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. Two cases of bacteriemia caused by nontoxigenic, non-O1, non-O139 Vibrio cholerae isolates in Ho Chi Minh City, Vietnam.

    PubMed

    Lan, Nguyen Phu Huong; Nga, Tran Vu Thieu; Yen, Nguyen Thi Thu; Dung, Le Thi; Tuyen, Ha Thanh; Campbell, James I; Whitehorn, Jamie; Thwaites, Guy; Chau, Nguyen Van Vinh; Baker, Stephen

    2014-10-01

    The toxigenic bacterium Vibrio cholerae belonging to the O1 and O139 serogroups is commonly associated with epidemic diarrhea in tropical settings; other diseases caused by this environmental pathogen are seldom identified. Here we report two unassociated cases of nonfatal, nontoxigenic V. cholerae non-O1, non-O139 bacteremia in patients with comorbidities in Ho Chi Minh City, Vietnam, that occurred within a 4-week period. PMID:25122858

  3. Two Cases of Bacteriemia Caused by Nontoxigenic, Non-O1, Non-O139 Vibrio cholerae Isolates in Ho Chi Minh City, Vietnam

    PubMed Central

    Lan, Nguyen Phu Huong; Nga, Tran Vu Thieu; Yen, Nguyen Thi Thu; Dung, Le Thi; Tuyen, Ha Thanh; Campbell, James I.; Whitehorn, Jamie; Thwaites, Guy; Chau, Nguyen Van Vinh

    2014-01-01

    The toxigenic bacterium Vibrio cholerae belonging to the O1 and O139 serogroups is commonly associated with epidemic diarrhea in tropical settings; other diseases caused by this environmental pathogen are seldom identified. Here we report two unassociated cases of nonfatal, nontoxigenic V. cholerae non-O1, non-O139 bacteremia in patients with comorbidities in Ho Chi Minh City, Vietnam, that occurred within a 4-week period. PMID:25122858

  4. Osteosynthesis-Associated Bone Infection Caused by a Nonproteolytic, Nontoxigenic Clostridium botulinum-Like Strain

    PubMed Central

    Carlier, Jean-Philippe; K'ouas, Guylčne; Lozniewski, Alain; Sirveaux, François; Cailloux, Philippe; Mory, Francine

    2004-01-01

    A nonproteolytic, nontoxigenic Clostridium botulinum strain identified by conventional and molecular techniques as type B-, E-, or F-like (BEF-like) was isolated from a human postsurgical wound. All previous reports of such strains have been from environmental sources. Since toxin production is the main taxonomic denominator for C. botulinum, a new name is needed for nonproteolytic, nontoxigenic BEF-like clinical isolates. PMID:14715812

  5. 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...

  6. Mould-ripened meat products: New selection scheme for non-toxigenic Penicillium spp

    Microsoft Academic Search

    M Gareis; R Rotheneder; W Rödel

    1999-01-01

    Species belonging to the genusPenicillium are known to produce a variety of mycotoxins. The use of non-toxigenic isolates is therefore of a major concern when selecting\\u000a strains for improving mould-ripened food products. For initial selection 249 different strains of the genusPenicillium originally isolated from food products have been used in this study. The isolates were grouped according to the pattern

  7. Contribution of Rare Copy Number Variants to Isolated Human Malformations

    PubMed Central

    Serra-Juhé, Clara; Rodríguez-Santiago, Benjamín; Cuscó, Ivon; Vendrell, Teresa; Camats, Núria; Torán, Núria; Pérez-Jurado, Luis A.

    2012-01-01

    Background Congenital malformations are present in approximately 2–3% of liveborn babies and 20% of stillborn fetuses. The mechanisms underlying the majority of sporadic and isolated congenital malformations are poorly understood, although it is hypothesized that the accumulation of rare genetic, genomic and epigenetic variants converge to deregulate developmental networks. Methodology/Principal Findings We selected samples from 95 fetuses with congenital malformations not ascribed to a specific syndrome (68 with isolated malformations, 27 with multiple malformations). Karyotyping and Multiplex Ligation-dependent Probe Amplification (MLPA) discarded recurrent genomic and cytogenetic rearrangements. DNA extracted from the affected tissue (46%) or from lung or liver (54%) was analyzed by molecular karyotyping. Validations and inheritance were obtained by MLPA. We identified 22 rare copy number variants (CNV) [>100 kb, either absent (n?=?7) or very uncommon (n?=?15, <1/2,000) in the control population] in 20/95 fetuses with congenital malformations (21%), including 11 deletions and 11 duplications. One of the 9 tested rearrangements was de novo while the remaining were inherited from a healthy parent. The highest frequency was observed in fetuses with heart hypoplasia (8/17, 62.5%), with two events previously related with the phenotype. Double events hitting candidate genes were detected in two samples with brain malformations. Globally, the burden of deletions was significantly higher in fetuses with malformations compared to controls. Conclusions/Significance Our data reveal a significant contribution of rare deletion-type CNV, mostly inherited but also de novo, to human congenital malformations, especially heart hypoplasia, and reinforce the hypothesis of a multifactorial etiology in most cases. PMID:23056206

  8. Isolation and characterization of a variant of ovomucoid.

    PubMed Central

    Waheed, A; Salhuddin, A

    1975-01-01

    A simple procedure, which can be used on a preparative scale, for the isolation and purification of a major variant of ovomucoid from egg white is described. Ovomucoid was precipitated by salt, and further fractionated by chromatography on sulphoethyl-Sephadex. It showed size homogeneity as revealed by gel chromatography and sodium dodecyl sulphate-polyacrylamide-gel electrophoresis where the mobility was consistent with a molecular weight of 28 300+/-2300. The inhibitor showed full antiryptic but no antichymotryptic activity. The u.v.-absorption and fluorescence characteristics indicated the absence of tryptophan. Polyacrylamide-gel electrophoresis in the presence of 9M-urea demonstrated absence of charge heterogeneity. The intrinsic viscosity of ovomucoid was 5.36ml/g which yielded an equivalent hydrodynamic radius (2.9nm), axial ratio (6.0) and frictional ratio (1.31) of the molecule. The Stokes radius (3.5nm), diffusion coefficient (7.8 times 10(-7 cm2/s) and frictional ratio (1.35) were calculated from gel-filtration data. These results suggest that ovomucoid exists in non-globular conformation under native conditions and that the deviation from the behaviour of a typical globular protein seems to be due both to asymmetry and hydration. Images PLATE 1 PMID:1171685

  9. Assessment of Virulence of Pigeon Isolates of Salmonella enterica subsp. enterica Serovar Typhimurium Variant Copenhagen for Humans

    Microsoft Academic Search

    Frank Pasmans; Filip Van Immerseel; Katleen Hermans; Marc Heyndrickx; Jean-Marc Collard; Richard Ducatelle; Freddy Haesebrouck

    2004-01-01

    Salmonella enterica serovar Typhimurium variant Copenhagen was isolated from 5 of 152 (3.3%) feral pigeons from the city of Ghent (Belgium) and from 26 pooled fecal samples from 114 pigeon lofts (22.8%). These isolates belonged to phage type (PT) 99. Seven of the pigeon isolates were further compared in vitro to five human variant Copenhagen isolates, 2 isolates of PT

  10. Isolation and Characterization of HL-A Variants in Cultured Human Lymphoid Cells

    Microsoft Academic Search

    Donald Pious; Pamela Hawley; Gary Forrest

    1973-01-01

    We have developed a procedure for immune selection in an established human lymphoid cell line based on HL-A, the major human histocompatibility locus. After a single brief exposure to selective conditions, HL-A2 variant clones were isolated from an HL-A2\\/HL-A3 heterozygous line. The variant clones occurred at a frequency of about 1 × 10-6. The variant phenotype was stable during prolonged

  11. Isolation and morphological studies of a variant of Ceratodon purpureus

    Microsoft Academic Search

    M. Larpent-Gourgaud; M. P. Aumaitre

    1982-01-01

    Summary Morphological variants from protonema ofCeratodon purpureus (Hedw.) were obtained using nitrosoguanidine (NTG). In one of the variants, reduced growth was accompagnied by hyperbranching and inhibition of caulogenesis. The deposition of branches in this strain can be studied by enzymatic analysis.

  12. Two Novel Salmonella Genomic Island 1 Variants in Proteus mirabilis Isolates from Swine Farms in China.

    PubMed

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

    2015-07-01

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

  13. 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

  14. Isolation of monoclonal antibody charge variants by displacement chromatography.

    PubMed

    McAtee, C Patrick; Hornbuckle, Jacob

    2012-08-01

    This unit discusses the important parameters in designing and optimizing a separation of monoclonal antibody (mAb) charge variants from process streams by ion-exchange displacement chromatography, including sample preparation and selection of matrix, column, and appropriate buffer. A protocol is provided for determination of optimal column binding and displacement conditions, including cleaning and regeneration of the displacement columns. PMID:22851499

  15. Isolation of Highly Heat-Resistant Listeria monocytogenes Variants by Use of a Kinetic Modeling-Based Sampling Scheme ?

    PubMed Central

    Van Boeijen, Ineke K. H.; Francke, Christof; Moezelaar, Roy; Abee, Tjakko; Zwietering, Marcel H.

    2011-01-01

    Stable high-hydrostatic-pressure (HHP)-resistant Listeria monocytogenes LO28 variants were previously isolated and characterized. These HHP variants were also more resistant to heat. In addition, nonlinear heat inactivation kinetics pointed toward the existence of heat-resistant variants, although these could not be isolated so far. In this study, we used kinetic modeling of inactivation curves of two isolated HHP variants and their wild type, and this revealed that the probability of finding resistant variants should depend on the nature of the inactivation treatment and the time of exposure. At specific heat and HHP conditions, resistant LO28 and EGDe variants were indeed isolated. Resistant LO28 variants were even isolated after a heat inactivation at 72°C in milk, and these variants showed high resistance to standard pasteurization conditions. The increased resistance of part of the isolated LO28 and EGDe variants was due to mutations in their ctsR genes. For the variants whose ctsR genes and upstream regions were not altered, the mechanisms leading to increased resistance remain to be elucidated. This research showed the strength of kinetic modeling in unraveling the causes of nonlinear inactivation and facilitating the isolation of heat-resistant L. monocytogenes variants. PMID:21357432

  16. Murine Coronaviruses: Isolation and Characterization of Two Plaque Morphology Variants of the JHM Neurotropic Strain

    Microsoft Academic Search

    STEPHEN A. STOHLMAN; PETER R. BRAYTON; JOHN O. FLEMING; LESLIE P. WEINER; MICHAEL M. C. LAI

    1982-01-01

    SUMMARY Two plaque-size variants of the neurotropic JHM strain of mouse hepatitis virus have been isolated from the virus stock after eight serial passages in suckling mouse brain. One variant, JHM-DL, produces large plaques, while the other, JHM-DS, produces small plaques in tissue culture. DS replicates more slowly, has a lower virus yield in vitro, and is less virulent for

  17. Isolation and characterization of therapeutic antibody charge variants using cation exchange displacement chromatography.

    PubMed

    Zhang, Taylor; Bourret, Justin; Cano, Tony

    2011-08-01

    In this report, we have demonstrated the isolation and enrichment of charge variants of a monoclonal antibody IgG1 using cation exchange displacement chromatography. We successfully achieved the separation of acidic, main and basic charge variants with high recovery (>70%) and purity (>90%) by using a commercially available stationary phase in conjunction with a commercially available displacer. In addition, we have isolated and enriched a trace methionine-oxidized variant of the monoclonal antibody allowing a secondary means of identification of this variant while providing sufficient enrichment for further analysis, stability tests and potency determination. Further characterization of the displacement trains by SEC indicate the possibility of enrichment of high and low molecular weight species. Glycan analysis of the displacement fractions indicates minimal variation in glycan distribution patterns among a wide spectrum of charge variants. These results provide a case study demonstrating the utility of cation exchange displacement chromatography as a viable approach to isolate and enrich antibody charge variants for enhanced molecular characterization. PMID:21700290

  18. 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

  19. 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

  20. Classification and nomenclature system for Human Alphapapillomavirus variants: general features, nucleotide landmarks and assignment of HPV6 and HPV11 isolates to variant lineages

    PubMed Central

    Burk, R. D.; Chen, Z.; Harari, A.; Smith, B. C.; Kocjan, B. J.; Maver, P. J.; Poljak, M.

    2013-01-01

    Background Papillomaviruses constitute a family of viruses that can be classified into genera, species and types based on their viral genome heterogeneity. Currently circulating infectious human Alphapapillomaviruses (alpha-PVs) constitute a set of viral genomes that have evolved from archaic times and display features of host co-speciation. Viral variants are more recently evolved genomes that require a standardized classification and nomenclature. Objectives To describe a system for the classification and nomenclature of HPV viral variants and provide landmarks for the numbering of nucleotide positions. Methods The complete 8 kb genomes of the alpha-9 species group and HPV6 and 11 types, collected from isolates throughout the world were obtained from published reports and GenBank. Complete genomes for each HPV type were aligned using the E1 start codon and sequence divergence was calculated by global and pairwise alignments using the MUSCLE program. Phylogenetic trees were constructed from the aligned sequences using a maximum likelihood method (RAxML). Results Pairwise comparisons of nucleotide differences between complete genomes of each type from alpha-9 HPV isolates (HPV16, 31, 33, 35, 52, 58 and 67) revealed a trimodal distribution. Maximum heterogeneity for variants within a type varied from 0.6%-2.3%. Nucleotide differences of approximately 1.0%-10.0% and 0.5%-1.0% of the complete genomes were used to define variant lineages and sublineages, respectively. Analysis of 43 HPV6 complete genomes indicated the presence of 2 variant lineages, whereas 32 HPV11 isolates were highly similar and clustered into 2 sublineages. A table was constructed of the human alpha-PV landmark nucleotide sequences for future reference and alignments. Conclusions A proposed nomenclature system for viral variants and coordination of nucleotide positions will facilitate the comparison of variants across geographic regions and amongst different populations. In addition, this system will facilitate study of pathogenic, tissue tropism and functional differences amongst variant lineages of and polymorphisms within HPV variants. PMID:22131111

  1. Detection and characterization of variant Salmonella genomic island 1s from Salmonella Derby isolates.

    PubMed

    Akiba, Masato; Nakamura, Kotaro; Shinoda, David; Yoshii, Noriyo; Ito, Hiroya; Uchida, Ikuo; Nakazawa, Muneo

    2006-10-01

    The purpose of this study is to investigate the distribution and structure of Salmonella genomic island 1 (SGI1) among Salmonella enterica serovar Derby isolates from swine and their rearing environment. Three variants of SGI1s, specifically SGI1-A, C, and I, were identified by PCR mapping. The results of macro-restriction analysis and DNA sequencing of SGI1 flanking regions revealed that there are at least two genomic lineages of Derby strains bearing SGI1s. PMID:17060705

  2. A Severe Hellenic CMV Tomato Isolate: Symptom Variability in Tobacco, Characterization and Discrimination of Variants

    Microsoft Academic Search

    A. P. Sclavounos; A. E. Voloudakis; Ch. Arabatzis; P. E. Kyriakopoulou

    2006-01-01

    A severe strain of Cucumber mosaic virus (CMV) originating from an infected tomato plant (Gastouni-Olympia, Greece) was isolated in tobacco (Nicotiana tabacum cv. Xanthi nc), after three serial local lesion passages in Chenopodium quinoa and designated CMV-G. CMV-G induces yellow mosaic (YM) symptoms in tobacco. When CMV-G was passed mechanically through C. quinoa, phenotypic variants inducing YM or green mild

  3. 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

  4. A truncating PET100 variant causing fatal infantile lactic acidosis and isolated cytochrome c oxidase deficiency.

    PubMed

    Oláhová, Monika; Haack, Tobias B; Alston, Charlotte L; Houghton, Jessica Ac; He, Langping; Morris, Andrew Am; Brown, Garry K; McFarland, Robert; Chrzanowska-Lightowlers, Zofia Ma; Lightowlers, Robert N; Prokisch, Holger; Taylor, Robert W

    2015-07-01

    Isolated mitochondrial complex IV (cytochrome c oxidase) deficiency is an important cause of mitochondrial disease in children and adults. It is genetically heterogeneous, given that both mtDNA-encoded and nuclear-encoded gene products contribute to structural components and assembly factors. Pathogenic variants within these proteins are associated with clinical variability ranging from isolated organ involvement to multisystem disease presentations. Defects in more than 10 complex IV assembly factors have been described including a recent Lebanese founder mutation in PET100 in patients presenting with Leigh syndrome. We report the clinical and molecular investigation of a patient with a fatal, neonatal-onset isolated complex IV deficiency associated with multiorgan involvement born to consanguineous, first-cousin British Asian parents. Exome sequencing revealed a homozygous truncating variant (c.142C>T, p.(Gln48*)) in the PET100 gene that results in a complete loss of enzyme activity and assembly of the holocomplex. Our report confirms PET100 mutation as an important cause of isolated complex IV deficiency outside of the Lebanese population, extending the phenotypic spectrum associated with abnormalities within this gene. PMID:25293719

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

    PubMed

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

    2009-10-01

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

  6. Nontoxigenic Highly Pathogenic Clone of Corynebacterium diphtheriae, Poland, 2004–2012

    PubMed Central

    2013-01-01

    Twenty-five cases of nontoxigenic Corynebacterium diphtheriae infection were recorded in Poland during 2004–2012, of which 18 were invasive. Alcoholism, homelessness, hepatic cirrhosis, and dental caries were predisposing factors for infection. However, for 17% of cases, no concomitant diseases or predisposing factors were found. PMID:24209492

  7. Multidisciplinary analysis of a nontoxigenic Clostridium difficile strain with stable resistance to metronidazole.

    PubMed

    Moura, Ines; Monot, Marc; Tani, Chiara; Spigaglia, Patrizia; Barbanti, Fabrizio; Norais, Nathalie; Dupuy, Bruno; Bouza, Emilio; Mastrantonio, Paola

    2014-08-01

    Stable resistance to metronidazole in a nontoxigenic Clostridium difficile strain was investigated at both the genomic and proteomic levels. Alterations in the metabolic pathway involving the pyruvate-ferredoxin oxidoreductase were found, suggesting that reduction of metronidazole, required for its activity, may be less efficient in this strain. Proteomic studies also showed a cellular response to oxidative stress. PMID:24913157

  8. Multidisciplinary Analysis of a Nontoxigenic Clostridium difficile Strain with Stable Resistance to Metronidazole

    PubMed Central

    Moura, Ines; Monot, Marc; Tani, Chiara; Barbanti, Fabrizio; Norais, Nathalie; Dupuy, Bruno; Bouza, Emilio; Mastrantonio, Paola

    2014-01-01

    Stable resistance to metronidazole in a nontoxigenic Clostridium difficile strain was investigated at both the genomic and proteomic levels. Alterations in the metabolic pathway involving the pyruvate-ferredoxin oxidoreductase were found, suggesting that reduction of metronidazole, required for its activity, may be less efficient in this strain. Proteomic studies also showed a cellular response to oxidative stress. PMID:24913157

  9. Verotoxins in Bovine and Meat Verotoxin-Producing Escherichia coli Isolates: Type, Number of Variants, and Relationship to Cytotoxicity?

    PubMed Central

    Krüger, Alejandra; Lucchesi, Paula M. A.; Parma, Alberto E.

    2011-01-01

    In this study, we determined vt subtypes and evaluated verotoxicity in basal as well as induced conditions of verotoxin-producing Escherichia coli (VTEC) strains isolated from cattle and meat products. Most (87%) of the 186 isolates carried a vt2 gene. Moreover, the vt2 subtype, which is associated with serious disease, was present in 42% of our VTEC collection. The other vt subtypes detected were vt1, vt1d, vt2vha, vt2vhb, vt2O118, vt2d (mucus activatable), and vt2g. A total of 41 (22%) of the isolates possessed more than one vt subtype in its genome, and among them the most frequent combination was vt1/vt2, but we also observed multiple combinations among vt2 subtypes. Differences in verotoxicity titers were found among a selection of 54 isolates. Among isolates with a single vt2 variant, those carrying the vt2 subtype had high titers under both uninduced and induced conditions. However, the highest increase in cytotoxicity under mitomycin C treatment was detected among the strains carrying vt2vha or vt2hb variants. Notably, the isolates carrying the vt1 subtype showed a lesser increase than that of most of the vt2-positive VTEC strains. Furthermore, the presence of more than one vt gene variant in the same isolate was not reflected in higher titers, and generally the titers were lower than those for strains with only one gene variant. The main observation was that both basal and induced cytotoxic effects seemed to be associated with the type and number of vt variants more than with the serotype or origin of the isolate. PMID:21037301

  10. Assessment of Virulence of Pigeon Isolates of Salmonella enterica subsp. enterica Serovar Typhimurium Variant Copenhagen for Humans

    PubMed Central

    Pasmans, Frank; Van Immerseel, Filip; Hermans, Katleen; Heyndrickx, Marc; Collard, Jean-Marc; Ducatelle, Richard; Haesebrouck, Freddy

    2004-01-01

    Salmonella enterica serovar Typhimurium variant Copenhagen was isolated from 5 of 152 (3.3%) feral pigeons from the city of Ghent (Belgium) and from 26 pooled fecal samples from 114 pigeon lofts (22.8%). These isolates belonged to phage type (PT) 99. Seven of the pigeon isolates were further compared in vitro to five human variant Copenhagen isolates, 2 isolates of PT 208, 1 isolate each of PT 120 and U302, and a nontypeable isolate. No differences in invasiveness in human intestinal epithelial Caco-2 cells were found. The human strains, however, were able to multiply significantly more inside human THP-1 macrophages than the pigeon strains. After inoculation of mice with a pigeon PT 99 strain, high numbers of Salmonella bacteria were shed with the feces, the internal organs were heavily colonized, and the animals showed severe clinical symptoms resulting in death. In conclusion, the less-pronounced ability of the pigeon variant Copenhagen strains to multiply inside human macrophages than human strains as well as the lack of human PT 99 isolates during 2002, despite the relatively high frequency of this PT in the pigeon population, suggest these strains to be of low virulence to humans. However, the high virulence for mice of the tested strain implies that rodents may act as reservoirs. PMID:15131161

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. Vacuolating Cytotoxin and Variants in Atg16L1 that Disrupt Autophagy Promote Helicobacter pylori Infection in Humans

    PubMed Central

    Raju, D; Hussey, S; Ang, M; Terebiznik, M.R.; Sibony, M; Galindo-Mata, E; Gupta, V; Blanke, S.R.; Delgado, A; Romero-Gallo, J; Ramjeet, M; Mascarenhas, H; Peek, R.M.; Correa, P; Streutker, C; Hold, G; Kunstmann, E; Yoshimori, T; Silverberg, M. S.; Girardin, S.E.; Philpott, D.J.; El Omar, E; Jones, N.L.

    2012-01-01

    Background & Aims The Helicobacter pylori toxin vacuolating cytotoxin (VacA) promotes gastric colonization and its presence (VacA+) is associated with more-severe disease. The exact mechanisms by which VacA contributes to infection are unclear. We previously found that limited exposure to VacA induces autophagy of gastric cells, which eliminates the toxin; we investigated whether autophagy serves as a defense mechanism against H pylori infection. Methods We investigated the effect of VacA on autophagy in human gastric epithelial cells (AGS) and primary gastric cells from mice. Expression of p62, a marker of autophagy, was also assessed in gastric tissues from patients infected with toxigenic (VacA+) or nontoxigenic strains. We analyzed the effect of VacA on autophagy in peripheral blood monocytes obtained from subjects with different genotypes of ATG16L1, which regulates autophagy. We performed genotyping for ATG16L1 in two cohorts of infected and uninfected subjects. Results Prolonged exposure of AGS and mouse gastric cells to VacA disrupted induction of autophagy in response to the toxin, because the cells lacked cathepsin-D in autophagosomes. Loss of autophagy resulted in the accumulation of p62 and reactive oxygen species. Gastric biopsies samples from patients infected with VacA+, but not nontoxigenic strains of H pylori, had increased levels of p62. Peripheral blood monocytes isolated from individuals with polymorphisms in ATG16L1 that increase susceptibility to Crohn's disease had reduced induction of autophagy in response to VacA+ compared to cells from individuals that did not have these polymorphisms. The presence of the ATG16L1 Crohn’s disease risk variant increased susceptibility to H pylori infection in 2 separate cohorts. Conclusions Autophagy protects against infection with H pylori; the toxin VacA disrupts autophagy to promote infection, which could contribute to inflammation and eventual carcinogenesis. PMID:22333951

  17. 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

  18. Literature review on the safety of Toyocerin ®, a non-toxigenic and non-pathogenic Bacillus cereus var. toyoi preparation

    Microsoft Academic Search

    Lonnie D. Williams; George A. Burdock; Guillermo Jiménez; Marisol Castillo

    2009-01-01

    Bacillus cereus var. toyoi is a naturally occurring, non-toxigenic and non-pathogenic strain of B. cereus. Safety studies were conducted on a B. toyoi preparation (Toyocerin®), including but not limited to enterotoxicity, eye irritation, genotoxicity, acute, subchronic and chronic toxicity studies and human clinical trials. In rabbits, Toyocerin® did not exhibit enterotoxicity and was only slightly irritating to the eyes. It

  19. Isolation and transposon mutagenesis of a Pseudomonas putida KT2442 toluene-resistant variant: involvement of an efflux system in solvent resistance

    Microsoft Academic Search

    Fumiyasu Fukumori; Hisako Hirayama; Hideto Takami; Akira Inoue; Koki Horikoshi

    1998-01-01

    A toluene-resistant variant of Pseudomonas putida KT2442, strain TOL, was isolated after liquid cultivation under xylene followed by toluene for 1 month in each condition.\\u000a Almost all the populations of the variant strain formed small but readily visible colonies under toluene within 24 h at 30?C.\\u000a The toluene-resistant strain also showed an increase in resistance to some unrelated antibiotics. Several

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. 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

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

    PubMed Central

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

    2015-01-01

    ABSTRACT A change in viral hemagglutinin (HA) receptor binding specificity from ?2,3- to ?2,6-linked sialic acid is necessary for highly pathogenic avian influenza (AI) virus subtype H5N1 to become pandemic. However, details of the human-adaptive change in the H5N1 virus remain unknown. Our database search of H5N1 clade 2.2.1 viruses circulating in Egypt identified multiple HA mutations that had been selected in infected patients. Using reverse genetics, we found that increases in both human receptor specificity and the HA pH threshold for membrane fusion were necessary to facilitate replication of the virus variants in human airway epithelia. Furthermore, variants with enhanced replication in human cells had decreased HA stability, apparently to compensate for the changes in viral receptor specificity and membrane fusion activity. Our findings showed that H5N1 viruses could rapidly adapt to growth in the human airway microenvironment by altering their HA properties in infected patients and provided new insights into the human-adaptive mechanisms of AI viruses. PMID:25852160

  4. Characterization of Sucrose-Negative Pasteurella multocida Variants, Including Isolates from Large-Cat Bite Wounds

    PubMed Central

    Christensen, Henrik; Bisgaard, Magne; Angen, Řystein; Frederiksen, Wilhelm; Olsen, John Elmerdahl

    2005-01-01

    To validate the identification of Pasteurella multocida-like bacteria negative for acid formation from sucrose, including isolates from bite wounds caused by large cats, 17 strains were phenotypically and genotypically characterized. Phylogenetic analysis of partially sequenced rpoB and infB genes showed the monophyly of the strains characterized and the reference strains of P. multocida. The sucrose-negative strains formed two groups, one related to reference strains of P. multocida and the other related to a separate species-like group (taxon 45 of Bisgaard). DNA-DNA hybridization further documented the species-like nature of this group. Ribotyping showed the heterogeneity of all strains except four strains that shared the same ribotype and that were isolated from bovine lungs. Phylogenetic analysis by 16S rRNA sequence comparison showed the monophyly of the strains characterized and the reference strains of P. multocida. Two strains isolated from leopard bite wounds were related to the type strain of P. dagmatis; however, they represented a new taxon (taxon 46 of Bisgaard), in accordance with their distinct phenotypic and genotypic identifications. The present study documents that sucrose-negative strains of P. multocida-like bacteria belong to two genotypically distinct groups. The study further confirms the phenotypic heterogeneity of P. multocida strains and documents two new species-like taxa of Pasteurella related to P. multocida. Until diagnostic tools have been further elaborated, special care should be taken in the identification of Pasteurella-like bacteria isolated from bite wounds caused by large cats. The evidence of phenotypic and genotypic divergence calls for the further development of PCR tests and DNA sequencing to document doubtful isolates. PMID:15634981

  5. Antigenic variants of rabies virus in isolates from eastern, central and northern Canada.

    PubMed Central

    Webster, W A; Casey, G A; Charlton, K M; Wiktor, T J

    1985-01-01

    Street rabies virus isolated from 51 specimens from Ontario, Quebec, Manitoba and the Northwest Territories have been typed by a panel of 36 antinucleocapsid monoclonal antibodies. Three main groups were found. The first group comprised those terrestrial mammals originating in Ontario, Quebec and the Northwest Territories. The second group was found in terrestrial mammals from Manitoba. The third heterogenous group was made up of bats from Ontario. PMID:3893660

  6. Morphology of griseofulvin-resistant isolates of Mongolian variant of Trichophyton schoenleini.

    PubMed

    Zheng, Y C

    1990-06-01

    Clinical, experimental and electronmicroscopic observations, and computer-enhanced images were made on 5 patients with tinea favosa resistant to griseofulvin. The pathologic fungus was identified as the Mongolian variant of Trichophyton schoenleini. The results of physical examinations, routine tests of blood, urine and stool, liver and immunologic function examinations were normal in all of the 5 patients. Under scanning electron microscopy, the surface of the spore showed pineapple-like form, the cluster of the acrogenous spores presented flower shape, and the antler-like hyphae appeared twisted in the culture. They were observed by transmission electron microscope and the images were processed by microcomputer. It was found that the cell walls of the fungi consisted of 8 layers, among which the inner layer was loose and contained cytoplasm. It was also found that all structures within the cytoplasm possessed a 1-3 layer intact envelope and there was chromatin in the nucleus. These may be contributing factors in the development of resistance to griseofulvin. This multiple-layered thick cell wall may act as a barrier responsible for the impermeability of the cell of fungi to griseofulvin. PMID:2119962

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

    PubMed

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

    2009-08-01

    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 (<0.1%) in 2,265 controls. We then examined a second, independent TOF cohort (n = 398) for additional CNVs at these loci. We identified CNVs at chromosome 1q21.1 in 1% (5/512, P = 0.0002, OR = 22.3) of nonsyndromic sporadic TOF cases. We also identified recurrent CNVs at 3p25.1, 7p21.3 and 22q11.2. CNVs in a single subject with TOF occurred at six loci, two that encode known (NOTCH1, JAG1) disease-associated genes. Our findings predict that at least 10% (4.5-15.5%, 95% confidence interval) of sporadic nonsyndromic TOF cases result from de novo CNVs and suggest that mutations within these loci might be etiologic in other cases of TOF. PMID:19597493

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

    PubMed

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

    2009-05-01

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

  9. 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

  10. Serotypes, Virulence Genes, and Intimin Types of Shiga Toxin (Verotoxin)-Producing Escherichia coli Isolates from Cattle in Spain and Identification of a New Intimin Variant Gene (eae-?)

    PubMed Central

    Blanco, M.; Blanco, J. E.; Mora, A.; Dahbi, G.; Alonso, M. P.; González, E. A.; Bernárdez, M. I.; Blanco, J.

    2004-01-01

    A total of 514 Shiga toxin-producing Escherichia coli (STEC) isolates from diarrheic and healthy cattle in Spain were characterized in this study. PCR showed that 101 (20%) isolates carried stx1 genes, 278 (54%) possessed stx2 genes, and 135 (26%) possessed both stx1 and stx2. Enterohemolysin (ehxA) and intimin (eae) virulence genes were detected in 326 (63%) and in 151 (29%) of the isolates, respectively. STEC isolates belonged to 66 O serogroups and 113 O:H serotypes (including 23 new serotypes). However, 67% were of one of these 15 serogroups (O2, O4, O8, O20, O22, O26, O77, O91, O105, O113, O116, O157, O171, O174, and OX177) and 52% of the isolates belonged to only 10 serotypes (O4:H4, O20:H19, O22:H8, O26:H11, O77:H41, O105:H18, O113:H21, O157:H7, O171:H2, and ONT:H19). Although the 514 STEC isolates belonged to 164 different seropathotypes (associations between serotypes and virulence genes), only 12 accounted for 43% of isolates. Seropathotype O157:H7 stx2 eae-?1 ehxA (46 isolates) was the most common, followed by O157:H7 stx1 stx2 eae-?1 ehxA (34 isolates), O113:H21 stx2 (25 isolates), O22:H8 stx1 stx2 ehxA (15 isolates), O26:H11 stx1 eae-?1 ehxA (14 isolates), and O77:H41 stx2 ehxA (14 isolates). Forty-one (22 of serotype O26:H11) isolates had intimin ?1, 82 O157:H7 isolates possessed intimin ?1, three O111:H- isolates had intimin type ?2, one O49:H- strain showed intimin type ?, 13 (six of serotype O103:H2) isolates had intimin type ? and eight (four of serotype O156:H-) isolates had intimin ?. We have identified a new variant of the eae intimin gene designated ? (xi) in two isolates of serotype O80:H-. The majority (85%) of bovine STEC isolates belonged to serotypes previously found for human STEC organisms and 54% to serotypes associated with STEC organisms isolated from patients with hemolytic uremic syndrome. Thus, this study confirms that cattle are a major reservoir of STEC strains pathogenic for humans. PMID:14766831

  11. Identification of a novel gene and a common variant associated with uric acid nephrolithiasis in a Sardinian genetic isolate.

    PubMed

    Gianfrancesco, Fernando; Esposito, Teresa; Ombra, Maria Neve; Forabosco, Paola; Maninchedda, Giuseppe; Fattorini, Mauro; Casula, Stefania; Vaccargiu, Simona; Casu, Giuseppina; Cardia, Francesco; Deiana, Ivo; Melis, Paola; Falchi, Mario; Pirastu, Mario

    2003-06-01

    Uric acid nephrolithiasis (UAN) is a common disease with an established genetic component that presents a complex mode of inheritance. While studying an ancient founder population in Talana, a village in Sardinia, we recently identified a susceptibility locus of approximately 2.5 cM for UAN on 10q21-q22 in a relatively small sample that was carefully selected through genealogical information. To refine the critical region and to identify the susceptibility gene, we extended our analysis to severely affected subjects from the same village. We confirm the involvement of this region in UAN through identical-by-descent sharing and autozygosity mapping, and we refine the critical region to an interval of approximately 67 kb associated with UAN by linkage-disequilibrium mapping. After inspecting the genomic sequences available in public databases, we determined that a novel gene overlaps this interval. This gene is divided into 15 exons, spanning a region of approximately 300 kb and generating at least four different proteins (407, 333, 462, and 216 amino acids). Interestingly, the last isoform was completely included in the 67-kb associated interval. Computer-assisted analysis of this isoform revealed at least one membrane-spanning domain and several N- and O-glycosylation consensus sites at N-termini, suggesting that it could be an integral membrane protein. Mutational analysis shows that a coding nucleotide variant (Ala62Thr), causing a missense in exon 12, is in strong association with UAN (P=.0051). Moreover, Ala62Thr modifies predicted protein secondary structure, suggesting that it may have a role in UAN etiology. The present study underscores the value of our small, genealogically well-characterized, isolated population as a model for the identification of susceptibility genes underlying complex diseases. Indeed, using a relatively small sample of affected and unaffected subjects, we identified a candidate gene for multifactorial UAN. PMID:12740763

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

    PubMed Central

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

    2014-01-01

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

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

    Microsoft Academic Search

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

    2006-01-01

    Summary.  Variants of Coconut cadang-cadang viroid have been identified in a plantation oil palm growing in Malaysia. Three size classes are described, comprising 297, 293,\\u000a and 270?nt. Compared with the 296-nt form of coconut cadang-cadang viroid (CCCVd), all variants substituted C31???U in the pathogenicity domain and A175???C in the right-hand terminus. Other mutations and deletions accounted for the different sizes. These

  14. Enterocin AS-48RJ: a variant of enterocin AS-48 chromosomally encoded by Enterococcus faecium RJ16 isolated from food.

    PubMed

    Abriouel, Hikmate; Lucas, Rosario; Ben Omar, Nabil; Valdivia, Eva; Maqueda, Mercedes; Martínez-Cańamero, Magdalena; Gálvez, Antonio

    2005-07-01

    The bacteriocinogenic strain RJ16 isolated from goat cheese has been identified as Enterococcusfaecium by species-specific PCR, DNA-rRNA hybridization and rDNA sequencing. Purified bacteriocin from strain RJ16 is a carboxypeptidase A-resistant peptide with a molecular mass (7125 Da) very close to the cyclic peptide enterocin AS-48. Bacteriocin from strain RJ16 and AS-48 show identical antibacterial spectra, although the former is slightly less active on strains of Listeria monocytogenes and Bacillus cereus. Producer strains show cross-immunity. PCR amplification of total DNA from strain RJ16 with primers for the AS-48 structural gene and sequencing of the amplified fragment revealed an almost identical sequence (99.5%), except for a single mutation that predicts the change of Glu residue at position 20 of AS-48 to Val. Therefore, bacteriocin produced by E. faecium RJ16 should be considered a variant of AS-48, which we call AS-48RJ. PCR amplification revealed that strain RJ16 contains the complete as-48. gene cluster. Hybridization with probes for as-48 gene cluster revealed a chromosomal location of as-48 genes in strain RJ16, being the first example of a chromosomal location of this bacteriocin trait. Strain RJ16 produced enzymes of interest in food processing (esterase, esterase lipase and phytase activities), and did not decarboxylate amino acids precursors for biogenic amines. Strain RJ16 did not exhibit haemolytic or gelatinase activities, and PCR amplification revealed the lack of genes encoding for known virulence determinants (aggregation substance, collagen adhesin, enterococcal surface protein, endocarditis antigens, as well as haemolysin and gelatinase production). Strain RJ16 was resistant to ciprofloxacin (MIC > 2 mgl(-1)) and levofloxacin (MIC > 4 mgl(-1)) and showed intermediate resistance to nitrofurantoin and erythromycin, but was sensitive to ampicillin, penicillin, streptomycin, gentamicin, rifampicin, chloramphenicol, tetracycline, quinupristin/dalfopristin, vancomycin and teicoplanin. Altogether, results from this study suggest that this broad-spectrum bacteriocin-producing strain may have a potential use in food preservation. PMID:16094865

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

    PubMed

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

    2015-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Lee, Youngwon; Kim, Myoung Hee [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.

  18. 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

  19. Characteristics of Staphylococcus aureus small colony variant and its parent strain isolated from chronic mastitis at a dairy farm in Beijing, China.

    PubMed

    Alkasir, Rashad; Liu, Xiuquan; Zahra, Mohammad; Ferreri, Miro; Su, Jingliang; Han, Bo

    2013-04-01

    Staphylococcus aureus is a major pathogen associated to bovine mastitis and has the ability to form a slow-growing population termed the small colony variants (SCVs). From 20 samples of 5 chronic S. aureus cases, 1 SCV isolate (SCV102) was recovered simultaneously with 1 of 8 S. aureus isolates. SCV102 showed auxotrophy for thymidine and had a slow growth rate. Intracellular persistence in human mammary epithelial cells (HBL100cell line) monolayer revealed that SCV102 isolate had minimal cytopathological effects compared with its parent strains. SCV102 isolate and its parent strain S. aureus 101 indicate similar resistant pattern to four antibiotics. On the contrary, the minimal inhibitory concentrations values for chloramphenicol and sulfadimethoxine were much higher in SCV102 than that of S. aureus 101. To the best of our knowledge this is the first time the isolation of S. aureus SCV102 from a persistent bovine mastitis has been reported in Beijing (China). This study suggests that SCV102 isolate may be an important contributor to persistent bovine mastitis. PMID:23140248

  20. NDM-12, a novel New Delhi metallo-?-lactamase variant from a carbapenem-resistant Escherichia coli clinical isolate in Nepal.

    PubMed

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

    2014-10-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2003-01-01

    Phage type 99 of Salmonella enterica subsp. enterica serovar Typhimurium variant Copenhagen strains isolated 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 XbaI and four closely related patterns with BlnI were obtained with the pigeon strains, whereas 16 XbaI patterns were found with the other strains. The XbaI patterns of the pigeon strains showed a low genetic similarity to the patterns of the porcine, poultry, and human strains and invariably showed a low-molecular-weight band that was absent in the majority of the other strains. The virulence genes shdA, spvR, pefA, sopE, and spvB were uniformly present in six pigeon isolates representing the genetic diversity found with BlnI. These six pigeon-derived strains were highly cytotoxic for pigeon macrophages compared to three porcine strains. After experimental infection of pigeons with a pigeon strain, clinical symptoms, fecal shedding, and colonization of internal organs were more pronounced than those after infection with a porcine strain. These data suggest that the phage type 99 strains used in this study are highly adapted to pigeons and should be classified as a host-restricted lineage of the serovar Typhimurium. PMID:14500532

  3. Highly divergent molecular variants of human T-lymphotropic virus type I from isolated populations in Papua New Guinea and the Solomon Islands.

    PubMed Central

    Gessian, A; Yanagihara, R; Franchini, G; Garruto, R M; Jenkins, C L; Ajdukiewicz, A B; Gallo, R C; Gajdusek, D C

    1991-01-01

    To determine the molecular genetic relationship between Melanesian strains of human T-lymphotropic virus type I (HTLV-I) and cosmopolitan prototype HTLV-I, we amplified by PCR, then cloned, and sequenced a 522-base-pair region of the HTLV-I env gene in DNA extracted from uncultured (fresh) and cultured peripheral blood mononuclear cells obtained from six seropositive Melanesian Papua New Guineans and Solomon Islanders, including a Solomon Islander with HTLV-I myeloneuropathy. Unlike isolates of HTLV-I from Japan, the West Indies, the Americas, and Africa, which share greater than or equal to 97% sequence homology, the Melanesian strains of HTLV-I were only 91.8%-92.5% identical with a prototype Japanese HTLV-IATK-1. The nucleotide sequence of proviral DNA from the Solomon Islander with HTLV-I myeloneuropathy also diverged markedly from that of HTLV-I isolated from Japanese patients with HTLV-I-associated myelopathy and from Jamaican patients with tropical spastic paraparesis, suggesting that these variant viruses are capable of causing disease. The HTLV-I variants from Papua New Guineans, in turn, differed by nearly 4% from the Melanesian variants from Solomon Islanders, indicating the existence of another HTLV-I quasi-species. By contrast, HTLV-I strains from two residents of Bellona Island, a Polynesian Outlier within the Solomon Islands, were closely related to cosmopolitan prototype HTLV-I (greater than or equal to 97% sequence identity), suggesting recent introduction, possibly during this century. These findings are consistent with a proto-Melanesian HTLV-I strain of archaic presence, which evolved independently of contemporary cosmopolitan strains, and pose new questions about the origin and global dissemination of HTLV-I. Images PMID:1881912

  4. Draft Genome Sequences of Vibrio cholerae O1 ElTor Strains 2011EL-301 and P-18785, Isolated in Russia

    PubMed Central

    Vodop’ianov, Sergey O.; Markelov, Mikhail L.; Dedkov, Vladimir G.; Kermanov, Anton V.; Kruglikov, Vladimir D.; Vodop’ianov, Alexey S.; Pisanov, Ruslan V.; Mazrukho, Alexey B.; Shipulin, German A.

    2013-01-01

    We report the draft whole-genome sequences of two Vibrio cholerae O1 strains, the environmental toxigenic strain 2011EL-301 and the clinical nontoxigenic strain P-18785, both isolated in Russia. Some basic data comparing the two against the GenBank repository are provided. PMID:23969060

  5. Rupestris stem pitting associated virus isolates are composed by mixtures of genomic variants which share a highly conserved coat protein

    Microsoft Academic Search

    G. Nolasco; C. Santos; N. Petrovic; M. Teixeira Santos; I. Cortez; F. Fonseca; J. Boben; A. M. Nazaré Pereira; O. Sequeira

    2006-01-01

    Broad spectrum primers were used to amplify a fragment comprising the CP gene and putative ORF6 by RT-PCR from ds-RNA templates originating from 46 Portuguese varieties, totalling 190 samples, including some wild Vitis ssp sylvestris vines, and 2 vines from Slovenia. SSCP analysis was used as a preliminary screen to avoid cloning and sequencing very similar variants. Four groups of

  6. Comparative biological activities of a plaque-purified variant and a Turkish native isolate of SpliNPV-B against Spodoptera littoralis (Lepidoptera: Noctuidae).

