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PubMed2006

A novel, resistance-linked ovine PrP variant and its equivalent mouse variant modulate the in vitro cell-free conversion of rPrP to PrP(res).

Prion diseases are associated with the conversion of the normal cellular prion protein, PrP(c), to the abnormal, disease-associated form, PrP(Sc). This conversion can be mimicked in vitro by using a cell-free conversion assay. It has recently been shown that this assay can be modified to use bacterial recombinant PrP as substrate and mimic the in vivo transmission characteristics of rodent scrapie. Here, it is demonstrated that the assay replicates the ovine polymorphism barriers of scrapie transmission. In addition, the recently identified ovine PrP variant ARL(168)Q, which is associated with resistance of sheep to experimental BSE, modulates the cell-free conversion of ovine recombinant PrP to PrP(res) by three different types of PrP(Sc), reducing conversion efficiencies to levels similar to those of the ovine resistance-associated ARR variant. Also, the equivalent variant in mice (L(164)) is resistant to conversion by 87V scrapie. Together, these results suggest a significant role for this position and/or amino acid in conversion.

Amino Acid Substitution↗

PubMed1989

Purification and characterization of five variants of phospholipase A2 and complete primary structure of the main phospholipase A2 variant in Heloderma suspectum (Gila monster) venom.

1. Five increasingly anionic variants (Pa1-Pa5) of Ca2+-dependent phospholipase A2 were purified to homogeneity from the venom of the lizard Heloderma suspectum (Gila monster). The purification procedure was based on semi-preparative reverse-phase HPLC followed by anion-exchange HPLC and analytical reverse-phase HPLC. 2. Their Mr were 17,000-18,000, as deduced by SDS/PAGE. Specific activities tested by the capacity to hydrolyze phosphatidylcholines at pH 8.5 decreased as follows: Pa3 greater than Pa5 greater than Pa4 greater than Pa1 greater than Pa2. These activities showed the same optimum pH (9.0), were mainly of the phospholipase A2 type and were lost upon p-bromophenacyl bromide treatment. 3. All five phospholipases efficiently stimulated amylase release from dispersed rat pancreatic acini at pH 7.4, their potency decreasing as follows: Pa2 greater than Pa1 approximately equal to Pa4 greater than Pa3 approximately equal to Pa5. No deleterious effect was apparent based on the lack of lactate dehydrogenase release. 4. The five variants, Pa1-Pa5, differed significantly in amino acid composition and this, together with distinct antigenic properties of Pa2 and Pa5, establishes the subheterogeneity of this new type of phospholipase A2, despite the fact that the N-terminal amino acid sequence (31 residues) of Pa1-Pa5 was exactly the same. 5. The full sequence of the major variant, Pa5, showed that this 142-amino-acid protein exhibited greater similarity to the bee venom enzyme than to any class I or class II secretory phospholipase A2 from snake venom and mammalian pancreas. While Pa5 displayed the highly conserved region between Asp30 and Cys39 (the essential active site of all phospholipases A2), its salient original points included 10 half-cystine residues only, an incomplete N-terminal sequence, large changes in the putative calcium loop, several alterations after the active site and a C-terminal extension never seen in other phospholipases A2, with the only exception being bee venom.

Amino Acid Sequence↗

PubMed1991

Isolation of chick tenascin variants and fragments. A C-terminal heparin-binding fragment produced by cleavage of the extra domain from the largest subunit splicing variant.

The extracellular-matrix glycoprotein, tenascin, consists of disulfide-linked subunits of 190, 200 and 230 kDa (the three splicing variants reported in chicken) and usually exists as a six-armed structure under the electron microscope. We used monoclonal antibodies to isolate and characterize different splicing variants and proteolytic fragments obtained from the native protein. Purified monomeric tenascin has a native molecular mass of 216 kDa and is structured as single arms. Tenascin fragments obtained by pepsin digestion bind to monoclonal antibody (mAb) TnM1 which is directed against epidermal-growth-factor-like repeats in the N-terminal half of all subunits. These fragments represent the thin proximal part of the tenascin arms and they are still partially linked to dimers and trimers via disulfide bridges. Using mAb Tn68, that reacts with a fibronectin-type-III repeat towards the C-terminus, a tenascin fragment, generated by treatment with pronase, can be isolated. Ultrastructurally, this fragment looks like the thicker distal part of the tenascin arms. Only the 230-kDa variant of tenascin gives rise to this distal fragment after cleavage within the alternatively spliced fibronectin-type-III repeats. Native tenascin and all fragments containing the distal part of its arms bind to heparin-agarose, whereas the proximal fragments do not. Oligomeric and monomeric tenascin inhibit fibronectin-mediated fibroblast spreading with comparable efficiency when added to the culture medium, while the proximal fragment has no effect. The distal fragment as well as reduced and alkylated tenascin are active in this assay, but only at higher molar concentrations when compared to the native protein.

