Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “hypervariable regions”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources
PubMed1996

Sequence divergence in a family of variant surface glycoprotein genes from trypanosomes: coding region hypervariability and downstream recombinogenic repeats.

The surface of the parasitic protozoan Trypanosoma brucei spp. is covered with a dense coat consisting of a single type of glycoprotein molecule, the variant surface glycoprotein (VSG). There may be as many as 1,000 genes for VSG within the genome of T. brucei, and the switch of expression from one to another is the phenomenon of antigenic variation. As an approach to understanding the evolution of VSG genes we have determined the genomic DNA sequences of the eight genes encoding the variant surface glycoprotein 117 (VSG) family. From these data we have observed a number of features concerning the relationships between these genes: (1) there is a region of high variability confined to the N-terminus of the coding sequence, and comparison of the sequences with the available X-ray diffraction crystal structures suggests that two of the most variable stretches within the N-terminal domain are present on surface-exposed loops, indicating a role for epitope selection in evolution of these genes; (2) the 29 nucleotides surrounding the splice acceptor site are absolutely conserved in all eight 117 VSG genes; (3) numerous insertion/deletion mutations are located within or immediately downstream of the C-terminal protein-coding sequences: (4) within 500 bp downstream of the insertion/deletion mutations are one or two copies of a repeat motif highly homologous to the recombinogenic 76-bp repeat sequences present upstream of many VSG basic copy genes and the expression-linked copy.

Amino Acid Sequence↗
PubMed1986

Antigenic domains of the streptococcal Pep M5 protein. Localization of epitopes crossreactive with type 6 M protein and identification of a hypervariable region of the M molecule.

Pep M5, the pepsin-derived N-terminal half of the group A streptococcal type 5 M protein exhibits immunologic crossreaction with type 6 M protein, localizing some of the M6-crossreactive epitope(s) within this segment of the M5 protein. Based on the amino acid sequence of the Pep M5 protein, two structurally distinct domains have been recognized within its coiled-coil structure. We have now found that peptides derived from both the structurally distinct domains of the Pep M5 protein contain antigenic epitopes. Furthermore, only the peptides from the C-terminal domain of the Pep M5 protein crossreacted with rabbit anti-M6 sera, whereas those from the N-terminal domain did not. Consistent with this, sequence analyses of the arginyl peptides of the Pep M6 protein, the pepsin-derived N-terminal half of the M6 protein, revealed extensive homology of some of these peptides with regions within the C-terminal domain of the Pep M5 molecule. While an arginyl peptide of the Pep M6 protein exhibits 84% homology with region 150-186 of the Pep M5 protein, the C-terminal hexadecapeptide of the Pep M6 protein is virtually identical with the corresponding region of the Pep M5 protein. These results are suggestive of conformational similarities in the region around the pepsin-susceptible site within the M5 and M6 proteins. In addition, one or more epitopes of the M5 protein that are crossreactive with the M6 protein may be placed close to the pepsin-susceptible site of the M5 protein. Previous studies have suggested the N-terminal half of the M proteins to be the variable part of the molecule among the different M protein serotypes. The present results suggest that the N-terminal quarter of the M protein may represent the hypervariable domain of the M molecule.

Amino Acid Sequence↗
PubMed1992

Linkage between rheumatoid arthritis susceptibility and the presence of HLA-DR4 and DR beta allelic third hypervariable region sequences in southern Chinese persons.

OBJECTIVE: To analyze HLA-DR and DQ associations with rheumatoid arthritis (RA) in patients from southern China. METHODS: In 66 patients and 45 controls, restriction fragment length polymorphism studies were performed using DRB, DQA, and DQB probes, and DRB allele-specific typing of polymerase chain reaction-amplified DRB DNA: RESULTS: The frequency of HLA-DR4 was significantly increased among RA patients (42.4% versus 17.8%). Increased frequencies of the DQA3 allele (77.8% versus 48.9%) and the DQB1*0302 allele (71.0% versus 46.3%), which are in linkage disequilibrium with DR4, were also found. Oligonucleotide typing showed that the amino acid sequence LLEQRRAA, spanning amino acid positions 67-74 of the DR beta molecule, was found in 19 of 49 patients and 5 of 32 controls. The main DR4 allelic subtypes found in the population were DRB1*0404 and DRB1*0405, both of which carried the sequence. There was no difference in subtype distribution between patients and controls. CONCLUSION: Chinese RA patients have an increased frequency of HLA-DR4 alleles which possess the same DRB third allelic hypervariable sequence shown to be associated with susceptibility in Caucasian RA patients.

Alleles↗
PubMed1999

Hypervariable region diversity of hepatitis C virus and humoral response: comparison between patients with or without cirrhosis.