    PubMed

    Toprak, Umut; Bayram, Serife; Gürkan, Oktay M

    2006-01-01

    The noctuid moth Spodoptera littoralis (Boisduval) is an important pest of many cultivated plants worldwide and five different geographical Nucleopolyhedrovirus (NPV) strains of this pest have been isolated to date. Two of these, a plaque-purified variant of the S. littoralis NPV from Morocco (SpliNPV-M2) and a SpliNPV isolated from field-infected S. littoralis larvae found in Turkey (SpliNPV-TR1), were compared biologically in terms of infectiveness (median lethal dose, LD50) for third instars and in terms of virulence (median lethal time, LT50) for neonates and third-instar S. littoralis larvae. The LD50 values of SpliNPV-TR1 and SpliNPV-M2 were 20.73 and 185.21 occlusion bodies (OBs)/larva, respectively, with non-overlapping confidence limits indicating they were significantly different. Thus, SpliNPV-M2 was found to be significantly less infective (about nine times higher LD50) than SpliNPV-TR1. The LT50 values of neonates for SpliNPV-M2 and SpliNPV-TR1 were 37 and 43.9 h at a concentration of 10(6) OBs ml(-1), respectively. For these same isolates, the LT50 values at a concentration of 3 x 10(6) OBs ml(-1) were calculated as 35.6 and 41.7 h, respectively. The LT(50) values of third instars for SpliNPV-M2 and SpliNPV-TR1 were 147.4 and 160.5 h, respectively, at a dose of 3000 OBs/larva and 145.4 and 152.4 h, respectively, for the same isolates at a dose of 20,000 OBs/larva. On the other hand, Helicoverpa armigera (Hübner) and Agrotis ipsilon (Hufnagel) revealed a lack of lethality of the SpliNPV-TR1 isolate. PMID:16235266

  7. Expression Analysis of a Highly Adherent and Cytotoxic Small Colony Variant of Pseudomonas aeruginosa Isolated from a Lung of a Patient with Cystic Fibrosis†

    PubMed Central

    von Götz, Franz; Häussler, Susanne; Jordan, Doris; Saravanamuthu, Senthil Selvan; Wehmhöner, Dirk; Strüßmann, André; Lauber, Joerg; Attree, Ina; Buer, Jan; Tümmler, Burkhard; Steinmetz, Ivo

    2004-01-01

    The heterogeneous environment of the lung of the cystic fibrosis (CF) patient gives rise to Pseudomonas aeruginosa small colony variants (SCVs) with increased antibiotic resistance, autoaggregative growth behavior, and an enhanced ability to form biofilms. In this study, oligonucleotide DNA microarrays were used to perform a genome-wide expression study of autoaggregative and highly adherent P. aeruginosa SCV 20265 isolated from a CF patient's lung in comparison with its clonal wild type and a revertant generated in vitro from the SCV population. Most strikingly, SCV 20265 showed a pronounced upregulation of the type III protein secretion system (TTSS) and the respective effector proteins. This differential expression was shown to be biologically meaningful, as SCV 20265 and other hyperpiliated and autoaggregative SCVs with increased TTSS expression were significantly more cytotoxic for macrophages in vitro and were more virulent in a mouse model of respiratory tract infection than the wild type. The observed cytotoxicity and virulence of SCV 20265 required exsA, an important transcriptional activator of the TTSS. Thus, the prevailing assumption that P. aeruginosa is subject to selection towards reduced cytotoxicity and attenuated virulence during chronic CF lung infection might not apply to all clonal variants. PMID:15175297

  8. Novel plasmid and its variant harboring both a bla(NDM-1) gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii.

    PubMed

    Hu, Hongyan; Hu, Yongfei; Pan, Yuanlong; Liang, Hui; Wang, Haiyan; Wang, Xiumei; Hao, Qinfang; Yang, Xiaoli; Yang, Xi; Xiao, Xue; Luan, Chunguang; Yang, Yi; Cui, Yujun; Yang, Ruifu; Gao, George F; Song, Yajun; Zhu, Baoli

    2012-04-01

    The spread of the bla(NDM-1) gene is gaining worldwide attentions. This gene is usually carried by large plasmids and has been discovered in diverse bacteria since it was originally found in Klebsiella pneumoniae. Here we report the complete sequences of a bla(NDM-1)-bearing plasmid, pNDM-BJ01, and its variant, pNDM-BJ02, isolated from clinical Acinetobacter lwoffii strains. The plasmid pNDM-BJ01 is 47.3 kb in size and cannot be classified into any known plasmid incompatibility group, thus representing a novel plasmid with an unknown maintenance mechanism. This plasmid contains both a bla(NDM-1) gene and a type IV secretion system (T4SS) gene cluster. The T4SS is assigned to the P-type T4SS group, which usually encode a short, rigid pilus, and the bla(NDM-1) gene is located within a composite transposon flanked by two insertion elements of ISAba125. Plasmid pNDM-BJ02 is nearly identical to pNDM-BJ01 except that one copy of the ISAba125 element is missing, and it is therefore regarded as a variant of pNDM-BJ01. Sequence alignment indicated that this bla(NDM-1)-containing composite transposon, which can also be captured by other mobile elements, was probably a product of multiple recombination events and can move as a whole by transposition. PMID:22290961

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

    PubMed

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

    2015-07-01

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

  10. Isolation of a Chinese hamster fibroblast variant defective in dihydroxyacetonephosphate acyltransferase activity and plasmalogen biosynthesis: use of a novel two-step selection protocol.

    PubMed

    Nagan, N; Hajra, A K; Larkins, L K; Lazarow, P; Purdue, P E; Rizzo, W B; Zoeller, R A

    1998-05-15

    We have developed a two-step selection protocol to generate a population of Chinese hamster ovary (CHO) cell variants that are plasmalogen-deficient, but contain intact, functional peroxisomes (plasmalogen-/peroxisome+). This involved sequential exposures of a mutagenized cell population to photodynamic damage by using two different pyrene-labelled sensors, 9-(1'-pyrene)nonanol and 12-(1'-pyrene)dodecanoic acid. By this procedure we generated several isolates, all except one of which displayed a severe decrease in plasmalogen biosynthesis. Further characterization of one of the plasmalogen-deficient isolates, NRel-4, showed that it contained intact, functional peroxisomes. Whole-cell homogenates from NRel-4 displayed severely decreased dihydroxyacetone phosphate acyltransferase, which catalyses the first step in plasmalogen biosynthesis. NRel-4 and another, recently described, plasmalogen-deficient cell line, NZel-1 [Nagan, Hajra, Das, Moser, Moser, Lazarow, Purdue and Zoeller (1997) Proc. Natl. Acad. Sci. U.S. A. 94, 4475-4480] were hypersensitive to singlet oxygen, supporting the notion of plasmalogens as radical oxygen scavengers. Wild-type-like resistance could be conferred on NRel-4 upon restoration of plasmalogen content by supplementation with a bypass compound, sn-1-hexadecylglycerol. NRel-4 and other plasmalogen-/peroxisome+ strains will allow us to examine further the role of ether lipids in cellular functions without complications associated with peroxisome deficiency, and might serve as an animal cell model for certain forms of the human genetic disorder rhizomelic chondrodysplasia punctata. PMID:9576878

  11. On the purification of notexin. Isolation of a single amino acid variant from the venom of Notechis scutatus scutatus.

    PubMed

    Chwetzoff, S; Mollier, P; Bouet, F; Rowan, E G; Harvey, A L; Ménez, A

    1990-02-26

    Venom of the Australian tiger snake, Notechis scutatus scutatus was fractionated by conventional ion-exchange chromatography. The fraction containing notexin, a well-known single-chain toxic phospholipase A2, was further purified by reverse-phase high-performance liquid chromatography. Two main components were isolated and the major one corresponded to notexin. The other component, designated as notechis Ns, was an isoform of notexin. Notechis Ns and notexin possessed similar in vitro esterase activity, in vitro neuromuscular activity and in vivo lethality. Amino acid composition and sequence of the Staphylococcus aureus V8-protease peptides demonstrated that primary structures of notechis Ns and notexin differed from each other by a single substitution amongst 119 amino acids: Lys----Arg at position 16. PMID:2155818

  12. Novel variants of AbaR resistance islands with a common backbone in Acinetobacter baumannii isolates of European clone II.

    PubMed

    Seputiene, Vaida; Povilonis, Justas; Suziedeliene, Edita

    2012-04-01

    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

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

    PubMed Central

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

    2015-01-01

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

  14. 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

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

    PubMed Central

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

    2014-01-01

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

  16. Antiviral susceptibility of variant influenza A(H3N2)v viruses isolated in the United States from 2011 to 2013.

    PubMed

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

    2014-01-01

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

  17. A Novel Variant, NDM-5, of the New Delhi Metallo-?-Lactamase in a Multidrug-Resistant Escherichia coli ST648 Isolate Recovered from a Patient in the United Kingdom?

    PubMed Central

    Hornsey, Michael; Phee, Lynette; Wareham, David W.

    2011-01-01

    A new variant of the New Delhi metallo-enzyme (NDM) carbapenemase was identified in a multidrug-resistant Escherichia coli ST648 isolate recovered from the perineum and throat of a patient in the United Kingdom with a recent history of hospitalization in India. NDM-5 differed from existing enzymes due to substitutions at positions 88 (Val?Leu) and 154 (Met?Leu) and reduced the susceptibility of E. coli TOP10 transformants to expanded-spectrum cephalosporins and carbapenems when expressed under its native promoter. PMID:21930874

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

    PubMed Central

    2013-01-01

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

  19. 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

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Fast Variants of RSA

    Microsoft Academic Search

    Dan Boneh; Hovav Shacham

    2002-01-01

    We survey three variants of RSA designed to speed up RSA decryption. These variants are backwards compatible in the sense that a system using one of these variants can interoperate with a system using standard RSA.

  4. Complex Serology and Immune Response of Mice to Variant High-Molecular-Weight O Polysaccharides Isolated from Pseudomonas aeruginosa Serogroup O2 Strains

    Microsoft Academic Search

    KAZUE HATANO; GERALD B. PIER

    The O antigen of the Pseudomonas aeruginosa lipopolysaccharide is the optimal target for protective anti- bodies, but the unusual and complex nature of their sugar substituents has made it difficult to define the range of these structures needed in an effective vaccine. Most clinical isolates of P. aeruginosa can be classified into 10 O-antigen serogroups, but slight chemical differences among

  5. 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.

    , isolated from a soil in Alberta, Canada, from a location with a history of severe grasshopper infestations, was evaluated for pathogenicity in bioassays of living grasshoppers. Mortality in treated individuals drawn from. anisopliae var. acridum (IMI 330189). Experimental infection of field-collected grasshoppers under laboratory

  6. Macrophage Tropism and Cytopathicity of HIV-1 Variants Isolated Sequentially from a Long-Term Survivor Infected with nef-Deleted Virus

    PubMed Central

    Gorry, Paul R; McPhee, Dale A; Wesselingh, Steven L; Churchill, Melissa J

    2007-01-01

    Long-term survival of human immunodeficiency virus type 1 (HIV-1) infection has been noted in rare cohorts of individuals infected with nef-deleted virus. Enhanced macrophage tropism and cytopathicity contribute to pathogenicity of wild type HIV-1. To better understand the pathogenesis of nef-deleted HIV-1, we analyzed the replication capacity and macrophage cytopathicity of nef-deleted HIV-1 isolated sequentially from a long-term survivor during progression to AIDS (n=6 isolates). Compared with controls, all nef-deleted viruses replicated to low levels in peripheral blood mononu-clear cells and monocyte-derived macrophages (MDM). One nef-deleted virus that was isolated on the development of AIDS caused high levels of syncytia in MDM similar to control viruses, but five viruses isolated from earlier times prior to AIDS onset caused only minimal cytopathicity. Together, these results suggest that enhanced cytopathicity of nef-deleted HIV-1 for MDM can occur independently of replication capacity, and may contribute to the pathogenesis of nef-deleted HIV-1 infection. PMID:19088897

  7. 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

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

    PubMed Central

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

    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 necessary for resistance to cefepime. PMID:14982805

  9. Characterization of Tn5801.Sag, a variant of Staphylococcus aureus Tn916 family transposon Tn5801 that is widespread in clinical isolates of Streptococcus agalactiae.

    PubMed

    Mingoia, Marina; Morici, Eleonora; Tili, Emily; Giovanetti, Eleonora; Montanari, Maria Pia; Varaldo, Pietro E

    2013-09-01

    Tn5801, originally detected in Staphylococcus aureus Mu50, is a Tn916 family element in which a unique int gene (int5801) replaces the int and xis genes in Tn916 (int916 and xis916). Among 62 tet(M)-positive tetracycline-resistant Streptococcus agalactiae isolates, 43 harbored Tn916, whereas 19 harbored a Tn5801-like element (Tn5801.Sag, ?20.6 kb). Tn5801.Sag was characterized (PCR mapping, partial sequencing, and chromosomal integration) and compared to other Tn5801-like elements. Similar to Tn5801 from S. aureus Mu50, tested in parallel, Tn5801.Sag was unable to undergo circularization and conjugal transfer. PMID:23817370

  10. Characterization of Tn5801.Sag, a Variant of Staphylococcus aureus Tn916 Family Transposon Tn5801 That Is Widespread in Clinical Isolates of Streptococcus agalactiae

    PubMed Central

    Mingoia, Marina; Morici, Eleonora; Tili, Emily; Giovanetti, Eleonora; Montanari, Maria Pia

    2013-01-01

    Tn5801, originally detected in Staphylococcus aureus Mu50, is a Tn916 family element in which a unique int gene (int5801) replaces the int and xis genes in Tn916 (int916 and xis916). Among 62 tet(M)-positive tetracycline-resistant Streptococcus agalactiae isolates, 43 harbored Tn916, whereas 19 harbored a Tn5801-like element (Tn5801.Sag, ?20.6 kb). Tn5801.Sag was characterized (PCR mapping, partial sequencing, and chromosomal integration) and compared to other Tn5801-like elements. Similar to Tn5801 from S. aureus Mu50, tested in parallel, Tn5801.Sag was unable to undergo circularization and conjugal transfer. PMID:23817370

  11. Selection during cefepime treatment of a new cephalosporinase variant with extended-spectrum resistance to cefepime in an Enterobacter aerogenes clinical isolate.

    PubMed

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

    2004-03-01

    Enterobacter aerogenes resistant to cefepime (MIC, 32 microg/ml) was isolated from a patient treated with cefepime for an infection caused by a strain of E. aerogenes overproducing its AmpC beta-lactamase (MIC of cefepime, 0.5 microg/ml). The AmpC beta-lactamase of the resistant strain had an L-293-P amino acid substitution and a high k(cat)/K(m) ratio for cefepime. Both of these modifications were necessary for resistance to cefepime. PMID:14982805

  12. In Vitro Activities of Cephalosporins and Quinolones against Escherichia coli Strains Isolated from Diarrheic Dairy Calves

    PubMed Central

    Orden, José Antonio; Ruiz-Santa-Quiteria, José Antonio; García, Silvia; Cid, Dolores; de la Fuente, Ricardo

    1999-01-01

    The in vitro activities of several cephalosporins and quinolones against 195 strains of Escherichia coli isolated from dairy calves affected by neonatal diarrhea were determined. One hundred thirty-seven of these strains produced one or more potential virulence factors (F5, F41, F17, cytotoxic necrotizing factor, verotoxin, and the eae gene), but the remaining 58 strains did not produce any of these factors. From 11 to 18% of the E. coli strains were resistant to cephalothin, nalidixic acid, enoxacin, and enrofloxacin. However, cefuroxime, cefotaxime, and cefquinome were highly effective against the E. coli isolates tested. Some significant differences (P < 0.05) in resistance to quinolones between the strains producing potential virulence factors and nonfimbriated, nontoxigenic, eae-negative strains were found. Thus, eae-positive, necrotoxigenic, and verotoxigenic (except for nalidixic acid) E. coli strains were significantly more sensitive to nalidixic acid, enoxacin, and enrofloxacin than nonfimbriated, nontoxigenic, eae-negative strains. Moreover, eae-positive strains were significantly more sensitive to enoxacin and enrofloxacin than F5-positive strains. Thus, the results of this study suggest that the bovine E. coli strains that produce some potential virulence factors are more sensitive to quinolones than those that do not express these factors. PMID:10049259

  13. In vitro activities of cephalosporins and quinolones against Escherichia coli strains isolated from diarrheic dairy calves.

    PubMed

    Orden, J A; Ruiz-Santa-Quiteria, J A; García, S; Cid, D; De La Fuente, R

    1999-03-01

    The in vitro activities of several cephalosporins and quinolones against 195 strains of Escherichia coli isolated from diary calves affected by neonatal diarrhea were determined. One hundred thirty-seven of these strains produced one or more potential virulence factors (F5, F41, F17, cytotoxic necrotizing factor, verotoxin, and the eae gene), but the remaining 58 strains did not produce any of these factors. From 11 to 18% of the E. coli strains were resistant to cephalothin, nalidixic acid, enoxacin, and enrofloxacin. However, cefuroxime, cefotaxime, and cefquinome were highly effective against the E. coli isolates tested. Some significant differences (P < 0.05) in resistance to quinolones between the strains producing potential virulence factors and nonfimbriated, nontoxigenic, eae-negative strains were found. Thus, eae-positive, necrotoxigenic, and verotoxigenic (except for nalidixic acid) E. coli strains were significantly more sensitive to nalidixic acid, enoxacin, and enrofloxacin than nonfimbriated, nontoxigenic, eae-negative strains. Moreover, eae-positive strains were significantly more sensitive to enoxacin and enrofloxacin than F5-positive strains. Thus, the result of this study suggest that the bovine E. coli strains that produce some potential virulence factors are more sensitive to quinolones than those that do not express these factors. PMID:10049259

  14. 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

  15. Charge variants in IgG1

    PubMed Central

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

    2010-01-01

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

  16. Reproductive Isolation Isolating Barriers

    E-print Network

    Cruzan, Mitchell B.

    ;Isolating Barriers Premating barriers. Spatial. Geographical isolation Habitat isolation. Temporal. OverlapReproductive Isolation Isolating Barriers: Premating Postmating-Prezygotic Postzygotic #12 in flowering times. Antirrhinum majus striatum Antirrhinum majus pseudomajus #12;Isolating Barriers Premating

  17. Mucopolysaccharidosis: A New Variant?

    ERIC Educational Resources Information Center

    Primrose, D. A.

    1972-01-01

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

  18. 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

  19. Evaluation of a commercial modified live virus fowl pox vaccine for the control of "variant" fowl poxvirus infections.

    PubMed

    Fatunmbi, O O; Reed, W M

    1996-01-01

    Three-week-old specific-pathogen-free chickens were vaccinated with either a commercial modified live virus fowl pox vaccine or five "variant" poxvirus field isolates. Immunity engendered by the commercial modified vaccine or field isolates was challenged with either the variant isolates or commercial modified vaccine virus. The commercial modified vaccine did not adequately protect vaccinates against challenge with the variant isolates. The percentages of vaccinated chickens protected following challenge with each of the variant isolates were 70%, 20%, 30%, 20%, and 25%. However, when the isolates were applied as vaccines, 100% of the vaccinates were protected against challenge from the modified vaccine virus. Furthermore, the variant poxvirus isolates offered excellent protection from challenge with homologous variant isolates. The modified live virus vaccine was expected to offer significant protection against challenge from the variant pox isolates, but in this experiment it did not. The variant isolates tested may be good vaccine candidates to prevent the vaccine breaks currently encountered in previously pox-vaccinated flocks. PMID:8883788

  20. 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

  1. Clostridium difficile genotypes other than ribotype 078 that are prevalent among human, animal and environmental isolates

    PubMed Central

    2012-01-01

    Background Characterising the overlap of C. difficile genotypes in different reservoirs can improve our understanding of possible transmission routes of this pathogen. Most of the studies have focused on a comparison of the PCR ribotype 078 isolated from humans and animals. Here we describe for the first time a comparison of C. difficile genotypes isolated during longer time intervals from different sources including humans, animals and the non-hospital environment. Results Altogether 786 isolates from time interval 2008-2010 were grouped into 90 PCR ribotypes and eleven of them were shared among all host types and the environment. Ribotypes that were most common in humans were also present in water and different animals (014/020, 002, 029). Interestingly, non-toxigenic isolates were very common in the environment (30.8%) in comparison to humans (6.5%) and animals (7.7%). A high degree of similarity was observed for human and animal isolates with PFGE. In human isolates resistance to erithromycin, clindamycin and moxifloxacin was detected, while all animal isolates were susceptible to all antibiotics tested. Conclusion Our results show that many other types in addition to PCR Ribotype 078 are shared between humans and animals and that the most prevalent genotypes in humans have the ability to survive also in the environment and several animal hosts. The genetic relatedness observed with PFGE suggests that transmission of given genotype from one reservoir to the other is likely to occur. PMID:22452857

  2. Splicing variants of porcine synphilin-1?

    PubMed Central

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

    2015-01-01

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

  3. Splicing variants of porcine synphilin-1.

    PubMed

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

    2015-09-01

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

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

    Microsoft Academic Search

    LUIS RUBIO; MARIA ANGELES AYLLON; P. Kong; A. Fernandez; M. Polek; J. Guerri; P. Moreno; B. W. Falk

    2001-01-01

    We examined the population structure and genetic variation of four genomic regions within and between 30 Citrus tristeza virus (CTV) isolates from Spain and California. Our analyses showed that most isolates con- tained a population of sequence variants, with one being predominant. Four isolates showed two major sequence variants in some genomic regions. The two major variants of three of

  5. Comparability of Essay Question Variants

    ERIC Educational Resources Information Center

    Bridgeman, Brent; Trapani, Catherine; Bivens-Tatum, Jennifer

    2011-01-01

    Writing task variants can increase test security in high-stakes essay assessments by substantially increasing the pool of available writing stimuli and by making the specific writing task less predictable. A given prompt (parent) may be used as the basis for one or more different variants. Six variant types based on argument essay prompts from a…

  6. Molecular characterization of a Chinese isolate of potato virus A (PVA) and evidence of a genome recombination event between PVA variants at the 3'-proximal end of the genome.

    PubMed

    He, Changzheng; Zhang, Wei; Hu, Xinxi; Singh, Mathuresh; Xiong, Xingyao; Nie, Xianzhou

    2014-09-01

    Potato plants that exhibited mosaic symptoms were collected in Xiangxi, Hunan province, China. Multiplex RT-PCR screening for common viruses revealed the presence of potato virus A (PVA) in these samples. ELISA with virus-specific antibodies confirmed infection by PVA in the plants. Rod-shaped virions of ~750 nm in length and ~13 nm in width were observed by transmission electron microscopy. One virus isolate (designated PVA-Hunan) was subjected to molecular characterization. The viral genome consisted of 9,567 nucleotides, excluding the poly(A) tail, and encoded a polyprotein of 3,059 amino acids. A second characteristic potyvirus open reading frame (ORF), pretty interesting Potyviridae ORF (pipo), was located at nucleotides 2,834-3,139. The isolate shared 84% to 98% and 93% to 99% sequence identity with other PVA isolates at the nucleotide and amino acid level, respectively. Phylogenetic analysis demonstrated that, within the PVA group, PVA-Hunan clustered most closely with the Finnish isolate Her, then with isolates 143, U, Ali, M and B11. The isolate TamMV stood alone at a separate branch. However, scanning of complete genome sequences using SimPlot revealed 99%-sequence identity between PVA-Hunan and TamMV in the 3'-proximal end of the genome (~nt 9,160 to the 3'end) and a 50%-94% (average~83%) identity upstream of nt 9,160. In contrast, 98% identity between PVA-Hunan and isolates M and B11 was detected for nucleotides 1 to ~9,160, but only ~94% for the 3'-proximal region, suggesting a genome recombination event (RE) at nt 9,133. The recombination breakpoint also was identified by the Recombination Detection Program (RDP). The RE was further confirmed by analysis of the CP gene, where the apparent RE was located. PMID:24722969

  7. The Phylloplane as a Source of Bacillus thuringiensis Variants

    PubMed Central

    Smith, Robert A.; Couche, Graham A.

    1991-01-01

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

  8. 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...

  9. ENZYMATIC VARIANTS OF INFLUENZA VIRUS

    PubMed Central

    Padgett, Billie L.; Walker, Duard L.

    1958-01-01

    The rate of elution of the variant virus from chicken RBC is progressively decreased as the temperature of incubation is increased above 25°C. The activity of the parent virus, on the other hand, is increased as the temperature is increased up to 40°C. The major cause of the decreased activity of the variant at temperatures above 2S°C. is an inhibition of the variant enzyme rather than its inactivation. The activity of the variant enzyme is stimulated in the presence of strontium, calcium, and barium ions. Manganese has only a slight effect, and magnesium has no stimulatory effect on the elution of the variant virus. Elution of the variant at 37°C. is progressively inhibited at pH values above 7, while the parent virus is still active at pH 8. In the absence of calcium the variant enzyme, hemagglutinin, and infectivity are more heat labile than those of the parent virus. The addition of calcium increases the heat stability of all three properties of the variant, and in the presence of calcium the infectivity of the variant is as stable as that of the parent virus. PMID:13587849

  10. The variant course of the suprascapular artery.

    PubMed

    Naidoo, N; Lazarus, L; De Gama, B Z; Satyapal, K S

    2014-05-01

    The suprascapular artery (SSA) has been identified to be of clinical relevance in surgical intervention and fracture healing of the shoulder. Despite the classic description of its course and relation to the superior transverse scapular ligament, it is subject to much variation. The aims of this study were: (i) to describe the course of the SSA in relation to the superior transverse scapular ligament, (ii) tob determine the prevalence of the course of the SSA in relation to the superior transverse scapular ligament, (iii) to determine the prevalence of the variant origin of the SSA in cases presenting with variant course of the latter, and (iv) to establish a difference in laterality and that between adults and foetuses. The course of the SSA was investigated through the macro- and micro dissection of the antero-andpostero-superior shoulder regions of 31 adult and 19 foetal cadaveric specimens (n = 100). The SSA was observed to pass inferior to the superior transverse scapular ligament accompanied by the suprascapular nerve (20%), which corroborated the findings of previous studies. Subsequently, this variant course of the SSA also appeared to present with the variant origin of it in many instances (13%): from the 3rd part of the subclavian artery (4%), 1st part of the axillary artery (2%), 2nd part of the axillary artery (5%) and SSA (2%). Injury to the SSA may cause more serious trauma than that of arteries which are isolated from the great vessels, therefore the recognition and knowledge of variation in the origin and course of the SSA is significant in the treatment of diseases in the shoulder and cervical regions. Furthermore, the accompaniment of the suprascapular nerve with the SSA at the suprascapular notch inferior to the superior transverse scapular ligament may lead to neuropathy syndromes due to the pulsation of the artery against the nerve within the confined notch. PMID:24902100

  11. Sequencing of Peach Latent Mosaic Viroid Variants from Nine North American Peach Cultivars Shows that This RNA Folds into a Complex Secondary Structure

    Microsoft Academic Search

    M. Pelchat; D. Lévesque; J. Ouellet; S. Laurendeau; S. Lévesque; J. Lehoux; D. A. Thompson; K. C. Eastwell; L. J. Skrzeczkowski; J. P. Perreault

    2000-01-01

    We sequenced 34 new peach latent mosaic viroid (PLMVd) variants isolated from nine different peach cultivars. This study provides the widest view of PLMVd diversity reported to date and includes the original characterization of North American variants, which cannot be differentiated from European sequences. PLMVd appears as a species in which each isolate is a complex mixture of RNAs. Analysis

  12. 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

  13. 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.

  14. Rare Copy Number Variants

    PubMed Central

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

    2015-01-01

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

  15. 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

  16. Variant view: visualizing sequence variants in their gene context.

    PubMed

    Ferstay, Joel A; Nielsen, Cydney B; Munzner, Tamara

    2013-12-01

    Scientists use DNA sequence differences between an individual's genome and a standard reference genome to study the genetic basis of disease. Such differences are called sequence variants, and determining their impact in the cell is difficult because it requires reasoning about both the type and location of the variant across several levels of biological context. In this design study, we worked with four analysts to design a visualization tool supporting variant impact assessment for three different tasks. We contribute data and task abstractions for the problem of variant impact assessment, and the carefully justified design and implementation of the Variant View tool. Variant View features an information-dense visual encoding that provides maximal information at the overview level, in contrast to the extensive navigation required by currently-prevalent genome browsers. We provide initial evidence that the tool simplified and accelerated workflows for these three tasks through three case studies. Finally, we reflect on the lessons learned in creating and refining data and task abstractions that allow for concise overviews of sprawling information spaces that can reduce or remove the need for the memory-intensive use of navigation. PMID:24051821

  17. Gene Variants Reduce Opioid Risks

    MedlinePLUS

    ... Prevention Research Training Treatment Research Trends and Statistics Drugs of Abuse Alcohol Amphetamines Bath Salts Club Drugs Cocaine Emerging ... this article APA style citation National Institute on Drug Abuse. Gene Variants Reduce Opioid Risks Retrieved from http:// ...

  18. 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

  19. Complete Genome Sequences of Two Genetically Distinct Variants of Porcine Epidemic Diarrhea Virus in the Eastern Region of Thailand

    PubMed Central

    Cheun-Arom, Thaniwan; Temeeyasen, Gun; Srijangwad, Anchalee; Tripipat, Thitima; Sangmalee, Suphattra; Vui, Dam Thi; Chuanasa, Taksina; Tantituvanont, Angkana

    2015-01-01

    Porcine epidemic diarrhea virus (PEDV) has continued to cause sporadic outbreaks in Thailand since 2007. Previously, PEDV in Thailand was a new variant containing an insertion and deletion in the spike gene. Herein, full-length genome sequences are reported for two variants of PEDV isolates from pigs displaying diarrhea in Thailand. PMID:26112783

  20. Complete Genome Sequences of Two Genetically Distinct Variants of Porcine Epidemic Diarrhea Virus in the Eastern Region of Thailand.

    PubMed

    Cheun-Arom, Thaniwan; Temeeyasen, Gun; Srijangwad, Anchalee; Tripipat, Thitima; Sangmalee, Suphattra; Vui, Dam Thi; Chuanasa, Taksina; Tantituvanont, Angkana; Nilubol, Dachrit

    2015-01-01

    Porcine epidemic diarrhea virus (PEDV) has continued to cause sporadic outbreaks in Thailand since 2007. Previously, PEDV in Thailand was a new variant containing an insertion and deletion in the spike gene. Herein, full-length genome sequences are reported for two variants of PEDV isolates from pigs displaying diarrhea in Thailand. PMID:26112783

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

    PubMed Central

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

    2015-01-01

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

  2. Xanthan gum production by altered pathogenicity variants of Xanthomonas campestris

    Microsoft Academic Search

    Maria Eugenia Ramírez; Leopoldo Fucikovsky; Federico García-Jiménez; Rodolfo Quintero; Enrique Galindo

    1988-01-01

    Several morphologically different isolates of Xanthomonas campestris pv. campestris were obtained by treatment with N-methyl-N'-nitro-N-nitrosoguanidine. These variants were used to infect Brassica plants where several degrees of virulence were found. The strains were cultured in order to produce polysaccharide, which was recovered by precipitation and subjected to physical and chemical characterization. A relationship was noted between virulence and parameters such

  3. A novel antigenic variant of Canine parvovirus from a Vietnamese dog

    Microsoft Academic Search

    M. Nakamura; Y. Tohya; T. Miyazawa; M. Mochizuki; H. T. T. Phung; N. H. Nguyen; L. M. T. Huynh; L. T. Nguyen; P. N. Nguyen; P. V. Nguyen; N. P. T. Nguyen; H. Akashi

    2004-01-01

    Summary. Nine isolates of Canine parvovirus (CPV) were obtained from Vietnamese dogs and cats. One canine isolate showed a unique antigenic property which indicates a novel antigenic variant of CPV-2b when examined with hemagglutination inhibition tests using our monoclonal antibodies, 21C3 and 19D7, which were recently developed. This isolate had an amino acid substitution of residue 426, Asp to Glu,

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

    PubMed

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

    2015-05-01

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

  5. Multiple splice variants of phosphodiesterase PDE4C cloned from human lung and testis

    Microsoft Academic Search

    Rena Obernolte; James Ratzliff; Preston A Baecker; Donald V Daniels; Patti Zuppan; Kurt Jarnagin; Earl R Shelton

    1997-01-01

    Four closely related cyclic-nucleotide specific phosphodiesterase (PDE4) genes have been identified in both humans and rats: PDE4A, 4B, 4C and 4D. We have now cloned cDNAs for multiple splice variants of human PDE4C. Two splice variants, PDE4C-791 and PDE4C-426, were isolated from a fetal lung library. The longest open reading frame (ORF) of 791 amino acids (aa) is encoded by

  6. Distribution of histone variants in the sea urchin chromatin fractions obtained by selective micrococcal nuclease digestion.

    PubMed

    Jasinskiene, N E; Jasinskas, A L; Gineitis, A A

    1985-10-01

    Chromatin fractions differing in their transcriptional activity were isolated by selective micrococcal nuclease digestion of nuclei from sea urchin embryos (Strongylocentrotus droebachiensis) at the gastrula and pluteus stage. The electrophoretic analysis of the chromatin proteins at the gastrula stage showed that a soluble, transcriptionally active fraction of chromatin was enriched with early variants of histones H1 and H2A. The early and late variants of histone H2A at the pluteus stage were distributed randomly between chromatin fractions. However, the content of both variants of histone H1 was essentially decreased in the soluble transcriptionally active fraction of chromatin. PMID:4069105

  7. Comprehensive Assessment of Genetic Variants Within TCF4 in Fuchs' Endothelial Corneal Dystrophy

    PubMed Central

    Wieben, Eric D.; Aleff, Ross A.; Eckloff, Bruce W.; Atkinson, Elizabeth J.; Baheti, Saurabh; Middha, Sumit; Brown, William L.; Patel, Sanjay V.; Kocher, Jean-Pierre A.; Baratz, Keith H.

    2014-01-01

    Purpose. The single nucleotide variant (SNV), rs613872, in the transcription factor 4 (TCF4) gene was previously found to be strongly associated (P = 6 × 10?26) with Fuchs' endothelial corneal dystrophy (FECD). Subsequently, an intronic expansion of the repeating trinucleotides, TGC, was found to be even more predictive of disease. We performed comprehensive sequencing of the TCF4 gene region in order to identify the best marker for FECD within TCF4 and to identify other novel variants that may be associated with FECD. Methods. Leukocyte DNA was isolated from 68 subjects with FECD and 16 unaffected individuals. A custom capture panel was used to isolate the region surrounding the two previously validated markers of FECD. Sequencing of the TCF4 coding region, introns and flanking sequence, spanning 465 kb was performed at >1000× average coverage using the Illumina HiSequation 2000. Results. TGC expansion (>50 repeats) was present in 46 (68%) FECD-affected subjects and one (6%) normal subject. A total of 1866 variants, including 1540 SNVs, were identified. Only two previously reported SNVs resided in the TCF4 coding region, neither of which segregated with disease. No variant, including TGC expansion, correlated perfectly with disease status. Trinucleotide repeat expansion was a better predictor of disease than any other variant. Conclusions. Complete sequencing of the TCF4 genomic region revealed no single causative variant for FECD. The intronic trinucleotide repeat expansion within TCF4 continues to be more strongly associated with FECD than any other genetic variant. PMID:25168903

  8. Different subcellular localizations and functions of human ARD1 variants.

    PubMed

    Seo, Ji Hae; Park, Ji-Hyeon; Lee, Eun Ji; Kim, Kyu-Won

    2015-02-01

    ARD1 is present in various species and has several variants derived from alternative splicing of mRNA. Previously, we reported differential biological functions and cellular distributions of mouse ARD1 (mARD1) variants. However, in comparison to mARD1 variants, human ARD1 (hARD1) variants have been rarely studied. In this study, we characterized a hARD1 variant, hARD1(131) and investigated its cellular activities. hARD1(131) mRNA was isolated from HeLa cells and sequenced. Sequence alignment revealed that, compared to hARD1(235), the most common form of hARD1, the mRNA sequence encoding hARD1131 possesses an altered reading frame due to a 46-bp deletion. Thus, hARD1(131) and hARD1(235) differ in their C-terminal regions with a partially deleted acetyltransferase domain at the C-terminus of hARD1(131). Moreover, hARD1(131) and hARD1(235) showed different subcellular localizations and biological functions. hARD1(131) was mostly localized in the cell nucleus, whereas hARD1(235) was primarily localized in the cytoplasm. In addition, hARD1(235) stimulated cell proliferation by upregulation of cyclin D1, however hARD1(131) had no influence on cyclin D1 expression and cell growth. Because hARD1(235) enhances cell proliferation by its autoacetylation activity, we examined the autoacetylation activity of hARD1(131) and observed that this function was absent in hARD1(131). These results suggest that human ARD1 variants have different effects on cell prolifer-ation, which may result from distinct subcellular localizations and autoacetylation activities. PMID:25421966

  9. Genetic Variants Associated with Port-Wine Stains

    PubMed Central

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

    2015-01-01

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

  10. The isolation of ovomucoid variants differing in carbohydrate composition

    PubMed Central

    Beeley, J. G.

    1971-01-01

    Three major and two minor species of ovomucoid were separated by chromatography on sulphoethyl-Sephadex. The predominant sialic acid-free species was further resolved into three fractions by DEAE-cellulose chromatography. Although all species of ovomucoid had closely similar trypsin-inhibiting activity, immunochemical properties and amino acid composition, they differ in carbohydrate composition. Wide variation was observed in the content of galactose, N-acetylglucosamine and sialic acid. Charge heterogeneity was related, in part, to variation in sialic acid content. The implications of variable carbohydrate composition for the structure and function of ovomucoid are discussed. ImagesFig. 3.Fig. 4. PMID:5001592

  11. Plasmodium falciparum Variant Surface Antigen Expression Patterns during Malaria

    PubMed Central

    2005-01-01

    The variant surface antigens expressed on Plasmodium falciparum–infected erythrocytes are potentially important targets of immunity to malaria and are encoded, at least in part, by a family of var genes, about 60 of which are present within every parasite genome. Here we use semi-conserved regions within short var gene sequence “tags” to make direct comparisons of var gene expression in 12 clinical parasite isolates from Kenyan children. A total of 1,746 var clones were sequenced from genomic and cDNA and assigned to one of six sequence groups using specific sequence features. The results show the following. (1) The relative numbers of genomic clones falling in each of the sequence groups was similar between parasite isolates and corresponded well with the numbers of genes found in the genome of a single, fully sequenced parasite isolate. In contrast, the relative numbers of cDNA clones falling in each group varied considerably between isolates. (2) Expression of sequences belonging to a relatively conserved group was negatively associated with the repertoire of variant surface antigen antibodies carried by the infected child at the time of disease, whereas expression of sequences belonging to another group was associated with the parasite “rosetting” phenotype, a well established virulence determinant. Our results suggest that information on the state of the host–parasite relationship in vivo can be provided by measurements of the differential expression of different var groups, and need only be defined by short stretches of sequence data. PMID:16304608

  12. Evaluation of Perceived Threat Differences Posed by Filovirus Variants

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2014-03-01

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

  14. Analysis of a SHA256 Variant

    Microsoft Academic Search

    Hirotaka Yoshida; Alex Biryukov

    2005-01-01

    \\u000a SHA-256 is a cryptographic hash function which was proposed in 2000 as a new generation of SHA functions and was adopted as\\u000a FIPS standard in 2002. In this paper we will consider a SHA-256 variant and a SHACAL-2 variant in which every arithmetic addition\\u000a is replaced by XOR operation. We call the SHA-256 variant SHA-2-XOR and the SHACAL-2 variant SHACAL-2-XOR

  15. Union de variants abstraits Jacques Garrigue

    E-print Network

    Garrigue, Jacques

    Union de variants abstraits Jacques Garrigue Nagoya University, Grad. Sch. of Mathematics avec Romain Bardou, E.N.S. Cachan #12;J. Garrigue, R. Bardou -- Union de variants abstraits 1 Union concr -> show_v y val show : t -> unit #12;J. Garrigue, R. Bardou -- Union de variants abstraits 2 Union concr

  16. Finding palindromes: variants and Johan Jeuring

    E-print Network

    Utrecht, Universiteit

    Finding palindromes: variants and algorithms Johan Jeuring Technical Report UU-CS-2013.089 3508 TB Utrecht The Netherlands #12;Finding palindromes: variants and algorithms Johan Jeuring1,2 1 of finding palindromes in strings appears in many variants: find exact palindromes, ignore punctuation

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Unusual variants of malignant melanoma

    Microsoft Academic Search

    Cynthia M Magro; A Neil Crowson; Martin C Mihm

    2006-01-01

    A potential diagnostic pitfall in the histologic assessment of melanoma is the inability to recognize unusual melanoma variants. Of these, the more treacherous examples include the desmoplastic melanoma, the nevoid melanoma, the so-called ‘minimal-deviation melanoma,’ melanoma with prominent pigment synthesis or ‘animal-type melanoma,’ and the malignant blue nevus. Also problematic are the unusual phenotypic profiles seen in vertical growth phase

  6. Isolated genital annular lichen planus.

    PubMed

    Badri, T; Kenani, N; Benmously, R; Debbiche, A; Mokhtar, I; Fenniche, S

    2011-01-01

    Annular lichen planus is a rarely reported variant of lichen planus (LP). Although genital lesions are frequent in patients with LP, isolated genital LP is rarely reported. We present a case of a 29-year- -old circumcised man with an asymptomatic annular lesion of the penis. Histopathological features were consistent with LP. Topical clobetasol was prescribed, with clinical improvement. It is important to consider annular LP among the possible diagnoses of individual annular genital lesions. PMID:21879203

  7. 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

  8. Growth control variant cell line having increased serum requirement and decreased response to platelet-derived growth factor: reversion by 5- azacytidine

    Microsoft Academic Search

    DANIEL S. STRAUS; DONALD L. COPPOCK

    1984-01-01

    Variants of the mouse embryo fibroblast x melanoma hybrid clone 100A have been isolated by a procedure that selects against cells that are able to grow in medium containing low concentrations of serum plus insulin. Three variant clones derived from this selection were found to have a much higher serum requirement than the parental clone 100A cells, as evidenced by

  9. 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

  10. SEQUENCE ANALYSIS OF THE SMALL RNA SEGMENT OF GUINEA PIG-PASSAGED PICHINDE VIRUS VARIANTS

    Microsoft Academic Search

    LIHONG ZHANG; KATHLEEN MARRIOTT; JUDITH F. ARONSON

    1999-01-01

    The established animal model for Lassa fever is based on the new world arenavirus Pichinde (PIC). Natural isolates of PIC virus are attenuated in guinea pigs, but serial guinea pig passage renders them extremely virulent in that host. We have compared the nucleotide sequences of the small RNA segments of two attenuated, low- passage variants of the PIC virus Munchique

  11. 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

  12. The KRAS-Variant and miRNA Expression in RTOG Endometrial Cancer Clinical Trials 9708 and 9905

    PubMed Central

    Uduman, Mohamed; Winter, Kathryn; Boeke, Marta; Greven, Kathryn M.; King, Stephanie; Burke, Thomas W.; Underhill, Kelly; Kim, Harold; Boulware, Raleigh J.; Yu, Herbert; Parkash, Vinita; Lu, Lingeng; Gaffney, David; Dicker, Adam P.; Weidhaas, Joanne

    2014-01-01

    Objective To explore the association of a functional germline variant in the 3?-UTR of KRAS with endometrial cancer risk, as well as the association of microRNA (miRNA) signatures and the KRAS-variant with clinical characteristics and survival outcomes in two prospective RTOG endometrial cancer trials. Methods/Materials The association of the KRAS-variant with endometrial cancer risk was evaluated by case-control analysis of 467 women with type 1 or 2 endometrial cancer and 582 age-matched controls. miRNA and DNA were isolated for expression profiling and genotyping from tumor specimens of 46 women with type 1 endometrial cancer enrolled in RTOG trials 9708 and 9905. miRNA expression levels and KRAS-variant genotype were correlated with patient and tumor characteristics, and survival outcomes were evaluated by variant allele type. Results The KRAS-variant was not significantly associated with overall endometrial cancer risk (14% controls and 17% type 1 cancers), although was enriched in type 2 endometrial cancers (24%, p?=?0.2). In the combined analysis of RTOG 9708/9905, miRNA expression differed by age, presence of lymphovascular invasion and KRAS-variant status. Overall survival rates at 3 years for patients with the variant and wild-type alleles were 100% and 77% (HR 0.3, p?=?0.24), respectively, favoring the variant. Conclusions The KRAS-variant may be a genetic marker of risk for type 2 endometrial cancers. In addition, tumor miRNA expression appears to be associated with patient age, lymphovascular invasion and the KRAS-variant, supporting the hypothesis that altered tumor biology can be measured by miRNA expression, and that the KRAS-variant likely impacts endometrial tumor biology. PMID:24732316

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

    PubMed Central

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

    2014-01-01

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

  14. 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, Tőnu; 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?ąą?). 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

  15. 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...

  16. 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...

  17. 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

  18. Vibration isolation

    NASA Technical Reports Server (NTRS)

    Bastin, Paul

    1990-01-01

    Viewgraphs on vibration isolation are presented. Techniques to control and isolate centrifuge disturbances were identified. Topics covered include: disturbance sources in the microgravity environment; microgravity assessment criteria; life sciences centrifuge; flight support equipment for launch; active vibration isolation system; active balancing system; and fuzzy logic control.

