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PubMed2005

KIT and RCC are useful in distinguishing chromophobe renal cell carcinoma from the granular variant of clear cell renal cell carcinoma.

The distinction between chromophobe renal cell carcinoma, the granular cell variant of clear cell renal cell carcinoma, and renal oncocytoma is a common diagnostic dilemma. The usefulness of KIT, CD10, RCC, and RON in the differential diagnosis of these renal epithelial tumors was investigated. KIT was 100% positive in chromophobe renal cell carcinoma (11 of 11) and renal oncocytoma (12 of 12). The KIT staining pattern was identical in both tumor types, with cytoplasmic membrane attenuation, and fine granular cytoplasmic staining. In contrast, KIT was absent in all granular cell variants of clear cell renal cell carcinoma (0 of 6). RCC was observed in more than 80% of the granular cell variant of clear cell renal cell carcinoma (5 of 6) but was negative in all chromophobe renal cell carcinomas (0 of 11) and renal oncocytomas (0 of 12). CD10 was expressed in 100% of the granular cell variant of clear cell renal cell carcinoma (6 of 6), 72% of chromophobe renal cell carcinomas (8 of 11), and 58% of renal oncocytomas (7 of 12). RON was 100% positive in the chromophobe renal cell carcinomas (11 of 11) and renal oncocytomas (12 of 12) but only 50% positive in the granular cell variant of clear cell renal cell carcinoma (3 of 6). Colloidal iron was diffusely and strongly positive in more than 80% of the chromophobe renal cell carcinomas (9 of 11), focally and weakly positive in 41% of the renal oncocytomas (5 of 12) but negative in all granular cell variant of clear cell renal cell carcinoma (0 of 6). The above results demonstrate that: 1) KIT is a very sensitive marker for both chromophobe renal cell carcinoma and renal oncocytoma; 2) immunohistochemistry using antibodies to KIT combined with RCC was sufficient to discriminate between chromophobe renal cell carcinoma and the granular cell variant of clear cell renal cell carcinoma; and 3) neither RON, nor KIT, nor a combination of this panel can be used to distinguish chromophobe renal cell carcinoma from renal oncocytoma. Colloidal iron staining aided in this distinction for the majority of the chromophobe renal cell carcinomas (more than 80% positive) and renal oncocytomas (close to 60% negative).

Adenocarcinoma, Clear Cell↗

PubMed1987

Selection of coxsackievirus B4 variants with monoclonal antibodies results in attenuation.

Inoculation of suckling mice with coxsackievirus B4 (CB4) results in the death of a majority of the animals. In this study we selected antigenic variants of CB4 in the presence of neutralizing monoclonal antibodies and tested them to see whether they were attenuated. Antigenic variants selected with a single antibody showed little or no attenuation by producing a high mortality (60 to 100%). A double variant selected with two antibodies showed considerable attenuation by causing only 25% mortality. A triple variant selected with three antibodies was almost completely attenuated (killed only 5% of the animals). Polypeptides from these variants were tested for their ability to interact with the monoclonal antibodies used for their selection. These studies showed that resistance of variant virus to neutralization in general was due to the inability of the antibody to bind to the virus. However, one of the antibodies could bind but not neutralize the virus, perhaps due to an alteration in the epitope. It is concluded that selection of CB4 variants using more than one neutralizing monoclonal antibody can lead to attenuation of the virus.

Animals↗

PubMed1988

The peplomer protein E2 of coronavirus JHM as a determinant of neurovirulence: definition of critical epitopes by variant analysis.

We selected murine coronavirus JHM variants specifically changed in defined antigenic sites of the peplomer protein E2. Variants were isolated from the supernatants of monoclonal antibody hybridoma cell cultures which continued to secrete neutralizing antibodies after being infected with JHM. Comparative antigenic analysis and biological tests were performed in order to refine an operational epitope map and to characterize functional domains important for pathogenicity. The reaction patterns (neutralization, inhibition of cell fusion, immunofluorescence and binding in ELISA) between the variant viruses and the panel of monoclonal antibodies were very similar. Four groups of variants were characterized each of which revealed distinct changes affecting one defined antigenic site. These observations indicated that at least four independently mutable antigenic sites were associated with domains involved in cell fusion, neutralization and pathogenicity (E2-Aa, -Ab, -Ba and -Bb). JHM variants with alterations in the E2-Aa, -Ab or -Bb sites were similar to wild-type virus. These variants caused acute hepatitis and encephalomyelitis in mice. In contrast, JHM variants with changes in site E2-Ba had a strong propensity to induce chronic disease accompanied by demyelination persisting for several months.

