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1

Molecular analyses of Vibrio cholerae O1 clinical strains, including new nontoxigenic variants isolated in Mexico during the Cholera epidemic years between 1991 and 2000.  

PubMed

We studied the evolution of Vibrio cholerae O1 during the 1991 to 2000 cholera epidemic in Mexico by biochemical, serological, and molecular characterization of strains collected during this period. Strains were divided into toxigenic and nontoxigenic groups according to the presence or absence of genes encoding cholera toxin. As previously reported, we characterized two populations among toxigenic strains, which were present from the first year of the epidemic. BglI rRNA analysis revealed that these strains had ribotype profiles, denoted M5 and M6 in our study, that were identical to those previously designated Koblavi B5 or Popovic 5 and Popovic 6a or Tamayo B21a, respectively. Ribotype M5 was isolated between 1991 and 1993. This ribotype had a low level of genetic variation as detected by pulsed-field gel electrophoresis (PFGE). Ribotype M6 persisted from 1991 to 2000. However, PFGE profiles suggested that two epidemiologically unrelated strains coexisted within this single ribotype from 1995 until the end of the epidemic. We identified three new BglI ribotypes, Mx1, Mx2, and Mx3, from nontoxigenic V. cholerae O1 strains isolated between 1998 and 2000; one of them grouped strains positive for the toxin-coregulated pilus island. They differed from nontoxigenic clones isolated in Latin America and on the U.S. Gulf Coast and are probably autochthonous Mexican V. cholerae O1 variants. Most of these new variants were isolated from states surrounding the Gulf of Mexico, where the highest incidence of cholera in the country was recorded. Thus, the Mexican Gulf Coast, like the U.S. Gulf Coast, may act as an environmental reservoir of V. cholerae O1. PMID:19213700

Lizárraga-Partida, Marcial Leonardo; Quilici, Marie-Laure

2009-02-11

2

Molecular Analyses of Vibrio cholerae O1 Clinical Strains, Including New Nontoxigenic Variants Isolated in Mexico during the Cholera Epidemic Years between 1991 and 2000?  

PubMed Central

We studied the evolution of Vibrio cholerae O1 during the 1991 to 2000 cholera epidemic in Mexico by biochemical, serological, and molecular characterization of strains collected during this period. Strains were divided into toxigenic and nontoxigenic groups according to the presence or absence of genes encoding cholera toxin. As previously reported, we characterized two populations among toxigenic strains, which were present from the first year of the epidemic. BglI rRNA analysis revealed that these strains had ribotype profiles, denoted M5 and M6 in our study, that were identical to those previously designated Koblavi B5 or Popovic 5 and Popovic 6a or Tamayo B21a, respectively. Ribotype M5 was isolated between 1991 and 1993. This ribotype had a low level of genetic variation as detected by pulsed-field gel electrophoresis (PFGE). Ribotype M6 persisted from 1991 to 2000. However, PFGE profiles suggested that two epidemiologically unrelated strains coexisted within this single ribotype from 1995 until the end of the epidemic. We identified three new BglI ribotypes, Mx1, Mx2, and Mx3, from nontoxigenic V. cholerae O1 strains isolated between 1998 and 2000; one of them grouped strains positive for the toxin-coregulated pilus island. They differed from nontoxigenic clones isolated in Latin America and on the U.S. Gulf Coast and are probably autochthonous Mexican V. cholerae O1 variants. Most of these new variants were isolated from states surrounding the Gulf of Mexico, where the highest incidence of cholera in the country was recorded. Thus, the Mexican Gulf Coast, like the U.S. Gulf Coast, may act as an environmental reservoir of V. cholerae O1.

Lizarraga-Partida, Marcial Leonardo; Quilici, Marie-Laure

2009-01-01

3

Molecular Analyses of Vibrio cholerae O1 Clinical Strains, Including New Nontoxigenic Variants Isolated in Mexico during the Cholera Epidemic Years between 1991 and 2000  

Microsoft Academic Search

We studied the evolution of Vibrio cholerae O1 during the 1991 to 2000 cholera epidemic in Mexico by biochemical, serological, and molecular characterization of strains collected during this period. Strains were divided into toxigenic and nontoxigenic groups according to the presence or absence of genes encoding cholera toxin. As previously reported, we characterized two populations among toxigenic strains, which were

Marcial Leonardo Lizarraga-Partida; Marie-Laure Quilici

4

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

PubMed Central

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

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

1991-01-01

5

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...

6

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

7

Nontoxigenic Vibrio parahaemolyticus Strains Causing Acute Gastroenteritis  

PubMed Central

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

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

2012-01-01

8

Alkaline protease from a non-toxigenic mangrove isolate of Vibrio sp. V26 with potential application in animal cell culture.  

PubMed

Vibrio sp. V26 isolated from mangrove sediment showed 98 % similarity to 16S rRNA gene of Vibrio cholerae, V. mimicus, V. albensis and uncultured clones of Vibrio. Phenotypically also it resembled both V. cholerae and V. mimicus. Serogrouping, virulence associated gene profiling, hydrophobicity, and adherence pattern clearly pointed towards the non-toxigenic nature of Vibrio sp. V26. Purification and characterization of the enzyme revealed that it was moderately thermoactive, nonhemagglutinating alkaline metalloprotease with a molecular mass of 32 kDa. The application of alkaline protease from Vibrio sp. V26 (APV26) in sub culturing cell lines (HEp-2, HeLa and RTG-2) and dissociation of animal tissue (chick embryo) for primary cell culture were investigated. The time required for dissociation of cells as well as the viable cell yield obtained by while administering APV26 and trypsin were compared. Investigations revealed that the alkaline protease of Vibrio sp. V26 has the potential to be used in animal cell culture for subculturing cell lines and dissociation of animal tissue for the development of primary cell cultures, which has not been reported earlier among metalloproteases of Vibrios. PMID:22717659

Manjusha, K; Jayesh, P; Jose, Divya; Sreelakshmi, B; Priyaja, P; Gopinath, Prem; Saramma, A V; Bright Singh, I S

2012-06-21

9

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

PubMed Central

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.

Carlier, Jean-Philippe; K'ouas, Guylene; Lozniewski, Alain; Sirveaux, Francois; Cailloux, Philippe; Mory, Francine

2004-01-01

10

Culture-Negative Prosthetic Valve Endocarditis with Concomitant Septicemia Due to a Nontoxigenic Corynebacterium diphtheriae Biotype Gravis Isolate in a Patient with Multiple Risk Factors.  

PubMed

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

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

2013-09-04

11

Molecular characterization of environmental and nontoxigenic strains of Vibrio cholerae.  

PubMed Central

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

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

1981-01-01

12

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...

13

Isolation and characterization of Bordetella avium phase variants.  

PubMed Central

Two spontaneous phase variants of Bordetella avium were isolated at a frequency of 2 x 10(-4) by colony immunoblot assay of B. avium with antibody against B. avium dermonecrotic toxin. The two phase variants, designated GOBL309 and GOBL312, lack dermonecrotic toxin and four outer membrane proteins with molecular masses of 93, 48, 38, and 27 kDa but retain the ability to agglutinate guinea pig erythrocytes. The proteins which are not expressed by GOBL309 and GOBL312 correspond to five proteins which are phenotypically modulated in B. avium by growth in the presence of nicotinic acid or MgSO4. Growth of the phase variants in supplemented Stainer-Scholte media containing nicotinamide did not alter expression of these five proteins. Intranasal inoculation of the spontaneous phase variants into 3-day-old turkeys and reisolation of B. avium at 2 weeks postinoculation resulted in the recovery of B. avium which had the wild-type phenotype, colonized the turkey tracheas, and produced the four outer membrane proteins and dermonecrotic toxin. Hybridization of B. avium and B. avium-like chromosomal DNA with internal portions of the Bordetella pertussis virulence regulatory genes, bvgA and bvgS, revealed that B. avium and B. avium-like isolates contain 5.3- and 5.7-kb DNA fragments, respectively, which are homologous to bvgS. B. avium and B. avium-like chromosomal DNA failed to hybridize to B. pertussis bvgA. Images

Gentry-Weeks, C R; Provence, D L; Keith, J M; Curtiss, R

1991-01-01

14

[Isolation of an autotrophic variant of Nocardia opaca].  

PubMed

A hydrogen-oxidizing autotrophic actinomycete, strain Z-766, was isolated from the neuston of a marsh near Moscow. The organism was identified as Nocardia opaca Z-766 according to its morphologo-physiological properties. The spectrum of organic compounds used by the strain, its cultural characteristics and growth are similar to those of the monotypical autotrophic microorganism N. opaca 1b described earlier. Repeated isolation of the autotrophic variant of N. opaca Z-766 suggests that the ability of this species for autotrophic growth is not a unique phenomenon. It would be expedient to construct a taxon of the subspecial range, N. opaca var. autotrophica, for autotrophic variants of N. opaca. PMID:155775

Kriukov, V R

15

Draft Genome Sequences of Five Yersinia pseudotuberculosis ST19 Isolates and One Isolate Variant  

PubMed Central

We report the first draft genome sequences of five Yersinia pseudotuberculosis isolates of sequence type (ST) 19 and of a variant from one of the five isolates. The total length of assemblies ranged from 4,226,485 bp to 4,274,148 bp, including between 3,808 and 3,843 predicted coding sequences.

Platonov, Mikhail E.; Blouin, Yann; Evseeva, Vera V.; Afanas'ev, Maxim V.; Pourcel, Christine; Balakhonov, Sergey V.

2013-01-01

16

Identification and molecular discrimination of toxigenic and nontoxigenic diphtheria Corynebacterium strains by combined real-time polymerase chain reaction assays.  

PubMed

With the recognition of several diphtheria outbreaks and the emergence of nontoxigenic corynebacteria strains, there has been renewed interest in the development of laboratory diagnostic methods. Previously reported polymerase chain reaction (PCR) assays can have low diagnostic sensitivity or give species misidentifications among clinical isolates. The aim of the present study was the development of combined real-time PCR assays, based on the tox and rpoB genes, for the detection and differentiation of toxigenic and nontoxigenic corynebacteria. By the PCR tox assay, it was possible to perform the direct identification of DT tox gene of Corynebacterium diphtheriae and Corynebacterium ulcerans, while the PCR rpoB assay differentiated C. diphtheriae from C. ulcerans, irrespective of their toxigenic status. In addition, we detected the DT toxin of Corynebacterium pseudotuberculosis for the first time. These assays revealed high sensitivity, specificity, and reproducibility, and the availability of plasmid controls will facilitate further research into the diagnostics of diphtheria corynebacteria. PMID:22494559

Mancini, Fabiola; Monaco, Monica; Pataracchia, Marco; von Hunolstein, Christina; Pantosti, Annalisa; Ciervo, Alessandra

2012-04-10

17

Contribution of Rare Copy Number Variants to Isolated Human Malformations  

PubMed Central

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.

Serra-Juhe, Clara; Rodriguez-Santiago, Benjamin; Cusco, Ivon; Vendrell, Teresa; Camats, Nuria; Toran, Nuria; Perez-Jurado, Luis A.

2012-01-01

18

Isolation and characterization of a variant of ovomucoid.  

PubMed Central

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

Waheed, A; Salhuddin, A

1975-01-01

19

Isolation of abscisic acid-resistant variants from tobacco cell cultures  

Microsoft Academic Search

Variant clones were isolated from Nicotiana silvestris Speg. et Comes cell cultures at low frequencies following severe abscisic-acid (ABA) or mannitol-induced water-stress treatments of plated cells. N. tabacum L. variants were not recovered. Variants from the ABA selection experiments exhibited a 10-fold increase in resistance to the hormone. This trait was stable in non-selective conditions for as long as was

James R. Wong; Ian M. Sussex

1980-01-01

20

Increased constrictor response to acetylcholine of the isolated coronary arteries from patients with variant angina  

Microsoft Academic Search

The aim of this study was to determine whether isolated coronary arteries from patients with variant angina show hyperreactivity and\\/or supersensitivity to acetylcholine in vitro. Coronary arterial rings were obtained at autopsy within 3 h after death from six coronary arteries having spasm in four patients with variant angina and from 22 coronary arteries in 14 control patients with non-cardiac

Kiyotaka Kugiyama; Toyoaki Murohara; Hirofumi Yasue; Tadashi Kimura; Naritsugu Sakaino; Masamichi Ohgushi; Seigo Sugiyama; Ken Okumura

1995-01-01

21

The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae.  

PubMed Central

The DNA sequences of the asd genes from 45 isolates of Vibrio cholerae (19 clinical O1 isolates, 2 environmental nontoxigenic O1 isolates, and 24 isolates with different non-O1 antigens) were determined. No differences were found within either sixth- or seventh-pandemic isolates; however, variation was found between the two forms and among the non-O1 isolates. O139 isolates had sequences identical to those of seventh-pandemic isolates. Phylogenetic trees with Vibrio mimicus as the outgroup suggest that the sixth-pandemic, seventh-pandemic, and U.S. Gulf isolates are three clones that have evolved independently from different lineages of environmental, nontoxigenic, non-O1 V. cholerae isolates. There is evidence for horizontal transfer of O antigen, since isolates with nearly identical asd sequences had different O antigens, and isolates with the O1 antigen did not cluster together but were found in different lineages. We also found evidence for recombination events within the asd gene of V. cholerae. V. cholerae may have a higher level of genetic exchange and a lower level of clonality than species such as Salmonella enterica and Escherichia coli.

Karaolis, D K; Lan, R; Reeves, P R

1995-01-01

22

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

PubMed Central

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

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

2011-01-01

23

Characterisation of an Australian bat lyssavirus variant isolated from an insectivorous bat  

Microsoft Academic Search

In 1996 a variant lyssavirus was isolated from an insectivorous bat (yellow bellied, sheath tail bat—Saccolaimus flaviventris) in Australia. The nucleocapsid protein (N), matrix protein (M), phosphoprotein (P), glycoprotein (G) and polymerase (L) genes of the Australian bat lyssavirus (ABL) insectivorous isolate were compared with that previously described from a frugivorous bat (Pteropus sp.), and showed sequence divergence at both

Allan R Gould; Jacqueline A Kattenbelt; Sarah G Gumley; Ross A Lunt

2002-01-01

24

Clinical importance and representation of toxigenic and non-toxigenic Clostridium difficile cultivated from stool samples of hospitalized patients  

PubMed Central

The aim of this study was to fortify the clinical importance and representation of toxigenic and non-toxigenic Clostridium difficile isolated from stool samples of hospitalized patients. This survey included 80 hospitalized patients with diarrhea and positive findings of Clostridium difficile in stool samples, and 100 hospitalized patients with formed stool as a control group. Bacteriological examination of a stool samples was conducted using standard microbiological methods. Stool sample were inoculated directly on nutrient media for bacterial cultivation (blood agar using 5% sheep blood, Endo agar, selective Salmonella Shigella agar, Selenite-F broth, CIN agar and Skirrow’s medium), and to selective cycloserine-cefoxitin-fructose agar (CCFA) (Biomedics, Parg qe tehnicologico, Madrid, Spain) for isolation of Clostridium difficile. Clostridium difficile toxin was detected by ELISA-ridascreen Clostridium difficile Toxin A/B (R-Biopharm AG, Germany) and ColorPAC ToxinA test (Becton Dickinson, USA). Examination of stool specimens for the presence of parasites (causing diarrhea) was done using standard methods (conventional microscopy), commercial concentration test Paraprep S Gold kit (Dia Mondial, France) and RIDA®QUICK Cryptosporidium/Giardia Combi test (R-Biopharm AG, Germany). Examination of stool specimens for the presence of fungi (causing diarrhea) was performed by standard methods. All stool samples positive for Clostridium difficile were tested for Rota, Noro, Astro and Adeno viruses by ELISA – ridascreen (R-Biopharm AG, Germany). In this research we isolated 99 Clostridium difficile strains from 116 stool samples of 80 hospitalized patients with diarrhea. The 53 (66.25%) of patients with diarrhea were positive for toxins A and B, one (1.25%) were positive for only toxin B. Non-toxigenic Clostridium difficile isolated from samples of 26 (32.5%) patients. However, other pathogenic microorganisms of intestinal tract cultivated from samples of 16 patients. Examination of cultivated colonies revealed that most of cultivated species belonged to genera of Campylobacter spp., Salmonella spp., and Candida spp.. In control group, toxigenic Clostridium difficile cultivated from stool samples of two patients (2%) and non-toxigenic Clostridium difficile from samples of five patients (5%). This research confirmed clinical importance of toxigenic Clostridium difficile found in liquid stool samples of hospitalized patient, and the possibility of asymptomatic carriage in 2% of patients with formed stool.

Predrag, Stojanovic; Branislava, Kocic; Miodrag, Stojanovic; Biljana, Miljkovic - Selimovic; Suzana, Tasic; Natasa, Miladinovic - Tasic; Tatjana, Babic

2012-01-01

25

Nucleotide sequence of a hop stunt viroid variant isolated from citrus growing in Taiwan.  

PubMed

The 303 nucleotide sequence of HSVd-citrus(T), a hop stunt viroid (HSVd) variant present in Etrog citron growing in Taiwan, was determined from cDNAs amplified by the polymerase chain reaction. HSVd-citrus(T) is very similar to several HSVd isolates previously recovered from citrus or cucumber, and exhibits microsequence heterogeneity at positions 154 and 181. Phylogenetic analysis using maximum parsimony grouped HSVd-citrus(T) with seven other isolates from citrus and cucumber in a large cluster of "citrus-type" isolates. A similar analysis revealed marked differences in both the extent and distribution of sequence variation among naturally occurring isolates of potato spindle tuber viroid. PMID:7732666

Hsu, Y H; Chen, W; Owens, R A

1995-01-01

26

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

PubMed

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

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

2011-01-31

27

Highly resistant Burkholderia pseudomallei small colony variants isolated in vitro and in experimental melioidosis  

Microsoft Academic Search

Burkholderia pseudomallei is the causative agent of melioidosis, a disease in which treatment failures and relapses are common. This study reports\\u000a on slow growing B. pseudomallei `small colony variants' (SCVs), isolated either in vitro after exposure to ceftazidime, ciprofloxacin or gentamicin or from\\u000a the spleen and liver in a mouse model of melioidosis after treatment with ceftazidime. Interestingly, SCVs isolated

Susanne Häußler; Manfred Rohde; Ivo Steinmetz

1999-01-01

28

Characterization of Small-Colony Variants of Enterococcus faecalis Isolated from Chickens with Amyloid Arthropathy?  

PubMed Central

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

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

2008-01-01

29

Virulence Attenuation of Candida albicans Genetic Variants Isolated from a Patient with a Recurrent Bloodstream Infection  

PubMed Central

The incidence of Candida albicans infections and the relapse episodes after antifungal treatment have increased in recent decades. Recurrences are mainly due to the persistence of the original infecting strain that may present genetic and genomic rearrangements during interaction with the host, reflecting strain adaptation. In this study, four isolates recovered from a patient during recurrent candidemia episodes were genotyped by microsatellite length polymorphism (MLP) and by multilocus sequence typing (MLST) and found to be genetic variants of the same strain. Using experimental mouse infections, a progressive reduction in the virulence of the four isolates was observed, with the first two isolates more virulent than the third and fourth. Additionally, in the mouse model, the first isolate resisted host control more efficiently, resulting in higher kidney fungal burdens and necrosis as compared to the third isolate. The resolution of inflammation was delayed in mice challenged with the first isolate and the message for IFN-? and TNF-? in the spleen was lower within the first few hours post-infection. Original and recurrent isolates also displayed different phenotypes regarding activity of secreted enzymes and response to stress agents. Overall, the comparative analysis indicated that the virulence decrease of these isolates was related to a lower ability to resist to the host anticandida effector mechanisms. We showed for the first time that C. albicans genetic variants of the same strain, sequentially isolated from an immunocompromised patient, underwent adaptations in the human host that resulted in virulence attenuation when tested in mice.

Sampaio, Paula; Santos, Marlene; Correia, Alexandra; Amaral, Fabio E.; Chavez-Galarza, Julio; Costa-de-Oliveira, Sofia; Castro, Antonio G.; Pedrosa, Jorge; Pais, Celia

2010-01-01

30

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

PubMed Central

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.

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

2013-01-01

31

Identification and functional characterization of NODAL rare variants in heterotaxy and isolated cardiovascular malformations  

PubMed Central

NODAL and its signaling pathway are known to play a key role in specification and patterning of vertebrate embryos. Mutations in several genes encoding components of the NODAL signaling pathway have previously been implicated in the pathogenesis of human left–right (LR) patterning defects. Therefore, NODAL, a member of TGF-? superfamily of developmental regulators, is a strong candidate to be functionally involved in congenital LR axis patterning defects or heterotaxy. Here we have investigated whether variants in NODAL are present in patients with heterotaxy and/or isolated cardiovascular malformations (CVM) thought to be caused by abnormal heart tube looping. Analysis of a large cohort of cases (n = 269) affected with either classic heterotaxy or looping CVM revealed four different missense variants, one in-frame insertion/deletion and two conserved splice site variants in 14 unrelated subjects (14/269, 5.2%). Although similar with regard to other associated defects, individuals with the NODAL mutations had a significantly higher occurrence of pulmonary valve atresia (P = 0.001) compared with cases without a detectable NODAL mutation. Functional analyses demonstrate that the missense variant forms of NODAL exhibit significant impairment of signaling as measured by decreased Cripto (TDGF-1) co-receptor-mediated activation of artificial reporters. Expression of these NODAL proteins also led to reduced induction of Smad2 phosphorylation and impaired Smad2 nuclear import. Taken together, these results support a role for mutations and rare deleterious variants in NODAL as a cause for sporadic human LR patterning defects.

Mohapatra, Bhagyalaxmi; Casey, Brett; Li, Hua; Ho-Dawson, Trang; Smith, Liana; Fernbach, Susan D.; Molinari, Laura; Niesh, Stephen R.; Jefferies, John Lynn; Craigen, William J.; Towbin, Jeffrey A.; Belmont, John W.; Ware, Stephanie M.

2009-01-01

32

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

PubMed

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

Zahra, Mohammad; Ferreri, Miro; Alkasir, Rashad; Yin, Jinhua; Han, Bo; Su, Jingliang

2013-07-17

33

SHV-14, a Novel ?-Lactamase Variant in Klebsiella pneumoniae Isolates from Nijmegen, The Netherlands  

PubMed Central

Four ceftazidime-resistant isolates of a Klebsiella pneumoniae strain were collected from intensive care unit patients in Nijmegen, The Netherlands. These isolates had TEM-29 and SHV-14 ?-lactamases. SHV-14 is a novel variant, with two substitutions compared with the sequence of SHV-1: Ile8Phe and Arg43Ser. Its gene also had a silent C?T mutation at nucleotide 481. The SHV-14 enzyme had slightly higher Vmax rates than SHV-1 for oxyimino-aminothiazolyl cephalosporins, but this activity was insufficient for the enzyme to count as an extended-spectrum ?-lactamase.

Yuan, Meifang; Hall, Lucinda M. C.; Hoogkamp-Korstanje, Jaa; Livermore, David M.

2001-01-01

34

Natural killer sensitivity of tumor cells isolated from primary and metastatic lesions of four Bomirski melanoma variants  

Microsoft Academic Search

Natural killer (NK) sensitivity of melanoma cells isolated from primary and metastatic lesions of four Bomirski melanoma variants was compared. The hamster melanomas differed in their growth rate and metastatic pattern. We found that during tumor growth of all the variants tested, NK sensitivity of melanoma cells at the metastasis formation stage was significantly lower in both primary and metastatic

J. BIGDAt; A. My?liwski; D. Sosnowska; P. Romanowski; A. Bomirski

1991-01-01

35

Characterization of a small plaque variant of West Nile virus isolated in New York in 2000.  

PubMed

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

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

2007-07-06

36

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

PubMed Central

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

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

2007-01-01

37

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

PubMed

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

Pan, Yongfei; Tian, Xiaoyan; Li, Wei; Zhou, Qingfeng; Wang, Dongdong; Bi, Yingzuo; Chen, Feng; Song, Yanhua

2012-09-12

38

Isolation and quantification of highly acid resistant variants of Listeria monocytogenes.  

PubMed

Heterogeneity in stress response of bacteria is one of the biggest challenges posed by minimal processing, which aims at finding the balance between microbiologically stable foods while maintaining the characteristics of fresh products. In this study, exposure of Listeria monocytogenes LO28 to acid stress, which can be encountered in the food processing environment as well as in the human body upon ingestion, led to inactivation kinetics showing considerable tailing, which was described by a biphasic inactivation model. Stable acid resistant variants of L. monocytogenes LO28 were isolated after exposure of late-exponential phase cells to pH3.5 for 90min. The resulting 23 stable resistant isolates could be divided in three groups: (a) highly increased acid resistance (<1log10 reduction, n=16), (b) slightly increased acid resistance (1-3log10 reduction, n=6), and (c) one isolate showing a variable acid stress response. The highly acid resistant group showed increased resistance to the tested pH range of 2.5 to 3.5 in both late-exponential and stationary phase. Increased acid resistance showed to be significantly correlated to reduced growth rate. The Weibull model was reparameterized, resulting in improved parameter estimation, and was used to estimate the inactivation kinetics at mild pH. Studying the growth boundaries of the wild type and a representative set of variants indicated that the increased resistance of the variants was only related to survival of severe pH stress but did not allow for better growth or survival at mild pH stress. This study shows that acid exposure of late-exponential phase cells reveals the presence of acid resistant subpopulations and that there is a phenotypic diversity amongst them. The occurrence of heterogeneity and stress resistant subpopulations may lead to a higher number of surviving microorganisms than expected. Also, stress resistant subpopulations can become part of the domestic flora in a food production line. The currently isolated acid resistant variants are a new group of stress resistant variants and underline the importance of gaining more insight in the mechanisms underlying this heterogeneity and increased resistance. PMID:24051176

Metselaar, Karin I; den Besten, Heidy M W; Abee, Tjakko; Moezelaar, Roy; Zwietering, Marcel H

2013-08-19

39

Staphylococcus aureus Isolates Encode Variant Staphylococcal Enterotoxin B Proteins That Are Diverse in Superantigenicity and Lethality  

PubMed Central

Staphylococcus aureus produces superantigens (SAgs) that bind and cross-link T cells and APCs, leading to activation and proliferation of immune cells. SAgs bind to variable regions of the ?-chains of T cell receptors (V?-TCRs), and each SAg binds a unique subset of V?-TCRs. This binding leads to massive cytokine production and can result in toxic shock syndrome (TSS). The most abundantly produced staphylococcal SAgs and the most common causes of staphylococcal TSS are TSS toxin-1 (TSST-1), and staphylococcal enterotoxins B and C (SEB and SEC, respectively). There are several characterized variants of humans SECs, designated SEC1-4, but only one variant of SEB has been described. Sequencing the seb genes from over 20 S. aureus isolates show there are at least five different alleles of seb, encoding forms of SEB with predicted amino acid substitutions outside of the predicted immune-cell binding regions of the SAgs. Examination of purified, variant SEBs indicates that these amino acid substitutions cause differences in proliferation of rabbit splenocytes in vitro. Additionally, the SEBs varied in lethality in a rabbit model of TSS. The SEBs were diverse in their abilities to cause proliferation of human peripheral blood mononuclear cells, and differed in their activation of subsets of T cells. A soluble, high-affinity V?-TCR, designed to neutralize the previously characterized variant of SEB (SEB1), was able to neutralize the variant SEBs, indicating that this high-affinity peptide may be useful in treating a variety of SEB-mediated illnesses.

Kohler, Petra L.; Greenwood, Seth D.; Nookala, Suba; Kotb, Malak; Kranz, David M.; Schlievert, Patrick M.

2012-01-01

40

Identification and functional characterization of NODAL rare variants in heterotaxy and isolated cardiovascular malformations.  

PubMed

NODAL and its signaling pathway are known to play a key role in specification and patterning of vertebrate embryos. Mutations in several genes encoding components of the NODAL signaling pathway have previously been implicated in the pathogenesis of human left-right (LR) patterning defects. Therefore, NODAL, a member of TGF-beta superfamily of developmental regulators, is a strong candidate to be functionally involved in congenital LR axis patterning defects or heterotaxy. Here we have investigated whether variants in NODAL are present in patients with heterotaxy and/or isolated cardiovascular malformations (CVM) thought to be caused by abnormal heart tube looping. Analysis of a large cohort of cases (n = 269) affected with either classic heterotaxy or looping CVM revealed four different missense variants, one in-frame insertion/deletion and two conserved splice site variants in 14 unrelated subjects (14/269, 5.2%). Although similar with regard to other associated defects, individuals with the NODAL mutations had a significantly higher occurrence of pulmonary valve atresia (P = 0.001) compared with cases without a detectable NODAL mutation. Functional analyses demonstrate that the missense variant forms of NODAL exhibit significant impairment of signaling as measured by decreased Cripto (TDGF-1) co-receptor-mediated activation of artificial reporters. Expression of these NODAL proteins also led to reduced induction of Smad2 phosphorylation and impaired Smad2 nuclear import. Taken together, these results support a role for mutations and rare deleterious variants in NODAL as a cause for sporadic human LR patterning defects. PMID:19064609

Mohapatra, Bhagyalaxmi; Casey, Brett; Li, Hua; Ho-Dawson, Trang; Smith, Liana; Fernbach, Susan D; Molinari, Laura; Niesh, Stephen R; Jefferies, John Lynn; Craigen, William J; Towbin, Jeffrey A; Belmont, John W; Ware, Stephanie M

2008-12-08

41

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

SciTech Connect

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

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

1984-10-01

42

Association of Genetic Variants with Isolated Fasting Hyperglycaemia and Isolated Postprandial Hyperglycaemia in a Han Chinese Population  

PubMed Central

Background Though multiple single nucleotide polymorphisms (SNPs) associated with type 2 diabetes have been identified, the genetic bases of isolated fasting hyperglycaemia (IFH) and isolated postprandial hyperglycaemia (IPH) were still unclear. In present study, we aimed to investigate the association of genome-wide association study-validated genetic variants and IFH or IPH in Han Chinese. Methods/Principal Findings We genotyped 27 validated SNPs in 6,663 unrelated individuals comprising 341 IFH, 865 IPH, 1,203 combined fasting hyperglycaemia and postprandial hyperglycaemia, and 4,254 normal glycaemic subjects of Han ancestry. The distributions of genotype frequencies of FTO, CDKAL1 and GCKR were significant different between individuals with IFH and those with IPH (SNP(ptrend): rs8050136(0.0024), rs9939609(0.0049), rs7756992(0.0122), rs780094(0.0037)). Risk allele of FTO specifically increased the risk of IFH (rs8050136: OR 1.403 [95% CI 1.125–1.750], p?=?0.0027; rs9939609: 1.398 [1.120–1.744], p?=?0.0030). G allele of CDKAL1 specifically increased the risk of IPH (1.217 [1.092–1.355], p?=?0.0004). G allele of GCKR increased the risk of IFH (1.167 [0.999–1.362], p?=?0.0513), but decreased the risk of IPH (0.891 [0.801–0.991], p?=?0.0331). In addition, TCF7L2 and KCNQ1 increased the risk of both IFH and IPH. When combined, each additional risk allele associated with IFH increased the risk for IFH by 1.246-fold (p<0.0001), while each additional risk allele associated with IPH increased the risk for IPH by 1.190-fold (p<0.0001). Conclusion/Significance Our results indicate that genotype distributions of variants from FTO, GCKR, CDKAL1 were different between IPH and IFH in Han Chinese. Variants of genes modulating insulin sensitivity (FTO, GCKR) contributed to the risk of IFH, while variants of genes related to beta cell function (CDKAL1) increase the risk of IPH.

Chen, Ying; Chen, Li; Zhao, Zhigang; Li, Qiang; Ge, Jiapu; Chen, Gang; Guo, Xiaohui; Lu, Juming; Weng, Jianping; Jia, Weiping; Ji, Linong; Xiao, Jianzhong; Shan, Zhongyan; Liu, Jie; Tian, Haoming; Ji, Qiuhe; Zhu, Dalong; Zhou, Zhiguang; Shan, Guangliang; Yang, Wenying

2013-01-01

43

Distribution of Allelic Variants of the Chromosomal Gene bla OXA-114-like in Achromobacter xylosoxidans Clinical Isolates.  

PubMed

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

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

2013-06-15

44

[Immunoloical aspects of the antropogenic response to the antigens of symbiotic non-toxigenic diphtherial corynebacteria].  

PubMed

Corynebacteria, being ancient symbionts of open cavities of human body, carry unique, balanced immunogenic stimuli, formed in the process of evolution, thus maintaining non-specific resistance at a certain level. They favor formation of human microcenotic communities as a normal biological and physiological phenomenon. Codivak, a preparation of natural antigens of a symbiotic strain of non-toxigenic diphtherial corynebacteria, is able to correct not only disturbances of oropharyngeal immunity, but also general cell-mediated and humoral immunity disorders. PMID:16496952

Shmeleva, E A; Popkova, S M; Makarova, S I; Baturina, I G

2006-01-01

45

Naturally occurring NS gene variants in an avian influenza virus isolate.  

PubMed

The A/Turkey/Wisconsin/68 (H5N9) isolate of avian influenza (AI) consists of two virus populations which have different NS genes and differ in their biological responses in chicken embryos. They were classified as being either rapidly embryo-lethal (REL) or slowly embryo-lethal (SEL), (Avian Dis., 33 (1989) 695-706). In this study, sequence analysis identified only two nucleotide differences between the two NS genes, creating single amino acid differences in both the NS1 and the NS2 protein. The difference in the NS1 protein appears to be neutral, while the differences in the NS2 places a phenylalanine at position 48. This amino acid has not been previously demonstrated at this position in an NS2 sequence and its presence results in a distinct hydrophobic shift in the region. The sequence specifying the phenylalanine also creates an EcoRI site in the cDNA of the REL NS gene. Analysis of several clones showed that this site appears to co-segregate with the REL characteristic. Molecular differences between the two NS gene variants were reflected by differences in the kinetics of early protein synthesis in infected cells. In particular, the NS2 protein is in higher concentration (relative to the NS1) in SEL-infected cells than in REL-infected cells. No differences were detectable, however, in the rates of viral replication, either in cell culture or in embryos. Also, the REL or SEL rate was established early during infection of the embryo and could not be competed out by the other variant population 3 h after inoculation. Thus, these two natural NS gene variants appear to specify early differences which influence the time of death of an infected embryo but the differences do not appear to influence virus replication. PMID:1320795

Perdue, M L

1992-05-01

46

Identification and characterization of porcine kobuvirus variant isolated from suckling piglet in gansu province, china.  

PubMed

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

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

2013-10-18

47

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

PubMed Central

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

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

2013-01-01

48

Population Turnover in a Microcystis Bloom Results in Predominantly Nontoxigenic Variants Late in the Season? †  

PubMed Central

Surface samples of the 2007 Microcystis bloom occurring in Copco Reservoir on the Klamath River in Northern California were analyzed genetically by sequencing clone libraries made with amplicons at three loci: the internal transcribed spacer of the rRNA operon (ITS), cpcBA, and mcyA. Samples were taken between June and October, during which time two cell count peaks occurred, in mid-July and early September. The ITS and cpcBA loci could be classified into four or five allele groups, which provided a convenient means for describing the Microcystis population and its changes over time. Each group was numerically dominated by a single, highly represented sequence. Other members of each group varied by changes at 1 to 3 nucleotide positions, while groups were separated by up to 30 nucleotide differences. As deduced by a partial sampling of the clone libraries, there were marked population turnovers during the season, indicated by changes in allele composition at both the ITS and cpcBA loci. Different ITS and cpcBA genotypes appeared to be dominant at the two population peaks. Toxicity (amount of microcystin per cell) and toxigenic potential (mcyB copy number) were lower during the second peak, and the mcyB copy number fell further as the bloom declined.

Bozarth, Connie S.; Schwartz, Andrew D.; Shepardson, Jonathan W.; Colwell, Frederick S.; Dreher, Theo W.

2010-01-01

49

Mechanistic variations among reverse transcriptases of simian immunodeficiency virus variants isolated from African green monkeys.  

PubMed

Here we report enzymatic variations among the reverse transcriptases (RTs) of five simian immunodeficiency virus (SIV) strains, Sab-1, 155-4, Gri-1, 9063-2, and Tan-1, which were isolated from four different species of naturally infected African green monkeys living in different regions across Africa. First, Sab-1 RT exhibits the most efficient dNTP incorporation efficiency at low dNTP concentrations, whereas the other four SIVagm RT proteins display different levels of reduced polymerase activity at low dNTP concentrations. Tan-1 RT exhibited the most restricted dNTP incorporation efficiency. Indeed, the pre-steady state analysis revealed that Sab-1 RT displays tight dNTP binding affinity (K(d) approximately 1-5 microM), comparable to values observed for NL4-3 and HXB2 HIV-1 RTs, whereas the dNTP binding affinity of Tan-1 RT is 6.2, approximately 34.8-fold lower than that of Sab-1 RT. Second, Tan-1 RT fidelity was significantly higher than that of Sab-1 RT. Indeed, Tan-1 RT enzymatically mimics oncoretroviral murine leukemia virus RT which is characterized by its low dNTP binding affinity and high fidelity. This study reports that simultaneous changes in dNTP binding affinity and fidelity of RTs appear to occur among natural SIV variants isolated from African green monkeys. PMID:19408961

Skasko, Mark; Diamond, Tracy L; Kim, Baek

2009-06-16

50

cagA gene variants in Malaysian Helicobacter pylori strains isolated from patients of different ethnic groups  

Microsoft Academic Search

Helicobacter pylori infection of a distinct subtype of cagA may lead to different pathological manifestation. The aim of this study is to determine the presence of cagA gene and its variants in H. pylori infection among different ethnic groups and its effect on gastroduodenal diseases. Overall detection of cagA among the 205 clinical isolates of H. pylori was 94%. Variations

Mohamed Ramelah; Ahmad Aminuddin; Hanafiah Alfizah; Mohd Rose Isa; Ali Yaakob Jasmi; Huck Joo Tan; A. Jamal A. Rahman; Abdul Manap Rizal; M. Zawawi Mazlam

2005-01-01

51

Isolated well-formed intestinal tissue in the umbilical cord. A variant of cyst of omphalomesenteric duct.  

PubMed

An extremely rare abnormality, a variant of omphalomesenteric duct, was observed in the umbilical cord 1 cm from the entry point into the abdominal wall, which itself was as an isolated mass of well-formed intestinal tissue free of structural defects. This intestinal tissue seems to be the remnant of an intestinal loop from caudal limb of midgut following physiological herniation during the third month of gestation. PMID:3728013

Iwasaki, I; Yu, T J; Itahashi, K; Nito, A; Yamaguchi, H; Onoki, J

1986-04-01

52

A molecular epidemiological investigation of isolates of the variant avian paramyxovirus type 1 virus (PPMV-1) responsible for the 1978 to present panzootic in pigeons  

Microsoft Academic Search

A sequence of 375 nucleotides, which included the region encoding the cleavage activation site and signal peptide of the fusion protein gene, was determined for 178 isolates of the pigeon variant strain of Newcastle disease virus (PPMV-1). These were compared with the sequences of 47 similar isolates published by GenBank, which included 30 isolates from pigeons and 17 representatives from

E. W. Aldous; C. M. Fuller; J. K. Mynn; D. J. Alexander

2004-01-01

53

Genetic relatedness of clinical and environmental Vibrio cholerae isolates based on triple housekeeping gene analysis.  

PubMed

Sequence analysis of dnaE, hlyA, and asd housekeeping genes were used to determine the genetic relatedness of our collection of Vibrio cholerae isolated from patients and surface waters over a 5-year period in Iran. The results showed 41, 17, and 9 variable sites throughout the sequenced fragments of dnaE (837 bp), hlyA (495 bp), and asd (295 bp), respectively. The results from sequence typing showed that all our clinical isolates were grouped in the same cluster. Eleven genotypes were identified among the environmental isolates. One environmental isolate was found to be in close genetic relatedness with our clinical isolates. One V. cholerae isolate showed a single-locus variant in the dnaE. For each of the studied genetic loci 10, 7, and 7 sequence types were observed for dnaE, hlyA, and asd, respectively. Only asd sequence analysis could make the distinction between the classical and El Tor isolates which emphasizes on selection of housekeeping locus with better discrimination power for analysis of different groups of isolates. Overall, the results indicated that surface waters in Tehran are a pool of non-toxigenic V. cholerae strains which are rarely related to clinical toxigenic isolates. In addition, our results verified that housekeeping gene sequence analysis could be a suitable approach for determination of the relatedness between clinical and environmental V. cholerae isolates. PMID:23397220

Dashtbani-Roozbehani, Abolfazl; Bakhshi, Bita; Pourshafie, Mohammad Reza

2013-02-09

54

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

PubMed Central

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.

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

55

Isolation and Partial Characterization of Lactate Dehydrogenase Isozymes from Normal and Variant Rainbow Trout Livers.  

National Technical Information Service (NTIS)

The homotetrameric lactate dehydrogenase (LDH) isozymes, B2 prime and B2 double prime, from normal and variant rainbow trout livers have been purified to homogeneity by affinity chromatography using a Sepharose-linked oxamate ligand. The two isozymes have...

Y. H. J. Kao

1977-01-01

56

Isolation and characterization of Chinese hamster ovary cell variants deficient in the expression of fibronectin receptor.  