  19. Simulating realistic genomic data with rare variants

    PubMed Central

    Xu, Yaji; Wu, Yinghua; Song, Chi; Zhang, Heping

    2012-01-01

    Increasing evidence suggests that rare and generally deleterious genetic variants might have strong impact on disease risks of not only Mendelian disease, but also many common diseases. However, identifying such rare variants remains to be challenging, and novel statistical methods and bioinformatic software must be developed. Hence, we have to extensively evaluate various methods under reasonable genetic models. While there are abundant genomic data, they are not most helpful for the evaluation of the methods because the disease mechanism is unknown. Thus, it is imperative that we simulate genomic data that mimic the real data containing rare variants and that enable us to impose a known disease penetrance model. Although resampling simulation methods have shown their advantages in computational efficiency and in preserving important properties such as linkage disequilibrium (LD) and allele frequency, they still have limitations as we demonstrated. We propose an algorithm that combines a regression-based imputation with resampling to simulate genetic data with both rare and common variants. Logistic regression model was employed to fit the relationship between a rare variant and its nearby common variants in the 1000 Genomes Project data and then applied to the real data to fill in one rare variant at a time using the fitted logistic model based on common variants. Individuals then were simulated using the real data with imputed rare variants. We compared our method with existing simulators and demonstrated that our method performed well in retaining the real sample properties, such as LD and minor allele frequency, qualitatively. PMID:23161487

  20. Small colony variants of Staphylococcus aureus--review.

    PubMed

    Melter, O; Radojevi?, B

    2010-11-01

    Bacterial variants of Staphylococcus aureus called small colony variants (SCVs) originate by mutations in metabolic genes, resulting in emergence of auxotrophic bacterial subpopulations. These variants are not particularly virulent but are able to persist viable inside host cells. SCVs show their characteristic auxotrophic growth deficiency and depressed ?-cytotoxin activity. Environmental pressure such as antibiotics, select for isogenic SCV cells that are frequently found coexisting with their parent wild-type strains in a mixed bacterial culture. SCV strains often grow on blood agar as non-pigmented or pinpoint pigmented colonies and their key biochemical tests are often non-reactive. Their altered metabolism or auxotrophism can result in long generation time and thus SCV phenotype, more often than not SCV can be overgrown by their wild-type counterparts and other competitive respiratory flora. This could affect laboratory detection. Thus, molecular methods, such as 16S rRNA partial sequencing or amplification of species-specific DNA targets (e.g. coagulase, nuclease) directly from clinical material or isolated bacterial colonies, become the method of choice. Patients at risk of infection by S. aureus SCVs include cystic fibrosis patients (CF), patients with skin and foreign-body related infections and osteomyelitis, as they suffer from chronic staphylococcal infections and are subject to long-term antibiotic therapy. Molecular evidence of SCV development has not been found except for some random mutations of the thymidylate synthase gene (thyA) described in SCV S. aureus strains of CF patients. These variants are able to bypass the antibiotic effect of folic acid antagonists such as sulfonamides and trimethoprim. Resistance to gentamicin and aminoglycosides in the hemin or menadione auxotrophic SCVs was hypothesized as being due to decreased influx of the drugs into cells as a result of decreased ATP production and decreased electrochemical gradient on cell membranes. PMID:21253898

  1. Population structure of Citrus tristeza virus from field Argentinean isolates.

    PubMed

    Iglesias, Néstor G; Gago-Zachert, Selma P; Robledo, Germán; Costa, Norma; Plata, María Inés; Vera, Osmar; Grau, Oscar; Semorile, Liliana C

    2008-02-01

    We studied the genetic variability of three genomic regions (p23, p25 and p27 genes) from 11 field Citrus tristeza virus isolates from the two main citrus growing areas of Argentina, a country where the most efficient vector of the virus, Toxoptera citricida, is present for decades. The pathogenicity of the isolates was determinated by biological indexing, single-strand conformation polymorphism analysis showed that most isolates contained high intra-isolate variability. Divergent sequence variants were detected in some isolates, suggesting re-infections of the field plants. Phylogenetic analysis of the predominant sequence variants of each isolate revealed similar grouping of isolates for genes p25 and p27. The analysis of p23 showed two groups contained the severe isolates. Our results showed a high intra-isolate sequence variability suggesting that re-infections could contribute to the observed variability and that the host can play an important role in the selection of the sequence variants present in these isolates. PMID:17999168

  2. Standard and Swedish variant types of the hybrid alder Phytophthora attacking alder in Hungary.

    PubMed

    Nagy, Zoltán A; Bakonyi, József; Ersek, Tibor

    2003-04-01

    A new Phytophthora disease of common alder (Alnus glutinosa) similar to that previously reported in several countries in Europe has been observed in Hungary. Based on these earlier studies, the alder Phytophthora was considered likely to be a hybrid between P cambivora and a P fragariae-like species: across Europe a range of new alder Phytophthora is spreading that comprise a range of heteroploid hybrids including a 'standard' hybrid type and several other hybrid types termed 'variants'. Phenotypic and molecular features of the pathogen in Hungary were characterised and compared with isolates from elsewhere. The morphologies of five isolates from one region (Hévíz) resembled the common, 'standard' type, whereas the three isolates from another region (Hanság) exhibited traits similar to those of one of the 'variant' types, ie the Swedish 'variant'. Molecular markers of these two groups of Hungarian isolates also represented a good fit to those of the standard type and the Swedish variant, respectively. Isozyme patterns and profiles of restriction fragments of the entire internal transcribed spacer (ITS) region or mitochondrial DNAs and of RAPD-PCR products did not differ within a group, but distinct polymorphisms were exhibited between the two groups of isolates. Southern analysis of random amplified polymorphic DNA (RAPD) revealed the homologous nature of co-migrating bands of P cambivora and the isolates of alder Phytophthora. Furthermore, restriction fragment profiles of the ITS region of ribosomal DNAs and the mtDNAs were consistent with reported biparental origin of alder Phytophthora. The hybrid status of these continuously evolving pathogens raises many issues and challenges concerning efficient control measures. PMID:12701711

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Yan, Xinghong

    1993-09-01

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

  5. 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

  6. Efficient Variants of the ICP Algorithm

    Microsoft Academic Search

    Szymon Rusinkiewicz; Marc Levoy

    2001-01-01

    The ICP (Iterative Closest Point) algorithm is widely used for ge- ometric alignment of three-dimensional models when an initial estimate of the relative pose is known. Many variants of ICP have been proposed, affecting all phases of the algorithm from the se- lection and matching of points to the minimization strategy. We enumerate and classify many of these variants, and

  7. Physiological responses of somaclonal variants of triploid bermudagrass (Cynodon transvaalensis x Cynodon dactylon) to drought stress.

    PubMed

    Lu, Shaoyun; Chen, Chuanhao; Wang, Zhongcheng; Guo, Zhenfei; Li, Haihang

    2009-03-01

    Eight somaclonal variants with enhanced drought tolerance were isolated from regenerated plants of triploid bermudagrass (Cynodon dactylon x Cynodon transvaalensis cv., TifEagle). Three of them (10-17, 89-02, 117-08) with strong drought tolerance were selected for investigations of physiological responses to drought stress. Compared to the parent control, TifEagle, the somaclonal variants had higher relative water contents and relative growth, and lower ion leakages in the greenhouse tests, while no difference in evapotranspirational water losses and soil water contents was observed between the variants and TifEagle. The variants also had less leaf firing in the field tests under drought stress. Superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities decreased gradually in responses to drought stress in all plants and exhibited negative correlations with ion leakage, indicating that the declined activities of these antioxidant enzymes were associated with drought injury in the triploid bermudagrass. However, CAT activities were significantly higher in all three variants than in TifEagle during drought stress. Two variants, 10-17 and 89-02, also had significantly higher APX activities than TifEagle before and during the first 4 days of drought treatments. These two lines also showed higher SOD activities after prolonged drought stress. Proline, total soluble sugars and sucrose were accumulated under drought stress in all plants and exhibited positive correlations with ion leakage. More proline and sugars were accumulated in TifEagle than in the variants. The results indicated that higher activities of the antioxidant enzymes in the variants during drought stress are associated with their increased drought tolerance. PMID:19050896

  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. Assessment of aflatoxin and cyclopiazonic acid production by Aspergillus flavus isolates from Hungary

    Microsoft Academic Search

    J. L. Richard; Deepak Bhatnagar; S. Peterson; G. Sandor

    1992-01-01

    Thirty-two isolates of Aspergillus flavus were obtained from various sources in Hungary. All isolates were morphologically identified as A. flavus and three atypical variants were confirmed as A. flavus by comparing their DNA with an ex type culture of A. flavus. None of these isolates produced aflatoxins when tested on coconut agar or grown on rice medium and culture extracts

  10. Isolated Storage

    Microsoft Academic Search

    Fabio Claudio Ferracchiati; Emanuele Garofalo

    \\u000a The isolated storage in Silverlight for Windows Phone 7 follows in some ways the architectural model used for the desktop\\u000a version. The concept of this storage is to isolate the physical memory of one application from another. Isolated storage undoubtedly\\u000a has its advantages: the application’s data is available only to us, which means that no one else can compromise security

  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. Measuring missing heritability: Inferring the contribution of common variants

    E-print Network

    Golan, David

    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 ...

  13. 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

  14. Two distinct sites are essential for virulent infection and support of variant satellite RNA replication in spontaneous beet black scorch virus variants.

    PubMed

    Xu, Jin; Wang, Xianbing; Shi, Lindan; Zhou, Yuan; Li, Dawei; Han, Chenggui; Zhang, Ziding; Yu, Jialin

    2012-12-01

    Spontaneous point mutations of virus genomes are important in RNA virus evolution and often result in modifications of their biological properties. Spontaneous variants of beet black scorch virus (BBSV) and its satellite (sat) RNA were generated from cDNA clones by serial propagation in Chenopodium amaranticolor and Nicotiana benthamiana. Inoculation with recombinant RNAs synthesized in vitro revealed BBSV variants with divergent infectious phenotypes that affected either symptom expression or replication of satRNA variants. Sequence alignments showed a correlation between the phenotypes and distinct BBSV genomic loci in the 3'UTR or in the domain encoding the viral replicase. Comparative analysis between a virulent variant, BBSV-m294, and the wild-type (wt) BBSV by site-directed mutagenesis indicated that a single-nucleotide substitution of a uridine to a guanine at nt 3477 in the 3'UTR was responsible for significant increases in viral pathogenicity. Gain-of-function analyses demonstrated that the ability of the BBSV variants to support replication of variant satRNAs was mainly determined by aa 516 in the P82 replicase. In this case, an arginine substitution for a glutamine residue was essential for high levels of replication, and alterations of other residues surrounding position 516 in the wtBBSV isolate led to only minor phenotypic effects. These results provide evidence that divergence of virus functions affecting pathogenicity and supporting parasitic replication can be determined by a single genetic site, either a nucleotide or an amino acid. The results suggest that complex interactions occur between virus and associated satRNAs during virus evolution. PMID:22971822

  15. Guillain-Barré Syndrome and Variants

    PubMed Central

    Barohn, Richard J.

    2014-01-01

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

  16. Environmental responses mediated by histone variants.

    PubMed

    Talbert, Paul B; Henikoff, Steven

    2014-11-01

    Fluctuations in the ambient environment can trigger chromatin disruptions, involving replacement of nucleosomes or exchange of their histone subunits. Unlike canonical histones, which are available only during S-phase, replication-independent histone variants are present throughout the cell cycle and are adapted for chromatin repair. The H2A.Z variant mediates responses to environmental perturbations including fluctuations in temperature and seasonal variation. Phosphorylation of histone H2A.X rapidly marks double-strand DNA breaks for chromatin repair, which is mediated by both H2A and H3 histone variants. Other histones are used as weapons in conflicts between parasites and their hosts, which suggests broad involvement of histone variants in environmental responses beyond chromatin repair. PMID:25150594

  17. Molecular analysis of the nucleoprotein gene of canine distemper virus isolated from clinical cases of the disease in foxes, minks and dogs.

    PubMed

    Adaszek, ?; Winiarczyk, S; Maj, J; Jankowski, ?; Zietek-Barszcz, A; Skrzypczak, M

    2009-01-01

    In this study, we used RT-PCR to detect and characterize canine distemper virus isolated from 9 naturally infected foxes, 3 minks and 3 dogs in Poland by amplifying and sequencing a portion of the NP gene. A 293-bp fragment of the CDV NP gene was amplified by RT-PCR. Sequencing of the PCR products from the isolates led to the identification of 3 sequence variants. The mostly representative polymorphic variant No. 1 showed high homology with Chinese isolate of CDV with a accession number EF 375619. The sequences of all isolates from this polymorphic variants compared with the sequences of other polymorphic variants obtained in the study and with European and American isolates sequences from GenBank showed the conservative nucleotides changes in positions 57, 132, 143, 159 and 237. These mutations can indicate that in this part of Europe there are new variants of CDV. PMID:20169915

  18. 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

  19. GM2 gangliosidosis variant B1

    Microsoft Academic Search

    Salvatore Grosso; Maria Angela Farnetani; Rosario Berardi; Maria Margollicci; Paolo Galluzzi; Rossella Vivarelli; Guido Morgese; Paolo Ballestri

    2003-01-01

    .   Variant B1 is a rare type of GM2 gangliosidosis. Clinically, it shows a wide spectrum of forms ranging from infantile to\\u000a juvenile. We report the first magnetic resonance imaging (MRI) findings from three patients affected by GM2 gangliosidosis\\u000a variant B1, two presenting with the infantile form and one with the juvenile form. The MRI appearances of the two patients

  20. Sequence variation of human 28S rRNA and expression of variants in different tissues

    SciTech Connect

    Sylvester, J.E.; Gonzalez, I.L.; Gillespie, D.A. [Hahnemann Univ., Philadelphia, PA (United States)] [and others

    1994-09-01

    There are 400 or so copies of the ribosomal RNA (rRNA) gene in humans. Previous studies have shown that human 28S encoding rDNA, and therefore rRNAs, vary in sequence at specific locations termed variable regions; these variations appear in a population and within an individual. This study asked the following questions regarding one variable region (V5) within 28S rRNA gene sequence variation in a single individual: (1) what is the extent and nature of the sequence variation at the DNA level?; (2) are these variant rRNA genes expressed?; (3) does rRNA gene sequence variation result in rRNA structural variation?; (4) is there evidence of differential expression of variant rRNA genes?. To address these four questions, genomic copies of the V5 region were cloned from the individual and sequenced. Six unique sequences were found among seven V5 clones, each differing only in the number of repeats of simple sequences (CGG), (TG), (T), and (C) at a specific site of the V5 region. Computer-generated secondary structure models of each of these variants indicated that the basic structure was not compromised. To test for V5 variant expression in different tissues of an individual, RNAs isolated from different tissues were used to protect each of the cloned V5 variant probes in the RNase protection assay (RPA). We conclude from the RPA results that different variants are present in proportionately different amounts in each tissue tested; however, the relative proportion of variants are similar in these tissues.

  1. 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

  2. Characterization of susceptibility variants of influenza virus grown in the presence of T-705.

    PubMed

    Daikoku, Tohru; Yoshida, Yoshihiro; Okuda, Tomoko; Shiraki, Kimiyasu

    2014-01-01

    T-705 (favipiravir) is a potent inhibitor of RNA polymerases of influenza viruses. Susceptibility variants were isolated during passages in the presence of T-705. Nine variants with 0.4 to 2.1 times the 50% inhibitory concentration for plaque formation of the parent A/PR/8/34 (H1N1) strain had amino acid variations in the PB1, PB2, and PA genes of the RNA polymerase complex. However, the variation patterns in the RNA polymerase complex indicated that T-705 does not work as a mutagen, and resistant mutants were not isolated, possibly because a mutation leading to resistance would be lethal to the RNA polymerase function. PMID:25296868

  3. Demography and the Age of Rare Variants

    PubMed Central

    Mathieson, Iain; McVean, Gil

    2014-01-01

    Large whole-genome sequencing projects have provided access to much rare variation in human populations, which is highly informative about population structure and recent demography. Here, we show how the age of rare variants can be estimated from patterns of haplotype sharing and how these ages can be related to historical relationships between populations. We investigate the distribution of the age of variants occurring exactly twice ( variants) in a worldwide sample sequenced by the 1000 Genomes Project, revealing enormous variation across populations. The median age of haplotypes carrying variants is 50 to 160 generations across populations within Europe or Asia, and 170 to 320 generations within Africa. Haplotypes shared between continents are much older with median ages for haplotypes shared between Europe and Asia ranging from 320 to 670 generations. The distribution of the ages of haplotypes is informative about their demography, revealing recent bottlenecks, ancient splits, and more modern connections between populations. We see the effect of selection in the observation that functional variants are significantly younger than nonfunctional variants of the same frequency. This approach is relatively insensitive to mutation rate and complements other nonparametric methods for demographic inference. PMID:25101869

  4. Characterizing genetic variants for clinical action.

    PubMed

    Ramos, Erin M; Din-Lovinescu, Corina; Berg, Jonathan S; Brooks, Lisa D; Duncanson, Audrey; Dunn, Michael; Good, Peter; Hubbard, Tim J P; 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

    2014-03-01

    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 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

  5. Full-Length Genome Sequence of a Variant Porcine Epidemic Diarrhea Virus Strain, CH/GDZQ/2014, Responsible for a Severe Outbreak of Diarrhea in Piglets in Guangdong, China, 2014

    PubMed Central

    Song, Deping; Chen, Yanjun; Peng, Qi; Huang, Dongyan; Zhang, Tiansheng; Huang, Tao; Zhang, Fanfan; Zhou, Xinrong

    2014-01-01

    The full-length genome sequence of a variant porcine epidemic diarrhea virus (PEDV) strain, CH/GDZQ/2014, was determined. The isolate was a variant strain with a relatively far relationship with the PEDV strains previously identified in the same area between 2011 and 2012 and was genetically distinct from the CV777-based vaccine strain currently being used in China. PMID:25477403

  6. 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

  7. Super Spy variants implicate flexibility in chaperone action.

    PubMed

    Quan, Shu; Wang, Lili; Petrotchenko, Evgeniy V; Makepeace, Karl At; Horowitz, Scott; Yang, Jianyi; Zhang, Yang; Borchers, Christoph H; Bardwell, James Ca

    2014-01-01

    Experimental study of the role of disorder in protein function is challenging. It has been proposed that proteins utilize disordered regions in the adaptive recognition of their various binding partners. However apart from a few exceptions, defining the importance of disorder in promiscuous binding interactions has proven to be difficult. In this paper, we have utilized a genetic selection that links protein stability to antibiotic resistance to isolate variants of the newly discovered chaperone Spy that show an up to 7 fold improved chaperone activity against a variety of substrates. These "Super Spy" variants show tighter binding to client proteins and are generally more unstable than is wild type Spy and show increases in apparent flexibility. We establish a good relationship between the degree of their instability and the improvement they show in their chaperone activity. Our results provide evidence for the importance of disorder and flexibility in chaperone function. DOI: http://dx.doi.org/10.7554/eLife.01584.001. PMID:24497545

  8. Social isolation.

    PubMed

    Cacioppo, John T; Hawkley, Louise C; Norman, Greg J; Berntson, Gary G

    2011-08-01

    Social species, by definition, form organizations that extend beyond the individual. These structures evolved hand in hand with behavioral, neural, hormonal, cellular, and genetic mechanisms to support them because the consequent social behaviors helped these organisms survive, reproduce, and care for offspring sufficiently long that they too reproduced. Social isolation represents a lens through which to investigate these behavioral, neural, hormonal, cellular, and genetic mechanisms. Evidence from human and nonhuman animal studies indicates that isolation heightens sensitivity to social threats (predator evasion) and motivates the renewal of social connections. The effects of perceived isolation in humans share much in common with the effects of experimental manipulations of isolation in nonhuman social species: increased tonic sympathetic tonus and HPA activation; and decreased inflammatory control, immunity, sleep salubrity, and expression of genes regulating glucocorticoid responses. Together, these effects contribute to higher rates of morbidity and mortality in older adults. PMID:21651565

  9. Yield of stool culture with isolate toxin testing versus a two-step algorithm including stool toxin testing for detection of toxigenic Clostridium difficile.

    PubMed

    Reller, Megan E; Lema, Clara A; Perl, Trish M; Cai, Mian; Ross, Tracy L; Speck, Kathleen A; Carroll, Karen C

    2007-11-01

    We examined the incremental yield of stool culture (with toxin testing on isolates) versus our two-step algorithm for optimal detection of toxigenic Clostridium difficile. Per the two-step algorithm, stools were screened for C. difficile-associated glutamate dehydrogenase (GDH) antigen and, if positive, tested for toxin by a direct (stool) cell culture cytotoxicity neutralization assay (CCNA). In parallel, stools were cultured for C. difficile and tested for toxin by both indirect (isolate) CCNA and conventional PCR if the direct CCNA was negative. The "gold standard" for toxigenic C. difficile was detection of C. difficile by the GDH screen or by culture and toxin production by direct or indirect CCNA. We tested 439 specimens from 439 patients. GDH screening detected all culture-positive specimens. The sensitivity of the two-step algorithm was 77% (95% confidence interval [CI], 70 to 84%), and that of culture was 87% (95% CI, 80 to 92%). PCR results correlated completely with those of CCNA testing on isolates (29/29 positive and 32/32 negative, respectively). We conclude that GDH is an excellent screening test and that culture with isolate CCNA testing detects an additional 23% of toxigenic C. difficile missed by direct CCNA. Since culture is tedious and also detects nontoxigenic C. difficile, we conclude that culture is most useful (i) when the direct CCNA is negative but a high clinical suspicion of toxigenic C. difficile remains, (ii) in the evaluation of new diagnostic tests for toxigenic C. difficile (where the best reference standard is essential), and (iii) in epidemiologic studies (where the availability of an isolate allows for strain typing and antimicrobial susceptibility testing). PMID:17804652

  10. Efficacy of commercial canarypox vaccine for protecting Hawai'i 'Amakihi from field isolates of Avipoxvirus

    USGS Publications Warehouse

    Atkinson, Carter T.; Wiegand, Kimberly C.; Triglia, Dennis; Jarvi, Susan I.

    2010-01-01

    At least three variants of avian pox virus are present in Hawai‘i - Fowlpox from domestic poultry and a group of genetically distinct viruses that cluster within two clades (Pox Variant 1 and Pox Variant 2) that are most similar to Canarypox based on DNA sequence of the virus 4b core protein gene. We tested whether Hawai‘i ‘Amakihi can be protected from wild virus isolates with an attenuated live Canarypox vaccine that is closely related to isolates that cluster within clade 1 (Pox Variant 1) based on sequence of the attenuated Canarypox virus 4b core protein. Thirty-one (31) Hawai`i ‘Amakihi (Hemignathus virens) with no prior physical evidence of pox infection were collected on Mauna Kea from xeric, high elevation habitats with low pox prevalence and randomly divided into two groups. One group of 16 was vaccinated with Poximmune C® while the other group received a sham vaccination with virus diluent. Four of 15 (27%) vaccinated birds developed potentially life-threatening disseminated lesions or lesions of unusually long duration, while one bird never developed a vaccine-associated lesion or "take". After vaccine-associated lesions healed, vaccinated birds were randomly divided into three groups of five and challenged with either a wild isolate of Fowlpox, a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 1 (Pox Variant 1) or a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 2 (Pox Variant 2). Similarly, three random groups of five unvaccinated ‘Amakihi were challenged with the same virus isolates. Vaccinated and unvaccinated ‘Amakihi challenged with Fowlpox had transient infections with no clinical signs of infection. Mortality in vaccinated ‘Amakihi that were challenged with Pox Variant 1 and Pox Variant 2 ranged from 0% (0/5) for Pox Variant 1 to 60% (3/5) for Pox Variant 2. Mortality in unvaccinated ‘Amakihi ranged from 40% (2/5) for Pox Variant 1 to 100% (5/5) for Pox Variant 2. While the vaccine provided some protection against Pox Variant 1, serious side effects and low efficacy against Pox Variant 2 make it risky to use in captive or wild honeycreepers.

  11. [Natural pathogenicity for man of an antigenic variant of Soldado virus from Morocco (author's transl)].

    PubMed

    Chastel, C; Bailly-Choumara, H; Le Lay, G

    1981-01-01

    Pathogenicity of Soldado virus was clearly established in the past for seabirds but remained questionable for man. In a scientist, repeatedly bitten by Ornithodoros (A.) maritimus larvae at Essaouira (Morocco), the association of fever of unknown origin and of neutralizing antibody against an antigenic variant of Soldado virus isolated from the same place, lead to the conclusion that this virus may act as a pathogen for man. Epidemiological implications of such an observation are briefly discussed. PMID:6274527

  12. 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.

  13. Plasmodium falciparum Parasites Expressing Pregnancy-Specific Variant Surface Antigens Adhere Strongly to the Choriocarcinoma Cell Line BeWo

    PubMed Central

    Haase, Rikke N.; Megnekou, Rosette; Lundquist, Maja; Ofori, Michael F.; Hviid, Lars; Staalsoe, Trine

    2006-01-01

    Placenta-sequestering Plasmodium falciparum parasites causing pregnancy-associated malaria express pregnancy-specific variant surface antigens (VSAPAM). We report here that VSAPAM-expressing patient isolates adhere strongly to the choriocarcinoma cell line BeWo and that the BeWo line can be used to efficiently select for VSAPAM expression in vitro. PMID:16622246

  14. Consensus sequence determination and elucidation of the evolutionary history of a rotavirus Wa variant reveal a close relationship to various Wa variants derived from the original Wa strain.

    PubMed

    Wentzel, Johannes F; Yuan, Lijuan; Rao, Shujing; van Dijk, Alberdina A; O'Neill, Hester G

    2013-12-01

    The consensus nucleotide sequence of a human rotavirus Wa strain, with only a partially known passage history, was determined with sequence-independent amplification and next generation 454® pyrosequencing. This rotavirus Wa strain had the expected genome constellation of G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and was designated RVA/Human-tc/USA/WaCS/1974/G1P[8]. Phylogenetic analyses revealed a close relationship to four human rotavirus Wa variants (Wag5re, Wag7/8re, ParWa and VirWa) derived from the original 1974 human isolate. There were rearrangements in the Wag5re- and Wag7/8re variants in genome segments 5 (Wag5re) and 7 and 8 (Wag7/8re), which were not present in WaCS. Pairwise comparisons and a combined molecular clock for the Wa rotavirus genome indicated a close relationship between WaCS and ParWa and VirWa. These results suggest that WaCS is most probably an early cell culture adapted variant from the initial gnotobiotic pig passaged Wa isolate. Evolutionary pressure analysis identified a possible negative selected amino acid site in VP1 (genome segment 1) and a likely positive selected site in VP4 (genome segment 4). The WaCS may be more appropriate as a rotavirus Wa reference sequence than the current composite Wa reference genome. PMID:24056015

  15. Heat sensitivity in a bentgrass variant. Failure to accumulate a chloroplast heat shock protein isoform implicated in heat tolerance.

    PubMed

    Wang, Dongfang; Luthe, Dawn S

    2003-09-01

    Two variants of creeping bentgrass (Agrostis stolonifera cv palustris), developed using tissue culture, have been used to determine the roles of chloroplast-localized small heat shock proteins (CP-sHSPs) in heat tolerance. Results from previous research indicate that the heat-tolerant variant expressed two additional CP-sHSP isoforms not expressed in the heat-sensitive variant, that accumulation of the additional CP-sHSP isoforms was genetically linked to thermotolerance, and that the presence of the additional isoforms in the heat-tolerant variant provided greater protection to photosystem II during heat stress. To determine the basis of the differential expression, we isolated the genes encoding the CP-sHSPs from both variants and characterized their structure and expression. Two genes, ApHsp26.2 and ApHsp26.7a, were isolated from the heat-tolerant variant, and three genes, ApHsp26.2m, ApHsp26.8, and ApHsp26.7b, were isolated from the heat-sensitive variant. The sequence of ApHsp26.2m from the heat-sensitive variant was identical to ApHsp26.2, except for a point mutation that generated a premature stop codon. Therefore, the protein product of ApHsp26.2m did not accumulate in the heat-sensitive line. Mass spectrometry analysis confirmed that ApHsp26.2 encoded for the CP-sHSP isoforms unique to the heat-tolerant variant. An identical mutation was detected in one of the three parental lines used to develop the creeping bentgrass variants. This suggests that ApHsp26.2m was inherited from this parent and did not arise from a mutation that occurred during tissue culture. The presence of two isoforms encoded by the same gene might be due to differential processing of the N-terminal amino acids during or after import into the chloroplast. PMID:12970497

  16. Allele Variants of Enterotoxigenic Escherichia coli Heat-Labile Toxin Are Globally Transmitted and Associated with Colonization Factors

    PubMed Central

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

    2014-01-01

    Enterotoxigenic Escherichia coli (ETEC) is a significant cause of morbidity and mortality in the developing world. ETEC-mediated diarrhea is orchestrated by heat-labile toxin (LT) and heat-stable toxins (STp and STh), acting in concert with a repertoire of more than 25 colonization factors (CFs). LT, the major virulence factor, induces fluid secretion after delivery of a monomeric ADP-ribosylase (LTA) and its pentameric carrier B subunit (LTB). A study of ETEC isolates from humans in Brazil reported the existence of natural LT variants. In the present study, analysis of predicted amino acid sequences showed that the LT amino acid polymorphisms are associated with a geographically and temporally diverse set of 192 clinical ETEC strains and identified 12 novel LT variants. Twenty distinct LT amino acid variants were observed in the globally distributed strains, and phylogenetic analysis showed these to be associated with different CF profiles. Notably, the most prevalent LT1 allele variants were correlated with major ETEC lineages expressing CS1 + CS3 or CS2 + CS3, and the most prevalent LT2 allele variants were correlated with major ETEC lineages expressing CS5 + CS6 or CFA/I. LTB allele variants generally exhibited more-stringent amino acid sequence conservation (2 substitutions identified) than LTA allele variants (22 substitutions identified). The functional impact of LT1 and LT2 polymorphisms on virulence was investigated by measuring total-toxin production, secretion, and stability using GM1–enzyme-linked immunosorbent assays (GM1-ELISA) and in silico protein modeling. Our data show that LT2 strains produce 5-fold more toxin than LT1 strains (P < 0.001), which may suggest greater virulence potential for this genetic variant. Our data suggest that functionally distinct LT-CF variants with increased fitness have persisted during the evolution of ETEC and have spread globally. PMID:25404692

  17. Molecular genetics of glycophorin MNS variants.

    PubMed

    Blumenfeld, O O; Huang, C H

    1997-07-01

    The antigens for the MNS blood group system are Glycophorins A and B (GPA,GPB), products of the GPA gene family. The existence of close to 40 variant phenotypes of this blood group system has been documented by serological analyses. Here is summarized the molecular basis for a large number of variants, including all the variants of the Miltenberger complex and several isoforms of Sta; also, Dantu, Sat, He, Mg, and deletion variants Ena, S-s-U- and Mk. The diversity is based predominantly on gene recombinations, namely unequal homologous recombinations and/or gene conversions, often coupled to pre-mRNA splicing. Most rearrangements occurred between GPA and GPB alleles, and were confined to hot-spots within the 4 kb region coding for the extracellular domain. The homologous region in GPE, the third member of the gene family, was involved only rarely. Sites of the variant epitopes are mapped to new intra- and inter-exon junctions or to patches of previously silenced sequences that become expressed following recombination. PMID:9269716

  18. ?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

  19. Heterologous expression of the allelic variant mu-class glutathione transferases mu and psi.

    PubMed Central

    Widersten, M; Pearson, W R; Engström, A; Mannervik, B

    1991-01-01

    cDNA encoding the more acidic form, glutathione transferase (GST) psi, of the polymorphic Mu-class GSTs discovered in liver, was mutated in the 5'-end to create an NcoI site, facilitating cloning into the expression plasmid pKK233-2. The protein expressed from this construct has a point mutation Pro-2----Ala-2, but gives a catalytically functional protein. Back-mutation of the codon for amino acid residue 2 gave rise to a plasmid expressing the wild-type enzyme GST psi, or GST Mu1b-1b. A variant cDNA, differing only in specifying lysine rather than asparagine in position 173 of the coding region, was generated by site-directed mutagenesis. The variant sequence corresponds to another cDNA clone isolated from a human liver cDNA library and expresses the near-neutral GST mu, or GST Mu1a-1a. The two recombinant proteins GST Mu1a-1a and GST Mu1b-1b, by physicochemical as well as kinetic criteria, were found to be indistinguishable from GST mu and GST psi respectively, isolated from human liver. It is therefore concluded that the recombinant proteins correspond to the allelic variants observed in the human population. The two forms have different isoelectric points and correspond to the allelic variants observed in the human population. The two forms have different isoelectric points and their protein subunits can be separated by h.p.l.c. on a reverse-phase column. With standard substrates and inhibitors no differences in kinetic parameters between the two variants were detected. The mutated GST Mu1b-1b (Pro-2----Ala) was not significantly different in catalytic properties from the wild-type enzyme, even though Pro-2 is a well conserved amino acid residue in the known Mu-class GSTs. Images Fig. 3. PMID:2049077

  20. Novel Human Butyrylcholinesterase Variants: Toward Organophosphonate Detoxication

    PubMed Central

    2015-01-01

    Human butyrylcholinesterase (hBChE) is currently being developed as a detoxication enzyme for stoichiometric binding and/or catalytic hydrolysis of organophosphates. Herein, we describe the use of a molecular evolution method to develop novel hBChE variants with increased resistance to stereochemically defined nerve agent model compounds of soman, sarin, and cyclosarin. Novel hBChE variants (Y332S, D340H, and Y332S/D340H) were identified with an increased resistance to nerve agent model compounds that retained robust intrinsic catalytic efficiency. Molecular dynamics simulations of these variants revealed insights into the mechanism by which these structural changes conferred nerve agent model compound resistance. PMID:24902043

  1. Biomechanical modeling of English /r/ variants.

    PubMed

    Stavness, Ian; Gick, Bryan; Derrick, Donald; Fels, Sidney

    2012-05-01

    This study reports an investigation of the well-known context-dependent variation in English /r/ using a biomechanical tongue-jaw-hyoid model. The simulation results show that preferred /r/ variants require less volume displacement, relative strain, and relative muscle stress than variants that are not preferred. This study also uncovers a previously unknown mechanism in tongue biomechanics for /r/ production: Torque in the sagittal plane about the mental spine. This torque enables raising of the tongue anterior for retroflexed [Symbol: see text] by activation of hyoglossus and relaxation of anterior genioglossus. The results provide a deeper understanding of the articulatory factors that govern contextual phonetic variation. PMID:22559452

  2. Anatomical variants and pathologies of the vermix

    PubMed Central

    Deshmukh, Swati; Verde, Franco; Johnson, Pamela T.; Fishman, Elliot K.

    2015-01-01

    The appendix may demonstrate a perplexing range of normal and abnormal appearances on imaging exams. Familiarity with the anatomy and anatomical variants of the appendix is helpful in identifying the appendix on ultrasound, computed tomography, and magnetic resonance imaging. Knowledge of the variety of pathologies afflicting the appendix and of the spectrum of imaging findings may be particularly useful to the emergency radiologist for accurate diagnosis and appropriate guidance regarding clinical and surgical management. In this pictorial essay, we review appendiceal embryology, anatomical variants such as Amyand hernias, and pathologies from appendicitis to carcinoid, mucinous, and nonmucinous epithelial neoplasms. PMID:24570122

  3. Isolated galaxies

    Microsoft Academic Search

    G. Vettolani; R. de Souza; G. Chincarini

    1986-01-01

    Using a catalogue of galaxies complete to mz <= 14.5, the authors investigate the possibility of extracting a sample of nonclustered galaxies and identifying it with a homogeneous background of objects. They conclude, in agreement with previous findings, that such a background does not exist observationally and stress the fact that the sample of isolated galaxies listed in this paper

  4. 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

  5. Comparison of the pathogenicity in three different Korean canine parvovirus 2 (CPV-2) isolates.

    PubMed

    Moon, H-S; Lee, S-A; Lee, S-G; Choi, R; Jeoung, S-Y; Kim, D; Hyun, C

    2008-09-18

    Canine parvovirus type 2 (CPV-2) is a major pathogen inducing acute hemorrhagic gastroenteritis in dogs. Despite the identification of numerous CPV-2 variants (from CPV-2a to CPV-2c), the pathogenic differences among the CPV-2 variants in dogs have not been evaluated. The aim of this study was to compare the pathogenicity of CPV-2 variants (CPV-2a-I, CPV-2a-V and CPV-2b) isolated mainly from Korea. We evaluated the pathogenicity of three different CPV-2 variants, by performing clinical, hematological, serological and histopathological examinations after experimentally inoculating three types of CPV-2 variants into young puppies. We found that the overall pathogenicity of the CPV-2a variants (CPV-2a-I and 2a-V) was severer compared to the CPV-2b variant. In addition, there was no significant difference in pathogenicity between the two CPV-2a variants. Our findings indicate that there are differences in the pathogenicity of CPV-2 variants in dogs, which may be useful to understand the different pathobiology of the CPV-2 variants. PMID:18400421

  6. An efficient variant of the RSA cryptosystem

    Microsoft Academic Search

    Cesar Alison; Monteiro Paixao

    2003-01-01

    We describe an efficient combination of two variants of RSA cryptosystem (MPrime and Rebalanced RSA) analysed by Boneh and Schacham (2). The decryption process resultant is (for 2048-bits moduli) about 8 times faster than that presented by Quisquater and Couvreur (9) and about 27 times faster than original cryptosystem. In this article we present an extension of the work of

  7. An efficient variant of the RSA cryptosystem

    Microsoft Academic Search

    Cesar Alison; Monteiro Paix; D ´ ecio; Luiz Gazzoni Filho

    We describe an efficient combination of two variants of the RSA cryptosystem (MPrime and Rebalanced RSA) analyzed by Boneh and Shacham (Boneh and Shacham 2002). For 2048-bit moduli, the resulting de- cryption process is about 8 times faster than that presented by Quisquater and Couvreur (Quisquater and Couvreur 1982) and about 27 times faster than the original cryptosystem.

  8. 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

  9. Odynophagia Secondary to Variant Thyroid Cartilage Anatomy

    Microsoft Academic Search

    Doris Lin; Nancy Fischbein; David W. Eisele

    2005-01-01

    We present a case of a displaced superior cornu of the thyroid cartilage causing odynophagia and a foreign body sensation of the pharynx. Diagnosis was made by computed tomography (CT) scan and confirmed by direct endoscopic examination. We review the literature that addresses possible etiologies of this variant anatomy and review treatment options.

  10. The foamy variant of pancreatic intraepithelial neoplasia

    Microsoft Academic Search

    Jorge Albores-Saavedra; Mariana Weimersheimer-Sandoval; Fredy Chable-Montero; Daniel Montante-Montes de Oca; Ralph H. Hruban; Donald Earl Henson

    2008-01-01

    Foamy gland adenocarcinoma is a variant of pancreatic ductal carcinoma, whose precursor has not been described. We describe here the morphologic and immunohistochemical features of the pancreatic intraepithelial neoplasia (PanIN) lesions associated with invasive foamy pancreatic adenocarcinoma. The staining properties and morphologic and immunohistochemical features of 3 foamy PanIN lesions were compared with those of 7 pancreatic foamy gland adenocarcinomas.

  11. 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.

  12. Analysis of simplified variants of SHA256

    Microsoft Academic Search

    Krystian Matusiewicz; Josef Pieprzyk; Norbert Pramstaller; Christian Rechberger; Vincent Rijmen

    2005-01-01

    In this paper we analyse the role of some of the building blocks of SHA-256. We show that the disturbance-correction strategy is applicable to the SHA-256 archi- tecture and we prove that functions , are vital for the security of SHA-256 by showing that for a variant without them it is possible to find collisions with complex- ity 264 hash

  13. A condition assessment method for time-variant structures with incomplete measurements

    NASA Astrophysics Data System (ADS)

    Ding, Y.; Zhao, B. Y.; Wu, B.; Xu, G. S.; Lin, Q.; Jiang, H. B.; Miao, Q. S.

    2015-06-01

    The structural damage incurred in a seismic event is always time-variant. In this paper, a new time-variant structural system identification method is proposed based on a two-stage strategy and incomplete structural acceleration responses. In the first stage, an external excitation identification method is developed for a time-variant structural system. The unknown structural response could be re-constructed with the average acceleration discrete algorithm in this stage. In the second stage, structural parameter is identified and updated with a reduced extended Kalman filter which can improve the computational effort. The re-constructed structural response and identified external excitation are used in the second stage for the damage identification and model updating. The proposed method is validated numerically with the simulation of a fifteen-storey shear frame structure subject to earthquake excitation. A model of a fourteen-storey concrete shear wall building was also studied experimentally with shaking table tests to further validate the proposed method. This shear wall building has a two-storey steel frame on top with base isolation. Both the stiffness of the model and the interface force in the isolator at the bottom of the steel frame during the seismic excitation were estimated with the proposed method. Results from both numerical simulations and laboratory tests indicate that the proposed method can be used to identify structural parameters and external excitations effectively based on a few number of polluted structural acceleration measurements.

  14. 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

  15. AN EFFICIENT VARIANT OF RSA CRYPTOSYSTEM SahadeoPadhye

    E-print Network

    faster than the standard RSA [1]. Some other variants are Batch RSA [4], Mprime RSA [3], Mpower RSA [8 and Shacham [1] gave a nice survey on all four variants (Batch RSA, Mprime RSA, Mpower RSA, Rebalanced RSA

  16. Automating Product-Line Variant Selection for Mobile Devices

    Microsoft Academic Search

    Jules White; Douglas C. Schmidt; Egon Wuchner; Andrey Nechypurenko

    2007-01-01

    Abstract—Product-line architectures (PLAs) designed for mobile devices create a unique challenge for automated product variant selection engines since variants must be derived on-the-fly as devices are discovered. Current automation techniques do not incorporate device resource consumption constraints into variant selection and do not address how,a PLA can be designed to improve automated variant selection speed. This paper presents a tool

  17. No evidence of the Chlamydia trachomatis variant in the UK

    Microsoft Academic Search

    M Sillis; S Skidmore; H Mallinson; T Todd; L Coupland; P Oliver; I Robinson; D Saunders; L Hesketh

    2007-01-01

    Objectives: The discovery of a variant strain of Chlamydia trachomatis (Ct) in Sweden has raised awareness of its possible undetected spread in the UK. The assays that fail to detect this variant are widely used in this country. This study aimed to determine if this variant is circulating in the UK.Method: 1680 genital specimens tested negative by the Roche assays

  18. Neuroradiological findings in GM2 gangliosidosis variant B1

    PubMed Central

    Bano, Shahina; Prasad, Akhila; Yadav, Sachchida Nand; Chaudhary, Vikas; Garga, Umesh Chandra

    2011-01-01

    GM2 gangliosidosis variant B1 is a very rare lysosomal disorder. As per our knowledge, to date, only one article depicting the magnetic resonance imaging (MRI) findings of GM2 gangliosidosis variant B1 is available in the literature. We are the first to describe the neuroradiological findings in an Indian patient diagnosed with GM2 gangliosidosis variant B1. PMID:22408656

  19. Rare Variants in Ischemic Stroke: An Exome Pilot Study

    Microsoft Academic Search

    John W. Cole; O. Colin Stine; Xinyue Liu; Abhishek Pratap; Yuching Cheng; Luke J. Tallon; Lisa K. Sadzewicz; Nicole Dueker; Marcella A. Wozniak; Barney J. Stern; James F. Meschia; Braxton D. Mitchell; Steven J. Kittner; Jeffrey R. OConnell

    2012-01-01

    The genetic architecture of ischemic stroke is complex and is likely to include rare or low frequency variants with high penetrance and large effect sizes. Such variants are likely to provide important insights into disease pathogenesis compared to common variants with small effect sizes. Because a significant portion of human functional variation may derive from the protein-coding portion of genes

  20. Modeling and analysis of product-line variants

    Microsoft Academic Search

    Shamim Ripon; Keya Azad; Sk Jahir Hossain; Mehidee Hassan

    2012-01-01

    Formal verification of variant requirements has gained much interest in the software product line (SPL) community. Feature diagrams are widely used to model product line variants. However, there is a lack of precisely defined formal notation for representing and verifying such models. This paper presents an approach to modeling and analyzing SPL variant feature diagrams using first-order logic. It provides

  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. Variant Influenza Associated with Live Animal Markets, Minnesota.

    PubMed

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

    2015-08-01

    Variant influenza viruses are swine-origin influenza A viruses that cause illness in humans. Surveillance for variant influenza A viruses, including characterization of exposure settings, is important because of the potential emergence of novel influenza viruses with pandemic potential. In Minnesota, we have documented variant influenza A virus infections associated with swine exposure at live animal markets. PMID:24931441

  4. 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

  5. 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

  6. The Identification and Characterization of Copy Number Variants in the Bovine Genome 

    E-print Network

    Doan, Ryan

    2013-06-26

    ........................................................................................ 66 Variant Confirmation................................................................................... 68 Genetic Variant Annotation and Analysis .................................................... 71 Genotyping for Known Mutations..................................................................................... 72 Variant Identification and Annotation .......................................................... 74 Functional Analysis of Variants .................................................................. 83 Genotyping for Known Mutations...