Animals↗

PubMed1989

Use of a monoclonal antibody specific for wild-type yellow fever virus to identify a wild-type antigenic variant in 17D vaccine pools.

Monoclonal antibodies (MAbs) against the Asibi wild-type strain of yellow fever (YF) virus were prepared and characterized. One of the MAbs (designated MAb 117) was shown, by cross-immunofluorescence tests with flaviviruses, to be specific for wildtype YF virus. This MAb was used in indirect immunofluorescence tests to identify wild-type antigenic variants in several different YF vaccine pools. Simultaneously, a vaccine-specific MAb prepared previously (MAb 864) was used to identify YF strain 17D vaccine type variants in the wild-type Asibi virus preparation. One variant, isolated by plaque purification from a 17D vaccine pool, possessed the wild-type epitope and was neurovirulent in infant mice whereas other variants, lacking the wild-type epitope but with vaccine-specific epitopes (identified by MAb 411), were avirulent in infant mice. Avirulent variants were able to infect mice and induce antibody. Virus-specific antigen was still detected in the brains of these mice 4 weeks after inoculation, suggesting that persistent infections were developing. These results to the potential risk of selection of wild-type variants in YF vaccine preparations. They also point to the potential risk of selection of wild-type variants in YF vaccine preparations and re-emphasize the need for modernization of techniques and more effective control measures to be taken during the production of YF vaccine.

Animals↗

PubMed1998

In vivo analysis of the stability and fitness of variants recovered from foot-and-mouth disease virus quasispecies.

We have analysed the ability to infect pigs of two foot-and-mouth disease virus (FMDV) variants isolated at low frequencies from virus populations (quasispecies) generated in pigs on infection with a parental virus, C-S8c1. A monoclonal antibody-resistant mutant (MARM21), and a variant isolated at early times post-infection (S-3T1), each exhibiting a unique amino acid substitution in VP1, were able to cause disease in pigs, both by direct inoculation or by contact transmission. The symptoms developed were similar to those produced by C-S8c1 or the related virus C-S15c1. The VP1 sequence of viral RNA directly recovered from lesions of infected animals confirmed the stability of the variant genotypes. Pigs infected with S-3T1 consistently showed an advance of 12 to 24 h in the emergence of fever and lesions when compared to animals infected with C-S8c1 or the remaining variants, an observation consistent with its early isolation. The ability of FMDV variants to compete in vivo with C-S8c1 was investigated in co-infection experiments. Analysis of the proportion of each of the competitors in lesions of co-infected pigs revealed that none of the variants was completely overgrown by the parent. However, co-infection with C-S8c1 and MARM21 resulted in lesions in which C-S8c1 was predominant, indicating a selective disadvantage of this variant in swine. In contrast, lesions from swine co-infected with C-S8c1 and S-3T1 contained similar proportions of the two viruses. These results document fitness variations in vivo among components of the mutant spectrum of FMDV quasispecies.

Animals↗

PubMed2000

Molecular variants of human papillomavirus types 16 and 18 preferentially associated with cervical neoplasia.