PubMed

Chinese hamster ovary cell populations were enriched for cells displaying low surface expression of the 140-kD integrin fibronectin receptor (FnR) by means of fluorescence-activated cell sorting using monoclonal anti-FnR antibodies. Selected cells were cloned by limiting dilution, and the resulting clones were screened for low cell surface FnR expression by ELISA. Two multiply sorted populations gave rise to variant clones possessing approximately 20 or 2% FnR expression, respectively, compared with wild-type cells. Growth rates of the "20%" and "2%" clones on serum-coated plastic dishes were similar to that of wild-type cells. Variant cells expressing 20% FnR could attach and spread on substrata coated with purified fibronectin, although somewhat more slowly than wild-type cells, while cells expressing 2% FnR could not attach or spread. Cells from all variant clones attached normally to vitronectin substrata, but some of the 2% clones displayed altered morphology on this type of substratum. Motility assays in blind well chambers showed a correlation of movement with level of expression of FnR. The number of cells migrating in response to fibronectin was greatly reduced compared with wild-type cells for the 20% FnR variant clones, while variant clones with 2% FnR showed virtually no migratory activity. Surface labeling with 125I and immunoaffinity purification of FnR showed reduced levels of intact FnR on the plasma membranes of variants with 20% FnR, while none was detected in variants expressing 2% FnR. Nevertheless, beta subunits were detected on the surfaces of all variant clones. Immunoblots of cell lysates from wild-type cells and from both types of variant clones showed substantial amounts of FnR beta chain as well as enhanced amounts of a pre-beta moiety in the variants. alpha chain was markedly reduced in the 20% variants and essentially absent in the 2% variants, indicating that failure to assemble intact FnR in these variants was due to deficiencies of alpha chain production. Dot blots of total mRNA from a representative clone expressing 20% FnR showed reduced levels of material hybridizing to an 0.97-kb hamster FnR alpha chain cDNA probe as compared with wild type, while mRNA from a representative clone expressing 2% FnR had no detectable hybridizable RNA; this seems to agree well with the results obtained by immunoblotting. Thus, the defect in the variant clones seems to be due to reduced levels of alpha chain mRNA leading to a deficit of mature FnR and consequent alterations in cell adhesion and motility on fibronectin substrata. PMID:2531750

Schreiner, C L; Bauer, J S; Danilov, Y N; Hussein, S; Sczekan, M M; Juliano, R L

1989-12-01

57

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

PubMed Central

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

Liao, H; McKenzie, T; Hageman, R

1986-01-01

58

Biochemical classification of Clostridium botulinum type C and D strains and their nontoxigenic derivatives.  

PubMed

The biochemical properties of 11 toxigenic and 10 nontoxigenic type C and D strains of Clostridium botulinum were studied. All of the strains examined were motile and hemolytic and produced lipase and liquid gelatin. Fermentation of several sugars and the production of lecithinase, indole, and hydrogen sulfide varied with the strain. The strains were classified into four groups based on their sugar fermentation profiles. The resulting classification was identical to the classification which had been proposed from the relationship between toxin production and phages and similar to the grouping based on the nature of toxin antigenic structures. Lecithinase production was negative in the cells belonging to group III, and indole and hydrogen sulfide production was negative in the cells of groups III and IV. Strains belonging to groups III and IV have many characteristics different from those of groups I and II. PMID:3513703

Oguma, K; Yamaguchi, T; Sudou, K; Yokosawa, N; Fujikawa, Y

1986-02-01

59

Isolation and preliminary characterization of erythromycin-resistant variants of Legionella micdadei and Legionella pneumophila.  

PubMed Central

Erythromycin-resistant Legionella spp. variants were obtained by a single passage of the naturally occurring bacteria on medium containing various concentrations of erythromycin. By disk diffusion susceptibility testing, at least three different phenotypic patterns of cross-resistance to macrolide, lincosamide, and streptogramin B antibiotics were observed among the 26 erythromycin-resistant strains examined.

Dowling, J N; McDevitt, D A; Pasculle, A W

1985-01-01

60

Complete Genome Sequence of a Variant Porcine Epidemic Diarrhea Virus Strain Isolated in Central China  

PubMed Central

We report here the complete genome sequence of the porcine epidemic diarrhea virus strain CH/ZMDZY/11 isolated from central China. Our data, together with sequence data of porcine epidemic diarrhea virus (PEDV) isolates from other parts in China, will help to understand better the epidemiology and genetic diversity of PEDV field isolates in China.

Wang, Xiao-Meng; Niu, Bei-Bei; Yan, He; Gao, Dong-Sheng; Huo, Jin-Yao; Chen, Lu; Chang, Hong-Tao; Wang, Chuan-qing

2013-01-01

61

Complete genome sequence of a variant porcine epidemic diarrhea virus strain isolated in central china.  

PubMed

We report here the complete genome sequence of the porcine epidemic diarrhea virus strain CH/ZMDZY/11 isolated from central China. Our data, together with sequence data of porcine epidemic diarrhea virus (PEDV) isolates from other parts in China, will help to understand better the epidemiology and genetic diversity of PEDV field isolates in China. PMID:23469356

Wang, Xiao-Meng; Niu, Bei-Bei; Yan, He; Gao, Dong-Sheng; Huo, Jin-Yao; Chen, Lu; Chang, Hong-Tao; Wang, Chuan-Qing; Zhao, Jun

2013-02-21

62

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

Microsoft Academic Search

Tetralogy of Fallot (TOF), the most common severe congenital heart malformation, occurs sporadically, without other anomaly, and from unknown cause in 70% of cases. Through a genome-wide survey of 114 subjects with TOF and their unaffected parents, we identified 11 de novo copy number variants (CNVs) that were absent or extremely rare (o0.1%) in 2,265 controls. We then examined a

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

2009-01-01

63

Characterization of a Variant of Human T-Lymphotropic Virus Type I Isolated from a Healthy Member of a Remote, Recently Contacted Group in Papua New Guinea  

Microsoft Academic Search

We report the characterization of a variant of human T-lymphotropic virus type I (HTLV-I) isolated from an interleukin 2-dependent, CD8^+ T-cell line derived from peripheral blood mononuclear cells of a healthy member of a remote, recently contacted hunter-horticulturalist group (Hagahai) in Madang province of Papua New Guinea. Antigenic characterization of this variant, designated PNG-1, by immunofluorescence, indicated no expression of

Richard Yanagihara; Vivek R. Nerurkar; Ralph M. Garruto; Mark A. Miller; Marta E. Leon-Monzon; Carol L. Jenkins; Raymond C. Sanders; Pawel P. Liberski; Michael P. Alpers; D. Carleton Gajdusek

1991-01-01

64

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

PubMed Central

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

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

2002-01-01

65

Necrobacillosis resulting in isolated carotid thrombosis and massive stroke: A unique Lemierre variant?  

Microsoft Academic Search

We describe a healthy, young adult male patient who developed isolated carotid artery thrombosis and occlusion following acute pharyngitis due to Fusobacterium necrophorum. We believe this is the first case of isolated occlusion of internal carotid artery (ICA) with F.necrophorum without associated internal jugular vein (IJV) thrombosis. Lemierre's syndrome (LS) is characterized by a history of recent oropharyngeal infection in

Munish Kumar Goyal; Gyanendra Kumar; Robert Burger

2009-01-01

66

Molecular characterization of seven Chinese isolates of infectious bursal disease virus: classical, very virulent, and variant strains.  

PubMed

Seven infectious bursal disease virus (IBDV) strains isolated from China have been characterized in this study, including a classical strain CJ801, an attenuated strain GZ911, a variant strain GZ902, and four very virulent strains G9201, G9302, F9502, and HK46. With the use of reverse transcription-polymerase chain reaction, the full-length VP2 genes were amplified and the hypervariable regions were sequenced. Protein sequences of the hypervariable region (a.a. 143-382) of the field isolates confirmed their identities. CJ801 has the highest identity to the classical strains STC and 52/70. GZ902 has the highest identity to the American variant strains A, E, and GLS, and they share unique amino acid residue at positions 249K and 254S, which are not present in standard serotype 1 strains. Attenuated strain GZ911, like other cell culture-adapted strains, has substitutions at positions 279(D to N) and 284 (A to T) as well as in the serine-rich heptapeptide region. Hence, these substitutions may take an important role in the reduced virulence of these strains. The four very virulent strains have the highest identity to the European very virulent strain UK661 and Japanese strain OKYM. These strains share unique amino acid residues at positions 222A, 256I, and 294I, which are not present in other less virulent strains. The very virulent strains isolated in Guangdong (G9201, G9303) and Fujian (F9502) Provinces have one to five amino acid substitutions at the two hydrophilic domains of VP2 comparing with UK661 and OKYM, indicating that new very virulent strains are evolving. Phylogenetic analysis suggests that Chinese very virulent IBDVs and European very virulent strains are derived from similar origin. PMID:9645325

Cao, Y C; Yeung, W S; Law, M; Bi, Y Z; Leung, F C; Lim, B L

67

Identification of the Genetic Basis for Clinical Menadione-Auxotrophic Small-Colony Variant Isolates of Staphylococcus aureus?  

PubMed Central

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

Lannergard, Jonas; von Eiff, Christof; Sander, Gunnar; Cordes, Tina; Seggewi?, Jochen; Peters, Georg; Proctor, Richard A.; Becker, Karsten; Hughes, Diarmaid

2008-01-01

68

Isolation and characterization of mouse testis specific serine/threonine kinase 5 possessing four alternatively spliced variants.  

PubMed

Phosphorylation on serine/threonine or tyrosine residues of target proteins is an essential and significant regulatory mechanism in signal transduction during many cellular and life processes, including spermatogenesis, oogenesis and fertilization. In the present work, we reported the isolation and characterization of mouse testis-specific serine/threonine kinase 5 (Tssk5), which contains four alternatively spliced variants including, Tssk5alpha, Tssk5beta, Tssk5gamma and Tssk5delta. Moreover, the locus of Tssk5 is on chromosome 14qC3 and the four variants had a similar high expression in the testis and the heart; however, had a low expression in other tissues, except for Tssk5alpha which also had comparably high expression in the spleen. Each variant of Tssk5 expression began in the testis 16 days after birth. Aside from TSSK5alpha, the other isoforms have an insertion of ten amino acid residues (RLTPSLSAAG) in region VIb (HRD domain) (His-Arg-Asp). Moreover, only TSSK5alpha exhibited kinase activity and consistently, a further Luciferase Reporter Assay demonstrated that TSSK5beta, TSSK5gamma and TSSK5delta cannot be stimulated at the CREB/CRE responsive pathway in cmparison to TSSK5alpha. These findings suggest that TSSK5beta, TSSK5gamma, TSSK5delta may be pseudokinases due to the insertion, which may damage the structure responsible for active kinase activity. Pull-down assay experiments indicated that TSSK5beta, TSSK5gamma and TSSK5delta can directly interact with TSSK5alpha. In summary, these four isoforms with similar expression patterns may be involved in spermatogenesis through a coordinative way in testis. PMID:17927909

Wei, Youheng; Fu, Guolong; Hu, Hairong; Lin, Gang; Yang, Jingchun; Guo, Jinhu; Zhu, Qiquan; Yu, Long

2007-09-30

69

CCR5, GPR15, and CXCR6 are major coreceptors of human immunodeficiency virus type 2 variants isolated from individuals with and without plasma viremia.  

PubMed

Human immunodeficiency virus type 2 (HIV-2) is generally considered capable of using a broad range of coreceptors. Since HIV-2 variants from individuals with nonprogressive infection were not studied previously, the possibility that broad coreceptor usage is a property of variants associated with progressive infection could not be excluded. To test this, we determined the coreceptor usage of 43 HIV-2 variants isolated from six long-term-infected individuals with undetectable plasma viremia. Using GHOST indicator cells, we showed for the first time that the only coreceptors efficiently used by low-pathogenic HIV-2 variants are CCR5, GPR15 (BOB), and CXCR6 (BONZO). Surprisingly, control HIV-2 variants (n = 45) isolated from seven viremic individuals also mainly used these three coreceptors, whereas use of CCR1, CCR2b, or CCR3 was rare. Nearly a quarter of all HIV-2 variants tested could infect the parental GHOST cells, which could be partially explained by CXCR4 usage. Use of CXCR4 was observed only for HIV-2 variants from viremic individuals. Thirty-eight variants from aviremic and viremic HIV-2-infected individuals were additionally tested in U87 cells. All except one were capable of infecting the parental U87 cells, often with high efficiency. When virus production in parental cells was regarded as background in the coreceptor-transduced cell lines, the results in U87 cells were largely in agreement with the findings in GHOST cells. HIV-2 isolates from aviremic individuals commonly use as coreceptors CCR5, GPR15, and CXCR6, as well as an unidentified receptor expressed by U87 cells. Broad coreceptor usage, therefore, does not appear to be associated with pathogenicity of HIV-2. PMID:15650194

Blaak, H; Boers, P H M; Gruters, R A; Schuitemaker, H; van der Ende, M E; Osterhaus, A D M E

2005-02-01

70

CCR5, GPR15, and CXCR6 Are Major Coreceptors of Human Immunodeficiency Virus Type 2 Variants Isolated from Individuals with and without Plasma Viremia  

PubMed Central

Human immunodeficiency virus type 2 (HIV-2) is generally considered capable of using a broad range of coreceptors. Since HIV-2 variants from individuals with nonprogressive infection were not studied previously, the possibility that broad coreceptor usage is a property of variants associated with progressive infection could not be excluded. To test this, we determined the coreceptor usage of 43 HIV-2 variants isolated from six long-term-infected individuals with undetectable plasma viremia. Using GHOST indicator cells, we showed for the first time that the only coreceptors efficiently used by low-pathogenic HIV-2 variants are CCR5, GPR15 (BOB), and CXCR6 (BONZO). Surprisingly, control HIV-2 variants (n = 45) isolated from seven viremic individuals also mainly used these three coreceptors, whereas use of CCR1, CCR2b, or CCR3 was rare. Nearly a quarter of all HIV-2 variants tested could infect the parental GHOST cells, which could be partially explained by CXCR4 usage. Use of CXCR4 was observed only for HIV-2 variants from viremic individuals. Thirty-eight variants from aviremic and viremic HIV-2-infected individuals were additionally tested in U87 cells. All except one were capable of infecting the parental U87 cells, often with high efficiency. When virus production in parental cells was regarded as background in the coreceptor-transduced cell lines, the results in U87 cells were largely in agreement with the findings in GHOST cells. HIV-2 isolates from aviremic individuals commonly use as coreceptors CCR5, GPR15, and CXCR6, as well as an unidentified receptor expressed by U87 cells. Broad coreceptor usage, therefore, does not appear to be associated with pathogenicity of HIV-2.

Blaak, H.; Boers, P. H. M.; Gruters, R. A.; Schuitemaker, H.; van der Ende, M. E.; Osterhaus, A. D. M. E.

2005-01-01

71

Characterization of herpes simplex virus clinical isolate Y3369 as a glycoprotein G variant and its bearing on virus typing  

PubMed Central

Background Herpes simplex viruses exist as two major serotypes, type 1 (HSV-1) and type 2 (HSV-2). Determination of type, either HSV-1 or HSV-2, is important in accurate diagnosis and clinical control of transmission. Several tests are available for typing HSV, including a monoclonal antibody specific for glycoprotein G and several PCR assays. Findings A clinical isolate was identified as herpes simplex virus, but tested negative for both HSV-1 and HSV-2 antigens using type-specific monoclonal antibody assays. The isolate was determined to be HSV-1 by PCR analysis. A mutation which likely caused the monoclonal antibody non-reactivity was found in glycoprotein G. Phylogenetic analysis revealed two groups of HSV, one with the mutation and one without. Three population studies examining mutations in HSV-1 glycoprotein G were analyzed by chi-squared test. To this point, the epitope which the monoclonal antibody recognizes was only found in HSV-1 isolates from human European populations (p < 0.0001). Conclusions These findings suggest that the PCR-based methods for HSV typing may be more useful than the standard monoclonal antibody test in areas of the world where the variant in glycoprotein G is more prevalent.

2011-01-01

72

Characterization of Small-Colony-Variant Stenotrophomonas maltophilia Isolated from the Sputum Specimens of Five Patients with Cystic Fibrosis?  

PubMed Central

Cystic fibrosis (CF) patients are predisposed to chronic respiratory infection by nonfermentative gram-negative bacilli, including Stenotrophomonas maltophilia. S. maltophilia is highly resistant to most antibiotics, with the exception of sulfamethoxazole-trimethoprim (SXT). SXT-resistant S. maltophilia has been reported, but the mechanism of resistance is not well defined. Repeated findings of suspected small-colony-variant (SCV) S. maltophilia isolates from the sputa of five CF patients were confirmed by partial 16S rRNA gene sequencing. The SCV S. maltophilia isolates were the only S. maltophilia isolates in these cultures, and none were clonally related. DNA fingerprint analysis confirmed that once established, the SCV S. maltophilia strains persisted. Nutritional studies of SCV S. maltophilia have suggested auxotrophy in hemin, methionine, and thymidine associated with resistance to multiple antibiotics, including SXT. The phenotypic switch from wild-type to SCV S. maltophilia was reproducible in vitro by exposure to SXT, suggesting that prolonged exposure to antibiotics may select for both the SCV S. maltophilia phenotype and SXT resistance by interference with the dihydrofolate reductase pathway. Recovery of SCV S. maltophilia from the sputum of CF patients has implications for both laboratory testing and patient management.

Anderson, Scott W.; Stapp, Jennifer R.; Burns, Jane L.; Qin, Xuan

2007-01-01

73

Isolated granulomatous renal arteritis: a variant form of giant cell arteritis with few macrophages.  

PubMed

A 64-year-old woman with hypertension and hyperlipidemia was admitted to our hospital for the investigation and management of general fatigue, anorexia, a 5-kg weight loss, and a 4-week history of high-grade fever. She had no symptoms of headache, myalgia, or arthralgia, and the physical examination was unremarkable. The laboratory tests revealed renal dysfunction with urine abnormalities that had not been observed 1 year earlier. A renal biopsy showed granulomatous small arteritis without necrotic lesions or glomerular pathology. An immunohistochemical study of the infiltrating leukocytes showed a predominance of CD4+ T cells followed by CD8+ T cells, and only a few macrophages. The condition drastically improved after treatment with 30 mg/day of oral prednisolone. The granulomatous renal arteritis was considered a variant of giant cell arteritis, because it showed the peculiar finding of a few macrophages in the granulomatous lesions. PMID:20075589

Watanabe, Ryu; Nakaya, Izaya; Kudo, Hiroki; Yahata, Mayumi; Sakuma, Tsutomu; Soma, Jun

2010-01-15

74

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

PubMed

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

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

2011-08-12

75

Effect of Light Intensity on the Relative Dominance of Toxigenic and Nontoxigenic Strains of Microcystis aeruginosa ?  

PubMed Central

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

LeBlanc Renaud, Susan; Pick, Frances R.; Fortin, Nathalie

2011-01-01

76

Genome Sequences of Listeria monocytogenes Serotype 4b Variant Strains Isolated from Clinical and Environmental Sources.  

PubMed

Listeria monocytogenes strains that show a novel PCR serotyping profile (IVb-v1) have been reported recently. Here, we announce the draft genome sequences of five L. monocytogenes IVb-v1 strains isolated from the United States and Australia that harbor a 6.3-kb DNA cassette characteristic of serotype 1/2a strains. PMID:24136844

Laksanalamai, Pongpan; Steyert, Susan R; Burall, Laurel S; Datta, Atin R

2013-10-17

77

Genome Sequences of Listeria monocytogenes Serotype 4b Variant Strains Isolated from Clinical and Environmental Sources  

PubMed Central

Listeria monocytogenes strains that show a novel PCR serotyping profile (IVb-v1) have been reported recently. Here, we announce the draft genome sequences of five L. monocytogenes IVb-v1 strains isolated from the United States and Australia that harbor a 6.3-kb DNA cassette characteristic of serotype 1/2a strains.

Laksanalamai, Pongpan; Steyert, Susan R.; Burall, Laurel S.

2013-01-01

78

Complete genome sequence of a variant porcine epidemic diarrhea virus strain isolated in China.  

PubMed

Since October 2010, an outbreak of porcine epidemic diarrhea (PED) has been observed in some provinces of China. Here we report the complete genome sequence of porcine epidemic diarrhea virus (PEDV) strain LC, which was recently isolated from sucking piglets that suffered from severe watery diarrhea in Guangdong. It will help in understanding the epidemiological and molecular characteristics of PEDV in China. PMID:23087112

Chen, Feng; Pan, Yongfei; Zhang, Xiangbin; Tian, Xiaoyan; Wang, Dongdong; Zhou, Qingfeng; Song, Yanhua; Bi, Yingzuo

2012-11-01

79

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

PubMed

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

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

2012-05-12

80

Isolation of a variant infectious bronchitis virus in Australia that further illustrates diversity among emerging strains  

Microsoft Academic Search

Summary.  Australian infectious bronchitis viruses (IBV) have undergone a separate evolution due to geographic isolation. Consequently,\\u000a changes occurring in Australian IBV illustrate, independently from other countries, types of variability that could occur\\u000a in emerging IBV strains. Previously, we have identified two distinct genetic groups of IBV, designated subgroups 1 and 2.\\u000a IBV strains of subgroup 1 have S1 and N proteins

J. Ignjatovic; G. Gould; S. Sapats

2006-01-01

81

Rat nicastrin gene: cDNA isolation, mRNA variants and expression pattern analysis  

Microsoft Academic Search

Nicastrin is a type 1 transmembrane glycoprotein that interacts with presenilin, Aph-1, and Pen-2 proteins to form a high molecular complex with gamma secretase activity. Then, nicastrin has a central role in presenilin-mediated processing of beta-amyloid precursor protein and in some aspects of Notch\\/glp-1 signaling in vivo. Here, we isolated a rat nicastrin cDNA and investigated gene expression in embryonic

Annamaria Confaloni; Alessio Crestini; Diego Albani; Paola Piscopo; Lorenzo Malvezzi Campeggi; Liana Terreni; Marco Tartaglia; Gianluigi Forloni

2005-01-01

82

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

Microsoft Academic Search

BackgroundCongenital malformations involving the Müllerian ducts are observed in around 5% of infertile women. Complete aplasia of the uterus, cervix, and upper vagina, also termed Müllerian aplasia or Mayer–Rokitansky–Kuster–Hauser (MRKH) syndrome, occurs with an incidence of around 1 in 4500 female births, and occurs in both isolated and syndromic forms. Previous reports have suggested that a proportion of cases, especially

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

2011-01-01

83

A NEW GENETIC VARIANT OF LA CROSSE VIRUS (BUNYAVIRIDAE) ISOLATED FROM NEW ENGLAND  

Microsoft Academic Search

Abstract. La Crosse virus (LACV) is found,primarily in the Midwestern,and,Appalachian regions of the United States where,it is a leading cause of mosquito-borne,encephalitis in children. To determine,whether,the distribution of this virus extends further east into New England, we analyzed a bunyavirus that was isolated from a pool of eastern tree-hole mosquitoes, Ochlerotatus triseriatus ( Aedes triseriatus), collected from Fairfield, Connecticut (CT)

Philip M. Armstrong; Theodore G. Andreadis

84

New Variant of CTX-M-Type Extended-Spectrum ?-Lactamases, CTX-M-71, with a Gly238Cys Substitution in a Klebsiella pneumoniae Isolate from Bulgaria?  

PubMed Central

A single Klebsiella pneumoniae strain isolated in a Bulgarian hospital was found to produce CTX-M-71, a new CTX-M variant characterized by one amino acid substitution from glycine to cysteine at position 238 in comparison to CTX-M-15. This exchange decreased the hydrolytic activity of the ?-lactamase for cefotaxime, ceftazidime, and cefepime.

Schneider, Ines; Queenan, Anne Marie; Markovska, Rumyana; Markova, Boyka; Keuleyan, Emma; Bauernfeind, Adolf

2009-01-01

85

Three antigenic variant groups in human respiratory syncytial virus subgroup B isolated in Japan.  

PubMed

Nineteen hybridomas producing monoclonal antibodies (MAbs) against the structural proteins of strain 58-17, a subgroup B field strain of respiratory syncytial virus (RSV) isolated in Japan, were obtained by fusion of X63 myeloma cells with spleen cells from BALB/c mice immunized with the virus-infected HEp-2 cells. Seven clones were found to produce antibodies against the fusion protein (F), five against the large glycoprotein (G), five against the nucleoprotein (NP) and two against the 22k protein by radioimmunoprecipitation assay. By competitive binding assay with the MAbs, at least seven, two, three and one epitopes were defined on the F, G, NP and 22k protein components of subgroup B strain, respectively. Of these epitopes, three, two and one epitopes on the F, G and NP components were different from subgroup A strain, respectively. Fifty-three other field strains of subgroup B isolated in Sapporo, Japan, during nine epidemic years from 1980 to 1989, were examined for reactivity with the MAbs by ELISA. Different reactivity to one anti-NP antibody suggested that the 53 strains can be divided into three groups (B-a: 26 strains, B-b: 26 strains, and one other strain). The dominant strain prevailing during the 1984 to 1988 epidemic years had changed from B-a to B-b. All of the 53 subgroup B strains reacted similarly with the other 18 MAbs. PMID:7678192

Nagai, K; Tsutsumi, H; Yamazaki, H; Pattamadilok, S; Chiba, S

1993-01-01

86

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

PubMed

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

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

2009-02-19

87

Contrasting Use of CCR5 Structural Determinants by R5 and R5X4 Variants within a Human Immunodeficiency Virus Type 1 Primary Isolate Quasispecies  

PubMed Central

Macrophagetropic R5 human immunodeficiency virus type 1 (HIV-1) isolates often evolve into dualtropic R5X4 variants during disease progression. The structural basis for CCR5 coreceptor function has been studied in a limited number of prototype strains and suggests that R5 and R5X4 Envs interact differently with CCR5. However, differences between unrelated viruses may reflect strain-specific factors and do not necessarily represent changes resulting from R5 to R5X4 evolution of a virus in vivo. Here we addressed CCR5 domains involved in fusion for a large set of closely related yet functionally distinct variants within a primary isolate swarm, employing R5 and R5X4 Envs derived from the HIV-1 89.6PI quasispecies. R5 variants of 89.6PI could fuse using either N-terminal or extracellular loop CCR5 sequences in the context of CCR5/CXCR2 chimeras, similar to the unrelated R5 strain JRFL, but R5X4 variants of 89.6PI were highly dependent on the CCR5 N terminus. Similarly, R5 89.6PI variants and isolate JRFL tolerated N-terminal CCR5 deletions, but fusion by most R5X4 variants was markedly impaired. R5 89.6PI Envs also tolerated multiple extracellular domain substitutions, while R5X4 variants did not. In contrast to CCR5 use, fusion by R5X4 variants of 89.6PI was largely independent of the CXCR4 N-terminal region. Thus, R5 and R5X4 species from a single swarm differ in how they interact with CCR5. These results suggest that R5 Envs possess a highly plastic capacity to interact with multiple CCR5 regions and support the concept that viral evolution in vivo results from the emergence of R5X4 variants with the capacity to use the CXCR4 extracellular loops but demonstrate less-flexible interactions with CCR5 that are strongly dependent on the N-terminal region.

Yi, Yanjie; Singh, Anjali; Shaheen, Farida; Louden, Andrew; Lee, ChuHee; Collman, Ronald G.

2003-01-01

88

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

PubMed Central

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

Sara, M; Pum, D; Kupcu, S; Messner, P; Sleytr, U B

1994-01-01

89

Common Variant in Myocilin Gene Is Associated with High Myopia in Isolated Population of Kor?ula Island, Croatia  

PubMed Central

Aim To study the association between genetic variants in myocilin and collagen type I alpha 1 genes and high myopia in an isolated island population. Methods A total of 944 examinees from the genetic epidemiology study conducted on the island of Kor?ula, Croatia, were included in the study. We selected 2 short nucleotide polymorphisms (SNP) available in our genome-wide scan set of SNPs that were previously associated with high myopia and used them to replicate previous claims of possible association. Results Nineteen cases of high myopia, defined as the refraction of ?-6.00 diopters, were identified and included in the analysis. We showed that rs2075555 in the COL1A1 gene was not associated with high myopia. In contrast, rs2421853 in the myocilin gene was significantly associated in both bivariate (P?=?0.006) and age- and sex-adjusted analysis (P?=?0.049). Conclusion Myocilin seems to be a very strong candidate for explaining some of the pathophysiological pathways leading to the development of both glaucoma and high myopia. As our finding was obtained in a relatively under-powered sample, further research and replication of these results is needed.

Vatavuk, Zoran; Skunca Herman, Jelena; Bencic, Goran; Andrijevic Derk, Biljana; Lacmanovic Loncar, Valentina; Petric Vickovic, Ivanka; Bucan, Kajo; Mandic, Kresimir; Mandic, Antonija; Skegro, Ivan; Pavicic Astalos, Jasna; Merc, Ivana; Martinovic, Miljenka; Kralj, Petra; Knezevic, Tamara; Barac-Juretic, Katja; Zgaga, Lina

2009-01-01

90

Influenza H3N2 variant viruses with pandemic potential: Preventing catastrophe in remote and isolated Canadian communities.  

PubMed

OBJECTIVE: To evaluate the impact of age-specific cross-reactive antibody protection levels on the outcomes of a pandemic outbreak of new variants of H3N2 influenza A viruses (H3N2v). METHODS: We calibrated a previously validated agent-based model of human-to-human transmission of influenza viruses to project the outcomes of various protection levels in a remote and isolated Canadian community, when demographics are drawn from the Statistics Canada census data. We then compared the outcomes with a scenario in which demographic variables were shifted to resemble an urban structure. This comparative evaluation was conducted using in-silico computer simulations, where the epidemiological data were drawn from relevant estimates in published literature. RESULTS: Simulations, using estimates of transmissibility for the 2009 H1N1 pandemic strain in the study population, show that the epidemic size is primarily affected by the cross-reactive protection levels of young children. A lower number of secondary infections at the early stages of an outbreak does not necessarily correspond to a lower epidemic size. CONCLUSIONS: Demographic variables could play a significant role in determining the outcomes of an outbreak. The findings strongly suggest that, when an H3N2v-specific vaccine becomes available, children below the age of 17 should be prioritized for vaccination. This prioritization is essential in population settings with a low average age, including aboriginal communities in northern latitudes. PMID:23628518

Laskowski, Marek; Duvvuri, Venkata R; Buckeridge, David L; Wu, Gillian; Wu, Jianhong; Moghadas, Seyed M

2013-04-28

91

Rapid Enzyme Immunoassay for Determination of Toxigenicity among Clinical Isolates of Corynebacteria  

PubMed Central

A rapid enzyme immunoassay (EIA) was developed for the phenotypic detection of diphtheria toxin among clinical isolates of corynebacteria. The assay uses equine polyclonal antitoxin as the capture antibody and an alkaline phosphatase-labeled monoclonal antibody, specific for fragment A of the toxin molecule, as the detecting antibody. The assay is rapid, sensitive, and specific: a final result is available within 3 h of colony selection, and the limits of detection are 0.1 ng of pure diphtheria toxin/ml. Toxigenicity could be detected with isolates grown on a diverse range of culture media, including selective agars. Toxin detection using the EIA was compared to that with the Elek test and PCR detection of fragment A of the diphtheria toxin (tox) gene, using 245 isolates of corynebacteria. The results for the EIA were in complete concordance with those of the Elek test: 87 toxigenic and 158 nontoxigenic isolates. Ten of the phenotypically nontoxigenic strains were found to contain fragment A of the tox gene but did not express the toxin protein. These isolates were found to be nontoxigenic in the Vero cell tissue culture cytotoxicity assay and were therefore nontoxigenic for diagnostic purposes. The EIA is a simple rapid phenotypic test which provides a definitive result on toxigenicity within one working day.

Engler, Kathryn H.; Efstratiou, Androulla

2000-01-01

92

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

PubMed

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

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

2006-02-10

93

Isolation and pathogenic characterization of an OB1 variant of Babesia rodhaini which has a glycophorin A-independent pathway to murine red blood cells.  

PubMed

Recent studies using several Babesia spp. have demonstrated that these species commonly recognize host sialic acids of red blood cells (RBCs) for their invasion. Glycophorin A (GPA), which is a major carrier of the sialic acids on RBCs, is a possible invasive receptor for Babesia parasites. In the present study, a variant of Babesia rodhaini was successfully isolated from a GPA homozygous knockout (GPA(-/-)) mouse infected with an Australian strain of B. rodhaini which had originally been unable to replicate in GPA(-/-) mice. The isolated parasite (designated as an OB1 variant) caused lethal infection to wild-type mice, as in the case of the parent Australian strain. However, although the growth of the OB1 variant in GPA(-/-) mice was comparable with that in wild-type mice at 1-4 days after infection, the growth was significantly inhibited from day 5 onward, leading to the eventual survival of the GPA(-/-) mice. Resistance of GPA(-/-) mice against OB1 infection was lost by splenectomy, although the cytokine responses to the infection in the sera of GPA(-/-) mice were similar to those of wild-type mice. The autoantibody levels to GPA-defective RBCs in the sera of GPA(-/-) mice were depressed at a lower level at 0-2 days after infection than those of wild-type mice, while the levels of GPA(-/-) mice progressively increased and reached comparable levels to those of wild-type mice at day 3 or later. These results indicate that the isolated OB1 variant has a GPA-independent invasion pathway into murine RBCs and suggest that the resistance of GPA(-/-) mice against infection with the OB1 variant may be attributed to the effective clearance of the parasitized RBCs lacking GPA in the spleen, possibly mediated by preferential autoantibody binding to the RBC membrane. PMID:19084340

Takabatake, Noriyuki; Iseki, Hiroshi; Ikehara, Yuzuru; Kanuka, Hirotaka; Yokoyama, Naoaki; Sekimizu, Kazuhisa; Igarashi, Ikuo

2008-10-15

94

Common MFRP sequence variants are not associated with moderate to high hyperopia, isolated microphthalmia, and high myopia  

PubMed Central

Purpose The membrane-type frizzled-related protein (MFRP) gene is selectively expressed in the retinal pigment epithelium and ciliary body, and mutations of this gene cause nanophthalmos. The MFRP gene may not be essential for retinal function but has been hypothesized to play a role in ocular axial length regulation. The involvement of the MFRP gene in moderate to high hyperopic, isolated microphthalmic/anophthalmic, and high myopic patients was tested in two phases: a mutation screening/sequence variant discovery phase and a genetic association study phase. Methods Eleven hyperopic, ten microphthalmic/anophthalmic, and seven non-syndromic high-grade myopic patients of varying ages and 11 control subjects participated in the mutation screening phase. Sixteen primer pairs were designed to amplify the 13 exons of the MFRP gene including intron/exon boundaries. Polymerase chain reactions were performed, and amplified products were sequenced using standard techniques. Normal and affected individual DNA sequences were compared alongside the known reference sequence (UCSC genome browser) for the MFRP gene. The genetic association study included 146 multiplex non-syndromic high-grade myopia families. Seventeen intragenic and flanking single nucleotide polymorphisms (SNPs) were chosen for the MFRP gene and genotyped in the large data set using the Taqman® allelic discrimination assay. The family-based association Pedigree Disequilibrium Test (PDT) and GenoPDT were performed. Results The average spherical refractive error of the hyperopic patient cohort was +4.21 diopters (D; range +2.00 to +9.25 D) and of the myopic patient cohort was ?12.36 D (range ?8.25 to ?14.50 D). A total of 16 SNPs were identified by direct sequencing. No significant association was determined between the 16 MFRP gene SNPs and the moderate to high hyperopia, microphthalmia/anophthalmia affection status, and high myopia. Family based association analysis did not reveal any association between the 17 SNPs genotyped in the larger family data set for any refractive error type. Conclusions Sequence variants of the MFRP gene do not appear to be associated with either the less severe forms of hyperopia, extreme forms of limited eye growth and development, or high myopia. These results indicate that the MFRP gene may not play a role in regulating ocular axial length in these phenotypes.

Metlapally, Ravikanth; Li, Yi-Ju; Tran-Viet, Khanh-Nhat; Bulusu, Anuradha; White, Tristan R.; Ellis, Jaclyn; Kao, Daniel

2008-01-01

95

First-Time Isolation and Characterization of a Bacteriophage Encoding the Shiga Toxin 2c Variant, Which Is Globally Spread in Strains of Escherichia coli O157  

Microsoft Academic Search

A bacteriophage encoding the Shiga toxin 2c variant (Stx2c) was isolated from the human Escherichia coli O157 strain CB2851 and shown to form lysogens on the E. coli K-12 laboratory strains C600 and MG1655. Production of Stx2c was found in the wild-type E. coli O157 strain and the K-12 lysogens and was inducible by growing bacteria in the presence of

Eckhard Strauch; Christoph Schaudinn; Lothar Beutin

2004-01-01

96

Serotyping and Genotyping of Genital Chlamydia trachomatis Isolates Reveal Variants of Serovars Ba, G, and J as Confirmed by omp1 Nucleotide Sequence Analysis  

PubMed Central

Urogenital isolates (n = 93) of Chlamydia trachomatis were differentiated into serovars and variants by serotyping with monoclonal antibodies and genotyping by restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified omp1 gene, respectively. The types of 87 of the 93 isolates (94%) were identical, as determined by both methods. Among these 87 isolates, 3 isolates were identified as the recently described new serovariant Ga/IOL-238 by omp1 nucleotide sequence analysis of the variable domains. Of the remaining six isolates, three isolates serotyped as both L2 and Ba but were identified as Ba/A-7 by genotyping by RFLP analysis of omp1. The omp1 nucleotide sequences of variable domains VD1, VD2, and VD4 of these urogenital Ba strains were identical to the sequences of the variable domains of Ba/J160, an ocular Ba type. The three remaining isolates were serotyped as J, but the patterns obtained by RFLP analysis of omp1, which were identical for the three isolates, differed from that of prototype serovar J/UW36. omp1 nucleotide sequence analysis revealed that these strains are genovariants of serovar J/UW36. Nucleotide sequence differences between serovar J/UW36 and this J genovariant, designated Jv, were found in both variable and constant domains. In conclusion, this study shows that the PCR-based genotyping of clinical C. trachomatis isolates by RFLP analysis of omp1 has a higher discriminatory power and is more convenient than serotyping. Variants of C. trachomatis serovars Ba, G, and J were identified and characterized.

Morre, Servaas A.; Ossewaarde, Jacobus M.; Lan, Jar; van Doornum, Gerard J. J.; Walboomers, Jan M. M.; MacLaren, David M.; Meijer, Chris J. L. M.; van den Brule, Adriaan J. C.

1998-01-01

97

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

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.

Blanco, M.; Blanco, J. E.; Mora, A.; Dahbi, G.; Alonso, M. P.; Gonzalez, E. A.; Bernardez, M. I.; Blanco, J.

2004-01-01

98

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

Microsoft Academic Search

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

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

2006-01-01

99

Dissemination of Clinical Isolates of Klebsiella oxytoca Harboring CMY-31, VIM-1, and a New OXY-2-Type Variant in the Community ?  

PubMed Central

The aim of the present study was to investigate the epidemiological link of multidrug-resistant Klebsiella oxytoca isolates causing community-onset infections among patients attending our outpatient department and to investigate the underlying resistance mechanisms. The isolates were tested by agar dilution MICs, phenotypic carbapenemase testing, enterobacterial repetitive intergenic consensus-PCR, and pulsed-field gel electrophoresis (PFGE). PCR assays and nucleotide sequencing were employed for the identification of bla gene types and the mapping of the integron-containing metallo-?-lactamase (MBL) gene. During the study period (January 2005 to April 2007), nine broad-spectrum cephalosporin-resistant K. oxytoca clinical isolates were prospectively collected from separate outpatients with urinary tract infections. In all cases, the patients had been hospitalized or exposed to health care facilities during the preceding year. Molecular typing revealed that all isolates belonged to the same K. oxytoca clonal type, which contained five PFGE subtypes. A novel chromosomal OXY-2 ?-lactamase type variant (OXY-2-9) was detected in all isolates, but no mutations in the promoter region justifying blaOXY gene overproduction were detected. In addition, all isolates harbored the plasmidic CMY-31 (LAT-4) AmpC cephalosporinase, while three of them harbored VIM-1 MBL in a class 1 integron structure. This is the first study to present the dissemination in the community of multidrug-resistant K. oxytoca isolates causing extrahospital infections.

Tsakris, Athanassios; Poulou, Aggeliki; Markou, Fani; Pitiriga, Vassiliki; Piperaki, Evangelia-Theophano; Kristo, Ioulia; Pournaras, Spyros

2011-01-01

100

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

SciTech Connect

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.

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

101

A novel post-translational modification of the peptide antibiotic subtilin: isolation and characterization of a natural variant from Bacillus subtilis A.T.C.C. 6633.  

PubMed Central

A variant of the peptide antibiotic subtilin has been isolated from Bacillus subtilis A.T.C.C. 6633, and its structure has been shown to be [N alpha-succinyl-Trp1]subtilin. The chemical structure of a fragment derived by tryptic hydrolysis of the variant is shown to be N alpha-succinyl-Trp-Lys by 1H and 13C n.m.r., fast-atom-bombardment m.s. and total chemical synthesis [N alpha-Succinyl-Trp1]-subtilin is produced later in the growth of the bacterium than is subtilin; reverse-phase h.p.l.c. analysis shows that after 24 h growth the ratio subtilin/[N alpha-succinyl-Trp1]subtilin is approx. 1:2. Although [N alpha-succinyl-Trp1]subtilin retains significant antibacterial activity, it is 10-20 times less active than subtilin.

Chan, W C; Bycroft, B W; Leyland, M L; Lian, L Y; Roberts, G C

1993-01-01

102

Characterization of Vibrio cholerae O1 El Tor Biotype Variant Clinical Isolates from Bangladesh and Haiti, Including a Molecular Genetic Analysis of Virulence Genes ?  

PubMed Central

Vibrio cholerae serogroup O1, the causative agent of the diarrheal disease cholera, is divided into two biotypes: classical and El Tor. Both biotypes produce the major virulence factors toxin-coregulated pilus (TCP) and cholera toxin (CT). Although possessing genotypic and phenotypic differences, El Tor biotype strains displaying classical biotype traits have been reported and subsequently were dubbed El Tor variants. Of particular interest are reports of El Tor variants that produce various levels of CT, including levels typical of classical biotype strains. Here, we report the characterization of 10 clinical isolates from the International Centre for Diarrhoeal Disease Research, Bangladesh, and a representative strain from the 2010 Haiti cholera outbreak. We observed that all 11 strains produced increased CT (2- to 10-fold) compared to that of wild-type El Tor strains under in vitro inducing conditions, but they possessed various TcpA and ToxT expression profiles. Particularly, El Tor variant MQ1795, which produced the highest level of CT and very high levels of TcpA and ToxT, demonstrated hypervirulence compared to the virulence of El Tor wild-type strains in the infant mouse cholera model. Additional genotypic and phenotypic tests were conducted to characterize the variants, including an assessment of biotype-distinguishing characteristics. Notably, the sequencing of ctxB in some El Tor variants revealed two copies of classical ctxB, one per chromosome, contrary to previous reports that located ctxAB only on the large chromosome of El Tor biotype strains.