  7. 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

  8. A variant of Wiener's attack on RSA

    E-print Network

    Dujella, Andrej

    2008-01-01

    Wiener's attack is a well-known polynomial-time attack on a RSA cryptosystem with small secret decryption exponent d, which works if dRSA cryptosystem to be broken when d is a few bits longer than n^{0.25}. They all have the run-time complexity (at least) O(D^2), where d=Dn^{0.25}. Here we propose a new variant of Wiener's attack, which uses results on Diophantine approximations of the form |\\alpha - p/q| < c/q^2, and "meet-in-the-middle" variant for testing the candidates (of the form rq_{m+1} + sq_m) for the secret exponent. This decreases the run-time complexity of the attack to O(D log(D)) (with the space complexity O(D)).

  9. MULTIPLE MENKES COPPER ATPASE (ATP7A) TRANSCRIPT AND PROTEIN VARIANTS ARE INDUCED BY IRON DEFICIENCY IN RAT DOUDENAL ENTEROCYTES

    PubMed Central

    Lu, Yan; Kim, Changae; Collins, James F.

    2013-01-01

    The Menkes copper ATPase (Atp7a) pumps copper into the trans-Golgi for cuproenzyme synthesis, and translocates to the basolateral membrane of enterocytes for copper export. Recent studies demonstrated that three 5’ end splice variants of the Atp7a transcript exist in rat duodenum, all of which are strongly induced during iron deprivation. To explore a possible role for Atp7a (and copper) in intestinal iron absorption, the current studies were undertaken to test the hypothesis that multiple Atp7a transcript and protein variants exist in intestinal epithelial cells. Northern blot analyses using probes generated from the full-length Atp7a cDNA revealed several specific hybridization bands, all of which were more intense in RNA samples extracted from duodenal enterocytes isolated from iron-deficient rats. A PCR-based approach, using forward primers specific for the alternative 5’ end splice variants and a reverse primer in exon 23, demonstrated that 3 full-length transcripts exist in rat IEC-6 cells. To identify possible Atp7a protein variants, three distinct polyclonal antisera were utilized. The specificity of the antisera was first established by western blotting and immunoprecipitation studies using samples derived from isolated rat enterocytes and Atp7a knockdown IEC-6 cells. Several specific immunoreactive bands were documented, and a unique Atp7a protein distribution in cytosolic vesicle-like structures was noted. In conclusion, multiple Atp7a transcript and protein variants exist in rodent intestinal epithelial cells and are induced by dietary iron deprivation. Further studies will be designed to determine the subcellular distribution of Atp7a protein variants and possible unique functions of each. PMID:22579041

  10. Phosphotriesterase variants with high methylphosphonatase activity and strong negative trade-off against phosphotriesters.

    PubMed

    Briseńo-Roa, Luis; Timperley, Christopher M; Griffiths, Andrew D; Fersht, Alan R

    2011-01-01

    The most lethal organophosphorus nerve agents (NA), like sarin, soman, agent-VX and Russian-VX, share a methylphosphonate moiety. Pseudomonas diminuta phosphotriesterase (PTE) catalyses the hydrolysis of methylphosphonate NA analogues with a catalytic efficiency orders of magnitude lower than that towards the pesticide paraoxon. With a view to obtaining PTE variants that more readily accept methylphosphonate NA, ~75,000 PTE variants of the substrate-binding residues Gly-60, Ile-106, Leu-303 and Ser-308 were screened with fluorogenic analogues of the NA Russian-VX and cyclosarin. Seven new PTE variants were isolated, purified and their k(cat)/K(M) determined against five phosphotriesters and five methylphosphonate analogues of sarin, cyclosarin, soman, agent-VX and Russian-VX. The novel PTE variants exhibited as much as a 10-fold increase in activity towards the methylphosphonate compounds--many reaching a k(cat)/K(M) of 10? M?ą s?ą--and as much as a 29,000-fold decrease in their phosphotriesterase activity. The mutations found in two of the variants, SS0.5 (G60V/I106L/S308G) and SS4.5 (G60V/I106A/S308G), were modelled into a high-resolution structure of PTE-wild type and docked with analogues of cyclosarin and Russian-VX using Autodock 4.2. The kinetic data and docking simulations suggest that the increase in activity towards the methylphosphonates and the loss of function against the phosphotriesters were due to an alteration of the shape and hydrophobicity of the binding pocket that hinders the productive binding of non-chiral racemic phosphotriesters, yet allows the binding of the highly asymmetric methylphosphonates. PMID:21037279

  11. Stability and Cu(II) binding of prion protein variants related to inherited human prion diseases.

    PubMed

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

    2003-03-01

    All inherited forms of human prion diseases are linked with mutations in the prion protein (PrP) gene. Here we have investigated the stability and Cu(II) binding properties of three recombinant variants of murine full-length PrP(23-231)-containing destabilizing point mutations that are associated with human Gerstmann-Sträussler-Scheinker disease (F198S), Creutzfeld-Jakob disease (E200K), and fatal familial insomnia (D178N) by electron paramagnetic resonance and circular dichroism spectroscopy. Furthermore, we analyzed the variants H140S, H177S, and H187S of the isolated C-terminal domain of murine PrP, mPrP(121-231), to test a role of the histidine residues in Cu(II) binding. The F198S and E200K variants of PrP(23-231) differed in Cu(II) binding from the wild-type mPrP(23-231). However, circular dichroism spectroscopy indicated that the variants and the wild type did not undergo conformational changes in the presence of Cu(II). The D178N variant showed a high tendency to aggregate at pH 7.4 both with and without Cu(II). At lower pH values, it showed the same Cu(II) binding behavior as the wild type. The analysis allowed for a better location of the Cu(II) binding sites in the C-terminal part of the protein. Our present data indicate that hereditary forms of prion diseases cannot be rationalized on the basis of altered Cu(II) binding or mutation-induced protein destabilization alone. PMID:12609901

  12. Uterine artery emerging variants - angiographic aspects

    PubMed Central

    ALBULESCU, DANA; CONSTANTIN, C.; CONSTANTIN, CONSTANTIN

    2014-01-01

    Uterine artery embolization as a therapeutic method in fibromyoma requires a good knowledge of the origin of the uterine artery to the success of this procedure involving selective catheterization. This study presents a classification of anatomical variants of uterine artery as a retrospective review of consecutive arteriogram, complete with various aspects of the origin of the uterine artery in cadaver dissection, in the Department of Anatomy. PMID:25729609

  13. Uterine artery emerging variants - angiographic aspects.

    PubMed

    Albulescu, Dana; Constantin, C; Constantin, Constantin

    2014-01-01

    Uterine artery embolization as a therapeutic method in fibromyoma requires a good knowledge of the origin of the uterine artery to the success of this procedure involving selective catheterization. This study presents a classification of anatomical variants of uterine artery as a retrospective review of consecutive arteriogram, complete with various aspects of the origin of the uterine artery in cadaver dissection, in the Department of Anatomy. PMID:25729609

  14. MRI anatomical variants of mammillary bodies.

    PubMed

    Tagliamonte, Micaela; Sestieri, Carlo; Romani, Gian Luca; Gallucci, Massimo; Caulo, Massimo

    2015-01-01

    The mammillary bodies (MBs) are classically defined as a pair of small round structures located on the undersurface of the diencephalon. The systematic observation of MR brain images of patients with neurological diseases, but also of healthy subjects enrolled in research protocols, reveals, however, a greater anatomical variability. The aim of the present study was to define the spectrum of such variability using spatial normalized 3D TFE T1-weighted MR images in a group of 151 healthy right-handed young subjects (78 females, age range 16-39 years). The MBs were identified on reformatted coronal and axial images and classified according to morphological, positional and numerical criteria. On the basis of coronal images, MBs were first divided into symmetrical (86.1 %) and asymmetrical (13.9 %), depending on their respective height. Symmetrical MBs were further subdivided into three variants [type A (2.7 %), B (76.2 %), C (7.3 %)] according to the depth of the intermammillary sulcus. Two morphological variants were defined on axial images, depending on whether the MBs were circular (63.6 %) or elliptic (36.4 %). This latter group was further divided in two subgroups, depending on whether the MBs were parallel (21.9 %) or convergent (14.6 %). Finally, two subjects (1.3 %) presented a supernumeral MB. The transverse size of the third ventricle was greater in the type A compared to the type B and C groups. Gender did not significantly affect the frequency of MBs variants, except for the three symmetrical subgroups in which the variants A and C were more frequent in males than in females. These findings suggest the presence of an anatomical variability of the MBs, in contrast to their classical definition. Therefore, atypical presentation of MBs can be the expression of this variability rather than a marker of neurological disorders (i.e. cerebral malformation, mesial temporal sclerosis, Wernicke-Korsakoff syndrome). PMID:24072163

  15. 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

  16. Association of genetic variants with diabetic nephropathy.

    PubMed

    Rizvi, Saliha; Raza, Syed Tasleem; Mahdi, Farzana

    2014-12-15

    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

  17. Characterization of blaOXA-143 variants in Acinetobacter baumannii and Acinetobacter pittii.

    PubMed

    Zander, Esther; Bonnin, Rémy A; Seifert, Harald; Higgins, Paul G

    2014-05-01

    The acquired carbapenem-hydrolyzing oxacillinase (OXA) OXA-143 has thus far been detected only in Acinetobacter baumannii isolates from Brazil. The aim of this study was to characterize three OXA-143 variants: OXA-231 and OXA-253 from carbapenem-resistant A. baumannii isolates and OXA-255 in a carbapenem-susceptible Acinetobacter pittii isolate originating from Brazil, Honduras, and the United States, respectively. The 5' rapid amplification of cDNA ends (RACE) technique identified the same transcription initiation site for all blaOXA-143-like genes and revealed differences in the putative promoter regions. However, all cloned OXA-143 variants conferred carbapenem resistance on A. baumannii ATCC 17978 and OXA-255 conferred carbapenem resistance on A. pittii SH024, which was correlated with blaOXA-255 gene expression. This is the first description of OXA-143-like outside A. baumannii. Detection of OXA-143-like in the United States and Honduras indicates its dissemination through the American continent. PMID:24566181

  18. Characterization of blaOXA-143 Variants in Acinetobacter baumannii and Acinetobacter pittii

    PubMed Central

    Zander, Esther; Bonnin, Rémy A.; Seifert, Harald

    2014-01-01

    The acquired carbapenem-hydrolyzing oxacillinase (OXA) OXA-143 has thus far been detected only in Acinetobacter baumannii isolates from Brazil. The aim of this study was to characterize three OXA-143 variants: OXA-231 and OXA-253 from carbapenem-resistant A. baumannii isolates and OXA-255 in a carbapenem-susceptible Acinetobacter pittii isolate originating from Brazil, Honduras, and the United States, respectively. The 5? rapid amplification of cDNA ends (RACE) technique identified the same transcription initiation site for all blaOXA-143-like genes and revealed differences in the putative promoter regions. However, all cloned OXA-143 variants conferred carbapenem resistance on A. baumannii ATCC 17978 and OXA-255 conferred carbapenem resistance on A. pittii SH024, which was correlated with blaOXA-255 gene expression. This is the first description of OXA-143-like outside A. baumannii. Detection of OXA-143-like in the United States and Honduras indicates its dissemination through the American continent. PMID:24566181

  19. 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

  20. Microsatellite Instability Use in Mismatch Repair Gene Sequence Variant Classification

    PubMed Central

    Thompson, Bryony A.; Spurdle, Amanda B.

    2015-01-01

    Inherited mutations in the DNA mismatch repair genes (MMR) can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI) is the defining molecular signature of MMR deficiency. The clinical classification of identified MMR gene sequence variants has a direct impact on the management of patients and their families. For a significant proportion of cases sequence variants of uncertain clinical significance (also known as unclassified variants) are identified, constituting a challenge for genetic counselling and clinical management of families. The effect on protein function of these variants is difficult to interpret. The presence or absence of MSI in tumours can aid in determining the pathogenicity of associated unclassified MMR gene variants. However, there are some considerations that need to be taken into account when using MSI for variant interpretation. The use of MSI and other tumour characteristics in MMR gene sequence variant classification will be explored in this review. PMID:25831438

  1. In vitro selection of variants of human immunodeficiency virus type 1 resistant to 3'-azido-3'-deoxythymidine and 2',3'-dideoxyinosine.

    PubMed Central

    Gao, Q; Gu, Z X; Parniak, M A; Li, X G; Wainberg, M A

    1992-01-01

    Drug-resistant variants of human immunodeficiency virus type 1 (HIV-1) have been isolated by in vitro selection. MT-4 cells were infected with either a laboratory strain (HIV-IIIB) or a clinical isolate (no. 187) of HIV-1 and maintained in medium containing subeffective concentrations of the drugs 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxyinosine (ddI). By gradually increasing the drug concentration in the culture medium during propagation of the virus on fresh MT-4 cells, we were able to isolate variants of HIV-IIIB and clinical isolate 187 which showed up to 100-fold increases in resistance to the drugs. The drug resistance phenotypes remained stable after propagation of the variants in the absence of drug pressure for over 2 months. However, variants resistant to one drug showed little or no cross-resistance to the other, suggesting that the genetic bases for resistance to the compounds differed. Genotypic analysis of these nucleoside-resistant variants by polymerase chain reaction (PCR) with primer pairs previously shown to correspond to mutations responsible for resistance to AZT was also carried out. A heterogeneity of genotypes was observed, with known mutations at pol codons 70 and 215 occurring in most of the AZT-resistant variants generated from either HIV-IIIB or clinical strain 187. However, mutations in codons 67 and 219 were less frequently detected, and none of these changes were observed in each of four variants resistant to ddI. Cloning and sequencing studies of the reverse transcriptase coding region of two of the isolates were also performed and confirmed the PCR data that had been obtained. In addition to previously described mutation sites responsible for resistance to AZT, an HIV-IIIB-resistant variant was shown to be mutated at positions 108 (Val----Ala) and 135 (Ile----Thr), while a resistant variant of strain 187 was mutated at positions 50 (Ile----Val) and 135 (Ile----Val). Images PMID:1727474

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

    Microsoft Academic Search

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

    2006-01-01

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

  3. Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins.

    PubMed

    Yourshaw, Michael; Taylor, S Paige; Rao, Aliz R; Martín, Martín G; Nelson, Stanley F

    2015-03-01

    High-throughput DNA sequencing has become a mainstay for the discovery of genomic variants that may cause disease or affect phenotype. A next-generation sequencing pipeline typically identifies thousands of variants in each sample. A particular challenge is the annotation of each variant in a way that is useful to downstream consumers of the data, such as clinical sequencing centers or researchers. These users may require that all data storage and analysis remain on secure local servers to protect patient confidentiality or intellectual property, may have unique and changing needs to draw on a variety of annotation data sets and may prefer not to rely on closed-source applications beyond their control. Here we describe scalable methods for using the plugin capability of the Ensembl Variant Effect Predictor to enrich its basic set of variant annotations with additional data on genes, function, conservation, expression, diseases, pathways and protein structure, and describe an extensible framework for easily adding additional custom data sets. PMID:24626529

  4. Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans

    PubMed Central

    Hussin, Julie; Idaghdour, Youssef; Bruat, Vanessa; de Maillard, Thibault; Grenier, Jean-Cristophe; Gbeha, Elias; Hamdan, Fadi F.; Girard, Simon; Spinella, Jean-François; Larivičre, Mathieu; Saillour, Virginie; Healy, Jasmine; Fernández, Isabel; Sinnett, Daniel; Michaud, Jacques L.; Rouleau, Guy A.; Haddad, Elie; Le Deist, Françoise; Awadalla, Philip

    2013-01-01

    Whole-exome or gene targeted resequencing in hundreds to thousands of individuals has shown that the majority of genetic variants are at low frequency in human populations. Rare variants are enriched for functional mutations and are expected to explain an important fraction of the genetic etiology of human disease, therefore having a potential medical interest. In this work, we analyze the whole-exome sequences of French-Canadian individuals, a founder population with a unique demographic history that includes an original population bottleneck less than 20 generations ago, followed by a demographic explosion, and the whole exomes of French individuals sampled from France. We show that in less than 20 generations of genetic isolation from the French population, the genetic pool of French-Canadians shows reduced levels of diversity, higher homozygosity, and an excess of rare variants with low variant sharing with Europeans. Furthermore, the French-Canadian population contains a larger proportion of putatively damaging functional variants, which could partially explain the increased incidence of genetic disease in the province. Our results highlight the impact of population demography on genetic fitness and the contribution of rare variants to the human genetic variation landscape, emphasizing the need for deep cataloguing of genetic variants by resequencing worldwide human populations in order to truly assess disease risk. PMID:24086152

  5. 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

  6. Acquisition of Five High-M r Penicillin-Binding Protein Variants during Transfer of High-Level b-Lactam Resistance from Streptococcus mitis to Streptococcus pneumoniae

    Microsoft Academic Search

    REGINE HAKENBECK; ANDREA KONIG; IZABELLA KERN; MARK VAN DER LINDEN; WOLFGANG KECK; DANIELLE BILLOT-KLEIN; RAYMOND LEGRAND; BERNARD SCHOOT; LAURENT GUTMANN

    1998-01-01

    Penicillin-resistant isolates of Streptococcus pneumoniae generally contain mosaic genes encoding the low- affinity penicillin-binding proteins (PBPs) PBP2x, PBP2b, and PBP1a. We now present evidence that PBP2a and PBP1b also appear to be low-affinity variants and are encoded by distinct alleles in b-lactam-resistant trans- formants of S. pneumoniae obtained with chromosomal donor DNA from a Streptococcus mitis isolate. Different lineages of

  7. Pathogenicity and phylogenetic evaluation of the variant Newcastle disease viruses termed “pigeon PMV-1 viruses” based on the nucleotide sequence of the fusion protein gene

    Microsoft Academic Search

    M. S. Collins; I. Strong; D. J. Alexander

    1996-01-01

    Summary The nucleotide sequences of the entire F genes of two isolates of the pigeon PMV-1 (PPMV-1) variant of Newcastle disease virus (NDV) were determined using RTPCR. The deduced amino acid sequences of the F0 protein showed four differences between isolate 760\\/83 which had been passaged 4 times in chickens and gave an intravenous pathogenicity index in chickens (IVPI) of

  8. Fluoroquinolone Efflux by the Plasmid-Mediated Multidrug Efflux Pump QacB Variant QacBIII in Staphylococcus aureus?

    PubMed Central

    Nakaminami, Hidemasa; Noguchi, Norihisa; Sasatsu, Masanori

    2010-01-01

    Plasmids that carry the multidrug efflux genes qacA and qacB are widely distributed in methicillin-resistant Staphylococcus aureus (MRSA). Although the QacA and QacB proteins are similar to each other, their respective substrate specificities may differ. We investigated the variability and structure-function relationships of QacA and QacB in MRSA isolates. The amino acid sequences of 7 QacA and 25 QacB proteins showed that QacB was present in three variants, designated QacBII, QacBIII, and QacBIV, that were different from the prototypic QacB variant encoded by plasmid pSK23, which was named QacBI, while QacA was present in two variants. When cloned and expressed in S. aureus, the strain carrying qacBIII exhibited higher susceptibility to dyes and decreased susceptibility to norfloxacin and ciprofloxacin compared to strains carrying the other QacB variants. Site-directed mutagenesis experiments revealed that the residue at position 320 in QacB plays an important role in the resistance phenotypes to dyes and fluoroquinolones. Furthermore, the accumulation of norfloxacin and ciprofloxacin in the strain carrying qacBIII was significantly decreased. Our data demonstrate that the plasmid-mediated multidrug efflux pump QacB variant QacBIII confers the capability for fluoroquinolone efflux on S. aureus. PMID:20660673

  9. Phylogenetically related, clinically different: human papillomaviruses 6 and 11 variants distribution in genital warts and in laryngeal papillomatosis.

    PubMed

    Godínez, J M; Nicolás-Párraga, S; Pimenoff, V N; Mengual-Chuliá, B; Muńoz, N; Bosch, F X; Sánchez, G I; McCloskey, J; Bravo, I G

    2014-06-01

    Genital warts (GWs) and laryngeal papillomatosis (LP) are two usually benign pathologies related to infection with human papillomaviruses (HPVs), mainly HPV6 and HPV11. The aim of this work was to describe the genetic diversity of HPV6 and HPV11 isolates found in GWs and LPs, and to analyse the differential involvement of viral variants in either lesion. A total of 231 samples diagnosed as GWs (n = 198) or LP (n = 33) and caused by HPV6 or HPV11 monoinfections were analysed. The phylogenetic relationships of the retrieved viral sequences were explored. We have identified the long control region and the intergenic E2-L2 region as the two most variable regions in both HPV6 and HPV11 genomes. We have generated new HPV6 (n = 166) or HPV11 (n = 65) partial sequences from GWs and LPs lesions spanning both regions and studied them in the context of all available sequences of both types (final n = 412). Our results show a significant (p <0.01) differential presence of HPV6 variants among both pathologies, with HPV6 B variants being preferentially found in GW versus LP samples. No differential involvement of HPV11 variants was observed. Our findings suggest that different HPV6 variants may either show differential tropism or have different potential to induce lesions in different epithelia. PMID:24118667

  10. Derivation and characterization of an efficiently myocarditic reovirus variant.

    PubMed Central

    Sherry, B; Schoen, F J; Wenske, E; Fields, B N

    1989-01-01

    A reovirus variant, 8B, was isolated from a neonatal mouse which had been inoculated with a mixture of two reovirus strains: type 1 Lang (T1L) and type 3 Dearing (T3D) (E. A. Wenske, S.J. Chanock, L. Krata, and B. N. Fields, J. Virol. 56:613-616, 1985). 8B is a reassortant containing eight gene segments derived from the T1L parent and two gene segments derived from the T3D parent. Upon infection of neonatal mice, 8B produced a generalized infection characteristic of many reoviruses, but it also efficiently induced numerous macroscopic external cardiac lesions, unlike either of its parents. Microscopic examination of hearts from infected mice revealed myocarditis with necrotic myocytes and both polymorphonuclear and mononuclear cellular infiltration. Electron microscopy revealed viral arrays in necrotic myocytes and dystrophic calcification accompanying late lesions. Determination of viral titers in hearts from T1L-, T3D-, or 8B-infected mice indicated that growth was not the primary determinant of myocardial necrosis. Results from inoculations of athymic mice demonstrated that T cells were not a requirement for the 8B-induced myocarditis. Finally, 8B was more cytopathic than either of the parent viruses in cultured mouse L cells. Together, the data suggest that 8B-induced myocardial necrosis is due to a direct effect of reovirus on myocytes. Reovirus thus provides a useful model for the study of viral myocarditis. Images PMID:2552157

  11. Evaluation of the molecular basis of pathogenicity of the variant Newcastle disease viruses termed “pigeon PMV-1 viruses”

    Microsoft Academic Search

    M. S. Collins; I. Strong; D. J. Alexander

    1994-01-01

    Summary The amino acid sequence at the F2\\/F1 cleavage site was determined for 15 strains of the so-called pigeon PMV-1 (PPMV-1) variant of Newcastle disease virus (NDV) which showed close antigenic identity, determined by their reactions with a panel of 28 monoclonal antibodies, but considerable variation in their pathogenicity for chickens. Thirteen of the isolates possessed the motif112G-R-Q-K-R-F117. This motif

  12. HmGlu 1d, a novel splice variant of the human type I metabotropic glutamate receptor

    Microsoft Academic Search

    David J. Laurie; Hendrikus W. G. M. Boddeke; Raphaela Hiltscher; Bernd Sommer

    1996-01-01

    A novel splice variant, hmGlu1d, of the human mGlu1 metabotropic glutamate receptor has been isolated from a human brain library. This clone is identical to human mGlu1a except that it lacks 35 nucleotides in the 3? coding sequence, which predicts a truncated protein and a novel carboxy terminus. After injection of the encoding sequence into mouse A9 fibroblasts, quisqualate and

  13. Cloning of novel kinectin splice variants with alternative C-termini: Structure, distribution and evolution of mouse kinectin

    Microsoft Academic Search

    Euphemia Leung; Cristin G Print; David AD Parry; David N Closey; Peter J Lockhart; Stephen JM Skinner; David C Batchelor; Geoffrey W Krissansen

    1996-01-01

    The analysis of cDNA clones encoding novel variant forms of mouse kinectin, an endoplasmic reticulum (ER)-bound receptor for the motor protein kinesin, is reported. Kinesin and cytoplasmic dynein are involved in mediating the anterograde and retrograde movements of intracellular vesicles along the microtubule network. The amino acid sequence deduced from kinectin cDNA isolated from mouse spleen cell and testis libraries

  14. Phenotypic and Genome-Wide Analysis of an Antibiotic-Resistant Small Colony Variant (SCV) of Pseudomonas aeruginosa

    Microsoft Academic Search

    Qing Wei; Saeed Tarighi; Andreas Dötsch; Susanne Häussler; Mathias Müsken; Victoria J. Wright; Miguel Cámara; Paul Williams; Steven Haenen; Bart Boerjan; Annelies Bogaerts; Evy Vierstraete; Peter Verleyen; Liliane Schoofs; Ronnie Willaert; Valérie N. De Groote; Jan Michiels; Ken Vercammen; Aurélie Crabbé; Pierre Cornelis

    2011-01-01

    BackgroundSmall colony variants (SCVs) are slow-growing bacteria, which often show increased resistance to antibiotics and cause latent or recurrent infections. It is therefore important to understand the mechanisms at the basis of this phenotypic switch.Methodology\\/Principal FindingsOne SCV (termed PAO-SCV) was isolated, showing high resistance to gentamicin and to the cephalosporine cefotaxime. PAO-SCV was prone to reversion as evidenced by emergence

  15. Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals

    PubMed Central

    Wright, Meredith S.; Perez, Federico; Brinkac, Lauren; Jacobs, Michael R.; Kaye, Keith; Cober, Eric; van Duin, David; Marshall, Steven H.; Hujer, Andrea M.; Rudin, Susan D.; Hujer, Kristine M.

    2014-01-01

    Genome sequencing of carbapenem-resistant Klebsiella pneumoniae isolates from regional U.S. hospitals was used to characterize strain diversity and the blaKPC genetic context. A phylogeny based on core single-nucleotide variants (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups. The primary differences between the groups are in the capsular polysaccharide locus (cps) and their plasmid contents. A strict association between clade and KPC variant was found. The blaKPC gene was found on variants of two plasmid backbones. This study indicates that highly similar K. pneumoniae subpopulations coexist within the same hospitals over time. PMID:24913165

  16. 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

  17. 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

  18. 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

  19. Genomic variant representation in a Chlamydia population is dynamic and adaptive with dependence on in vitro and in vivo passage

    PubMed Central

    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

  20. 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

  1. Clinical variants of idiopathic torsion dystonia.

    PubMed Central

    Fahn, S

    1989-01-01

    Some patients with dystonic movements and postures not known to be caused by environmental or degenerative disorders can be segregated from classical-appearing idiopathic torsion dystonia on the basis of distinctive clinical and pharmacologic features. Many of them should be considered within the family of dystonia, as clinical variants of idiopathic torsion dystonia, while others are better classified as being part of other families of dyskinesias. In the former group are paradoxical dystonia, myoclonic dystonia, diurnal dystonia, and dopa-responsive dystonia. The latter group consists of dystonic tics and the various entities comprising paroxysmal dystonia, namely kinesigenic, nonkinesigenic and hypnogenic dystonia. PMID:2666583

  2. Molecular typing of monophasic Salmonella 4,[5]:i:- strains isolated in Belgium (2008-2011).

    PubMed

    Boland, Cécile; Bertrand, Sophie; Mattheus, Wesley; Dierick, Katelijne; Wattiau, Pierre

    2014-01-31

    To assess the distribution of Salmonella 4,[5]:i:- subtypes in the Belgian food chain and compare it to the subtypes associated with human infections, a molecular assessment was initiated. Two hundred fifty-three Salmonella isolates serotyped as 4,[5]:i:- during the period 2008-2011 in Belgium and originating from animal productions, food or human clinical samples were analysed by a specific duplex PCR. One hundred ninety-four isolates (76.7%) fit the profile of a S. Typhimurium monophasic variant as defined by the European Food Safety Authority. The other isolates possessed but did not express the phase II flagellin gene (23.3%). Multiple Locus Variable Number of Tandem Repeats Analysis (MLVA) revealed many but closely related profiles in the fljB-negative S. Typhimurium monophasic variant isolates. Some MLVA types were associated with both human and animal isolates but no unique source of human contamination could be demonstrated. PMID:24398228

  3. RcsB contributes to the distinct stress fitness among Escherichia coli O157:H7 curli variants of the 1993 hamburger-associated outbreak strains.

    PubMed

    Carter, Michelle Q; Parker, Craig T; Louie, Jacqueline W; Huynh, Steven; Fagerquist, Clifton K; Mandrell, Robert E

    2012-11-01

    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

  4. Ribavirin-Resistant Variants of Foot-and-Mouth Disease Virus: the Effect of Restricted Quasispecies Diversity on Viral Virulence

    PubMed Central

    Zeng, Jianxiong; Wang, Haiwei; Xie, Xiaochun; Li, Chen; Zhou, Guohui; Yang, Decheng

    2014-01-01

    ABSTRACT Mutagenic nucleoside analogues can be used to isolate RNA virus high-fidelity RNA-dependent RNA polymerase (RdRp) variants, the majority of which are attenuated in vivo. However, attenuated foot-and-mouth disease virus (FMDV) high-fidelity RdRp variants have not been isolated, and the correlations between RdRp fidelity and virulence remain unclear. Here, the mutagen ribavirin was used to select a ribavirin-resistant population of FMDV, and 4 amino acid substitutions (D5N, A38V, M194I, and M296V) were identified in the RdRp-coding region of the population. Through single or combined mutagenesis using a reverse genetics system, we generated direct experimental evidence that the rescued D5N, A38V, and DAMM mutants but not the M194I and M296V mutants are high-fidelity RdRp variants. Mutagen resistance assays revealed that the higher replication fidelity was associated with higher-level resistance to ribavirin. In addition, significantly attenuated fitness and virulence phenotypes were observed for the D5N, A38V, and DAMM mutants. Based on a systematic quantitative analysis of fidelity and virulence, we concluded that higher replication fidelity is associated with a more attenuated virus. These data suggest that the resulting restricted quasispecies diversity compromises the adaptability and virulence of an RNA virus population. The modulation of replication fidelity to attenuate virulence may represent a general strategy for the rational design of new types of live, attenuated vaccine strains. IMPORTANCE The ribavirin-isolated poliovirus (PV) RdRp G64S variant, the polymerases of which were of high replication fidelity, was attenuated in vivo. It has been proposed (M. Vignuzzi, E. Wendt, and R. Andino, Nat. Med. 14:154–161, http://dx.doi.org/10.1038/nm1726) that modulation of replication fidelity is a promising approach for engineering attenuated virus vaccines. The subsequently mutagen-isolated RdRp variants also expressed the high-fidelity polymerase, but not all of them were attenuated. Few studies have shown the exact correlation between fidelity and virulence. The present study investigates the effect of restricted quasispecies diversity on viral virulence via several attenuated FMDV high-fidelity RdRp variants. Our findings may aid in the rational design of a new type of vaccine strain. PMID:24453363

  5. 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

  6. [Antigen profile of rabies virus isolated from different species of non-hematophagous bats in the region of Presidente Prudente, State of Săo Paulo].

    PubMed

    Albas, Avelino; Souza, Edson Aroldo Novaes de; Lourenço, Rúbia Anzolin; Favoretto, Silvana Regina; Sodré, Miriam Martos

    2009-01-01

    Using the monoclonal antibody technique, the Clinical and Molecular Virology Laboratory of the Institute of Biomedical Sciences of the University of Săo Paulo typed 18 rabies virus samples from non-hematophagous bats of several species from the region of Presidente Prudente, SP, Brazil. Among these samples, 15 (82.3%) were defined as variant 3 (compatible with samples isolated from Desmodus rotundus bats) and three (16.7%) as variant 4 (compatible with samples isolated from Tadarida brasiliensis bats). PMID:19287929

  7. Factors affecting the incidence of non-metrical skeletal variants.

    PubMed Central

    Berry, A C

    1975-01-01

    Non-metrical variants of the human cranium have been studied in 186 London crania of known age, sex and date of birth. The incidence of several variants was different in the two sexes, and these results were compared with those of other workers from different parts of the world. Few variants persistently favoured one sex: the majority behaved inconsistently. Age dependency was only demonstrated for one variant, while year of birth, presence of rickets, and spina bifida occulta, showed negligible influence on variant incidence. 20% of vertebral columns examined included an anomalous vertebra, usually sacral spina bifida occulta. Although family studies were largely inconclusive, this investigation provides no reason to doubt the basic genetical control of these variants. PMID:129447

  8. VIRUS NOMENCLATURE BELOW THE SPECIES LEVEL: A STANDARDIZED NOMENCLATURE FOR LABORATORY ANIMAL-ADAPTED STRAINS AND VARIANTS OF VIRUSES ASSIGNED TO THE FAMILY FILOVIRIDAE

    PubMed Central

    Kuhn, Jens H.; Bao, Yiming; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander A.; Caě, Yíngyún; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Gonzalez, Jean-Paul; Formenty, Pierre; Freiberg, Alexander N.; Hensley, Lisa E.; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Karl M.; Klenk, Hans-Dieter; Kobinger, Gary; Lackemeyer, Matthew G.; Leroy, Eric M.; Lever, Mark S.; Lofts, Loreen L.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

    2013-01-01

    The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( <isolation host-suffix>///variant designation>-<isolate designation>) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed. PMID:23358612

  9. [Transferrin variants: significance and identification in paternity cases (author's transl)].

    PubMed

    Mauff, G; Doppelfeld, E; Weber, W

    1975-08-01

    Transferrin phenotypes were determined in 3380 sera of unrelated persons of the western region of Germany with 97.60 percent for TfC and 2.40 percent for Tf variants. Identification was achieved by immunochemical means or through autoradiography. Relative mobilities in some variants were measured using Tf B2C (0.7) as reference. Application of Tf variants is demonstrated in paternity cases. PMID:171873

  10. Association of SORL1 gene variants with Alzheimer's disease

    Microsoft Academic Search

    Heike Kölsch; Frank Jessen; Jens Wiltfang; Piotr Lewczuk; Martin Dichgans; Stefan J. Teipel; Johannes Kornhuber; Lutz Frölich; Isabella Heuser; Oliver Peters; Birgitt Wiese; Hanna Kaduszkiewicz; Hendrik van den Bussche; Michael Hüll; Alexander Kurz; Eckhart Rüther; Fritz A. Henn; Wolfgang Maier

    2009-01-01

    SORL1 gene variants were described as risk factor of Alzheimer's disease (AD) additionally SORL1 gene variants were associated with altered A?42 CSF levels in AD patients. In the present study we investigated the association of SORL1 gene variants (rs2070045 (SNP19), SORL1-18ex26 (SNP21), rs3824968 (SNP23), rs1010159 (SNP25)) with AD risk by using Cox proportional hazard model and Kaplan–Meier survival analysis in

  11. Clinical relevance of hepatitis B virus variants

    PubMed Central

    Gao, Shan; Duan, Zhong-Ping; Coffin, Carla S

    2015-01-01

    The hepatitis B virus (HBV) is a global public health problem with more than 240 million people chronically infected worldwide, who are at risk for end-stage liver disease and hepatocellular carcinoma. There are an estimated 600000 deaths annually from complications of HBV-related liver disease. Antiviral therapy with nucleos/tide analogs (NA) targeting the HBV polymerase (P) can inhibit disease progression by long-term suppression of HBV replication. However, treatment may fail with first generation NA therapy due to the emergence of drug-resistant mutants, as well as incomplete medication adherence. The HBV replicates via an error-prone reverse transcriptase leading to quasispecies. Due to overlapping open reading frames mutations within the HBV P can cause concomitant changes in the HBV surface gene (S) and vice versa. HBV quasispecies diversity is associated with response to antiviral therapy, disease severity and long-term clinical outcomes. Specific mutants have been associated with antiviral drug resistance, immune escape, liver fibrosis development and tumorgenesis. An understanding of HBV variants and their clinical relevance may be important for monitoring chronic hepatitis B disease progression and treatment response. In this review, we will discuss HBV molecular virology, mechanism of variant development, and their potential clinical impact. PMID:26052397

  12. Clinical relevance of hepatitis B virus variants.

    PubMed

    Gao, Shan; Duan, Zhong-Ping; Coffin, Carla S

    2015-05-18

    The hepatitis B virus (HBV) is a global public health problem with more than 240 million people chronically infected worldwide, who are at risk for end-stage liver disease and hepatocellular carcinoma. There are an estimated 600000 deaths annually from complications of HBV-related liver disease. Antiviral therapy with nucleos/tide analogs (NA) targeting the HBV polymerase (P) can inhibit disease progression by long-term suppression of HBV replication. However, treatment may fail with first generation NA therapy due to the emergence of drug-resistant mutants, as well as incomplete medication adherence. The HBV replicates via an error-prone reverse transcriptase leading to quasispecies. Due to overlapping open reading frames mutations within the HBV P can cause concomitant changes in the HBV surface gene (S) and vice versa. HBV quasispecies diversity is associated with response to antiviral therapy, disease severity and long-term clinical outcomes. Specific mutants have been associated with antiviral drug resistance, immune escape, liver fibrosis development and tumorgenesis. An understanding of HBV variants and their clinical relevance may be important for monitoring chronic hepatitis B disease progression and treatment response. In this review, we will discuss HBV molecular virology, mechanism of variant development, and their potential clinical impact. PMID:26052397

  13. 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

  14. The spread of sequence variants in Rattus satellite DNAs.

    PubMed Central

    Epstein, D A; Witney, F R; Furano, A V

    1984-01-01

    The genus Rattus has two related families of satellite DNA: Satellite I consists of tandem arrays of a 370 base pair repeat unit which is a dimer of two 185 base pair portions (a, b) which are about 60% homologous. Satellite I' consists of tandem arrays of a 185 base pair repeat unit (a') which is about 85% homologous to a and 60% homologous to b. R. norvegicus contains only satellite I but R. rattus contains both satellites I and I'. We examined certain aspects of satellite DNA evolution by comparing the spacing at which variant repeat units of each satellite have spread among non-variant repeat units in these two species. With but one exception, in R. rattus, 15 different variant repeat units have spread among non-variant repeat units of satellite I, with a spacing equal to the length of the (a,b) dimer. Similarly, fourteen different variant repeat units of the monomeric satellite I' have mixed among non-variant repeat units with a spacing equal to the length of the (a') monomer. These results suggest that a mechanism involving homologous interaction among satellite sequences could account for the spread of variant family members. We also found that a sequence variant present in certain portions of the dimeric repeat unit of satellite I is more efficiently amplified (or less efficiently corrected) than variants occurring in other regions. This was not true for the monomeric repeat unit of satellite I'. Images PMID:6320128

  15. 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

  16. Six host range variants of the xenotropic/polytropic gammaretroviruses define determinants for entry in the XPR1 cell surface receptor

    PubMed Central

    Yan, Yuhe; Liu, Qingping; Kozak, Christine A

    2009-01-01

    Background The evolutionary interactions between retroviruses and their receptors result in adaptive selection of restriction variants that can allow natural populations to evade retrovirus infection. The mouse xenotropic/polytropic (X/PMV) gammaretroviruses rely on the XPR1 cell surface receptor for entry into host cells, and polymorphic variants of this receptor have been identified in different rodent species. Results We screened a panel of X/PMVs for infectivity on rodent cells carrying 6 different XPR1 receptor variants. The X/PMVs included 5 well-characterized laboratory and wild mouse virus isolates as well as a novel cytopathic XMV-related virus, termed Cz524, isolated from an Eastern European wild mouse-derived strain, and XMRV, a xenotropic-like virus isolated from human prostate cancer. The 7 viruses define 6 distinct tropisms. Cz524 and another wild mouse isolate, CasE#1, have unique species tropisms. Among the PMVs, one Friend isolate is restricted by rat cells. Among the XMVs, two isolates, XMRV and AKR6, differ from other XMVs in their PMV-like restriction in hamster cells. We generated a set of Xpr1 mutants and chimeras, and identified critical amino acids in two extracellular loops (ECLs) that mediate entry of these different viruses, including 3 residues in ECL3 that are involved in PMV entry (E500, T507, and V508) and can also influence infectivity by AKR6 and Cz524. Conclusion We used a set of natural variants and mutants of Xpr1 to define 6 distinct host range variants among naturally occurring X/PMVs (2 XMV variants, 2 PMVs, 2 different wild mouse variants). We identified critical amino acids in XPR1 that mediate entry of these viruses. These gammaretroviruses and their XPR1 receptor are thus highly functionally polymorphic, a consequence of the evolutionary pressures that favor both host resistance and virus escape mutants. This variation accounts for multiple naturally occurring virus resistance phenotypes and perhaps contributes to the widespread distribution of these viruses in rodent and non-rodent species. PMID:19811656

  17. [Phenotypic and genetic features of cultural-morphologic variants of Bacillus anthracis].

    PubMed

    Tsygankova, O I; Eremenko, E I; Tsygankova, E A; Buravtseva, N P; Riazanova, A G

    2008-01-01

    Comparative analysis of MVLA-genotypes of 6 Bacillus anthracis strains and 40 their variants differing on capsule- and toxin synthesis, hemolytic, proteolytic and lecitinase activity, nutritional requirements, susceptibility to anthrax bacteriophages, virulence, immunogenicity, and presence of genes for capsule and toxin synthesis was performed. Results of phylogenetic analysis of 5 chromosome locuses and plasmid locus pXO1aat which are variable for this sample of B. anthracis cultures showed that all strains divided on 2 main clusters - A and B. Cluster A consisted of 5 genotypes whereas cluster B - of 1 genotype. All highly virulent original strains and variants with characteristic phenotype Cap(CO2)(+)(O2)(-)Tox(+)ProtA(+)Hly(+) Lec(-)Trp(+) had identical genotype in 4 groups and in 5th group differences were present only in vrrA locus. All original strains and variants with the most atypical complex of phenotypic characteristics Cap (CO2)(+)(O2)(+)Tox(-)ProtA(-)Hly(-)Lec(-)Trp(-) also had the same genotype belonging to cluster B and diverged on characteristic of 5 chromosomal VNTR locuses and pXO1aat locus from typical strains. Absence of toxin production in vitro was not related to loss of genetic determinants of toxin components. Cultures with typical characteristics, one of which was ability to produce toxin in vitro, had larger sizes of amplicons of pXO1aat locus (135 and 132 nbp), whereas atoxigenic original strains and variants with complex of atypical characteristics and identical chromosome genotype had the smallest sizes (123 bnp). All original cultures were isolated in Russia, their genotypes are described for the first time. PMID:18822496

  18. Naturally Occurring Variants of Human ?9 Nicotinic Receptor Differentially Affect Bronchial Cell Proliferation and Transformation

    PubMed Central

    Chikova, Anna; Grando, Sergei A.

    2011-01-01

    Isolation of polyadenilated mRNA from human immortalized bronchial epithelial cell line BEP2D revealed the presence of multiple isoforms of RNA coded by the CHRNA9 gene for ?9 nicotinic acetylcholine receptor (nAChR). BEP2D cells were homozygous for the rs10009228 polymorphism encoding for N442S amino acid substitution, and also contained mRNA coding for several truncated isoforms of ?9 protein. To elucidate the biologic significance of the naturally occurring variants of ?9 nAChR, we compared the biologic effects of overexpression of full-length ?9 N442 and S442 proteins, and the truncated ?9 variant occurring due to a loss of the exon 4 sequence that causes frame shift and early termination of the translation. These as well as control vector were overexpressed in the BEP2D cells that were used in the assays of proliferation rate, spontaneous vs. tobacco nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-induced cellular transformation, and tumorigenicity in cell culture and mice. Overexpression of the S442 variant significantly increased cellular proliferation, and spontaneous and NNK-induced transformation. The N442 variant significantly decreased cellular transformation, without affecting proliferation rate. Overexpression of the truncated ?9 significantly decreased proliferation and suppressed cellular transformation. These results suggested that ?9 nAChR plays important roles in regulation of bronchial cell growth by endogenous acetylcholine and exogenous nicotine, and susceptibility to NNK-induced carcinogenic transformation. The biologic activities of ?9 nAChR may be regulated at the splicing level, and genetic polymorphisms in CHRNA9 affecting protein levels, amino acid sequence and RNA splicing may influence the risk for lung cancer. PMID:22125646

  19. Comparison of mammalian and bacterial expression library screening to detect recombinant alpha-1 proteinase inhibitor variants with enhanced thrombin inhibitory capacity?.