In order to determine geographically related intratypic variation in human papillomavirus (HPV) type 16 and 18 isolates that could be associated with lesion development, data were analysed from an ongoing cohort study of the natural course of infection of HPVs and cervical neoplasia. Testing for HPVs was carried out by PCR and molecular variants of these HPVs were characterized by sequence analysis of the long control region and by dot blot hybridization of the E6 and L1 genes. Tests for HPV were done in multiple first-year specimens from 1690 women enrolled in a cancer screening program from 1993 to 1997. Subjects were followed-up by cytology and cervicography for detection of cervical lesions. Seven variants of HPV-16 and four of HPV-18 were detected in one or more specimens from 65 subjects. The same variant was found in specimens taken on different visits from each case of persistent infection. Overall, non-European variants tended to persist more frequently [odds ratio (OR)=4.5; 95% confidence interval (CI), 1.6-12.4] than European (E) variants (OR=2.5; 95% CI, 1.3-4.9), relative to the risk of persistence for non-oncogenic HPVs. In addition, non-E variants were more strongly associated with risk of both prevalent (age- and race-adjusted OR=172.2; 95% CI, 47.1-630.1) and incident [relative risk (RR)=22.5; 95% CI, 6.0-83.9] high-grade lesions than E variants (prevalent lesions OR=46.3; 95% CI, 15.5-138.0 and incident lesons RR=6.1; 95% CI, 1.3-27.4), relative to the risk for HPV-negative women. Although consistent, the latter differences were not statistically significant. If confirmed in other populations, measurement of intratypic variation of HPV-16 and -18 has the potential to serve as an ancillary tool in cervical cancer screening.

Age Factors↗

PubMed1993

Macrophage chemiluminescence induced by interaction with transparent and opaque colonial variants of Mycobacterium intracellulare.

Macrophage (M phi) chemiluminescence (CL) induced by interaction with the two types of colonial variants of Mycobacterium intracellulare was studied. A smooth, opaque and dome-shaped (SmD) colonial variant triggered more intense M phi CL than did a smooth, transparent and flat colonial variant (SmT). M phi CL-inducing activity of the SmD variant was reduced by heating or by treatments with either Pronase P, some endoglycosidases or Tween 80, thereby indicating that the SmD variant possesses M phi CL-inducing substance(s) having peptide, sugar and/or lipid-like moieties. Treatment of the SmD variant organism with some endoglycosidases, such as cellulase, pectinase, dextranase or alpha-amylase decreased its M phi CL-inducing ability. On the other hand, M phi CL-inducing activity of the SmT variant was not affected by any of above treatments except that it was slightly increased by Pronase P treatment and reduced by alpha-amylase and dextranase.

Animals↗

PubMed2002

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

The obligately intracellular chlamydiae are bacterial pathogens that occupy intracellular vacuoles, termed inclusions, as they develop and multiply. Typical Chlamydia trachomatis isolates occupy inclusions that fuse with other C. trachomatis inclusions within cells infected with multiple elementary bodies (wild-type phenotype). The authors of this study have recently described C. trachomatis isolates that form multiply-lobed, non-fusogenic inclusions within single cells infected with multiple elementary bodies (variant phenotype). Inclusions formed by these isolates uniformly lacked the protein IncA on the inclusion membrane (IM). In the present work, the study of the C. trachomatis inclusion phenotype has been expanded to include 27 variant and 13 wild-type isolates. Twenty-four of the 27 variant isolates were IncA-negative, as detected by fluorescence microscopy and immunoblotting, but three variants localized IncA to the IM. The IncA-positive variants formed inclusions that fused, at a reduced rate, with those occupied by wild-type isolates and with inclusions formed by other IncA-positive variants. Nucleotide-sequence analysis of the incA sequences from the variant isolates identified a variety of distinct sequence polymorphisms relative to incA from wild-type strains. The authors also demonstrate that a second Inc protein, CT223p, is not found in the IM in selected C. trachomatis isolates. No change in the structure or the fusogenicity of the inclusions was associated with the presence or absence of CT223p.

Bacterial Proteins↗

PubMed2004

Distribution of human papillomavirus type 16 variants in human immunodeficiency virus type 1-positive and -negative women.

The prevalence of human papillomavirus type 16 E6 variant lineages was characterized in a cross-sectional study of 24 human immunodeficiency virus type 1 (HIV)-positive and 33 HIV-negative women in New Orleans. The European prototype was the predominant variant in the HIV-negative women (39.4 %), while in the HIV-positive women the European 350G variant was predominant (29.1 %). In exact logistic regression models, HIV-positive women were significantly more likely to harbour any variant with a nucleotide G-350 mutation compared with HIV-negative women [58.3 % vs 21.1 %; adjusted odds ratio (AOR)=6.28, 95 % confidence interval (CI)=1.19-46.54]. Models also revealed a trend towards increased prevalence of Asian-American lineage in HIV-positive women compared with HIV-negative women (25.0 % vs 6.0 %; AOR=6.35, 95 % CI=0.77-84.97). No association was observed between any variant and cytology or CD4 cell counts or HIV-1 viral loads. These observations reflect a difference in the distribution of HPV-16 variants among HIV-positive and -negative women, indicating that HIV-positive status may lead to increased prevalence of a subset of variants.