Son, Mike S.; Megli, Christina J.; Kovacikova, Gabriela; Qadri, Firdausi; Taylor, Ronald K.

2011-01-01

103

Identification of novel subgroup A variants with enhanced receptor binding and replicative capacity in primary isolates of anaemogenic strains of feline leukaemia virus  

PubMed Central

Background The development of anaemia in feline leukaemia virus (FeLV)-infected cats is associated with the emergence of a novel viral subgroup, FeLV-C. FeLV-C arises from the subgroup that is transmitted, FeLV-A, through alterations in the amino acid sequence of the receptor binding domain (RBD) of the envelope glycoprotein that result in a shift in the receptor usage and the cell tropism of the virus. The factors that influence the transition from subgroup A to subgroup C remain unclear, one possibility is that a selective pressure in the host drives the acquisition of mutations in the RBD, creating A/C intermediates with enhanced abilities to interact with the FeLV-C receptor, FLVCR. In order to understand further the emergence of FeLV-C in the infected cat, we examined primary isolates of FeLV-C for evidence of FeLV-A variants that bore mutations consistent with a gradual evolution from FeLV-A to FeLV-C. Results Within each isolate of FeLV-C, we identified variants that were ostensibly subgroup A by nucleic acid sequence comparisons, but which bore mutations in the RBD. One such mutation, N91D, was present in multiple isolates and when engineered into a molecular clone of the prototypic FeLV-A (Glasgow-1), enhanced replication was noted in feline cells. Expression of the N91D Env on murine leukaemia virus (MLV) pseudotypes enhanced viral entry mediated by the FeLV-A receptor THTR1 while soluble FeLV-A Env bearing the N91D mutation bound more efficiently to mouse or guinea pig cells bearing the FeLV-A and -C receptors. Long-term in vitro culture of variants bearing the N91D substitution in the presence of anti-FeLV gp70 antibodies did not result in the emergence of FeLV-C variants, suggesting that additional selective pressures in the infected cat may drive the subsequent evolution from subgroup A to subgroup C. Conclusions Our data support a model in which variants of FeLV-A, bearing subtle differences in the RBD of Env, may be predisposed towards enhanced replication in vivo and subsequent conversion to FeLV-C. The selection pressures in vivo that drive the emergence of FeLV-C in a proportion of infected cats remain to be established.

2012-01-01

104

Detection and Characterization of VIM-31, a New Variant of VIM-2 with Tyr224His and His252Arg Mutations, in a Clinical Isolate of Enterobacter cloacae  

PubMed Central

We report the first description of the metallo-?-lactamase VIM-31, a new variant of VIM-2 with Tyr224His and His252Arg mutations, in Enterobacter cloacae 11236, which was isolated from blood specimens of a patient with colonic adenocarcinoma in Belgium. blaVIM-31 was found on a class 1 integron located on a self-transferable but not typeable 42-kb plasmid. Compared to values published elsewhere for VIM-2, the purified VIM-31 enzyme showed weaker catalytic efficiency against all the tested beta-lactam agents (except for ertapenem), resulting from lower kcat (except for ertapenem) and higher Km values for VIM-31.

Bebrone, Carine; Huang, Te-Din; Bouchahrouf, Warda; DeGheldre, Yves; Deplano, Ariane; Hoffmann, Kurt; Glupczynski, Youri

2012-01-01

105

Time course of virus-like particles (VLPs) double-stranded rna accumulation in toxigenic and non-toxigenic strains of Aspergillus flavus  

Microsoft Academic Search

Two strains of Aspergillus flavus, non-toxigenic NRRL 6550 and toxigenic NRRL 5940, were studied over a period of 44 days, in order to detect the presence of virus-like particles (VLPs) by means of electron microscopy (EM) and nucleic acids electrophoresis. Only the toxigenic strain contained VLPs, presenting three-segmented dsRNA. An increase in VLPs number was observed during the exponential phase

Valéria N. Silva; Edison Luiz Durigon; Maria de Fátima Costa Pires; Alexandre Lourenço; Maria Jacinta de Faria; Benedito Corrêa

2001-01-01

106

HCV Variants.  

National Technical Information Service (NTIS)

HCV variants are described. The variants include polynucleotides comprising non-naturally occurring HCV sequences and HCV variants that have a transfection efficiency and ability to survive subpassage greater than HCV that have wild-type polyprotein codin...

C. M. Rice K. J. Blight

2005-01-01

107

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

PubMed Central

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

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

1991-01-01

108

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

PubMed Central

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

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

1991-01-01

109

Characterization of Two New CTX-M-25-Group Extended-Spectrum ?-Lactamase Variants Identified in Escherichia coli Isolates from Israel  

PubMed Central

Objectives We characterized two new CTX-M-type extended-spectrum ?-lactamase (ESBL) variants in Escherichia coli isolates from stool samples of two elderly patients admitted at the Tel Aviv Sourasky Medical Center, Israel. Both patients underwent treatment with cephalosporins prior to isolation of the E. coli strains. Methods ESBLs were detected by the double-disk synergy test and PCR-sequencing of ?-lactamase genes. The blaCTX-M genes were cloned into the pCR-BluntII-TOPO vector in E. coli TOP10. The role of amino-acid substitutions V77A and D240G was analyzed by site-directed mutagenesis of the blaCTX-M-94 and blaCTX-M-100 genes and comparative characterization of the resulting E. coli recombinants. MICs of ?-lactams were determined by Etest. Plasmid profiling, mating experiments, replicon typing and sequencing of blaCTX-M flanking regions were performed to identify the genetic background of the new CTX-M variants. Results The novel CTX-M ?-lactamases, CTX-M-94 and -100, belonged to the CTX-M-25-group. Both variants differed from CTX-M-25 by the substitution V77A, and from CTX-M-39 by D240G. CTX-M-94 differed from all CTX-M-25-group enzymes by the substitution F119L. Glycine-240 was associated with reduced susceptibility to ceftazidime and leucine-119 with increased resistance to ceftriaxone. blaCTX-M-94 and blaCTX-M-100 were located within ISEcp1 transposition units inserted into ?93 kb non-conjugative IncFI and ?130 kb conjugative IncA/C plasmids, respectively. The plasmids carried also different class 1 integrons. Conclusions This is the first report on CTX-M-94 and -100 ESBLs, novel members of the CTX-M-25-group.

Vervoort, Jascha; Baraniak, Anna; Gazin, Muriel; Sabirova, Julia; Lammens, Christine; Kazma, Meital; Grabowska, Anna; Izdebski, Radoslaw; Carmeli, Yehuda; Kumar-Singh, Samir; Gniadkowski, Marek; Goossens, Herman; Malhotra-Kumar, Surbhi

2012-01-01

110

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

PubMed Central

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

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

1999-01-01

111

Host adaptation of pigeon isolates of Salmonella enterica subsp. enterica serovar Typhimurium variant Copenhagen phage type 99 is associated with enhanced macrophage cytotoxicity.  

PubMed

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

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

2003-10-01

112

Human spleen histone H1. Isolation and amino acid sequence of a main variant, H1b.  

PubMed

The complete amino acid sequence of a main variant, H1b, of human spleen histone H1 was determined, following previous determinations of human spleen histones H2B, H2A, H3, and H4. High-performance liquid chromatography on C8 silica of the H1 fraction yielded the homogeneous H1b subfraction; this variant was estimated to account for 60% of the total of the four H1 variants. The sequence determination was performed with four main fragments, I to IV, obtained by limited chymotryptic digestion of H1b. Together with direct sequencing by automated Edman degradation of fragments II, III, and IV, fragment I, blocked at the N-terminal, and fragment IV, the C-terminal half the H1b molecule, were sequenced after further digestion with staphylococcal protease and others. The four fragments were aligned with three overlapping peptides each derived from chymotryptic partial fragments, I-II and I-II-III, and intact H1b. Carboxypeptidase digestion of intact H1b confirmed the C-terminal sequence of the molecule. Thus, the total sequence of H1b was completely determined; it consists of a total of 218 amino acid residues, has a molecular weight of 21,734 in the unmodified form, and is completely acetylated at the N-terminal serine residue and partially methylated at the lysine residue 25. This sequence is compared with two mammalian somatic H1 sequences. PMID:3782055

Ohe, Y; Hayashi, H; Iwai, K

1986-08-01

113

Isolation and Characterization of a Salmonella enterica Serotype Typhi Variant and Its Clinical and Public Health Implications  

Microsoft Academic Search

We report the isolation and characterization of a member of the family Enterobacteriaceae isolated from the gallbladder pus of a food handler. Conventional biochemical tests suggested Salmonella enterica serotype Typhi, but the isolate agglutinated with poly(O), 2O, 9O, and Vi Salmonella antisera but not with poly(H) or any individual H Salmonella antisera. 16S rRNA gene sequencing showed that there were

PATRICK C. Y. WOO; AMI M. Y. FUNG; SAMSON S. Y. WONG; HOI-WAH TSOI; KWOK-YUNG YUEN

2001-01-01

114

Characterization of non-membrane-damaging cytotoxin of non-toxigenic Vibrio cholerae O1 and its relevance to disease.  

PubMed

The non-membrane-damaging cytotoxin which causes dramatic cell rounding of cultured HeLa cells was purified to homogeneity from a clinical strain (WO5) of non-toxigenic Vibrio cholerae O1 Inaba belonging to the E1 Tor biotype. The purified protein has a denatured molecular weight of 35 kDa and a native molecular weight of approximately 37 kDa indicating the monomeric nature of the protein. The 15 N-terminal amino acid sequence of non-membrane-damaging cytotoxin showed complete homology to the hemagglutinin protease previously purified and characterized from V. cholerae O1. Purified non-membrane-damaging cytotoxin from V. cholerae O1 was immunologically and biochemically identical to that previously purified from V. cholerae O26. Non-membrane-damaging cytotoxin was found to be enterotoxic in rabbit ileal loop assay inducing accumulation of non-hemorrhagic fluid at 100 micrograms and elicited a concentration dependent increase in short circuit current and tissue conductance of rabbit ileal mucosa mounted on Ussing chambers. A significant serum immunoglobulin G response against non-membrane-damaging cytotoxin was elicited by patients infected with V. cholerae O139 but not with V. cholerae O1. These properties make non-membrane-damaging cytotoxin a potential virulence factor of V. cholerae which should be taken into consideration while making live, attenuated recombinant vaccine strains against cholera. PMID:9868778

Mitra, R; Saha, P K; Basu, I; Venkataraman, A; Ramakrishna, B S; Albert, M J; Takeda, Y; Nair, G B

1998-12-15

115

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

PubMed Central

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

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

2011-01-01

116

A Novel FexA Variant from a Canine Staphylococcus pseudintermedius Isolate That Does Not Confer Florfenicol Resistance.  

PubMed

Transposon Tn558 integrated in the chromosomal radC gene was detected for the first time in Staphylococus pseudintermedius. It carried a novel fexA variant (fexAv) that confers only chloramphenicol resistance. The exporter FexAv exhibited two amino acid substitutions, Gly33Ala and Ala37Val, both of which seem to be important for substrate recognition. Site-directed mutagenesis that reverted the mutated base pairs to those present in the original fexA gene restored the chloramphenicol-plus-florfenicol resistance phenotype. PMID:23979755

Gómez-Sanz, Elena; Kadlec, Kristina; Feßler, Andrea T; Zarazaga, Myriam; Torres, Carmen; Schwarz, Stefan

2013-08-26

117

Novel Plasmid and Its Variant Harboring both a blaNDM-1 Gene and Type IV Secretion System in Clinical Isolates of Acinetobacter lwoffii  

PubMed Central

The spread of the blaNDM-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 blaNDM-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 blaNDM-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 blaNDM-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 blaNDM-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.

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.

2012-01-01

118

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

PubMed Central

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

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

2012-01-01

119

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

PubMed Central

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

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

2010-01-01

120

Isolation and characterization of an estrogen-inhibited variant derived from the MCF-7 breast cancer cell line.  

PubMed

The mechanism by which pharmacological concentrations of estrogen can paradoxically inhibit the growth of human breast cancer is unknown. We have selected for a variant line of MCF-7 which may help to understand this process. The variant was selected by exposing MCF-7 cells to high-specific-activity 16 alpha-[125I]iodoestradiol. These cells were viably frozen for two isotopic half-lives, defrosted once, then reexposed to 16 alpha-[125I]iodoestradiol to allow maximal radiation damage mediated by isotope associated with binding sites. This cell line (113) is one of 55 lines cloned from MCF-7 cells that survived this treatment. The growth response to estradiol of the 113 breast cancer cells grown in monolayer is normal for 4 to 6 days, and then the cell number plateaus as the cells appear to round up and detach. Concomitantly, a decrease in [3H]thymidine incorporation occurs. The cells cannot be rescued by removing estradiol from the medium. The inhibition is dose dependent and can be seen in concentrations of estradiol as low as 10(-10) M. The 113 cells are also inhibited by antiestrogens. They have normal levels of estrogen receptors which bind to DNA cellulose with activation. Progesterone receptors are estrogen inducible, although the levels are one-third that of wild-type MCF-7 cells. The morphological changes determined by electron microscopy of estrogen-treated cells are typical of degenerative cells. To investigate the possibility that inhibitory factors are secreted into the medium by 113 cells, conditioned medium from estrogen-exposed 113 cells is added to normal MCF-7 and 113 cells. No decrease in [3H]thymidine incorporation compared to controls is observed. When the secreted proteins are labeled with [35S]methionine and analyzed by sodium dodecyl sulfate-acrylamide gels, no major differences are apparent in the 113 and MCF-7 cells. Thus, the source of the defect is still unknown. It remains to be seen if the growth-inhibitory effects of 17 beta-estradiol on this cell line are receptor mediated or related to specific gene products which can be identified. PMID:6744309

Bronzert, D A; Triche, T J; Gleason, P; Lippman, M E

1984-09-01

121

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

PubMed Central

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

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

1992-01-01

122

Laboratory investigation of an Escherichia coli O157:H7 strain possessing a vtx2c gene with an IS1203 variant insertion sequence isolated from an asymptomatic food handler in Japan.  

PubMed

We isolated an Escherichia coli O157:H7 strain that was negative for verocytotoxin production, but positive for the vtx2 gene using commercial kits, from an asymptomatic food handler. The laboratory investigations revealed that a 1310-bp insertion sequence, IS1203 variant, was present in the B subunit-coding region of the vtx2c gene. PMID:23891550

Harada, Tetsuya; Hirai, Yuji; Itou, Takeshi; Hayashida, Mizuho; Seto, Kazuko; Taguchi, Masumi; Kumeda, Yuko

2013-07-26

123

New variant of CTX-M-type extended-spectrum beta-lactamases, CTX-M-71, with a Gly238Cys substitution in a Klebsiella pneumoniae isolate from Bulgaria.  

PubMed

A single Klebsiella pneumoniae strain isolated in a Bulgarian hospital was found to produce CTX-M-71, a new CTX-M variant characterized by one amino acid substitution from glycine to cysteine at position 238 in comparison to CTX-M-15. This exchange decreased the hydrolytic activity of the beta-lactamase for cefotaxime, ceftazidime, and cefepime. PMID:19620330

Schneider, Ines; Queenan, Anne Marie; Markovska, Rumyana; Markova, Boyka; Keuleyan, Emma; Bauernfeind, Adolf

2009-07-20

124

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

PubMed

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

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

2012-11-14

125

Activation of the fibrinogen binding site on platelets isolated from a patient with the Strasbourg I variant of Glanzmann's thrombasthenia.  

PubMed

One proposed ligand binding site on platelet integrin alpha IIb beta 3 is the region of the beta 3 subunit encompassing amino acids 211-221. However, we recently showed that synthetic peptides corresponding to amino acids 211-221 inhibit fibrinogen binding to alpha IIb beta 3 by binding to alpha IIb beta 3 and not to fibrinogen. In this study, we show that AP6, a monoclonal antibody (MoAb) directed against amino acids 214-221 of beta 3, bound to immobilized active alpha IIb beta 3 but did not inhibit fibrinogen binding to the complex. We then determined whether nonfunctional alpha IIb beta 3 on platelets with a beta 3 Arg-214-->Trp mutation (Strasbourg I variant of Glanzmann's thrombasthenia or GTV) could be induced to aggregate after treatment with dithiothreitol (DTT). DTT has been shown to expose the fibrinogen receptor on normal platelets. DTT treatment of GTV platelets did result in the formation of the fibrinogen binding site as indicated by the binding of pI-55, an MoAb that only binds to the activated form of alpha IIb beta 3. Furthermore, DTT-treated GTV platelets aggregated in the presence of fibrinogen and divalent cations. This aggregation was inhibited by EDTA, RGDS, and the selective alpha IIb beta 3 antagonist, Ro 43-5054. These data show that Arg-214 of beta 3 is not required for fibrinogen binding or for platelet aggregation. However, this amino acid appears to be critical for the formation and for the maintenance of the correct tertiary structure of the fibrinogen binding site on alpha IIb beta 3. PMID:8049427

Kouns, W C; Steiner, B; Kunicki, T J; Moog, S; Jutzi, J; Jennings, L K; Cazenave, J P; Lanza, F

1994-08-15

126

Partial biochemical and biological characterization of purified chicken growth hormone (cGH). Isolation of cGH charge variants and evidence that cGH is phosphorylated.  

PubMed

Chicken growth hormone (cGH) was purified from frozen pituitary glands obtained from recently sacrificed broilers. Glands were homogenized in a protease inhibitor solution (0.5 mM PMSF, 50 KIU/ml aprotinin, pH 7.2); extract was taken to pH 9.0 with calcium hydroxide and the supernatant was differentially precipitated with 20% (fraction A) and 50% (fraction B) ammonium sulfate. cGH (fraction B-DE-1) was obtained in pure form from fraction B after DEAE-cellulose chromatography at pH 8.6, with a yield of 2.9 mg/g tissue. Three charge variants of cGH (Rf = 0.23, 0.30, and 0.35) could be isolated by electroelution after semipreparative nondenaturing polyacrylamide gel electrophoresis of fraction B-DE-1. These charge variants showed the same apparent molecular weight (26,300 Da) by sodium dodecyl sulfate polyacrylamide gel electrophoresis under reducing conditions. Isoelectric focusing of fraction B-DE-1 revealed two major components (pI = 7.2 and 7.4) and four minor bands (pI = 6.2, 6.7, 7.1, and 7.5). It was found that fraction B-DE-1 contained a significant amount of esterified phosphate (1 nmol PO4/3.5 nmol protein) similar to that reported previously for ovine GH. The functional integrity of the cGH obtained here was characterized by two heterologous and one homologous bioassays. High activity was shown by fraction B-DE-1 in the tibia assay (1.76 UI/mg) and in the liver ornithine decarboxylase assay (sixfold over control), both made in hypophysectomized rats; and it also stimulated lipolysis (138 and 215% at 10 and 100 ng/ml, respectively) on chicken abdominal adipose tissue explants. PMID:2591723

Arámburo, C; Carranza, M; Sanchez, R; Perera, G

1989-11-01

127

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?  

PubMed Central

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 to the common coagulase-negative group. In some cases they turned out to be opportunistic pathogens present in wound infections. MICs were determined for 12 antibiotics, and antibiotic resistance genes were detected by microarray. At hospital admission, horses harbored staphylococci that were susceptible to antibiotics or resistant to one group of drugs, mainly due to the presence of new variants of the methicillin and macrolide resistance genes mecA and mph(C), respectively. After 3 days, the percentage of Staphylococcus isolates displaying antibiotic resistance, as well as the number of resistance genes per isolate, increased moderately in hospitalized horses without surgery or penicillin treatment but dramatically in hospitalized horses after colic surgery as well as penicillin treatment. Staphylococcus species displaying multiple resistance were found to harbor mainly genes conferring resistance to ?-lactams (mecA and blaZ), aminoglycosides [str and aac(6?)-Ie-aph(2?)-Ia], and trimethoprim [dfr(A) and dfr(D)]. Additional genes conferring resistance to macrolides [mph(C), erm(C), and erm(B)], tetracycline [tet(K) and tet(M)], chloramphenicol [cat(pC221) and cat(pC223)], and streptothricin (sat4) appeared in several strains. Hospitalization and preventive penicillin use were shown to act as selection agents for multidrug-resistant commensal staphylococcal flora.

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

2006-01-01

128

MRSA Variant in Companion Animals  

PubMed Central

Methicillin-resistant Staphylocoocus aureus (MRSA) harboring mecALGA251 has been isolated from humans and ruminants. Database screening identified this MRSA variant in cats, dogs, and a guinea pig in Germany during 2008–2011. The novel MRSA variant is not restricted to ruminants or humans, and contact with companion animals might pose a zoonotic risk.

Wieler, Lothar H.; Vincze, Szilvia; Antao, Esther-Maria; Brandenburg, Anja; Stamm, Ivonne; Kopp, Peter A.; Kohn, Barbara; Semmler, Torsten; Lubke-Becker, Antina

2012-01-01

129

Identification and functional analysis of sequence variants in the long control region and the E2 open reading frame of bovine papillomavirus type 1 isolated from equine sarcoids.  

PubMed

BPV-1 DNA is the predominant viral type detected in equine sarcoids and represents the only reported natural cross species infection of papillomaviruses. In this study, nucleotide variations in the LCR and the E2 regions of equine sarcoid-associated BPV-1 were characterised by sequence analysis. Variants particular to sarcoid BPV-1 were identified in both the LCR and E2 sequence. The functionality of the most common LCR variant was examined in equine and bovine cells. These studies showed that the activity of the variant LCR was higher in equine cells than bovine cells; the activity of the variant LCR in the presence of the E2 variant was similar to the reference/wild-type sequences in equine cells, whereas in bovine cells the variant function was reduced by 50%. These data suggest the viral BPV variants commonly detected in sarcoids have an enhanced function in equine cells compared to their function in bovine cells. PMID:17412385

Nasir, L; Gault, E; Morgan, I M; Chambers, G; Ellsmore, V; Campo, M S

2007-04-06

130

Analysis of Vibrio cholerae Genome Sequences Reveals Unique rtxA Variants in Environmental Strains and an rtxA-Null Mutation in Recent Altered El Tor Isolates  

PubMed Central

ABSTRACT Vibrio cholerae genome sequences were analyzed for variation in the rtxA gene that encodes the multifunctional autoprocessing RTX (MARTX) toxin. To accommodate genomic analysis, a discrepancy in the annotated rtxA start site was resolved experimentally. The correct start site is an ATG downstream from rtxC resulting in a gene of 13,638 bp and deduced protein of 4,545 amino acids. Among the El Tor O1 and closely related O139 and O37 genomes, rtxA was highly conserved, with nine alleles differing by only 1 to 6 nucleotides in 100 years. In contrast, 12 alleles from environment-associated isolates are highly variable, at 1 to 3% by nucleotide and 3 to 7% by amino acid. The difference in variation rates did not represent a bias for conservation of the El Tor rtxA compared to that of other strains but rather reflected the lack of gene variation in overall genomes. Three alleles were identified that would affect the function of the MARTX toxin. Two environmental isolates carry novel arrangements of effector domains. These include a variant from RC385 that would suggest an adenylate cyclase toxin and from HE-09 that may have actin ADP-ribosylating activity. Within the recently emerged altered El Tor strains that have a classical ctxB gene, a mutation arose in rtxA that introduces a premature stop codon that disabled toxin function. This null mutant is the genetic background for subsequent emergence of the ctxB7 allele resulting in the strain that spread into Haiti in 2010. Thus, similar to classical strains, the altered El Tor pandemic strains eliminated rtxA after acquiring a classical ctxB.

Dolores, Jazel; Satchell, Karla J. F.

2013-01-01

131

The Genome-Sequenced Variant of Campylobacter jejuni NCTC 11168 and the Original Clonal Clinical Isolate Differ Markedly in Colonization, Gene Expression, and Virulence-Associated Phenotypes  

PubMed Central

The genome sequence of the enteric bacterial pathogen Campylobacter jejuni NCTC 11168 (11168-GS) was published in 2000, providing a valuable resource for the identification of C. jejuni-specific colonization and virulence factors. Surprisingly, the 11168-GS clone was subsequently found to colonize 1-day-old chicks following oral challenge very poorly compared to other strains. In contrast, we have found that the original clinical isolate from which 11168-GS was derived, 11168-O, is an excellent colonizer of chicks. Other marked phenotypic differences were also identified: 11168-O invaded and translocated through tissue culture cells far more efficiently and rapidly than 11168-GS, was significantly more motile, and displayed a different morphology. Serotyping, multiple high-resolution molecular genotyping procedures, and subtractive hybridization did not yield observable genetic differences between the variants, suggesting that they are clonal. However, microarray transcriptional profiling of these strains under microaerobic and severely oxygen-limited conditions revealed dramatic expression differences for several gene families. Many of the differences were in respiration and metabolism genes and operons, suggesting that adaptation to different oxygen tensions may influence colonization potential. This correlates biologically with our observation that anaerobically priming 11168-GS or aerobically passaging 11168-O caused an increase or decrease, respectively, in colonization compared to the parent strain. Expression differences were also observed for several flagellar genes and other less well-characterized genes that may participate in motility. Targeted sequencing of the sigma factors revealed specific DNA differences undetected by the other genomic methods. These observations highlight the capacity of C. jejuni to adapt to multiple environmental niches, the likelihood that this adaptation involves genetic evolution, and provides the first whole-genome molecular exploration of the effect of laboratory culture and storage on colonization and virulence properties of this pathogen.

Gaynor, Erin C.; Cawthraw, Shaun; Manning, Georgina; MacKichan, Joanna K.; Falkow, Stanley; Newell, Diane G.

2004-01-01

132

Comparative studies on the pathogenicity and tissue distribution of three virulence variants of classical swine fever virus, two field isolates and one vaccine strain, with special regard to immunohistochemical investigations  

PubMed Central

Background The aim of this study was to compare the tissue distribution and pathogenicity of three virulence variants of classical swine fever virus (CSFV) and to investigate the applicability of various conventional diagnostic procedures. Methods 64 pigs were divided into three groups and infected with the highly virulent isolate ISS/60, the moderately virulent isolate Wingene'93 and the live attenuated vaccine strain Riems, respectively. Clinical signs, gross and histopathological changes were compared in relation to time elapsed post infection. Virus spread in various organs was followed by virus isolation, by immunohistochemistry, applying monoclonal antibodies in a two-step method and by in situ hybridisation using a digoxigenin-labelled riboprobe. Results The tissue distribution data are discussed in details, analyzing the results of the various diagnostic approaches. The comparative studies revealed remarkable differences in the onset of clinical signs as well as in the development of the macro- and microscopical changes, and in the tissue distribution of CSFV in the three experimental groups. Conclusion The present study demonstrates that in the case of highly and moderately virulent virus variants the virulence does not affect the pattern of the viral spread, however, it influences the outcome, the duration and the intensity of the disease. Immunohistochemistry has the advantage to allow the rapid detection and localisation of the virus, especially in cases of early infection, when clinical signs are still absent. Compared to virus isolation, the advantage of this method is that no cell culture facilities are required. Thus, immunohistochemistry provides simple and sensitive tools for the prompt detection of newly emerging variants of CSFV, including the viruses of very mild virulence.

Belak, Katinka; Koenen, Frank; Vanderhallen, Hans; Mittelholzer, Christian; Feliziani, Francesco; De Mia, Gian Mario; Belak, Sandor

2008-01-01

133

Occurrence of Efflux Mechanism and Cephalosporinase Variant in a Population of Enterobacter aerogenes and Klebsiella pneumoniae Isolates Producing Extended-Spectrum  -Lactamases  

Microsoft Academic Search

We investigated the occurrence of multidrug resistance in 44 Enterobacter aerogenes and Klebsiella pneumoniae clinical isolates. Efflux was involved in resistance in E. aerogenes isolates more frequently than in K. pneumoniae isolates (100 versus 38% of isolates) and was associated with the expression of phenylalanine arginine -naphthylamide-susceptible active efflux. AcrA-TolC overproduction in E. aerogenes isolates was noted. An analysis of

Que-Tien Tran; Myrielle Dupont; Jean-Philippe Lavigne; Jacqueline Chevalier; Jean-Marie Pages; Albert Sotto; Anne Davin-Regli

2009-01-01

134

Human spleen histone H1. Isolation and amino acid sequences of three minor variants, H1a, H1c, and H1d.  

PubMed

Following the previous determination of the main variant H1b of human spleen histone H1, we have determined the complete amino acid sequence of another variant, H1d. Limited chymotryptic digestion of H1d produced four fragments, I to IV, and one partial fragment I-II, as in the case of H1b. These fragments were aligned with two overlapping peptides, produced by another enzyme from the intact H1d. We also confirmed the C-terminal sequence of H1d by carboxypeptidase digestion. This H1d has an acetylated N-terminal serine, equimolar alanine or valine residue at 17, and is composed of 212 residues. The molecular weight was 21,233 for the alanine variant and 21,261 for the valine variant in the unmodified form. We also deduced the total sequences of H1a and H1c in a similar way, considering the maximum homology with H1b and H1d. Each N-terminal serine residue is acetylated, too. H1a consists of 222 amino acid residues and has a molecular weight of 22,178 in its unmodified form; the H1c consists of 220 residues and has a molecular weight of 22,218 in that form. The human spleen H1 sequences varied to about the same extent in the N-terminal 40 and C-terminal 110 residues. However, the sequences of the about 70 internal residues are well conserved between the variants. The extent of differences among the human H1 variants is similar to, or rather smaller than, those among the mammalian somatic H1 species. The implications of these differences in the sequence for H1 function are discussed from the evolutionary viewpoint. PMID:2613692

Ohe, Y; Hayashi, H; Iwai, K

1989-11-01

135

Segment2 sequence analysis and cross-neutralization studies on some Indian bluetongue viruses suggest isolates are VP2-variants of serotype 23  

Microsoft Academic Search

Sequence analysis of segment 2 (seg-2) of three Indian bluetongue virus (BTV) isolates, Dehradun, Rahuri and Bangalore revealed\\u000a 99% nucleotide identity amongst them and 96% with the reference BTV 23. Phylogenetic analysis grouped the isolates in ‘nucleotype\\u000a D’. The deduced amino acid (aa) sequence of the Bangalore isolate showed a high variability in a few places compared to other\\u000a isolates.

Prabhakar A. Tembhurne; Bimalendu Mondal; Kunj B. Pathak; Sanchay K. Biswas; Aniket Sanyal; Mahendra P. Yadav; Santanu K. Bandyopadhyay; Raj K. Singh

2010-01-01

136

Scimitar variant.  

PubMed

In the classic scimitar syndrome, a pulmonary vein draining all or part of the right lung enters the inferior vena cava. A variant is described with the same roentgenographic appearance, but with drainage of the anomalous pulmonary vein into both the inferior vena cava and the left atrium; the atrial septum was intact. This case, together with six others reported elsewhere, reminds us that the scimitar sign has both false positives and false negatives. Therefore, the diagnosis of scimitar syndrome cannot be made with certainty from a plain x-ray film. PMID:3628070

Pearl, W

1987-01-01

137

Identification and functional analysis of sequence variants in the long control region and the E2 open reading frame of bovine papillomavirus type 1 isolated from equine sarcoids  

Microsoft Academic Search

BPV-1 DNA is the predominant viral type detected in equine sarcoids and represents the only reported natural cross species infection of papillomaviruses. In this study, nucleotide variations in the LCR and the E2 regions of equine sarcoid-associated BPV-1 were characterised by sequence analysis. Variants particular to sarcoid BPV-1 were identified in both the LCR and E2 sequence. The functionality of

L. Nasir; E. Gault; I. M. Morgan; G. Chambers; V. Ellsmore; M. S. Campo

2007-01-01

138

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

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.

2013-01-01

139

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

Microsoft Academic Search

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

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

2001-01-01

140

Complete nucleotide sequence of an Amerindian human T-cell lymphotropic virus type II (HTLV-II) isolate: identification of a variant HTLV-II subtype b from a Guaymi Indian.  

PubMed Central

The complete nucleotide sequence of a human T-cell lymphotropic virus type II (HTLV-II) isolate from a Panamanian Guaymi Indian was determined and analyzed. When this new viral isolate (HTLV-IIG12) was compared with prototypic HTLV-IIMoT, the overall nucleotide sequence similarity was 95.4%, while the predicted amino acid sequence similarity was 97.5%. Although the overall percentage of nucleotide and amino acid identity with prototypic HTLV-IIMoT (subtype a) was high, HTLV-IIG12 displayed several distinctive features that defined it as an HTLV-II subtype b. However, there were several characteristics unique to this isolate, which included a cluster of nucleotide substitutions in the pre-gag region and changes in restriction enzyme sites within the pre-gag region and the gag, pol, env, and pX genes. In addition, two nucleotide changes in the C terminus of the Tax protein coding sequence inserted an Arg residue for a stop codon and appeared to result in a larger tax gene product in HTLV-IIG12. Although the HTLV-IIG12 isolate appears to be a variant of the prototypic HTLV-IIb, this information represents the first complete nucleotide sequence of any HTLV-II subtype b. These data will allow further studies on the evolutionary relationships between the HTLV-II subtypes and between HTLV-I and HTLV-II.

Pardi, D; Switzer, W M; Hadlock, K G; Kaplan, J E; Lal, R B; Folks, T M

1993-01-01

141

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...

142

Human isolates of Aeromonas possess Shiga toxin genes (stx1 and stx2) highly similar to the most virulent gene variants of Escherichia coli.  

PubMed

Strains producing Shiga toxins, encoded by stx1 and stx2 genes, can cause diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome. PCR screening of 80 clinical Aeromonas strains showed that 19 were stx1-positive and only one was positive for both stx1 and stx2. PCR bands were very faint for some strains and negative results were obtained after subculturing. The obtained sequences of Aeromonas stx1 and stx2 genes were highly similar to those of the most virulent stx gene variants of Shiga toxin-producing Escherichia coli. These results may lead to a better understanding of the potential pathogenicity and virulence mechanisms of Aeromonas. PMID:20219084

Alperi, A; Figueras, M J

2010-10-01

143

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

Microsoft Academic Search

Aspergillus oryzae NRRL 35191 was isolated as an endophyte from coffee leaves and found to produce kojic acid (KA) in culture. When inoculated\\u000a into cacao seedlings (Theobroma cacao), A. oryzae grew endophytically and synthesized KA in planta. Cacao seedlings inoculated with A. oryzae produced higher levels of caffeine than non-inoculated ones. Aspergillus oryzae may be a useful endophyte to introduce

Fabio C. Chaves; Thomas J. Gianfagna; Madhu Aneja; Francisco Posada; Stephen W. Peterson; Fernando E. Vega

144

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

PubMed

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

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

2013-08-12

145

Molecular identification and phylogenetic study of coxsackievirus A24 variant isolated from an outbreak of acute hemorrhagic conjunctivitis in India in 2010.  

PubMed

An outbreak of acute hemorrhagic conjunctivitis (AHC) occured in India between August and October 2010. Molecular typing by RT-PCR and sequencing of a partial VP1 region identified coxsackievirus A24 variant (CV A24v) as the serotype involved in this outbreak. Phylogenetic analysis based on the VP1 and 3C genes revealed that CV A24v strains associated with the 2010 AHC outbreak in India were genetically similar to strains from Central and South America that caused outbreaks of AHC in Cuba between 2008 and 2009 and Brazil in 2009. The result shows that the Indian strain of CV A24v may be responsible for the recent AHC outbreak in Marseille, France, in 2012. PMID:23124888

Shukla, Deepti; Kumar, Arvind; Srivastava, Shalini; Dhole, Tapan N

2012-11-04

146

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

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

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

147

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

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

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

2006-01-01

148

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

Microsoft Academic Search

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

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

2004-01-01

149

OXA-15, an Extended-Spectrum Variant of OXA-2 bLactamase, Isolated from aPseudomonas aeruginosaStrain  

Microsoft Academic Search

Pseudomonas aeruginosa AH, isolated in Ankara, Turkey, was highly resistant to ceftazidime (MIC, 128 mg\\/ml) and produced a b-lactamase that gave a doublet of bands at pIs 8.7 and 8.9. b-Lactamase production was transferable toP. aeruginosaPU21 by conjugation and was determined by a ca. 450-kb plasmid, pMLH54. The transconjugant andEscherichia colitransformed with the cloned gene showed increased resistance to ceftazi-

FRANCK DANEL; LUCINDA M. C. HALL; DENIZ GUR; ANDDAVID M. LIVERMORE

1997-01-01

150

A new variant of blepharospasm.  

PubMed Central

Ten patients who were unable to initiate or sustain eye opening in the absence of overt spasm of the orbicularis oculi, were investigated. In five, the problem was isolated. Three had Parkinson's disease and two progressive supra-nuclear palsy for between one to six years before the eye opening difficulty developed. The clinical features and electrophysiological investigation suggested that the disorder is a variant of blepharospasm due to abnormal contraction in the pre-tarsal orbicularis oculi.

Elston, J S

1992-01-01

151

A new variant of blepharospasm.  

PubMed

Ten patients who were unable to initiate or sustain eye opening in the absence of overt spasm of the orbicularis oculi, were investigated. In five, the problem was isolated. Three had Parkinson's disease and two progressive supra-nuclear palsy for between one to six years before the eye opening difficulty developed. The clinical features and electrophysiological investigation suggested that the disorder is a variant of blepharospasm due to abnormal contraction in the pre-tarsal orbicularis oculi. PMID:1602309

Elston, J S

1992-05-01

152

Mitochondrial variants of Neurospora intermedia from nature.  

PubMed

From a sample of 122 natural isolates of Neurospora intermedia collected recently from around the world, five variants had erratic stop-start growth patterns reminiscent of the phenotype of "stopper" laboratory extranuclear mutants of Neurospora crassa. Like laboratory isolated mutants, the natural "stopper" variants were sterile as protoperithecial parents and transmitted the variant growth phenotypes very inefficiently, if at all, as male parents. Heterokaryon tests could not be made because of strain incompatibilities. Four of the variants have mitochondrial cytochrome aa3 and b deficiencies. These four variants are all defective in mitochondrial ribosome assembly and have abnormal ratios of large to small subunits. Restriction enzyme analyses revealed some similarity of N. intermedia to N. crassa mtDNA. One normal and four variant strains had additional DNA in comparison to a standard normal strain. Cumulatively, the results indicate that the genetic alterations which cause stopper phenotypes of these natural isolates of N. intermedia are of mitochondrial rather than nuclear origin. PMID:6303535

Rieck, A; Griffiths, A J; Bertrand, H

1982-01-01

153

Chapter 4: Variant descriptions  

Treesearch

Research & Development ... Title: Chapter 4: Variant descriptions ... This report documents differences between geographic variants of the FFE. ... You may send email to rschneider@fs.fed.us to request a hard copy of this publication. (Please ...

154

Isolation of SPO12–1 and SPO13–1 from a Natural Variant of Yeast That Undergoes a Single Meiotic Division  

PubMed Central

ATCC4117 is a strain of S. cerevisiae that undergoes a single nuclear division during sporulation to produce asci containing two diploid ascospores (Grewal and Miller 1972). All clones derived from these spores are sporulation-capable and, like the parental strain, form two-spored asci. In this paper, we describe the genetic analysis of ATCC4117. In tetraploid hybrids of vegetative cells of the ATCC4117 diploid and a/a or ?/? diploids, the production of two-spored asci is recessive. From these tetraploids, we have isolated two recessive alleles, designated spo12–1 and spo13–1, each of which alone results in the production of asci with two diploid or near-diploid spores. These alleles are unlinked and segregate as single nuclear genes. spo12–1 is approximately 22 cM from its centromere; spo13–1 has been localized to within 1 cM of arg4 on chromosome VIII. This analysis also revealed that ATCC4117 carries a diploidization gene allelic to or closely linked to HO, modifiers that reduce the number of haploid spores per ascus and alleles affecting the total level of sporulation.

Klapholz, Sue; Esposito, Rochelle Easton

1980-01-01

155

Immunoselection of tumor variants resistant to antibody-mediated cytotoxicity  

Microsoft Academic Search

The immunological characteristics of two series of metastatic variants of restricted genetic origin were related to their lung-colony-forming potential. A series of metastatic variants was isolated from a tumor-cell population in which heterogeneity appeared following short-term in vivo passage, while a second series of variants were immunoselected in vitro for resistance to antibody-complement-mediated cell lysis. In the case of the

Jean R. Starkey; William C. Davis; James E. Talmadge

1982-01-01

156

Reversion of CTL escape–variant immunodeficiency viruses in vivo  

Microsoft Academic Search

Engendering cytotoxic T-lymphocyte (CTL) responses is likely to be an important goal of HIV vaccines. However, CTLs select for viral variants that escape immune detection. Maintenance of such escape variants in human populations could pose an obstacle to HIV vaccine development. We first observed that escape mutations in a heterogeneous simian immunodeficiency virus (SIV) isolate were lost upon passage to

Thomas C Friedrich; Elizabeth J Dodds; Levi J Yant; Lara Vojnov; Richard Rudersdorf; Candice Cullen; David T Evans; Ronald C Desrosiers; Bianca R Mothé; John Sidney; Alessandro Sette; Kevin Kunstman; Steven Wolinsky; Michael Piatak; Jeffrey Lifson; Austin L Hughes; Nancy Wilson; David H O'Connor; David I Watkins

2004-01-01

157

Charge variants in IgG1  

PubMed Central

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.