    PubMed

    Gierczak, Richard F; Bhakta, Varsha; Xie, Michael; Sheffield, William P

    2015-08-20

    Serpins are a widely distributed family of serine proteases. A key determinant of their specificity is the reactive centre loop (RCL), a surface motif of ?20 amino acids in length. Expression libraries of variant serpins could be rapidly probed with proteases to develop novel inhibitors if optimal systems were available. The serpin variant alpha-1 proteinase inhibitor M358R (API M358R) inhibits the coagulation protease thrombin, but at sub-maximal rates compared to other serpins. Here we compared two approaches to isolate functional API variants from serpin expression libraries, using the same small library of API randomized at residue 358 (M358X): flow cytometry of transfected HEK 293 cells expressing membrane-displayed API; and a thrombin capture assay (TCA) performed on pools of bacterial lysates expressing soluble API. No enrichment for specific P1 residues was observed when the RCL codons of the 1% of sorted transfected 293 cells with the highest fluorescent thrombin-binding signals were subcloned and sequenced. In contrast, screening of 16 pools of bacterial API-expressing transformants led to the facile identification of API M358R and M358K as functional variants. Kinetic characterization showed that API M358R inhibited thrombin 17-fold more rapidly than API M358K. Reducing the incubation time with immobilized thrombin improved the sensitivity of TCA to detect supra-active API M358R variants and was used to screen a hypervariable library of API variants expressing 16 different amino acids at residues 352-357. The most active variant isolated, with TLSATP substituted for FLEAI, inhibited thrombin 2.9-fold more rapidly than API M358R. Our results indicate that flow cytometric approaches used in protein engineering of antibodies are not appropriate for serpins, and highlight the utility of the optimized TCA for serpin protein engineering. PMID:26043905

  20. Isolation and characterization of acid- and bile-tolerant isolates from strains of Lactobacillus acidophilus.

    PubMed

    Chou, L S; Weimer, B

    1999-01-01

    Lactic acid bacteria have been reported to be useful as a health adjunct and are commonly added to food as the delivery mechanism. The literature contains many conflicting observations for their proposed benefits, and the mechanism of action is undefined. One source of variation is the large number of strains used without proper controls supplemented. Additionally, many of the organisms are not characterized for their acid shock response or the acid-tolerance response, which are known to vary among bacterial species. Our objective was to isolate acid-resistant and bile-resistant variants of Lactobacillus acidophilus and to determine the phenotypic changes. The acid- and bile-tolerant isolates were obtained using natural selection techniques after sequential exposure to hydrochloric acid (pH 3.5 to 7.0) and mixed bile salts. The acid- and bile-tolerant isolates retained their ability to grow at pH 3.5 with 0.3% bile after the selective pressure was removed and reapplied. Isolates varied from their parents for stability in freezing, lactose utilization, protease activity, aminopeptidase activity, plasmid profile, and cell-wall fatty acid profile. These data suggest that the isolated acid- and bile-tolerant isolates possess growth advantages over that of the parents under stress conditions and may be considered as candidates for probiotic strains after further characterization with animal models. PMID:10022003

  1. Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU

    PubMed Central

    Metselaar, Karin I.; den Besten, Heidy M. W.; Boekhorst, Jos; van Hijum, Sacha A. F. T.; Zwietering, Marcel H.; Abee, Tjakko

    2015-01-01

    The dynamic response of microorganisms to environmental conditions depends on the behavior of individual cells within the population. Adverse environments can select for stable stress resistant subpopulations. In this study, we aimed to get more insight in the diversity within Listeria monocytogenes LO28 populations, and the genetic basis for the increased resistance of stable resistant fractions isolated after acid exposure. Phenotypic cluster analysis of 23 variants resulted in three clusters and four individual variants and revealed multiple-stress resistance, with both unique and overlapping features related to stress resistance, growth, motility, biofilm formation, and virulence indicators. A higher glutamate decarboxylase activity correlated with increased acid resistance. Whole genome sequencing revealed mutations in rpsU, encoding ribosomal protein S21 in the largest phenotypic cluster, while mutations in ctsR, which were previously shown to be responsible for increased resistance of heat and high hydrostatic pressure resistant variants, were not found in the acid resistant variants. This underlined that large population diversity exists within one L. monocytogenes strain and that different adverse conditions drive selection for different variants. The finding that acid stress selects for rpsU variants provides potential insights in the mechanisms underlying population diversity of L. monocytogenes. PMID:26005439

  2. Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU.

    PubMed

    Metselaar, Karin I; den Besten, Heidy M W; Boekhorst, Jos; van Hijum, Sacha A F T; Zwietering, Marcel H; Abee, Tjakko

    2015-01-01

    The dynamic response of microorganisms to environmental conditions depends on the behavior of individual cells within the population. Adverse environments can select for stable stress resistant subpopulations. In this study, we aimed to get more insight in the diversity within Listeria monocytogenes LO28 populations, and the genetic basis for the increased resistance of stable resistant fractions isolated after acid exposure. Phenotypic cluster analysis of 23 variants resulted in three clusters and four individual variants and revealed multiple-stress resistance, with both unique and overlapping features related to stress resistance, growth, motility, biofilm formation, and virulence indicators. A higher glutamate decarboxylase activity correlated with increased acid resistance. Whole genome sequencing revealed mutations in rpsU, encoding ribosomal protein S21 in the largest phenotypic cluster, while mutations in ctsR, which were previously shown to be responsible for increased resistance of heat and high hydrostatic pressure resistant variants, were not found in the acid resistant variants. This underlined that large population diversity exists within one L. monocytogenes strain and that different adverse conditions drive selection for different variants. The finding that acid stress selects for rpsU variants provides potential insights in the mechanisms underlying population diversity of L. monocytogenes. PMID:26005439

  3. Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks.

    PubMed

    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

    2014-02-01

    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

  4. 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

  5. Epidermal growth factor-nonresponsive 3T3 variants do not contain epidermal growth factor receptor-related antigens or mRNA

    SciTech Connect

    Schneider, C.A.; Lim, R.W.; Terwilliger, E.; Herschman, H.R.

    1986-01-01

    The authors have previously isolated three independent variants of Swiss 3T3 cells that are unable to generate a mitogenic response to epidermal growth factor (EGF). Each of the variants is unable to bind /sup 125/I-labeled EGF; each lacks a functional EGF receptor. They used an antiserum to murine EGF receptor to look for an EGF-receptor gene product in wild-type 3T3 cells and in the three EGF-nonresponsive variants. No cross-reactive material could be detected in any of the three variants, either in /sup 125/I-labeled cell extracts or in (/sup 35/S)methionine metabolically labeled cells. 3T3 cells contained mRNA molecules homologous to a cDNA probe for the human EGF-receptor coding region. In contrast, no homologous RNA could be detected in any of the three variants. Analysis of genomic Southern blots of the DNA from 3T3 cells and the three EGF-nonresponsive variants indicated sequences from the EGF-receptor gene are present in the DNA of all four cell lines. These EGF-nonresponsive lines, which demonstrate proliferative responses to a variety of mitogens, will be ideal recipients for structure-function studies of the EGF receptor by transfection of the cloned gene.

  6. Detection of mixed populations of wild-type and YMDD hepatitis B variants by pyrosequencing in acutely and chronically infected patients

    PubMed Central

    2012-01-01

    Background Lamivudine (LAM) is associated with the highest known rate of resistance mutations among nucleotide analogs used to treat chronic hepatitis B virus (HBV) infection. Despite this, LAM continues in widespread use, especially in combination therapies. The primary LAM resistance mutation (rtM204V/I) occurs in the YMDD motif of HBV polymerase. The aim of this study was to characterize Brazilian HBV isolates from acute and chronic cases by direct sequencing, and to identify HBV quasispecies in the YMDD motif using a pyrosequencing method capable of detecting single-nucleotide polymorphisms. HBV DNA from serum samples of 20 individuals with acute HBV infection and 44 with chronic infection undergoing antiviral therapies containing LAM were analyzed by direct sequencing and pyrosequencing methods. Results Phylogenic analyses of direct-sequenced isolates showed the expected genotypes (A, D and F) for the Brazilian population in both acute and chronic infections. However, within genotype A isolates, subgenotype A2 was more frequently detected in acute cases than in chronic cases (P?=?0.012). As expected, none of the individuals with acute hepatitis B had LAM-resistant isolates as a dominant virus population, whether detected by direct sequencing or pyrosequencing. However, pyrosequencing analyses showed that 45% of isolates (9/20) had minor subpopulations (4-17%) of LAM-resistant isolates. Among chronic patients undergoing LAM treatment, YMDD mutants were frequently found as a dominant virus population. In cases where wild-type virus was the dominant population, subpopulations of YMDD variants were usually found, demonstrating the complexity of HBV quasispecies. Conclusions YMDD variants were frequently detected as a minor population in acute HBV infection. The occurrence of pre-existing variants may lead to a high frequency of resistant mutants during antiviral therapy in the chronic phase. In chronic infection, detection of YMDD variants before virological or biochemical breakthrough might contribute to making better therapy choices and thus improving treatment outcome. PMID:22672436

  7. Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.

    PubMed

    Dubey, J P; Choudhary, S; Tilahun, G; Tiao, N; Gebreyes, W A; Zou, X; Su, C

    2013-09-01

    Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia. PMID:23411374

  8. Possible new variant of Nijmegen breakage syndrome

    SciTech Connect

    Der Kaloustian, V.M.; Booth, A.; Elliott, A.M. [Montreal Children`s Hospital and McGill Univ., Montreal (Canada)] [and others] [Montreal Children`s Hospital and McGill Univ., Montreal (Canada); and others

    1996-10-02

    We report on a child with microcephaly, small facial and body size, and immune deficiency. The phenotype is consistent with Nijmegen breakage syndrome (NBS), with additional clinical manifestations and laboratory findings not reported heretofore. Most investigations, including the results of radiation-resistant DNA synthesis, concurred with the diagnosis of NBS. Cytogenetic analysis documented abnormalities in virtually all cells examined. Along with the high frequency of breaks and rearrangements of chromosomes 7 and 14, we found breakage and monosomies involving numerous other chromosomes. Because of some variation in the clinical presentation and some unusual cytogenetic findings, we suggest that our patient may represent a new variant of Nijmegen breakage syndrome. 34 refs., 3 figs., 7 tabs.

  9. Variant terminology. [for aerospace information systems

    NASA Technical Reports Server (NTRS)

    Buchan, Ronald L.

    1991-01-01

    A system called Variant Terminology Switching (VTS) is set forth that is intended to provide computer-assisted spellings for terms that have American and British versions. VTS is based on the use of brackets, parentheses, and other symbols in conjunction with letters that distinguish American and British spellings. The symbols are used in the systems as indicators of actions such as deleting, adding, and replacing letters as well as replacing entire words and concepts. The system is shown to be useful for the intended purpose and also for the recognition of misspellings and for the standardization of computerized input/output. The VTS system is of interest to the development of international retrieval systems for aerospace and other technical databases that enhance the use by the global scientific community.

  10. Right temporal lobe variant of frontotemporal dementia.

    PubMed

    González-Caballero, G; Abellán-Miralles, I; Sáenz-Sanjuan, M J

    2015-07-01

    We present two women with the right temporal lobe variant (RTLV) of frontotemporal dementia (FTD) and analyse the clinical features that are determined by the anatomical distribution of atrophy. Each of our patients displayed different clinical and radiological profiles which were in line with findings reported by other authors. One of two patients carries a novel mutation in the granulin gene. FTD is heterogeneous with regard to clinical manifestation, genetics, distribution of cortical atrophy and underlying disease. Its clinical manifestations are related to the distribution of the cortical atrophy. The RTLV of FTD is an uncommon entity. There is no consensus about its name despite the fact that its clinical and radiological features are well-defined and distinguish it from other types of FTD including semantic dementia. PMID:25981552

  11. 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

  12. Integrative Annotation of Variants from 1092 Humans: Application to

    E-print Network

    Yu, Haiyuan

    of selection in DNA elements from the ENCODE project using the full spectrum of variants from 1092 individuals, Michael Wilson, Yali Xue, Fuli Yu, 1000 Genomes Project Consortium, Emmanouil T. Dermitzakis, Haiyuan Yu in the 1000 Genomes Project (Phase 1), includ- ing single-nucleotide variants (SNVs), short insertions

  13. Noise Analysis of Time Variant Shapers in Frequency Domain

    Microsoft Academic Search

    David Gascon; Sebastiŕ Bota; Angel Dieguez; Lluis Garrido; Eduardo Picatoste

    2011-01-01

    In this paper we discuss the noise analysis of time variant shapers in the frequency domain, based on well estab- lished concepts of the theory of time varying circuits. A frequency domain extension of the techniques typically adopted for noise analysis in detector instrumentation is proposed and applied to a classic time variant shaper: the gated integrator. In some cases,

  14. The bisection point across variants of the task.

    PubMed

    García-Pérez, Miguel A; Peli, Eli

    2014-08-01

    Bisection tasks are used in research on normal space and time perception and to assess the perceptual distortions accompanying neurological disorders. Several variants of the bisection task are used, which often yield inconsistent results, prompting the question of which variant is most dependable and which results are to be trusted. We addressed this question using theoretical and experimental approaches. Theoretical performance in bisection tasks is derived from a general model of psychophysical performance that includes sensory components and decisional processes. The model predicts how performance should differ across variants of the task, even when the sensory component is fixed. To test these predictions, data were collected in a within-subjects study with several variants of a spatial bisection task, including a two-response variant in which observers indicated whether a line was transected to the right or left of the midpoint, a three-response variant (which included the additional option to respond "midpoint"), and a paired-comparison variant of the three-response format. The data supported the model predictions, revealing that estimated bisection points were least dependable with the two-response variant, because this format confounds perceptual and decisional influences. Only the three-response paired-comparison format can separate out these influences. Implications for research in basic and clinical fields are discussed. PMID:24811039

  15. A Variant of Poly1305 MAC and Its Security Proof

    Microsoft Academic Search

    Dayin Wang; Dongdai Lin; Wenling Wu

    2005-01-01

    \\u000a We give a variant of Poly1305 MAC and prove its security viewing this MAC as a Carter-Wegman MAC. The proposed variant not\\u000a only keeps all the good properties of the Poly1305, but also makes Poly1305 deterministic.

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

    PubMed

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

    2014-07-01

    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

  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. Common Genetic Variants Modulate Pathogen-Sensing Responses in

    E-print Network

    Napp, Nils

    Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells Mark N. Lee to complex human diseases. The genetic basis of such variation is poorly understood. Here, we identify a global map linking human genetic variants to specific immuno- logical processes. FIGURES IN THE FULL

  19. 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.

  20. 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)

    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.

  1. Hepatitis E virus variant in farmed mink, Denmark.

    PubMed

    Krog, Jesper S; Breum, Solvej Ř; Jensen, Trine H; Larsen, Lars E

    2013-12-01

    Hepatitis E virus (HEV) is a zoonotic virus for which pigs are the primary animal reservoir. To investigate whether HEV occurs in mink in Denmark, we screened feces and tissues from domestic and wild mink. Our finding of a novel HEV variant supports previous findings of HEV variants in a variety of species. PMID:24274600

  2. Hepatitis E Virus Variant in Farmed Mink, Denmark

    PubMed Central

    Breum, Solvej Ř.; Jensen, Trine H.; Larsen, Lars E.

    2013-01-01

    Hepatitis E virus (HEV) is a zoonotic virus for which pigs are the primary animal reservoir. To investigate whether HEV occurs in mink in Denmark, we screened feces and tissues from domestic and wild mink. Our finding of a novel HEV variant supports previous findings of HEV variants in a variety of species. PMID:24274600

  3. 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. Segrč; 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 Jřrgensen; 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 Sparsř; 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; Inęs 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.

  4. LMP1 Strain Variants: Biological and Molecular Properties

    PubMed Central

    Mainou, Bernardo A.; Raab-Traub, Nancy

    2006-01-01

    The ubiquitous herpesvirus Epstein-Barr virus (EBV) is linked to the development of several malignancies, including nasopharyngeal carcinoma. Latent membrane protein 1 (LMP1) is considered the EBV oncogene as it is necessary for EBV-induced transformation of B lymphocytes and is able to transform Rat-1 fibroblasts. LMP1 can activate a wide array of signaling pathways, including phosphatidylinositol 3-kinase (PI3K)-Akt and NF-?B. Six sequence variants of LMP1, termed Alaskan, China 1, China 2, Med+, Med?, and NC, have been identified, and individuals can be infected with multiple variants. The frequencies of detection of these variants differ for various EBV-associated malignancies from different geographic regions. In this study, the biological and signaling properties of the LMP1 variants have been characterized. All of the LMP1 variants transformed Rat-1 fibroblasts, induced increased motility of HFK cells, and induced increased homotypic adhesion of BJAB cells. While all the variants activated the PI3K-Akt signaling pathway to similar extents, the Alaskan, China 1, and Med+ variants had limited binding to the E3 ubiquitin ligase component homologue of Slimb and had slightly enhanced NF-?B signaling. These findings indicate that the signature amino acid changes of the LMP1 variants do not hinder or enhance their in vitro transforming potentials or affect their signaling properties. PMID:16775333

  5. Histone variants as emerging regulators of embryonic stem cell identity.

    PubMed

    Turinetto, Valentina; Giachino, Claudia

    2015-07-01

    Dynamic regulation of chromatin structure is an important mechanism for balancing the pluripotency and cell fate decision in embryonic stem cells (ESCs). Indeed ESCs are characterized by unusual chromatin packaging, and a wide variety of chromatin regulators have been implicated in control of pluripotency and differentiation. Genome-wide maps of epigenetic factors have revealed a unique epigenetic signature in pluripotent ESCs and have contributed models to explain their plasticity. In addition to the well known epigenetic regulation through DNA methylation, histone posttranslational modifications, chromatin remodeling, and non-coding RNA, histone variants are emerging as important regulators of ESC identity. In this review, we summarize and discuss the recent progress that has highlighted the central role of histone variants in ESC pluripotency and ESC fate, focusing, in particular, on H1 variants, H2A variants H2A.X, H2A.Z and macroH2A and H3 variant H3.3. PMID:26114724

  6. Clinical and Laboratory Update on the DEL Variant.

    PubMed

    Nuchnoi, Pornlada; Thongbus, Jairak; Srisarin, Apapan; Kerdpin, Usanee; Prachayasittikul, Virapong

    2014-01-01

    Serological assays for the RhD blood group are based on detection of the RhD antigen on human red blood cells using a specific anti-D antibody. The weak expression of the RhD antigen in the DEL variant hinders the sensitivity of conventional serological assays. Evidence of anti-D immunization in patients with D-negativity who have received DEL-variant blood units has been reported in various populations. This observation has prompted the need for genetic epidemiological and clinical data on the DEL variant in the development of DEL molecular diagnostic testing. This review highlights the molecular features of the DEL variant, the clinical consequences of DEL-blood transfusion, and current approaches for detection of the DEL-variant for donor screening and transfusion. PMID:25316658

  7. Temporal Variant Frontotemporal Dementia Is Associated with Globular Glial Tauopathy

    PubMed Central

    Clark, Camilla N.; Lashley, Tammaryn; Mahoney, Colin J.; Warren, Jason D.; Revesz, Tamas

    2015-01-01

    Frontotemporal dementia (FTD) is a clinically and pathologically heterogeneous neurodegenerative disorder associated with atrophy of the frontal and temporal lobes. Most patients with focal temporal lobe atrophy present with either the semantic dementia subtype of FTD or the behavioral variant subtype. For patients with temporal variant FTD, the most common cause found on post-mortem examination has been a TDP-43 (transactive response DNA-binding protein 43 kDa) proteinopathy, but tauopathies have also been described, including Pick’s disease and mutations in the microtubule-associated protein tau (MAPT) gene. We report the clinical and imaging features of 2 patients with temporal variant FTD associated with a rare frontotemporal lobar degeneration pathology known as globular glial tauopathy. The pathologic diagnosis of globular glial tauopathy should be considered in patients with temporal variant FTD, particularly those who have atypical semantic dementia or an atypical parkinsonian syndrome in association with the right temporal variant. PMID:26102999

  8. Revealing histone variant induced changes via quantitative proteomics.

    PubMed

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

    2011-08-01

    Histone variants are isoforms of linker and core histone proteins that differ in their amino acid sequences. These variants have distinct genomic locations and posttranslational 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 posttranslational 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

  9. 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

  10. FOXO3 gene variants and human aging: coding variants may not be key players.

    PubMed

    Donlon, Timothy A; Curb, J David; He, Qimei; Grove, John S; Masaki, Kamal H; Rodriguez, Beatriz; Elliott, Ayako; Willcox, D Craig; Willcox, Bradley J

    2012-11-01

    FOXO3 is generally recognized as a "master" gene in aging since its association with longevity has been replicated in multiple organisms and human populations. A group of single nucleotide polymorphisms in linkage disequilibrium with a coding region has been associated with human longevity, but the actual functional variant is unidentified. Therefore, we sequenced the coding region in our long-lived Japanese American population in order to enhance resources for fine mapping this region. We demonstrate that of 38 published variants, 6 are misalignments with homologous nonallelic sequences from FOXO3B (ZNF286B), a pseudogene on a different chromosome; 2 are attributable to ZNF286B only, and the remaining 30 were unconfirmed, indicating that they are very rare and not likely involved in longevity. Furthermore, we identified a novel, unique, nonsynonymous coding variant in exon 3 (Gly566Ala; rs138174682) that is prevalent in multiple ethnic groups but appeared too rare for major longevity effects in our study populations. PMID:22459618

  11. 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

  12. Asparagine-requiring tumor cell lines and their non-requiring variants: cytogenetics, biochemistry and population dynamics.

    PubMed

    Colofiore, J; Morrow, J; Patterson, M K

    1973-11-01

    Asparagine-requiring Jensen and Walker rat tumor cells and their asparagine-independent variants have been analyzed. The following results were obtained: (1) Both cell lines have very low levels of asparagine synthetase, and non-requiring revertants isolated from these lines have elevated levels of the enzyme. (2) No differences in chromosome number were detected between the parent Jensen line and five Jensen non-requiring revertants isolated from it. (3) Both Jensen and Walker cells undergo asparagineless death when deprived of this amino acid, although the Jensen cells do so at a more rapid rate. (4) Jensen requiring lines are at a selective advantage when grown in competition with non-requiring variants in complete medium, and their growth rate is more rapid when grown separately. The selective coefficients for the variant with respect to the asparagine-requiring parent ASN(-) line were 0.94 for the competition experiments and 0.83 for growth rate estimates. (5) A somatic cell hybrid between Chinese hamster cells (which require asparagine at low densities, and posses measurable synthetase activity) and the Walker line was found to be asparagine-independent, and it possessed enzyme levels equivalent to the hamster parent. The results of these investigations suggest a parallel with microbial auxotrophic mutants and can be understood in terms of alterations within nuclear structural genes. PMID:4798091

  13. Detection of novel chromosome-SCCmec variants in Methicillin Resistant Staphylococcus aureus and their inclusion in PCR based screening

    PubMed Central

    2011-01-01

    Findings To facilitate automation, a novel DNA extraction method for MRSA was adopted. The MRSA specific chromosome-SCCmec PCR was adapted, additional primers were added, and the performance was validated. From various laboratories in The Netherlands we received a total of 86 MRSA clinical isolates, that were negative in commercially available tests. We identified 14 MRSA strains with new variant chromosome-SCCmec junctions by sequence analysis. These MRSA strains appeared to carry SCCmec sequences with a high degree of homology to SCC regions of S. epidermidis and S. haemolyticus. All were included for detection in chromosome-SCCmec based PCR. Background Efficient management of Methicillin Resistant Staphylococcus aureus (MRSA) in the hospital is needed to prevent dissemination. It is important that MRSA can be rapidly identified, and effective infection control measures can be initiated. Equally important is a rapid MRSA negative report, especially for patients in isolation. For negative screening we implemented fully automated high through-put molecular screening for MRSA. Conclusions Fourteen variant chromosome-SCCmec junctions in MRSA, that are not detected in commercially available MRSA detection kits were added to our PCR to detect all currently known variant SCC-mec types of MRSA. PMID:21615900

  14. Stem pitting and seedling yellows symptoms of Citrus tristeza virus infection may be determined by minor sequence variants.

    PubMed

    Cerni, Silvija; Rusci?, Jelena; Nolasco, Gustavo; Gatin, Zivko; Krajaci?, Mladen; Skori?, Dijana

    2008-02-01

    The isolates of Citrus tristeza virus (CTV), the most destructive viral pathogen of citrus, display a high level of variability. As a result of genetic bottleneck induced by the bud-inoculation of CTV-infected material, inoculated seedlings of Citrus wilsonii Tanaka displayed different symptoms. All successfully grafted plants showed severe symptoms of stem pitting and seedling yellows, while plants in which inoculated buds died displayed mild symptoms. Since complex CTV population structure was detected in the parental host, the aim of this work was to investigate how it changed after the virus transmission, and to correlate it with observed symptoms. The coat protein gene sequence of the predominant genotype was identical in parental and grafted plants and clustered to the phylogenetic group 5 encompassing severe reference isolates. In seedlings displaying severe symptoms, the low-frequency variants clustering to other phylogenetic groups were detected, as well. Indicator plants were inoculated with buds taken from unsuccessfully grafted C. wilsonii seedlings. Surprisingly, they displayed no severe symptoms despite the presence of phylogenetic group 5 genomic variants. The results suggest that the appearance of severe symptoms in this case is probably induced by a complex CTV population structure found in seedlings displaying severe symptoms, and not directly by the predominant genomic variant. PMID:18074213

  15. Occurrence of ssl genes in isolates of Staphylococcus aureus from animal infection.

    PubMed

    Smyth, Davida S; Meaney, William J; Hartigan, Patrick J; Smyth, Cyril J

    2007-03-01

    The occurrence of 7 of the 11 known ssl genes that are found within the vSaalpha genomic island of Staphylococcus aureus and encode the novel Ssl family of exoproteins was examined in isolates from cows (42 isolates), goats (4 isolates), sheep (1 isolate), rabbits (3 isolates) and chickens (2 isolates). Based on seven S. aureus genome sequences for human strains NCTC 8325, N315, Mu50, COL, MRSA 252, MW2 and MSSA-476, and bovine strain RF122, along with the ssl reference gene sequences from strains NCTC 6571, FRI326 and NCTC 8325, ClustalW-generated alignments were used to design PCR primers for unique regions of the ssl genes that are present in the allelic variants of each, except for the ssl4 gene for which specific primers for the set2 and set9 allelic variants were designed individually. The genotypes of isolates were determined using random amplified polymorphic DNA (RAPD) typing. All of the animal-associated S. aureus isolates contained an ssl locus, but there were minor variations in the number of ssl genes present. Forty-nine of the animal isolates possessed a vSaalpha genomic island containing the ssl3 (set8), ssl5 (set3/set10), ssl7 (set1/set11), ssl8 (set12), ssl9 (set5/set13) and ssl10 (set4/set14) genes. One bovine and one goat isolate lacked the ssl3 gene. The ssl9 gene was absent in one bovine isolate. The goat isolate lacking the ssl3 gene was the only animal isolate that possessed the set2 allele of the ssl4 gene. PCR for the set9 allele of the ssl4 gene was inconclusive. Isolates that showed identical RAPD fingerprints had the same complement of ssl genes, but the ssl gene pattern was not RAPD-type specific. Southern blot hybridization showed similar ssl gene RFLPs in isolates of the same RAPD type. PMID:17314375

  16. Characterization of Bartonella strains isolated from black-tailed prairie dogs (Cynomys ludovicianus).

    PubMed

    Bai, Ying; Kosoy, Michael; Martin, Andrew; Ray, Chris; Sheff, Kelly; Chalcraft, Linda; Collinge, Sharon K

    2008-01-01

    Thirty bartonella strains were isolated from the blood of black-tailed prairie dogs (Cynomys ludovicianus) from Boulder County, Colorado, USA. The bacteria appeared as small, fastidious, aerobic, Gram-negative rods. The partial sequences of the citrate synthase gene (gltA) demonstrated five unique genetic variants. Phylogenetic analysis based on sequences of gltA, 16S rRNA, rpoB, ftsZ, and ribC showed that the black-tailed prairie dog-related Bartonella variants comprise a distinct monophyletic clade that is closely related to Bartonella washoensis, a species isolated from a human patient and subsequently from ground squirrels. These variants, however, are grouped together in 100% of the bootstrapped trees. These variants were not found in other small mammals trapped during the same study, showing some evidence of host specificity. We believe that the group being described here is typical of the black-tailed prairie dog. We propose to name the bacteria Candidatus Bartonella washoensis subsp. cynomysii. The type strain is CL8606co(T)(=ATCC BAA-1342(T) = CCUG 53213(T)), which is the representative isolate of the dominant variant of the characterized group. PMID:18237261

  17. 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

  18. Evaluating the impact of genotype errors on rare variant tests of association

    E-print Network

    Cook, Kaitlyn

    The new class of rare variant tests has usually been evaluated assuming perfect genotype information. In reality, rare variant genotypes may be incorrect, and so rare variant tests should be robust to imperfect data. Errors ...

  19. A geometric framework for evaluating rare variant tests of association.

    PubMed

    Liu, Keli; Fast, Shannon; Zawistowski, Matthew; Tintle, Nathan L

    2013-05-01

    The wave of next-generation sequencing data has arrived. However, many questions still remain about how to best analyze sequence data, particularly the contribution of rare genetic variants to human disease. Numerous statistical methods have been proposed to aggregate association signals across multiple rare variant sites in an effort to increase statistical power; however, the precise relation between the tests is often not well understood. We present a geometric representation for rare variant data in which rare allele counts in case and control samples are treated as vectors in Euclidean space. The geometric framework facilitates a rigorous classification of existing rare variant tests into two broad categories: tests for a difference in the lengths of the case and control vectors, and joint tests for a difference in either the lengths or angles of the two vectors. We demonstrate that genetic architecture of a trait, including the number and frequency of risk alleles, directly relates to the behavior of the length and joint tests. Hence, the geometric framework allows prediction of which tests will perform best under different disease models. Furthermore, the structure of the geometric framework immediately suggests additional classes and types of rare variant tests. We consider two general classes of tests which show robustness to noncausal and protective variants. The geometric framework introduces a novel and unique method to assess current rare variant methodology and provides guidelines for both applied and theoretical researchers. PMID:23526307

  20. Private Mitochondrial DNA Variants in Danish Patients with Hypertrophic Cardiomyopathy

    PubMed Central

    Hagen, Christian M.; Aidt, Frederik H.; Havndrup, Ole; Hedley, Paula L.; Jensen, Morten K.; Kanters, Jřrgen K.; Pham, Tam T.; Bundgaard, Henning; Christiansen, Michael

    2015-01-01

    Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disease primarily caused by mutations in genes coding for sarcomeric proteins. A molecular-genetic etiology can be established in ~60% of cases. Evolutionarily conserved mitochondrial DNA (mtDNA) haplogroups are susceptibility factors for HCM. Several polymorphic mtDNA variants are associated with a variety of late-onset degenerative diseases and affect mitochondrial function. We examined the role of private, non-haplogroup associated, mitochondrial variants in the etiology of HCM. In 87 Danish HCM patients, full mtDNA sequencing revealed 446 variants. After elimination of 312 (69.9%) non-coding and synonymous variants, a further 109 (24.4%) with a global prevalence > 0.1%, three (0.7%) haplogroup associated and 19 (2.0%) variants with a low predicted in silico likelihood of pathogenicity, three variants: MT-TC: m.5772G>A, MT-TF: m.644A>G, and MT-CYB: m.15024G>A, p.C93Y remained. A detailed analysis of these variants indicated that none of them are likely to cause HCM. In conclusion, private mtDNA mutations are frequent, but they are rarely, if ever, associated with HCM. PMID:25923817

  1. Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments

    PubMed Central

    Qi, Yuan; Liu, Xiuping; Liu, Chang-gong; Wang, Bailing; Hess, Kenneth R.; Symmans, W. Fraser; Shi, Weiwei; Pusztai, Lajos

    2015-01-01

    Nucleotide alterations detected by next generation sequencing are not always true biological changes but could represent sequencing errors. Even highly accurate methods can yield substantial error rates when applied to millions of nucleotides. In this study, we examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA. We performed targeted sequencing of all known human protein kinase genes (kinome) (~3.2 Mb) using the SOLiD v4 platform. Seventeen breast cancer samples were sequenced in duplicate (n=14) or triplicate (n=3) to assess concordance of all calls and single nucleotide variant (SNV) calls. The concordance rates over the entire sequenced region were >99.99%, while the concordance rates for SNVs were 54.3-75.5%. There was substantial variation in basic sequencing metrics from experiment to experiment. The type of nucleotide substitution and genomic location of the variant had little impact on concordance but concordance increased with coverage level, variant allele count (VAC), variant allele frequency (VAF), variant allele quality and p-value of SNV-call. The most important determinants of concordance were VAC and VAF. Even using the highest stringency of QC metrics the reproducibility of SNV calls was around 80% suggesting that erroneous variant calling can be as high as 20-40% in a single experiment. The sequence data have been deposited into the European Genome-phenome Archive (EGA) with accession number EGAS00001000826. PMID:26136146

  2. Generating thermal stable variants of protein domains through phage display.

    PubMed

    Pershad, Kritika; Kay, Brian K

    2013-03-15

    Often in protein design research, one desires to generate thermally stable variants of a protein or domain. One route to identifying mutations that yield domains that remain folded and active at a higher temperature is through the use of directed evolution. A library of protein domain variants can be generated by mutagenic PCR, expressed on the surface of bacteriophage M13, and subjected to heat, such that the unfolded forms of the domain, showing reduced or no binding activity, are lost during subsequent affinity selection, whereas variants that still retain binding to their target are selected and enriched with each subsequent round of affinity selection. This approach takes advantage of the fact that bacteriophage M13 particles are heat stable and resistant to many proteases and protein denaturants. We present the application of this general approach to generating thermally stable variants of a eukaryotic peptide-binding domain. The benefits of producing such variants are that they typically express at high levels in Escherichia coli (30-60 mg/L shake flask) and remain soluble in solution at higher concentrations for longer periods of time than the wild-type form of the domain. The process of library generation and screening generally requires about one month of effort, and yields variants with >10 °C increase in thermal stability, as measured in a simple fluorescence-based thermal shift assay. It is anticipated that thermally stable variants will serve as excellent scaffolds for generating affinity reagents to a variety of targets of interest. PMID:23276752

  3. Robust and Powerful Affected Sibpair Test for Rare Variant Association.

    PubMed

    Lin, Keng-Han; Zöllner, Sebastian

    2015-07-01

    Advances in DNA sequencing technology facilitate investigating the impact of rare variants on complex diseases. However, using a conventional case-control design, large samples are needed to capture enough rare variants to achieve sufficient power for testing the association between suspected loci and complex diseases. In such large samples, population stratification may easily cause spurious signals. One approach to overcome stratification is to use a family-based design. For rare variants, this strategy is especially appropriate, as power can be increased considerably by analyzing cases with affected relatives. We propose a novel framework for association testing in affected sibpairs by comparing the allele count of rare variants on chromosome regions shared identical by descent to the allele count of rare variants on nonshared chromosome regions, referred to as test for rare variant association with family-based internal control (TRAFIC). This design is generally robust to population stratification as cases and controls are matched within each sibpair. We evaluate the power analytically using general model for effect size of rare variants. For the same number of genotyped people, TRAFIC shows superior power over the conventional case-control study for variants with summed risk allele frequency f<0.05; this power advantage is even more substantial when considering allelic heterogeneity. For complex models of gene-gene interaction, this power advantage depends on the direction of interaction and overall heritability. In sum, we introduce a new method for analyzing rare variants in affected sibpairs that is robust to population stratification, and provide freely available software. PMID:25966809

  4. A variational Bayes discrete mixture test for rare variant association

    PubMed Central

    Logsdon, Benjamin A.; Dai, James Y.; Auer, Paul L.; Johnsen, Jill M.; Ganesh, Santhi K.; Smith, Nicholas L.; Wilson, James G.; Tracy, Russell P.; Lange, Leslie A.; Jiao, Shuo; Rich, Stephen S.; Lettre, Guillaume; Carlson, Christopher S.; Jackson, Rebecca D.; O’Donnell, Christopher J.; Wurfel, Mark M.; Nickerson, Deborah A.; Tang, Hua; Reiner, Alexander P.; Kooperberg, Charles

    2014-01-01

    Recently, many statistical methods have been proposed to test for associations between rare genetic variants and complex traits. Most of these methods test for association by aggregating genetic variations within a predefined region, such as a gene. Although there is evidence that “aggregate” tests are more powerful than the single marker test, these tests generally ignore neutral variants and therefore are unable to identify specific variants driving the association with phenotype. We propose a novel aggregate rare-variant test that explicitly models a fraction of variants as neutral, tests associations at the gene-level, and infers the rare-variants driving the association. Simulations show that in the practical scenario where there are many variants within a given region of the genome with only a fraction causal our approach has greater power compared to other popular tests such as the Sequence Kernel Association Test (SKAT), the Weighted Sum Statistic (WSS), and the collapsing method of Morris and Zeggini (MZ). Our algorithm leverages a fast variational Bayes approximate inference methodology to scale to exome-wide analyses, a significant computational advantage over exact inference model selection methodologies. To demonstrate the efficacy of our methodology we test for associations between von Willebrand Factor (VWF) levels and VWF missense rare-variants imputed from the National Heart, Lung, and Blood Institute’s Exome Sequencing project into 2,487 African Americans within the VWF gene. Our method suggests that a relatively small fraction (~10%) of the imputed rare missense variants within VWF are strongly associated with lower VWF levels in African Americans. PMID:24482836

  5. HIV-1 Genetic Diversity in Russia: CRF63_02A1, a New HIV Type 1 Genetic Variant Spreading in Siberia

    PubMed Central

    Bogachev, Vladislav V.; Gashnikova, Natalya M.

    2014-01-01

    Abstract 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. Isolation of useful variants in alloplasmic crop brassicas in the cytoplasmic background of Erucastrum gallicum

    Microsoft Academic Search

    Gadde U. Rao; Akshay K. Pradhan; Kundaranahalli R. Shivanna

    1998-01-01

    Alloplasmic Brassica juncea was synthesized by repeatedly backcrossing amphidiploid of Erucastrum gallicum B. juncea with\\u000a pollen of B. juncea. The E. gallicum cytoplasm was also transferred to B. napus and B. carinata through alloplasmic (E. gallicum)\\u000a B. juncea. RFLP analyses of organelle DNA confirmed the presence of E. gallicum cytoplasm in all the alloplasmics. The cytoplasm\\u000a of E. gallicum, though

  7. Nonradioactive heteroduplex tracking assay for the detection of minority-variant chloroquine-resistant Plasmodium falciparum in Madagascar

    PubMed Central

    Juliano, Jonathan J; Randrianarivelojosia, Milijaona; Ramarosandratana, Benjamin; Ariey, Frédéric; Mwapasa, Victor; Meshnick, Steven R

    2009-01-01

    Background Strains of Plasmodium falciparum genetically resistant to chloroquine (CQ) due to the presence of pfcrt 76T appear to have been recently introduced to the island of Madagascar. The prevalence of such resistant genotypes is reported to be low (< 3%) when evaluated by conventional PCR. However, these methods are insensitive to low levels of mutant parasites present in patients with polyclonal infections. Thus, the current estimates may be an under representation of the prevalence of the CQ-resistant P. falciparum isolates on the island. Previously, minority variant chloroquine resistant parasites were described in Malawian patients using an isotopic heteroduplex tracking assay (HTA), which can detect pfcrt 76T-bearing P. falciparum minority variants in individual patients that were undetectable by conventional PCR. However, as this assay required a radiolabeled probe, it could not be used in many resource-limited settings. Methods This study describes a digoxigenin (DIG)-labeled chemiluminescent heteroduplex tracking assay (DIG-HTA) to detect pfcrt 76T-bearing minority variant P. falciparum. This assay was compared to restriction fragment length polymorphism (RFLP) analysis and to the isotopic HTA for detection of genetically CQ-resistant parasites in clinical samples. Results Thirty one clinical P. falciparum isolates (15 primary isolates and 16 recurrent isolates) from 17 Malagasy children treated with CQ for uncomplicated malaria were genotyped for the pfcrt K76T mutation. Two (11.7%) of 17 patients harboured genetically CQ-resistant P. falciparum strains after therapy as detected by HTA. RFLP analysis failed to detect any pfcrt K76T-bearing isolates. Conclusion These findings indicate that genetically CQ-resistant P. falciparum are more common than previously thought in Madagascar even though the fitness of the minority variant pfcrt 76T parasites remains unclear. In addition, HTAs for malaria drug resistance alleles are promising tools for the surveillance of anti-malarial resistance. The use of a non-radioactive label allows for the use of HTAs in malaria endemic countries. PMID:19291288

  8. 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

  9. Variant selection and transformation texture in zirconium alloy Excel

    NASA Astrophysics Data System (ADS)

    Sattari, M.; Holt, R. A.; Daymond, M. R.

    2014-10-01

    The crystallographic texture and variant selection during phase transformations in zirconium alloy Excel (Zr-3.5% Sn-0.8% Mo-0.8% Nb) was investigated. It was shown that upon water-quenching from ?Zr + ?Zr or fully ?Zr regions, variant selection occurs during ?Zr ? ??Zr martensitic transformation. Also during air-cooling from the ?Zr + ?Zr region, only a partial memory effect and some transformation texture with variant selection was observed which is contrary to previous reports on zirconium alloys heat treated in the ?Zr + ?Zr region.

  10. Selection, isolation, and characterization of cadmium-resistant Datura innoxia suspension cultures

    Microsoft Academic Search

    P. J. Jackson; E. J. Roth; P. R. McClure; C. M. Naranjo

    1984-01-01

    Datura innoxia cells from suspension cultures were selected for their ability to grow and divide rapidly in normally lethal concentrations of cadmium. Cells resistant to 12.5, 25, 50, 100, 160, 200, and 250 micromolar cadmium chloride were isolated and utilized to initiate cell suspension cultures resistant to this toxic metal ion. Variant cell lines retained their ability to grow in

  11. 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

  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. 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

  14. First report of a variant bovine papillomavirus type 2 (BPV-2) in cattle in the Iberian Peninsula.

    PubMed

    Escudero, Clara; Vázquez, Rocío; Doménech, Ana; Gómez-Lucía, Esperanza; Benítez, Laura

    2014-01-01

    Infections caused by bovine papillomavirus (BPV) have been described worldwide. Some types, like BPV-1 and BPV-2, have been reported in association with skin warts and fibropapillomas in cattle and sarcoids in equids. In this study we have investigated the presence of BPV in cutaneous warts isolated from a steer in Spain. Cutaneous fibropapillomatosis was confirmed by histopathological analysis. Complete genome was amplified by multiple-primed rolling circle and the L1, E5 and E6 genes were sequenced. The isolate was classified as a variant of BPV-2 on the basis of the L1 gene sequences. Genetic variability of L1, E5 and E6 genes was compared with BPV-2 isolates from different hosts in several continents. Some mutations involved non-synonymous substitutions when compared to the prototype strain. One of these non-conservative mutations was located in the jelly roll ?-barrel of the EF loop of the capsid protein (encoded by L1). This study presents the first report of a variant of BPV-2 infection in the Iberian Peninsula and contributes to extend the knowledge of the spreading and circulation of BPV. PMID:25273965

  15. 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

  16. Analysis of mitochondrial DNA variants in Japanese patients with schizophrenia.

    PubMed

    Ueno, Hitomi; Nishigaki, Yutaka; Kong, Qing-Peng; Fuku, Noriyuki; Kojima, Shuji; Iwata, Nakao; Ozaki, Norio; Tanaka, Masashi

    2009-11-01

    To test the hypothesis that mitochondrial DNA (mtDNA) variants contribute to the susceptibility to schizophrenia, we sequenced the entire mtDNAs from 93 Japanese schizophrenic patients. Three non-synonymous homoplasmic variants in subunit six of the ATP synthase (MT-ATP6) gene that were detected only in patients but not in controls were suggested to be slightly deleterious, because (1) their original amino acid residues (AA) were highly conserved and (2) the physicochemical differences between the original and altered AA were relatively high. In addition, we detected three novel heteroplasmic variants that were potentially pathogenic. Although functional analysis is needed, rare variants in the mtDNA may convey susceptibility to schizophrenia. PMID:19563917

  17. Comparative sequence studies of variants of avocado sunblotch viroid.

    PubMed

    Rakowski, A G; Symons, R H

    1989-11-01

    The nucleotide sequences of 16 variants of the 247 nucleotide avocado sunblotch viroid (ASBV), purified from leaves of three avocado trees in separate locations, have been determined and compared with that of the previously published ASBV SB-1 sequence (Symons, R. H., Nucl. Acids Res. 9, 6527-6537, 1981). Most of the nucleotide differences were found to occur in the left- and right-hand loops of the ASBV molecule. The number of residues in the sequence variants varied from 246 to 251. Two sequence variants contained nucleotide changes in the double hammerhead-like self-cleaving structure identified in ASBV RNA. RNA transcripts of dimeric cDNA clones of these sequence variants retained their in vitro self-cleavage activity. PMID:2815589

  18. 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.

  19. 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.