Animals↗

PubMedDate not supplied

Variant frequency in flap production. A corpus analysis of variant frequency in American English flap production.

This study examined the distribution of allophonic variants [t], [I] or [U], of medial /t/ using a corpus of conversational speech. We utilized a large conversational speech database to generate statistics about the frequency of occurrence of medial flaps. Results confirmed the prevalence of flapping in American English. Low frequency words showed a redistribution of variants from [U] to [t] compared to dominant flapping in high frequency words. A similar redistribution of variant production occurred for morphologically complex words (e.g. dirty) compared with morphologically simple words (e.g. water). A second analysis examining vowel length prior to medial /t/ and medial /d/ showed that, while both stops were pronounced as a flap, the vowel preceding medial /d/ tended to the longer. These results were discussed in reference to potential processes in recognizing spoken words.

Female↗

PubMed1976

Distribution of G6PD types in the population of southwest France: common variants and new variants.

Glucose-6-phosphate dehydrogenase was purified from blood samples originating from 33 subjects living in the 'Midi-Pyrenees' region (Southwest France). Biochemical and electrophoretic characteristics of several enzymatic variants were revealed. The distribution of the mutations in the subjects studied gave the following results: (1) Meditteranean Gd(-) and Gd(-)A identified variants; they constitute the main part of our observations. (2) Two original variants confirmed by the WHO International Reference Laboratory, that is: Gd(-) Toulouse and Gd(+) Luz-Saint-Sauveur; the latter mutation did not produce any haematological disorder. Absence of chronic haemolytic anaemia as well as a high rate of favism could be found in the families studied. As it is generally observed in Mediterranean regions, Southwest France population is characterized by a certain heterogeneity in biochemical and genetic mutations.

Erythrocytes↗

PubMed2006

A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degeneration.

PURPOSE: Two biologically related factors, complement factor H (CFH) and C-reactive protein (CRP), have been associated with AMD. The Y402H variant of CFH is located within the binding site of CFH for CRP. Although plasma CRP levels have been related to AMD and plasma CRP levels are partly determined by genetic variation, there is no information on whether genetic variants in CRP are associated with AMD. METHODS: A prospective analysis was performed of 111 men who eventually developed AMD and 401 men who remained free of AMD, all participants in the Physicians' Health Study. Genotypes were determined for the common T-->C single nucleotide polymorphism (SNP) in exon 9 of CFH (rs1061170; protein Y402H), as well as seven previously described CRP SNPs (rs3093059, rs2794521, rs3091244, rs1417938, rs1800947, rs1130864, and rs1205). Logistic regression analysis was used to evaluate individual SNPs, as well as six CRP haplotypes for association with AMD. RESULTS: The high-risk C allele of CFH was present in 45% of cases and 34% of controls. An odds ratio (OR) of 1.46 was observed for AMD (95% confidence interval [CI]: 1.05-2.04) for TC heterozygotes and an OR of 2.13 (95% CI: 1.10-4.16) for CC homozygotes, assuming a multiplicative (log-additive) model and attributable fraction of 25% (95% CI: 1% to 44%) was calculated. For CRP, single-marker or haplotype-based analysis failed to reveal any significant associations with a risk of AMD. CONCLUSIONS: These prospective data confirmed an association between the Y402H variant of CFH and a risk of AMD. In contrast, although a biologically plausible, genetic variation in CRP does not appear to be associated with a risk of AMD. Further prospective studies of a larger number of subjects are needed to substantiate available information on the genetic epidemiology of AMD.