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

158

Novel Variant of Tickborne Encephalitis Virus, Russia  

PubMed Central

We isolated a novel strain of tickborne encephalitis virus (TBEV), Glubinnoe/2004, from a patient with a fatal case in Russia. We sequenced the strain, whose landmark features included 57 amino acid substitutions and 5 modified cleavage sites. Phylogenetically, Glubinnoe/2004 is a novel variant that belongs to the Eastern type of TBEV.

Ternovoi, Vladimir A.; Protopopova, Elena V.; Chausov, Eugene V.; Novikov, Dmitry V.; Leonova, Galina N.; Netesov, Sergey V.

2007-01-01

159

Infectious bursal disease virus variant from commercial Leghorn pullets.  

PubMed

An infectious bursal disease virus (IBDV) was isolated from 39-to-43-day-old commercial leghorn pullets suspected of having infectious bursal disease (IBD). These chickens had been vaccinated with a commercial live IBDV vaccine at 28 and 35 days of age. An isolate designated IN was recovered using specific-pathogen-free (SPF) chickens and the BGM-70 established cell line. Experimental studies using SPF chickens vaccinated with either inactivated vaccines made from the vaccine strain used in the problem flock or a standard-type vaccine indicated no protection against the IN isolate. However, two variants and another standard-type vaccine induced protection against the IN isolate. Cross-neutralization tests indicated that the IN isolate differed antigenically from commercial vaccine strains and was related to the variant IBDV strains recently isolated from broilers. To our knowledge, this is the first report of a variant IBDV recovered from commercial layer chickens in the United States. PMID:2157389

Ismail, N M; Saif, Y M; Wigle, W L; Havenstein, G B; Jackson, C

160

Human papillomavirus genome variants.  

PubMed

Amongst the human papillomaviruses (HPVs), the genus Alphapapillomavirus contains HPV types that are uniquely pathogenic. They can be classified into species and types based on genetic distances between viral genomes. Current circulating infectious HPVs constitute a set of viral genomes that have evolved with the rapid expansion of the human population. Viral variants were initially identified through restriction enzyme polymorphisms and more recently through sequence determination of viral fragments. Using partial sequence information, the history of variants, and the association of HPV variants with disease will be discussed with the main focus on the recent utilization of full genome sequence information for variant analyses. The use of multiple sequence alignments of complete viral genomes and phylogenetic analyses have begun to define variant lineages and sublineages using empirically defined differences of 1.0-10.0% and 0.5-1.0%, respectively. These studies provide the basis to define the genetics of HPV pathogenesis. PMID:23998342

Burk, Robert D; Harari, Ariana; Chen, Zigui

2013-08-31

161

Variant Creutzfeldt Jakob Disease  

Microsoft Academic Search

The young and stable median age of those who die of variant Creutzfeldt-Jakob disease has been attributed to age-dependent infection rates. This analysis shows that an influence of age on risk for death after infection better explains age patterns, suggesting that biologic factors peaking in the third decade of life may hasten disease. T he epidemic of variant Creutzfeldt-Jakob disease

M. J. Painter

2000-01-01

162

Generation of Virulence Factor Variants in Staphylococcus aureus Biofilms?  

PubMed Central

Several serious diseases are caused by biofilm-associated Staphylococcus aureus. Colonial variants occur in biofilms of other bacterial species, and S. aureus variants are frequently isolated from biofilm-associated infections. Thus, we studied the generation of variants with altered expression of virulence factors in S. aureus biofilms. We observed that the number of variants found in biofilms, as measured by hemolytic activity, varied for different strains. Further study of hemolytic activity and signaling by the accessory gene regulator (Agr) quorum-sensing system in one S. aureus strain revealed three primary biofilm subpopulations: nonhemolytic (Agr deficient), hemolytic (Agr positive), and hyperhemolytic (also Agr positive). The nonhemolytic variant became the numerically dominant subpopulation in the biofilm. The nonhemolytic variant phenotype was stable and heritable, indicating a genetic perturbation, whereas the hyperhemolytic phenotype was unstable, suggesting a phase variation. Transcription profiling revealed that expression of the agr locus and many extracellular virulence factors was repressed in the nonhemolytic variant. Expression of the agr-activating gene, sarU, was also repressed in the nonhemolytic variant, suggesting one potential regulatory pathway responsible for the Agr-deficient phenotype. We suggest that the development of these variants in biofilms may have important clinical implications.

Yarwood, Jeremy M.; Paquette, Kara M.; Tikh, Ilya B.; Volper, Esther M.; Greenberg, E. Peter

2007-01-01

163

(Alkylamino) piperidine bis(heteroaryl)piperizine analogs are potent, broad-spectrum nonnucleoside reverse transcriptase inhibitors of drug-resistant isolates of human immunodeficiency virus type 1 (HIV-1) and select for drug-resistant variants of HIV-1IIIB with reduced replication phenotypes.  

PubMed Central

The (alkylamino)piperidine bis(heteroaryl)piperizines (AAP-BHAPs) are a new class of human immunodeficiency virus type 1 (HIV-1)-specific inhibitors which were identified by targeted screening of recombinant reverse transcriptase (RT) enzymes carrying key nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance-conferring mutations and NNRTI-resistant variants of HIV-1. Phenotypic profiling of the two most potent AAP-BHAPs, U-95133 and U-104489, against in vitro-selected drug-resistant HIV-1 variants carrying the NNRTI resistance-conferring mutation (Tyr->Cys) at position 181 of the HIV-1 RT revealed submicromolar 90% inhibitory concentration estimates for these compounds. Moreover, U-104489 demonstrated potent activity against BHA-P-resistant HIV-1MF harboring the Pro-236->Leu RT substitution and significantly suppressed the replication of clinical isolates of HIV-1 resistant to both delavirdine (BHAP U-90152T) and zidovudine. Biochemical and phenotypic characterization of AAP-BHAPresistant HIV-1IIIB variants revealed that high-level resistance to the AAP-BHAPs was mediated by a Gly-190->Glu substitution in RT, which had a deleterious effect on the integrity and enzymatic activity of virion-associated RT heterodimers, as well as the replication capacity of these resistant viruses.

Olmsted, R A; Slade, D E; Kopta, L A; Poppe, S M; Poel, T J; Newport, S W; Rank, K B; Biles, C; Morge, R A; Dueweke, T J; Yagi, Y; Romero, D L; Thomas, R C; Sharma, S K; Tarpley, W G

1996-01-01

164

Occurrence of Genetic Variants of Listeria monocytogenes Strains.  

PubMed

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

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

2013-09-01

165

Classification and diagnostic criteria of variants of Hirschsprung's disease.  

PubMed

"Variants of Hirschsprung's disease" are conditions that clinically resemble Hirschsprung's disease (HD), despite the presence of ganglion cells in rectal suction biopsies. The diagnosis and management of these patients can be challenging. Specific histological, immunohistochemical and electron microscopic investigations are required to characterize this heterogeneous group of functional bowel disorders. Variants of HD include intestinal neuronal dysplasia, intestinal ganglioneuromatosis, isolated hypoganglionosis, immature ganglia, absence of the argyrophil plexus, internal anal sphincter achalasia and congenital smooth muscle cell disorders such as megacystis microcolon intestinal hypoperistalsis syndrome. This review article systematically classifies variants of HD based on current diagnostic criteria with an additional focus on pathogenesis, epidemiology, clinical presentation, management and outcome. PMID:23943250

Friedmacher, Florian; Puri, Prem

2013-09-01

166

LDH variants in India  

Microsoft Academic Search

17 examples of genetically controlled variation of LDH have been encountered in a survey of 1331 Indian blood samples collected in Calcutta and Madras. 15 of the variants (10 in Calcutta and 5 in Madras) were identical and have been given the trivial name ‘Calcutta-1’. The other 2 examples were found in Madras and have been called ‘Madras-1’. ‘Calcutta-1’ is

S. R. Das; B. N. Mukherjee; S. K. Das; R. ANANTHAKRISItNAN; N. M. Blake; R. L. Kirk

1970-01-01

167

Virulence aspects of Listeria monocytogenes LO28 high pressure-resistant variants.  

PubMed

High pressure treatment is a novel food processing approach for reducing pathogens in foods and food ingredients. However, relatively little is known about the pathogenic potential of organisms that survive the treatment. Twelve previously isolated and characterized variants of Listeria monocytogenes LO28 obtained after a high pressure treatment were assessed for their virulence potential and antibiotic susceptibility. Ten variants showed attenuated virulence while two variants retained full virulence in a mouse model of infection. Seven of the attenuated variants demonstrated a reduction in virulence factor activity. Compared to the wild type, all variants exhibited similar or increased susceptibility to multiple antibiotics commonly used in listeriosis treatment. PMID:23603274

Van Boeijen, Ineke K H; Casey, Pat G; Hill, Colin; Moezelaar, Roy; Zwietering, Marcel H; Gahan, Cormac G M; Abee, Tjakko

2013-04-17

168

Morphological Variants of Proteus hauseri  

Microsoft Academic Search

SUMMARY Cultures of Proteus hauseri may consist of one or more of five colonial variants. Population pressure experiments started with one variant eventually yielded all other variants. Y variants form raised non-swarming colonies on a MacConkey-type agar at 37O, but swarm in concentric step-like rings at room temperature on this medium; they swarm in step-like concentric rings on nutrient agar

J. N. COETZEE; T. G. SACKS

1960-01-01

169

Persistence of newly detected human papillomavirus type 31 infection, stratified by variant lineage.  

PubMed

Variants of human papillomavirus (HPV) type 31 have been shown to be related both to risk of cervical lesions and racial composition of a population. It is largely undetermined whether variants differ in their likelihood of persistence. Study subjects were women who participated in the ASCUS-LSIL Triage Study and who had a newly detected HPV31 infection during a two-year follow-up with six-month intervals. HPV31 isolates were characterized by sequencing and assigned to one of three variant lineages. Loss of the newly detected HPV31 infection was detected in 76 (47.5%) of the 160 women (32/67 with A variants, 16/27 with B variants and 28/66 with C variants). The adjusted hazard ratio associating loss of the infection was 1.2 (95% CI, 0.7-2.1) for women with A variants and 2.1 (95% CI, 1.2-3.5) for women with B variants when compared with those with C variants. Infections with A and C variants were detected in 50 and 41 Caucasian women and in 15 and 23 African-American women, respectively. The likelihood of clearance of the infection was significantly lower in African-American women with C variants than in African-American women with A variants (p = 0.05). There was no difference in the likelihood of clearance between A and C variants among Caucasian women. Our data indicated that infections with B variants were more likely to resolve than those with C variants. The difference in clearance of A vs. C variants in African-Americans, but not in Caucasians, suggests a possibility of the race-related influence in retaining the variant-specific infection. PMID:22729840

Xi, Long Fu; Schiffman, Mark; Koutsky, Laura A; He, Zhonghu; Winer, Rachel L; Hulbert, Ayaka; Lee, Shu-Kuang; Ke, Yang; Kiviat, Nancy B

2012-07-11

170

Engineering of Kex2 variants exhibiting altered substrate specificity.  

PubMed

Engineering of secreted protease variants exhibiting altered substrate specificity is a challenging task because effective screening methods for the desired property are not available yet. In this study, we sought to obtain variants of Kex2, a yeast Golgi protease, which exhibit altered P2 specificity. We first randomly mutated three Asp residues (D176, D210, and D211) that constitute the S2 pocket of Kex2 and then isolated from the resulting library Kex2 variants that preferred substrates with Met (poorly preferred by wild type Kex2) at the P2 position using a yeast-based screening method. The Kex2 variants isolated from this initial screening were further tested against various substrate sequences. Four out of the 16 isolated Kex2 variants showed greater preference for Met than for Lys (preferred by the wild-type Kex2) at the P2 position. We therefore suggest that our method might serve as an efficient tool for engineering and directing the evolution of secreted proteases. PMID:16229820

Han, Hye-Eun; Rho, Seong-Hwan; Lee, Yong Jae; Park, Woo Jin

2005-10-06

171

Identification of Aspergillus flavus isolates as potential biocontrol agents of aflatoxin contamination in crops.  

PubMed

Aspergillus flavus, a haploid organism found worldwide in a variety of crops, including maize, cottonseed, almond, pistachio, and peanut, causes substantial and recurrent worldwide economic liabilities. This filamentous fungus produces aflatoxins (AFLs) B1 and B2, which are among the most carcinogenic compounds from nature, acutely hepatotoxic and immunosuppressive. Recent efforts to reduce AFL contamination in crops have focused on the use of nonaflatoxigenic A. flavus strains as biological control agents. Such agents are applied to soil to competitively exclude native AFL strains from crops and thereby reduce AFL contamination. Because the possibility of genetic recombination in A. flavus could influence the stability of biocontrol strains with the production of novel AFL phenotypes, this article assesses the diversity of vegetative compatibility reactions in isolates of A. flavus to identify heterokaryon self-incompatible (HSI) strains among nonaflatoxigenic isolates, which would be used as biological controls of AFL contamination in crops. Nitrate nonutilizing (nit) mutants were recovered from 25 A. flavus isolates, and based on vegetative complementation between nit mutants and on the microscopic examination of the number of hyphal fusions, five nonaflatoxigenic (6, 7, 9 to 11) and two nontoxigenic (8 and 12) isolates of A. flavus were phenotypically characterized as HSI. Because the number of hyphal fusions is reduced in HSI strains, impairing both heterokaryon formation and the genetic exchanges with aflatoxigenic strains, the HSI isolates characterized here, especially isolates 8 and 12, are potential agents for reducing AFL contamination in crops. PMID:23726204

Rosada, L J; Sant'anna, J R; Franco, C C S; Esquissato, G N M; Santos, P A S R; Yajima, J P R S; Ferreira, F D; Machinski, M; Corrêa, B; Castro-Prado, M A A

2013-06-01

172

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

PubMed

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

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

2013-02-01

173

Comparative Intracellular Activity of 11 Antistaphylococcal Antibiotics (AABS) against a Stable, Thymidine-dependent Small Colony Variant (SCV) and its Normal Phenotype Isolate (NP) Counterpart from a Cystic Fibrosis Patient  

Microsoft Academic Search

Objectives: SCVs are able to persist more efficiently within host cells making infections difficult to eradicate. We therefore compare the intracellular activities of AABs against a SCV and its NP counterpart. Methods: Mec A negative SCV and NP were isolated from the same patient and showed identical PFGE profiles. MICs were measured by microdilution in MHB. Intracellular activities were determined

H. A. Nguyen; O. Denis; A. Vergison; P. M. Tulkens; M. Struelens; F. Van Bambeke

174

Variant angina in an adolescent  

Microsoft Academic Search

We describe a case of variant angina associated with acute myocardial ischemia in an adolescent presenting with severe chest pain and transient ST elevation. Subsequent cardiac catheterization revealed normal coronary anatomy, and the patient has been asymptomatic since discharge on calcium channel blockers. Variant angina is a rare cause of chest pain in adolescents.

D. Ivy; J. Kaye; D. Flitter; J. Wiggins

1994-01-01

175

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

PubMed

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

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

2012-06-07

176

The Naturally Occurring Variant of Estrogen Receptor (ER) ER E7 Suppresses Estrogen-Dependent Transcriptional Activation by Both Wild-Type ER  and ER  

Microsoft Academic Search

We have isolated and functionally characterized the exon 7-skipped variant (ERE7) of estrogen receptor (ER), which has emerged as the predominant variant expressed in multi- ple normal and tumoral tissues. However, to date no function has been established for this variant in mammalian cells. ERE7 exhibits a negligible ability to bind ligands, insensi- tivity to allosteric modulation by estrogen and

JUANA M. GARCÍA PEDRERO; PEDRO ZUAZUA; CARLOS MARTÍNEZ-CAMPA; PEDRO S. LAZO; SOFIA RAMOS

2003-01-01

177

Separation of time variant vibration sources by short time coherent output power  

NASA Astrophysics Data System (ADS)

This effort describes the use of time variant coherence causality based analysis to separate the effects of nonstationary time variant vibration excitation sources. A time variant coherence function using the Short Time Fourier Transform (STFT) is first discussed. The concept of a time variant coherent output power for source separation of systems with time variant transfer functions is developed. A parametric study is performed to examine the coherent output power separation capabilities with respect to the data processing parameters. The study guided the selection of the time-frequency processing parameters judged to provide a suitable compromise between the time event localization and output amplitude source separation. The time variant coherent output power is then applied to separate the effects of the two possible excitation sources on the prototype vibration isolation floor. The application was a subscale prototype isolation floor for a proposed vibration sensitive equipment site adjacent to a busy freight rail line. The moving train created time variant transmission paths. As there was a direct line of sight between the prototype floor and the rail line there was an airborne acoustic excitation path in addition to a ground path. The short time coherent output power was applied to separate prototype isolation floor vibration into respective components related to the two candidate sources. The analysis and discussion of the results focuses upon the interpretation and issues in such a complicated realistic environment. Ultimately the application was successful providing an explanation as to why the observed vibration isolation was degraded at higher frequencies.

Trethewey, Martin W.

2011-02-01

178

Heteromorphic variants of chromosome 9  

PubMed Central

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

2013-01-01

179

The Herpes Simplex Virus Type 1 BgKL Variant, Unlike the BgOL Variant, Shows a Higher Association with Orolabial Infection than with Infections at Other Sites, Supporting the Variant-Dispersion-Replacement Hypothesis  

Microsoft Academic Search

The identification and geographic distribution of the herpes simplex virus type 1 (HSV-1) BglII restriction fragment length polymorphism (RFLP) variants named BgKL and BgOL in clinical isolates from orolabial and cutaneous sites were described in our previous reports, in which the dispersion and replacement of HSV-1 variants were proposed. The base substitution sites deduced from the BgKL multiple RFLP variations

Shigeru Ozawa; Hiroyuki Eda; Yasuyuki Ishii; Fumihiko Ban; Toshiyuki Funabashi; Seiichiro Hata; Kozaburo Hayashi; Hiroki Iga; Takao Ikushima; Hiroaki Ishiko; Tomoo Itagaki; Rinji Kawana; Shunsaku Kobayashi; Takeo Ogino; Tsuyoshi Sekizawa; Yoshikazu Shimomura; Hiroshi Shiota; Ryoichi Mori; Takashi Nakakita; Yoshio Numazaki; Yoshikatsu Ozaki; Shigeru Yamamoto; Kamesaburo Yoshino; Kazuo Yanagi

2007-01-01

180

[Variants of hermaphroditism (clinical findings)].  

PubMed

False and true hermaphroditism (FH and TH) are often encountered in surgery for hypospadia. A clinically validated classification of various types and variants of hermaphroditism is proposed. FH is divided into male FH and female FH. TH also falls into two categories: TH without anomalies of external genitalia and that with these anomalies. The latter category has three variants: 1) all genitalia of males or females and some genitalia of the other sex; 2) some female and male organs in various combinations; 3) all organs of both sexes. All TH variants are illustrated by 5 case reports. These patients were thoroughly examined and their sex was surgically corrected. PMID:14708246

Derevianko, I M; Derevianko, T I; Ryzhkov, V V

181

Variants of beta-glucosidase  

DOEpatents

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

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

2009-12-29

182

Variant View: Visualizing Sequence Variants in their Gene Context.  

PubMed

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

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

2013-12-01

183

A Common Property of Amyotrophic Lateral Sclerosis-associated Variants  

PubMed Central

At least 119 mutations in the gene encoding copper/zinc superoxide dismutase (SOD1) cause amyotrophic lateral sclerosis by an unidentified toxic gain of function. We compared the dynamic properties of 13 as-isolated, partially metallated, SOD1 variant enzymes using hydrogen-deuterium exchange. We identified a shared property of these familial amyotrophic lateral sclerosis-related SOD1 variants, namely structural and dynamic change affecting the electrostatic loop (loop VII) of SOD1. Furthermore, SOD1 variants that have severely compromised metal binding affinities demonstrated additional structural and dynamic changes to the zinc-binding loop (loop IV) of SOD1. Although the biological consequences of increased loop VII mobility are not fully understood, this common property is consistent with the hypotheses that SOD1 mutations exert toxicity via aggregation or aberrant association with other cellular constituents.

Molnar, Kathleen S.; Karabacak, N. Murat; Johnson, Joshua L.; Wang, Qi; Tiwari, Ashutosh; Hayward, Lawrence J.; Coales, Stephen J.; Hamuro, Yoshitomo; Agar, Jeffrey N.

2009-01-01

184

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

Microsoft Academic Search

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

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

2009-01-01

185

Developing a DNA variant database.  

PubMed

Disease- and locus-specific variant databases have been a valuable resource to clinical and research geneticists. With the recent rapid developments in technologies, the number of DNA variants detected in a typical molecular genetics laboratory easily exceeds 1,000. To keep track of the growing inventory of DNA variants, many laboratories employ information technology to store the data as well as distributing the data and its associated information to clinicians and researchers via the Web. While it is a valuable resource, the hosting of a web-accessible database requires collaboration between bioinformaticians and biologists and careful planning to ensure its usability and availability. In this chapter, a series of tutorials on building a local DNA variant database out of a sample dataset will be provided. However, this tutorial will not include programming details on building a web interface and on constructing the web application necessary for web hosting. Instead, an introduction to the two commonly used methods for hosting web-accessible variant databases will be described. Apart from the tutorials, this chapter will also consider the resources and planning required for making a variant database project successful. PMID:18453092

Fung, David C Y

2008-01-01

186

Structure, tissue distribution and estrogen regulation of splice variants of the sea bream estrogen receptor ? gene.  

PubMed

Estrogen actions are mainly mediated by specific nuclear estrogen receptors (ERs), for which different genes and a diversity of transcript variants have been identified, mainly in mammals. In this study, we investigated the presence of ER splice variants in the teleost fish gilthead sea bream (Sparus auratus), by comparison with the genomic organization of the related species Takifugu rubripes. Two exon2-deleted ER? transcript variants were isolated from liver cDNA of estradiol-treated fish. The ?E2 variant lacks ER? exon 2, generating a premature termination codon and a putative C-terminal truncated receptor, while the ?E2,3* variant contains an in-frame deletion of exon 2 and part of exon 3 and codes for a putative ER? protein variant lacking most of the DNA-binding domain. Both variants were expressed at very low levels in several female and male sea bream tissues, and their expression was highly inducible in liver by estradiol-17? treatment with a strong positive correlation with the typical wild-type (wt) ER? response in this tissue. These findings identify novel estrogen responsive splice variants of fish ER?, and provide the basis for future studies to investigate possible modulation of wt-ER actions by splice variants. PMID:22579469

Pinto, P I S; Teodósio, R; Socorro, S; Power, D M; Canário, A V M

2012-05-03

187

Evaluation of selective competitive binding of basic drugs to alpha1-acid glycoprotein variants.  

PubMed

We examined the binding of various basic drugs to the F(1)S and A genetic variants of alpha(1)-acid glycoprotein (AGP), which were isolated from native human commercial AGP (total AGP) by chromatography on an immobilized copper(II) affinity adsorbent. The values of the dissociation constant (K(d)) of some basic drugs with the F(1)S variant in equilibrium dialysis differed characteristically from those with the A variant. The selective binding to these variants was evaluated by measuring the displacement ratio of dicumarol bound to the F(1)S variant or that of acridine orange bound to the A variant, using circular dichroism spectroscopy. There was reasonably good agreement between the K(d) values and displacement ratios. There was a characteristic difference between the values of inhibition constant (K(i)) of basic drugs towards dipyridamole binding to F(1)S and towards disopyramide binding to A in total AGP. We found that the K(i) values for dipyridamole binding were well correlated with the K(d) values for the F(1)S variant, whereas those for disopyramide binding were well correlated with the K(d) values for the A variant. In conclusion, the higher the affinity of basic drugs for AGP, the more they inhibit the binding of other basic drugs, and further, the inhibitory potency depends on the selectivity of binding to the AGP variants. PMID:20045943

Ishizaki, Junko; Fukaishi, Akiko; Fukuwa, Chie; Yamazaki, Satoko; Tabata, Mayu; Ishida, Takuya; Suga, Yukio; Arai, Kunizo; Yokogawa, Koichi; Miyamoto, Ken-ichi

2010-01-01

188

Global Distribution of a Variant of the Circumsporozoite Gene of Plasmodium vivax. (Reannouncement with New Availability Information).  

National Technical Information Service (NTIS)

The global distribution of a newly described variant of the Plasmodium vivax circumsporozoite (CS) gene was determined by genetic analysis of wild isolates. Whole blood specimens were collected on filter paper from patients infected with P. vivax in South...

K. C. Kain J. Keystone E. D. Franke D. E. Lanar

1991-01-01

189

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

PubMed Central

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

2012-01-01

190

Flashlamp for NIF: Russian variant  

SciTech Connect

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

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

1996-11-01

191

Are isolated wetlands isolated?  

USGS Publications Warehouse

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

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

2011-01-01

192

Association between variant plasmid formation and senescence in retroplasmid-containing strains of Neurospora spp.  

PubMed

Serial transfer of Neurospora strains harboring the Mauriceville and Varkud mitochondrial retroplasmids frequently displays erratic growth and senescence. Growth impairment is associated with the formation of variant forms of the retroplasmids that can integrate into the mitochondrial genome, resulting in mtDNA rearrangements and eventual loss of respiratory function. Here, we evaluate the rate at which variant plasmids arise in subcultures of the Mauriceville strain of N. crassa and their association with the senescent phenotype. Although variant plasmid formation preceded senescence, subcultures were found to tolerate variant plasmids for variable lengths of time and no correlation could be made between the specific sequence inserted in the plasmids and the rate or frequency of senescence. In addition, many cultures were found to contain more than one variant plasmid. The lack of concordance between the timing of variant plasmid formation and growth cessation distinguishes these two events, and provides additional insight into the etiology of senescence. We also detected differences in the frequency of senescence between retroplasmid-containing strains of N. crassa and N. intermedia and report the isolation of a strain in which senescence occurs in the absence of variant plasmid formation or detectable alterations in mtDNA. Our findings indicate there are multiple pathways that lead to senescence and suggest there are host-specific mechanisms that suppress the deleterious effects of the variant plasmids. PMID:11405101

Fox, A N; Kennell, J C

2001-04-01

193

Stability, Entrapment and Variant Formation of Salmonella Genomic Island 1  

PubMed Central

Background The Salmonella genomic island 1 (SGI1) is a 42.4 kb integrative mobilizable element containing several antibiotic resistance determinants embedded in a complex integron segment In104. The numerous SGI1 variants identified so far, differ mainly in this segment and the explanations of their emergence were mostly based on comparative structure analyses. Here we provide experimental studies on the stability, entrapment and variant formation of this peculiar gene cluster originally found in S. Typhimurium. Methodology/Principal Findings Segregation and conjugation tests and various molecular techniques were used to detect the emerging SGI1 variants in Salmonella populations of 17 Salmonella enterica serovar Typhimurium DT104 isolates from Hungary. The SGI1s in these isolates proved to be fully competent in excision, conjugal transfer by the IncA/C helper plasmid R55, and integration into the E. coli chromosome. A trap vector has been constructed and successfully applied to capture the island on a plasmid. Monitoring of segregation of SGI1 indicated high stability of the island. SGI1-free segregants did not accumulate during long-term propagation, but several SGI1 variants could be obtained. Most of them appeared to be identical to SGI1-B and SGI1-C, but two new variants caused by deletions via a short-homology-dependent recombination process have also been detected. We have also noticed that the presence of the conjugation helper plasmid increased the formation of these deletion variants considerably. Conclusions/Significance Despite that excision of SGI1 from the chromosome was proven in SGI1+ Salmonella populations, its complete loss could not be observed. On the other hand, we demonstrated that several variants, among them two newly identified ones, arose with detectable frequencies in these populations in a short timescale and their formation was promoted by the helper plasmid. This reflects that IncA/C helper plasmids are not only involved in the horizontal spreading of SGI1, but may also contribute to its evolution.

Kiss, Janos; Nagy, Bela; Olasz, Ferenc

2012-01-01

194

Biologically diverse molecular variants within a single HIV1 isolate  

Microsoft Academic Search

AIDS is a disorder characterized by a slow progressive impairment of immune function and by infection of human immunodeficiency viruses (HIV-1, HIV-2)1-4. Our knowledge of how these viruses cause disease in man, or how the related lentiviruses (visna and equine infectious anaemia virus) cause disease in animals, is still fragmentary. In particular, the significance of genetic variation in HIV-1, occurring

Amanda G. Fisher; Barbara Ensoli; David Looney; Andrea Rose; Robert C. Gallo; Michael S. Saag; George M. Shaw; Beatrice H. Hahn; Flossie Wong-Staal

1988-01-01

195

Isolation of a variant of subtilosin A with hemolytic activity.  

PubMed

Bacillus subtilis produces an anionic bacteriocin called subtilosin A that possesses antibacterial activity against certain gram-positive bacteria. In this study, we uncovered a hemolytic mutant of B. subtilis that produces an altered form of subtilosin A. The mutant bacteriocin, named subtilosin A1, has a replacement of threonine at position 6 with isoleucine. In addition to the hemolytic activity, subtilosin A1 was found to exhibit enhanced antimicrobial activity against specific bacterial strains. The B. subtilis albB mutant that does not produce a putative immunity peptide was more sensitive to both subtilosin A and subtilosin A1. A spontaneous suppressor mutation of albB that restored resistance to subtilosin A and subtilosin A1 was obtained. The sbr (subtilosin resistance) mutation conferring the resistance is not linked to the sboA-alb locus. The sbr mutation does not increase the resistance of B. subtilis to other cell envelope-targeted antimicrobial agents, indicating that the mutation specifically confers the resistance to subtilosins. The findings suggest possible bioengineering approaches for obtaining anionic bacteriocins with enhanced and/or altered bactericidal activity. Furthermore, future identification of the subtilosin-resistant mutation could provide insights into the mechanism of subtilosin A activity. PMID:19633086

Huang, Tai; Geng, Hao; Miyyapuram, Venugopal R; Sit, Clarissa S; Vederas, John C; Nakano, Michiko M

2009-07-24

196

Isolation of a Variant of Subtilosin A with Hemolytic Activity?  

PubMed Central

Bacillus subtilis produces an anionic bacteriocin called subtilosin A that possesses antibacterial activity against certain gram-positive bacteria. In this study, we uncovered a hemolytic mutant of B. subtilis that produces an altered form of subtilosin A. The mutant bacteriocin, named subtilosin A1, has a replacement of threonine at position 6 with isoleucine. In addition to the hemolytic activity, subtilosin A1 was found to exhibit enhanced antimicrobial activity against specific bacterial strains. The B. subtilis albB mutant that does not produce a putative immunity peptide was more sensitive to both subtilosin A and subtilosin A1. A spontaneous suppressor mutation of albB that restored resistance to subtilosin A and subtilosin A1 was obtained. The sbr (subtilosin resistance) mutation conferring the resistance is not linked to the sboA-alb locus. The sbr mutation does not increase the resistance of B. subtilis to other cell envelope-targeted antimicrobial agents, indicating that the mutation specifically confers the resistance to subtilosins. The findings suggest possible bioengineering approaches for obtaining anionic bacteriocins with enhanced and/or altered bactericidal activity. Furthermore, future identification of the subtilosin-resistant mutation could provide insights into the mechanism of subtilosin A activity.

Huang, Tai; Geng, Hao; Miyyapuram, Venugopal R.; Sit, Clarissa S.; Vederas, John C.; Nakano, Michiko M.

2009-01-01

197

Bacterial Phenotype Variants in Group B Streptococcal Toxic Shock Syndrome1  

PubMed Central

We conducted genetic and functional analyses of isolates from a patient with group B streptococcal (GBS) necrotizing fasciitis and toxic shock syndrome. Tissue cultures simultaneously showed colonies with high hemolysis (HH) and low hemolysis (LH). Conversely, the HH and LH variants exhibited low capsule (LC) and high capsule (HC) expression, respectively. Molecular analysis demonstrated that the 2 GBS variants were of the same clonal origin. Genetic analysis found a 3-bp deletion in the covR gene of the HH/LC variant. Functionally, this isolate was associated with an increased growth rate in vitro and with higher interleukin-8 induction. However, in whole blood, opsonophagocytic and intracellular killing assays, the LH/HC phenotype demonstrated higher resistance to host phagocytic killing. In a murine model, LH/HC resulted in higher levels of bacteremia and increased host mortality rate. These findings demonstrate differences in GBS isolates of the same clonal origin but varying phenotypes.

Johansson, Linda; Dahesh, Samira; Van Sorge, Nina M.; Darenberg, Jessica; Norgren, Mari; Sjolin, Jan; Nizet, Victor; Norrby-Teglund, Anna

2009-01-01

198

Molecular Characterization of Mycobacterium tuberculosis H37Rv/Ra Variants: Distinguishing the Mycobacterial Laboratory Strain†  

PubMed Central

The Mycobacterium tuberculosis strains H37Rv and H37Ra are the most commonly used controls for M. tuberculosis identification in the clinical and research laboratory setting. To reduce the likelihood of misidentification and possible cross-contamination with this laboratory neotype, it is important to be able to distinguish H37 from clinical isolates. To provide a reference for identifying H37, we used multiple molecular techniques to characterize H37 strains, including 18 of the most frequently used variants available through the American Type Culture Collection. Isolates were genotyped using gene probes to IS6110 and IS1085. In addition, we performed polymorphic GC-rich sequence typing (PGRS), spoligotyping, determination of variable number of tandem repeats (VNTR), and PCR amplification of the mtp40, msx4, and mpp8 polymorphic regions. Southern hybridization with IS6110 provided the most discrimination, differentiating the 18 H37 isolates into 10 discrete patterns made up of 9 H37Rv variants and 1 H37Ra variant. PGRS, IS1085, mpp8, and spoligotyping were not able to distinguish any H37 variants, while VNTR and msx4 discriminated two. Only IS6110 and spoligotyping could distinguish the H37 strain from clinical isolates. In summary, spoligotyping and IS6110 provide a rapid and accurate way to identify H37 contamination, though IS6110 can, in addition, classify many of the H37 variants that would otherwise require phenotypic segregation.

Bifani, P.; Moghazeh, S.; Shopsin, B.; Driscoll, J.; Ravikovitch, A.; Kreiswirth, B. N.

2000-01-01

199

Variant Humicola grisea CBH1.1  

DOEpatents

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.

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

2011-05-31

200

Variant Humicola grisea CBH1.1  

DOEpatents

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.

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

2008-12-02

201

Fecal influenza in mammals: selection of novel variants.  

PubMed

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

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

2013-08-21

202

Evaluation of perceived threat differences posed by filovirus variants.  

PubMed

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

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

2011-11-09

203

GCPII variants, paralogs and orthologs.  

PubMed

Glutamate carboxypeptidase II (GCPII) and its splice variants, paralogs and human homologs represent a family of proteins with diverse tissue distribution, cellular localization and largely unknown function which have been explored only recently. While GCPII itself has been thoroughly studied from different perspectives, as clearly documented in this series of reviews, very little is known about other members of its family, even though they might be biologically relevant. Differential expression of individual GCPII splice variants is associated with tumor progression and prognosis of prostate cancer. The best studied GCPII homolog, GCPIII or NAALADase II, may be a valid pharmaceutical target for itself since it may compensate for a lack of normal GCPII enzymatic activity. Detailed molecular characterization of this family of proteins is thus very important not only with respect to the potential therapeutic use of GCPII inhibitors, but also for better understanding of the biological role of GCPII within as well as outside the nervous system. PMID:22304710

Hlouchová, K; Navrátil, V; Tykvart, J; Sácha, P; Konvalinka, J

2012-01-01

204

Pigmented pilomatricoma: an underrecognized variant.  

PubMed

The presence of melanin pigment and/or melanocytes in pilomatricoma has been rarely documented. In this study, we analyzed the incidence and clinicopathological features of pigmented pilomatricoma. Fifty-seven consecutive pilomatricoma cases from 53 Japanese patients were examined in this study. In fourteen cases (24.6%), pigmentation was observed in pilomatricoma. This variant equally affected in males and females, and the common locations were the upper arm and face. Proliferation of dendritic melanocytes was observed within basaloid cell nests in all cases, and melanin pigment was also present within the cytoplasm of the basaloid cells in 11 cases. Melanin pigment was also present in the shadow cells in 7 cases. The incidence of pigmented pilomatricoma as documented in previous reports is approximately 10%. However, our analysis revealed that pigmented pilomatricoma was found in 24.6% of Japanese cases of pilomatricoma, thus, this variant is not uncommon and may be under-recognized. PMID:24040455

Ishida, Mitsuaki; Okabe, Hidetoshi

2013-08-15

205

Pigmented pilomatricoma: an underrecognized variant  

PubMed Central

The presence of melanin pigment and/or melanocytes in pilomatricoma has been rarely documented. In this study, we analyzed the incidence and clinicopathological features of pigmented pilomatricoma. Fifty-seven consecutive pilomatricoma cases from 53 Japanese patients were examined in this study. In fourteen cases (24.6%), pigmentation was observed in pilomatricoma. This variant equally affected in males and females, and the common locations were the upper arm and face. Proliferation of dendritic melanocytes was observed within basaloid cell nests in all cases, and melanin pigment was also present within the cytoplasm of the basaloid cells in 11 cases. Melanin pigment was also present in the shadow cells in 7 cases. The incidence of pigmented pilomatricoma as documented in previous reports is approximately 10%. However, our analysis revealed that pigmented pilomatricoma was found in 24.6% of Japanese cases of pilomatricoma, thus, this variant is not uncommon and may be under-recognized.

Ishida, Mitsuaki; Okabe, Hidetoshi

2013-01-01

206

Navigation Stability: A New Isolation Level in ORDBMSs  

Microsoft Academic Search

SUMMARY In order to enhance the performance, many database management systems (DBMSs) execute transactions at isolation level 2rather than at isolation level 3, the strict two phase locking, even if it sacrifices consistency to a certain de- gree. Cursor stability, a variant of isolation level 2in relational DBMSs (RDBMSs), has been widely used as a useful technique for obtaining concurrency

Hong-Suk SEO; Kyu-Young WHANG; Yang-Sae MOON; Ji-Woong CHANG; Eui-Kyung HONG

2001-01-01

207

[Stiff man syndrome and variants].  

PubMed

Stiff man syndrome (SMS) and its variants are rare neurological disorders with unusual, often awkward motor and psychological symptoms. Misdiagnoses are frequent and differentiation from psychogenic movement disorder may be difficult. Clinical suspicion can be substantiated by neurophysiological and immunological testing. Autoimmunity against certain proteins of inhibitory synapses appears to be a key feature that links SMS to other autoimmune encephalopathies and endocrinopathies. According to retrospective analyses a front-loaded long-term methylprednisolone treatment appears to be most effective. PMID:23568166

Meinck, H-M

2013-04-01

208

Variant forms of autoimmune hepatitis  

Microsoft Academic Search

Variant forms of autoimmune hepatitis have features that are intermixed with another disorder (overlap syndrome) or findings\\u000a that are inconsistent with or insufficient for a confident diagnosis of classic disease (outlier syndrome). Diagnostic criteria\\u000a have not been codified, but application of a modified scoring system provides a template that can be combined with clinical\\u000a findings to ensure uniform evaluation and

Albert J. Czaja

1999-01-01

209

Variant Creutzfeldt-Jakob disease.  

PubMed

It is clear that the prion strain causing bovine spongiform encephalopathy (BSE) in cattle has infected human beings, manifesting itself as a novel human prion disease, variant Creutzfeldt-Jakob disease (CjD). Studies of the incubation periods seen in previous epidemics of human prion disease and of the effect of transmission barriers limiting spread of these diseases between species, suggest that the early variant CJD cases may have been exposed during the preclinical phase of the BSE epidemic. It must therefore be considered that many cases may follow from later exposure in an epidemic that would be expected to evolve over decades. Since the number of people currently incubating this disease is unknown, there are concerns that prions might be transmitted iatrogenically via blood transfusion, tissue donation, and, since prions resist routine sterilisation, contamination of surgical instruments. Such risks remain unquantified. Although variant CJD can be diagnosed during life by tonsil biopsy, a prion-specific blood test is needed to assess and manage this potential threat to public health. The theoretical possibility that BSE prions might have transferred to other species and continue to present a risk to human health cannot be excluded at present. PMID:10440324

Collinge, J

1999-07-24

210

Keratin variants associate with progression of fibrosis during chronic hepatitis C infection.  

PubMed

Keratins 8 and 18 (K8/K18) protect the liver from various forms of injury. Studies of liver explants from a large cohort of U.S. patients showed that K8/K18 mutations confer a risk to developing end-stage liver diseases, though which diseases are preferentially involved is unknown. We tested the hypothesis that K8/K18 variants are associated with chronic hepatitis C (CHC) and that their presence correlates with progression of fibrosis. Genomic DNA was isolated from peripheral blood of a well-characterized German cohort of 329 patients with CHC infection. Exonic regions were PCR-amplified and analyzed using denaturing high-performance liquid chromatography and DNA sequencing. Our findings showed: (1) amino acid altering keratin heterozygous variants in 24 of 329 CHC patients (7.3%) and non-coding heterozygous variants in 26 patients (7.8%), and (2) 3 new exonic K8 variants (T26R/G55A/A359T); 6 novel non-coding variants and one K18 coding variant (K18 S230T; 2 patients). The most common variants were K8 R341H (10 patients), K8 G62C (6 patients) and K8 I63V (4 patients). A novel and exclusive association of an intronic KRT8 IVS7+10delC deletion in all 10 patients with K8 R341H was observed. Notably, there was a significant association of exonic, but not of intronic K8 variants with increased fibrosis. In conclusion, previously described and novel K8 variants are present in a German population and collectively associate with progression of fibrosis in CHC infection. The unique 100% segregation of the most common K8 variant, R341H, with an intronic deletion suggests that one of these two genetic changes might lead to the other. PMID:16729313

Strnad, Pavel; Lienau, Tim C; Tao, Guo-Zhong; Lazzeroni, Laura C; Stickel, Felix; Schuppan, Detlef; Omary, M Bishr

2006-06-01

211

agr function in clinical Staphylococcus aureus isolates.  