  20. Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples

    PubMed Central

    Betge, Johannes; Kerr, Grainne; Miersch, Thilo; Leible, Svenja; Erdmann, Gerrit; Galata, Christian L.; Zhan, Tianzuo; Gaiser, Timo; Post, Stefan; Ebert, Matthias P.; Horisberger, Karoline; Boutros, Michael

    2015-01-01

    Next generation sequencing (NGS) is an emerging technology becoming relevant for genotyping of clinical samples. Here, we assessed the stability of amplicon sequencing from formalin-fixed paraffin-embedded (FFPE) and paired frozen samples from colorectal cancer metastases with different analysis pipelines. 212 amplicon regions in 48 cancer related genes were sequenced with Illumina MiSeq using DNA isolated from resection specimens from 17 patients with colorectal cancer liver metastases. From ten of these patients, paired fresh frozen and routinely processed FFPE tissue was available for comparative study. Sample quality of FFPE tissues was determined by the amount of amplifiable DNA using qPCR, sequencing libraries were evaluated using Bioanalyzer. Three bioinformatic pipelines were compared for analysis of amplicon sequencing data. Selected hot spot mutations were reviewed using Sanger sequencing. In the sequenced samples from 16 patients, 29 non-synonymous coding mutations were identified in eleven genes. Most frequent were mutations in TP53 (10), APC (7), PIK3CA (3) and KRAS (2). A high concordance of FFPE and paired frozen tissue samples was observed in ten matched samples, revealing 21 identical mutation calls and only two mutations differing. Comparison of these results with two other commonly used variant calling tools, however, showed high discrepancies. Hence, amplicon sequencing can potentially be used to identify hot spot mutations in colorectal cancer metastases in frozen and FFPE tissue. However, remarkable differences exist among results of different variant calling tools, which are not only related to DNA sample quality. Our study highlights the need for standardization and benchmarking of variant calling pipelines, which will be required for translational and clinical applications. PMID:26010451

  1. 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

  2. ANOMALOUS DOPAMINE RELEASE ASSOCIATED WITH A HUMAN DOPAMINE TRANSPORTER CODING VARIANT

    PubMed Central

    Mazei-Robison, M.S.; Bowton, E.; Holy, M.; Schmudermaier, M.; Freissmuth, M.; Sitte, H.H.; Galli, A.; Blakely, R.D.

    2008-01-01

    Dopamine (DA) signaling at synapses is tightly coordinated through opposing mechanisms of vesicular fusion-mediated DA release and transporter-mediated DA clearance. Altered brain DA signaling is suspected to underlie multiple brain disorders including schizophrenia, Parkinson’s disease, bipolar disorder and attention-deficit hyperactivity disorder (ADHD). We identified a pedigree containing two male children diagnosed with ADHD who share a rare human DA transporter (DAT, SLC6A3) coding variant, Ala559Val. Among over 1000 control and affected subjects, the Val559 variant has only been isolated once previously, in a female subject with bipolar disorder. Although hDAT Ala559Val supports normal DAT protein and cell surface expression, as well as normal DA uptake, the variant exhibits anomalous DA efflux from DA loaded cells. We also demonstrate that hDAT Ala599Val exhibits increased sensitivity to intracellular Na+, but not intracellular DA, and displays exaggerated DA efflux at depolarized potentials. Remarkably, the two most common ADHD medications, amphetamine and methylphenidate, both block hDAT Ala559Val-mediated DA efflux, whereas these drugs have opposite actions at wildtype hDAT. Our findings reveal that DA efflux, typically associated with amphetamine-like psychostimulants, can be produced through a heritable change in hDAT structure. As multiple gene products are known to coordinate to support amphetamine-mediated DA efflux, the properties of hDAT Ala559Val may have broader significance in identifying a new mechanism through which DA signaling disorders arise. Additionally, they suggest that block of inappropriate neurotransmitter efflux may be an unsuspected mechanism supporting the therapeutic actions of existing transporter-directed medications. PMID:18614672

  3. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics*

    PubMed Central

    Li, Jing; Su, Zengliu; Ma, Ze-Qiang; Slebos, Robbert J. C.; Halvey, Patrick; Tabb, David L.; Liebler, Daniel C.; Pao, William; Zhang, Bing

    2011-01-01

    Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics. PMID:21389108

  4. Thermal unfolding of two designed monomeric ? Cro repressor variants

    Microsoft Academic Search

    Heinz Fabian; Klaus Gast; Vladimir V. Filimonov; Dmitry F. Zamyatkin; Vladimir V. Rogov

    2005-01-01

    The thermal unfolding of the wild-type ? Cro repressor and of two designed variants, Cro K56-[DGEVK] and Cro K56-[DGEVK] Q16L, was studied by Fourier transform infrared spectroscopy and dynamic light scattering. The engineered Cro K56-[DGEVK] monomer has five additional amino acids inserted after position 56 of the wild-type sequence, while the K56-[DGEVK] Q16L variant differs only in one position (Gln-16

  5. 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

  6. G-6-PD variants in Chinese in Thailand.

    PubMed

    Panich, V; Na-Nakorn, S; Wasi, P

    1980-06-01

    Partial purified erythrocyte G-6-PD from 25 G-6-PD deficient southern Chinese male residents in Thailand was characterized. Five G-6-PD variants were found : G-6-PDs Canton (8), Dhon (or Taipei-Hakka) (8), Mahidol (or B (-) Chinese) (6), Haad Yai (1), and Hong Kong (1). One person whose enzyme was not fully characterized might have G-6-PD Haad Yai or a new variant. PMID:7434076

  7. Recent advances using green and red fluorescent protein variants

    Microsoft Academic Search

    Annette Müller-Taubenberger; Kurt I. Anderson

    2007-01-01

    Fluorescent proteins have proven to be excellent tools for live-cell imaging. In addition to green fluorescent protein (GFP)\\u000a and its variants, recent progress has led to the development of monomeric red fluorescent proteins (mRFPs) that show improved\\u000a properties with respect to maturation, brightness, and the monomeric state. This review considers green and red spectral variants,\\u000a their paired use for live-cell

  8. Unusual histologic and clinical variants of melanoma: Implications for therapy

    Microsoft Academic Search

    A. Neil Crowson; Cynthia Magro; Martin C. Mihm Jr

    2007-01-01

    Unusual histologic variants of melanoma may be problematic to the histopathologist. Several of these variants are sufficiently\\u000a rare that their biologic behavior remains obscure. As identification of some of these melanoma subtypes has specific implications\\u000a for the therapeutic approach, and as some may mimic other forms of epithelial or mesenchymal neoplasia, their recognition\\u000a is key to patient management.

  9. 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

  10. Signaling from novel splice variants of hormone receptors in cancer

    Microsoft Academic Search

    Wei-Qun Ding; Laurence J. Miller

    2002-01-01

    A number of splice variants of hormone receptors have recently been described in malignant neoplasms. Signaling by these novel\\u000a receptor isoforms differ from their wild type counterparts, raising interesting questions as to possible roles in the initiation,\\u000a progression, and metastatic potential of various tumors. This review summarizes recent findings on the signaling of novel\\u000a variants of hormone receptors, including human

  11. 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

  12. Analysis of mitochondrial DNA variants in Japanese patients with schizophrenia

    Microsoft Academic Search

    Hitomi Ueno; Yutaka Nishigaki; Qing-Peng Kong; Noriyuki Fuku; Shuji Kojima; Nakao Iwata; Norio Ozaki; Masashi Tanaka

    2009-01-01

    To test the hypothesis that mitochondrial DNA (mtDNA) variants contribute to the susceptibility to schizophrenia, we sequenced the entire mtDNAs from 93 Japanese schizophrenic patients. Three non-synonymous homoplasmic variants in subunit six of the ATP synthase (MT-ATP6) gene that were detected only in patients but not in controls were suggested to be slightly deleterious, because (1) their original amino acid

  13. Better prediction of functional effects for sequence variants

    PubMed Central

    2015-01-01

    Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classifier that improves over the state-of-the-art in distinguishing between effect and neutral variants. Our method's improved performance results from screening many potentially relevant protein features and from refining our development data sets. Cross-validated on >100k experimentally annotated variants, SNAP2 significantly outperformed other methods, attaining a two-state accuracy (effect/neutral) of 83%. SNAP2 also outperformed combinations of other methods. Performance increased for human variants but much more so for other organisms. Our method's carefully calibrated reliability index informs selection of variants for experimental follow up, with the most strongly predicted half of all effect variants predicted at over 96% accuracy. As expected, the evolutionary information from automatically generated multiple sequence alignments gave the strongest signal for the prediction. However, we also optimized our new method to perform surprisingly well even without alignments. This feature reduces prediction runtime by over two orders of magnitude, enables cross-genome comparisons, and renders our new method as the best solution for the 10-20% of sequence orphans. SNAP2 is available at: https://rostlab.org/services/snap2web Definitions used Delta, input feature that results from computing the difference feature scores for native amino acid and feature scores for variant amino acid; nsSNP, non-synoymous SNP; PMD, Protein Mutant Database; SNAP, Screening for non-acceptable polymorphisms; SNP, single nucleotide polymorphism; variant, any amino acid changing sequence variant. PMID:26110438

  14. RAREMETAL: fast and powerful meta-analysis for rare variants

    PubMed Central

    Feng, Shuang; Liu, Dajiang; Zhan, Xiaowei; Wing, Mary Kate; Abecasis, Gonçalo R.

    2014-01-01

    Summary: RAREMETAL is a computationally efficient tool for meta-analysis of rare variants genotyped using sequencing or arrays. RAREMETAL facilitates analyses of individual studies, accommodates a variety of input file formats, handles related and unrelated individuals, executes both single variant and burden tests and performs conditional association analyses. Availability and implementation: http://genome.sph.umich.edu/wiki/RAREMETAL for executables, source code, documentation and tutorial. Contact: sfengsph@umich.edu or goncalo@umich.edu PMID:24894501

  15. African-American factor VII-deficient variants in Georgia (FVII variants).

    PubMed

    Krauss, J S; Matthews, A; Oliver, J; Lightsey, A; Jonah, M H; Pantazis, C G

    1994-11-01

    We studied African-American Factor (FVII)-deficient variants and carriers in Georgia by measuring their levels of FVII antigen (FVIIAG) and FVII procoagulant (FVIIC). Factor VIIAG was determined using enzyme-linked immunoassay (ELISA), whereas FVIIC was measured in two ways: 1) by fibrin clotting methods that employed human recombinant (HRFVIIC), human placental (HPFVIIC), rabbit brain (RBFVIIC), and bovine brain (BBFVIIC) thromboplastins; and 2) by an amidolytic method (AMFVIIC). Prothrombin time tests (PT) were also performed by standard methods. These 4 FVII-deficient patients and 3 carriers demonstrated the following results: PT: 18.2 +/- 6.5 sec; FVIIAG: 73.0 +/- 14.9%; HRFVIIC: 30.6 +/- 20.3%; HPFVIIC: 30.5 +/- 21.4%; RBFVIIC: 25.3 +/- 21.4%; BBFVIIC: 30.6 +/- 17.5%; AMFVIIC: 44.1 +/- 18.3%. We conclude that a group of clinically mild African-American FVII-deficient variants exists in Georgia. This group is characterized by the presence of FVIIAG and decreased FVIIC, using a variety of thromboplastins; and excellent correlation was noted for both human thromboplastins. PMID:7942793

  16. The study of hyperostosic variants: significance of hyperostotic variants of human skulls in anthropology

    PubMed Central

    Srivastava, Dhirendra; Singh, Davinder; Raheja, Shashi

    2012-01-01

    Minor variations in the ossicles, foramina and ridges of the cranium have aroused the curiosity of anatomists for many decades. These non-metric variants help us to study the genetic relationships among ancient populations. Since these traits show considerable frequency differences in different populations, they can be used as anthropological characters in epidemiological studies. These variants indirectly reflect the part of underlying genotype of a given population thus implying their usefulness in biological comparisons of related groups. They can be used for the assessment of the existence of the parental structures within a community or as taxonomic indicators. For anthropological studies, the traits should be genetically determined, vary in frequency between different populations and should not show age, sex, and side dependency. The present study was conducted on hundred dry adult human skulls from Northern India. They were sexed and studied for the presence of hyperostotic traits (double hypoglossal canal, jugular foramen bridging, and paracondylar process). Sexual and side dimorphism was observed. None of the traits had shown statistically significant side and sexual dimorphism. Since the dimorphism is exhibited by none of them, it can be postulated that these traits are predominantly under genetic control and can be effectively used for population studies. PMID:23301194

  17. Rare genetic variant analysis on blood pressure in related samples

    PubMed Central

    2014-01-01

    The genetic variants associated with blood pressure identified so far explain only a small proportion of the total heritability of this trait. With recent advances in sequencing technology and statistical methodology, it becomes feasible to study the association between blood pressure and rare genetic variants. Using real baseline phenotype data and imputed dosage data from Genetic Analysis Workshop 18, we performed a candidate gene association analysis. We focused on 8 genes shown to be associated with either systolic or diastolic blood pressure to identify the association with both common and rare genetic variants, and then did a genome-wide rare-variant analysis on blood pressure. We performed association analysis for rare coding and splicing variants within each gene region and all rare variants in each sliding window, using either burden tests or sequence kernel association tests accounting for familial correlation. With a sample size of only 747, we failed to find any novel associated genetic loci. Consequently, we performed analyses on simulated data, with knowledge of the underlying simulating model, to evaluate the type I error rate and power for the methods used in real data analysis. PMID:25519320

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. Variants affecting exon skipping contribute to complex traits.

    PubMed

    Lee, Younghee; Gamazon, Eric R; Rebman, Ellen; Lee, Yeunsook; Lee, Sanghyuk; Dolan, M Eileen; Cox, Nancy J; Lussier, Yves A

    2012-01-01

    DNA variants that affect alternative splicing and the relative quantities of different gene transcripts have been shown to be risk alleles for some Mendelian diseases. However, for complex traits characterized by a low odds ratio for any single contributing variant, very few studies have investigated the contribution of splicing variants. The overarching goal of this study is to discover and characterize the role that variants affecting alternative splicing may play in the genetic etiology of complex traits, which include a significant number of the common human diseases. Specifically, we hypothesize that single nucleotide polymorphisms (SNPs) in splicing regulatory elements can be characterized in silico to identify variants affecting splicing, and that these variants may contribute to the etiology of complex diseases as well as the inter-individual variability in the ratios of alternative transcripts. We leverage high-throughput expression profiling to 1) experimentally validate our in silico predictions of skipped exons and 2) characterize the molecular role of intronic genetic variations in alternative splicing events in the context of complex human traits and diseases. We propose that intronic SNPs play a role as genetic regulators within splicing regulatory elements and show that their associated exon skipping events can affect protein domains and structure. We find that SNPs we would predict to affect exon skipping are enriched among the set of SNPs reported to be associated with complex human traits. PMID:23133393

  4. 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

  5. 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.

  6. Catecholaminergic Gene Variants: Contribution in ADHD and Associated Comorbid Attributes in the Eastern Indian Probands

    PubMed Central

    Sarkar, Kanyakumarika; Bhaduri, Nipa; Sarkar, Keka; Sinha, Swagata; Mukhopadhyay, Kanchan

    2013-01-01

    Contribution of genes in attention deficit hyperactivity disorder (ADHD) has been explored in various populations, and several genes were speculated to contribute small but additive effects. We have assessed variants in four genes, DDC (rs3837091 and rs3735273), DRD2 (rs1800496, rs1801028, and rs1799732), DRD4 (rs4646984 and rs4646983), and COMT (rs165599 and rs740603) in Indian ADHD subjects with comorbid attributes. Cases were recruited following the Diagnostic and Statistical Manual for Mental Disorders-IV-TR after obtaining informed written consent. DNA isolated from peripheral blood leukocytes of ADHD probands (N = 170), their parents (N = 310), and ethnically matched controls (n = 180) was used for genotyping followed by population- and family-based analyses by the UNPHASED program. DRD4 sites showed significant difference in allelic frequencies by case-control analysis, while DDC and COMT exhibited bias in familial transmission (P < 0.05). rs3837091 “AGAG,” rs3735273 “A,” rs1799732 “C,” rs740603 “G,” rs165599 “G” and single repeat alleles of rs4646984/rs4646983 showed positive correlation with co-morbid characteristics (P < 0.05). Multi dimensionality reduction analysis of case-control data revealed significant interactive effects of all four genes (P < 0.001), while family-based data showed interaction between DDC and DRD2 (P = 0.04). This first study on these gene variants in Indo-Caucasoid ADHD probands and associated co-morbid conditions indicates altered dopaminergic neurotransmission in ADHD. PMID:24163823

  7. Structural, catalytic and stabilizing consequences of aromatic cluster variants in human carbonic anhydrase II.

    PubMed

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

    2013-11-01

    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 Ĺ 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 (18)O-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

  8. [Protoplast culture and plant regeneration of the methionine resistant variant of Astragalus cicer L].

    PubMed

    Zhang, Gai Na; Wang, Ying Hua; Wang, Xue Ren; He, Tao; Hao, Jian Guo; Jia, Jing Fen

    2006-06-01

    A protoplast-to-plant system for the methionine resistant variant of Astragalus cicer L. has been developed. The friable calli induced from stem segments of variant plants were used as materials for protoplast isolation through enzyme digestion. The effects of different media and plating densities on protoplast divisions and plant regeneration were studied. Sustained cell divisions and colony formation from the protoplasts of the methionine resistant cell line of Astragalus cicer L. were obtained by a DPD medium containing 2.0 mg/L 2,4- dichlorophenoxyacetic acid (2,4-D), 0.2 mg/L 6 -benzylaminopurine(6-BA), 0.3 mol/L mannitol, 200 mg/L casein hydrolysate and 2% (W/V) sucrose at a plating density of 2x10(5) /ml. The division frequency was 38.3%. At the same time, different dividing types of protoplasts were found. Organogenesis and shoot formation from the protoplast-derived calli were induced on MS medium supplemented with 0.5 mg/L NAA, 10 mg/L KT and 2% (W/V) sucrose. The protoplast-derived calli still expressed resistance to methionine. The protoplast to plant regeneration protocol developed in this study might provide the foundation for the resistant cell line as a parent for somatic hybridization. PMID:16944592

  9. Helicobacter pylori cagA gene variants in Malaysians of different ethnicity.

    PubMed

    Mohamed, Ramelah; Hanafiah, Alfizah; Rose, Isa M; Manaf, Mohd Rizal A; Abdullah, Shiekh Anwar; Sagap, Ismail; van Belkum, A; Yaacob, Jasmi A

    2009-07-01

    We have defined DNA repeat variability in the 3'-terminus of the cagA gene of Helicobacter pylori strains from Malaysian patients of different ethnicities. We identified different alleles based on the EPIYA repeats. cagA types A-B-D and A-B-B-D are more similar to the sequence of Japanese strains, whereas cagA types A-B-C, A-B-C-C, A-B and A-C displayed similarity to strain 26695 sequences. A significant association was found between cagA genotypes and patients' ethnicity, with cagA type A-B-D being predominantly isolated from Chinese patients and cagA type A-B-C from Malays and Indians. Our data further corroborate the possibility that variant biological activity of CagA may affect the host specificity and/or pathogenicity of H. pylori. PMID:19247698

  10. Virus nomenclature below the species level: a standardized nomenclature for filovirus strains and variants rescued from cDNA

    PubMed Central

    Kuhn, Jens H.; Bŕo, Y?míng; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brauburger, Kristina; Brister, J. Rodney; Bukreyev, Alexander A.; Caě, Yíngyún; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Gonzalez, Jean-Paul; Formenty, Pierre; Freiberg, Alexander N.; Hensley, Lisa E.; Hoenen, Thomas; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Karl M.; Klenk, Hans-Dieter; Kobinger, Gary; Lackemeyer, Matthew G.; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Volchkova, Valentina A.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

    2013-01-01

    Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratory-adapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming, (/)<isolation host-suffix>///variant designation>-<isolate designation>, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to “Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1” (with the suffix “rec” identifying the recombinant nature of the virus and “abc1” being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as “EBOVH.sap/COD/95/Kik-abc1”) and abbreviations (such as “EBOV/Kik-abc1”) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed. PMID:24190508

  11. Virus nomenclature below the species level: a standardized nomenclature for filovirus strains and variants rescued from cDNA.

    PubMed

    Kuhn, Jens H; Bŕo, Y?míng; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brauburger, Kristina; Rodney Brister, J; Bukreyev, Alexander A; Caě, Yíngyún; Chandran, Kartik; Davey, Robert A; Dolnik, Olga; Dye, John M; Enterlein, Sven; Gonzalez, Jean-Paul; Formenty, Pierre; Freiberg, Alexander N; Hensley, Lisa E; Hoenen, Thomas; Honko, Anna N; Ignatyev, Georgy M; Jahrling, Peter B; Johnson, Karl M; Klenk, Hans-Dieter; Kobinger, Gary; Lackemeyer, Matthew G; Leroy, Eric M; Lever, Mark S; Mühlberger, Elke; Netesov, Sergey V; Olinger, Gene G; Palacios, Gustavo; Patterson, Jean L; Paweska, Janusz T; Pitt, Louise; Radoshitzky, Sheli R; Ryabchikova, Elena I; Saphire, Erica Ollmann; Shestopalov, Aleksandr M; Smither, Sophie J; Sullivan, Nancy J; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S; van der Groen, Guido; Volchkov, Viktor E; Volchkova, Valentina A; Wahl-Jensen, Victoria; Warren, Travis K; Warfield, Kelly L; Weidmann, Manfred; Nichol, Stuart T

    2014-05-01

    Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratory-adapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming, (/)<isolation host-suffix>///variant designation>-<isolate designation>, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to "Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1" (with the suffix "rec" identifying the recombinant nature of the virus and "abc1" being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as "EBOV H.sap/COD/95/Kik-abc1") and abbreviations (such as "EBOV/Kik-abc1") could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. "EBOV" would suffice if only one EBOV strain/variant/isolate is addressed. PMID:24190508

  12. 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

  13. Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV1 envelope glycoprotein variants from patients with AIDS

    Microsoft Academic Search

    Jasminka Sterjovski; Melissa J Churchill; Anne Ellett; Lachlan R Gray; Michael J Roche; Rebecca L Dunfee; Damian FJ Purcell; Nitin Saksena; Bin Wang; Secondo Sonza; Steven L Wesselingh; Ingrid Karlsson; Eva-Maria Fenyo; Dana Gabuzda; Anthony L Cunningham; Paul R Gorry

    2007-01-01

    BACKGROUND: CCR5-restricted (R5) human immunodeficiency virus type 1 (HIV-1) variants cause CD4+ T-cell loss in the majority of individuals who progress to AIDS, but mechanisms underlying the pathogenicity of R5 strains are poorly understood. To better understand envelope glycoprotein (Env) determinants contributing to pathogenicity of R5 viruses, we characterized 37 full-length R5 Envs from cross-sectional and longitudinal R5 viruses isolated

  14. Two genetic variants of the crustacean hyperglycemic hormone (CHH) from the Australian crayfish, Cherax destructor: detection of chiral isoforms due to posttranslational modification

    Microsoft Academic Search

    Patrick Bulau; Iris Meisen; Barbara Reichwein-Roderburg; Jasna Peter-Katalini?; Rainer Keller

    2003-01-01

    From sinus glands of the Australian crayfish Cherax destructor, two genetic variants of the crustacean hyperglycemic hormone (CHH) were isolated by HPLC and fully characterized by mass spectrometry and Edman sequencing. Both CHH A (8350.38Da) and CHH B (8370.34Da) consist of 72 amino acid residues, with pyroGlu as N-terminus and an amidated (Val-NH2) C-terminus. They differ in 14 residues (81%

  15. Volume 15 Number 11 1987 Nucleic Acids Research Characterization of a cDNA clone coding for a sea urchin histone H2A variant related to the

    E-print Network

    Ernst, Susan G.

    , 1987 ABSTRACT A cDNA clone coding for a sea urchin histone H2A variant has been isolated. The coding in chickens. The nucleotide sequence of the sea urchin H2A.F/Z is 74% conserved when compared to chicken H2A.F and 51% conserved compared to sea urchin H2A early and 60% compared to sea urchin H2A late

  16. DNA length variants contiguous to the 3? end of a vitellogenin gene in Drosophila grimshawi laboratory stocks from different Hawaiian Islands

    Microsoft Academic Search

    Polydefkis Hatzopoulos; Elysse M. Craddock; Michael P. Kambysellis

    1989-01-01

    Two V3 vitellogenin clones isolated from genomic libraries ofDrosophila grimshawi (G1, Auwahi, Maui) were found to differ in length. Structural comparison of the two clones established that the length difference could be attributed to two insertions\\/deletions of about 200 bp each, both within the 3' flanking sequences of the gene. The two length variants appeared to be polymorphic in the

  17. Amino Acid Insertions near Gag Cleavage Sites Restore the Otherwise Compromised Replication of Human Immunodeficiency Virus Type 1 Variants Resistant to Protease Inhibitors

    Microsoft Academic Search

    Sadahiro Tamiya; Sek Mardy; Mark F. Kavlick; Kazuhisa Yoshimura; Hiroaki Mistuya

    2004-01-01

    A variety of amino acid substitutions in the protease and Gag proteins have been reported to contribute to the development of human immunodeficiency virus type 1 (HIV-1) resistance to protease inhibitors. In the present study, full-length molecular infectious HIV-1 clones were generated by using HIV-1 variants isolated from heavily drug-experienced and therapy-failed AIDS patients. Of six full-length infectious clones generated,

  18. Somatic cell scores and clinical signs following experimental intramammary infection of dairy cows with a Staphylococcus aureus small colony variant ( S. aureus SCV) in comparison to other bovine strains

    Microsoft Academic Search

    Heba Atalla; Carlton Gyles; Bruce Wilkie; Ken Leslie; Bonnie Mallard

    2009-01-01

    A recently isolated bovine Staphylococcus aureus small colony variant (SCV) was shown to persist within cultured endothelial cells. However, the clinical importance of S. aureus SCV in persistent infection of the mammary gland is unknown. The hypothesis tested here was a naturally occurring bovine S. aureus SCV, Heba3231, and a Newbould hemB mutant that was an artificially created SCV would

  19. 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

  20. Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

    PubMed

    de Beer, Tjaart A P; Laskowski, Roman A; Parks, Sarah L; Sipos, Botond; Goldman, Nick; Thornton, Janet M

    2013-01-01

    The 1000 Genomes Project data provides a natural background dataset for amino acid germline mutations in humans. Since the direction of mutation is known, the amino acid exchange matrix generated from the observed nucleotide variants is asymmetric and the mutabilities of the different amino acids are very different. These differences predominantly reflect preferences for nucleotide mutations in the DNA (especially the high mutation rate of the CpG dinucleotide, which makes arginine mutability very much higher than other amino acids) rather than selection imposed by protein structure constraints, although there is evidence for the latter as well. The variants occur predominantly on the surface of proteins (82%), with a slight preference for sites which are more exposed and less well conserved than random. Mutations to functional residues occur about half as often as expected by chance. The disease-associated amino acid variant distributions in OMIM are radically different from those expected on the basis of the 1000 Genomes dataset. The disease-associated variants preferentially occur in more conserved sites, compared to 1000 Genomes mutations. Many of the amino acid exchange profiles appear to exhibit an anti-correlation, with common exchanges in one dataset being rare in the other. Disease-associated variants exhibit more extreme differences in amino acid size and hydrophobicity. More modelling of the mutational processes at the nucleotide level is needed, but these observations should contribute to an improved prediction of the effects of specific variants in humans. PMID:24348229

  1. Soluble variants of human recombinant glutaminyl cyclase.

    PubMed

    Castaldo, Cristiana; Ciambellotti, Silvia; de Pablo-Latorre, Raquel; Lalli, Daniela; Porcari, Valentina; Turano, Paola

    2013-01-01

    Recombinant human Glutaminyl Cyclase expressed in E. coli is produced as inclusion bodies. Lack of glycosylation is the main origin of its accumulation in insoluble aggregates. Mutation of single isolated hydrophobic amino acids into negative amino acids was not able to circumvent inclusion bodies formation. On the contrary, substitution with carboxyl-terminal residues of two or three aromatic residues belonging to extended hydrophobic patches on the protein surface provided soluble but still active forms of the protein. These mutants could be expressed in isotopically enriched forms for NMR studies and the maximal attainable concentration was sufficient for the acquisition of (1)H-(15)N HSQC spectra that represent the starting point for future drug development projects targeting Alzheimer's disease. PMID:23977104

  2. Genomic architecture of aggression: rare copy number variants in intermittent explosive disorder.

    PubMed

    Vu, Tiffany H; Coccaro, Emil F; Eichler, Evan E; Girirajan, Santhosh

    2011-12-01

    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. PMID:21812102

  3. 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

  4. 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 Conceiçăo 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

  5. 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

  6. Clinical Clostridium difficile: Clonality and Pathogenicity Locus Diversity

    PubMed Central

    Dingle, Kate E.; Griffiths, David; Didelot, Xavier; Evans, Jessica; Vaughan, Alison; Kachrimanidou, Melina; Stoesser, Nicole; Jolley, Keith A.; Golubchik, Tanya; Harding, Rosalind M.; Peto, Tim E.; Fawley, Warren; Walker, A. Sarah; Wilcox, Mark; Crook, Derrick W.

    2011-01-01

    Clostridium difficile infection (CDI) is an important cause of mortality and morbidity in healthcare settings. The major virulence determinants are large clostridial toxins, toxin A (tcdA) and toxin B (tcdB), encoded within the pathogenicity locus (PaLoc). Isolates vary in pathogenicity from hypervirulent PCR-ribotypes 027 and 078 with high mortality, to benign non-toxigenic strains carried asymptomatically. The relative pathogenicity of most toxigenic genotypes is still unclear, but may be influenced by PaLoc genetic variant. This is the largest study of C. difficile molecular epidemiology performed to date, in which a representative collection of recent isolates (n?=?1290) from patients with CDI in Oxfordshire, UK, was genotyped by multilocus sequence typing. The population structure was described using NeighborNet and ClonalFrame. Sequence variation within toxin B (tcdB) and its negative regulator (tcdC), was mapped onto the population structure. The 69 Sequence Types (ST) showed evidence for homologous recombination with an effect on genetic diversification four times lower than mutation. Five previously recognised genetic groups or clades persisted, designated 1 to 5, each having a strikingly congruent association with tcdB and tcdC variants. Hypervirulent ST-11 (078) was the only member of clade 5, which was divergent from the other four clades within the MLST loci. However, it was closely related to the other clades within the tcdB and tcdC loci. ST-11 (078) may represent a divergent formerly non-toxigenic strain that acquired the PaLoc (at least) by genetic recombination. This study focused on human clinical isolates collected from a single geographic location, to achieve a uniquely high density of sampling. It sets a baseline of MLST data for future comparative studies investigating genotype virulence potential (using clinical severity data for these isolates), possible reservoirs of human CDI, and the evolutionary origins of hypervirulent strains. PMID:21625511

  7. 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

  8. 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

  9. Optimal tests for rare variant effects in sequencing association studies

    PubMed Central

    Lee, Seunggeun; Wu, Michael C.; Lin, Xihong

    2012-01-01

    With development of massively parallel sequencing technologies, there is a substantial need for developing powerful rare variant association tests. Common approaches include burden and non-burden tests. Burden tests assume all rare variants in the target region have effects on the phenotype in the same direction and of similar magnitude. The recently proposed sequence kernel association test (SKAT) (Wu, M. C., and others, 2011. Rare-variant association testing for sequencing data with the SKAT. The American Journal of Human Genetics 89, 82–93], an extension of the C-alpha test (Neale, B. M., and others, 2011. Testing for an unusual distribution of rare variants. PLoS Genetics 7, 161–165], provides a robust test that is particularly powerful in the presence of protective and deleterious variants and null variants, but is less powerful than burden tests when a large number of variants in a region are causal and in the same direction. As the underlying biological mechanisms are unknown in practice and vary from one gene to another across the genome, it is of substantial practical interest to develop a test that is optimal for both scenarios. In this paper, we propose a class of tests that include burden tests and SKAT as special cases, and derive an optimal test within this class that maximizes power. We show that this optimal test outperforms burden tests and SKAT in a wide range of scenarios. The results are illustrated using simulation studies and triglyceride data from the Dallas Heart Study. In addition, we have derived sample size/power calculation formula for SKAT with a new family of kernels to facilitate designing new sequence association studies. PMID:22699862

  10. Adenosquamous variant of metaplastic carcinoma of breast - an unusual histological variant.

    PubMed

    Swathy, P U; Arunalatha, P; Chandramouleeswari, K; Lily, S Mary; Ramya, S

    2015-02-01

    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. PMID:25859463

  11. Genetic complementation in somatic cell hybrids of four variants of infantile G M2 gangliosidosis

    Microsoft Academic Search

    S. Sonderfeld; S. Brendler; K. Sandhoff; H. Galjaard; A. T. Hoogeveen

    1985-01-01

    Summary  Cell hybridizations between fibroblasts of four variants (B, O, AB, and B1) of infantile GM2 gangliosidosis were performed. Cocultivated as well as hybrid cells were analyzed for their capability to degrade exogenously\\u000a added [3H]-GM2. Hybridization of variant AB fibroblasts with fibroblasts of variant O, variant B, or variant B1 resulted in an enhanced\\u000a rate of GM2 hydrolysis, showing intergenic complementation.

  12. 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

  13. Genomic Structure of Three Phenotypically Different Isolates of Peach Latent Mosaic Viroid: Implications of the Existence of Constraints Limiting the Heterogeneity of Viroid Quasispecies

    PubMed Central

    Ambrós, S.; Hernández, C.; Desvignes, J. C.; Flores, R.

    1998-01-01

    The peach latent mosaic viroid (PLMVd) is used to study the interactions between a viroid containing hammerhead ribozymes and its natural host, peach. To gain insight into the molecular basis of the phenotypic effects observed upon viroid infection, sequence variants from three PLMVd isolates that differ in symptom expression on the peach indicator GF-305 have been characterized. Analysis of the primary structures of a total of 29 different sequence variants derived from a severe and two latent isolates has revealed a large number of polymorphic positions in the viroid molecule. The variability pattern indicates that preservation of the stability of both hammerhead structures and conservation of a branched secondary structure of the viroid molecule may be factors limiting sequence heterogeneity in PLMVd. Moreover, compensatory mutations in two hairpin loops of the proposed secondary structure, suggesting that a pseudoknot-like interaction may exist between them, have also been observed. Phylogenetic analysis has allowed the allocation of PLMVd molecules into three major groups. This clustering does not strictly correlate with the source isolate from which the variants were obtained, providing insights into the complex mixture of molecules which make up each isolate. Bioassays of individual PLMVd sequence variants on GF-305 peach seedlings have shown that the biological properties of the PLMVd isolates may be correlated with both the complexity of their viroid populations and the presence of specific sequence variants. PMID:9696836

  14. Proportion of antigenic variants induced by in vitro UV irradiation differs in clones derived from a single tumor

    SciTech Connect

    Hostetler, L.W.; Kripke, M.L.

    1988-01-15

    The purpose of this study was to examine the capacity of different clones derived from the same tumor to generate highly antigenic cells after in vitro exposure to UV radiation. Cells from the metastatic murine melanoma K1735 and clones of K1735 differing in metastatic potential were exposed to UV radiation in vitro, cloned, and tested for antigenic properties in vivo. Approximately half of the clones isolated after UV irradiation of parental K1735 melanoma cells were highly antigenic (five of nine). Similar treatment of cells of a nonmetastatic clone of K1735 generated clones that were all antigenic (nine of nine). In contrast, only one of nine clones derived from UV-irradiated cells of a highly metastatic clone of K1735 were antigenic. Clones derived from unirradiated cultures were not antigenic variants. The increased antigenicity of cells derived from UV-irradiated cultures did not correlate with an increase in expression of cell surface class I major histocompatibility complex antigens. These results demonstrate that the frequency of antigenic variant production after UV irradiation is an intrinsic property of the particular cell line used, and that even cloned cell lines derived from a single tumor differ in their ability to generate antigenic variants after UV irradiation. In addition, they indicate that the increased antigenicity is not necessarily due to a UV-induced increase in expression of cell surface class I histocompatibility antigens.

  15. Vibration isolation technology experiment

    NASA Technical Reports Server (NTRS)

    Keckler, C. R.

    1984-01-01

    The objectives of the vibration isolation technology experiment are to demonstrate the viability of the magnetic suspension technology in providing the isolation of large structures elements from the external environment and to quantify the degree of isolation provided by this system. The approach proposed for this experiment is to mount a six-degrees-of-freedom magnetic bearing suspension system at the free end of a shuttle-attached flexible structure such as MAST. The disturbance generator, located on top of the isolation system, will be energized at selected and broadband frequencies to simulate a typical spacecraft vibration environment. Sensors located on the isolation system and the flexible structures element will be used to quantify the degree of isolation provided by this system.

  16. Cell Culture Adaptation of Hepatitis C Virus and In Vivo Viability of an Adapted Variant?

    PubMed Central

    Kaul, Artur; Woerz, Ilka; Meuleman, Philip; Leroux-Roels, Geert; Bartenschlager, Ralf

    2007-01-01

    Production of infectious hepatitis C virus in cell culture has become possible because of the unique properties of the JFH1 isolate. However, virus titers are rather low, limiting the utility of this system. Here we describe the generation of cell culture-adapted JFH1 variants yielding higher titers of infectious particles and enhanced spread of infection in cultured cells. Sequence analysis of adapted genomes revealed a complex pattern of mutations that differed in two independent experiments. Adaptive mutations were observed both in the structural and in the nonstructural regions, with the latter having the highest impact on enhancement of virus titers. The major adaptive mutation was identified in NS5A, and it enhanced titers of three intergenotypic chimeras consisting of the structural region of a genotype 1a, 1b, or 3a isolate and the remainder of the JFH1 isolate. The mutation resides at the P3 position of the NS5A-B cleavage site and slows down processing, implying that subtle differences in replication complex formation appear to determine the efficiency of virus formation. Highly adapted JFH1 viruses carrying six mutations established a robust infection in uPA-transgenic SCID mice xenografted with human hepatocytes. However, the mutation in NS5A which enhanced virus titers in cell culture the most had reverted to wild type in nearly half of the viral genomes isolated from these animals at 15 weeks postinoculation. These results argue for some level of impaired fitness of this mutant in vivo. PMID:17881454

  17. Reducing the search space for causal genetic variants with VASP

    PubMed Central

    Field, Matthew A.; Cho, Vicky; Cook, Matthew C.; Enders, Anselm; Vinuesa, Carola G.; Whittle, Belinda; Andrews, T. Daniel; Goodnow, Chris C.

    2015-01-01

    Motivation: Increasingly, cost-effective high-throughput DNA sequencing technologies are being utilized to sequence human pedigrees to elucidate the genetic cause of a wide variety of human diseases. While numerous tools exist for variant prioritization within a single genome, the ability to concurrently analyze variants within pedigrees remains a challenge, especially should there be no prior indication of the underlying genetic cause of the disease. Here, we present a tool, variant analysis of sequenced pedigrees (VASP), a flexible data integration environment capable of producing a summary of pedigree variation, providing relevant information such as compound heterozygosity, genome phasing and disease inheritance patterns. Designed to aggregate data across a sequenced pedigree, VASP allows both powerful filtering and custom prioritization of both single nucleotide variants (SNVs) and small indels. Hence, clinical and research users with prior knowledge of a disease are able to dramatically reduce the variant search space based on a wide variety of custom prioritization criteria. Availability and implementation: Source code available for academic non-commercial research purposes at https://github.com/mattmattmattmatt/VASP. Contact: matt.field@anu.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25755272

  18. 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

  19. The ARVD/C genetic variants database: 2014 update.

    PubMed

    Lazzarini, Elisabetta; Jongbloed, Jan D H; Pilichou, Kalliopi; Thiene, Gaetano; Basso, Cristina; Bikker, Hennie; Charbon, Bart; Swertz, Morris; van Tintelen, J Peter; van der Zwaag, Paul A

    2015-04-01

    Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disease characterized by myocardial atrophy, fibro-fatty replacement, and a high risk of ventricular arrhythmias that lead to sudden death. In 2009, genetic data from 57 publications were collected in the arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) Genetic Variants Database (freeware available at http://www.arvcdatabase.info), which comprised 481 variants in eight ACM-associated genes. In recent years, deep genetic sequencing has increased our knowledge of the genetics of ACM, revealing a large spectrum of nucleotide variations for which pathogenicity needs to be assessed. As of April 20, 2014, we have updated the ARVD/C database into the ARVD/C database to contain more than 1,400 variants in 12 ACM-related genes (PKP2, DSP, DSC2, DSG2, JUP, TGFB3, TMEM43, LMNA, DES, TTN, PLN, CTNNA3) as reported in more than 160 references. Of these, only 411 nucleotide variants have been reported as pathogenic, whereas the significance of the other approximately 1,000 variants is still unknown. This comprehensive collection of ACM genetic data represents a valuable source of information on the spectrum of ACM-associated genes and aims to facilitate the interpretation of genetic data and genetic counseling. PMID:25676813

  20. Common genetic variants influence human subcortical brain structures

    PubMed Central

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivičres, 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-Santiańez, 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

  1. An intron 9 containing splice variant of PAX2

    PubMed Central

    Busse, Antonia; Rietz, Anika; Schwartz, Stefan; Thiel, Eckhard; Keilholz, Ulrich

    2009-01-01

    Background PAX2 is a transcription factor with an important role in embryogenic development. However, PAX2 expression was frequently identified in neoplasia responsible for the growth and survival of cancer cells. Due to alternative splicing of exon 6, exon 10 and exon 12 four isoforms of PAX2 are described so far. Methods The expression of an intron 9 containing PAX2 splice variant was analyzed in neoplastic B cell and solid tumor cell lines as well as in primary tumor samples by quantitative RT-PCR. PAX2 proteins were detected by Western Blot in a subset of cell lines. Results All 14 lymphoma cell lines expressed an undescribed PAX2 splice variant containing the entire intron 9 sequence and the exon 10 sequence. This splice variant could also be detected in 35 solid tumor cell lines, in leukemia and lymphoma as well as in colon carcinoma and melanoma patient samples and in blood samples of healthy donors. Expression of this new splice variant on protein level was verified by Western Blot analysis. Conclusion We discovered a previously undescribed intron 9 and exon 10 containing splice variant of PAX2 in B-cell neoplasia and in solid tumors on mRNA and protein level. PMID:19467152

  2. Enhanced activity of human serotonin transporter variants associated with autism

    PubMed Central

    Prasad, Harish C.; Steiner, Jennifer A.; Sutcliffe, James S.; Blakely, Randy D.

    2008-01-01

    Rare, functional, non-synonymous variants in the human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT) gene (SLC6A4) have been identified in both autism and obsessive–compulsive disorder (OCD). Within autism, rare hSERT coding variants associate with rigid–compulsive traits, suggesting both phenotypic overlap with OCD and a shared relationship with disrupted 5-HT signalling. Here, we document functional perturbations of three of these variants: Ile425Leu; Phe465Leu; and Leu550Val. In transiently transfected HeLa cells, the three variants confer a gain of 5-HT transport phenotype. Specifically, enhanced SERT activity was also observed in lymphoblastoid lines derived from mutation carriers. In contrast to previously characterized Gly56Ala, where increased transport activity derives from catalytic activation, the three novel variants exhibit elevated surface density as revealed through both surface antagonist-binding and biotinylation studies. Unlike Gly56Ala, mutants Ile425Leu, Phe465Leu and Leu550Val retain a capacity for acute PKG and p38 MAPK regulation. However, both Gly56Ala and Ile425Leu demonstrate markedly reduced sensitivity to PP2A antagonists, suggesting that deficits in trafficking and catalytic modulation may derive from a common basis in perturbed phosphatase regulation. When expressed stably from the same genomic locus in CHO cells, both Gly56Ala and Ile425Leu display catalytic activation, accompanied by a striking loss of SERT protein. PMID:18957375

  3. Separating Instability from Aggregation Propensity in ?S-Crystallin Variants

    PubMed Central

    Brubaker, William D.; Freites, J. Alfredo; Golchert, Kory J.; Shapiro, Rebecca A.; Morikis, Vasilios; Tobias, Douglas J.; Martin, Rachel W.