Adult↗

PubMed2005

Differential splicing of E6 within human papillomavirus type 18 variants and functional consequences.

Persistent infections of the uterine cervix with 'high-risk' human papillomavirus (HPV) are now recognized as necessary for the development of cervical cancer. Among them, HPV types 16 and 18 exhibit numerous variants associated with different risks for cervical cancer development. In this study, the questions of whether different HPV type 18 variants exhibit changes in early gene transcription and the molecular mechanisms underlying these differences were investigated. It was shown that, indeed, type 18 variants exhibited singular differences in E6 transcripts in vivo. Higher levels of the E6*I transcript were detected regularly in clones harbouring the African variant, as opposed to low levels of this transcript detected in clones containing the reference clone (Asian-Amerindian), where significantly higher levels of full-length E6 transcript were usually observed. As a direct consequence, higher levels of p53 protein were found in the presence of African E6, as opposed to the low levels of p53 observed with the Asian-Amerindian E6. These variations in consequence affected the levels of cellular proteins regulated by p53, such as Bax. Similar changes in the relative levels of E6 transcripts were observed when tumours containing type 18 E6 variants were analysed. The different ability of cells containing variant E6 genes to form tumours in nude mice was suggested by the fact that tumour volumes were considerably higher when cells expressed the Asian-Amerindian E6. Mutagenesis analysis of the reference clone showed that a C491A change reverts the phenotype. These results suggest that different splicing patterns of E6 within HPV type 18 variants may possibly have biological implications in viral tumorigenesis.

Animals↗

PubMed2002

Evidence for a fast, intrachromosomal conversion mechanism from mapping of nucleotide variants within a homogeneous alpha-satellite DNA array.

Assuming that patterns of sequence variants within highly homogeneous centromeric tandem repeat arrays can tell us which molecular turnover mechanisms are presently at work, we analyzed the alpha-satellite tandem repeat array DXZ1 of one human X chromosome. Here we present accurate snapshots from this dark matter of the genome. We demonstrate stable and representative cloning of the array in a P1 artificial chromosome (PAC) library, use samples of higher-order repeats subcloned from five unmapped PACs (120-160 kb) to identify common variants, and show that such variants are presently in a fixed transition state. To characterize patterns of variant spread throughout homogeneous array segments, we use a novel partial restriction and pulsed-field gel electrophoresis mapping approach. We find an older large-scale (35-50 kb) duplication event supporting the evolutionarily important unequal crossing-over hypothesis, but generally find independent variant occurrence and a paucity of potential de novo mutations within segments of highest homogeneity (99.1%-99.3%). Within such segments, a highly nonrandom variant clustering within adjacent higher-order repeats was found in the absence of haplotypic repeats. Such variant clusters are hardly explained by interchromosomal, fixation-driving mechanisms and likely reflect a fast, localized, intrachromosomal sequence conversion mechanism.

Animals↗

PubMed1991

Multiplicity of histone h3 variants in wheat, barley, rice, and maize.

Histone H3 proteins were purified to near homogeneity from etiolated seedlings of wheat (Triticum aestivum), barley (Hordeum vulgare), rice (Oryza sativa), maize (Zea mays), and alfalfa (Medicago sativa) to determine the number of histone H3 variants. Five distinct histone H3 variants were identified by gradient gel electrophoresis and reversed phase chromatography. These variants occur in various combinations of two to four forms in each plant species. One minor histone variant form (variant III, named H3.2 in alfalfa) appeared present and identical in all mono- and dicotyledonous plant species tested to date. All H3 proteins were acetylated to multiple levels and in every species the variant III form was acetylated most extensively. The level of histone H3 acetylation showed an inverse correlation with plant genome size. These observations support the idea that acetylated histones and especially variant III proteins are an element of transcriptionally active chromatin.