PubMed

The accessory gene regulator (agr) of Staphylococcus aureus is a global regulator of the staphylococcal virulon, which includes secreted virulence factors and surface proteins. The agr locus is important for virulence in a variety of animal models of infection, and has been assumed by inference to have a major role in human infection. Although most human clinical S. aureus isolates are agr(+), there have been several reports of agr-defective mutants isolated from infected patients. Since it is well known that the agr locus is genetically labile in vitro, we have addressed the question of whether the reported agr-defective mutants were involved in the infection or could have arisen during post-isolation handling. We obtained a series of new staphylococcal isolates from local clinical infections and handled these with special care to avoid post-isolation mutations. Among these isolates, we found a number of strains with non-haemolytic phenotypes owing to mutations in the agr locus, and others with mutations elsewhere. We have also obtained isolates in which the population was continuously heterogeneous with respect to agr functionality, with agr(+) and agr(-) variants having otherwise indistinguishable chromosomal backgrounds. This finding suggested that the agr(-) variants arose by mutation during the course of the infection. Our results indicate that while most clinical isolates are haemolytic and agr(+), non-haemolytic and agr(-) strains are found in S. aureus infections, and that agr(+) and agr(-) variants may have a cooperative interaction in certain types of infections. PMID:18667559

Traber, Katrina E; Lee, Elsie; Benson, Sarah; Corrigan, Rebecca; Cantera, Mariela; Shopsin, Bo; Novick, Richard P

2008-08-01

212

Micropapillary Variant of Urothelial Carcinoma  

PubMed Central

Micropapillary carcinoma (MPC) of urinary tract is an uncommon variant of urothelial carcinoma with significant diagnostic and prognostic implications. Though MPC shows characteristic microscopic features, there exists interobserver variability and also it needs to be differentiated from the metastasis from other organs. The prognosis is generally poor, depending on the proportion of the micropapillary component in some reports. Early cystectomy in cases with only lamina propria invasion may be indicated according to recent studies. This review outlines the general features of this entity and briefly comments on the controversies and the recent development.

Kwon, Ghee Young; Ro, Jae Y.

2011-01-01

213

Atypical toxin variant of Clostridium botulinum type B associated with infant botulism.  

PubMed Central

An atypical toxin variant of Clostridium botulinum (strain 657) was isolated from the feces of a 6-week-old female infant whose symptoms and clinical history were consistent with infant botulism. Toxin detected in the feces and the toxin produced by isolates from the feces and from two rectal swabs could be neutralized by type B botulinal antitoxin only at very high ratios of of antitoxin to toxin in the neutralization mixture. One international unit of type B antitoxin neutralized only about 10 lethal doses of 657 toxin as compared with approximately 10,000 lethal doses of conventional type B toxin from the Beans strain. Antitoxin prepared against 657 toxin was 10 times more effective against the conventional toxin than against the homologous toxin. Toxoid-antitoxin-binding studies indicate that both 657 toxin and type B toxin are heterogeneous and that both toxins may contain the same molecular variants, but that the proportions of the variants are different in each.

Hatheway, C L; McCroskey, L M; Lombard, G L; Dowell, V R

1981-01-01

214

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

PubMed Central

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.

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

2011-01-01

215

Physical maps and virulence of Anticarsia gemmatalis nucleopolyhedrovirus genomic variants  

Microsoft Academic Search

Summary.  ?Seventeen plaque purified isolates of two viral preparations of Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV), were analyzed in terms of the genomic changes after digestion of their DNAs with\\u000a HindIII and PstI restriction enzymes. The 1979 AgMNPV wild type preparation (AgMNPV-’79) resulted in six different variants\\u000a and the 1985 viral commercial preparation (AgMNPV-’85), in eleven. The genomic variation of all the

J. E. Maruniak; A. Garcia-Maruniak; M. L. Souza; P. M. A. Zanotto; F. Moscardi

1999-01-01

216

Three Splicing Variants of Tomosyn and Identification of Their Syntaxin-Binding Region  

Microsoft Academic Search

We have recently isolated a neural tissue-specific syntaxin-1-binding protein, named tomosyn, which is capable of dissociating Munc18\\/n-Sec1\\/rbSec1 from syntaxin-1 to form a 10S tomosyn complex, an intermediate complex converted to the 7S SNARE complex. We isolated here two splicing variants of tomosyn: one had 36 amino acids (aa) insertion and another had 17 aa deletion. We named original one m-tomosyn,

Shigekazu Yokoyama; Hiromichi Shirataki; Toshiaki Sakisaka; Yoshimi Takai

1999-01-01

217

Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants  

PubMed Central

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common cause of gastroenteritis in humans. Here, we report the draft genome sequences of 10 isolates of an S. Typhimurium phage type 135 variant that is linked to egg-associated outbreaks in Tasmania, Australia.

Hogg, Geoff; Dimovski, Karolina; Hiley, Lester

2013-01-01

218

Antigenic Differences between Metastatic and Nonmetastatic BSp73 Rat Tumor Variants Characterized by Monoclonal Antibodies  

Microsoft Academic Search

Variants AS and ASMI of the BSp73 rat tumor differ markedly with respect to morphologyand to the capacity for spontaneous metastasis via the lymphatics. Monoclonal antibodies (MAbs) were raised in order to identify surface molecules associated with both phenotypes. Mice were immunizedwith either whole cells or isolated membranes and hybridoma supernatants were screened according to the criteria of selective binding

Siegfried Matzku; Achini Wenzel; Sida Liu

219

[PSI+] Prion Variant Establishment in Yeast  

PubMed Central

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

Sharma, Jaya; Liebman, Susan W.

2012-01-01

220

Hereditary Amyloid Cardiomyopathy Caused by a Variant Apolipoprotein A1  

PubMed Central

Autosomal dominant hereditary amyloidosis with a unique cutaneous and cardiac presentation and death from heart failure by the sixth or seventh decade was found to be associated with a previously unreported point mutation (thymine to cytosine, nt 1389) in exon 4 of the apolipoprotein A1 (apoA1) gene. The predicted substitution of proline for leucine at amino acid position 90 was confirmed by structural analysis of amyloid protein isolated from cardiac deposits of amyloid. The subunit protein is composed exclusively of NH2-terminal fragments of the variant apoA1 with the longest ending at residue 94 in the wild-type sequence. Amyloid fibrils derived from four previously described apoA1 variants are composed of similar fragments with carboxyl-terminal heterogeneity, but contrary to those variants, which all carry one extra positive charge, the substitution Leu90Pro does not result in any charge modification. It is unlikely, therefore, that amyloid fibril formation is related to change of charge for a specific residue of the precursor protein. This is in agreement with studies on transthyretin amyloidosis in which no unifying factor such as change of charge for amino acid residues has been noted.

Hamidi Asl, Ladan; Liepnieks, Juris J.; Hamidi Asl, Kamran; Uemichi, Tomoyuki; Moulin, Georges; Desjoyaux, Emmanuel; Loire, Robert; Delpech, Marc; Grateau, Gilles; Benson, Merrill D.

1999-01-01

221

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

PubMed Central

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

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

2013-01-01

222

Characterization of a novel variant of Mycobacterium chimaera.  

PubMed

In this study, nonchromogenic mycobacteria were isolated from pulmonary samples of three patients in the Netherlands. All isolates had identical, unique 16S rRNA gene and 16S-23S ITS sequences, which were closely related to those of Mycobacterium chimaera and Mycobacterium marseillense. The biochemical features of the isolates differed slightly from those of M. chimaera, suggesting that the isolates may represent a possible separate species within the Mycobacterium avium complex (MAC). However, the cell-wall mycolic acid pattern, analysed by HPLC, and the partial sequences of the hsp65 and rpoB genes were identical to those of M. chimaera. We concluded that the isolates represent a novel variant of M. chimaera. The results of this analysis have led us to question the currently used methods of species definition for members of the genus Mycobacterium, which are based largely on 16S rRNA or rpoB gene sequencing. Definitions based on a single genetic target are likely to be insufficient. Genetic divergence, especially in the MAC, yields strains that cannot be confidently assigned to a specific species based on the analysis of a single genetic target. PMID:22700551

van Ingen, J; Hoefsloot, W; Buijtels, P C A M; Tortoli, E; Supply, P; Dekhuijzen, P N R; Boeree, M J; van Soolingen, D

2012-06-14

223

Fibrolamellar variant of hepatocellular carcinoma.  

PubMed

The fibrolamellar variant of hepatocellular carcinoma is a rare primary liver cancer occurring in adolescents and young adults without chronic liver disease or known risk factors. Histologically, it is defined by lamellar bands of fibrosis surrounding well-differentiated tumor cells. Radiologic imaging typically demonstrates a large, solitary mass with calcifications and a central scar. Lymph node metastases in the porta hepatis are frequently diagnosed upon presentation. More patients with fibrolamellar carcinoma are candidates for surgical resection than those with conventional hepatocellular carcinoma, owing to their young age and absence of cirrhosis. The most important prognostic factor is surgical resection, which results in 5-year overall survival rates ranging between 50 and 76 %. Despite complete surgical resection, relapse rates are high, and novel therapies are needed to prevent and treat recurrent disease. PMID:22941016

Chun, Yun Shin; Zimmitti, Giuseppe

2013-01-01

224

PCR/RFLP-based allelic variants of streptokinase and their plasminogen activation potencies.  

PubMed

PCR-restriction fragment length polymorphism (PCR/RFLP)-based analysis of ?-domain variable region of streptokinase genes (sk) has previously identified 14 sk alleles (sk1-sk14) in group A (GAS), C (GCS) and G (GGS) streptococci isolates from a few geographically distinct regions. However, the relation of sk allelic variants to their plasminogen activation potencies remained as a matter of debate. Herein, employing the same PCR/RFLP assay, we analysed sk allelic variants of GAS and GCS/GGS isolates from Iranian patients. In total, 21 sk allelic variants including 14 new alleles (sk14-sk28) were identified. Results implied the horizontal gene transfer of sk fragments between GAS and GCS/GGS strains and did not prove the specificity of particular sk alleles to GCS/GGS or GAS groups. Measurement of streptokinase (SK) activity in streptococcal culture supernatants by colorimetric assay (S2251 substrate) ranged from 9 to 182 IU mL(-1). Although some strains with the highest SK activity were detected in definite variants, no significant correlation between sk alleles and plasminogen activation was detected (P value > 0.05). Analysis of DNA sequences and restriction site mapping of selective sk variants with similar SK activity pointed to the inadequacy of the currently available PCR/RFLP method for differentiation of critical/silent nucleotides to precisely categorize sk alleles for their functional properties. PMID:22812485

Keramati, Malihe; Roohvand, Farzin; Eslaminejad, Zahra; Mirzaie, Amir; Nikbin, Vajihe Sadat; Aslani, Mohammad Mehdi

2012-08-29

225

Comments on Integral Variants of ISS  

Microsoft Academic Search

This note discusses two integral variants of the input-to-state stability (ISS) property, which represent nonlinear generalizations of L, stability, in much the same way that ISS generalizes L, stability. Both variants are equivalent to ISS for linear systems. For general nonlinear systems, it is shown that one of the new properties is strictly weaker than ISS, while the other one

Eduardo D. Sontag

1998-01-01

226

Pathology of Variant Creutzfeldt-Jakob Disease  

Microsoft Academic Search

Variant Creutzfeldt-Jakob disease (CJD) is a novel form of human prion disease that appears to result from oral infection by the bovine spongiform encephalopathy (BSE) agent. Variant CJD is also unique in human prion diseases in that infectivity and accumulation of the disease-associated isoform of prion protein are readily detectable outside the central nervous system, perhaps reflecting the peripheral pathogenesis

James W. Ironside

227

Rare and common variants: twenty arguments  

Microsoft Academic Search

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

Greg Gibson

2012-01-01

228

In search of low-frequency and rare variants affecting complex traits.  

PubMed

The allelic architecture of complex traits is likely to be underpinned by a combination of multiple common frequency and rare variants. Targeted genotyping arrays and next-generation sequencing technologies at the whole-genome sequencing (WGS) and whole-exome scales (WES) are increasingly employed to access sequence variation across the full minor allele frequency (MAF) spectrum. Different study design strategies that make use of diverse technologies, imputation and sample selection approaches are an active target of development and evaluation efforts. Initial insights into the contribution of rare variants in common diseases and medically relevant quantitative traits point to low-frequency and rare alleles acting either independently or in aggregate and in several cases alongside common variants. Studies conducted in population isolates have been successful in detecting rare variant associations with complex phenotypes. Statistical methodologies that enable the joint analysis of rare variants across regions of the genome continue to evolve with current efforts focusing on incorporating information such as functional annotation, and on the meta-analysis of these burden tests. In addition, population stratification, defining genome-wide statistical significance thresholds and the design of appropriate replication experiments constitute important considerations for the powerful analysis and interpretation of rare variant association studies. Progress in addressing these emerging challenges and the accrual of sufficiently large data sets are poised to help the field of complex trait genetics enter a promising era of discovery. PMID:23922232

Panoutsopoulou, Kalliope; Tachmazidou, Ioanna; Zeggini, Eleftheria

2013-08-06

229

In search of low-frequency and rare variants affecting complex traits  

PubMed Central

The allelic architecture of complex traits is likely to be underpinned by a combination of multiple common frequency and rare variants. Targeted genotyping arrays and next-generation sequencing technologies at the whole-genome sequencing (WGS) and whole-exome scales (WES) are increasingly employed to access sequence variation across the full minor allele frequency (MAF) spectrum. Different study design strategies that make use of diverse technologies, imputation and sample selection approaches are an active target of development and evaluation efforts. Initial insights into the contribution of rare variants in common diseases and medically relevant quantitative traits point to low-frequency and rare alleles acting either independently or in aggregate and in several cases alongside common variants. Studies conducted in population isolates have been successful in detecting rare variant associations with complex phenotypes. Statistical methodologies that enable the joint analysis of rare variants across regions of the genome continue to evolve with current efforts focusing on incorporating information such as functional annotation, and on the meta-analysis of these burden tests. In addition, population stratification, defining genome-wide statistical significance thresholds and the design of appropriate replication experiments constitute important considerations for the powerful analysis and interpretation of rare variant association studies. Progress in addressing these emerging challenges and the accrual of sufficiently large data sets are poised to help the field of complex trait genetics enter a promising era of discovery.

Panoutsopoulou, Kalliope; Tachmazidou, Ioanna; Zeggini, Eleftheria

2013-01-01

230

Minority Variants of Drug-Resistant HIV  

PubMed Central

Minor drug-resistant variants exist in every HIV-infected patient. Since these minority variants are usually present at very low levels, they cannot be detected and quantified using conventional genotypic and phenotypic tests. Recently, several assays have been developed to characterize these low-abundance drug-resistant variants in the large genetically complex population present in every HIV-infected individual. The most important issue is, what results generated by these assays can predict clinical or treatment outcomes and might guide patient management in clinical practice. Cutoff-values for the detection of these low-abundance viral variants that predict increased risk of treatment failure should be determined. These thresholds may be specific for each mutation and treatment regimen. In this review we summarize the attributes and limitations of the currently available detection assays and review the existing information about both acquired and transmitted drug resistant minority variants.

Gianella, Sara; Richman, Douglas D.

2010-01-01

231

Human spleen cysteineproteinase inhibitor. Purification, fractionation into isoelectric variants and some properties of the variants.  

PubMed

The papain inhibitor from human spleen was purified by extraction in isotonic sucrose, acetone fractionation, papain-Sepharose affinity chromatography and gel filtration on Sephadex G-50. The purified inhibitor was fractionated by electrofocusing into four major isoelectric variants with pI values of 4.7, 5.0, 6.0 and 6.5. These variants can be classified into two groups: the acidic type, comprising the variants with pI 4.7 and 5.0, and the neutral type, comprising the variants with pI 6.0 and 6.5. The following properties distinguish the two types: 1. Immunological properties: antibodies raised against either of the neutral variants precipitated both of these, but not the acidic variants. The antiserum against the human epidermal cysteineproteinase inhibitor precipitated the acidic variants, but not the neutral variants. 2. Molecular size: two-dimensional electrophoresis of the purified inhibitor gave molecular weights of 11400 for the acidic variants and 12000 for the neutral variants. The pI 6.0 variant contained two compounds with molecular weights of 12000 and 12800. 3. Enzyme spectrum: human cathepsin B was inhibited by the acidic type, while the neutral type was a poor inhibitor. Both types inhibited cathepsin H, papain, ficin and bromelain, although the inhibition of bromelain did not exceed 70%. Human cathepsin D, bovine trypsin and chymotrypsin and porcine elastase were not inhibited by either type. PMID:6184075

Järvinen, M; Rinne, A

1982-11-01

232

Enhancement of Nitrogen-Fixation with Rhizobial Tan Variants.  

National Technical Information Service (NTIS)

Legumes inoculated with tryptophan catabolic variants (tan variants) of wild-type bradyrhizobia are characterized by an enhanced capacity to fix atmospheric nitrogen as compared to parent strains. Responses of the symbiotic system to the variants include ...

T. Kaneshiro

1986-01-01

233

Splicing Variants of Estrogen Receptor in Breast Cancer.  

National Technical Information Service (NTIS)

Results are summarized from the analysis of ER-a splicing variants in breast tumor cells. A highly diverse population of variants were observed representing primarily exon-skipped transcripts, but also including novel variants resulting from promiscuous o...

R. J. Miksicek

1999-01-01

234

Antigenic variants of rabies virus  

Microsoft Academic Search

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

T. J. WIKTOR; H. KOPROWSKI

1980-01-01

235

Synthesis of spatially variant lattices.  

PubMed

It is often desired to functionally grade and/or spatially vary a periodic structure like a photonic crystal or metamaterial, yet no general method for doing this has been offered in the literature. A straightforward procedure is described here that allows many properties of the lattice to be spatially varied at the same time while producing a final lattice that is still smooth and continuous. Properties include unit cell orientation, lattice spacing, fill fraction, and more. This adds many degrees of freedom to a design such as spatially varying the orientation to exploit directional phenomena. The method is not a coordinate transformation technique so it can more easily produce complicated and arbitrary spatial variance. To demonstrate, the algorithm is used to synthesize a spatially variant self-collimating photonic crystal to flow a Gaussian beam around a 90° bend. The performance of the structure was confirmed through simulation and it showed virtually no scattering around the bend that would have arisen if the lattice had defects or discontinuities. PMID:22772224

Rumpf, Raymond C; Pazos, Javier

2012-07-01

236

Variants of cerebral arteries - anterior circulation  

PubMed Central

Summary Advances in imaging techniques allow for in vivo identification of abnormalities and normal variants of cerebral arteries. These arterial variations can be asymptomatic and uncomplicated although, some of them increase the risk of aneurysm formation, acute intracranial hemorrhage, play a vital role in neurosurgical planning or can be misidentified as serious pathology and medical errors. The goal of this publication is to discuss arterial anomalies of anterior cerebral circulation, their prevalence and demonstrate radiological images of some of those variants. In this article we will discuss variants of internal carotid artery, anterior cerebral artery, anterior communicating artery, middle cerebral artery, persistent stapedial artery and fenestration.

Makowicz, Grzegorz; Poniatowska, Renata; Lusawa, Malgorzata

2013-01-01

237

Genotypes Associated with Virulence in Environmental Isolates of Vibrio cholerae  

PubMed Central

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

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

2001-01-01

238

Immunological characterization of metallothioneins in mouse LMTK cells and in a variant resistant to cadmium  

SciTech Connect

A cadmium-resistant variant isolated from mouse fibroblast LMTK cells can grow in the presence of 40 ..mu..M Cd/sup 2 +/. This variant retained its properties in the absence of selecting agent. Induction of metallothionein was measured in cell extracts by radioimmunoassay. The maximum amount of metallothioneins in the cells was reached after 36 hours. The cadmium resistant variant produced two times more metallothionein than the wild-type when exposed to 10-20 ..mu..MCd/sup 2 +/. By Ouchterlony double diffusion, the metallothioneins from cultured cells formed a line of partial identity with the mouse liver serotype and a line of complete identity with one of the two mouse kidney serotypes. These observations raise the possibility of a tissue-specific expression of metallothionein genes.

Maiti; I.; Mbikay, M.; Marengo, C.; Thirion, J.-P.

1982-07-01

239

Evaluation of FM-9 Antimisting Kerosene Variants.  

National Technical Information Service (NTIS)

The results of an experimental effort on evaluation of /fm-9 antimisting kerosene (AMK) variants developed by Imperial Chemical Industries (ICI) to improve the dissolution rate of mist suppression polymers in Jet A are described. Dissolution rate characte...

A. Yavrouian P. Parikh L. Bernal V. Sarohia

1986-01-01

240

Variant (Swine Origin) Influenza Viruses in Humans  

MedlinePLUS

... en... Favorites Delicious Digg Google Bookmarks Variant (Swine Origin) Influenza Viruses in Humans On This Page Background Reporting ... Prevention Toolkit Other Flu Websites CDC Resources for Pandemic Flu Pandemic Flu Preparedness Tools Influenza Risk Assessment Tool ...

241

Directed Evolution of Streptavidin Variants Using IVC  

PubMed Central

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

Levy, M.; Ellington, A.D.

2008-01-01

242

Population structure of Citrus tristeza virus from field Argentinean isolates.  

PubMed

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

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

2007-11-13

243

Kuru and "new variant" CJD.  

PubMed

Acquired transmissible spongiform encephalopathies in humans include Kuru (a disease which was associated with ritualistic cannibalism in Papua New Guinea), iatrogenic Creutzfeldt-Jakob disease and a newly recognized variant form of Creutzfeldt-Jakob disease (nvCJD). Clinical and neuropathological features of nvCJD are reminiscent of Kuru: early and progressive cerebellar ataxia and numerous characteristic Kuru-type amyloid plaques surrounded by spongiform change. In contrast to typical cases of sporadic CJD, Kuru and nvCJD affect young patients. The newly recognized form of CJD has been identified in ten young people in the UK in 1996, approximately 10 years after the beginning of the bovine spongiform encephalopathy (BSE) epidemic in the UK. Molecular analysis has shown that nvCJD has strain characteristics that are distinct from other types of CJD but similar to those of BSE. In the UK an estimated half a million BSE-infected cows entered the human food chain before the bovine offal ban of 1989. To be effective the oral route probably requires high-infectivity titers which are encountered only in the brain, spinal cord and eyes of naturally infected cows. In patients with Kuru, titers of more than 10(8) infectious doses per gram were reported in the brain tissues. As a result of the estimated very long incubation period of nvCJD (10 to 30 years or more) the predicted nvCJD epidemic will have the shape of a normal distribution curve with a peak expected in 2009. The epidemic may extend until 2030. There is already an example to illustrate such a curve in its descending line: the decline of Kuru deaths following the interruption of ritual cannibalism. PMID:9561604

Verdrager, J

1997-09-01

244

Bisalbuminemia. A new molecular variant, albumin Vancouver.  

PubMed

Of 18 members of a Fiji Indian family investigated, eight of the 12 males and two of the six females had an electrophoretically slow-type bisalbuminemia (alloalbuminemia). The albumin was characterized by the hiterto unique ratio of the two bands (Al A 35%: variant 65%), and by dye-binding studies and electrophoretic mobility in different media. The data suggest that this is a new variant, which we propose to call albumin Vancouver (Al Va). PMID:709819

Frohlich, J; Kozier, J; Campbell, D J; Curnow, J V; Tárnoky, A L

1978-11-01

245

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

PubMed

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

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

2012-01-06

246

Implication of common and disease specific variants in CLU, CR1, and PICALM.  

PubMed

Two recent genome-wide association studies (GWAS) for late onset Alzheimer's disease (LOAD) revealed 3 new genes: clusterin (CLU), phosphatidylinositol binding clathrin assembly protein (PICALM), and complement receptor 1 (CR1). In order to evaluate association with these genome-wide association study-identified genes and to isolate the variants contributing to the pathogenesis of LOAD, we genotyped the top single nucleotide polymorphisms (SNPs), rs11136000 (CLU), rs3818361 (CR1), and rs3851179 (PICALM), and sequenced the entire coding regions of these genes in our cohort of 342 LOAD patients and 277 control subjects. We confirmed the association of rs3851179 (PICALM) (p = 7.4 × 10(-3)) with the disease status. Through sequencing we identified 18 variants in CLU, 3 of which were found exclusively in patients; 8 variants (out of 65) in CR1 gene were only found in patients and the 16 variants identified in PICALM gene were present in both patients and controls. In silico analysis of the variants in PICALM did not predict any damaging effect on the protein. The haplotype analysis of the variants in each gene predicted a common haplotype when the 3 single nucleotide polymorphisms rs11136000 (CLU), rs3818361 (CR1), and rs3851179 (PICALM), respectively, were included. For each gene the haplotype structure and size differed between patients and controls. In conclusion, we confirmed association of CLU, CR1, and PICALM genes with the disease status in our cohort through identification of a number of disease-specific variants among patients through the sequencing of the coding region of these genes. PMID:22402018

Ferrari, Raffaele; Moreno, Jorge H; Minhajuddin, Abu T; O'Bryant, Sid E; Reisch, Joan S; Barber, Robert C; Momeni, Parastoo

2012-03-07

247

Exposed epitopes on a Trypanosoma equiperdum variant surface glycoprotein altered by point mutations.  

PubMed Central

African trypanosomes are covered by a dense protein layer that is immunologically distinct on different trypanosome isolates and is termed the variant surface glycoprotein (VSG). The different VSGs are expressed in a general order, where some VSGs appear preferentially early in infection and others only later. The exposed epitopes on a late antigen, VSG 78, of T.equiperdum were studied by the technique of monoclonal antibody (MAb) escape selection. MAbs that neutralize trypanosomes bearing VSG 78 reacted with the VSG only when it was attached to the trypanosome surface, suggesting that the most immunogenic surface epitopes are conformational. Trypanosome clones resistant to one of the MAbs yet still expressing VSG 78 or 78(20) were isolated in vitro. Two independent variants resistant to MAb H3 changed Ser192 to Arg by a single base change in the VSG gene and a variant resistant to MAb H21 had a single base change that converted Gln172 to Glu. A variant resistant to MAb H7 had several changes in the VSG gene, a gene conversion in the 5' region and an isolated mutation in codon 220 that is proposed to be responsible for the resistance phenotype. The isotypic bias of the MAbs against VSG 78 and an analysis of the natural variants that are resistant to MAb 78H21 suggest that glycosylation plays a role in the immunogenicity of these proteins. The analysis defines some of the exposed amino acid residues and demonstrates that VSG genes are altered by mutations and small gene conversions as well as replaced by large gene conversion-like events. The results provide biological data supporting the model of VSG structure obtained by crystallographic studies. Images

Baltz, T; Giroud, C; Bringaud, F; Eisen, H; Jacquemot, C; Roth, C W

1991-01-01

248

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

PubMed Central

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

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

2011-01-01

249

Meningococcal Factor H-Binding Protein Variants Expressed by Epidemic Capsular Group A, W-135, and X Strains from Africa  

PubMed Central

Background Meningococcal epidemics in Africa are generally caused by capsular group A strains, but W-135 or X strains also cause epidemics in this region. Factor H–binding protein (fHbp) is a novel antigen being investigated for use in group B vaccines. Little is known about fHbp in strains from other capsular groups. Methods We investigated fHbp in 35 group A, W-135, and X strains from Africa. Results The 22 group A isolates, which included each of the sequence types (STs) responsible for epidemics since 1963, and 4 group X and 3 group W-135 isolates from recent epidemics had genes encoding fHbp in antigenic variant group 1. The remaining 6 W-135 isolates had fHbp variant 2. Within each fHbp variant group, there was 92%–100% amino acid identity, and the proteins expressed conserved epitopes recognized by bactericidal monoclonal antibodies. Serum samples obtained from mice vaccinated with native outer membrane vesicle vaccines from mutants engineered to express fHbp variants had broad bactericidal activity against group A, W-135, or X strains. Conclusions Despite extensive natural exposure of the African population, fHbp is conserved among African strains. A native outer membrane vesicle vaccine that expresses fHbp variants can potentially elicit protective antibodies against strains from all capsular groups that cause epidemics in the region.

Beernink, P. T.; Caugant, D. A.; Welsch, J. A.; Koeberling, O.; Granoff, D. M.

2010-01-01

250

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

PubMed Central

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

2012-01-01

251

Characterization of novel ybjG and dacC variants in Escherichia coli.  

PubMed

A total of 69 strains of Escherichia coli from patients in the Taizhou Municipal Hospital, China, were isolated, and 11 strains were identified that were resistant to bacitracin, chloramphenicol, tetracycline and erythromycin. These strains were PCR positive for at least two out of three genes, ybjG, dacC and mdfA, by gene mapping with conventional PCR detection. Conjugation experiments demonstrated that these genes existed in plasmids that conferred resistance. Novel ybjG and dacC variants were isolated from E. coli strains EC2163 and EC2347, which were obtained from the sputum of intensive care unit patients. Genetic mapping showed that the genes were located on 8200 kb plasmid regions flanked by EcoRI restriction sites. Three distinct genetic structures were identified among the 11 PCR-positive strains of E. coli, and two contained the novel ybjG and dacC variants. The putative amino acid differences in the ybjG and dacC gene variants were characterized. These results provide evidence for novel variants of ybjG and dacC, and suggest that multiple drug resistance in hospital strains of E. coli depends on the synergistic function of ybjG, dacC and mdfA within three distinct genetic structures in conjugative plasmids. PMID:23912810

Wang, Dongguo; Hu, Enping; Chen, Jiayu; Tao, Xiulin; Gutierrez, Katelyn; Qi, Yongxiao

2013-08-02

252

Identification of growth hormone molecular variants in chicken serum.  

PubMed

It has been described that pituitary growth hormone shows molecular and functional heterogeneity. In birds, size and charge variants of chicken growth hormone (cGH) have been shown in the chicken pituitary gland and in purified preparations of the hormone. Here we demonstrate the existence of cGH molecular isoforms in chicken serum, thus suggesting that they are secreted from the gland. The isolation of total cGH present in sera was performed by immunoaffinity chromatography employing a specific monoclonal antibody against cGH. Different analytical electrophoretic methods (SDS-polyacrylamide gel electrophoresis, isoelectric focusing, bidimensional polyacrylamide gel electrophoresis) followed by Western blot and immunostaining were employed to characterize the serum cGH isoforms, and compared to those present in a fresh pituitary extract. Several identical immunoreactive bands comigrated in both serum and the gland extract in the different systems (SDS-PAGE, MW 16, 22, 26, 29, 52, 62, 66 kDa; IEF, pIs 8.1, 7.5, 7.1, 6.8, 6.2), thus revealing a high correspondence of molecular isoforms of the hormone in the two tissues. Additionally, a glycosylated variant of chicken growth hormone (G-cGH) was also revealed in the serum after concanavalin A-Sepharose chromatography. PMID:1478445

Montiel, J L; Berghman, L R; Arámburo, C

1992-11-01

253

Biochemical Characterization of a Neuroserpin Variant Associated with Hereditary Dementia  

PubMed Central

Neuroserpin isolated from inclusion bodies in the brain of a patient with a neurodegenerative disease was characterized biochemically. The protein consisted of residues 20 to 410 of the neuroserpin precursor deduced from its cDNA sequence indicating the entire molecule was deposited. A minor amount started with residue 19 of the precursor, and the carboxyl terminus was heterogeneous ending at residues 405, 407, 409, and 410. Arg was present at position 52. No normal Ser52 was found indicating that only mutant neuroserpin was present in the inclusion bodies. The three potential Asn glycosylation sites all contained carbohydrate. DNA sequence analysis of exons 2 to 9 of the neuroserpin gene in the proband showed the published normal neuroserpin sequence except for the presence of both adenine and cytosine at the first position of codon 52, that indicates heterozygosity for both the normal Ser(AGT) and variant Arg(CGT) at this position in the expressed protein. Restriction fragment length polymorphism analysis of a polymerase chain reaction product from exon 2 revealed the propositus and his affected sibling both were heterozygous for the mutation whereas 100 unaffected controls were negative. Chemical characterization of the variant neuroserpin will significantly enhance the understanding of this protein in both normal physiology and neurodegenerative diseases.

Yazaki, Masahide; Liepnieks, Juris J.; Murrell, Jill R.; Takao, Masaki; Guenther, Brian; Piccardo, Pedro; Farlow, Martin R.; Ghetti, Bernardino; Benson, Merrill D.

2001-01-01

254

[Immunologic analysis of the antigenic properties of neuraminidase from drift-variants of influenza virus B].  

PubMed

The antigenic features of neuraminidases of several drift variants of influenza B virus were studied by enzyme immunoassay using antiserum to influenza B/USSR/100/83 virus neuraminidase isolated by pronase. Studies using immunosorption and competitive solid-phase enzyme immunoassay showed the presence in the antineuraminidase serum of at least two antibody subpopulations capable to inhibiting the activity of the enzyme and interacting with neuraminidase antigenic determinants: one detecting the antigenic determinant common for B/100/83 and B/Lee/40 viruses, and the other characterizing the antigenic determinant inherent in neuraminidase of B/100/83 virus and enzymes of drift variants isolated in 1970-1986 and lacking in the enzyme of B/Lee/40 virus. PMID:3073569

Rovnova, Z I; Rogacheva, T A; Platonova, A L; Isaeva, E I

255

Identifying the Source of Unknown Microcystin Genes and Predicting Microcystin Variants by Comparing Genes within Uncultured Cyanobacterial Cells?  

PubMed Central

While multiple phylogenetic markers have been used in the culture-independent study of microcystin-producing cyanobacteria, in only a few instances have multiple markers been studied within individual cells, and in all cases these studies have been conducted with cultured isolates. Here, we isolate and evaluate large DNA fragments (>6 kb) encompassing two genes involved in microcystin biosynthesis (mcyA2 and mcyB1) and use them to identify the source of gene fragments found in water samples. Further investigation of these gene loci from individual cyanobacterial cells allowed for improved analysis of the genetic diversity within microcystin producers as well as a method to predict microcystin variants for individuals. These efforts have also identified the source of the novel mcyA genotype previously termed Microcystis-like that is pervasive in the Laurentian Great Lakes and they predict the microcystin variant(s) that it produces.

Allender, Christopher J.; LeCleir, Gary R.; Rinta-Kanto, Johanna M.; Small, Randall L.; Satchwell, Michael F.; Boyer, Gregory L.; Wilhelm, Steven W.

2009-01-01

256

The Chicago variant of clinical galactosemia.  

PubMed

A new variant of clinical galactosemia with two hitherto unidentified alleles on the transferase locus in one family is described. This new clinical variant of transferase has 25% of normal control activity in blood and in skin fibroblasts, and the patient accumulates galactose-1-phosphate in blood on an unrestricted galactose diet. Using starch gel electrophoresis on the hemolysate of the family members, a fast-moving transferase with mobility in between those of the normal control and of the Duarte variant is identified. This new allele is designated as GALTC1 (fast-moving Chicago variant). In addition, a second new allele was documented in this family by studying the instability of the transferase enzyme in hemolysates of family members at 50 degrees C for various time intervals. This new allele is designated as GALTC2 (heat-labile Chicago variant). On the basis of these studies, the transferase genotype of this patient is thought to be a double heterozygote compound, GALTC1/GALTG. PMID:885545

Chacko, C M; Wappner, R S; Brandt, I K; Nadler, H L

1977-07-26

257

The logopenic variant of primary progressive aphasia  

PubMed Central

Purpose The aim of this review is to explore the evolution of the logopenic variant of primary progressive aphasia as a distinct clinical entity and to outline recent advances that have clarified its clinical characteristics, neural underpinnings and potential genetic and pathological bases. This is particularly relevant as researchers attempt to identify clinico-pathological relationships in subtypes of primary progressive aphasia in hopes of utilizing language phenotype as a marker of underlying disease. Recent findings Recent work has served to refine and expand upon the clinical phenotype of the logopenic variant. Logopenic patients show a unique pattern of spared and impaired language processes that reliably distinguish this syndrome from other variants of progressive aphasia. Specifically, they exhibit deficits in naming and repetition in the context of spared semantic, syntactic and motor speech abilities. Further, there is a growing body of evidence indicating a possible link between the logopenic variant phenotype and specific pathological and genetic correlates. Summary Findings indicate that the logopenic variant is a distinct subtype of progressive aphasia that may hold value as a predictor of underlying pathology. Additional research, however, is warranted in order to further clarify the cognitive-linguistic profile and to confirm its relation to certain pathological and genetic processes.

Henry, M.L.; Gorno-Tempini, M.L.

2010-01-01

258

Sensitive Phenotypic Detection of Minor Drug-Resistant Human Immunodeficiency Virus Type 1 Reverse Transcriptase Variants  

Microsoft Academic Search

Detection of drug-resistant variants is important for the clinical management of human immunodeficiency virus type 1 (HIV-1) infection and for studies on the evolution of drug resistance. Here we show that hybrid elements composed of the Saccharomyces cerevisiae retrotransposon Ty1 and the reverse transcriptase (RT) of HIV-1 are useful tools for detecting, monitoring, and isolating drug-resistant reverse transcriptases. This sensitive

Dwight V. Nissley; Elias K. Halvas; Nicole L. Hoppman; David J. Garfinkel; John W. Mellors; Jeffrey N. Strathern

2005-01-01

259

Identification and analysis of U5 snRNA variants in Drosophila  

Microsoft Academic Search

Distinct isoforms of spliceosomal RNAs may be involved in regulating pre-messenger RNA splicing in eukaryotic cells. During a large-scale effort to identify small noncoding RNAs in Drosophila, we isolated a U5 snRNA-like molecule containing a 50 segment identical to that of the canonical (major) U5 snRNA but with a variant Sm binding site and a distinct 30 hairpin sequence. Based

LI CHEN; DENNIS J. LULLO; ENBO MA; SUSAN E. CELNIKER; DONALD C. RIO; JENNIFER A. DOUDNA

2005-01-01

260

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

PubMed

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

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

261

R factor variants with enhanced sex factor activity in Pseudomonas aeruginosa  

Microsoft Academic Search

The R factor R68 readily promotes chromosome transfer in Pseudomonas aeruginosa strain PAT, but shows little such sex factor activity in strain PAO. A variant of this plasmid, R68.45, has been isolated which produces recombinants in PAO plate matings at frequencies of 10-3–10-5 per donor cell for markers in the 0–60 min region of the chromosome. Little or no chromosome

Dieter Haas; Bruce W. Holloway

1976-01-01

262

Small-colony variants: a novel mechanism for triclosan resistance in methicillin-resistant Staphylococcus aureus  

Microsoft Academic Search

Objectives: A little-understood mode of antimicrobial resistance in Staphylococcus aureus is the evolution of a sub-population of small-colony variants (SCVs). SCVs are a cause of persistent and recurring infections refractory to antimicrobial chemotherapy. Following the inadvertent isolation of suspected SCVs growing in the presence of triclosan we set out to evaluate the formation of these colonial mutants and assess their

Paul F. Seaman; Dietmar Ochs; Martin J. Day

2007-01-01

263

The sub- and super-equivalence method of isotope dilution XIII. Theoretical error of the CVC and VCC variants  

Microsoft Academic Search

The theoretical error of both the CVC and VCC variants at non-quantitative complex forming reaction M+LML has been studied. The erros of analysis for the following analytical curve determinations are considered: (1) measurement with constant error of the analytical function, (2) measurement with registration of a constant number of disintegrations, (3) measurement at constant time of radioactivity measurement of isolated

J. Klas; Z. Kore?ová; J. Tölgyessy

1987-01-01

264

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

Microsoft Academic Search

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 (P. falciparum isolates on the island. Previously, minority variant chloroquine resistant parasites were described in Malawian patients using an isotopic heteroduplex

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

2009-01-01

265

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

Microsoft Academic Search

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

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

1996-01-01

266

Prevalence of hepatitis C virus sequence variants in South-East Asia.  

PubMed

The nature and distribution of hepatitis C virus (HCV) genotypic variants present in south-east Asia have not been extensively investigated. We analysed HCV RNA obtained from 67 clinical serum samples from Singapore, Thailand, Indonesia, the Philippines and South Korea. All samples were amplified by semi-nested RT-PCR and the nucleotide sequence determined for four regions within the E1, E2/NS1, NS4 and NS5 genes. Each isolate had a unique nucleotide and deduced amino acid sequence, consistent with the genetic heterogeneity of this virus. There was remarkably little amino acid sequence variation between isolates of the same genotype, apart from variable domains within putative envelope glycoproteins that are likely to be under immune pressure. All isolates could be classified according to the currently recognized genotypes of HCV, with the exception of one Singapore isolate that defined a new group 3 subtype. The 1b genotype, which predominates in Japan, was the most widely distributed genotype and accounted for 58% of all isolates sequenced. Regional variations in HCV genotype distribution were observed, with type 3a being found almost exclusively in Thailand. By contrast, the 1a genotype, which predominates in the USA was the most prevalent genotype in the Philippines. Genotype 1a was found less commonly among the Thai isolates, presumably having been introduced from the West in stored blood products or by sporadic transmission. The significant prevalence of HCV types 2 and 3 restates the need for variant genotypes to be included in immunodiagnostic and vaccine development strategies. This study reveals that the 1b genotype of HCV, previously found to be the major variant present in east Asia, also predominantes in the south-east Asian region, and may be the major HCV type found worldwide. PMID:7844535

Greene, W K; Cheong, M K; Ng, V; Yap, K W

1995-01-01

267

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

PubMed

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

Wang, Dongfang; Luthe, Dawn S

2003-09-01

268

Heat Sensitivity in a Bentgrass Variant. Failure to Accumulate a Chloroplast Heat Shock Protein Isoform Implicated in Heat Tolerance1  

PubMed Central

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.

Wang, Dongfang; Luthe, Dawn S.

2003-01-01

269

Genetic variants associated with Crohn's disease.  