Aged↗

PubMed2005

Serotypes, intimin variants and other virulence factors of eae positive Escherichia coli strains isolated from healthy cattle in Switzerland. Identification of a new intimin variant gene (eae-eta2).

BACKGROUND: Enteropathogenic Escherichia coli (EPEC) and Shigatoxin-producing Escherichia coli (STEC) share the ability to introduce attaching-and-effacing (A/E) lesions on intestinal cells. The genetic determinants for the production of A/E lesions are located on the locus of enterocyte effacement (LEE), a pathogenicity island that also contains the genes encoding intimin (eae). This study reports information on the occurrence of eae positive E. coli carried by healthy cattle at the point of slaughter, and on serotypes, intimin variants, and further virulence factors of isolated EPEC and STEC strains. RESULTS: Of 51 eae positive bovine E. coli strains, 59% were classified as EPEC and 41% as STEC. EPEC strains belonged to 18 O:H serotypes, six strains to typical EPEC serogroups. EPEC strains harbored a variety of intimin variants with eae-beta1 being most frequently found. Moreover, nine EPEC strains harbored astA (EAST1), seven bfpA (bundlin), and only one strain was positive for the EAF plasmid. We have identified a new intimin gene (eta2) in three bovine bfpA and astA-positive EPEC strains of serotype ONT:H45. STEC strains belonged to seven O:H serotypes with one serotype (O103:H2) accounting for 48% of the strains. The majority of bovine STEC strains (90%) belonged to five serotypes previously reported in association with hemolytic uremic syndrom (HUS), including one O157:H7 STEC strain. STEC strains harbored four intimin variants with eae-epsilon1 and eae-gamma1 being most frequently found. Moreover, the majority of STEC strains carried only stx1 genes (13 strains), and was positive for ehxA (18 strains) encoding for Enterohemolysin. Four STEC strains showed a virulence pattern characteristic of highly virulent human strains (stx2 and eae positive). CONCLUSION: Our data confirm that ruminants are an important source of serologically and genetically diverse intimin-harboring E. coli strains. Moreover, cattle have not only to be considered as important asymptomatic carriers of O157 STEC but can also be a reservoir of EPEC and eae positive non-O157 STEC, which are described in association with human diseases.

Adhesins, Bacterial↗

PubMed2003

Large-scale association studies of variants in genes encoding the pancreatic beta-cell KATP channel subunits Kir6.2 (KCNJ11) and SUR1 (ABCC8) confirm that the KCNJ11 E23K variant is associated with type 2 diabetes.

The genes ABCC8 and KCNJ11, which encode the subunits sulfonylurea receptor 1 (SUR1) and inwardly rectifying potassium channel (Kir6.2) of the beta-cell ATP-sensitive potassium (K(ATP)) channel, control insulin secretion. Common polymorphisms in these genes (ABCC8 exon 16-3t/c, exon 18 T/C, KCNJ11 E23K) have been variably associated with type 2 diabetes, but no large ( approximately 2,000 subjects) case-control studies have been performed. We evaluated the role of these three variants by studying 2,486 U.K. subjects: 854 with type 2 diabetes, 1,182 population control subjects, and 150 parent-offspring type 2 diabetic trios. The E23K allele was associated with diabetes in the case-control study (odds ratio [OR] 1.18 [95% CI 1.04-1.34], P = 0.01) but did not show familial association with diabetes. Neither the exon 16 nor the exon 18 ABCC8 variants were associated with diabetes (1.04 [0.91-1.18], P = 0.57; 0.93 [0.71-1.23], P = 0.63, respectively). Meta-analysis of all case-control data showed that the E23K allele was associated with type 2 diabetes (K allele OR 1.23 [1.12-1.36], P = 0.000015; KK genotype 1.65 [1.34-2.02], P = 0.000002); but the ABCC8 variants were not associated. Our results confirm that E23K increases risk of type 2 diabetes and show that large-scale association studies are important for the identification of diabetes susceptibility alleles.

ATP-Binding Cassette Transporters↗

PubMed1999

[An unusual variant of urothelial carcinoma: the "nested variant of urothelial carcinoma." Report of two cases].