To investigate the potential clinical utility of antibody response to HVR1 of HCV, the genomic and amino acid diversity of HVR1 was compared between two groups of four chronic HCV carriers with or without liver cirrhosis. Peptides corresponding to the deduced COOH- and NH2-terminal amino acid sequences of HVR1 were synthesised to assess the reactivity of patient sera to autologous and homologous HVR1 epitopes by enzyme-linked immunosorbent assay. HCV chronic carriers had significantly more frequent cross-reactivity with homologous C- than N-terminal HVR1 peptides. Twelve cirrhotic and eleven noncirrhotic patients had a similar frequency of cross-reactivity with either C- or N-terminal HVR1 peptides. However, noncirrhotic patients had a significantly higher level of C-terminal HVR1 antibody cross-reactivity than cirrhotic patients. In HCV chronic carriers, the magnitude of the immune response to but not the frequency of cross-reactivity with C-terminus HVR1 peptides differ between patients with and without liver cirrhosis.

Adult↗
PubMed1985

T helper cell recognition of idiotopes on lambda 2 light chains of M315 and T952: evidence for dependence on somatic mutations in the third hypervariable region.

Previous work has indicated that BALB/c T helper cells (Th) recognize an idiotope expressed on a 88-114/117 fragment of V lambda 2 of BALB/c myeloma protein 315. In the present study the antigenic structure of this idiotope was further analyzed. Conventional carrier-specific Th elicited by immunization of BALB/c mice with free lambda 2(315) did not cross-react with the free lambda 2 chain of the BALB/c myeloma protein T952 which differs from lambda 2(315) in five amino acid positions (38, 94, 95, 96, 99). Similarly, Th primed with free lambda 2T952 did not respond to a boost with free lambda 2(315). Thus, BALB/c lambda 2(315)-specific Th recognize an idiotope that depends on some or all of the residues at positions 94, 95, 96 and 99. Furthermore, free lambda 2T952 contains an idiotope immunogenic to Th that depends on some or all of residues 38, 94, 95, 96 and 99. Th recognition of the free lambda 2T952 idiotope was quenched upon H + L chain assembly because Th elicited by free lambda 2T952 did not respond to a boost with the complete T952 myeloma protein. In contrast to the lack of Th cell cross-reactivity, some of the antisera from BALB/c mice immunized with free lambda 2T952 cross-reacted with free lambda 2(315), free lambda lJ558 and free lambda 3CBPC49 but not with free kappa W3129 or polyclonal L chains. The H chain of T952 (alpha, kappa 2) myeloma protein was abnormally short (Mr = 48 000) and T952 existed as a halfmere probably due to this H chain deletion. Furthermore, H and L chains were disulfide bonded to each other.

Animals↗
PubMed1986

Synthetic peptides and beta-chain gene rearrangements reveal a diversified T cell repertoire for a lambda light chain third hypervariable region.

Twelve L3T4+ Ly-2.2- subclones, derived from 4 independent BALB/c T cell lines, responded to a combination of the I-Ed molecule and a synthetic peptide corresponding to residues 91-108 of the lambda light chain from BALB/c myeloma protein M315 (alpha, lambda 2). Peptide analogues in which the mutated residues Arg95 or Asn96 were exchanged with the corresponding germ-line-encoded Ser95 or Thr96 had an abolished or greatly reduced capacity to stimulate T cell clones. However, responses of subclones to an analogue where the mutated Phe94 was substituted with the germ-line-encoded Tyr94 revealed three specificity patterns: 5 clones reacted only with the lambda 2(315) peptide, 6 clones responded equally well to both peptides and a single clone reacted better with the Tyr94 analogue. Analysis of the T cell receptor beta-chain gene rearrangements disclosed 7 distinct rearrangements, identical rearrangements only being found for subclones originating from the same line. At least 3 different V beta genes were used. Subclones with identical or nearly identical peptide specificity, major histocompatibility complex-restriction and alloreactivity could differ in their V beta or J beta gene segment utilization.

Amino Acid Sequence↗
PubMed2001

Influence of the dynamics of the hypervariable region 1 of hepatitis C virus (HCV) on the histological severity of HCV recurrence after liver transplantation.

Recurrence of hepatitis C virus (HCV) infection after liver transplantation is almost universal and usually leads to chronic hepatitis with different degrees of severity. The pathogenic mechanisms underlying the variable outcome of HCV infection recurrence are not well defined, but recent data suggest that the dynamics of HCV quasispecies may be involved. HCV quasispecies evolution was traced by longitudinal single strand conformation polymorphism, direct sequencing, and cloning analyses of pre- and post-transplant HCV-1b isolates from patients with histologically severe (seven cases) or mild or moderate (nine cases) HCV infection recurrence. Differences between the two groups of patients that concerned the level of viremia or the degree of HCV quasispecies complexity and diversity were not observed at any of the three time points analyzed. However, emergence of nucleotide and amino acid changes during the 12 months follow-up was significantly more frequent in patients with mild or moderate than in those with severe HCV infection recurrence. The ratio of non-synonymous to synonymous nucleotide substitutions 12 months after transplantation was also greater in the former, suggesting that the HVR1 of HCV is under stronger selective pressure in these subjects. These findings suggest that the degree of amino acid diversification in the HVR1 of HCV, which probably reflects the strength of immune pressure on HCV, is inversely related to the histological severity of HCV infection recurrence.