PubMed

Crohn's disease is an immune-related disorder characterized by inflammation of the gastrointestinal mucosa, which can occur in any area throughout the digestive tract. This life-long disease commonly presents with abdominal pain, diarrhea, vomiting, and weight loss. While the exact etiology of this disease is largely unknown, it is thought to arise from an interaction between microbial, immunological, and environmental factors in a genetically susceptible host, whereby the immune system attacks the intestine as it cross reacts against gut microbial antigens. The study of genetic variants associated with Crohn's disease has shed light on our understanding of disease pathophysiology. A large number of genetic variants identified in Crohn's disease are related to genes targeting microbial recognition and bacterial wall sensing, the most common being NOD2/CARD15 gene. This review will discuss the recent advance in our knowledge of genetic variants of this disease and how they influence the disease course and prognosis. PMID:23935379

Michail, Sonia; Bultron, Gilberto; Depaolo, R William

2013-07-16

270

Recognizing MSTAR target variants and articulations  

NASA Astrophysics Data System (ADS)

The focus of this paper is recognizing articulated vehicles and actual vehicle configuration variants in real SAR images from the MSTAR public data. Using SAR scattering center locations and magnitudes as features, the invariance of these features is shown with articulation (i.e. turret rotation for the T72 tank and ZSU 23/4 gun), with configuration variants and with a small change in depression angle. This scatterer location and magnitude quasi-invariance (e.g. location within one pixel, magnitude within about ten percent in radar cross- section) is used as a basis for development of a SAR recognition engine that successfully identified real articulated and non-standard configuration vehicles based on non-articulated, standard recognition models. Identification performance results are presented as vote space scatter plots and ROC curves for configuration variants, for articulated objects and for a small change in depression angle with the MSTAR data.

Bhanu, Bir; Jones, Grinnell

1999-08-01

271

Meshy meningioma: a potential novel variant.  

PubMed

A potential novel variant of meningioma is reported. The tumor was solid, hard, white-colored, well circumscribed in a fibrous capsule and fixed to the dura, showing no invasion into the brain parenchyma. Histopathological study presented a sparsely cellular tumor composed of cells with fine reticular or mesh-like cytoplasm, each containing an oval nucleus. Mitotic figures were rarely seen. Immunohistochemical studies of tumor cells showed positive immunoreactivity for vimentin and epithelial membrane antigen but were negative for GFAP, desmin, neurofilament, keratin, S-100, CD34 and CEA. Bipolar neoplastic cells and long processes were noted on ultrastructural observation; these were attached side by side to each other by desmosomes, resulting in a mesh-like configuration. Perinuclear cytoplasm and processes were rich in intermediate filaments and rough endoplasmic reticulum. These microscopic and ultrastructural features have never before been reported among the variants of meningioma. The name 'meshy meningioma' is proposed for this novel variant. PMID:11666022

Yamanouchi, H; Yokoo, H; Yoshida, T; Kamiya, M; Sasaki, A; Hirato, J; Nakazato, Y

2001-09-01

272

A phonetic explanation of pronunciation variant effects.  

PubMed

Effects of word-level phonetic variation on the recognition of words with different pronunciation variants (e.g., center produced with/(out) [t]) are investigated via the semantic- and pseudoword-priming paradigms. A bias favoring clearly articulated words with canonical variants ([nt]) is found. By reducing the bias, words with different variants show robust and equivalent lexical activation. The equivalence of different word forms highlights a snag for frequency-based theories of lexical access: How are words and word productions with vastly different frequencies recognized equally well by listeners? A process-based account is proposed, suggesting that careful speech induces bottom-up processing and casual speech induces top-down processing. PMID:23862902

Sumner, Meghan

2013-07-01

273

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

PubMed

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

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

2009-01-01

274

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

USGS Publications Warehouse

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.

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

2010-01-01

275

Epithelioid fibrous papule - a new variant.  

PubMed

Fibrous papules (FPs) are common benign lesions occurring most frequently on the nose. Multiple variants have been described, including classic, hypercellular, clear cell, pigmented, pleomorphic, inflammatory and granular FPs. We describe a group of FPs with characteristics that do not easily fit into any of the above categories, with diffuse sheets of distinctive epithelioid cells, causing potential diagnostic confusion. Immunoperoxidase stains show that the cells of this 'epithelioid fibrous papule' are reactive for procollagen, and are negative for NKI/C3, unlike previously described clear cell variants. PMID:17576337

Kucher, Cynthia; McNiff, Jennifer M

2007-07-01

276

Space-variant Fresnel transform optical correlator  

NASA Astrophysics Data System (ADS)

A space-variant optical correlator whose output depends on both the shape and the position of the input signal is introduced. This positionally sensitive correlator has potential applications in machine vision, cryptography, and optical logic. In this approach the input function undergoes a free-space Fresnel transform (which introduces the positional sensitivity) and is multiplied by an appropriate mask function. The Fourier transform of the product then obtains the desired output. The theoretical basis for the space-variant correlator, computer-simulated outputs, and experimental results for the case in which the mask is written onto a magneto-optic spatial light modulator are discussed.

Davis, Jeffrey A.; Cottrell, Don M.; Nestorovic, Ned; Highnote, Susan M.

1992-11-01

277

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

Microsoft Academic Search

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

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

2002-01-01

278

Mouse Col18a1 is Expressed in a Tissue-Specific Manner as Three Alternative Variants and is Localized in Basement Membrane Zones  

Microsoft Academic Search

We have isolated overlapping cDNAs encoding the N-terminal non-triple-helical region of mouse alpha1(XVIII) collagen and shown that three different variants of alpha1(XVIII) collagen exist. Each of the three variants shows characteristic tissue-specific expression patterns. Immunohistochemical studies show positive staining for alpha1(XVIII) collagen along the basement membrane zones of vessels in the intestinal villi, the choroid plexus, skin, liver, and kidney.

Yasuteru Muragaki; Sheila Timmons; C. May Griffith; Suk P. Oh; Bahaa Fadel; Thomas Quertermous; Bjorn R. Olsen

1995-01-01

279

Prevalence and Clinical Course in Invasive Infections with Meningococcal Endotoxin Variants  

PubMed Central

Background Meningococci produce a penta-acylated instead of hexa-acylated lipid A when their lpxL1 gene is inactivated. Meningococcal strains with such lipid A endotoxin variants have been found previously in adult meningitis patients, where they caused less blood coagulopathy because of decreased TLR4 activation. Methods A cohort of 448 isolates from patients with invasive meningococcal disease in the Netherlands were screened for the ability to induce IL-6 in monocytic cell Mono Mac 6 cells. The lpxL1 gene was sequenced of isolates, which show poor capacity to induce IL-6.. Clinical characteristics of patients were retrieved from hospital records. Results Of 448 patients, 29 (6.5%) were infected with meningococci expressing a lipid A variant strain. Lipid A variation was not associated with a specific serogroup or genotype. Infections with lipid A variants were associated with older age (19.3 vs. 5.9 (median) years, p?=?0.007) and higher prevalence of underlying comorbidities (39% vs. 17%; p?=?0.004) compared to wild-type strains. Patients infected with lipid A variant strains had less severe infections like meningitis or shock (OR 0.23; 95%CI 0.09–0.58) and were less often admitted to intensive care (OR 0.21; 95%CI 0.07–0.60) compared to wild-type strains, independent of age, underlying comorbidities or strain characteristics. Conclusions In adults with meningococcal disease lipid A variation is rather common. Infection with penta-acylated lipid A variant meningococci is associated with a less severe disease course.

Bogaert, Debby; Schipper, Kim; Groenwold, Rolf H. H.; Hamstra, Hendrik Jan; Westerhuis, Brenda M.; van de Beek, Diederik; van der Ley, Peter; Sanders, Elisabeth A. M.; van der Ende, Arie

2012-01-01

280

Social isolation  

PubMed Central

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.

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

2011-01-01

281

New variant for whole pancreas grafting  

SciTech Connect

A new variant for whole pancreas grafting is described in which a segment of the duodenum and the spleen is included in the graft. The graft is placed extraperitoneally as in kidney transplantation. The exocrine drainage is with side-to-side anastomosis between duodenum and bladder. The spleen is irradiated to prevent the occurrence of GVHD, as is reported in splenic transplantation.

Kootstra, G.; van Hooff, J.P.; Joerning, P.J.L.; Leunissen, K.M.; van der Linden, C.J.; Beukers, E.; Buurman, W.A.

1987-02-01

282

X-linked adrenoleukodystrophy: spinocerebellar variant  

Microsoft Academic Search

The phenotypic variability in X-linked adrenoleukodystrophy (X-ALD) can be wide and varied. Rarely, it can present with clinical signs of spinocerebellar degeneration. There are very few reported cases of selective predominant white matter disease of the cerebellum in these patients. We report a patient with a rare variant of adult onset ALD who was previously diagnosed as spinocerebellar ataxia. He

Eng-King Tan; Shih-Hui Lim; Ling-Ling Chan; Meng-Cheong Wong; Kim-Ping Tan

1999-01-01

283

Truncated variants of apolipoprotein B cause hypobetalipoproteinaemia.  

PubMed Central

Familial hypobetalipoproteinaemia is a rare autosomal dominant disorder in which levels of apo-B-containing plasma lipoproteins are approximately half-normal in heterozygotes and virtually absent in homozygotes. Here we describe mutations of the apo-B gene that cause two different truncated variants of apo-B in unrelated individuals with hypobetalipoproteinaemia. One variant, apo-B(His1795----Met-Trp-Leu-Val-Thr-Term) is predicted to be 1799 amino acids long and arises from deletion of a single nucleotide (G) from leucine codon 1794. This protein was found at low levels in very low density and low density lipoprotein fractions in the blood. The second, shorter variant, apo-B(Arg1306----Term), is caused by mutation of a CpG dinucleotide in arginine codon 1306 converting it to a stop codon and predicting a protein of 1305 residues. The product of this allele could not be detected in the circulation. The differences in size and behaviour of these two variants compared to apo-B100 or apo-B48 point to domains that may be important for the assembly, secretion or stability of apo-B-containing lipoproteins. Images

Collins, D R; Knott, T J; Pease, R J; Powell, L M; Wallis, S C; Robertson, S; Pullinger, C R; Milne, R W; Marcel, Y L; Humphries, S E

1988-01-01

284

Splicing analysis of unclassified variants in COL2A1 and COL11A1 identifies deep intronic pathogenic mutations.  

PubMed

UK NHS diagnostic service sequence analysis of genes generally examines and reports on variations within a designated region 5' and 3' of each exon, typically 30 bp up and downstream. However, because of the degenerate nature of the splice sites, intronic variants outside the AG and GT dinucleotides of the acceptor and donor splice sites (ASS and DSS) are most often classified as being of unknown clinical significance, unless there is some functional evidence of their pathogenicity. It is now becoming clear that mutations deep within introns can also interfere with normal processing of pre-mRNA and result in pathogenic effects on the mature transcript. In diagnostic laboratories, these deep intronic variants most often fall outside of the regions analysed and so are rarely reported. With the likelihood that next generation sequencing will identify more of these unclassified variants, it will become important to perform additional studies to determine the pathogenicity of such sequence anomalies. Here, we analyse variants detected in either COL2A1 or COL11A1 in patients with Stickler syndrome. These have been analysed both in silico and functionally using either RNA isolated from the patient's cells or, more commonly, minigenes as splicing reporters. We show that deep intronic mutations are not a rare occurrence, including one variant that results in multiple transcripts, where both de novo donor and ASS are created by the mutation. Another variant produces transcripts that result in either haploinsufficiency or a dominant negative effect, potentially modifying the disease phenotype. PMID:22189268

Richards, Allan J; McNinch, Annie; Whittaker, Joanne; Treacy, Becky; Oakhill, Kim; Poulson, Arabella; Snead, Martin P

2011-12-21

285

Splicing analysis of unclassified variants in COL2A1 and COL11A1 identifies deep intronic pathogenic mutations  

PubMed Central

UK NHS diagnostic service sequence analysis of genes generally examines and reports on variations within a designated region 5? and 3? of each exon, typically 30?bp up and downstream. However, because of the degenerate nature of the splice sites, intronic variants outside the AG and GT dinucleotides of the acceptor and donor splice sites (ASS and DSS) are most often classified as being of unknown clinical significance, unless there is some functional evidence of their pathogenicity. It is now becoming clear that mutations deep within introns can also interfere with normal processing of pre-mRNA and result in pathogenic effects on the mature transcript. In diagnostic laboratories, these deep intronic variants most often fall outside of the regions analysed and so are rarely reported. With the likelihood that next generation sequencing will identify more of these unclassified variants, it will become important to perform additional studies to determine the pathogenicity of such sequence anomalies. Here, we analyse variants detected in either COL2A1 or COL11A1 in patients with Stickler syndrome. These have been analysed both in silico and functionally using either RNA isolated from the patient's cells or, more commonly, minigenes as splicing reporters. We show that deep intronic mutations are not a rare occurrence, including one variant that results in multiple transcripts, where both de novo donor and ASS are created by the mutation. Another variant produces transcripts that result in either haploinsufficiency or a dominant negative effect, potentially modifying the disease phenotype.

Richards, Allan J; McNinch, Annie; Whittaker, Joanne; Treacy, Becky; Oakhill, Kim; Poulson, Arabella; Snead, Martin P

2012-01-01

286

Fluorescent Protein Variants and Methods for Making Same.  

National Technical Information Service (NTIS)

The present invention relates generally to variant fluorescent proteins, and more specifically to monomeric and dimeric forms of Anthozoan fluorescent proteins. In one aspect, the present invention provides variants of fluorescent proteins, where the vari...

G. S. Baird R. E. Campbell R. Y. Tsien

2006-01-01

287

Fluorescent Protein Variants and Methods for Making Same.  

National Technical Information Service (NTIS)

The present invention relates generally to variant fluorescent proteins, and more specifically to monomeric and dimeric forms of Anthozoan fluorescent proteins. In one aspect, the present invention provides variants of fluorescent proteins, where the vari...

R. Y. Tsien R. E. Campbell G. S. Baird

2002-01-01

288

Processing variant forms in spoken word recognition: The role of variant frequency  

Microsoft Academic Search

Recognition of a spoken word phonological variant—schwa vowel deletion (e.g., corporate ? corp’rate)— was investigated in vowel detection (absent\\/present) and syllable number judgment (two or three syllables) tasks. Variant\\u000a frequency corpus analyses (Patterson, LoCasto, & Connine, 2003) were used to select words with either high or low schwa vowel\\u000a deletion rates. Speech continua were created for each word in which

Cynthia M. Connine; Larissa J. Ranbom; David J. Patterson

2008-01-01

289

Functional and Computational Assessment of Missense Variants in the Ataxia-Telangiectasia Mutated (ATM) Gene: Mutations with Increased Cancer Risk  

PubMed Central

The functional consequences of missense variants are often difficult to predict. This becomes especially relevant when DNA sequence changes are used to determine a diagnosis or prognosis. To analyze the consequences of twelve missense variants in patients with mild forms of ataxia-telangiectasia (A-T), we employed site-directed mutagenesis of ATM cDNA followed by stable transfections into a single A-T cell line to isolate the effects of each allele on the cellular phenotype. After induction of the transfected cells with CdCl2, we monitored for successful ATM transcription and subsequently assessed: 1) intracellular ATM protein levels, 2) ionizing radiation (IR)-induced ATM kinase activity, and 3) cellular radiosensitivity. We then calculated SIFT and PolyPhen scores for the missense changes. Nine variants produced little or no correction of the A-T cellular phenotype and were interpreted to be ATM mutations; SIFT/PolyPhen scores supported this. Three variants corrected the cellular phenotype, suggesting that they represented benign variants or polymorphisms. SIFT and PolyPhen scores supported the functional analyses for one of these variants (c.1709T>C); the other two were predicted to be “not tolerated” (c.6188G>A, and c.6325T>G) and were classified as “operationally neutral”. Genotype/phenotype relationships were compared: three deleterious missense variants were associated with an increased risk of cancer (c.6679C>T, c.7271T>G and c.8494C>T). In situ mutagenesis represents an effective experimental approach for distinguishing deleterious missense mutations from benign or “operationally neutral” missense variants.

Mitui, M; Nahas, SA; Du, LT; Yang, Z; Lai, CH; Nakamura, K; Arroyo, S; Scott, S; Purayidom, A; Concannon, P; Lavin, M; Gatti, RA

2009-01-01

290

Isolation and cloning of two variant papillomaviruses from domestic pigs: Sus scrofa papillomaviruses type 1 variants a and b  

Microsoft Academic Search

The healthy skin of two female domestic pigs (Sus scrofa domestica) was sampled with cotton- tipped swabs. Total genomic DNA was extracted from the samples and subjected to PCR with degenerate papillomavirus (PV)-specific primers. Similarity searches performed with BLASTN showed that partial E1 and L1 sequences of two novel PVs were amplified. Subsequently, the complete genomes of these Sus scrofa

Hans Stevens; Annabel Rector; Kees Van Der Kroght; Marc Van Ranst

2008-01-01

291

Multiple rRNA variants in a single spore of the microsporidian Nosema bombi.  

PubMed

To understand the source of the multiple DNA sequence variants of Nosema bombi ribosomal RNA (rRNA) found in a single bumble bee host, we PCR amplified, cloned, and sequenced the partial rRNA gene from 125 clones, which were derived from four out of 46 spores individually isolated from a single host by laser microdissection. At least two rRNA variants, characterized by either (GTTT)(2) or (GTTT)(3) repeat units within the internal transcribed spacer (ITS) region, were found per spore in approximately equal proportions, variants which were also found in approximately equal proportions in 55 clones of the two DNA extracts of multiple spores from the same host. Firstly, we demonstrate for the first time that DNA sequences can be obtained from single-binucleate microsporidia. Secondly, it appears that concerted evolution has not homogenized the sequences of all rRNA copies within a single N. bombi spore or even within a single nucleus. We thereby demonstrate unequivocally that two or more rRNA sequence variants exist per N. bombi spore, and urge caution in the use of multicopy rRNA genes for population genetic and phylogenetic analysis of this and other Microsporidia unless homologous copies can be reliably typed. PMID:17300528

O'Mahony, Elaine M; Tay, Wee Tek; Paxton, Robert J

292

Case of primary localized cutaneous amyloidosis with protean clinical manifestations: lichen, poikiloderma-like, dyschromic and bullous variants.  

PubMed

Primary localized cutaneous amyloidosis (PLCA) commonly presents as macular and lichen variants. We present a case of a 27-year-old Chinese woman with cutaneous features of the rarely reported poikiloderma-like, dyschromic and bullous forms of PLCA, and the commoner lichen variant. There were no syndromic associations or systemic involvement, and the various morphological subtypes occurred in isolation from one another. We review the clinical spectrum of PLCA, highlight its protean clinical manifestations in this patient, and discuss its postulated pathogenesis in relation to its histopathological features. PMID:21933256

Chandran, Nisha Suyien; Goh, Boon-Kee; Lee, Siong-See; Goh, Chee-Leok

2011-09-20

293

A Three-Dimensional Interactive Atlas of Cerebral Arterial Variants  

Microsoft Academic Search

The knowledge of cerebrovascular variants is essential in education, training, diagnosis and treatment. The current way of\\u000a presentation of vasculature and, particularly, vascular variants is insufficient. Our purpose is to construct a three-dimensional\\u000a (3D) interactive atlas of cerebral arterial variants along with exploration tools allowing the investigator just with a few\\u000a clicks to better and faster understand the variants and

Wieslaw L. Nowinski; A. Thirunavuukarasuu; Ihar Volkau; Yevgen Marchenko; Bivi Aminah; Fiftarina Puspitasari; Val M. Runge

2009-01-01

294

Testing for rare variant associations in complex diseases  

PubMed Central

The study of rare variants holds the promise of accounting for some of the missing heritability in complex traits. Next-generation sequencing technologies enable probing of variation across the full spectrum of allele frequencies. Multiple methods for the analysis of rare variants have been proposed and, recently, Ionita-Laza et al. have presented an approach with the theoretical capacity to detect risk and protective variants. The identification of rare risk variants could have major implications in understanding complex disease etiopathogenesis.

2011-01-01

295

Human Papillomavirus Type 6 and 11 Genetic Variants Found in 71 Oral and Anogenital Epithelial Samples from Australia  

PubMed Central

Genetic variation of 49 human papillomavirus (HPV) 6 and 22 HPV11 isolates from recurrent respiratory papillomatosis (RRP) (n?=?17), genital warts (n?=?43), anal cancer (n?=?6) and cervical neoplasia cells (n?=?5), was determined by sequencing the long control region (LCR) and the E6 and E7 genes. Comparative analysis of genetic variability was examined to determine whether different disease states resulting from HPV6 or HPV11 infection cluster into distinct variant groups. Sequence variation analysis of HPV6 revealed that isolates cluster into variants within previously described HPV6 lineages, with the majority (65%) clustering to HPV6 sublineage B1 across the three genomic regions examined. Overall 72 HPV6 and 25 HPV11 single nucleotide variations, insertions and deletions were observed within samples examined. In addition, missense alterations were observed in the E6/E7 genes for 6 HPV6 and 5 HPV11 variants. No nucleotide variations were identified in any isolates at the four E2 binding sites for HPV6 or HPV11, nor were any isolates found to be identical to the HPV6 lineage A or HPV11 sublineage A1 reference genomes. Overall, a high degree of sequence conservation was observed between isolates across each of the regions investigated for both HPV6 and HPV11. Genetic variants identified a slight association with HPV6 and anogenital lesions (p?=?0.04). This study provides important information on the genetic diversity of circulating HPV 6 and HPV11 variants within the Australian population and supports the observation that the majority of HPV6 isolates cluster to the HPV6 sublineage B1 with anogenital lesions demonstrating an association with this sublineage (p?=?0.02). Comparative analysis of Australian isolates for both HPV6 and HPV11 to those from other geographical regions based on the LCR revealed a high degree of sequence similarity throughout the world, confirming previous observations that there are no geographically specific variants for these HPV types.

Danielewski, Jennifer A.; Garland, Suzanne M.; McCloskey, Jenny; Hillman, Richard J.; Tabrizi, Sepehr N.

2013-01-01

296

Processing of No-Release Variants in Connected Speech  

ERIC Educational Resources Information Center

|The cross modal repetition priming paradigm was used to investigate how potential lexically ambiguous no-release variants are processed. In particular we focus on segmental regularities that affect the variant's frequency of occurrence (voicing of the critical segment) and phonological context in which the variant occurs (status of the following…

LoCasto, Paul C.; Connine, Cynthia M.

2011-01-01

297

Statistical analysis strategies for association studies involving rare variants  

Microsoft Academic Search

The limitations of genome-wide association (GWA) studies that focus on the phenotypic influence of common genetic variants have motivated human geneticists to consider the contribution of rare variants to phenotypic expression. The increasing availability of high-throughput sequencing technologies has enabled studies of rare variants but these methods will not be sufficient for their success as appropriate analytical methods are also

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

2010-01-01

298

Properties of learning of a fuzzy ART variant  

Microsoft Academic Search

This paper discusses one variation of the fuzzy ART architecture, referred to as fuzzy ART variant. The fuzzy ART variant is a fuzzy ART algorithm, with a very large value for the choice parameter. Based on the geometrical interpretation of templates in fuzzy ART we present and prove useful properties of learning pertaining to the fuzzy ART variant. One of

Michael Georgiopoulos; I. Dagher; Gregory L. Heileman; George Bebis

1997-01-01

299

Identification of Constitutively Active Interleukin 33 (IL-33) Splice Variant*  

PubMed Central

IL-33/IL-1F11 is a new member of the IL-1 family ligand and provokes T helper-type immune responses. IL-33 is the ligand of ST2 and IL-1 receptor accessory protein (IL-1RAcP) that triggers nuclear factor-? light chain enhancer of activated B cells (NF-?B) and MAPK signaling. We discovered a novel short splice variant of IL-33 that was termed spIL-33. The new spIL-33 lacks exon 3 containing a proposed caspase-1 cleavage site. We isolated spIL-33 cDNA from the Huh7 human hepatocarcinoma cell line and expressed the recombinant spIL-33 protein in Escherichia coli. The recombinant spIL-33 and pro-IL-33 were not cleaved by caspase-1, unlike IL-18 (IL-1F4). The recombinant spIL-33 was constitutively active, and spIL-33-induced inflammatory cytokine production was caspase-1-independent in HMC-1 and Raw 264.7 cells. The recombinant spIL-33 induced the phosphorylation of IL-1 receptor-associated kinase (IRAK1), NF-?B, p38 MAPK, p44/42 MAPK, and JNK in a time- and dose-dependent manner. Anti-ST2 monoclonal antibody specifically blocked the spIL-33-induced cytokine production. In this study, we identified and characterized a new IL-33 splice variant, which was a constitutively active IL-33 isoform. The existence of constitutively active spIL-33 suggests that the biological activity of IL-33 could be triggered by diverse stimulations during immune responses. Further investigation of the spIL-33 expression pattern may contribute to understanding the involvement of IL-33 in inflammatory disorders.

Hong, Jaewoo; Bae, Suyoung; Jhun, Hyunjhung; Lee, Siyoung; Choi, Jida; Kang, Taebong; Kwak, Areum; Hong, Kwangwon; Kim, Eunsom; Jo, Seunghyun; Kim, Soohyun

2011-01-01

300

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

PubMed

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

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

2012-02-15

301

Lobular breast carcinoma and its variants.  

PubMed

Lobular carcinoma is a special type of breast cancer that shows distinct clinical presentation, morphologic and molecular features, and clinical behavior, and its incidence is rising in recent years. Infiltrating lobular carcinoma (ILC) and its precursor lesions may result in diagnostic difficulties, particularly in the screening settings and their management may be problematic. Variants of lobular carcinoma, such as the pleomorphic variant, although not common, exist and some show differences in behavior warranting their recognition in view of requirements for different management strategies. Here we present a review of lobular carcinomas with particular attention to lobular in situ lesions, epidemiology, subtypes, diagnosis, molecular pathology, and grading of ILC in addition to the clinical behavior, response to therapy, and outcome of patients with ILC. PMID:20306830

Rakha, Emad A; Ellis, Ian O

2010-02-01

302

Methylenetetrahydrofolate reductase variant and schizophrenia/depression.  

PubMed

Patients with methylenetetrahydrofolate reductase (MTHFR) deficiency often show psychiatric manifestations. Since a common variant of the MTHFR gene, T677(Ala), responsible for the thermolabile MTHFR with less than 50% specific MTHFR activity, has been reported, we examined whether the T677 allele is associated with psychiatric disorders in an unrelated Japanese population consisting of 297 schizophrenics, 32 patients with major depression, 40 patients with bipolar disorder, and 419 controls. The genotype homozygous for the T677 allele was significantly frequently observed in schizophrenics with an odds ratio of 1.9 (P = 0.0006), and in patients with major depression with an odds ratio of 2.8 (P = 0.005). Our data suggest associations of the MTHFR gene variant with schizophrenia and depression in the Japanese. PMID:9342205

Arinami, T; Yamada, N; Yamakawa-Kobayashi, K; Hamaguchi, H; Toru, M

1997-09-19

303

The equine fundus. III: Pathological variants.  

PubMed

A wide range of ophthalmoscopic variants are encountered during routine examination of the horse. Some result from minor anatomical anomalies, cause no significant effect on vision and may be considered to lie within the limits of 'biological normality'. Others are a consequence of pathological disruption of the anatomical integrity of the fundus, and may directly or indirectly affect the neurosensory retina and produce some degree of visual deficit. This paper illustrates the ophthalmoscopic appearance of a number of pathological variants of the anatomic fundus, and discusses their possible effect upon vision. Among the abnormalities discussed is peripapillary chorioretinitis, which commonly presents as the so-called peripapillary 'butterfly lesion'. It is concluded that, although this lesion may occur in conjunction with signs of more generalised posterior segment disease, eg posterior capsular cataract, in the absence of concurrent signs of anterior uveitis there is no reason to associate the lesion with equine recurrent uveitis (periodic ophthalmia). PMID:9079119

Matthews, A G; Crispin, S M; Parker, J

1990-09-01

304

Nuclear Receptor Variants in Liver Disease  

PubMed Central

This review aims to provide a snapshot of the actual state of knowledge on genetic variants of nuclear receptors (NR) involved in regulating important aspects of liver metabolism. It recapitulates recent evidence for the application of NR in genetic diagnosis of monogenic (“Mendelian”) liver disease and their use in clinical diagnosis. Genetic analysis of multifactorial liver diseases such as viral hepatitis or fatty liver disease identifies key players in disease predisposition and progression. Evidence from these analyses points towards a role of NR polymorphisms in common diseases, linking regulatory networks to complex and variable phenotypes. The new insights into NR variants also offer perspectives and cautionary advice for their use as handles towards diagnosis and treatment.

Mullenbach, Roman; Weber, Susanne N.; Lammert, Frank

2012-01-01

305

Toxin gene analysis of a variant strain of Clostridium difficile that causes human clinical disease.  

PubMed

A toxin variant strain of Clostridium difficile was isolated from two patients with C. difficile-associated disease (CDAD), one of whom died from extensive pseudomembranous colitis. This strain, identified by restriction endonuclease analysis (REA) as type CF2, was not detected by an immunoassay for C. difficile toxin A. Culture supernatants of CF2 failed to elicit significant enterotoxic activity in the rabbit ileal loop assay but did produce atypical cytopathic effects in cell culture assay. Southern hybridization, PCR amplification, and DNA sequence analyses were performed on the toxin A (tcdA) and toxin B (tcdB) genes of type CF2 isolate 5340. Type CF2 5340 tcdA exhibited a 1,821-bp truncation, due to three deletions in the 3' end of the gene, and a point mutation in the 5' end of the gene, resulting in a premature stop codon at tcdA position 139. Type CF2 5340 tcdB exhibited multiple nucleotide base substitutions in the 5' end of the gene compared to tcdB of the standard toxigenic strain VPI 10463. Type CF2 5340 toxin gene nucleotide sequences and deduced amino acid sequences showed a strong resemblance to those of the previously described variant C. difficile strain 1470, a strain reported to have reduced pathogenicity and no association with clinical illness in humans. REA of strain 1470 identified this strain as a distinct type (CF1) within the same REA group as the closely related type CF2. A review of our clinical-isolate collection identified five additional patients infected with type CF2, three of whom had documented CDAD. PCR amplification of the 3' end of tcdA demonstrated identical 1. 8-kb deletions in all seven type CF2 isolates. REA type CF2 is a toxin variant strain of C. difficile that retains the ability to cause disease in humans but is not detected in clinical immunoassays for toxin A. PMID:10992443

Sambol, S P; Merrigan, M M; Lyerly, D; Gerding, D N; Johnson, S

2000-10-01

306

Pullulan production by tropical isolates of Aureobasidium pullulans  

Microsoft Academic Search

Tropical isolates of Aureobasidium pullulans previously isolated from distinct habitats in Thailand were characterized for their capacities to produce the valuable polysaccharide,\\u000a pullulan. A. pullulans strain NRM2, the so-called “color variant” strain, was the best producer, yielding 25.1 g pullulan l?1 after 7 days in sucrose medium with peptone as the nitrogen source. Pullulan from strain NRM2 was less pigmented than those\\u000a from

Sehanat Prasongsuk; Mark A. Berhow; Christopher A. Dunlap; David Weisleder; Timothy D. Leathers; Douglas E. Eveleigh; Hunsa Punnapayak

2007-01-01

307

Variant Extensions to Prove MAS Behaviours  

Microsoft Academic Search

\\u000a In this article, it is shown how the behaviour of a multi-agent system can be validated thanks to proof. At first, the method\\u000a used is briefly presented [10]. Then, the variant notion is presented and an extension of this notion to prove MAS is introduced. In the third part, the proof technique is\\u000a illustrated for the prey-predator problem: the behaviour

Bruno Mermet; Dominique Fournier

2004-01-01

308

Sex steroids and variants of gender identity.  

PubMed

This article summarizes for the practicing endocrinologist the current literature on the psychobiology of the development of gender identity and its variants in individuals with disorders of sex development (DSD) or with non-DSD transgenderism. Gender reassignment remains the treatment of choice for strong and persistent gender dysphoria in both categories, but more research is needed on the short-term and long-term effects of puberty-suppressing medications and cross-sex hormones on brain and behavior. PMID:24011879

Meyer-Bahlburg, Heino F L

2013-09-01

309

Hfq variant with altered RNA binding functions  

Microsoft Academic Search

The interaction between Hfq and RNA is central to multiple regulatory processes. Using site-directed mutagenesis, we have found a missense mutation in Hfq (V43R) which strongly affects the RNA binding capacity of the Hfq protein and its ability to stimulate poly(A) tail elongation by poly(A)-polymerase in vitro. In vivo, overexpression of this Hfq variant fails to stimulate rpoS-lacZ expression and

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

2006-01-01

310

The modification and variants of histone  

Microsoft Academic Search

The modification of histone plays a crucial role in regulating chromatin states that conserve transcription programs and provide\\u000a a mechanism for chromatin states to be maintained as cells proliferate. A large number of factors and protein complexes are\\u000a now known to be involved in regulating the dynamic states of the modification and variants of histone. A fraction of histones\\u000a are

Changjun Mu; Heng Liu; Guo-Chang Zheng

2007-01-01

311

New Variant Famine: Reassessing Its Validity  

Microsoft Academic Search

Southern Africa has faced recurring food-crises since 2001. It has been recognised that HIV\\/AIDS is an important contributory factor, but the New Variant Famine (NVF) hypothesis places HIV\\/AIDS as a central factor. Critical analyses of NVF have failed to engage adequately with it. This paper interrogates the concept through a case study of Malawi in 2001\\/02. It argues that there

Andrew Gibbs

312

Human Prion Diseases with Variant Prion Protein  

Microsoft Academic Search

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

Tetsuyuki Kitamoto; Jun Tateishi

1994-01-01

313

Thymofibrolipoma. A histologic variant of thymolipoma.  

PubMed

We report two cases of a thymic neoplasm showing abundant fibroconnective tissue with focal areas of fatty tissue. The two patients, a 9-year-old girl and a 32-year-old man, were found to have an anterior mediastinal mass on routine chest roentgenograms. Surgical resection was performed in both cases. Because of the histologic features shown by these neoplasms, we believe that these cases represent a variant of thymolipoma, and we have named it thymofibrolipoma. PMID:8135632

Moran, C A; Zeren, H; Koss, M N

1994-03-01

314

Intracellular signaling by growth hormone variant (GHV)  

Microsoft Academic Search

Placental growth hormone, or growth hormone variant (GH-V), is a member of the growth hormone gene family. Its physiologic role during pregnancy remains undefined. Although extensive work has been done characterizing the signaling pathways activated by hGH, the signaling pathways which are activated by GH-V have not been characterized. We investigated cellular signaling by GH-V in model systems in which

Corinne M Silva; Michael T Kloth; Charles E Lyons; Christopher R Dunn; Susan E Kirk

2002-01-01

315

Characterisation of PCV2 isolates from Spain, Germany and France  

Microsoft Academic Search

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

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

2000-01-01

316

Antimicrobial Susceptibilities of Invasive Pediatric Abiotrophia and Granulicatella Isolates  

Microsoft Academic Search

Abiotrophia and Granulicatella species have been associated with various infections. Antimicrobial suscep- tibility data for these nutritionally variant streptococcus-like organisms, especially for pediatric isolates, are very limited. Little is known about the genetic bases of their resistance mechanisms. We report the results of identification to bacterial species level, antimicrobial susceptibility testing, macrolide resistance testing, and detection of genes encoding that

Xiaotian Zheng; Alexandra F. Freeman; Jay Villafranca; Dee Shortridge; Jill Beyer; William Kabat; Karen Dembkowski; Stanford T. Shulman

2004-01-01

317

Clear cell variant of squamous cell carcinoma of skin: A report of a case.  

PubMed

Clear cell squamous cell carcinoma (SCC) is a rare variant of SCC of skin in which ultraviolet radiation has been suggested as possible etiology. This case is that of a 62-year-old male concrete block maker/bricklayer who presented with a 6 months history of a non-healing ulcer on the left side of his face. Histology showed features of malignant epithelial neoplasm composed of islands of large oval to polyhedral malignant squamous cells with eosinophilic to amphophilic cytoplasm and vesicular nuclei and there were areas showing clear cell differentiation and isolated areas of keratin pearl formation. The lesion was also negative for periodic acid schiff, mucicarmine, and alcian blue stains but was strongly positive for AE1/AE3 (immuno-stain). This case showed an aggressive and bizarre clinical presentation but more report of cases are needed to have a better characterization of the clinical presentation and prognosis of this variant of SCC. PMID:23798842

Lawal, Ahmed Oluwatoyin; Adisa, Akinyele Olumuyiwa; Olajide, Mofoluwaso A; Olusanya, Adeola Adenike

2013-01-01

318

Clear cell variant of squamous cell carcinoma of skin: A report of a case  

PubMed Central

Clear cell squamous cell carcinoma (SCC) is a rare variant of SCC of skin in which ultraviolet radiation has been suggested as possible etiology. This case is that of a 62-year-old male concrete block maker/bricklayer who presented with a 6 months history of a non-healing ulcer on the left side of his face. Histology showed features of malignant epithelial neoplasm composed of islands of large oval to polyhedral malignant squamous cells with eosinophilic to amphophilic cytoplasm and vesicular nuclei and there were areas showing clear cell differentiation and isolated areas of keratin pearl formation. The lesion was also negative for periodic acid schiff, mucicarmine, and alcian blue stains but was strongly positive for AE1/AE3 (immuno-stain). This case showed an aggressive and bizarre clinical presentation but more report of cases are needed to have a better characterization of the clinical presentation and prognosis of this variant of SCC.

Lawal, Ahmed Oluwatoyin; Adisa, Akinyele Olumuyiwa; Olajide, Mofoluwaso A; Olusanya, Adeola Adenike

2013-01-01

319

Characterization of Macrolide Efflux Pump mef Subclasses Detected in Clinical Isolates of Streptococcus pyogenes Isolated between 1999 and 2005  

Microsoft Academic Search

The macrolide efflux mechanism of resistance, mef, was characterized in community-acquired respiratory tract infections with Streptococcus pyogenes. Fifty-four (4.6%) M phenotype isolates were screen tested as negative for mef(A). Of these 54 isolates, 5 (0.4%), 27 (2.3%), and 1 (0.1%) were considered to be mef(I) positive, a novel mosaic variant of mef, or a novel subclass of mef, respectively. This

J. Blackman Northwood; M. Del Grosso; L. R. Cossins; M. D. Coley; R. Creti; A. Pantosti; D. J. Farrell

2009-01-01

320

Antigenic drift in type A influenza virus: Peptide mapping and antigenic analysis of A/PR/8/34 (HON1) variants selected with monoclonal antibodies  

PubMed Central

Variants of A/PR/8/34 (HON1) influenza virus, having hemagglutinin molecules with probably a single altered antigenic determinant, were isolated by growing the virus in the presence of the monoclonal hybridoma antibody PEG-1. The variants were analyzed by peptide mapping and characterized antigenically by using PEG-1 and four other monoclonal hybridoma antibodies to PR8 hemagglutinin. Peptide maps of the large hemagglutinin polypeptide, HA1, from 8 out of 10 variants showed a single changed peptide. This peptide from two of the variants was analyzed, and in each case a serine residue in the wild-type hemagglutinin was replaced by leucine in the variant. Although these eight variants showed identical peptide maps, one could be discriminated antigenically from the others with one of the hybridomas. (The peptide maps represented about one-third of the HA1 molecule.) Of the other two variants, one gave the same HA1 map as the wild type, but could be distinguished antigenically from wild-type virus by two of the hybridomas. The other was unique, and could be distinguished, both antigenically and by peptide mapping, from the other variants. Since a large number of the variants selected with PEG-1 showed the same peptide change, it is likely that this alteration in amino acid sequence (serine to leucine) was responsible for the inability of the variants to bind PEG-1 monoclonal antibody. We do not know, however, whether the changed amino acids were located within the antigenic sites or whether the change occurred somewhere else in the hemagglutinin molecule and altered the determinants through conformational changes. Images

Laver, W. G.; Gerhard, W.; Webster, R. G.; Frankel, M. E.; Air, G. M.

1979-01-01

321

Variant influenza virus hemagglutinin that induces fusion at elevated pH.  

PubMed Central

The hemagglutinin (HA) glycoprotein of influenza virus performs two critical roles during infection: it binds virus to cell surface sialic acids, and under mildly acidic conditions it induces fusion of the virion with intracellular membranes, liberating the genome into the cytoplasm. The pH dependence of fusion varies for different influenza virus strains. Here we report the isolation and characterization of a naturally occurring variant of the X31 strain that fuses at a pH 0.2 units higher than the parent strain does and that is less sensitive to the effects of ammonium chloride, a compound known to elevate endosomal pH. The bromelain-solubilized ectodomain of the variant HA displayed a corresponding shift in the pH at which it changed conformation and bound to liposomes. Cloning and sequencing of the variant HA gene revealed amino acid substitutions at three positions in the polypeptide. Two substitutions were in antigenic determinants in the globular region of HA1, and the third occurred in HA2 near the base of the molecule. By using chimeric HA molecules expressed in CV-1 cells from simian virus 40-based vectors, we demonstrated that the change in HA2 was solely responsible for the altered fusion phenotype. This substitution, asparagine for aspartic acid at position 132, disrupted a highly conserved interchain salt bridge between adjacent HA2 subunits. The apparent role of this residue in stabilizing the HA trimer is consistent with the idea that the trimer dissociates at low pH. Furthermore, the results demonstrate that influenza virus populations contain fusion variants, raising the possibility that such variants may play a role in the evolution of the virus. Images

Doms, R W; Gething, M J; Henneberry, J; White, J; Helenius, A

1986-01-01

322

Positional identification of variants of Adamts16 linked to inherited hypertension  

PubMed Central

A previously reported blood pressure (BP) quantitative trait locus on rat Chromosome 1 was isolated in a short congenic segment spanning 804.6 kb. The 804.6 kb region contained only two genes, LOC306664 and LOC306665. LOC306664 is predicted to translate into A Disintegrin-like and Metalloproteinase with Thrombospondin Motifs-16 (Adamts16). LOC306665 is a novel gene. All predicted exons of both LOC306664 and LOC306665 were sequenced. Non-synonymous variants were identified in only one of these genes, LOC306664. These variants were naturally existing polymorphisms among inbred, outbred and wild rats. The full-length rat transcript of Adamts16 was detected in multiple tissues. Similar to ADAMTS16 in humans, expression of Adamts16 was prominent in the kidney. Renal transcriptome analysis suggested that a network of genes related to BP was differential between congenic and S rats. These genes were also differentially expressed between kidney cell lines with or without knock-down of Adamts16. Adamts16 is conserved between rats and humans. It is a candidate gene within the homologous region on human Chromosome 5, which is linked to systolic and diastolic BP in the Quebec Family Study. Multiple variants, including an Ala to Pro variant in codon 90 (rs2086310) of human ADAMTS16, were associated with human resting systolic BP (SBP). Replication study in GenNet confirmed the association of two variants of ADAMTS16 with SBP, including rs2086310. Overall, our report represents a high resolution positional cloning and translational study for Adamts16 as a candidate gene controlling BP.