We report two cases of a poorly known variant of transitional cell carcinoma, the "nested variant of urothelial carcinoma". This tumor is composed of small islands or nests of transitional cells, presenting little atypia and mimicking von Brünn's nests. This low grade tumoral variant seems to behave as a high grade tumor of the same stage. Deep biopsies are necessary to display tumoral invasion, which allows the diagnosis. Importance of the knowledge of this entity is highlighted in order to avoid misdiagnoses that could delay appropriate therapy.

Aged↗

PubMed1999

DAR, a new RhD variant involving exons 4, 5, and 7, often in linkage with ceAR, a new Rhce variant frequently found in African blacks.

The highly polymorphic Rh system is encoded by 2 homologous genes RHD and RHCE. Gene rearrangements, deletions, or point mutations may cause partial D and CE antigens. In this study, a new RHD variant, DAR, and a new RHCE variant, ceAR, are described in 4 Dutch African Blacks. Serologically, DAR showed weaker reactions with a monoclonal antibody and polyclonal antiserum against D. The DAR phenotype was characterized by complete loss of at least 9 of 37 Rh D epitopes. Erythrocytes expressing ceAR were all typed as VS(-), V(+). DNA analysis showed a partial D allele with only 3 mutations: C602G (exon 4), T667G (exon 5), and T1025C (exon 7). The ceAR allele carried G48C (exon 1), a hybrid exon 5 (A712G, C733G, A787G, and T800A), and A916G (exon 6). To study the frequency of these variants, 326 South-African Blacks was screened genomically. Of the 326 donors, 16 (4.9%) carried the DAR allele, 20 (6.1%) the ceAR allele, and 14 (4.3%) both mutated alleles. Five of these donors (1.5%) had the DAR phenotype, indicating that they carried the DAR allele homozygously or next to a D-negative allele. Immunogenicity of the D antigen for individuals with the DAR phenotype was proven, because 1 of the 4 Dutch individuals produced allo-antibodies against D after multiple transfusions with D-positive blood. In a multiethnic society, the prevalence of this D phenotype will increase and is therefore relevant in transfusion practice and in prevention of hemolytic disease of the newborn.

Africa↗

PubMed2000

PDGF B mRNA variants in human tumors with similarity to the v-sis oncogene: expression of cellular PDGF B protein is associated with exon 1 divergence, but not with a 3'UTR splice variant.

While platelet-derived growth factor, PDGF, is not regularly expressed in mesenchymal tissues, PDGF B mRNA is often found in tumors derived from these tissues. PDGF B protein is also present, but the protein levels in individual tumors do not appear to correlate well with those of the mRNA. PDGF B is homologous to the v-sis oncogene of simian sarcoma virus (SSV), and certain deletions confined to 3; and 5; non-coding sequences of PDGF B mRNA are consistently found in tumors induced by SSV and by a PDGF B retrovirus. Part of exon 1, including a non-coding GC-rich regulatory domain and the signal sequence as well as a 149 nucleotide long AU-rich stretch in the 3; non-coding region, are often lost. We hoped that this information could provide a clue to defective regulatory mechanisms present in human tumors and have searched for such mRNA variants in human sarcoma cell lines and soft tissue tumors. We identified a splice variant of PDGF B mRNA that, similar to v-sis, lacks the 149 nucleotide stretch and introduces an anomalous splice point between exons 6 and 7. This weakly abundant mRNA variant was co-expressed with the regular PDGF B mRNA, but its presence failed to show any association with increased levels of immunohistochemically detectable PDGF B protein. Instead, the highest levels of cellular PDGF B protein were found in samples with mRNAs showing exon 1 divergence. The changes in the 5; end of the mRNA were not accompanied by any genomic aberrations.

3' Untranslated Regions↗

PubMedDate not supplied

[Requirements for glucose, nitrate and phosphate and their variants in the analysis of the mixed culture of Pseudomonas aeruginosa variants].

The calibration data and sensitivity analysis for the variational model of Pseudomonas aeruginosa mixed culture containing R, S, and M phenotypic variants are presented. The model with calibrated parameters (requirements of the variants for glucose, nitrates, and phosphates) adequately describes the experiment. The sensitivity indices (the species abundances and total community size) changed least under the influence of the parameter variations in the one-way limitation areas. The variant proportions are more sensitive to variation of the requirements than the community size.