Amino Acid Sequence↗
PubMed1996

Conformation of the hypervariable region L3 without the key proline residue.

The refined structure of the Fab fragment of the monoclonal antibody CRIS-I (IgG2a kappa) against the leukocyte differentiation antigen CD5, determined at 1.9 A resolution with an agreement R-factor of 18.3%, reveals a variant of the canonical conformations proposed for the light chain complementarity determining region L3 (CDR-L3). This is the first Fab structure available with a kappa light chain in which the CDR-L3 lacks the key proline residue in either position 94 or 95. The conformation found could be significant for about 10% of the murine IgG molecules with kappa light chains without proline in their CDR-L3 sequences.

Animals↗
PubMed1998

Murine antibodies against E2 and hypervariable region 1 cross-reactively capture hepatitis C virus.

The absence of readily available animal and cell culture models for hepatitis C virus (HCV) replication has bottlenecked research on protective immunity to HCV infection. Antibodies reactive with HCV virions in vitro are assumed to be candidates for neutralizing or inhibitory antibodies against HCV. To find potentially neutralizing or inhibitory antibody candidates, anti-C, anti-E1, anti-E2, and anti-HVR1 antisera acquired from mice immunized with corresponding recombinant proteins or synthetic peptides were used to capture HCV viral particles in vitro based on antibody-virus interaction assays. Both anti-E2 and anti-HVR1 antibodies effectively captured HCV in vitro. Furthermore, it was found that anti-E2 and anti-HVR1 antibodies could immunoprecipitate an isolate of HCV unrelated to the original antigenic HCV isolate. ELISA confirmed that anti-HVR1 antibodies cross-reactively bind to these unrelated HVR1 peptides. These findings suggest that anti-E2 and anti-HVR1 antibodies induced in mice have the ability to bind with HCV particles in an isolate cross-reactive manner and highlight the possible application of combining several sequences of HVR1 to generate broadly reactive anti-HVR1 antibodies.

Amino Acid Sequence↗
PubMed1990

Variation in the size of human apolipoprotein(a) is due to a hypervariable region in the gene.

We have investigated whether the size heterogeneity of the human apolipoprotein(a) [apo(a)] is due to differences in the number of plasminogen kringle 4-like repeat units present in the different alleles. Using the Southern blot hybridization technique and a DNA probe for the kringle 4 domain of plasminogen, we have observed that in 31 different individuals a 5.8-kb PvuII restriction fragment band varies widely in intensity relative to other bands. A strong correlation (r = 0.76, P less than 0.001) was found between apo(a) protein size and the variation in intensity of the detected restriction fragment band. We confirmed this correlation in a large family where the parents are heterozygous for the apo(a) protein size isoforms. The specificity of the 5.8-kb band was established by using an apo(a)-specific oligonucleotide. These correlations strongly suggest that the observed size heterogeneity in apo(a) protein is due to different numbers of copies of the kringle 4 sequence in the apo(a) glycoprotein gene.

Alleles↗
PubMed1987

A hypervariable region at the D19S11 locus.

The polymorphic locus D19S11 consists of four closely linked RFLPs: alpha, beta, delta, and gamma on chromosome 19p13.2----19cen, revealed by subclones p13-1-82 and p13-2-21 from cosmid 1-13. Here, we report that p13-1-25, an additional subclone of c1-13, reveals three insertion/deletion RFLPs, alpha, epsilon, and phi, at the D19S11 locus. In situ hybridization of p13-1-25 to metaphase chromosomes from a carrier of a 19/X translocation with a breakpoint near the centromere confirms localization of D19S11 to 19p. Studies with hydatidiform moles have generated assignments of specific restriction fragments to these three loci, and genotypic studies in three-generation families have indicated that they are closely linked. Loci alpha (also detected by p13-1-82) and phi each have but two common alleles, whereas epsilon has at least 33 alleles, including a null allele. Fifty unrelated individuals tested displayed unique fragment patterns on Taq I blots probed with p13-1-25. Applications of this probe include monitoring loss of chromosome 19 during tumorigenesis, monitoring engraftment of donor bone marrow after transplantation, testing for paternity, and mapping disease genes on chromosome 19.