Joe, Bina; Saad, Yasser; Lee, Norman H.; Frank, Bryan C.; Achinike, Ovokeraye H.; Luu, Truong V.; Gopalakrishnan, Kathirvel; Toland, Edward J.; Farms, Phyllis; Yerga-Woolwine, Shane; Manickavasagam, Ezhilarasi; Rapp, John P.; Garrett, Michael R.; Coe, David; Apte, Suneel S.; Rankinen, Tuomo; Perusse, Louis; Ehret, Georg B.; Ganesh, Santhi K.; Cooper, Richard S.; O'Connor, Ashley; Rice, Treva; Weder, Alan B.; Chakravarti, Aravinda; Rao, Dabeeru C.; Bouchard, Claude

2009-01-01

323

Multiple Menkes copper ATPase (Atp7a) transcript and protein variants are induced by iron deficiency in rat duodenal enterocytes.  

PubMed

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

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

2012-05-10

324

Selection of variant hepatoma cells in liver-specific growth media: regulation at the mRNA level.  

PubMed

Three liver-specific growth media, respectively free of arginine (Arg-), tyrosine (Tyr-) and glucose (G-), have been used to characterize cells of the rat H4IIEC3, human HepG2 and mouse BW hepatoma lines. Cells of clone FaO, a derivative of line H4IIEC3, freely grew in Tyr- and G- media, and gave rise to stable variants in Arg- conditions. Cells of line HepG2 and clone BWTG3, a derivative of line BW, degenerated in all three media. Arg and tyr variants were however derived from HepG2 cells; their genesis appeared to be pathway specific, illustrating the complexity of the regulatory loops that are implicated in the control of the differentiated state. No variant was ever obtained with BWTG3 cells, demonstrating the stability of their deficiency in the post-natal hepatic functions that are involved in Arg-, Tyr- and G- selections. Variant clones of HepG2 and FaO cells that have been isolated in Arg- medium were characterized in details for liver-specific urea-cycle enzyme activities and mRNA. These variants were shown to be controlled at the mRNA level, most likely at transcription. Isolation of stable FaO and HepG2 variant clones as well as the converse demonstration of the stable deficiency of BWTG3 cells in post-natal hepatic functions were aimed at expression cloning. Our results are thus discussed in terms of transfection with full-length cDNA expression libraries and cloning of regulatory genes that could activate or extinguish liver specific genes. PMID:1322334

Armbruster, L; Cavard, C; Briand, P; Bertolotti, R

1992-05-01

325

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

PubMed Central

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.

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

2013-01-01

326

Monocytotropic human immunodeficiency virus type 1 (HIV-1) variants detectable in all stages of HIV-1 infection lack T-cell line tropism and syncytium-inducing ability in primary T-cell culture.  

PubMed Central

We previously demonstrated a correlation between the presence of syncytium-inducing (SI) human immunodeficiency virus type 1 (HIV-1) variants showing tropism for cell line H9 and the occurrence of rapid CD4 cell decline and progression to AIDS. In contrast, in stable asymptomatic individuals, we detected only isolates with low replication rates that were non-syncytium-inducing (NSI) and nontropic for the H9 cell line. Here, we investigated the monocytotropism of established HIV-1 isolates with a panel of isolates and with biological HIV-1 clones with distinct phenotypes. Moreover, the prevalence and biological phenotypes of monocytotropic HIV-1 variants in the course of HIV-1 infection were analyzed in comparative primary isolation studies on peripheral blood lymphocytes (PBL) and monocyte-derived macrophages (MDM). In cell-free infection studies with MDM from eight blood donors, 13 of 17 NSI isolates but only 4 of 14 SI isolates were able to infect MDM. NSI isolates also infected significantly more different donors than SI variants (median, 3 of 8 versus 0 of 8). This enhanced monocytotropism of NSI isolates was confirmed in experiments with biological HIV-1 clones with distinct phenotypes recovered from the same donor. To investigate the prevalence and biological phenotypes of monocytotropic variants in different stages of HIV-1 infection, sequential isolates from peripheral blood mononuclear cell samples from nine asymptomatic individuals, five of whom progressed to AIDS and seven of whom had a known time of seroconversion, were recovered by cocultivation with both PBL and MDM. Monocytotropic variants were obtained from 37 of 42 time points. All monocytotropic variants were NSI in PBL culture and non-T-cell-line tropic, even when SI, T-cell-line-tropic HIV-1 variants could be recovered from the same patient sample by cocultivation with PBL. We conclude that monocytotropic HIV-1 variants mostly have an NSI phenotype in PBL and, in contrast to SI variants, are present at all stages of HIV-1 infection. These results suggest an important role for monocytotropic variants in the persistence of HIV-1 infection.

Schuitemaker, H; Kootstra, N A; de Goede, R E; de Wolf, F; Miedema, F; Tersmette, M

1991-01-01

327

Suggestive linkage of ADHD to chromosome 18q22 in a young genetically isolated Dutch population  

Microsoft Academic Search

Attention deficit\\/hyperactivity disorder (ADHD) is a common, highly heritable, neuropsychiatric disorder among children. Linkage studies in isolated populations have proved powerful to detect variants for complex diseases, such as ADHD. We performed a genome-wide linkage scan for ADHD in nine patients from a genetically isolated population in the Netherlands, who were linked to each other within 10 generations through multiple

Najaf Amin; Yuri S Aulchenko; Marieke C Dekker; Robert F Ferdinand; Alwin van Spreeken; Alfons H Temmink; Frank C Verhulst; Ben A Oostra; Cornelia M van Duijn; CM van Duijn

2009-01-01

328

[Analysis of the antigenic properties of hemagglutinins of isolates of the influenza A virus (H1N1), isolated in 1986 in the Byelorussian SSR].  

PubMed

The influenza epidemic occurring in Minsk in the autumn of 1986 was caused by at least two drift variants of influenza A virus (H1N1 subtype) differing in two antigenic determinants of hemagglutinin from the viruses isolated in previous years (A/USSR/90/77, A/Dunedin/6/83). One of the epidemic drift variants was found to be identical in the antigenic properties of hemagglutinin with the reference A/Taiwan/1/86 virus. PMID:2480024

Rogacheva, T A; Khliustov, S V; Virinskaia, A S

329

Novel secondary Ig VH gene rearrangement and in-frame Ig heavy chain complementarity-determining region III insertion/deletion variants in de novo follicular lymphoma.  

PubMed

Human germinal center B cell tumors retain the ability of their nontransformed counterparts to somatically hypermutate Ig V genes by nucleotide substitution. Among a survey of 60 primary previously untreated, clonal, follicular lymphomas we have identified a rare V(H) rearrangement variant and two other in-frame nucleotide insertion/deletion variants within complementarity-determining region III of the Ig heavy chain. The neoplastic origin of the V(H) rearrangement variant was directly demonstrated in cells isolated by microdissection from malignant follicles. In all three cases a common clonal origin for the variants was demonstrated by complementarity-determining region III nucleotide sequence homology and shared somatic mutations in germline encoded positions in framework region IV. The monoclonal nature of the tumors was independently confirmed by demonstrating a single t(14;18) translocation breakpoint in the two cases with a detectable translocation. All the variants occurred in functional V(H) rearrangements, which in two cases were directly shown to encode functional Ab molecules. Both recombination-activating genes 1 and 2 were expressed in lymph node tumor cells containing the V(H) rearrangement variant, although recombination-activating gene expression among a panel of lymphomas was not limited to this variant. PMID:11160277

Kobrin, C; Bendandi, M; Kwak, L

2001-02-15

330

Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans.  

PubMed

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

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

2013-09-26

331

High genotypic diversity and a novel variant of human cytomegalovirus revealed by combined UL33/UL55 genotyping with broad-range PCR  

PubMed Central

The known strains of human cytomegalovirus (HCMV) represent genotypic variants of a single species, and HCMV genotypic variability has been studied in order to reveal correlations between different disease patterns and the presence of certain HCMV genotypes, either as single or as multiple infections. The methods used for the detection of HCMV genotypes have not always been sophisticated enough to achieve complete comprehensiveness, mainly because only one genotype is usually detected in a certain specimen, due to primer specificity and genome copy number. To improve detection of variant HCMV genotypes in mixed infections, we developed PCR assays with degenerate primers targeting two variable HCMV genes, glycoprotein B (gB, UL55) and the G-protein-coupled receptor gene UL33. Primers were designed to bind conserved sites in the genomes of HCMV variants and great ape CMVs. To analyse if samples contained one or more HCMV genotypic variants, PCR assays were supplemented with oligonucleotides containing locked nucleic acids. This broad-range PCR methodology and subsequent sequence analysis detected all gB/UL55 and UL33 genotypic variants known to date in primary clinical specimens, but also revealed that many samples contained genotype mixtures. Importantly, a novel UL33 genotypic variant could be discovered in several specimens, and one HCMV isolate was plaque-purified containing the novel UL33 genotype and a so far undescribed variant of gB.

2009-01-01

332

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

PubMed Central

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.

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

2013-01-01

333

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

PubMed Central

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.

Nakaminami, Hidemasa; Noguchi, Norihisa; Sasatsu, Masanori

2010-01-01

334

[Genetic variants of Borrelia afzelii, a pathogen of the ixodes tick borrelioses].  

PubMed

Borrelia afzelii is one of two most important pathogens of the ixodes tick borrelioses (ITB) in Russia and neighboring countries. This pathogen circulates in various ecosystems and has a wide range of reservoir hosts and transmitters. The results of studies of genetic heterogeneity of the spirochaetae B. afzelii are considered. A total of 139 primary isolates were studied. The isolates were isolated from three species of Ixodes ticks at different stages of development and obtained from the laboratory of infection transmitters, Gamaleya Scientific Research Institute of Epidemiology and Microbiology, Russran Academy of Medical Sciences, Moscow. The transmitters and reservoir hosts of borrelias were caught in natural foci of Russia (from Kaliningrad region irk the west to south Sakhalin in the east), Czechia, Lithuania, Estonia, Ukraine, and Moldavia. Analysis of genotype sequence similarity obtained by sequencing of the rrf(SS)-rrl(23S) spacer demonstrated that the B. afzelii genospecies incorporated no less than 10 genetic variants of spirochaetae, most variants being geographically widespread. PMID:16173394

Fadeeva, I A; Nefedova, V V; Korenberg, E I; Gorelova, N B

2005-01-01

335

A Variant Quorum Sensing System in Aeromonas veronii MTCC 3249  

PubMed Central

We have investigated the quorum sensing control in Aeromonas veronii MTCC 3249, originally isolated as A. culicicola from the midgut of Culex quinquefasciatus. Based on biosensor assays, the bacterium showed constant production of multiple acyl-homoserine lactones (AHLs) with increasing cell-density. The luxRI gene homologs, acuR (A. culicicola transcriptional Regulator) and acuI (A. culicicola autoInducer) were successfully amplified by inverse-PCR. Sequence analysis indicated acuRI were divergent from all known quorum sensing gene homologs in Aeromonas. Two localized regions in the C-terminal autoinducer binding domain of acuR showed indels suggesting variations in autoinducer specificity. Further, only a single copy of the quorum sensing genes was detected, suggesting a tight regulation of mechanisms under its control. Chromatography and further chemical analysis identified two AHLs in the culture supernatant: 6-carboxy-HHL (homoadipyl homoserine lactone), a novel AHL, and N-tetradecanoylhomoserine lactone. The existence of a potentially variant quorum sensing system might therefore, reflect in some way the ecological strategies adopted by this bacterium in the mosquito midgut.

Jangid, Kamlesh; Parameswaran, Perunninakulath S.; Shouche, Yogesh S.

2012-01-01

336

Clinical characterization of the HOXA1 syndrome BSAS variant  

PubMed Central

Background: The Bosley-Salih-Alorainy syndrome (BSAS) variant of the congenital human HOXA1 syndrome results from autosomal recessive truncating HOXA1 mutations. We describe the currently recognized spectrum of ocular motility, inner ear malformations, cerebrovascular anomalies, and cognitive function. Methods: We examined nine affected individuals from five consanguineous Saudi Arabian families, all of whom harbored the same I75-I76insG homozygous mutation in the HOXA1 gene. Patients underwent complete neurologic, neuro-ophthalmologic, orthoptic, and neuropsychological examinations. Six individuals had CT, and six had MRI of the head. Results: All nine individuals had bilateral Duane retraction syndrome (DRS) type 3, but extent of abduction and adduction varied between eyes and individuals. Eight patients were deaf with the common cavity deformity of the inner ear, while one patient had normal hearing and skull base development. Six had delayed motor milestones, and two had cognitive and behavioral abnormalities meeting Diagnostic and Statistical Manual of Mental Disorders-IV criteria for autism spectrum disorder. MRI of the orbits, extraocular muscles, brainstem, and supratentorial brain appeared normal. All six appropriately studied patients had cerebrovascular malformations ranging from unilateral internal carotid artery hypoplasia to bilateral agenesis. Conclusions: This report extends the Bosley-Salih-Alorainy syndrome phenotype and documents the clinical variability resulting from identical HOXA1 mutations within an isolated ethnic population. Similarities between this syndrome and thalidomide embryopathy suggest that the teratogenic effects of early thalidomide exposure in humans may be due to interaction with the HOX cascade.

Bosley, T.M.; Salih, M.A.; Alorainy, I.A.; Oystreck, D.T.; Nester, M.; Abu-Amero, K.K.; Tischfield, M.A.; Engle, E.C.

2010-01-01

337

Granulomatous variant of giant centrifugal miliaria profunda.  

PubMed

Two infants presented with multiple asymptomatic papules and geographic and annular plaques over the extensor aspect of the upper and lower extremities and trunk. Skin biopsy of both lesions showed plugged and hyperplastic dilated acrosryingia and deep dermal ducts, along with granulomatous inflammatory reaction. These lesions showed self-healing with complete resolution. A previous report described similar clinical and histopathologic features and labeled it giant centrifugal miliaria profunda. Because of the large granulomatous plaques and deep infiltrate, we propose that it was a granulomatous variant of giant centrifugal miliaria profunda. We report these cases for their rarity and self-healing nature. PMID:22276567

Doshi, Bhavana R; Mahajan, Sunanda; Kharkar, Vidya; Khopkar, Uday S

2012-01-26

338

Clinical variants of idiopathic torsion dystonia.  

PubMed Central

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.

Fahn, S

1989-01-01

339

Clinical variants of idiopathic torsion dystonia.  

PubMed

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

Fahn, S

1989-06-01

340

The herpes simplex virus type 1 BgKL variant, unlike the BgOL variant, shows a higher association with orolabial infection than with infections at other sites, supporting the variant-dispersion-replacement hypothesis.  

PubMed

The identification and geographic distribution of the herpes simplex virus type 1 (HSV-1) BglII restriction fragment length polymorphism (RFLP) variants named BgK(L) and BgO(L) in clinical isolates from orolabial and cutaneous sites were described in our previous reports, in which the dispersion and replacement of HSV-1 variants were proposed. The base substitution sites deduced from the BgK(L) multiple RFLP variations were mapped to the U(L)12 (DNase), R(L)2 (alpha0 transactivator), and latency-associated transcript genes in the present study. The results show that the relative frequencies (RFs) of BgK(L) are significantly higher in orolabial and cutaneous HSV-1 infections than in ocular infections. For the BgO(L) variant, the opposite was found; i.e., the RF of BgO(L) was significantly lower in orolabial and cutaneous infections than in ocular infections. No significant differences in the RFs of non-BgK(L):non-BgO(L) isolates were observed. The ratio of the BgK(L) RF to the BgO(L) RF was much higher for the orolabial and cutaneous infection groups than for the ocular infection group, whereas the BgK(L) RF-to-non-BgK(L):non-BgO(L) RF ratios for the former groups were slightly higher than those for the latter group. The higher efficiency of orolabial and cutaneous infections caused by BgK(L) compared to the efficiency of infections caused by BgO(L) allows BgK(L) to spread more efficiently in human populations and to displace BgO(L), because the mouth and lips are the most common HSV-1 infection sites in children. The present study supports our HSV-1 dispersion-and-replacement hypothesis and suggests that HSV-1, the latency-reactivation of which allows variants to accumulate in human populations, has evolved under competitive conditions, providing a new perspective on the polymorphism or variation of HSV-1. PMID:17475752

Ozawa, Shigeru; Eda, Hiroyuki; Ishii, Yasuyuki; Ban, Fumihiko; Funabashi, Toshiyuki; Hata, Seiichiro; Hayashi, Kozaburo; Iga, Hiroki; Ikushima, Takao; Ishiko, Hiroaki; Itagaki, Tomoo; Kawana, Rinji; Kobayashi, Shunsaku; Ogino, Takeo; Sekizawa, Tsuyoshi; Shimomura, Yoshikazu; Shiota, Hiroshi; Mori, Ryoichi; Nakakita, Takashi; Numazaki, Yoshio; Ozaki, Yoshikatsu; Yamamoto, Shigeru; Yoshino, Kamesaburo; Yanagi, Kazuo

2007-05-02

341

Infection of chickens with antimicrobial-resistant Salmonella enterica Typhimurium DT193 and monophasic Salmonella Typhimurium-like variants: an emerging risk to the poultry industry?  

PubMed

Antimicrobial-resistant Salmonella enterica poses a particular risk to public health, and in particular isolates belonging to clonal lineages such as Salmonella Typhimurium DT104 cause epidemics across species including poultry. In recent years, antimicrobial-resistant S. Typhimurium DT193 and specifically the monophasic S. Typhimurium-like variants of this phage type, serotypes 4,12:i:- and 4,5,12:i:-, have become an increasing risk to public health in Europe and the USA and now account for nearly one-half of human S. Typhimurium infections in the UK. Unlike S. Typhimurium that possesses two forms of flagella which can vary between phase 1 and phase 2 during infection, monophasic variants possess only phase 1 flagella. These monophasic antimicrobial-resistant variants have become a major problem in pig production but human cases have also been associated with poultry consumption and have been found in UK flocks through surveillance schemes since 2010. In this study we determined the ability of antimicrobial-resistant DT193 serotype 4,12:i:- and 4,5,12:i:- isolates from pigs to infect chickens. All isolates were found to colonize the caeca and liver. All but one isolate of serotype 4,5,12:i:- also infected the spleen. Levels of infection and pathology were comparable with those found with the virulent S. Typhimurium isolate 4/74. These findings indicate that both S. Typhimurium DT193 and monophasic variants of this phage type usually associated with pigs are capable of colonizing the chicken. This shows that both S. Typhimurium DT193 and monophasic variants represent a significant and potential emerging threat to poultry production from "spill-over" of these isolates from the pig industry or other sources. PMID:23930753

Parsons, B N; Crayford, G; Humphrey, T J; Wigley, P

2013-08-09

342

IN-VITRO SCREENING OF CISSUS QUADRANGULARIS L. VARIANT II AGAINST HELICOBACTER PYLORI  

PubMed Central

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

Austin, Anoop; Jegadeesan, M.; Gowrishankar, R.

2003-01-01

343

Structural and functional properties of reconstituted high density lipoprotein discs prepared with six apolipoprotein Al variants  

Microsoft Academic Search

Six apolipoprotein A-I (apoA-I) variants containing the following amino acid changes: Pros+Arg, Prop+Arg, Lys1o7+0 (Lys deletion) LyslO7-*Met, Pr016~+Arg, and Glulg8+ Lys, and the corresponding normal allele products, were isolated by preparative isoelectric focusing from heterozygous indivi- duals. The apoA-I samples were reconstituted with palmitoylo- leoyl phosphatidylcholine (POPC) or dipalmitoyl phosphatidyl- choline (DPPC), and small amounts of cholesterol, into dis- coidal

Ana Jonas; Arnold von Eckardstein; Armin Steinmetz; Gerd Assmannt

344

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

PubMed

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

Austin, Anoop; Jegadeesan, M; Gowrishankar, R

2003-07-01

345

Isolation and cryopreservation of O-methylthreonine-resistant Rosa cell lines altered in the feedback sensitivity of l-threonine deaminase  

Microsoft Academic Search

O-Methylthreonine (OMT) inhibits the growth of plated Rosa cells (ID50?6·10-6M). Isoleucine is able to reverse efficiently and specifically this OMT toxicity. From OMT-resistant colonies occurring at a frequency of 1.58·10-7 variants per cell plated at 10-4M OMT, the variant strains OMTR-1 and OMTR-2 were isolated, cloned via protoplasts and characterized. Both variants were ten times more resistant to OMT than

André Strauss; Heinz Fankhauser; Patrick J. King

1985-01-01

346

Isolating prompt photons with narrow cones  

NASA Astrophysics Data System (ADS)

We discuss the isolation of prompt photons in hadronic collisions by means of narrow isolation cones and the QCD computation of the corresponding cross sections. We reconsider the occurence of large perturbative terms with logarithmic dependence on the cone size and their impact on the fragmentation scale dependence. We cure the apparent perturbative violation of unitarity for small cone sizes, which had been noticed earlier in next-to-leading-order (NLO) calculations, by resumming the leading logarithmic dependence on the cone size. We discuss possible implications regarding the implementation of some hollow cone variants of the cone criterion, which simulate the experimental difficulty to impose isolation inside the region filled by the electromagnetic shower that develops in the calorimeter.

Catani, S.; Fontannaz, M.; Guillet, J. Ph.; Pilon, E.

2013-09-01

347

Plasmalogen status influences docosahexaenoic acid levels in a macrophage cell line: insights using ether lipid-deficient variants  

Microsoft Academic Search

Previously, this laboratory reported the isolation of variants, RAW.12 and RAW.108, from the macrophage- like cell line RAW 264.7 that are defective in plasmalogen biosynthesis ( Zoeller, R.A. et al. 1992. J. Biol. Chem. 267: 8299-8306). Fatty acid analysis showed significant changes in the mutants in the ethanolamine phospholipids (PE), the only phospholipid class in which the plasmalogen species, plasmenylethanolamine,

Daniel P. Gaposchkin; Raphael A. Zoeller

348

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

Microsoft Academic Search

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

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

1994-01-01

349

A VEGF-A splice variant defective for heparan sulfate and neuropilin-1 binding shows attenuated signaling through VEGFR-2  

Microsoft Academic Search

.  The development of functional blood and lymphatic vessels requires spatio-temporal coordination of the production and release\\u000a of growth factors such as vascular endothelial growth factors (VEGFs). VEGF family proteins are produced in multiple isoforms\\u000a with distinct biological properties and bind to three types of VEGF receptors. A VEGF-A splice variant, VEGF-A165b, has recently been isolated from kidney epithelial cells. This

S. Cébe Suarez; M. Pieren; L. Cariolato; S. Arn; U. Hoffmann; A. Bogucki; C. Manlius; J. Wood; K. Ballmer-Hofer

2006-01-01

350

Sumatriptan provokes coronary artery spasm in patients with variant angina: Possible involvement of serotonin 1B receptor  

Microsoft Academic Search

BackgroundSerotonin (5HT) can induce coronary artery spasm (CAS) in patients with variant angina (VA). We have previously reported that 5HT1B and 5HT2A receptors gene were expressed in human coronary arterial smooth muscle cells and that isolated coronary artery from a patient with VA showed the supersensitivity to sumatriptan (SMT), a 5HT1B\\/1D receptor agonist. The aim of the present study was

Masakatsu Shimizu; Katsuya Hata; Hideyuki Takaoka; Kenji Kanazawa; Toshiro Shinke; Hidenari Matsumoto; Satoshi Watanabe; Ryohei Yoshikawa; Hiroyuki Masai; Yoshitomo Miyamoto; Hozuka Akita; Mitsuhiro Yokoyama

2007-01-01

351

A Variant of Cucumber mosaic virus Is Restricted to Local Lesions in Inoculated Tobacco Leaves with a Hypersensitive Response  

Microsoft Academic Search

  A variant of Cucumber mosaic virus, CMV(Y\\/GM2), was isolated from a tobacco plant with mild green mosaic symptoms that was regenerated in vitro from a yellow strain of CMV [CMV(Y)]-infected tobacco leaves by tissue culture. CMV(Y\\/GM2) has two amino acid substitutions\\u000a at 36 and 111 positions in the coat protein encoded on RNA3. CMV, assembled by mixing in vitro transcribed

Hideki TAKAHASHI; Mitsuhiro SUGIYAMA; Akira KARASAWA; Shuu HASE; Yoshio EHARA

2000-01-01

352

eXtasy: variant prioritization by genomic data fusion.  

PubMed

Massively parallel sequencing greatly facilitates the discovery of novel disease genes causing Mendelian and oligogenic disorders. However, many mutations are present in any individual genome, and identifying which ones are disease causing remains a largely open problem. We introduce eXtasy, an approach to prioritize nonsynonymous single-nucleotide variants (nSNVs) that substantially improves prediction of disease-causing variants in exome sequencing data by integrating variant impact prediction, haploinsufficiency prediction and phenotype-specific gene prioritization. PMID:24076761

Sifrim, Alejandro; Popovic, Dusan; Tranchevent, Leon-Charles; Ardeshirdavani, Amin; Sakai, Ryo; Konings, Peter; Vermeesch, Joris R; Aerts, Jan; De Moor, Bart; Moreau, Yves

2013-09-29

353

Emergence of Anaplasma marginale Antigenic Variants during Persistent Rickettsemia  

Microsoft Academic Search

Anaplasma marginale is an ehrlichial pathogen of cattle, in the order Rickettsiales, that establishes persistent cyclic rickettsemia in the infected host. Within each rickettsemic cycle, A. marginale expressing antigenically variant major surface protein 2 (MSP2) emerge. By cloning 17 full-length msp2 transcripts expressed during cyclic rickettsemia, we determined that emergent variants have a single, central hypervariable region encoding variant B-cell

Dorothy M. French; Wendy C. Brown; Guy H. Palmer

1999-01-01

354

Pharmacognostical studies on Cissus quadrangularis L. variant I & II  

PubMed Central

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

Austin, Anoop; Kannan, R.; Jegadeesan, M.

2004-01-01

355

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

PubMed

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

Austin, Anoop; Kannan, R; Jegadeesan, M

2004-04-01

356

Melanocortin 1 Receptor Variants in an Irish Population  

Microsoft Academic Search

The identification of an association between variants in the human melanocortin 1 receptor (MC1R) gene and red hair and fair skin, as well as the relation between variants of this gene and coat color in animals, suggests that the MC1R is an integral control point in the normal pigmentation phenotype. In order to further define the contribution of MC1R variants

Rachel Smith; Eugene Healy; Shazia Siddiqui; Niamh Flanagan; Peter M Steijlen; Inger Rosdahl; Jon P Jacques; Sarah Rogers; Richard Turner; Ian J Jackson; Mark A Birch-Machin; Jonathan L Rees

1998-01-01

357

Functional diversity of SDF-1 splicing variants  

PubMed Central

SDF-1 is ubiquitously expressed in vertebrate tissues in a constitutive manner. It performs an essential role in cell migration and proliferation as well as participates in tissue-specific physiological processes such as neuromodulation. It is also involved in many pathological processes including: HIV infection, metastatic malignancy, chronic inflammatory disorders and benign proliferative diseases. SDF-1 is mostly regulated at the splicing, and not transcriptional level. Different splicing variants share agonist potency to their cognate receptor, CXCR4, but are characterized by distinct properties. SDF-1? is the predominant isoform found in all organs, but undergoes rapid proteolysis in blood. SDF-1? is more resistant to blood-dependent degradation, stimulates angiogenesis and is present in highly vascularized organs such as: the liver, spleen and kidneys. In contrast, SDF-1? is located in very active, less vascularized organs susceptible to infarction such as the heart and the brain. The understanding of the functional diversity of the different splicing variants will help in developing therapeutic strategies.

2009-01-01

358

Linker histone subtypes and their allelic variants.  

PubMed

Members of histone H1 family bind to nucleosomal and linker DNA to assist in stabilization of higher-order chromatin structures. Moreover, histone H1 is involved in regulation of a variety of cellular processes by interactions with cytosolic and nuclear proteins. Histone H1, composed of a series of subtypes encoded by distinct genes, is usually differentially expressed in specialized cells and frequently non-randomly distributed in different chromatin regions. Moreover, a role of specific histone H1 subtype might be also modulated by post-translational modifications and/or presence of polymorphic isoforms. While the significance of covalently modified histone H1 subtypes has been partially recognized, much less is known about the importance of histone H1 polymorphic variants identified in various plant and animal species, and human cells as well. Recent progress in elucidating amino acid composition-dependent functioning and interactions of the histone H1 with a variety of molecular partners indicates a potential role of histone H1 polymorphic variation in adopting specific protein conformations essential for chromatin function. The histone H1 allelic variants might affect chromatin in order to modulate gene expression underlying some physiological traits and, therefore could modify the course of diverse histone H1-dependent biological processes. This review focuses on the histone H1 allelic variability, and biochemical and genetic aspects of linker histone allelic isoforms to emphasize their likely biological relevance. PMID:23075301

Kowalski, Andrzej; Pa?yga, Jan

2012-11-01

359

RcsB Contributes to the Distinct Stress Fitness among Escherichia coli O157:H7 Curli Variants of the 1993 Hamburger-Associated Outbreak Strains  

PubMed Central

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.

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

2012-01-01

360

Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants.  

PubMed

BACKGROUND: The majority of coeliac disease (CD) patients are not being properly diagnosed and therefore remain untreated, leading to a greater risk of developing CD-associated complications. The major genetic risk heterodimer, HLA-DQ2 and DQ8, is already used clinically to help exclude disease. However, approximately 40% of the population carry these alleles and the majority never develop CD. OBJECTIVE: We explored whether CD risk prediction can be improved by adding non-HLA-susceptible variants to common HLA testing. DESIGN: We developed an average weighted genetic risk score with 10, 26 and 57 single nucleotide polymorphisms (SNP) in 2675 cases and 2815 controls and assessed the improvement in risk prediction provided by the non-HLA SNP. Moreover, we assessed the transferability of the genetic risk model with 26 non-HLA variants to a nested case-control population (n=1709) and a prospective cohort (n=1245) and then tested how well this model predicted CD outcome for 985 independent individuals. RESULTS: Adding 57 non-HLA variants to HLA testing showed a statistically significant improvement compared to scores from models based on HLA only, HLA plus 10 SNP and HLA plus 26 SNP. With 57 non-HLA variants, the area under the receiver operator characteristic curve reached 0.854 compared to 0.823 for HLA only, and 11.1% of individuals were reclassified to a more accurate risk group. We show that the risk model with HLA plus 26 SNP is useful in independent populations. CONCLUSIONS: Predicting risk with 57 additional non-HLA variants improved the identification of potential CD patients. This demonstrates a possible role for combined HLA and non-HLA genetic testing in diagnostic work for CD. PMID:23704318

Romanos, Jihane; Rosén, Anna; Kumar, Vinod; Trynka, Gosia; Franke, Lude; Szperl, Agata; Gutierrez-Achury, Javier; van Diemen, Cleo C; Kanninga, Roan; Jankipersadsing, Soesma A; Steck, Andrea; Eisenbarth, Georges; van Heel, David A; Cukrowska, Bozena; Bruno, Valentina; Mazzilli, Maria Cristina; Núñez, Concepcion; Bilbao, Jose Ramon; Mearin, M Luisa; Barisani, Donatella; Rewers, Marian; Norris, Jill M; Ivarsson, Anneli; Boezen, H Marieke; Liu, Edwin; Wijmenga, Cisca

2013-06-01

361

A unified phylogeny-based nomenclature for histone variants  

PubMed Central

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.

2012-01-01

362

Identifying rare variants associated with complex traits via sequencing.  

PubMed

Although genome-wide association studies have been successful in detecting associations with common variants, there is currently an increasing interest in identifying low-frequency and rare variants associated with complex traits. Next-generation sequencing technologies make it feasible to survey the full spectrum of genetic variation in coding regions or the entire genome. The association analysis for rare variants is challenging, and traditional methods are ineffective, however, due to the low frequency of rare variants, coupled with allelic heterogeneity. Recently a battery of new statistical methods has been proposed for identifying rare variants associated with complex traits. These methods test for associations by aggregating multiple rare variants across a gene or a genomic region or among a group of variants in the genome. In this unit, we describe key concepts for rare variant association for complex traits, survey some of the recent methods, discuss their statistical power under various scenarios, and provide practical guidance on analyzing next-generation sequencing data for identifying rare variants associated with complex traits. PMID:23853079

Li, Bingshan; Liu, Dajiang J; Leal, Suzanne M

2013-07-01

363

Histological variants of prostatic carcinoma and their significance.  

PubMed

The vast majority of prostatic cancers are acinar adenocarcinomas. Histological variants of prostatic carcinoma have been variably defined. One approach is to consider two groups of variants. The first group comprises histological variants of acinar adenocarcinoma and the second group non-acinar carcinoma variants or types. Variants of usual acinar adenocarcinoma defined in 2004 by the World Health Organization (WHO) include atrophic, pseudohyperplastic, foamy, colloid, signet ring, oncocytic and lymphoepithelioma-like carcinomas. The second group of non-acinar carcinoma histological variants or types of prostatic carcinoma accounts for about 5-10% of carcinomas that originate in the prostate. These include sarcomatoid carcinoma, ductal adenocarcinoma, urothelial carcinoma, squamous and adenosquamous carcinoma, basal cell carcinoma, and neuroendocrine tumours, specifically small-cell carcinoma. Recently characterized variants not present in the 2004 WHO classification, including microcystic adenocarcinoma, prostatic intraepithelial neoplasia-like adenocarcinoma, large-cell neuroendocrine carcinoma, and pleomorphic giant cell carcinoma, are also described. The aims of this review are to present the essential histomorphological diagnostic attributes of these variants, and to emphasize the clinical signficance of the variants, when different from usual acinar adenocarcinoma, including clinical presentation and outcome. PMID:22212078

Humphrey, Peter A

2012-01-01

364

Clinical and pathologic characteristics of focal segmental glomerulosclerosis pathologic variants.  

PubMed

Histologic variants of idiopathic focal segmental glomerulosclerosis (FSGS) may have prognostic value. A recent working classification system has distinguished five FSGS variants. We evaluated a cohort of adult patients with biopsy-proven FSGS diagnosed between March 1982 and July 2001 to determine if subtypes were associated with renal outcome. Renal biopsies were reviewed by two pathologists. Demographic and clinical data were obtained from charts. Outcomes were partial and complete remission of the nephrotic syndrome, and renal failure. The frequency of FSGS variants was: 3% cellular (N=6), 11% collapsing (N=22), 17% tip lesion (N=34), 26% perihilar (N=52), and 42% not otherwise specified (NOS) (N=83). Collapsing FSGS affected younger and more often black patients. Black race was uncommon in tip variant. Collapsing and tip variants had higher proteinuria and lower serum albumin than perihilar and NOS variants. Better renal function and less severe tubulointerstitial injury were observed in patients with tip variant. These patients were more likely to receive steroids and more often achieved complete remission (50%). After a median follow-up of 1.8 years, 23% of patients were on dialysis and 28% had renal failure. Collapsing FSGS had worse 1-year (74%) and 3-year (33%) renal survival compared to other variants (overall cohort renal survival at 1 and 3 years: 86 and 67%). Different histologic variants of FSGS have substantial differences in clinical features at the time of biopsy diagnosis and substantial differences in renal outcomes. PMID:16518352

Thomas, D B; Franceschini, N; Hogan, S L; Ten Holder, S; Jennette, C E; Falk, R J; Jennette, J C

2006-03-01

365

Identification and analysis of U5 snRNA variants in Drosophila  

PubMed Central

Distinct isoforms of spliceosomal RNAs may be involved in regulating pre-messenger RNA splicing in eukaryotic cells. During a large-scale effort to identify small noncoding RNAs in Drosophila, we isolated a U5 snRNA-like molecule containing a 5? segment identical to that of the canonical (major) U5 snRNA but with a variant Sm binding site and a distinct 3? hairpin sequence. Based on this finding, another six similar U5 snRNA-like sequences were identified within the Drosophila genome by sequence similarity to the invariant loop in the 5? half of U5. Interestingly, although all of these variants are expressed in vivo, each shows a distinct temporal expression profile during Drosophila development, and one is expressed primarily in fly heads. The presence of these U5 snRNA variants within RNP particles suggests their role in splicing and implies a possible connection to regulation of developmental and tissue-specific gene expression.

CHEN, LI; LULLO, DENNIS J.; MA, ENBO; CELNIKER, SUSAN E.; RIO, DONALD C.; DOUDNA, JENNIFER A.

2005-01-01

366

Identification and analysis of U5 snRNA variants in Drosophila.  

PubMed

Distinct isoforms of spliceosomal RNAs may be involved in regulating pre-messenger RNA splicing in eukaryotic cells. During a large-scale effort to identify small noncoding RNAs in Drosophila, we isolated a U5 snRNA-like molecule containing a 5' segment identical to that of the canonical (major) U5 snRNA but with a variant Sm binding site and a distinct 3' hairpin sequence. Based on this finding, another six similar U5 snRNA-like sequences were identified within the Drosophila genome by sequence similarity to the invariant loop in the 5' half of U5. Interestingly, although all of these variants are expressed in vivo, each shows a distinct temporal expression profile during Drosophila development, and one is expressed primarily in fly heads. The presence of these U5 snRNA variants within RNP particles suggests their role in splicing and implies a possible connection to regulation of developmental and tissue-specific gene expression. PMID:16199758

Chen, Li; Lullo, Dennis J; Ma, Enbo; Celniker, Susan E; Rio, Donald C; Doudna, Jennifer A

2005-10-01

367

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

PubMed

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

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

2013-02-22

368

[Anatomic variants of hepatic artery in metastatic affection of the liver].  

PubMed

On 39 nonfixed cadavers of patients, in whom hepatic metastatic affection was diagnosed in abdominal cavity tumors, there were studied up a hepatic artery anatomic variants and possible accesses. In 22 observations there was noted a typical variant of hepatic artery branching from a. hepatis communis, in 9--isolated blood supply of the left and right hepatic lobes, in 4--additional branches of various diameter from a. gastrica sinistra to the left hepatic lobe, in 2-- additional branches toward the right hepatic lobe, branching from a. mesenterica superior, in 1--the blood supply of the left hepatic lobe by arterial branch from splenic artery, while a lienalis-hepatic trunk have branched from truncus coeliacus. In one observation there was revealed the common hepatic artery branching on three trunks, while the median one have supplied a hepatic quadrate lobe. It is expedient in all observations perform en bloc lymph node dissection of hepatic hilus with the truncus coeliacus structures opening. The proposed order of activities while conduction of selective intraarterial polychemotherapy permits to take into account the anatomic variants as well and to eliminate the possible faults and complications occurrence. PMID:22629802

Ishchenko, R V; Sidiuk, A V; Lasachko, P S

2012-02-01

369

Molecular and functional characterization of voltage-gated sodium channel variants from Drosophila melanogaster  

PubMed Central

Extensive alternative splicing and RNA editing have been documented for the transcript of DmNaV (formerly para), the sole sodium channel gene in Drosophila melanogaster. However, the functional consequences of these post-transcriptional modifications are not well understood. In this study we isolated 64 full-length DmNaV cDNA clones from D. melanogaster adults. Based on the usage of 11 alternative exons, 64 clones could be grouped into 29 splice types. When expressed in Xenopus oocytes, 33 DmNaV variants generated sodium currents large enough for functional characterization. Among these variants, DmNaV5-1 and DmNaV7-1 channels activated at the most hyperpolarizing potentials, whereas DmNaV1-6 and DmNaV19 channels activated at the most depolarizing membrane potentials. We identified an A-to-I editing event in DmNaV5-1 that is responsible for its uniquely low-voltage-dependent activation. The wide range of voltage dependence of gating properties exhibited by DmNaV variants represents a rich resource for future studies to determine the role of DmNaV in regulating sodium channel gating, pharmacology, and neuronal excitability in insects.

Olson, Rachel O'Donnell; Liu, Zhiqi; Nomura, Yoshiko; Song, Weizhong; Dong, Ke

2011-01-01

370

Transforming potential of alternatively spliced variants of fibroblast growth factor receptor 2 in human mammary epithelial cells.  