Journal Article↗

PubMed2005

Groupoid of orientational variants.

Daughter crystals in orientation relationship with a parent crystal are called variants. They can be created by a structural phase transition (Landau or reconstructive), by twinning or by precipitation. Internal and external classes of transformations defined from the point groups of the parent and daughter phases and from a transformation matrix allow the orientations of the distinct variants to be determined. These are algebraically identified with left cosets and their number is given by the Lagrange formula. A simple equation links the numbers of variants of the direct and inverse transitions. The equivalence classes on the transformations between variants are isomorphic to the double cosets (operators) and their number is given by the Burnside formula. The orientational variants and the operators constitute a groupoid whose composition table acts as a crystallographic signature of the transition. A general method that determines if two daughter variants can be inherited from more than one parent crystal is also described. A computer program has been written to calculate all these properties for any structural transition; some results are given for Burgers transitions and for martensitic transitions in steels. The complexity, irreversibility and entropy of fractal systems constituted by orientational variants generated by thermal cycling are briefly discussed.

Journal Article↗

PubMed2004

Retarded protein folding of deficient human alpha 1-antitrypsin D256V and L41P variants.

alpha(1)-Antitrypsin is the most abundant protease inhibitor in plasma and is the archetype of the serine protease inhibitor superfamily. Genetic variants of human alpha(1)-antitrypsin are associated with early-onset emphysema and liver cirrhosis. However, the detailed molecular mechanism for the pathogenicity of most variant alpha(1)-antitrypsin molecules is not known. Here we examined the structural basis of a dozen deficient alpha(1)-antitrypsin variants. Unlike most alpha(1)-antitrypsin variants, which were unstable, D256V and L41P variants exhibited extremely retarded protein folding as compared with the wild-type molecule. Once folded, however, the stability and inhibitory activity of these variant proteins were comparable to those of the wild-type molecule. Retarded protein folding may promote protein aggregation by allowing the accumulation of aggregation-prone folding intermediates. Repeated observations of retarded protein folding indicate that it is an important mechanism causing alpha(1)-antitrypsin deficiency by variant molecules, which have to fold into the metastable native form to be functional.

Animals↗

PubMed2000

The familial aggregation of the lesser variant in biological and nonbiological relatives of PDD probands: a family history study.

OBJECTIVE: To determine the risk of the lesser variant (or PDD-like traits) in the biological and nonbiological second- and third-degree relatives of PDD probands using a screening questionnaire and to investigate the extent to which the risk of the lesser variant differs according to various characteristics of the proband. METHOD: The sample consists of a series of 34 nuclear families with 2 affected PDD children (multiplex, MPX), 44 families with a single PDD child (simplex, SPX), and 14 families who adopted a PDD child. Data on characteristics of the lesser variant in 1362 biological and 337 nonbiological second- and third-degree relatives were collected from parents by telephone interview and from several maternal and paternal relatives by questionnaire. RESULTS: All components of the lesser variant were more common in biological relatives (BR) than nonbiological relatives (NBR), confirming the familial aggregation of the traits. Proband characteristics associated with an increased risk of the lesser variant in relatives were a higher level of functioning and coming from a MPX family. CONCLUSIONS: These findings on the familial aggregation of the lesser variant suggest that the genes for PDD also confer susceptibility to the lesser variant and that PDD may be a genetically heterogeneous disorder.

Adolescent↗

PubMed1988

Restriction endonuclease DNA analysis of antigenic variants of leptospires selected by monoclonal antibodies.

The genome of antigenic variant CV (CT3)-1 derived from Leptospira interrogans serovar canicola was compared by cleavage with restriction endonucleases with the parent and serovar bafani, to which the variant was serologically most closely related. No differences were observed between the parent and variant in DNA restriction endonuclease patterns using eight restriction endonucleases. Serovar bafani was different in the patterns from the parent and antigenic variant CV (CT3)-1. The two antigenic variants derived from serovar hebdomadis, HV (H16)-1 and HV (H19)-1 which belonged serologically to serovars jules and hebdomadis, respectively, were compared by restriction endonuclease DNA analysis with the parent and serovar jules. No differences were observed between the parent and variants in DNA restriction endonuclease patterns using the same enzymes. But some differences were observed in DNA restriction endonuclease patterns between HV (H16)-1 and serovar jules. Thus, the antigenic variant selected from the parent by the anti-parent monoclonal antibody and serologically different from the parent, being identified either as a new serovar or as a known one, was found to be similar to the parent by the restriction endonuclease DNA analysis.