Bacteriological Techniques↗

PubMed1985

Some anatomical variants and pitfalls in computed tomography of the trachea and mainstem bronchi. II. Compression or anatomical variants?

472 computed tomographic (CT) examinations in 448 patients were reviewed for depression of the wall of the trachea and mainstem bronchi. Depression was defined as a neutral term, not indicating pressure exerted upon the wall. Such depressions appeared to occur very frequently as a variant. Special attention is paid to the so-called azygos vein indentation. The most marked depression variants in our series are reproduced. When a depression is found in contiguity with a pathological mass and does not exceed the range of the variants, one cannot be sure that the mass is indeed the cause of this depression. In patients with bronchogenic carcinoma, depression of the wall of the trachea or mainstem bronchus seems to be no better sign for the metastatic nature of lymphadenopathy than size per se.

Azygos Vein↗

PubMed1998

Different effects of Gsalpha splice variants on beta2-adrenoreceptor-mediated signaling. The beta2-adrenoreceptor coupled to the long splice variant of Gsalpha has properties of a constitutively active receptor.

The beta2-adrenoreceptor (beta2AR) couples to the G-protein Gs to mediate adenylyl cyclase activation. The splice variants of Gsalpha differ by a 15-amino acid insert between the Ras-like domain and the alpha-helical domain. The long splice variant of Gsalpha (GsalphaL) binds GDP with lower affinity than the short splice variant (GsalphaS), but the impact of this difference on the interaction of Gsalpha with the beta2AR is not known. We studied the beta2AR/Gsalpha interaction using receptor/G-protein fusion proteins (beta2ARGsalphaS and beta2ARGsalphaL) expressed in Sf9 cells. Fusion of the beta2AR to Gsalpha promotes efficient coupling as shown by high-affinity agonist binding and GTPase and adenylyl cyclase activation and ensures fixed stoichiometry between receptor and G-protein. Importantly, fusion does not change the fundamental properties of the beta2AR or Gsalpha. The beta2AR in beta2ARGsalphaL showed hallmarks of constitutive activity (increased potency and intrinsic activity of partial agonists, increased efficacy of inverse agonists, and increased basal GTPase activity) compared with the beta2AR in beta2ARGsalphaS. The apparent constitutive activity of the beta2AR in beta2ARGsalphaL may be due to the lower GDP affinity of GsalphaL compared with GsalphaS, i.e. GsalphaL is more often nucleotide-free than GsalphaS and, therefore, more frequently available to stabilize the beta2AR in the active (R*) state. This study demonstrates that subtle structural differences between closely related G-protein alpha-subunits can have important consequences for the functional properties of a G-protein-coupled receptor.

Adenylyl Cyclases↗

PubMedDate not supplied

Serum assay of soluble CD44 standard (sCD44-st), CD44 splice variant v5 (sCD44-v5), and CD44 splice variant v6 (sCD44-v6) in patients with epithelial ovarian cancer.

Different variants of the cell adhesion molecule CD44 have been involved in malignant transformation and cancer metastasis. In the present investigation we assessed the preoperative serum levels of soluble CD44 standard (sCD44-st), sCD44 splice variant 5 (sCD44-v5), and sCD44 splice variant 6 (sCD44-v6) in 51 patients with ovarian cancer. Median preoperative sCD44-st, sCD44v5, and sCD44-v6 levels were 417 ng/ml (range, 240- > 602 ng/ml), 78 ng/ml (range, 5-314 ng/ml), and 86 ng/ml (range, 1-243 ng/ml), respectively. No significant relationship was detected between sCD44-st concentrations and the common clinicopathological variables. Conversely, sCD44-v5 and sCD44-v6 levels were significantly lower in FIGO stage III-IV than in stage I disease (p < 0.0001 and p = 0.001, respectively). Moreover, with regard to advanced ovarian cancer, sCD44-v5 levels were lower in patients with poorly differentiated (G3) than in those with moderately (G2) or well (G1) differentiated tumors (p = 0.038), as well as in patients whose residual disease was > 2 cm than in those with smaller residuum (p = 0.025). Similarly, sCD44-v6 levels were lower in patients with large residual disease (p = 0.05). The median value of serum sCD44-v6 was lower in patients with G3 than in those with G1-G2 tumor, but the difference was not significant. In conclusion, sCD44-st, sCD44-v5, and sCD44-v6 are detectable in sera from patients with epithelial ovarian cancer. A reduction in preoperative sCD44-v5 and sCD44-v6 levels seems to be associated with advanced, poorly differentiated tumors and with large residual disease after first surgery, and it might reflect an increased biological aggressiveness of the malignancy.