    2011-01-01

    Molecular dynamics (MD) simulations, circular dichroism (CD), and dynamic light scattering (DLS) measurements were used to investigate the aggregation propensity of the eye-lens protein ?S-crystallin. The wild-type protein was investigated along with the cataract-related G18V variant and the symmetry-related G106V variant. The MD simulations suggest that local sequence differences result in dramatic differences in dynamics and hydration between these two apparently similar point mutations. This finding is supported by the experimental measurements, which show that although both variants appear to be mostly folded at room temperature, both display increased aggregation propensity. Although the disease-related G18V variant is not the most strongly destabilized, it aggregates more readily than either the wild-type or the G106V variant. These results indicate that ?S-crystallin provides an excellent model system for investigating the role of dynamics and hydration in aggregation by locally unfolded proteins. PMID:21244846

  4. Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

    PubMed Central

    Seth-Smith, Helena MB; Harris, Simon R; Persson, Kenneth; Marsh, Pete; Barron, Andrew; Bignell, Alexandra; Bjartling, Carina; Clark, Louise; Cutcliffe, Lesley T; Lambden, Paul R; Lennard, Nicola; Lockey, Sarah J; Quail, Michael A; Salim, Omar; Skilton, Rachel J; Wang, Yibing; Holland, Martin J; Parkhill, Julian; Thomson, Nicholas R; Clarke, Ian N

    2009-01-01

    Background Chlamydia trachomatis is the most common cause of sexually transmitted infections globally and the leading cause of preventable blindness in the developing world. There are two biovariants of C. trachomatis: 'trachoma', causing ocular and genital tract infections, and the invasive 'lymphogranuloma venereum' strains. Recently, a new variant of the genital tract C. trachomatis emerged in Sweden. This variant escaped routine diagnostic tests because it carries a plasmid with a deletion. Failure to detect this strain has meant it has spread rapidly across the country provoking a worldwide alert. In addition to being a key diagnostic target, the plasmid has been linked to chlamydial virulence. Analysis of chlamydial plasmids and their cognate chromosomes was undertaken to provide insights into the evolutionary relationship between chromosome and plasmid. This is essential knowledge if the plasmid is to be continued to be relied on as a key diagnostic marker, and for an understanding of the evolution of Chlamydia trachomatis. Results The genomes of two new C. trachomatis strains were sequenced, together with plasmids from six C. trachomatis isolates, including the new variant strain from Sweden. The plasmid from the new Swedish variant has a 377 bp deletion in the first predicted coding sequence, abolishing the site used for PCR detection, resulting in negative diagnosis. In addition, the variant plasmid has a 44 bp duplication downstream of the deletion. The region containing the second predicted coding sequence is the most highly conserved region of the plasmids investigated. Phylogenetic analysis of the plasmids and chromosomes are fully congruent. Moreover this analysis also shows that ocular and genital strains diverged from a common C. trachomatis progenitor. Conclusion The evolutionary pathways of the chlamydial genome and plasmid imply that inheritance of the plasmid is tightly linked with its cognate chromosome. These data suggest that the plasmid is not a highly mobile genetic element and does not transfer readily between isolates. Comparative analysis of the plasmid sequences has revealed the most conserved regions that should be used to design future plasmid based nucleic acid amplification tests, to avoid diagnostic failures. PMID:19460133

  5. 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

  6. Novel CLC3 transcript variants in blood eosinophils and increased CLC3 expression in nasal lavage and blood eosinophils of asthmatics

    PubMed Central

    Gaurav, Rohit; Bewtra, Againdra K; Agrawal, Devendra K

    2014-01-01

    Eosinophilia is a characteristic feature of allergic airway inflammation and remodeling. Chloride channel-3 (CLC3) in eosinophils has been associated with superoxide generation and respiratory burst. The CLC3 gene may produce multiple transcript variants through alternative splicing. However, the presence of CLC3 variants in human eosinophils is unknown. We examined the expression of CLC3 transcript variants in peripheral blood eosinophils of allergic asthmatics and healthy individuals. Potential of these obligatory dimers to form homo- or hetero-dimers was examined in HEK293 cells co-transfected with CLC3b-GFP and CLC3e-RFP. Eosinophils were isolated from peripheral blood by negative selection. Expression of CLC3 and CLC3 transcript variants was examined by qPCR, Western blot, and immunofluorescence. Confocal micrographs were analyzed with Image J software. Higher levels of novel transcript variants of CLC3 (CLC3b and CLC3e) were found in peripheral blood eosinophils of asthmatics compared to healthy non-atopic subjects. We also found higher CLC3 protein expression in the blood and nasal lavage eosinophils of asthmatics than healthy subjects. Both membranous and intracellular CLC3 expression were observed. Also, we found the presence of both homodimers and heterodimers of CLC3b-GFP and CLC3e-RFP in HEK293 cells. Higher and differential expression of novel CLC3 transcript variants in mild-to-moderate and moderate-to-severe asthmatic eosinophils suggest their critical role in allergic asthma. Membranous and intracellular (granular) expression of CLC3 in nasal lavage and peripheral blood eosinophils suggest their involvement in the activation and migration of eosinophils in allergic asthma. Moreover, homo- and hetero-dimerization of these transcript variants may change the channel properties to exhibit these states. Presence of CLC3 variants may serve as a biomarker in allergic asthma and additional knowledge of interaction between CLC3 transcript variants and their specific role in the activation and migration of eosinophils will allow to explore novel therapeutic approach in allergic asthma. PMID:25866628

  7. KD4v: comprehensible knowledge discovery system for missense variant

    PubMed Central

    Luu, Tien-Dao; Rusu, Alin; Walter, Vincent; Linard, Benjamin; Poidevin, Laetitia; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Raffelsberger, Wolfgang; Wicker, Nicolas; Lecompte, Odile; Thompson, Julie D.; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    A major challenge in the post-genomic era is a better understanding of how human genetic alterations involved in disease affect the gene products. The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants. The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates. These rules are interpretable by non-expert humans and are used to accurately predict the deleterious/neutral status of an unknown mutation. The web server is available at http://decrypthon.igbmc.fr/kd4v. PMID:22641855

  8. KD4v: Comprehensible Knowledge Discovery System for Missense Variant.

    PubMed

    Luu, Tien-Dao; Rusu, Alin; Walter, Vincent; Linard, Benjamin; Poidevin, Laetitia; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Raffelsberger, Wolfgang; Wicker, Nicolas; Lecompte, Odile; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-07-01

    A major challenge in the post-genomic era is a better understanding of how human genetic alterations involved in disease affect the gene products. The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants. The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates. These rules are interpretable by non-expert humans and are used to accurately predict the deleterious/neutral status of an unknown mutation. The web server is available at http://decrypthon.igbmc.fr/kd4v. PMID:22641855

  9. New Compstatin Variants through Two De Novo Protein Design Frameworks

    PubMed Central

    Bellows, M.L.; Fung, H.K.; Taylor, M.S.; Floudas, C.A.; López de Victoria, A.; Morikis, D.

    2010-01-01

    Abstract Two de novo protein design frameworks are applied to the discovery of new compstatin variants. One is based on sequence selection and fold specificity, whereas the other approach is based on sequence selection and approximate binding affinity calculations. The proposed frameworks were applied to a complex of C3c with compstatin variant E1 and new variants with improved binding affinities are predicted and experimentally validated. The computational studies elucidated key positions in the sequence of compstatin that greatly affect the binding affinity. Positions 4 and 13 were found to favor Trp, whereas positions 1, 9, and 10 are dominated by Asn, and position 11 consists mainly of Gln. A structural analysis of the C3c-bound peptide analogs is presented. PMID:20483343

  10. Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver

    PubMed Central

    Pham, Phillip H.; Shipman, William J.; Erikson, Galina A.; Schork, Nicholas J.; Torkamani, Ali

    2015-01-01

    Interpretation of human genomes is a major challenge. We present the Scripps Genome ADVISER (SG-ADVISER) suite, which aims to fill the gap between data generation and genome interpretation by performing holistic, in-depth, annotations and functional predictions on all variant types and effects. The SG-ADVISER suite includes a de-identification tool, a variant annotation web-server, and a user interface for inheritance and annotation-based filtration. SG-ADVISER allows users with no bioinformatics expertise to manipulate large volumes of variant data with ease – without the need to download large reference databases, install software, or use a command line interface. SG-ADVISER is freely available at genomics.scripps.edu/ADVISER. PMID:25706643

  11. Massively Parallel Functional Analysis of BRCA1 RING Domain Variants.

    PubMed

    Starita, Lea M; Young, David L; Islam, Muhtadi; Kitzman, Jacob O; Gullingsrud, Justin; Hause, Ronald J; Fowler, Douglas M; Parvin, Jeffrey D; Shendure, Jay; Fields, Stanley

    2015-06-01

    Interpreting variants of uncertain significance (VUS) is a central challenge in medical genetics. One approach is to experimentally measure the functional consequences of VUS, but to date this approach has been post hoc and low throughput. Here we use massively parallel assays to measure the effects of nearly 2000 missense substitutions in the RING domain of BRCA1 on its E3 ubiquitin ligase activity and its binding to the BARD1 RING domain. From the resulting scores, we generate a model to predict the capacities of full-length BRCA1 variants to support homology-directed DNA repair, the essential role of BRCA1 in tumor suppression, and show that it outperforms widely used biological-effect prediction algorithms. We envision that massively parallel functional assays may facilitate the prospective interpretation of variants observed in clinical sequencing. PMID:25823446

  12. A hierarchical particle swarm optimizer and its adaptive variant.

    PubMed

    Janson, Stefan; Middendorf, Martin

    2005-12-01

    A hierarchical version of the particle swarm optimization (PSO) metaheuristic is introduced in this paper. In the new method called H-PSO, the particles are arranged in a dynamic hierarchy that is used to define a neighborhood structure. Depending on the quality of their so-far best-found solution, the particles move up or down the hierarchy. This gives good particles that move up in the hierarchy a larger influence on the swarm. We introduce a variant of H-PSO, in which the shape of the hierarchy is dynamically adapted during the execution of the algorithm. Another variant is to assign different behavior to the individual particles with respect to their level in the hierarchy. H-PSO and its variants are tested on a commonly used set of optimization functions and are compared to PSO using different standard neighborhood schemes. PMID:16366251

  13. Engineering unnatural variants of plantazolicin through codon reprogramming

    PubMed Central

    Deane, Caitlin D.; Melby, Joel O.; Molohon, Katie J.; Susarrey, Aziz R.; Mitchell, Douglas A.

    2013-01-01

    Plantazolicin (PZN) is a polyheterocyclic natural product derived from a ribosomal peptide that harbors remarkable antibiotic selectivity for the causative agent of anthrax, Bacillus anthracis. To simultaneously establish the structure-activity relationship of PZN and the substrate tolerance of the biosynthetic pathway, an Escherichia coli expression strain was engineered to heterologously produce PZN analogs. Variant PZN precursor genes were produced by site-directed mutagenesis and later screened by mass spectrometry to assess posttranslational modification and export by E. coli. From a screen of 72 precursor peptides, 29 PZN variants were detected. This analog collection provided insight into the selectivity of the posttranslational modifying enzymes and established the boundaries of the natural biosynthetic pathway. Unlike other studied thiazole/oxazole-modified microcins, the biosynthetic machinery appeared to be finely tuned towards the production of PZN, such that the cognate enzymes did not process even other naturally occurring sequences from similar biosynthetic clusters. The modifying enzymes were exquisitely selective, installing heterocycles only at pre-defined positions within the precursor peptides while leaving neighboring residues unmodified. Nearly all substitutions at positions normally harboring heterocycles prevented maturation of a PZN variant, though some exceptions were successfully produced lacking a heterocycle at the penultimate residue. No variants containing additional heterocycles were detected, although several peptide sequences yielded multiple PZN variants as a result of varying oxidation states of select residues. Eleven PZN variants were produced in sufficient quantity to facilitate purification and assessment of their antibacterial activity, providing insight into the structure-activity relationship of PZN. PMID:23823732

  14. Engineering unnatural variants of plantazolicin through codon reprogramming.

    PubMed

    Deane, Caitlin D; Melby, Joel O; Molohon, Katie J; Susarrey, Aziz R; Mitchell, Douglas A

    2013-09-20

    Plantazolicin (PZN) is a polyheterocyclic natural product derived from a ribosomal peptide that harbors remarkable antibiotic selectivity for the causative agent of anthrax, Bacillus anthracis. To simultaneously establish the structure-activity relationship of PZN and the substrate tolerance of the biosynthetic pathway, an Escherichia coli expression strain was engineered to heterologously produce PZN analogues. Variant PZN precursor genes were produced by site-directed mutagenesis and later screened by mass spectrometry to assess post-translational modification and export by E. coli. From a screen of 72 precursor peptides, 29 PZN variants were detected. This analogue collection provided insight into the selectivity of the post-translational modifying enzymes and established the boundaries of the natural biosynthetic pathway. Unlike other studied thiazole/oxazole-modified microcins, the biosynthetic machinery appeared to be finely tuned toward the production of PZN, such that the cognate enzymes did not process even other naturally occurring sequences from similar biosynthetic clusters. The modifying enzymes were exquisitely selective, installing heterocycles only at predefined positions within the precursor peptides while leaving neighboring residues unmodified. Nearly all substitutions at positions normally harboring heterocycles prevented maturation of a PZN variant, though some exceptions were successfully produced lacking a heterocycle at the penultimate residue. No variants containing additional heterocycles were detected, although several peptide sequences yielded multiple PZN variants as a result of varying oxidation states of select residues. Eleven PZN variants were produced in sufficient quantity to facilitate purification and assessment of their antibacterial activity, providing insight into the structure-activity relationship of PZN. PMID:23823732

  15. Identification and characterization of Clostridium perfringens beta toxin variants with differing trypsin sensitivity and in vitro cytotoxicity activity.

    PubMed

    Theoret, James R; Uzal, Francisco A; McClane, Bruce A

    2015-04-01

    By producing toxins, Clostridium perfringens causes devastating diseases of both humans and animals. C. perfringens beta toxin (CPB) is the major virulence determinant for type C infections and is also implicated in type B infections, but little is known about the CPB structure-function relationship. Amino acid sequence comparisons of the CPBs made by 8 randomly selected isolates identified two natural variant toxins with four conserved amino acid changes, including a switch of E to K at position 168 (E168K) that introduces a potential trypsin cleavage site into the CPB protein of strain JGS1076. To investigate whether this potential trypsin cleavage site affects sensitivity to trypsin, a primary host defense against this toxin, the two CPB variants were assayed for their trypsin sensitivity. The results demonstrated a significant difference in trypsin sensitivity, which was linked to the E168K switch by using site-directed recombinant CPB (rCPB) mutants. The natural CPB variants also displayed significant differences in their cytotoxicity to human endothelial cells. This cytotoxicity difference was mainly attributable to increased host cell binding rather than the ability to oligomerize or form functional pores. Using rCPB site-directed mutants, differences in cytotoxicity and host cell binding were linked to an A300V amino acid substitution in the strain JGS1076 CPB variant that possessed more cytotoxic activity. Mapping of sequence variations on a CPB structure modeled using related toxins suggests that the E168K substitution is surface localized and so can interact with trypsin and that the A300V substitution is located in a putative binding domain of the CPB toxin. PMID:25643999

  16. Atypical clinical variants in New World cutaneous leishmaniasis: disseminated, erysipeloid, and recidiva cutis due to Leishmania (V.) panamensis.

    PubMed

    Calvopina, Manuel; Gomez, Eduardo A; Uezato, Hiroshi; Kato, Hirotomo; Nonaka, Shigeo; Hashiguchi, Yoshihisa

    2005-08-01

    In recent times, there has been an increase in the number of reports for new and rare variants of cutaneous leishmaniasis (CL). Here, we describe three unusual clinical forms of CL identified in Ecuadorian children. A total of 131 patients with CL were diagnosed over a 2-year period of active search. In 3 (2.29%), the lesions were very unusual; these included erysipeloid, recidiva cutis (LRC), and disseminated leishmaniasis (DL). The erysipeloid case is characterized by erythematous and indurated plaque seen on the face of a 5-year-old boy; the LRC one is differentiated by slowly progressing red-brown papules around large scars of healed sores in a 6-year-old girl, and the DL case is characterized by dozens of cutaneous ulcers distributed in the whole body of a 1-year-old girl. Leishmania parasites were isolated by lesion aspirate and analyzed by the technique multilocus enzyme electrophoresis (MLEE). All three isolates were identified as Leishmania (Viannia) panamensis. These distinct clinical variants rarely have been reported previously in the American cutaneous leishmaniasis, and for the first time L. (V.) panamensis was identified as the etiologic agent. Our cases extend the spectrum of clinical presentations in New World leishmaniasis. PMID:16103590

  17. Engineering of highly selective variants of Parvibaculum lavamentivorans alcohol dehydrogenase.

    PubMed

    Spickermann, Dominik; Hausmann, Sascha; Degering, Christian; Schwaneberg, Ulrich; Leggewie, Christian

    2014-09-22

    We present the development of highly selective variants of the Parvibaculum lavamentivorans alcohol dehydrogenase. Four amino acids (A158, N162, K202, L224) in the second sphere of the catalytic site were identified to determine the selectivity for 3-quinuclidone reduction significantly. The best variant (A158H/N162G/K202Q/L224W) was able to increase the ee for (R)-3-quinuclidinol production from 84.3?% (wild-type) to ?99?% and concomitantly to enhance conversion by 43.5?%. PMID:25169816

  18. Synaptotagmin 7 splice variants differentially regulate synaptic vesicle recycling

    PubMed Central

    Virmani, Tuhin; Han, Weiping; Liu, Xinran; Südhof, Thomas C.; Kavalali, Ege T.

    2003-01-01

    The speed of synaptic vesicle recycling determines the efficacy of neurotransmission during repetitive stimulation. Synaptotagmins are synaptic C2-domain proteins that are involved in exocytosis, but have also been linked to endocytosis. We now demonstrate that upon expression in transfected neurons, a short splice variant of synaptotagmin 7 that lacks C2-domains accelerates endocytic recycling of synaptic vesicles, whereas a longer splice variant that contains C2-domains decelerates recycling. These results suggest that alternative splicing of synaptotagmin 7 acts as a molecular switch, which targets vesicles to fast and slow recycling pathways. PMID:14532108

  19. Functional gene variants of CYP3A4.

    PubMed

    Werk, A N; Cascorbi, I

    2014-09-01

    Cytochrome P450 3A4 (CYP3A4) is involved in the metabolism of more drugs in clinical use than any other foreign compound-metabolizing enzyme in humans. Recently, increasing evidence has been found showing that variants in the CYP3A4 gene have functional significance and--in rare cases--lead to loss of activity, implying tremendous consequences for patients. This review article highlights the functional consequences of all CYP3A4 variants recognized by the Human Cytochrome P450 (CYP) Allele Nomenclature Database. PMID:24926778

  20. Isolated central vestibular syndrome.

    PubMed

    Kim, Sung-Hee; Park, Seong-Ho; Kim, Hyo-Jung; Kim, Ji-Soo

    2015-04-01

    Isolated vestibular syndrome may occur all along the vestibular pathways from the peripheral labyrinth to the brain. By virtue of recent developments in clinical neurotology and neuroimaging, however, diagnosis of isolated central vestibulopathy is increasing. Here, we review five distinct syndromes of isolated central vestibular syndrome from lesions restricted to the vestibular nuclei, the nucleus prepositus hypoglossi, the flocculus, the tonsil, and the nodulus, and introduce a new vestibular syndrome from isolated involvement of the inferior cerebellar peduncle. Decreased responses to head impulses do not exclude a central lesion as a cause of isolated vestibular syndrome. Brain imaging, including diffusion-weighted magnetic resonance imaging (MRI), may be falsely negative during the acute phase in patients with isolated vestibular syndrome because of a stroke. Central signs should be sought carefully in patients with isolated vertigo, even when the patients show the features of peripheral vestibulopathy and negative MRIs. Recognition of these isolated central vestibular syndromes would aid in defining the lesions responsible for various vestibular manifestations in central vestibulopathy. PMID:25735822

  1. Wrentit Genetic Isolation Map

    USGS Multimedia Gallery

    This map of the Thousand Oaks, Calif. area visualizes the degree of genetic isolation being experienced by the wrentit (Chamaea fasciata), a small songbird. USGS and National Park Service biologists discovered that as urban development fragmented the Santa Monica Mountains scrubland into isolated

  2. Isolation of Thermophilic Actinomycetes

    Microsoft Academic Search

    P. H. Gregory; Maureen E. Lacey

    1962-01-01

    To judge from reports in the literature, thermophilic Actinomycetes have proved difficult to isolate. For isolations from mouldy hay we have developed a convenient method which promises to be useful in other contexts1. The method uses the fact that dry air removes spores of the Streptomycetaceae in preference to bacteria. Instead of suspending the spores in water and plating dilutions

  3. [Persistent and recurrent skin infection with small-colony variant methicillin-resistant Staphylococcus aureus].

    PubMed

    Coman, Gabriela; Mardare, Nicoleta; Cop?cianu, Brîndu?a; Covic, Maria

    2008-01-01

    S. aureus is one of the problematic bacteria, capable to develop resistance mechanisms to all antibiotics that the bacteria are naturally susceptible. A particular phenotypic mechanism, especially against the antibiotics that repressed the synthesis of the cellular wall and aminoglycosides, was evidenced in subpopulations that grows in small-colonies and represents auxotrophic mutants for hemin, menadione or thymidine. This type of strains has been isolated most frequently from patients with osteomyelitis, septic arthritis or pulmonary infections after a long period of antibiotic treatment. The authors present the case of a patient with persistent and recurrent staphylococcal infection of the peritoneal dialysis exit site, treated with different antibiotics (ciprofloxacin, vancomycin, amoxicillin and clavulanic acid, cephalexin) from witch has been isolated a small-colony strain of methicillin-resistant S. aureus. Therapeutic failure can be explain by the slow multiplication of this strain in vivo, persistence into phagocytes and the protection offered by biofilm from the surface of the catheter. Bacteriologic diagnosis in these cases is difficult because of the culture, biochemical and susceptibility testing particularities of these strains. All these may lead failure to identification small colony variants of S. aureus and mis-evaluation of the frequency of infection with these strains in patients with long-term antibiotherapy. PMID:18677911

  4. Simulation-based decision support tool for electrification of isolated areas using a network with multiple renewable sources

    Microsoft Academic Search

    S. Keller; S. Naciri; A. Nejmi; J. Dos Ghali

    2007-01-01

    The Ecole Polytechnique Federale de Lausanne (EPFL), the Hassan II Institute of Agronomics and Veterinary Science (IAV) and Targa-Aid association (Rabat\\/Morocco) undertook a joint project to implement an electrification technique from different types of renewable sources, supplying small networks of isolated consumers. To help select the best solution among several production variants for satisfying the consumption, taking all of the

  5. Swine fever virus strains isolated in these atypical cases are virulent only for the foetus and the newborn piglet. In 50 p. ioo of these positive cases, seroneutralization tests showed that iso-

    E-print Network

    Paris-Sud XI, Université de

    Swine fever virus strains isolated in these atypical cases are virulent only for the foetus swine fever virus strains were characterized as serological variants. These strains are poorly FOR PREGNANT SOWS OF THE « THIVERVAI,» STRAIN FROM CLASSICAL SWINE FEVER VIRUS Isolated in tissue culture

  6. Induction of differential T-helper-cell responses in mice infected with variants of the parasitic nematode Trichuris muris.

    PubMed Central

    Bellaby, T; Robinson, K; Wakelin, D

    1996-01-01

    The resistance or susceptibility of mice to infection with the intestinal nematode parasite Trichuris muris is closely correlated with polarization of T helper (Th) cell responses to the type 2 (Th2) or type 1 (Th1) subset. Comparison of infections with three isolates of T. muris (E/K, E/N, and S) in three inbred strains of mice (CBA, C57BL/10, and B10.BR) has shown that host Th response phenotype can be parasite determined. Although the mouse strains used show genetically determined variation in ability to respond to T. muris (CBA > C57BL/10 > B10.BR), the speed of worm expulsion in a given strain depended upon the isolate used for infection (E/K > E/N > S). The two isolates that induced the most effective resistance (E/K and E/N) elicited parasite-specific host antibody responses that were dominated by immunoglobulin G1 (IgG1), and antigen-stimulated T cells from infected mice released interleukin-5 in vitro. With the isolate that induced the least host resistance (S), the dominant antibody response was IgG2a, and T cells released gamma interferon in vitro. These data show clearly that parasite variant-specific factors play a major role in Th subset polarization during infection. PMID:8641783

  7. Imaging appearances of musculoskeletal developmental variants in the pediatric population.

    PubMed

    Berko, Netanel S; Kurian, Jessica; Taragin, Benjamin H; Thornhill, Beverly A

    2015-01-01

    Variations in musculoskeletal development in children are commonly encountered. These variants often have a confusing appearance on imaging and may simulate pathologic conditions. However, in many instances, these normal variants have certain features that allow for confident determination of the benign nature of these entities. An awareness of the characteristic imaging features is therefore important for radiologists. In this review, we focus on 4 specific categories of variants in the development: (1) variations in the normal ossification of skeletal structures, (2) the appearance of tendinous and ligamentous insertions in the developing skeleton, (3) overlapping lines that can be confused with fractures or other pathologic conditions, and (4) variant orientation of normal bones. We review the etiology and imaging appearance of these entities and also describe methods of differentiating these benign entities from pathologic lesions. Although in certain cases, correlation with clinical parameters is needed to confidently diagnose the lesion as benign, in many cases, an appreciation of the characteristic imaging features alone would suffice and prevent a potentially costly workup. PMID:25512169

  8. Genetic associations of nonsynonymous exonic variants with psychophysiological endophenotypes.

    PubMed

    Vrieze, Scott I; Malone, Stephen M; Pankratz, Nathan; Vaidyanathan, Uma; Miller, Michael B; Kang, Hyun Min; McGue, Matt; Abecasis, Gonçalo; Iacono, William G

    2014-12-01

    We mapped ?85,000 rare nonsynonymous exonic single nucleotide polymorphisms (SNPs) to 17 psychophysiological endophenotypes in 4,905 individuals, including antisaccade eye movements, resting EEG, P300 amplitude, electrodermal activity, affect-modulated startle eye blink. Nonsynonymous SNPs are predicted to directly change or disrupt proteins encoded by genes and are expected to have significant biological consequences. Most such variants are rare, and new technologies can efficiently assay them on a large scale. We assayed 247,870 mostly rare SNPs on an Illumina exome array. Approximately 85,000 of the SNPs were polymorphic, rare (MAF?variant association tests identified a SNP in the PARD3 gene associated with theta resting EEG power. The sequence kernel association test, a gene-based test, identified a gene PNPLA7 associated with pleasant difference startle, the difference in startle magnitude between pleasant and neutral images. No other single nonsynonymous variant, or gene-based group of variants, was strongly associated with any endophenotype. PMID:25387709

  9. Power Spectra for Cold Dark Matter and Its Variants

    Microsoft Academic Search

    Daniel J. Eisenstein; Wayne Hu

    1999-01-01

    The bulk of recent cosmological research has focused on the adiabatic cold dark matter model and its simple extensions. Here we present an accurate fitting formula that describes the matter transfer functions of all common variants, including mixed dark matter models. The result is a function of wavenumber, time, and six cosmological parameters: the massive neutrino density, number of neutrino

  10. Optimal tests for rare variant effects in sequencing association studies

    E-print Network

    Lin, Xihong

    Optimal tests for rare variant effects in sequencing association studies Seunggeun Lee Department association tests. Common ap- proaches include burden and non-burden tests. Burden tests assume all rare. The recently proposed Sequence Kernel association Test (SKAT) [19] an extension of the C-alpha test [12

  11. Observational consequences of the standard model Higgs inflation variants

    SciTech Connect

    Popa, L.A., E-mail: lpopa@spacescience.ro [Institute for Space Sciences, Bucharest-Magurele, Ro-077125 Romania (Romania)

    2011-10-01

    We consider the possibility to observationally differentiate the Standard Model (SM) Higgs driven inflation with non-minimal coupling to gravity from other variants of SM Higgs inflation based on the scalar field theories with non-canonical kinetic term such as Galileon-like kinetic term and kinetic term with non-minimal derivative coupling to the Einstein tensor. In order to ensure consistent results, we study the SM Higgs inflation variants by using the same method, computing the full dynamics of the background and perturbations of the Higgs field during inflation at quantum level. Assuming that all the SM Higgs inflation variants are consistent theories, we use the MCMC technique to derive constraints on the inflationary parameters and the Higgs boson mass from their fit to WMAP7+SN+BAO data set. We conclude that a combination of the SM Higgs mass measurement by the LHC and accurate determination by the PLANCK satellite of the spectral index of curvature perturbations and tensor-to-scalar ratio will enable to distinguish among these models. We also show that the consistency relations of the SM Higgs inflation variants are distinct enough to differentiate among them.

  12. Telangiectatic focal nodular hyperplasia: a variant of hepatocellular adenoma

    Microsoft Academic Search

    Valerie Paradis; Asmae Benzekri; Delphine Dargčre; Ivan Bičche; Ingrid Laurendeau; Valerie Vilgrain; Jacques Belghiti; Michel Vidaud; Claude Degott; Pierre Bedossa

    2004-01-01

    Background & Aims: “Telangiectatic focal nodular hyperplasia” designate atypical lesions considered as variants of focal nodular hyperplasia (FNH). However, because “telangiectatic FNH” share several morphologic patterns with hepatocellular adenomas, classification of such lesions deserve further clarification. Therefore, the aim of the present study was to reconsider the classification of telangiectatic FNH with the help of a molecular approach. Methods: Ten

  13. Creutzfeldt - Jakob con debut oftalmológico: la variante Heidenhain

    Microsoft Academic Search

    I. del Barrio-Manso; Á. Toribio-García; M. Cordero-Coma; L. Tuńón; E. Baragańo

    2010-01-01

    Clinical caseWe report the case of a 67 year old female complaining of decreased vision and diagnosed with the Heidenhain variant of sporadic Creutzfeldt-Jakob disease. Her past medical history was unremarkable. She died less than three months after the onset.

  14. Missense variant in TREML2 protects against Alzheimer's disease

    PubMed Central

    Benitez, Bruno A.; Jin, Sheng Chih; Guerreiro, Rita; Graham, Rob; Lord, Jenny; Harold, Denise; Sims, Rebecca; Lambert, Jean-Charles; Gibbs, J. Raphael; Bras, Jose; Sassi, Celeste; Harari, Oscar; Bertelsen, Sarah; Lupton, Michelle K.; Powell, John; Bellenguez, Celine; Brown, Kristelle; Medway, Christopher; Haddick, Patrick CG.; van der Brug, Marcel P.; Bhangale, Tushar; Ortmann, Ward; Behrens, Tim; Mayeux, Richard; Pericak-Vance, Margaret A.; Farrer, Lindsay A.; Schellenberg, Gerard D.; Haines, Jonathan L.; Turton, Jim; Braae, Anne; Barber, Imelda; Fagan, Anne M.; Holtzman, David M.; Morris, John C.; Williams, Julie; Kauwe, John S.K.; Amouyel, Philippe; Morgan, Kevin; Singleton, Andy; Hardy, John; Goate, Alison M.; Cruchaga, Carlos

    2014-01-01

    TREM and TREM-like receptors are a structurally similar protein family encoded by genes clustered on chromosome 6p21.11. Recent studies have identified a rare coding variant (p.R47H) in TREM2 that confers a high risk for Alzheimer's disease (AD). In addition, common single nucleotide polymorphisms in this genomic region are associated with cerebrospinal fluid biomarkers for AD and a common intergenic variant found near the TREML2 gene has been identified to be protective for AD. However, little is known about the functional variant underlying the latter association or its relationship with the p.R47H. Here, we report comprehensive analyses using whole-exome sequencing data, cerebrospinal fluid biomarker analyses, meta-analyses (16,254 cases and 20,052 controls) and cell-based functional studies to support the role of the TREML2 coding missense variant p.S144G (rs3747742) as a potential driver of the meta-analysis AD-associated genome-wide association studies signal. Additionally, we demonstrate that the protective role of TREML2 in AD is independent of the role of TREM2 gene as a risk factor for AD. PMID:24439484

  15. Representing Numbers Using Fibonacci Variants Stephen K. Lucas

    E-print Network

    Lucas, Stephen

    Representing Numbers Using Fibonacci Variants Stephen K. Lucas Department of Mathematics Dunlap [4] and Va- jda [17]. Fibonacci numbers are defined by the recurrence relation fn = fn-1 + fn-2 of Fibonacci numbers is that every natural number can be uniquely represented by a sum of distinct non

  16. Genetic variants underlying risk of endometriosis: insights from

    E-print Network

    Nyholt, Dale R.

    variants underlying risk of endometriosis: insights from meta-analysis of eight genome-wide association; accepted on February 26, 2014 table of contents Introduction GWAS of endometriosis Sources-wide significant results across the studies Investigation of other reported GWAS associations in endometriosis loci

  17. Antenna optimization for time-variant MIMO systems

    Microsoft Academic Search

    Lars Reichardt; Juan Pontes; Yoke Leen Sit; Thomas Zwick

    2011-01-01

    The handling of the radio channel is an important aspect that determines the working capability of a mobile communication system. Since the channel behavior is influenced by the environment, which leads to a different behavior in different environments, the antenna design (synthesis) becomes environment dependent (time-variant) as well. In this paper, a capacity maximizing approach for the design of antenna

  18. Genetic variants in sporadic Parkinson's disease: East vs West.

    PubMed

    Peeraully, Tasneem; Tan, E K

    2012-01-01

    A number of gene variants or single nucleotide polymorphisms (SNPs) have been shown to modulate the risk of Parkinson's disease (PD). These variants are identified from genetic association studies of familial PD and candidate genes, and from genome wide association studies (GWAS). These include REP1 dinucleotide repeat polymorphism within the promoter region of the SNCA gene, and SNPs within the vicinity of SNCA and LRRK2 genes. A number of exonic variants of LRRK2 (G2385R, R1628P, S1647T, M1646T, A419V, R1398H, N551K, Y2189C) have been shown to influence PD risk in various ethnic populations. Numerous GWAS linked loci including BST1 (bone marrow stromal cell antigen 1), PARK16 (parkinson disease 16 susceptibility), GAK (cyclin G associated kinase), and HLA (human leukocyte antigen) have also been identified. The genetic variants have differential effect on PD risk in Eastern and Western populations. Knowing the basis behind ethnic-specific variances would further our understanding of the pathophysiologic mechanisms and help planning of genetic testing programmes. PMID:22166457

  19. A Variant of Evolution Strategies for Vector Optimization

    E-print Network

    Coello, Carlos A. Coello

    A Variant of Evolution Strategies for Vector Optimization Frank Kursawe University of Dortmund a new method based on evolution strategies has been developed which is capable of giving a good insight, game theory, one global replacement criterion and others [2, 3]. Many of these algorithms reduce

  20. Space-Variant Computer Vision: A Graph Theoretic Approach

    E-print Network

    Schwartz, Eric L.

    of the system ­ p.4/65 #12;Biological visual sampling The "Terrain Theory" of Hughes (1977) (a) Tree Kangaroo (b) Ground Kangaroo ­ p.5/65 #12;Biological visual sampling Problem: How to apply computer vision techniques to space-variant images? (a) 4-Connected (b) 8-Connected (c) Kangaroo ­ p.6/65 #12;Biological visual

  1. Linear analysis of rotationally invariant, radially variant tomographic imaging systems

    Microsoft Academic Search

    John R. Baker; Ronald H. Huesman; Thomas F. Budinger

    1990-01-01

    We describe a method to analyze the linear imaging characteristics of rotationally invariant, radially variant tomographic imaging systems using singular value decomposition (SVD). When the projection measurements from such a sysem are assumed to be samples from independent and identically distributed multi-normal random variables, the best estimate of the emission intensity is given by the unweighted lease squares estimator. The

  2. Kronecker Product and SVD Approximations for Separable Spatially Variant Blurs

    E-print Network

    Nagy, James

    variant blurs. An approximate singular value decomposition is then computed from this Kronecker, with singular values decaying to, and clustering at zero. Thus, because of the presence of noise, one cannot use). 8 In this case the integral equation is a convolution, and K is then a block Toeplitz matrix

  3. Oncogenic potential diverge among human papillomavirus type 16 natural variants

    SciTech Connect

    Sichero, Laura, E-mail: lsichero@gmail.com [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil) [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil); Department of Virology, Ludwig Institute for Cancer Research, Sao Paulo 01323-903 (Brazil); Simao Sobrinho, Joao [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil) [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil); Department of Virology, Ludwig Institute for Cancer Research, Sao Paulo 01323-903 (Brazil); Lina Villa, Luisa [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil) [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil); Department of Virology, Ludwig Institute for Cancer Research, Sao Paulo 01323-903 (Brazil); Department of Radiology, School of Medicine, University of Sao Paulo (Brazil)

    2012-10-10

    We compared E6/E7 protein properties of three different HPV-16 variants: AA, E-P and E-350G. Primary human foreskin keratinocytes (PHFK) were transduced with HPV-16 E6 and E7 and evaluated for proliferation and ability to grow in soft agar. E-P infected keratinocytes presented the lowest efficiency in colony formation. AA and E-350G keratinocytes attained higher capacity for in vitro transformation. We observed similar degradation of TP53 among HPV-16 variants. Furthermore, we accessed the expression profile in early (p5) and late passage (p30) transduced cells of 84 genes commonly involved in carcinogenesis. Most differences could be attributed to HPV-16 E6/E7 expression. In particular, we detected different expression of ITGA2 and CHEK2 in keratinocytes infected with AA and AA/E-350G late passage cells, respectively, and higher expression of MAP2K1 in E-350G transduced keratinocytes. Our results indicate differences among HPV-16 variants that could explain, at least in part, differences in oncogenic potential attributed to these variants.

  4. Spatially-Variant Anisotropic Morphological Filters Driven by Gradient Fields

    E-print Network

    Angulo,JesĂşs

    . We formalize the definition of spa- tially variant dilation/erosion and opening/closing for gray their orientation across the dominant direction of image structures. The orientation at each pixel is extracted basic operations of dilation, erosion, and their two products, and the three dualities (adjunction

  5. Linear-Work Greedy Parallel Approximate Set Cover and Variants

    E-print Network

    Blelloch, Guy E.

    Linear-Work Greedy Parallel Approximate Set Cover and Variants Guy E. Blelloch Richard Peng Kanat approximation algorithms for set cover and related problems. These algorithms build on an algorithm for solving of a key component in existing work on parallel set cover. We derive a randomized algorithm for Ma

  6. ORIGINAL PAPER Variant allometric scaling relationships between bud size

    E-print Network

    Paris-Sud XI, Université de

    ORIGINAL PAPER Variant allometric scaling relationships between bud size and secondary shoot growth populations of contrasting climates are poorly understood. We tested the hypotheses that bud size and stem area, apical bud mass, and number of buds) were measured in ten trees per site, and the relationships

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

    MedlinePLUS

    ... if I still have specific questions about GM2-gangliosidosis, AB variant? Ask the Genetic and Rare Diseases Information Center . Where can I ... Professionals What glossary definitions help with understanding GM2-gangliosidosis, AB ... Home Reference Glossary . See also Understanding Medical Terminology . ...

  8. A variant of Wiener's attack on RSA Andrej Dujella

    E-print Network

    Dujella, Andrej

    A variant of Wiener's attack on RSA Andrej Dujella Abstract Wiener's attack is a well-known polynomial-time attack on a RSA cryptosystem with small secret decryption exponent d, which works if d the public key (n, e). There are several extensions of Wiener's attack that allow the RSA cryptosystem

  9. Correlation between butyrylcholinesterase variants and sensitivity to soman toxicity.

    PubMed

    Dimov, Dimo; Kanev, Kamen; Dimova, Ivanka

    2012-01-01

    Butyrylcholinesterase (BChE) is synthesized in the liver and found in high concentrations in blood plasma, liver, heart, pancreas, vascular endothelium, skin, brain white matter, smooth muscle cells and adipocytes. BChE is a non specific enzyme that hydrolyzes different choline esters (succinylcholine, mivacurium) and many other drugs such as aspirin, cocaine and procaine. The enzyme is also considered as a bioscavenger due to its ability to neutralize the toxic effects of organophosphorus compounds (nervous system fs agents) such as soman. BChE displays several polymorphisms that influence its serum activity; therefore they could determine the individual sensitivity to chemical nerve agents. In this study, we investigated the correlation between BChE variants and the degree of enzyme inhibition and reactivation after soman application on blood samples of 726 individuals. The blood samples of individuals expressing abnormal variants, were more sensitive to soman compared to variants of homozygotes and heterozygotes for U-allele. We found significant differences in the degree of enzyme reactivation between different variants (with and without U-presence). PMID:22696303

  10. Coronary slow flow: is it a disease or normal variant?

    PubMed

    Cay, Serkan

    2010-10-01

    The exact pathophysiological mechanism of coronary slow flow remains unclear although some possible mechanisms such as altered microvascular tone, diffuse vascular pathology, and acute release of coronary vasoconstrictor mediators have been proposed. Therefore we need new studies regarding responsible etiologies to answer the question 'Is coronary slow flow a disease or normal variant?' PMID:19297037

  11. A new asymmetric, space variant distance metric Shobhit Saxena

    E-print Network

    Banerjee, Subhashis

    A new asymmetric, space variant distance metric Shobhit Saxena 2002407 Rahul Malik 2002442 January in feature space. As a con- sequence, the nature of clusters identified by a clustering algorithm is highly and Mahalanobis distance metrics have been used for machine learning applications. The Mahalanobis distance

  12. Variants of rectifiers with near sinusoidal input currents

    Microsoft Academic Search

    M. Pletea; N. R. Buzatu; A. Serediuc; C. Nedelcu; I. V. Pletea

    2011-01-01

    Based on the characteristics of the rectifiers with near sinusoidal input currents (RNSIC-1, with capacitors connected on the DC side and RNSIC-2, with capacitors connected on the AC side), the paper proposes a comparative analysis between the performances of the two variants of RNSIC converters with three- phase six pulse full-bridge diode rectifiers with passive filters. A comparative analysis between

  13. Variant selection in samples of austenitic stainless steel cold

    E-print Network

    Cambridge, University of

    Variant selection in samples of austenitic stainless steel cold rolled and deformed by tension texture of samples deformed by cold rolling. ­ Comparing texture measured by EBSD in cold rolled samples Tensor for deformation in a tension test Tensor for deformation by cold rolling #12;Austenitic stainless

  14. Tailored Source Code Transformations to Synthesize Computationally Diverse Program Variants

    E-print Network

    Paris-Sud XI, Université de

    of knowledge who can exploit it to spy or remotely control the program. Moving target defense ad- dresses the predictability about a program's control or data-flow. The success of moving target defense relies on two target defense proposes to use a large number of program variants and to continually shift be- tween them

  15. The Dominating Set Problem: (a few) variants and results

    E-print Network

    Stavrakakis, Ioannis

    The Dominating Set Problem: (a few) variants and results Gerasimos G. Pollatos gpol@di.uoa.gr 23 and a collection C of subsets of U. · Find the minimum number of members of C whose union is U. Dominating Set Set! · Running time is also fast! (O(nm2 )) #12;Connected Dominating Set Input: Connected graph G = (V, E), |V

  16. Inferring causative variants in microRNA target sites

    PubMed Central

    Thomas, Laurent F.; Saito, Takaya; Sćtrom, Pĺl

    2011-01-01

    MicroRNAs (miRNAs) regulate genes post transcription by pairing with messenger RNA (mRNA). Variants such as single nucleotide polymorphisms (SNPs) in miRNA regulatory regions might result in altered protein levels and disease. Genome-wide association studies (GWAS) aim at identifying genomic regions that contain variants associated with disease, but lack tools for finding causative variants. We present a computational tool that can help identifying SNPs associated with diseases, by focusing on SNPs affecting miRNA-regulation of genes. The tool predicts the effects of SNPs in miRNA target sites and uses linkage disequilibrium to map these miRNA-related variants to SNPs of interest in GWAS. We compared our predicted SNP effects in miRNA target sites with measured SNP effects from allelic imbalance sequencing. Our predictions fit measured effects better than effects based on differences in free energy or differences of TargetScan context scores. We also used our tool to analyse data from published breast cancer and Parkinson's disease GWAS and significant trait-associated SNPs from the NHGRI GWAS Catalog. A database of predicted SNP effects is available at http://www.bigr.medisin.ntnu.no/mirsnpscore/. The database is based on haplotype data from the CEU HapMap population and miRNAs from miRBase 16.0. PMID:21693556

  17. Lignin content in natural Populus variants affects sugar release

    E-print Network

    California at Riverside, University of

    Lignin content in natural Populus variants affects sugar release Michael H. Studera,b,1 , Jaclyn D fuels from lignocel- lulosic biomass is a plant's recalcitrance to releasing sugars bound in the cell and guaiacyl units (S/G ratio). This subset was tested for total sugar release through enzymatic hydrolysis

  18. Biomechanical modeling of English /r/ variants Ian Stavness

    E-print Network

    British Columbia, University of

    Biomechanical modeling of English /r/ variants Ian Stavness Department of Bioengineering, Stanford an investigation of the well-known con- text-dependent variation in English /r/ using a biomechanical tongue- jaw a previously unknown mechanism in tongue biomechanics for /r/ produc- tion: Torque in the sagittal plane about

  19. New common variants affecting susceptibility to basal cell carcinoma

    PubMed Central

    Stacey, Simon N; Sulem, Patrick; Masson, Gisli; Gudjonsson, Sigurjon A; Thorleifsson, Gudmar; Jakobsdottir, Margret; Sigurdsson, Asgeir; Gudbjartsson, Daniel F; Sigurgeirsson, Bardur; Benediktsdottir, Kristrun R; Thorisdottir, Kristin; Ragnarsson, Rafn; Scherer, Dominique; Hemminki, Kari; Rudnai, Peter; Gurzau, Eugene; Koppova, Kvetoslava; Botella-Estrada, Rafael; Soriano, Virtudes; Juberias, Pablo; Saez, Berta; Gilaberte, Yolanda; Fuentelsaz, Victoria; Corredera, Cristina; Grasa, Matilde; Höiom, Veronica; Lindblom, Annika; Bonenkamp, Johannes J; van Rossum, Michelle M; Aben, Katja K H; de Vries, Esther; Santinami, Mario; Di Mauro, Maria G; Maurichi, Andrea; Wendt, Judith; Hochleitner, Pia; Pehamberger, Hubert; Gudmundsson, Julius; Magnusdottir, Droplaug N; Gretarsdottir, Solveig; Holm, Hilma; Steinthorsdottir, Valgerdur; Frigge, Michael L; Blondal, Thorarinn; Saemundsdottir, Jona; Bjarnason, Hjördis; Kristjansson, Kristleifur; Bjornsdottir, Gyda; Okamoto, Ichiro; Rivoltini, Licia; Rodolfo, Monica; Kiemeney, Lambertus A; Hansson, Johan; Nagore, Eduardo; Mayordomo, José I; Kumar, Rajiv; Karagas, Margaret R; Nelson, Heather H; Gulcher, Jeffrey R; Rafnar, Thorunn; Thorsteinsdottir, Unnur; Olafsson, Jon H; Kong, Augustine; Stefansson, Kari