PubMed

A breast cancer cell line developed in our laboratory (SUM-52PE) has a 12-fold amplification and high-level overexpression of the oncogene fibroblast growth factor receptor 2 (FGFR2). Previously, nine different alternatively spliced FGFR2 variants were isolated from this cell line. Overexpression of two variants that differ only in their carboxyl termini (C1 and C3) has been successfully accomplished in the immortalized human mammary epithelial cell line H16N2. FGFR2 expression led to the activation of the mitogen-activated protein kinase and phosphatidylinositol 3-kinase signaling cascades. Phosphorylation of the adapter protein FGF receptor substrate 2 is much more robust in the cells expressing the C3 variant of FGFR2 compared with the C1 variant. H16N2 cells expressing the full-length FGFR2 with the C1 or C3 carboxyl terminus were tested for their ability to grow under epidermal growth factor (EGF)-independent conditions, in soft agar, and for their ability to invade naturally occurring basement membranes and compared with the parental SUM-52PE cell line. All three cell lines grew under EGF-independent conditions and all were inhibited by the FGFR family specific inhibitor PD173074. The full-length FGFR2-C1 and FGFR2-C3 variants grew robustly in soft agar similar to the parental cell line SUM-52PE. However, cells expressing the C3 variant formed large colonies in agar in both insulin-free and EGF-free medium, whereas the cells expressing the C1 variant required insulin for growth. Soft agar growth was also inhibited by PD173074. Because SUM-52PE was developed from a metastatic breast carcinoma, the FGFR2-overexpressing cell lines were assessed for their ability to invade sea urchin embryo cell membranes. H16N2 cells expressing the C1 carboxyl terminus failed to invade sea urchin embryo cell membranes. By contrast, FGFR2-C3-expressing cells were as invasive as the SUM-52 breast cancer cells and erbB-2-overexpressing H16N2 cells. These results indicate that FGFR2 is a transforming oncogene in human mammary epithelial cells when expressed to levels similar to that found in breast cancer cells with FGFR2 gene amplification. Furthermore, the results suggest that different splice variants have differing transforming activities and that signaling from variants expressing the C3 carboxyl terminus results in more autonomous signaling, cell growth, and invasion. PMID:15561780

Moffa, Allison B; Tannheimer, Stacey L; Ethier, Stephen P

2004-11-01

371

Molecular Evidence of Cholera Outbreak Caused by a Toxigenic Vibrio cholerae O1 El Tor Variant Strain in Kelantan, Malaysia ?  

PubMed Central

A total of 20 Vibrio cholerae isolates were recovered for investigation from a cholera outbreak in Kelantan, Malaysia, that occurred between November and December 2009. All isolates were biochemically characterized as V. cholerae serogroup O1 Ogawa of the El Tor biotype. They were found to be resistant to multiple antibiotics, including tetracycline, erythromycin, sulfamethoxazole-trimethoprim, streptomycin, penicillin G, and polymyxin B, with 35% of the isolates being resistant to ampicillin. All isolates were sensitive to ciprofloxacin, norfloxacin, chloramphenicol, gentamicin, and kanamycin. Multiplex PCR analysis confirmed the biochemical identification and revealed the presence of virulence genes, viz., ace, zot, and ctxA, in all of the isolates. Interestingly, the sequencing of the ctxB gene showed that the outbreak strain harbored the classical cholera toxin gene and therefore belongs to the newly assigned El Tor variant biotype. Clonal analysis by pulsed-field gel electrophoresis demonstrated that a single clone of a V. cholerae strain was responsible for this outbreak. Thus, we present the first molecular evidence that the toxigenic V. cholerae O1 El Tor variant has invaded Malaysia, highlighting the need for continuous monitoring to facilitate early interventions against any potential epidemic by this biotype.

Ang, Geik Yong; Yu, Choo Yee; Balqis, Kamarudin; Elina, Husni Tan; Azura, Hussin; Hani, Mat Hussin; Yean, Chan Yean

2010-01-01

372

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

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,

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

2006-01-01

373

Growth hormone size variants: changes in the pituitary during development of the chicken.  

PubMed

There is considerable evidence for the existence of structural variants of growth hormone (GH). The chicken is a useful model for investigating GH heterogeneity as both size and charge immunoreactive-(ir) variants have been observed in the pituitary and plasma. The present study examined the size distribution of ir-GH in the pituitary gland of chicken, from late embryogenesis through adulthood. Pituitaries were homogenized in the presence of protease inhibitor, and the GH size variants were separated by SDS-PAGE, transferred by Western blotting, immunostained with a specific antiserum to chicken GH, and quantitated by chemiluminescence followed by laser densitometry (chemiluminescent assay). Under nonreducing conditions ir-GH bands of 15, 22, 25, 44, 50, 66, 80, 98, 105 and >110 kDa were observed. Both the relative proportion of the GH size variants and the total pituitary content varied with developmental stage and age. The proportion of the 15-kDa fragment was greatest in the embryonic stage, and then it decreased. The proportion of the monomeric 22-kDa form was lowest at 18 days of embryogenesis (dE) and highest at 20 dE. In contrast, the high MW forms (>/=66 kDa) were lowest in embryos, and they increased (P < 0.05) after hatching. The 22-, 44-, 66-, and 80-kDa forms were assayed for activity by radioreceptor assay following isolation by semipreparative SDS-PAGE. Only the 22-kDa GH variant showed radioreceptor activity. Under reducing conditions for SDS-PAGE, ir-GH bands of 13, 15, 18, 23, 26, 36, 39, 44, 48, 59 and 72 kDa were oberved, but most of the high MW form disappeared. There was a concomitant increase in the proportion of the monomeric band and of several submonomeric forms. The present data indicate that the expression, processing, and/or release of some if not all size variants are under some differential control during growth and development of the chicken. PMID:10632963

Arámburo, C; Luna, M; Carranza, M; Reyes, M; Martínez-Coria, H; Scanes, C G

2000-01-01

374

Multiplex Real-Time PCR Assay for Detection and Classification of Klebsiella pneumoniae Carbapenemase Gene (blaKPC) Variants?  

PubMed Central

Carbapenem resistance mediated by plasmid-borne Klebsiella pneumoniae carbapenemases (KPC) is an emerging problem of significant clinical importance in Gram-negative bacteria. Multiple KPC gene variants (blaKPC) have been reported, with KPC-2 (blaKPC-2) and KPC-3 (blaKPC-3) associated with epidemic outbreaks in New York City and various international settings. Here, we describe the development of a multiplex real-time PCR assay using molecular beacons (MB-PCR) for rapid and accurate identification of blaKPC variants. The assay consists of six molecular beacons and two oligonucleotide primer pairs, allowing for detection and classification of all currently described blaKPC variants (blaKPC-2 to blaKPC-11). The MB-PCR detection limit was 5 to 40 DNA copies per reaction and 4 CFU per reaction using laboratory-prepared samples. The MB-PCR probes were highly specific for each blaKPC variant, and cross-reactivity was not observed using DNA isolated from several bacterial species. A total of 457 clinical Gram-negative isolates were successfully characterized by our MB-PCR assay, with blaKPC-3 and blaKPC-2 identified as the most common types in the New York/New Jersey metropolitan region. The MB-PCR assay described herein is rapid, sensitive, and specific and should be useful for understanding the ongoing evolution of carbapenem resistance in Gram-negative bacteria. As novel blaKPC variants continue to emerge, the MB-PCR assay can be modified in response to epidemiologic developments.

Chen, Liang; Mediavilla, Jose R.; Endimiani, Andrea; Rosenthal, Marnie E.; Zhao, Yanan; Bonomo, Robert A.; Kreiswirth, Barry N.

2011-01-01

375

Antibiotic and antimicrobial peptide combinations: synergistic inhibition of Pseudomonas fluorescens and antibiotic-resistant variants.  

PubMed

Variants resistant to penicillin G (RvP), streptomycin (RvS), lincomycin (RvL) and rifampicin (RvR) were developed from a colistin-sensitive isolate of Pseudomonas fluorescens LRC-R73 (P. fluorescens). Cell fatty acid composition, K(+) efflux and sensitivity to antimicrobial peptides (nisin Z, pediocin PA-1/AcH and colistin) alone or combined with antibiotics were determined. P. fluorescens was highly sensitive to kanamycin, tetracycline and chloramphenicol at minimal inhibitory concentrations of 0.366, 0.305 and 0.732 ?g/ml respectively. P. fluorescens, RvP, RvS, RvL and RvR were resistant to nisin Z and pediocin PA-1/AcH at concentrations ?100 ?g/ml but sensitive to colistin at 0.076, 0.043, 0.344, 0.344 and 0.258 ?g/ml respectively. A synergistic inhibitory effect (FICI ?0.5) was observed when resistant variants were treated with peptide/antibiotic combinations. No significant effect on K(+) efflux from the resistant variants in the presence of antibiotics or peptides alone or combined was observed. The proportion of C16:0 was significantly higher in antibiotic-resistant variants than in the parent strain, accounting for 32.3%, 46.49%, 43.3%, 40.1% and 44.1% of the total fatty acids in P. fluorescens, RvP, RvS, RvL and RvR respectively. Combination of antibiotics with antimicrobial peptides could allow reduced use of antibiotics in medical applications and could help slow the emergence of bacteria resistant to antibiotics. PMID:22172555

Naghmouchi, Karim; Le Lay, Christophe; Baah, John; Drider, Djamel

2011-11-27

376

Separation of time variant vibration sources by short time coherent output power  

Microsoft Academic Search

This effort describes the use of time variant coherence causality based analysis to separate the effects of nonstationary time variant vibration excitation sources. A time variant coherence function using the Short Time Fourier Transform (STFT) is first discussed. The concept of a time variant coherent output power for source separation of systems with time variant transfer functions is developed. A

Martin W. Trethewey

2011-01-01

377

Production of bacteriolytic activity in the oral cavity by nutritionally variant streptococci.  

PubMed Central

Microorganisms from the oral flora were examined for the production of bacteriolytic substances. Among human viridans group streptococci, only one group of strains with thiol-dependent properties was shown to secrete enzymes with bacteriolytic activity on heat-killed cells of Micrococcus luteus on double-layer nutrient agar plates. By morphology, culture requirements, and biochemical properties, they were found to conform to descriptions of nutritionally variant streptococci (NVS). Bacteriolytic activity was shown to be a constant property of all of the human oral NVS isolated and a property of some reference strains of NVS from clinical sources. No other known species of viridans group streptococci demonstrated bacteriolytic activity. Analysis of bacteriolytic activity could be a useful tool for both the isolation and identification of this fastidious group of microorganisms. Images

Pompei, R; Caredda, E; Piras, V; Serra, C; Pintus, L

1990-01-01

378

Hyperlexia: a variant of aphasia or dyslexia.  

PubMed

We report five patients with hyperlexia who presented for evaluation in the Learning Disabilities Clinic at the Medical College of Georgia over a two year period. Analysis of the data from the neurologic and neuropsychologic evaluations indicates that the primary and essential cognitive deficit in these children is a disorder in speech and language involving a severe deficit in their ability to comprehend language whether it be spoken or written, as opposed to a dyslexia syndrome involving only recognition and/or comprehension of written language. This finding is in contrast to the Nosology of Disorders of Higher Cerebral Function proposed by the Child Neurology Society which views hyperlexia as a variant of the language disorder subtype of dyslexia. PMID:2468342

Cohen, M; Campbell, R; Gelardo, M

379

[Uncommon variants of malignant melanocytic neoplasms].  

PubMed

Benign and malignant melanocytic neoplasms are relatively frequent and show a broad morphological heterogeneity. The spectrum of malignant melanomas comprises the four main types, superficial spreading malignant melanoma, nodular malignant melanoma, lentigo-maligna melanoma and acrolentiginous malignant melanoma. In addition the rare spitzoid malignant melanoma, desmoplastic malignant melanoma as well as some unusual variants of malignant melanoma can be distinguished. The latter include nevoid malignant melanoma, a form of malignant melanoma resembling benign melanocytic nevi, animal type malignant melanoma, an atypical melanocytic neoplasm with numerous melanophages and prominent melanosis resembling an atypical epithelioid blue naevus as well as regressive malignant melanoma, and representing a questionably distinct entity, balloon cell and signet-ring malignant melanomas, melanoma types with degenerative clear cell changes, as well as myxoid and osteogenic malignant melanomas that are characterized by unusual stromal changes. PMID:17846776

Mentzel, T

2007-11-01

380

Complex pattern of a variant hepatic artery.  

PubMed

Liver transplantation is the only solution for end-stage liver diseases. The common hepatic artery (CHA) arises from the coeliac trunk (CT), and the right (RHA) and left hepatic (LHA) arteries are its terminal branches. An abnormal arterial pattern would influence the surgical outcome. The anterior layer of the lesser omentum of a female cadaver was cleaned to identify the CHA, which was traced backwards for its origin and toward the porta hepatis for its terminal branches. In this case, the replaced RHA originated from the CT and ran posterior to the portal vein and the common bile duct. The replaced LHA arose from the left gastric artery. The CHA originated from the CT and branched out as the middle hepatic and gastroduodenal arteries. The replaced RHA and LHA with alteration in relation to the neighbouring structures is a complex and rare variant. Knowledge of this uncommon arterial anomaly is beneficial for hepatobiliary surgeons. PMID:23023911

Hlaing, Khin Pa Pa; Othman, Faizah

2012-09-01

381

Paratesticular rhabdomyoma: a morphologically distinct sclerosing variant.  

PubMed

Extracardiac rhabdomyomas, which currently are classified into fetal, adult, and genital types, are rare. We have identified 7 cases of a distinct morphologic variant of rhabdomyoma that affects mainly young men in the paratesticular region, seen in consultation between 2001 and 2011. The 7 male patients were adults (median age 24 y) and presented with tumors in paratesticular soft tissue (4 left-sided, 3 right-sided). Grossly, the median tumor size was 4.5 cm (range, 2.0 to 12 cm), and lesions were well circumscribed with a uniform tan-white cut surface. Microscopically, these rhabdomyomas were characterized by bundles of large well-differentiated skeletal muscle cells with copious eosinophilic cytoplasm that were variably round, polygonal, and occasionally strap shaped. The tumor cells were set in a dense hyalinized collagenous stroma, often with adjacent prominent lymphoplasmacytic aggregates. Tumor cells had round, occasionally vesicular, nuclei (sometimes binucleate or multinucleate) with small or inconspicuous nucleoli. All tumors lacked nuclear atypia and necrosis. Mitotic activity was virtually absent, although 1 tumor showed a count of 1 per 50 HPF. All tumors were diffusely positive for desmin, 4/4 were diffusely positive for fast myosin, and 1/1 examined was positive for myf-4. All patients were treated by local excision (5 with positive margins). Four patients with known follow-up data had no evidence of tumor recurrence or disease progression (median follow-up time 8.5 mo). The clinical course as determined thus far is benign, similar to other types of rhabdomyoma. However, this rare paratesticular subset of rhabdomyomas appears to be morphologically distinct from rhabdomyomas at other locations and appears to represent a separate variant. PMID:23887159

Jo, Vickie Y; Reith, John D; Coindre, Jean Michel; Fletcher, Christopher D M

2013-11-01

382

Early-onset Alzheimer disease clinical variants  

PubMed Central

Objective: To assess patterns of reduced cortical thickness in different clinically defined variants of early-onset Alzheimer disease (AD) and to explore the hypothesis that these variants span a phenotypic continuum rather than represent distinct subtypes. Methods: The case-control study included 25 patients with posterior cortical atrophy (PCA), 15 patients with logopenic progressive aphasia (LPA), and 14 patients with early-onset typical amnestic AD (tAD), as well as 30 healthy control subjects. Cortical thickness was measured using FreeSurfer, and differences and commonalities in patterns of reduced cortical thickness were assessed between patient groups and controls. Given the difficulty of using mass-univariate statistics to test ideas of continuous variation, we use multivariate machine learning algorithms to visualize the spectrum of subjects and to assess separation of patient groups from control subjects and from each other. Results: Although each patient group showed disease-specific reductions in cortical thickness compared with control subjects, common areas of cortical thinning were identified, mainly involving temporoparietal regions. Multivariate analyses permitted clear separation between control subjects and patients and moderate separation between patients with PCA and LPA, while patients with tAD were distributed along a continuum between these extremes. Significant classification performance could nevertheless be obtained when every pair of patient groups was compared directly. Conclusions: Analyses of cortical thickness patterns support the hypothesis that different clinical presentations of AD represent points in a phenotypic spectrum of neuroanatomical variation. Machine learning shows promise for syndrome separation and for identifying common anatomic patterns across syndromes that may signify a common pathology, both aspects of interest for treatment trials. Neurology® 2012;79:80–84

Lehmann, Manja; Barnes, Josephine; Rohrer, Jonathan D.; Warren, Jason D.; Crutch, Sebastian J.; Fox, Nick C.

2012-01-01

383

Characteristics of a Pathogenic Molecular Clone of an End-Stage Serum-Derived Variant of Simian Immunodeficiency Virus (SIVF359)  

PubMed Central

End-stage simian immunodeficiency virus (SIV) isolates are suggested to be the most fit of the evolved virulent variants that precipitate the progression to AIDS. To determine if there were common characteristics of end-stage variants which emerge from accelerated cases of AIDS, a molecular clone was derived directly from serum following in vivo selection of a highly virulent SIV isolate obtained by serial end-stage passage in rhesus monkeys (Macaca mulatta). This dominant variant caused a marked cytopathic effect and replicated to very high levels in activated but not resting peripheral blood lymphocytes. Furthermore, although this clone infected but did not replicate to detectable levels in rhesus monocyte-derived macrophages, these cells were able to transmit infection to autologous T cells upon contact. Interestingly, although at low doses this end-stage variant did not use any of the known coreceptors except CCR5, it was able to infect and replicate in human peripheral blood mononuclear cells homozygous for the ?32 deletion of CCR5, suggesting the use of a novel coreceptor. It represents the first pathogenic molecular clone of SIV derived from viral RNA in serum and provides evidence that not only the genetic but also the biological characteristics acquired by highly fit late-stage disease variants may be distinct in different hosts.

Holterman, Lennart; Dubbes, Rob; Mullins, James; Learn, Gerald; Niphuis, Henk; Koornstra, Wim; Koopman, Gerrit; Kuhn, Eva-Maria; Wade-Evans, Alison; Rosenwirth, Brigitte; Haaijman, Joost; Heeney, Jonathan

2001-01-01

384

A second albumin variant in an Irish population.  

PubMed

Three patients with bisalbuminemia of the slow type (relative mobility 0.94) were detected and the properties of the variant albumin investigated. Three additional patients possessing a fast type variant (relative mobility 1.05) have been detected since a previous report of 4 such cases and studies on these patients are also reported. PMID:3677425

Leahy, D T; McLaughlin, H

1987-10-15

385

Rare Hemoglobin Variant Hb Yaizu Observed in Turkey  

Microsoft Academic Search

Objective: To determine the characteristic features of the rare hemoglobin (Hb) variant Hb Yaizu to enable laboratory diagnosis of the hemoglobin variants during screening programs. Materials and Methods: Genomic DNA was obtained from the 4 members of a family living in Denizli province, an Aegean region of Turkey. Blood cell counts, hemoglobin composition, hemoglobin electrophoresis (both alkaline and acid), HPLC

Erol Ömer Atalay; Ayfer Atalay; Hasan Koyuncu; Onur Öztürk; Aylin Köseler; Anzel Özkan; Sanem Demirtepe

2008-01-01

386

Identification of New Sequence Variants in the Leptin Gene  

Microsoft Academic Search

The leptin gene (LEP) has been linked to extreme obesity. How- ever, no common obesity-related gene variants have been found to exist in the LEP. The present study was designed to investigate the LEP for variants by screening both the putative promoter and the coding region of this gene in obese Finnish subjects (n 5 200; body mass index, .27

MATTI K. KARVONEN; ULLAMARI PESONEN; PAULA HEINONEN; MARKKU LAAKSO; AILA RISSANEN; HANNU NAUKKARINEN; RAISA VALVE; MATTI I. J. UUSITUPA; MARKKU KOULU

1998-01-01

387

Identification of New Sequence Variants in the Leptin Gene  

Microsoft Academic Search

The leptin gene (LEP) has been linked to extreme obesity. How- ever, no common obesity-related gene variants have been found to exist in the LEP. The present study was designed to investigate the LEP for variants by screening both the putative promoter and the coding region of this gene in obese Finnish subjects (n 5 200; body mass index, .27

MATTI K. KARVONEN; ULLAMARI PESONEN; PAULA HEINONEN; MARKKU LAAKSO; AILA RISSANEN; HANNU NAUKKARINEN; RAISA VALVE; MATTI I. J. UUSITUPA; MARKKU KOULU

388

Continuous culture of Candida boidinii variant 60 growing on methanol  

Microsoft Academic Search

A new variant, Candida boidinii variant 60, which is less sensitive to methanol and formaldehyde shocks was grown in continuous cultures with methanol as sole carbon source. The substrate concentration in the feeding medium was either 1% methanol or 3% methanol. Biomass production, methanol consumption, the formation of formaldehyde and gas exchange were measured at different dilution rates. With low

W. Held; G. Schlanderer; J. Reimann; H. Dellweg

1978-01-01

389

Detecting Rare Variants in Case-Parents Association Studies  

PubMed Central

Despite the success of genome-wide association studies (GWASs) in detecting common variants (minor allele frequency ?0.05) many suggested that rare variants also contribute to the genetic architecture of diseases. Recently, researchers demonstrated that rare variants can show a strong stratification which may not be corrected by using existing methods. In this paper, we focus on a case-parents study and consider methods for testing group-wise association between multiple rare (and common) variants in a gene region and a disease. All tests depend on the numbers of transmitted mutant alleles from parents to their diseased children across variants and hence they are robust to the effect of population stratification. We use extensive simulation studies to compare the performance of four competing tests: the largest single-variant transmission disequilibrium test (TDT), multivariable test, combined TDT, and a likelihood ratio test based on a random-effects model. We find that the likelihood ratio test is most powerful in a wide range of settings and there is no negative impact to its power performance when common variants are also included in the analysis. If deleterious and protective variants are simultaneously analyzed, the likelihood ratio test was generally insensitive to the effect directionality, unless the effects are extremely inconsistent in one direction.

Cheng, Kuang-Fu; Chen, Jin-Hua

2013-01-01

390

A new variant for fission track dating (FTD)  

Microsoft Academic Search

One modify variant for FTD have proposed. The results of FTD by this procedure for three bloks of granite rocks have been presented. From intercomparison of different dating methods it's concluded that the proposed variant for FTD can be used as reference - method.

Nguyen Xuan Thang; Nguyen Tac Anh; Le Van Vuong; Duong Ba Cuong; Le Tien Dung

1995-01-01

391

Rare Variants Create Synthetic Genome-Wide Associations  

Microsoft Academic Search

A large number of different common variants has been associated with very modest increases of risk for various common diseases. A simulation study shows that rare variants with much greater impacts on disease risk may be responsible for some of these associations.

Samuel P. Dickson; Kai Wang; Ian Krantz; Hakon Hakonarson; David B. Goldstein

2010-01-01

392

Detecting rare variants in case-parents association studies.  

PubMed

Despite the success of genome-wide association studies (GWASs) in detecting common variants (minor allele frequency ?0.05) many suggested that rare variants also contribute to the genetic architecture of diseases. Recently, researchers demonstrated that rare variants can show a strong stratification which may not be corrected by using existing methods. In this paper, we focus on a case-parents study and consider methods for testing group-wise association between multiple rare (and common) variants in a gene region and a disease. All tests depend on the numbers of transmitted mutant alleles from parents to their diseased children across variants and hence they are robust to the effect of population stratification. We use extensive simulation studies to compare the performance of four competing tests: the largest single-variant transmission disequilibrium test (TDT), multivariable test, combined TDT, and a likelihood ratio test based on a random-effects model. We find that the likelihood ratio test is most powerful in a wide range of settings and there is no negative impact to its power performance when common variants are also included in the analysis. If deleterious and protective variants are simultaneously analyzed, the likelihood ratio test was generally insensitive to the effect directionality, unless the effects are extremely inconsistent in one direction. PMID:24086332

Cheng, Kuang-Fu; Chen, Jin-Hua

2013-09-26

393

Clinical and pathologic characteristics of focal segmental glomerulosclerosis pathologic variants  

Microsoft Academic Search

Histologic variants of idiopathic focal segmental glomerulosclerosis (FSGS) may have prognostic value. A recent working classification system has distinguished five FSGS variants. We evaluated a cohort of adult patients with biopsy-proven FSGS diagnosed between March 1982 and July 2001 to determine if subtypes were associated with renal outcome. Renal biopsies were reviewed by two pathologists. Demographic and clinical data were

D B Thomas; N Franceschini; S L Hogan; S ten Holder; C E Jennette; R J Falk; J C Jennette

2006-01-01

394

The histone minority report: the variant shall not be silenced.  

PubMed

In this issue of Cell, Meneghini et al. demonstrate that replacement of canonical histone H2A with the histone variant H2A.Z within euchromatin prevents silent chromatin proteins from migrating into regions of the chromosome that normally are transcriptionally active. Thus, this highly conserved histone variant is critical for defining chromatin domains. PMID:12628179

van Leeuwen, Fred; Gottschling, Daniel E

2003-03-01

395

Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis  

Microsoft Academic Search

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

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

2011-01-01

396

Fossil Alpha-Recoil Analysis of Certain Variant Radioactive Halos  

Microsoft Academic Search

The distribution of alpha-radioactivity in the vicinity of uranium and of certain variant radioactive halos in biotite was investigated by the fossil alpha-recoil method. Within the limits of the method I could not confirm a previously proposed hydrothermal mechanism for the origin of certain variant halo types due to polonium isotopes.

Robert V. Gentry

1968-01-01

397

Genetics Home Reference: GM2-gangliosidosis, AB variant  

MedlinePLUS

... activator. This protein is required for the normal function of an enzyme called beta-hexosaminidase A, which plays a critical ... AB variant. Because the AB variant impairs the function of a lysosomal enzyme and involves the buildup of GM2 ganglioside, this ...

398

CBH1 homologs and variant CBH1 cellulases  

DOEpatents

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.

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

2011-05-31

399

Assessing association between protein truncating variants and quantitative traits  

PubMed Central

Motivation: In sequencing studies of common diseases and quantitative traits, power to test rare and low frequency variants individually is weak. To improve power, a common approach is to combine statistical evidence from several genetic variants in a region. Major challenges are how to do the combining and which statistical framework to use. General approaches for testing association between rare variants and quantitative traits include aggregating genotypes and trait values, referred to as ‘collapsing’, or using a score-based variance component test. However, little attention has been paid to alternative models tailored for protein truncating variants. Recent studies have highlighted the important role that protein truncating variants, commonly referred to as ‘loss of function’ variants, may have on disease susceptibility and quantitative levels of biomarkers. We propose a Bayesian modelling framework for the analysis of protein truncating variants and quantitative traits. Results: Our simulation results show that our models have an advantage over the commonly used methods. We apply our models to sequence and exome-array data and discover strong evidence of association between low plasma triglyceride levels and protein truncating variants at APOC3 (Apolipoprotein C3). Availability: Software is available from http://www.well.ox.ac.uk/~rivas/mamba Contact: donnelly@well.ox.ac.uk

Rivas, Manuel A.; Pirinen, Matti; Neville, Matthew J.; Gaulton, Kyle J.; Moutsianas, Loukas; Lindgren, Cecilia M.; Karpe, Fredrik; McCarthy, Mark I.; Donnelly, Peter

2013-01-01

400

Expression of the CTL2 transcript variants in human peripheral blood cells and human tissues.  

PubMed

BACKGROUND: The HNA-3a antigen is an important antibody target in the pathophysiology of transfusion-related acute lung injury (TRALI). It is encoded by the choline transporter-like protein 2 (CTL2) gene, which exists in the two transcript variants TV1 and TV2, differing in the upstream promoter and coding region. Only TV1 has been demonstrated to enable choline transport across the cell membrane. STUDY DESIGN AND METHODS: The aim of this study was to determine the CTL2 transcript pattern in human peripheral blood cells and tissues and its capacity to bind HNA-3a antibodies. RNA was isolated from human whole blood, isolated neutrophils, mononuclear blood cells, leukoreduced platelets, human lung, liver, and colon. After reverse transcription, the single-stranded cDNA was amplified using primer combinations specific for the respective transcript. Plasmids containing the entire CTL2 coding cDNA of the transcript variant TV1 or TV2 served as controls. HEK293T cells expressing both variants were used to determine the binding of HNA-3a antibodies. RESULTS: The shorter TV2 transcript was demonstrated in each RNA sample derived from human peripheral blood tested so far, as well as in human lung and liver, whereas the longer TV1 transcript was only detected in human lung and colon. TV1 and TV2 had the same binding capacity to HNA-3a antibodies. CONCLUSION: The expression of TV1 and TV2 is tissue and cell specific, with peripheral blood cells expressing only TV2. This does not affect binding of HNA-3a antibodies. Whether the unequal expression might be relevant in the pathogenesis of TRALI remains to be investigated. PMID:23480595

Flesch, Brigitte K; Wesche, Jan; Berthold, Tom; Goldmann, Torsten; Hundt, Matthias; Greinacher, Andreas; Bux, Jürgen

2013-03-11

401

Quantitative analysis of cell walls of nutritionally variant streptococci grown under various growth conditions.  

PubMed Central

Strains of nutritionally variant streptococci are usually isolated from patients with subacute bacterial endocarditis. Only recently have these strains been subdivided into three serotypes; however, no group-specific antigen has been described. To understand the immunochemical basis for the serology of these microorganisms as well as set the groundwork for adherence studies, quantitative analysis of the cell walls of nutritionally variant streptococci was undertaken. The bacteria were grown in semisynthetic medium or pyridoxal-supplemented Todd-Hewitt broth and harvested during the exponential or stationary phase. Cell walls were isolated and analyzed for amino sugars, sugars, polyalcohols, amino acids, and phosphorus by gas chromatography, high-pressure liquid chromatography, or colorimetric assays. The peptidoglycans of the cell walls of the prototype strains from the three serotypes were representative of other streptococcal cell walls, including the presence of alanine as the possible cross-bridge. The composition of the peptidoglycan was similar for all three strains and included a decreased concentration of peptidoglycan in their cell walls during the stationary phase. Glucosamine, glucose, galactose, ribitol, and a small amount of rhamnose were found in each of the cell wall polysaccharides. Galactosamine was only found in serotype II and III cell walls and might be responsible for the previously described cross-reaction between these strains. The concentration of the other sugars and amino sugars varied in each of the cell wall preparations, depending on the growth conditions. Finally, all three strains expressed both ribitol and phosphorus in their cell walls, characteristic of the presence of a ribitol teichoic acid. Therefore the cell wall composition of the nutritionally variant streptococci varies depending on the growth conditions, and their composition appears similar to that of strains of Streptococcus mitis.

van de Rijn, I

1985-01-01

402

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

PubMed Central

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.

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

2009-01-01

403

High Lung-metastatic Variant of Human Osteosarcoma Cells, Selected by Passage of Lung Metastasis in Nude Mice, Is Associated with Increased Expression of ?v?3 Integrin.  

PubMed

Altered expression of ?v?3 integrin is associated with tumor progression and metastasis in several types of cancer, including metastatic osteosarcoma. In this study, we demonstrate that in vivo passaging of lung metastasis in nude mice can generate an aggressive variant of human osteosarcoma cells. Experimental metastases were established by injecting 143B human osteosarcoma cells, expressing green fluorescent protein (GFP) in the nucleus and red fluorescent protein (RFP) in the cytoplasm, in the tail vein of nude mice. Lung metastases were harvested under fluorescence microscopy from nude mice to establish cell lines which were then injected via the tail vein of additional nude mice. This procedure was repeated for four passages in order to isolate highly metastatic variant sublines. When the parental and metastatic variants were transplanted orthotopically into the tibia of nude mice, the 143B-LM4 variant had the highest metastatic rate, approximately 18-fold higher than the parent (p<0.01). ?v?3 integrin expression was increased approximately 5.6-fold in 143B-LM4 compared to parental cells (p<0.05). Thus, serial passage of lung metastases created a highly metastatic variant of human osteosarcoma cells which had increased expression of ?v?3 integrin, suggesting that ?v?3 integrin plays an essential role in osteosarcoma metastasis. With this highly metastatic variant overexpressing ?v?3 integrin, it will now be possible to further investigate the mechanism by which ?v?3 integrin facilitates metastasis. PMID:24023288

Tome, Yasunori; Kimura, Hiroaki; Maehara, Hiroki; Sugimoto, Naotoshi; Bouvet, Michael; Tsuchiya, Hiroyuki; Kanaya, Fuminori; Hoffman, Robert M

2013-09-01

404

Separation of phosphorylated histone H1 variants by high-performance capillary electrophoresis.  

PubMed

High-performance capillary electrophoresis (HPCE) was used to separate successfully distinct phosphorylated derivatives of individual histone H1 variants. With an untreated capillary (50 cm x 75 microns I.D.) the electrophoresis was performed in about 15 min. Inconvenient interactions of these highly basic proteins with the capillary wall were eliminated by using 0.1 M sodium phosphate buffer (pH 2.0) containing 0.03% hydroxypropylmethylcellulose. Under these experimental conditions the histone H1 variants H1b and H1c obtained from mitotic enriched NIH 3T3 fibroblasts and isolated by reversed-phase high-performance liquid chromatography were clearly separated in their non-phosphorylated and different phosphorylated forms. This result was confirmed by acid-urea gel electrophoresis, comparison with non-phosphorylated histones H1b and H1c, isolated from quiescent NIH 3T3 cells, and incubation of multi-phosphorylated histone H1b with alkaline phosphatase and subsequent acid-urea and capillary electrophoresis. The results illustrate that the application of HPCE to the analysis of histone modifications provides a new alternative to traditional gel electrophoresis. PMID:1430024

Lindner, H; Helliger, W; Dirschlmayer, A; Talasz, H; Wurm, M; Sarg, B; Jaquemar, M; Puschendorf, B

1992-09-11

405

Crystallographic variant selection in Ti-6Al-4V  

SciTech Connect

Transformation textures in the two-phase alloy Ti-6Al-4V have been studied. Samples were heated into the fully {beta} phase condition and then slow cooled to allow diffusional transformation to {alpha}. This produced a microstructure of grain boundary {alpha} encircling colonies of Widmanstaetten {alpha}. Electron backscattered diffraction (EBSD) texture measurements showed that the {alpha} texture was markedly sharper than that calculated on a basis of equal variant probability, indicating that significant variant selection was occurring during diffusional transformation. Investigation of the {alpha} variants produced across prior {beta} grain boundaries has shown that the selection of variants during transformation is highly dependant on the crystallography of those boundaries. The effect of this crystallographic variant selection on the transformation texture has been modelled.

Stanford, N. [Manchester Materials Science Centre, University of Manchester, Grosvenor Street, Manchester M1 7HS (United Kingdom); Bate, P.S. [Manchester Materials Science Centre, University of Manchester, Grosvenor Street, Manchester M1 7HS (United Kingdom)]. E-mail: pete.bate@man.ac.uk

2004-10-04

406

Antigenic and S-1 genomic characterization of the Delaware variant serotype of infectious bronchitis virus.  

PubMed

A previously unrecognized infectious bronchitis virus (IBV) serotype, referred to hereafter as the Delaware variant (DE var), was isolated from commercial broiler chickens during a severe, widespread respiratory disease epornitic in the Delmarva peninsula region of the United States in January-March 1992. The DE var serotype was found to be antigenically unrelated by virus-neutralization (VN) test to nine reference IBV serotypes from North America. Additional VN tests indicated that the DE var isolates (DE/072/92, DE/121/ 92, DE/152/92, and DE/174/92) from broilers were fully or partially neutralized by monospecific antisera prepared against themselves and against two IBV field isolates (DE/492/90 and DE/903/90) recovered from a Delmarva commercial layer flock experiencing egg production losses in 1990. Antigenic relatedness values determined by VN indicated layer isolate DE/492/90 was more closely related to the broiler DE var isolates than was layer isolate DE/903/90. Cross-challenge tests performed in specific-pathogen-free chickens also demonstrated the antigenic similarity of the broiler (DE/072/92 and DE/174/92) and the layer isolates (DE/492/90 and DE/903/90), with heterologous strain protection values ranging from 55% to 100%. Protection values of DE var isolates vs. Massachusetts 41 and Arkansas DPI were considerably lower (0-60%). The S-1 gene of the US/DE/072/92 isolate of the DE var serotype was amplified by reverse transcription polymerase chain reaction, cloned, and sequenced. The DE var S-1 gene sequence was compared with the S-1 gene sequences of IBV serotypes from North America, Europe, and Australia. A dendrogram based on this analysis supported the conclusion that the DE var serotype is highly novel among IBV. A high degree of similarity (> 88%) was observed between the S-1 genes of the DE var broiler isolates (DE/072/92 and DE/174/92) and layer isolates (DE/492/90 and DE/903/90). These data, taken with the VN and cross-challenge results, establish a genetic as well as an antigenic link between the isolates from layers and broilers and indicate the DE var serotype was responsible for both infectious bronchitis outbreaks. PMID:9356713

Gelb, J; Keeler, C L; Nix, W A; Rosenberger, J K; Cloud, S S

407

Bayesian detection of causal rare variants under posterior consistency.  

PubMed

Identification of causal rare variants that are associated with complex traits poses a central challenge on genome-wide association studies. However, most current research focuses only on testing the global association whether the rare variants in a given genomic region are collectively associated with the trait. Although some recent work, e.g., the Bayesian risk index method, have tried to address this problem, it is unclear whether the causal rare variants can be consistently identified by them in the small-n-large-P situation. We develop a new Bayesian method, the so-called Bayesian Rare Variant Detector (BRVD), to tackle this problem. The new method simultaneously addresses two issues: (i) (Global association test) Are there any of the variants associated with the disease, and (ii) (Causal variant detection) Which variants, if any, are driving the association. The BRVD ensures the causal rare variants to be consistently identified in the small-n-large-P situation by imposing some appropriate prior distributions on the model and model specific parameters. The numerical results indicate that the BRVD is more powerful for testing the global association than the existing methods, such as the combined multivariate and collapsing test, weighted sum statistic test, RARECOVER, sequence kernel association test, and Bayesian risk index, and also more powerful for identification of causal rare variants than the Bayesian risk index method. The BRVD has also been successfully applied to the Early-Onset Myocardial Infarction (EOMI) Exome Sequence Data. It identified a few causal rare variants that have been verified in the literature. PMID:23922764

Liang, Faming; Xiong, Momiao

2013-07-26

408

Rapid emergence of novel antigenic and genetic variants of equine infectious anemia virus during persistent infection.  

PubMed Central

Previous results from our laboratory have demonstrated that equine infectious anemia virus displays structural variations in its surface glycoproteins and RNA genome during passage and chronic infections in experimentally infected Shetland ponies (Montelaro et al., J. Biol. Chem. 259:10539-10544, 1984; Payne et al., J. Gen. Virol. 65:1395-1399, 1984). The present study was undertaken to obtain an antigenic and biochemical characterization of equine infectious anemia virus isolates recovered from an experimentally infected pony during sequential disease episodes, each separated by intervals of only 4 to 8 weeks. The virus isolates could be distinguished antigenically by neutralization assays with serum from the infected pony and by Western blot analysis with a monoclonal antibody against the major surface glycoprotein gp90, thus demonstrating that novel antigenic variants of equine infectious anemia virus predominate during each clinical episode. The respective virion glycoproteins displayed different electrophoretic mobilities on sodium dodecyl sulfate-polyacrylamide gels, indicating structural variation. Tryptic peptide and glycopeptide maps of the viral proteins of each virus isolate revealed biochemical alterations involving amino acid sequence and glycosylation patterns in the virion surface glycoproteins gp90 and gp45. In contrast, no structural variation was observed in the internal viral proteins pp15, p26, and p9 from any of the four virus isolates. Oligonucleotide mapping experiments revealed similar but unique RNase T1-resistant oligonucleotide fingerprints of the RNA genomes of each of the virus isolates. Localization of altered oligonucleotides for one virus isolate placed two of three unique oligonucleotides within the predicted env gene region of the genome, perhaps correlating with the structural variation observed in the envelope glycoproteins. Thus these results support the concept that equine infectious anemia virus is indeed capable of relatively rapid genomic variations during replication, some of which result in altered glycoprotein structures and antigenic variants which are responsible for the unique periodic disease nature observed in persistently infected animals. The findings of envelope specific differences in isolates of visna virus and of human T-cell lymphotropic virus III (acquired immune deficiency syndrome-related virus) suggest that this variation may be a common characteristic of the subfamily Lentivirinae. Images

Salinovich, O; Payne, S L; Montelaro, R C; Hussain, K A; Issel, C J; Schnorr, K L

1986-01-01

409

Common genetic variants associated with open-angle glaucoma.  

PubMed

Open-angle glaucoma (glaucoma) is a major eye disorder characterized by optic disc pathology. Recent genome-wide association studies identified new loci associated with clinically relevant optic disc parameters, such as the optic disc area and vertical cup-disc ratio (VCDR). We examined to what extent these loci are involved in glaucoma. The loci studied include ATOH7, CDC7/TGFBR3 and SALL1 for optic disc area, and CDKN2B, SIX1, SCYL1/LTBP3, CHEK2, ATOH7 and DCLK1 for VCDR. We performed a meta-analysis using data from six independent studies including: the Rotterdam Study (n= 5736), Genetic Research in Isolated Populations combined with Erasmus Rucphen Family study (n= 1750), Amsterdam Glaucoma Study (n= 296) and cohorts from Erlangen and Tübingen (n= 1363), Southampton (n= 702) and deCODE (n= 36 151) resulting in a total of 3161 glaucoma cases and 42 837 controls. Of the eight loci, we found significant evidence (P= 1.41 × 10(-8)) for the association of CDKN2B with glaucoma [odds ratio (OR) for those homozygous for the risk allele: 0.76; 95% confidence interval (CI): 0.70-0.84], for the role of ATOH7 (OR: 1.28; 95% CI: 1.12-1.47) and for SIX1 (OR: 1.20; 95% CI: 1.10-1.31) when adjusting for the number of tested loci. Furthermore, there was a borderline significant association of CDC7/TGFBR3 and SALL1 (both P= 0.04) with glaucoma. In conclusion, we found consistent evidence for three common variants (CDKN2B, ATOH7 and SIX1) significantly associated with glaucoma. These findings may shed new light on the pathophysiological protein pathways leading to glaucoma, and point to pathways involved in the growth and development of the optic nerve. PMID:21427129

Ramdas, Wishal D; van Koolwijk, Leonieke M E; Lemij, Hans G; Pasutto, Francesca; Cree, Angela J; Thorleifsson, Gudmar; Janssen, Sarah F; Jacoline, Ten Brink; Amin, Najaf; Rivadeneira, Fernando; Wolfs, Roger C W; Walters, G Bragi; Jonasson, Fridbert; Weisschuh, Nicole; Mardin, Christian Y; Gibson, Jane; Zegers, Richard H C; Hofman, Albert; de Jong, Paul