Chromosome Mapping↗
PubMed1994

Evaluation of mixed chimerism by two-step polymerase chain reaction amplification of hypervariable region MCT118 after allogeneic bone marrow transplantation.

We assessed the origin of peripheral blood cells and bone marrow cells of 92 samples obtained from 19 patients after allo BMT by two-step polymerase chain reaction (PCR) amplification of MCT118, one of the variable number of tandem repeat regions (VNTR) which has a different length in 19 of 32 sibling pairs examined, that can detect the DNA pattern of a minor cell population of only 1% without using radioisotopes. Mixed chimerism (MC) was detected in the hematopoietic cells of four patients. Two patients who showed progressive MC developed relapse of leukemia 3 months and 4 months after the detection of MC, and two patients died with bone marrow hypoplasia 61 days and 7 months after BMT. These data suggest the clinical importance of analyzing the correlation of MC and clinical complications after BMT by this method, which can be used to monitor MC in about two thirds of allo BMT patients with an adequate sensitivity.

Base Sequence↗
PubMed1994

[Hypervariable regions (HVR) as genetic markers in tumor diagnosis. Methodological principles and their use in pathologic diagnosis].

Variable number tandem repeats (VNTR) are highly polymorphic DNA sequences which can be used as genetic markers in different fields of medicine. In this report, we describe the methodology of VNTR in diagnostic molecular pathology, using a rapid, DNA-based approach involving polymerase chain reaction (PCR) amplification and electrophoresis of highly polymorphic DNA satellite sequences. As concrete examples of the application of this approach, we present two case reports: 1. A B-cell lymphoma of the porta hepatis developed in a 54-year-old man 4.5 months after orthotopic liver transplantation for liver failure due to chronic hepatitis C infection. Using DNA polymorphisms as genetic markers, we showed that the tumor was of donor origin. This finding may be important for the patient's subsequent management. 2. An immature teratoma of the left ovary was found during delivery by cesarean section in a 27-year-old woman. The female newborn survived for 9 weeks and then died from central dysregulation because of an intracranial immature teratoma. Because the synchronous tumors were of similar histology, clonal origin in maternal tissues and metastatic spread were initially suspected. Analysis of highly polymorphic DNA markers clearly indicated that the teratoma carried by the child was of independent genetic origin from the mother's tumor.

Brain↗
PubMed1992

Entamoeba histolytica extrachromosomal circular ribosomal DNA: analysis of clonal variation in a hypervariable region.

The ribosomal RNA genes of the protozoan parasite Entamoeba histolytica are highly repeated and display restriction fragment length polymorphism. Using a set of four DNA probes spanning the coding region and part of the flanking region of the E. histolytica ribosomal RNA genes, an analysis of the DNA bands generated by EcoRI digestion of Entamoeba DNA is presented. This analysis included five strains of E. histolytica, four strains of E. moshkovskii, and one strain each of E. invadens and E. terrapinae. No common bands were observed between E. histolytica and the other Entamoeba. Within E. histolytica, two bands were conserved in all strains while the others were polymorphic. Detailed analysis of DNA from independently isolated clones of the strain HM-1:IMSS of E. histolytica showed two bands to be highly polymorphic. Of these, the 4.4-kb band of clone 6 was further analyzed. Polymorphism in this band could even be demonstrated in cells of the same clone. Restriction enzyme analysis of this DNA band from two clones of HM-1:IMSS showed that the polymorphism may be due to variable numbers of DraI repeat units present in this DNA stretch.

Animals↗
PubMed1996

Vaccination with peptides from MHC class II beta chain hypervariable region causes allele-specific suppression of EAE.

In our earlier studies we showed that successful immunotherapy of EAE in SJL/J mice can be achieved either by the use of antibodies to MHC class II antigens or by vaccination with synthetic peptide analogs of the beta chain of MHC class II molecules. We proposed that inhibition of EAE following vaccination with synthetic peptides derived from the beta chain of mouse I-A, was in part due to the generation of auto-anti-MHC class II antibodies that interfered with T cell sensitization. In our present study we show that suppression of EAE following vaccination results in poor sensitization of MBP reactive T cells, and that the lack of immune response is allele-specific. In F1(SJL(I-AS) x Balb/cI-Ad) mice, in which susceptibility to EAE is linked closely to the I-AS allele, vaccination with peptides from beta chain of I-AS results in inhibition of proliferative response to MBP and prevents the development of EAE. Vaccination with peptide from the beta chain of I-Ad did not affect either the development of immune response to MBP or the induction of EAE, indicating allele-specific suppression. Since global immunosuppression is not induced by vaccination with I-A peptides, we propose that this strategy can be extended to human autoimmune diseases wherein a clear association between certain MHC class II alleles and autoimmune disease is evident.

Alleles↗