    2010-01-01

    In a follow-up to our previously reported genome-wide association study of cutaneous basal cell carcinoma (BCC)1, we describe here several new susceptibility variants. SNP rs11170164, encoding a G138E substitution in the keratin 5 (KRT5) gene, affects risk of BCC (OR = 1.35, P = 2.1 × 10?9). A variant at 9p21 near CDKN2A and CDKN2B also confers susceptibility to BCC (rs2151280[C]; OR = 1.19, P = 6.9 × 10?9), as does rs157935[T] at 7q32 near the imprinted gene KLF14 (OR = 1.23, P = 5.7 × 10?10). The effect of rs157935[T] is dependent on the parental origin of the risk allele. None of these variants were found to be associated with melanoma or fair-pigmentation traits. A melanoma- and pigmentation-associated variant in the SLC45A2 gene, L374F, is associated with risk of both BCC and squamous cell carcinoma. Finally, we report conclusive evidence that rs401681[C] in the TERT-CLPTM1L locus confers susceptibility to BCC but protects against melanoma. PMID:19578363

  20. Estrogen withdrawal, increased breast cancer risk and the KRAS-variant.

    PubMed

    McVeigh, Terri P; Jung, Song-Yi; Kerin, Michael J; Salzman, David W; Nallur, Sunitha; Nemec, Antonio A; Dookwah, Michelle; Sadofsky, Jackie; Paranjape, Trupti; Kelly, Olivia; Chan, Elcie; Miller, Nicola; Sweeney, Karl J; Zelterman, Daniel; Sweasy, Joann; Pilarski, Robert; Telesca, Donatello; Slack, Frank J; Weidhaas, Joanne B

    2015-07-01

    The KRAS-variant is a biologically functional, microRNA binding site variant, which predicts increased cancer risk especially for women. Because external exposures, such as chemotherapy, differentially impact the effect of this mutation, we evaluated the association of estrogen exposures, breast cancer (BC) risk and tumor biology in women with the KRAS-variant. Women with BC (n = 1712), the subset with the KRAS-variant (n = 286) and KRAS-variant unaffected controls (n = 80) were evaluated, and hormonal exposures, KRAS-variant status, and pathology were compared. The impact of estrogen withdrawal on transformation of isogenic normal breast cell lines with or without the KRAS-variant was studied. Finally, the association and presentation characteristics of the KRAS-variant and multiple primary breast cancer (MPBC) were evaluated. KRAS-variant BC patients were more likely to have ovarian removal pre-BC diagnosis than non-variant BC patients (p = 0.033). In addition, KRAS-variant BC patients also appeared to have a lower estrogen state than KRAS-variant unaffected controls, with a lower BMI (P < 0.001). Finally, hormone replacement therapy (HRT) discontinuation in KRAS-variant patients was associated with a diagnosis of triple negative BC (P < 0.001). Biologically confirming our clinical findings, acute estrogen withdrawal led to oncogenic transformation in KRAS-variant positive isogenic cell lines. Finally, KRAS-variant BC patients had greater than an 11-fold increased risk of presenting with MPBC compared to non-variant patients (45.39% vs 6.78%, OR 11.44 [3.42-37.87], P < 0.001). Thus, estrogen withdrawal and a low estrogen state appear to increase BC risk and to predict aggressive tumor biology in women with the KRAS-variant, who are also significantly more likely to present with multiple primary breast cancer. PMID:25961464

  1. Comparison of statistical approaches to rare variant analysis for quantitative traits

    PubMed Central

    2011-01-01

    With recent advances in technology, deep sequencing data will be widely used to further the understanding of genetic influence on traits of interest. Therefore not only common variants but also rare variants need to be better used to exploit the new information provided by deep sequencing data. Recently, statistical approaches for analyzing rare variants in genetic association studies have been proposed, but many of them were designed only for dichotomous outcomes. We compare the type I error and power of several statistical approaches applicable to quantitative traits for collapsing and analyzing rare variant data within a defined gene region. In addition to comparing methods that consider only rare variants, such as indicator, count, and data-adaptive collapsing methods, we also compare methods that incorporate the analysis of common variants along with rare variants, such as CMC and LASSO regression. We find that the three methods used to collapse rare variants perform similarly in this simulation setting where all risk variants were simulated to have effects in the same direction. Further, we find that incorporating common variants is beneficial and using a LASSO regression to choose which common variants to include is most useful when there is are few common risk variants compared to the total number of risk variants. PMID:22373209

  2. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

    PubMed Central

    Wilm, Andreas; Aw, Pauline Poh Kim; Bertrand, Denis; Yeo, Grace Hui Ting; Ong, Swee Hoe; Wong, Chang Hua; Khor, Chiea Chuen; Petric, Rosemary; Hibberd, Martin Lloyd; Nagarajan, Niranjan

    2012-01-01

    The study of cell-population heterogeneity in a range of biological systems, from viruses to bacterial isolates to tumor samples, has been transformed by recent advances in sequencing throughput. While the high-coverage afforded can be used, in principle, to identify very rare variants in a population, existing ad hoc approaches frequently fail to distinguish true variants from sequencing errors. We report a method (LoFreq) that models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population. Using simulated and real datasets (viral, bacterial and human), we show that LoFreq has near-perfect specificity, with significantly improved sensitivity compared with existing methods and can efficiently analyze deep Illumina sequencing datasets without resorting to approximations or heuristics. We also present experimental validation for LoFreq on two different platforms (Fluidigm and Sequenom) and its application to call rare somatic variants from exome sequencing datasets for gastric cancer. Source code and executables for LoFreq are freely available at http://sourceforge.net/projects/lofreq/. PMID:23066108

  3. Molecular characterization of canine parvovirus-2 variants circulating in Tunisia.

    PubMed

    Touihri, Leila; Bouzid, Imen; Daoud, Rahma; Desario, Costantina; El Goulli, Amel Founa; Decaro, Nicola; Ghorbel, Abderrazak; Buonavoglia, Canio; Bahloul, Chokri

    2009-04-01

    Canine parvovirus type 2 (CPV2) emerged in 1978 as a highly contagious and very serious disease in dogs. The characterization of CPV2 antigenic types is exclusively based on the identification of the amino acid residue at position 426 of the capsid protein VP2. Currently, three antigenic types CPV-2a (asparagine N(426)), CPV-2b (aspartic acid D(426)) and CPV-2c (glutamic acid E(426)) are circulating worldwide. In Tunisia, despite the fact that many clinical and few serological investigations clearly indicate that CPV is widespread and of major concerns in the local dog population, no molecular and antigenic type characterization of circulating variants has been carried out. This investigation showed that most of clinically presumed CPV infections were confirmed by classical or real-time PCR. When no real-time PCR facilities were affordable, classical PCR as reported here in association with restriction fragment length polymorphism (RFLP) with MboI and MboII can be very useful for screening and diagnosing CPV infections. A total of 50 variants were characterized by sequencing and an almost even representation of the different antigenic types, including CPV-2c and slightly more type 2b, were evidenced. Characterization of the Tunisian variants by MGB probe assays as reported was inefficient for most of CPV-2a variants because of their typical nucleotide mutation C(1269). Phylogenetic analysis showed that the Tunisian variants underwent evolution for a relatively long period of time inside the country. The analysis also showed some crossings of the different antigenic types, leaving both genotypic and phenotypic characteristic mutations. PMID:19112611

  4. Characterization of two pigeon paramyxovirus type 1 isolates in China.

    PubMed

    Awu, Abie; Shao, Meng-Yu; Liu, Meng-Meng; Hu, Yan-Xin; Qin, Zhuo-Ming; Tian, Fu-Lin; Zhang, Guo-Zhong

    2015-06-01

    For over three decades, there has been a continuing panzootic caused by a virulent variant avian paramyxovirus type 1 strain, the so-called pigeon paramyxovirus type 1. It is found primarily in racing pigeons, but it has also spread to wild birds and poultry. In this study, two pigeon paramyxovirus type 1 strains, SD12 and BJ13, obtained from diseased pigeons in China, were characterized. Phylogenetic analysis based on complete sequences allowed characterization of both strains as genotype VI, class II. Further phylogenetic analysis of a 374-nucleotide section of the fusion gene showed that SD12 fell into lineage VIbii-d and BJ13 into VIbii-f. The deduced amino acid sequence of the cleavage site of the fusion protein confirmed that both isolates contained the virulent motif (112)K/RRQKR?F(117) at the cleavage site. Nevertheless, the values of intracerebral pathogenicity indices showed the SD12 isolate to be a velogenic strain and BJ13 isolate to be a mesogenic strain. The SD12 isolate was further investigated via clinical observation, RNA detection, histopathology and viral serology in experimentally infected 3-week-old chickens. It showed a mild pathological phenotype in chickens, with viral replication restricted to a few tissues. The molecular mechanism for the SD12 isolate to have a virulent motif but low levels of virulence for chickens requires further study. PMID:25735628

  5. Heterogeneity of Host TLR2 Stimulation by Staphylocoocus aureus Isolates

    PubMed Central

    Hilmi, Dina; Parcina, Marijo; Stollewerk, Daniel; Ostrop, Jenny; Josten, Michaele; Meilaender, Alina; Zaehringer, Ulrich; Wichelhaus, Thomas A.; Bierbaum, Gabriele; Heeg, Klaus; Wolz, Christiane; Bekeredjian-Ding, Isabelle

    2014-01-01

    High lipoprotein expression and potent activation of host Toll-like receptor-2 (TLR2) are characteristic features of the staphylococcal species. Expression of TLR2 in the host is important for clearance of Staphylococcus aureus infection and host survival. Thus, we hypothesized that bacterial regulation of its intrinsic TLR2-stimulatory capacity could represent a means for immune evasion or host adaptation. We, therefore, compared clinical S. aureus isolates in regards to their TLR2 activation potential and assessed the bacterial factors that modulate TLR2-mediated recognition. S. aureus isolates displayed considerable variability in TLR2-activity with low to absent TLR2-activity in 64% of the isolates tested (68/106). Notably, strain-specific TLR2-activity was independent of the strain origin, e.g. no differences were found between strains isolated from respiratory specimen from cystic fibrosis patients or those isolated from invasive disease specimen. TLR2-activity correlated with protein A expression but not with the agr status. Capsule expression and small colony variant formation had a negative impact on TLR2-activity but any disruption of cell wall integrity enhanced TLR2 activation. Altogether, heterogeneity in host TLR2-activity reflects differences in metabolic activity and cell wall synthesis and/or remodeling. PMID:24810614

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

    E-print Network

    Altshuler, David

    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, ...

  7. Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

    E-print Network

    de Bakker, Paul

    is to pick a fixed allele- frequency threshold and perform an association test on the set of variants below variants, and it implicitly assumes that the log odds ratio is approximately inversely propor- tional

  8. Regenerative Estimation Variants of Response Times in Closed Networks of Queues

    E-print Network

    Katsaros, Panagiotis

    Regenerative Estimation Variants of Response Times in Closed Networks of Queues PANAJOTIS KATSAROS regenerative estimation variants of response times, in multivariate simulations of closed queuing networks. Key-Words: - Queuing networks, Regenerative method, Simulation output analysis, Sequential control

  9. Differentiation of BHV-1 isolates from vaccine virus by high-resolution melting analysis.

    PubMed

    Ostertag-Hill, Claire; Fang, Liang; Izume, Satoko; Lee, Megan; Reed, Aimee; Jin, Ling

    2015-02-16

    An efficacious bovine herpesvirus type-1 (BHV-1) vaccine has been used for many years. However, in the past few years, abortion and respiratory diseases have occurred after administration of the modified live vaccine. To investigate whether BHV-1 isolates from disease outbreaks are identical to those of the vaccines used, selected regions of the BHV-1 genome were investigated by high-resolution melting (HRM) analysis and PCR-DNA sequencing. When a target region within the thymidine kinase (TK) gene was examined by HRM analysis, 6 out of the 11 isolates from abortion cases and 22 out of the 25 isolates from bovine respiratory disease (BRD) cases had different melting curves compared to the vaccine virus. Surprisingly, when a conserved region within the US6 gene that encodes glycoprotein D (gD) was examined by HRM analysis, 5 out of the 11 abortion isolates and 18 out of the 23 BRD isolates had different melting curves from the vaccine virus. To determine whether SNPs within the coding regions of glycoprotein E (gE) and TK genes can be used to differentiate the isolates from the vaccine virus, PCR-DNA sequencing was used to examine these SNPs in all the isolates. This revealed that only 1 out of 11 of the abortion isolates and 4 out of 24 of the BRD isolates are different in the target region of gE from the vaccine virus, while 5 out of 11 abortion isolates and 4 out of 22 BRD isolates are different in the target region of TK from the vaccine virus. No DNA sequence differences were observed in glycoprotein G (gG) region between disease and vaccine isolates. Our study demonstrated that many disease isolates had genetic differences from the vaccine virus in regions examined by HRM and PCR-DNA sequencing analysis. In addition, many isolates contained more than one type of mutation and were composed of mixed variants. Our study suggests that a mixture of variants were present in isolates collected post-vaccination. HRM is a rapid diagnostic method that can be used for rapid differentiation of clinical isolates from vaccine strains. PMID:25556125

  10. Whole-brain white matter disruption in semantic and nonfluent variants of primary progressive aphasia.

    PubMed

    Schwindt, Graeme C; Graham, Naida L; Rochon, Elizabeth; Tang-Wai, David F; Lobaugh, Nancy J; Chow, Tiffany W; Black, Sandra E

    2013-04-01

    Semantic (svPPA) and nonfluent (nfPPA) variants of primary progressive aphasia are associated with distinct patterns of cortical atrophy and underlying pathology. Little is known, however, about their contrasting spread of white matter disruption and how this relates to grey matter (GM) loss. We undertook a structural MRI study to investigate this relationship. We used diffusion tensor imaging, tract-based spatial statistics, and voxel-based morphometry to examine fractional anisotropy (FA) and directional diffusivities in nine patients with svPPA and nine patients with nfPPA, and compared them to 16 matched controls after accounting for global GM atrophy. Significant differences in topography of white matter changes were found, with more ventral involvement in svPPA patients and more widespread frontal involvement in nfPPA individuals. However, each group had both ventral and dorsal tract changes, and both showed spread of diffusion abnormalities beyond sites of local atrophy. There was a clear dissociation in sensitivity of diffusion tensor imaging measures between groups. SvPPA patients showed widespread changes in FA and radial diffusivity, whereas changes in axial diffusivity were more restricted and proximal to sites of GM atrophy. NfPPA patients showed isolated changes in FA, but widespread axial and radial diffusivity changes. These findings reveal the extent of white matter disruption in these variants of PPA after accounting for GM loss. Further, they suggest that differences in the relative sensitivity of diffusion metrics may reflect differences in the nature of underlying white matter pathology in these two subtypes. PMID:22109837

  11. Investigation of the dominant positive effect of porcine farnesoid X receptor (FXR) splice variant 1.

    PubMed

    Gray, Matthew A; James Squires, E

    2015-04-10

    Pigs are well recognized as a model for humans in research studies due to similarities in metabolism and physiology between the two species. The potential for pigs to model humans in studying metabolic diseases is highly dependent on similarities in hepatic metabolism between the two species, including similarities in the farnesoid X receptor (FXR; NR1H4) which regulate bile acid homeostasis. During initial cloning of porcine FXR (pFXR), an alternative splice variant (pFXR-SV1) was isolated which contained a four amino acid (MYTG) insert that exerted a dominant positive effect on the wild type receptor (pFXR-WT). The current study investigated the role of this insert in the dominant positive effect. Individual point mutations were made to the first three amino acids of the MYTG insert. Mutations of the methionine (M) or threonine (T) to alanine (A) reduced the dominant positive effect, while mutation of the tyrosine (Y) to either A or phenylalanine (F) completely abolished the dominant positive effect. Treatment with the tyrosine phosphatase inhibitor sodium orthovanadate (Na3VO4) increased the dominant positive effect of pFXR-SV1 by about 30%. These results suggest that the dominant positive effect may be dependent on the phosphorylation status of the tyrosine in the MYTG insert. The human variant hFXR?+ has the same MYTG insert as pFXR-SV1, but did not cause a dominant positive effect on hFXR-WT and significantly reduced the activity of hFXR-WT. Thus, although the MYTG insert is conserved in both human and pig, the effects of this insert are different in the two species. PMID:25623328

  12. Computerized design and generation of space-variant holographic filters. II - Applications of space-variant filters to optical computing

    NASA Technical Reports Server (NTRS)

    Ambs, P.; Fainman, Y.; Esener, S.; Lee, S. H.

    1988-01-01

    Holographic optical elements (HOEs) of space-variant impulse response have been designed and generated using a computerized optical system. HOEs made of dichromated gelatin have been produced and used for spatial light modulator defect removal and optical interconnects. Experimental performance and characteristics are presented.

  13. Drug-resistant variants of Escherichia coli thymidylate synthase: effects of substitutions at Pro-254.

    PubMed

    Fantz, C; Shaw, D; Jennings, W; Forsthoefel, A; Kitchens, M; Phan, J; Minor, W; Lebioda, L; Berger, F G; Spencer, H T

    2000-02-01

    Drug-resistant variants of thymidylate synthase (TS) can potentially be used in gene therapy applications to decrease the myelosuppressive side effects of TS-directed anticancer agents or to select genetically modified cells in vivo. Mutations of proline 303 of human TS confer resistance to TS-directed fluoropyrimidines and antifolates (). We generated the corresponding variants in Escherichia coli TS (ecTS), position 254, to better understand the mechanism by which mutations at this residue confer resistance. In addition, because ecTS is intrinsically resistant to several antifolates when compared with human TS, we suspected that greater resistance could be achieved with the bacterial enzyme. The P254L enzyme conferred >100-fold resistance to both raltitrexed and 5-fluoro-2'-deoxyuridine (FdUrd) compared with wild-type ecTS. Four additional mutants (P254F, P254S, P254G, and P254D), each of which complemented growth of a TS-deficient cell line, were generated, isolated, and characterized. Steady-state values of K(m) for dUMP and k(cat) were not substantially different among the variants and were comparable with the wild-type values, but K(m) for methylenetetrahydrofolate (CH(2)H(4)PteGlu) was >10-fold higher for P254D. Values of k(on) and k(off) for nucleotide binding, which were obtained by stopped-flow spectroscopy, were virtually unchanged among the mutants. Drastic differences were observed for CH(2)H(4)PteGlu binding, with K(d) values >15-fold higher than observed with the wild-type enzyme; surprisingly, the proposed isomerization reaction that is very evident for the wild-type enzyme is not observed with P254S. The decrease in affinity for CH(2)H(4)PteGlu correlates well with K(i) values obtained for three TS-directed inhibitors. These results show that mutations at Pro-254 specifically affect the initial binding interactions between enzyme and cofactor and also alter the ability of the mutant enzymes to undergo conformational changes that occur on ternary complex formation. The crystal structure of P254S was determined at 1.5 A resolution and is the most precise structure of TS available. When compared with wild-type TS, the structure shows local conformational changes affecting mostly Asp-253; its carbonyl is rotated approximately 40 degrees, and the side chain forms an ion pair with Arg-225. PMID:10648646

  14. Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes

    PubMed Central

    2014-01-01

    Background Clarithromycin (CLR) is the key drug in eradication therapy of Helicobacter pylori (H. pylori) infection, and widespread use of CLR has led to an increase in primary CLR-resistant H. pylori. The known mechanism of CLR resistance has been established in A2146G and A2147G mutations in the 23S rRNA gene, but evidence of the involvement of other genetic mechanisms is lacking. Using the MiSeq platform, whole-genome sequencing of the 19 clinical strains and the reference strain ATCC26695 was performed to identify single nucleotide variants (SNVs) of multi-drug resistant efflux pump genes in the CLR-resistant phenotype. Results Based on sequencing data of ATCC26695, over one million sequencing reads with over 50-fold coverage were sufficient to detect SNVs, but not indels in the bacterial genome. Sequencing reads of the clinical isolates ranged from 1.82 to 10.8 million, and average coverage ranged from 90.9- to 686.3-fold, which were acceptable criteria for detecting SNVs. Utilizing the conventional approach of allele-specific PCR, point mutations in the 23S rRNA gene were detected in 12 clinical resistant isolates, but not in 7 clinical susceptible isolates. All sequencing reads of CLR-resistant strains had a G mutation in an identical position of the 23S rRNA gene. In addition, genetic variants of four gene clusters (hp0605-hp0607, hp0971-hp0969, hp1327-hp1329, and hp1489-hp1487) of TolC homologues, which have been implicated in multi-drug resistance, were examined. Specific SNVs were dominantly found in resistant strains. Conclusions Gene clusters of TolC homologues are involved in CLR susceptibility profiles in individual H. pylori strains. Whole-genome sequencing has yielded novel understanding of genotype-phenotype relationships. PMID:24995043

  15. The macrophage scavenger receptor CD163: endocytic properties of cytoplasmic tail variants

    Microsoft Academic Search

    Marianne Jensby Nielsen; Mette Madsen; Holger J. Mřller; Sřren K. Moestrup

    2006-01-01

    CD163 is the monocyte\\/macrophage- specific receptor for haptoglobin-hemoglobin (Hp- Hb) complexes. The cytoplasmic tail of human CD163 exists as a short tail variant and two long tail variants. Reverse transcriptase-polymerase chain reaction analysis indicated that all three CD163 variants are substantially expressed in blood, liver, and spleen, and the short tail variant is the predominant mRNA species. Using cell trans-

  16. Human follicle stimulating hormone receptor variants lacking transmembrane domains display altered post-translational conformations

    Microsoft Academic Search

    Andrew J Peterson; Barbara Lindau-Shepard; Howard A Brumberg; James A Dias

    2000-01-01

    Variant splicing of gonadotropin receptor mRNA commonly occurs, however expression of receptor protein variants and their trafficking has yet to be studied in detail. To determine receptor variant trafficking and intracellular processing in mammalian cells, the intracellular fate of intentionally truncated variants of human follicle stimulating hormone receptor (hFSH-R) expressed in CHO cells was examined. Monoclonal antibodies (mAbs) were made

  17. Extending the reflexion method for consolidating software variants into product lines

    Microsoft Academic Search

    Rainer Koschke; Pierre Frenzel; Andreas P. J. Breu; Karsten Angstmann

    2009-01-01

    Software variants emerge from ad-hoc copying in-the-large with adaptations to a specific context. As the number of variants\\u000a increases, maintaining such software variants becomes more and more difficult and expensive. In contrast to such ad-hoc reuse,\\u000a software product lines offer organized ways of reuse, taking advantage of similarities of different products. To re-gain control,\\u000a software variants may be consolidated as

  18. Competitive endothelial adhesion between Plasmodium falciparum isolates under physiological flow conditions

    PubMed Central

    Phiri, Happy; Montgomery, Jacqui; Molyneux, Malcolm; Craig, Alister

    2009-01-01

    Background Sequestration of parasitized red blood cells in the microvasculature of major organs involves a sequence of events that is believed to contribute to the pathogenesis of severe falciparum malaria. Plasmodium falciparum infections are commonly composed of multiple subpopulations of parasites with varied adhesive properties. A key question is: do these subpopulations compete for adhesion to endothelium? This study investigated whether, in a laboratory model of cytoadherence, there is competition in binding to endothelium between pRBC infected with P. falciparum of variant adhesive phenotypes, particularly under flow conditions. Methods Four different P. falciparum isolates, of known adherence phenotypes, were matched in pairs, mixed in different proportions and allowed to bind to cultured human endothelium. Using in vitro competitive static and flow-based adhesion assays, that allow simultaneous testing of the adhesive properties of two different parasite lines, adherence levels of paired P. falciparum isolates were quantified and analysed using either non-parametric Wilcoxon's paired signed rank test or Student paired test. Results Study findings show that P. falciparum parasite lines show marked differences in the efficiency of adhesion to endothelium. Conclusion Plasmodium falciparum variants will compete for adhesion to endothelia and variants can be ranked by their efficiency of binding. These findings suggest that variants from a mixed infection will not show uniform cytoadherence and so may vary in their ability to cause disease. PMID:19772553

  19. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

    PubMed Central

    Kuhn, Jens H.; Bao, Yiming; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander A.; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Hensley, Lisa; Honko, Anna N.; Jahrling, Peter B.; Johnson, Karl M.; Kobinger, Gary; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Saphire, Erica Ollmann; Smither, Sophie J.; Swanepoel, Robert; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis; Weidmann, Manfred; Nichol, Stuart T.

    2012-01-01

    The task of international expert groups is to recommend the classification and naming of viruses. The ICTV Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling. PMID:23001720

  20. CLUSTER PARAMETERS FOR TIME-VARIANT MIMO CHANNEL MODELS N. Czink1,2

    E-print Network

    Zemen, Thomas

    CLUSTER PARAMETERS FOR TIME-VARIANT MIMO CHANNEL MODELS N. Czink1,2 , R. Tian3 , S. Wyne3 , G models is to simulate the time-variant nature of the channel correctly. Cluster-based MIMO channel models-variant cluster parameters. In this paper we identify and track clusters from three dif- ferent measurements

  1. Investigation of the role of TCF4 rare sequence variants in schizophrenia.

    PubMed

    Basmanav, F Buket; Forstner, Andreas J; Fier, Heide; Herms, Stefan; Meier, Sandra; Degenhardt, Franziska; Hoffmann, Per; Barth, Sandra; Fricker, Nadine; Strohmaier, Jana; Witt, Stephanie H; Ludwig, Michael; Schmael, Christine; Moebus, Susanne; Maier, Wolfgang; Mössner, Rainald; Rujescu, Dan; Rietschel, Marcella; Lange, Christoph; Nöthen, Markus M; Cichon, Sven

    2015-07-01

    Transcription factor 4 (TCF4) is one of the most robust of all reported schizophrenia risk loci and is supported by several genetic and functional lines of evidence. While numerous studies have implicated common genetic variation at TCF4 in schizophrenia risk, the role of rare, small-sized variants at this locus-such as single nucleotide variants and short indels which are below the resolution of chip-based arrays requires further exploration. The aim of the present study was to investigate the association between rare TCF4 sequence variants and schizophrenia. Exon-targeted resequencing was performed in 190 German schizophrenia patients. Six rare variants at the coding exons and flanking sequences of the TCF4 gene were identified, including two missense variants and one splice site variant. These six variants were then pooled with nine additional rare variants identified in 379 European participants of the 1000 Genomes Project, and all 15 variants were genotyped in an independent German sample (n?=?1,808 patients; n?=?2,261 controls). These data were then analyzed using six statistical methods developed for the association analysis of rare variants. No significant association (P?variants in schizophrenia risk is warranted by the assessment of larger cohorts with higher statistical power to identify rare variant associations. © 2015 Wiley Periodicals, Inc. PMID:26010163

  2. Small Scale Variants of the AES C. Cid # , S. Murphy, and M.J.B. Robshaw

    E-print Network

    Small Scale Variants of the AES C. Cid # , S. Murphy, and M.J.B. Robshaw Information Security Group.Cid,S.Murphy,M.Robshaw}@rhul.ac.uk Abstract. In this paper we define small scale variants of the AES. These variants inherit the design features of the AES and provide a suitable framework for comparing di#erent cryptanalytic methods

  3. Compositions and methods comprising cellulase variants with reduced affinity to non-cellulosic materials

    DOEpatents

    Cascao-Pereira, Luis G.; Kaper, Thijs; Kelemen, Bradley R; Liu, Amy D.

    2012-08-07

    The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having reduced binding to non-cellulosic materials. Also described are nucleic acids encoding the cellulase, compositions comprising said cellulase, methods of identifying cellulose variants and methods of using the compositions.

  4. High-Throughput Association Testing on DNA Pools to Identify Genetic Variants that Confer Susceptibility

    E-print Network

    California at Berkeley, University of

    High-Throughput Association Testing on DNA Pools to Identify Genetic Variants that Confer designed for nine candidate genetic variants in DNA repair and cell cycle/apoptotic regulatory genes, including Cyclin D1 [codon 870 splice site variant (A>G)]; BRCA1, P871L; ERCC2, K751Q; FAS Ŕ1377 (G>A); h

  5. Variants in Melanogenesis Genes in Melanoma Susceptibility and Survival Promotionsfach: DKFZ (Deutschen Krebsforschungszentrum)

    E-print Network

    Kirches, Christian

    Jian Guan Dr. med. Variants in Melanogenesis Genes in Melanoma Susceptibility and Survival was mainly aimed at validating the genetic variants in susceptibility to melanoma through replication variants out of 27 loci were confirmed to have significant associations with risk of melanoma within both

  6. An efficient variant of the RSA cryptosystem Cesar Alison Monteiro Paix~ao

    E-print Network

    An efficient variant of the RSA cryptosystem Cesar Alison Monteiro Paix~ao capaixao combination of two variants of RSA cryptosystem (MPrime and Rebalanced RSA) analysed by Boneh and Schacham [2 present an extension of the work of Boneh and Shacham on some variants of the RSA cryptosystem. We review

  7. An e#cient variant of the RSA cryptosystem Cesar Alison Monteiro Paixao #

    E-print Network

    An e#cient variant of the RSA cryptosystem Cesar Alison Monteiro Paixâ?ťao # capaixao#cient combination of two variants of RSA cryptosystem (MPrime and Rebalanced RSA) analysed by Boneh and Schacham [2 present an extension of the work of Boneh and Shacham on some variants of the RSA cryptosystem. We review

  8. Small colony variants: a pathogenic form of bacteria that facilitates persistent and recurrent infections

    Microsoft Academic Search

    Christof von Eiff; Barbara C. Kahl; Karsten Becker; Peter McNamara; Mathias Herrmann; Georg Peters; Richard A. Proctor

    2006-01-01

    Small colony variants constitute a slow-growing subpopulation of bacteria with distinctive phenotypic and pathogenic traits. Phenotypically, small colony variants have a slow growth rate, atypical colony morphology and unusual biochemical characteristics, making them a challenge for clinical microbiologists to identify. Clinically, small colony variants are better able to persist in mammalian cells and are less susceptible to antibiotics than their

  9. Comparison of genotype clustering tools with rare variants

    PubMed Central

    2014-01-01

    Background Along with the improvement of high throughput sequencing technologies, the genetics community is showing marked interest for the rare variants/common diseases hypothesis. While sequencing can still be prohibitive for large studies, commercially available genotyping arrays targeting rare variants prove to be a reasonable alternative. A technical challenge of array based methods is the task of deriving genotype classes (homozygous or heterozygous) by clustering intensity data points. The performance of clustering tools for common polymorphisms is well established, while their performance when conducted with a large proportion of rare variants (where data points are sparse for genotypes containing the rare allele) is less known. We have compared the performance of four clustering tools (GenCall, GenoSNP, optiCall and zCall) for the genotyping of over 10,000 samples using the Illumina’s HumanExome BeadChip, which includes 247,870 variants, 90% of which have a minor allele frequency below 5% in a population of European ancestry. Different reference parameters for GenCall and different initial parameters for GenoSNP were tested. Genotyping accuracy was assessed using data from the 1000 Genomes Project as a gold standard, and agreement between tools was measured. Results Concordance of GenoSNP’s calls with the gold standard was below expectations and was increased by changing the tool’s initial parameters. While the four tools provided concordance with the gold standard above 99% for common alleles, some of them performed poorly for rare alleles. The reproducibility of genotype calls for each tool was assessed using experimental duplicates which provided concordance rates above 99%. The inter-tool agreement of genotype calls was high for approximately 95% of variants. Most tools yielded similar error rates (approximately 0.02), except for zCall which performed better with a 0.00164 mean error rate. Conclusions The GenoSNP clustering tool could not be run straight “out of the box” with the HumanExome BeadChip, as modification of hard coded parameters was necessary to achieve optimal performance. Overall, GenCall marginally outperformed the other tools for the HumanExome BeadChip. The use of experimental replicates provided a valuable quality control tool for genotyping projects with rare variants. PMID:24559245

  10. Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

    PubMed Central

    Vallania, Francesco; Ramos, Enrique; Cresci, Sharon; Mitra, Robi D.; Druley, Todd E.

    2012-01-01

    As DNA sequencing technology has markedly advanced in recent years2, it has become increasingly evident that the amount of genetic variation between any two individuals is greater than previously thought3. In contrast, array-based genotyping has failed to identify a significant contribution of common sequence variants to the phenotypic variability of common disease4,5. Taken together, these observations have led to the evolution of the Common Disease / Rare Variant hypothesis suggesting that the majority of the "missing heritability" in common and complex phenotypes is instead due to an individual's personal profile of rare or private DNA variants6-8. However, characterizing how rare variation impacts complex phenotypes requires the analysis of many affected individuals at many genomic loci, and is ideally compared to a similar survey in an unaffected cohort. Despite the sequencing power offered by today's platforms, a population-based survey of many genomic loci and the subsequent computational analysis required remains prohibitive for many investigators. To address this need, we have developed a pooled sequencing approach1,9 and a novel software package1 for highly accurate rare variant detection from the resulting data. The ability to pool genomes from entire populations of affected individuals and survey the degree of genetic variation at multiple targeted regions in a single sequencing library provides excellent cost and time savings to traditional single-sample sequencing methodology. With a mean sequencing coverage per allele of 25-fold, our custom algorithm, SPLINTER, uses an internal variant calling control strategy to call insertions, deletions and substitutions up to four base pairs in length with high sensitivity and specificity from pools of up to 1 mutant allele in 500 individuals. Here we describe the method for preparing the pooled sequencing library followed by step-by-step instructions on how to use the SPLINTER package for pooled sequencing analysis (http://www.ibridgenetwork.org/wustl/splinter). We show a comparison between pooled sequencing of 947 individuals, all of whom also underwent genome-wide array, at over 20kb of sequencing per person. Concordance between genotyping of tagged and novel variants called in the pooled sample were excellent. This method can be easily scaled up to any number of genomic loci and any number of individuals. By incorporating the internal positive and negative amplicon controls at ratios that mimic the population under study, the algorithm can be calibrated for optimal performance. This strategy can also be modified for use with hybridization capture or individual-specific barcodes and can be applied to the sequencing of naturally heterogeneous samples, such as tumor DNA. PMID:22760212

  11. Size heterogeneity among antigenically related Giardia lamblia variant-specific surface proteins is due to differences in tandem repeat copy number.

    PubMed Central

    Mowatt, M R; Nguyen, B Y; Conrad, J T; Adam, R D; Nash, T E

    1994-01-01

    Giardia lamblia undergoes antigenic variation by modulating the expression of the different genes that comprise the trophozoite's variant-specific surface protein (VSP) repertoire. We studied an epitope that is conserved among VSPs expressed by cloned trophozoite lines derived from the independent G. lamblia isolates WB, G3M, Be-2, and CAT. The epitope recognized by monoclonal antibody 6E7 lies entirely within the region of tandemly repeated 65-amino-acid units that is characteristic of these size-variant VSPs. Northern (RNA) hybridization, cDNA cloning, and DNA sequence analysis indicate that size heterogeneity among these VSPs is due to differences in the number of repetitive units. Images PMID:7510666

  12. Genetic characterization of hantaviruses isolated from Guizhou, China: evidence for spillover and reassortment in nature.

    PubMed

    Zou, Yang; Hu, Jing; Wang, Zhao-Xiao; Wang, Ding-Ming; Yu, Chun; Zhou, Jing-Zhu; Fu, Zhen F; Zhang, Yong-Zhen

    2008-06-01

    To gain more insights into the epidemiology of hantaviruses in the Guizhou province, China, rodents were captured in Guizhou during the period from 2001 to 2003. In addition, serum sample was collected from one patient. Virus isolation was attempted from human serum and rodent samples. Four hantaviruses were isolated successfully in cell culture from one human, two A. agrarius, and one R. norvegicus. The nucleotide sequences for the entire S and M and partial L segment were determined from these four isolates as well as six viruses isolated in 1980s. Phylogenetic analysis revealed that the S segment from all isolates belong to the Hantaan virus (HTNV) clade, regardless of the sources from which they were derived. According to the S sequences, these viruses could be divided into three distinct phylogroups, showing geographical clustering. Analysis of the entire M and the partial L segment sequences demonstrated that 8 out of the 10 isolates belong to the HTNV clade. However, two isolates (CGRn8316 and CGRn9415) isolated from R. norvegicus belong to the Seoul virus (SEOV) clade. In addition, these two isolates were distinct from other known members of SEOV clade. Together, the data suggest that at least three groups of HTNV are co-circulating and one new variant of SEOV may be present in Guizhou. Our results also suggest that HTNV from A. agrarius spilled over to R. norvegicus and natural reassortment between HTNV and SEOV occurred during or after the spillover. PMID:18428127

  13. Analysis of Salmonella typhi isolates from Southeast Asia by pulsed-field gel electrophoresis.

    PubMed Central

    Thong, K L; Puthucheary, S; Yassin, R M; Sudarmono, P; Padmidewi, M; Soewandojo, E; Handojo, I; Sarasombath, S; Pang, T

    1995-01-01

    Pulsed-field gel electrophoresis (PFGE) revealed that multiple genetic variants of Salmonella typhi are simultaneously present in Southeast Asia and are associated with sporadic cases of typhoid fever and occasional outbreaks. Comparative analysis of PFGE patterns also suggested that considerable genetic diversity exists among S. typhi strains and that some PFGE patterns are shared between isolates obtained from Malaysia, Indonesia, and Thailand, implying movement of these strains within these regions of Southeast Asia, where they are endemic. PMID:7665677

  14. Low-loss, high-isolation, fiber-optic isolator

    NASA Technical Reports Server (NTRS)

    Lutes, George F. (inventor)

    1988-01-01

    A low-loss, high-isolation, fiber-optic isolator for use in single-mode fiber systems utilizes a Faraday rotator and two polarizers, one at each end angularly oriented from each other at the angle of rotation for isolation, and two aspheric lens connectors to couple optical fibers to the Faraday isolator to reduce forward loss to about 2.5 dB and improve isolation to greater than 70 dB.

  15. [Rabies virus isolation in the salivary glands of insectivorous bats].

    PubMed

    Gury Dohmen, F; Beltrán, F

    2009-12-01

    This study determined the presence of the rabies virus in salivary glands, as well as its titre and antigenic characterisation and the level of exposure to the virus from contact between domestic animals and humans. Twenty-six positive brain samples were selected, 80% of which were from the Brazilian free-tailed bat, Tadarida brasiliensis, corresponding to the period 1999-2005. Antigenic characterisation was conducted on a panel of 19 monoclonal antibodies targeting the rabies virus nucleoprotein supplied by the Centers for Disease Control and Prevention in Atlanta in the United States of America. The results revealed a high percentage of isolations in salivary glands (76.9%). Their average titres were compared in a batch of positive samples of brain and salivary glands, giving values of 4.75 and 3.81 respectively (expressed as log LD50/0.03 ml). The isolated viruses corresponded principally to variant 4 associated with T brasiliensis and variant 6 associated with the hoary bat, Lasiurus cinereus, and the red bat, L. borealis, and their respective subvariants. The level of exposure in domestic animals and humans was 50% during the period under study. PMID:20462155

  16. Isolation of novel sequences targeting highly variable viral protein hemagglutinin?

    PubMed Central

    Xu, Zhiwu; Wu, Jieyu; Feng, Fan; Zhang, Xiaoxiao; Ma, Xiaoqian; Tang, Man; Huang, Yan; Zhang, Ying; Cao, Yongchang; Cao, Weiguo; He, Ran; Gao, Ye; Liu, Qiuyun

    2015-01-01

    Rapid evolution is a hallmark of the viral kingdom and a major concern for developing universal vaccines. The isolation of substantial numbers of viral sequence variants at highly variable viral protein domains remains a major challenge. We previously developed a combinatorial method for the isolation of novel sequences to cope with rapid viral variations at the G-H loop of Foot and Mouth Disease virus VP1 protein [1]. Here we present a modification of that method in its application in the randomization of the hemagglutinin gene from a H5N2 virus, namely: • removal of potentially stressful region which harbored a stretch of basic amino acids to increase the success rates of gene cloning, and to streamline the process of future engineering of novel viral variants. • clustered randomization in a full-length gene, as the positive rate for partial gene fragment libraries was extremely low before enrichment in the previous FMDV studies. • the use of fusion partner was avoided, which was used previously for protein expression, stabilization of clones and reduction of stresses on host cells. • the use of Poisson distribution is proposed to approximate sequencing output to achieve cost effectiveness.

  17. Engineered antibody Fc variants with enhanced effector function

    NASA Astrophysics Data System (ADS)

    Lazar, Greg A.; Dang, Wei; Karki, Sher; Vafa, Omid; Peng, Judy S.; Hyun, Linus; Chan, Cheryl; Chung, Helen S.; Eivazi, Araz; Yoder, Sean C.; Vielmetter, Jost; Carmichael, David F.; Hayes, Robert J.; Dahiyat, Bassil I.

    2006-03-01

    Antibody-dependent cell-mediated cytotoxicity, a key effector function for the clinical efficacy of monoclonal antibodies, is mediated primarily through a set of closely related Fc receptors with both activating and inhibitory activities. By using computational design algorithms and high-throughput screening, we have engineered a series of Fc variants with optimized Fc receptor affinity and specificity. The designed variants display >2 orders of magnitude enhancement of in vitro effector function, enable efficacy against cells expressing low levels of target antigen, and result in increased cytotoxicity in an in vivo preclinical model. Our engineered Fc regions offer a means for improving the next generation of therapeutic antibodies and have the potential to broaden the diversity of antigens that can be targeted for antibody-based tumor therapy. antibody-dependent cell-mediated cytotoxicity | FcR | protein engineering | cancer

  18. Dandy Walker Variant and Bipolar I Disorder with Graphomania

    PubMed Central

    Karaka? U?urlu, Görkem; Çakmak, Selcen

    2014-01-01

    Cerebellum is known to play an important role in coordination and motor functions. In some resent studies it is also considered to be involved in modulation of mood, cognition and psychiatric disorders. Dandy Walker Malformation is a congenital malformation that is characterized by hypoplasia or aplasia of the cerebellar vermis, cystic dilatation of the fourth ventricle and enlargement of the posterior fossa. When the volume of posterior fossa is normal, the malformation is called Dandy Walker Variant. Case is a 32 year old male with a 12 year history of Bipolar I Disorder presented with manic and depresive symptoms, including dysphoric and depressive affect, anhedonia, suicidal thoughts and behaviours, thoughts of fear about future, overtalkativeness and graphomania, increased energy, irregular sleep, loss of appetite, increased immersion in projects, irritability, agressive behavior, impulsivity. Cranial Magnetic Resonance Imaging was compatible to the morphological features of Dandy Walker Variant. PMID:25110509

  19. A case of cough variant asthma undiagnosed for 16 years

    PubMed Central

    Sridaran, Sankar; Gonzalez-Estrada, Alexei; Aronica, Mark A.

    2014-01-01

    A 64-year-old female patient presented with a 16-year history of persistent dry cough that was undiagnosed after workups at several healthcare facilities. The patient denies wheezing, shortness of breath or sputum production. Previous workups include chest imaging, transthoracic echocardiogram (TTE), laryngoscopy, spirometry and bronchoscopy, all of which were unremarkable. During her current evaluation, spirometry was ordered again for the patient, which showed a post-bronchodilator improvement in the FEV1 by 13%, strongly suggestive of asthma. The patient was started on pharmacological therapy for severe persistent asthma, which led to sustained symptomatic improvement per evaluation at follow-up after 2 months. Spirometric findings, clinical presentation and resolution of symptoms with adequate therapy for asthma suggest that this is a case of cough variant asthma that went undiagnosed for several years. This case report summarizes the workup for chronic cough and how the diagnosis of cough variant asthma can be missed. PMID:25988016

  20. Diagnosis and Management of Behavioral Variant Frontotemporal Dementia

    PubMed Central

    Pressman, Peter; Miller, Bruce L

    2014-01-01

    Frontotemporal dementia (FTD) was documented over a century ago. The last decade, however, has seen substantial changes in our conceptions of this increasingly recognized disorder. Different clinical variants have been delineated, the most common of which is the behavioral variant (bvFTD). Updated diagnostic criteria have been established. New histopathological findings and genetic etiologies have been discovered. Research continues to uncover molecular mechanisms by which abnormal proteins accumulate in degenerating brain tissue. Novel neuroimaging techniques suggest that functional networks are diminished in bvFTD that may be relevant to empathy and social behavior. Despite rapid advances in our understanding of bvFTD, the disease is still under-recognized and commonly misdiagnosed. The result is inappropriate patient care. Recognizing the various presentations of bvFTD and its histological and genetic subtypes may further diagnosis, treatment and research. PMID:24315411