Alternative Splicing↗

PubMed1998

Different effects of Gsalpha splice variants on beta2-adrenoreceptor-mediated signaling. The Beta2-adrenoreceptor coupled to the long splice variant of Gsalpha has properties of a constitutively active receptor.

The beta2-adrenoreceptor (beta2AR) couples to the G-protein Gs to mediate adenylyl cyclase activation. The splice variants of Gs alpha differ by a 15-amino acid insert between the Ras-like domain and the alpha-helical domain. The long splice variant of Gs alpha (Gs alphaL) binds GDP with lower affinity than the short splice variant (Gs alphaS), but the impact of this difference on the interaction of Gs alpha with the beta 2AR is not known. We studied the beta2 AR/Gs alpha interaction using receptor/G-protein fusion proteins (beta2 AR Gs alphaS and beta2 AR Gs alphaL) expressed in Sf9 cells. Fusion of the beta2 AR to Gs alpha promotes efficient coupling as shown by high-affinity agonist binding and GTPase and adenylyl cyclase activation and ensures fixed stoichiometry between receptor and G-protein. Importantly, fusion does not change the fundamental properties of the beta2 AR or Gs alpha. The beta2 AR in beta2 AR Gs alphaL showed hallmarks of constitutive activity (increased potency and intrinsic activity of partial agonists, increased efficacy of inverse agonists, and increased basal GTPase activity) compared with the beta2 AR in beta2 AR Gs alphaS. The apparent constitutive activity of the beta2 AR in beta2 AR Gs alphaL may be due to the lower GDP affinity of Gs alphaL compared with Gs alphaS, i.e. Gs alphaL is more often nucleotide-free than Gs alphaS and, therefore, more frequently available to stabilize the beta2 AR in the active (R*) state. This study demonstrates that subtle structural differences between closely related G-protein alpha-subunits can have important consequences for the functional properties of a G-protein-coupled receptor.

Adrenergic beta-Agonists↗

PubMed1988

Stable variant-specific transcripts of the variant cell surface glycoprotein gene 1.8 expression site in Trypanosoma brucei.

The structure and transcriptional regulation of the 1.8 variant cell surface glycoprotein (VSG) gene expression site located on a 430-kilobase (kb) chromosome was examined in a 430-kb-chromosome-specific library. Using 32P-labeled nascent transcripts generated by nuclear run-on, we selected recombinant clones derived from the 430-kb chromosome which were coordinately activated with the 1.8 VSG gene. The results show that a repetitive region with a minimum size of 27 kb is coordinately activated with the 1.8 VSG gene. As with the 1.8 VSG gene, transcription is by RNA polymerases that are insensitive to the drug alpha-amanitin at concentrations up to 1 mg/ml. Transcription results in the generation of several stable variant-specific mRNAs. These mRNAs most likely belong to a family of repetitive expression-site-associated genes.

Animals↗

PubMed1999

Association of unstable hemoglobin variants and heterozygous beta-thalassemia: example of a new variant Hb Acharnes or [beta53(D4) Ala --> Thr].

We report here the functional and structural characterization of Hb Acharnes [beta53(D4) Ala --> Thr], an unstable and electrophoretically silent variant, that was found associated in trans with a beta(0)-thalassemic mutation (IVSI-1 G --> A), in a patient with thalassemia intermedia syndrome. This case is discussed in comparison with other sporadic cases that we have previously investigated, resulting from the co-inheritance of a beta(0)-thalassemic mutation (CD39 C --> T) with two other types of unstable hemoglobins, Hb Köln [beta98(FG5) Val --> Met], and Hb Arta [beta45(CD4) Phe --> Cys]. It may be concluded that, in these associated forms, both the degree of instability of the variant and the altered oxygen binding properties (affecting the degree of tissue hypoxia) are major determinants of their clinical expression.

Child↗