Antibodies, Monoclonal↗

PubMed1993

Molecular basis of clinical and morphological heterogeneity in hereditary elliptocytosis (HE) with spectrin alpha I variants.

The impaired ability of spectrin dimers to self-associate into tetramers is one of the most frequent defects associated with hereditary elliptocytosis (HE) and its more serious form, hereditary pyropoikylocytosis (HPP). We previously described four proteic variants of the spectrin (Sp) alpha I tryptic domain associated with the Sp dimer self-association defect (Sp alpha I/78, Sp alpha I/74, Sp alpha I/65, Sp alpha I/46 variants). Following the characterization of proteic variants, genomic molecular defects were identified and most of the mutations appeared to lie either in or near the self-association site, i.e. in the alpha I tryptic domain or in the beta I tryptic domain. The clinical severity of these different mutations varies considerably and ranges from asymptomatic to severe haemolytic disease such as in heterozygous HPP patients and in some homozygous HE patients. Studies of 113 patients from 61 HE families showed a correlation among parameters and showed which factors modulate the clinical expression of the molecular defect. Our analysis indicated that the clinical expression was directly correlated with the severity of the spectrin dimer self-association defect as evaluated by the increase in the Sp dimer percentage found in the 4 degrees C extract. A critical threshold of 40-50% of unassembled Sp dimer was determined; above that, patients exhibited severe haemolysis requiring splenectomy. The percentage of Sp dimer depends, in turn, on two factors: (i) the nature of the variant in relation to the position of the mutation versus the tetramerization site; (ii) the relative amount of mutant spectrin present in the membrane (ranging from 15% to 80% in heterozygous patients). As for the severity of haemolysis, the ghost mechanical stability to shear stress, as measured by ektacyometer, was also found to depend on the Sp dimer self-association defect. In contrast, the decrease in erythrocyte deformability was not related to the amount of unassembled Sp dimer but appeared to be correlated with the amount of mutant spectrin whatever the variant. Concerning erythrocyte morphology and the number of elliptocytes, the Sp alpha I/65 variant appears to be the most 'elliptocytogenic' variant, indicating that erythrocyte shape abnormality is not linked to the Sp dimer self-association defect.

Electrophoresis, Polyacrylamide Gel↗

PubMed2005

High pressure liquid chromatography and electrospray ionization mass spectrometry are advantageously integrated into a two-levels approach to detection and identification of haemoglobin variants.

Detecting and correctly identifying haemoglobin (Hb) variants is typically achieved by a two-levels laboratory approach. We report our experience in dealing with 91 Hb variants, including a number of frequent and a few rare variants. Screening included akaline agarose gel electrophoresis (AGE), ion-exchange automated high-performance liquid chromatography (HPLC) and a test for deoxyhaemoglobin solubility. Identification was based on electrospray ionization-mass spectrometry (ESI-MS). Our results confirmed the advantages of HPLC over AGE for screening, because of the occurrence of some electrophoretically 'silent' variants. ESI-MS permitted the definitive identification of 90 of the 91 variants included in the study, in some cases (e.g. HbS) through the application of a simple protocol (direct injection of the sample), in other cases requiring the application of more demanding procedures (purification of the variant chain and peptide analysis after enzymatic or chemical cleavage). In an additional case (Hb J-Oxford), ESI-MS assay did not lead to definitive identification, but gave indications for designing the appropriate primers to focus DNA sequence analysis on the specific region of the gene. Deoxyhaemoglobin solubility test was positive only in the presence of HbS. We conclude that HPLC and ESI-MS are advantageously integrated into a two-level analytical system for the detection and confirmation of variant Hbs.

Chromatography, High Pressure Liquid↗