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PubMed1984

Structure and polymorphism of the HLA class II SB light chain genes.

The HLA Class II region contains at least three groups of loci, DR, DC and SB, which play an important role in the immune response. The antigens encoded at these loci are heterodimers composed of an alpha and a beta chain. The sequence of a complete Class II beta cDNA clone whose sequence agrees closely with the limited N-terminal protein sequence available for the SB beta chain is reported. In addition the structure and coding sequence of genomic SB beta clones of two different SB haplotypes has been obtained and allows definition of some polymorphic regions. The SB beta gene appears to undergo alternate splicing at its 3' end, resulting in expression of two different intracytoplasmic regions. Partial sequencing of a second non-allelic SB beta-like gene, SX beta, indicates that it is a pseudogene.

Amino Acid Sequence↗

PubMed1993

Structure and evolution of the promoter regions of the DQA genes.

HLA-DQ antigens are unique among the class II antigens in that their alpha chains are highly polymorphic. In the present study, we characterized the general structure of the promoter regions of the DQA genes derived from different DR haplotypes and defined their nucleotide sequence polymorphisms. The promoter of each DQA1 allele contains three sequence motifs which are not present in non-DQA related class II genes: one identical to a tumor necrosis factor (TNF alpha) response element, one similar to an NF kappa B binding element, and one similar to a W motif. All DQA alleles lack TATA and CCAAT boxes in the proximal promoter region but carry other sequence elements characteristic of MHC class II genes, including S, X, X2, and Y boxes, and a pyrimidine-rich tract upstream of the X box. Nucleotide sequence polymorphisms among the various DQA1 alleles were noted within the promoter region, with some of the differences mapping within, or close to, regulatory elements that are important for the expression of MHC class II genes. All DQA1 alleles carry an unrearranged, full length, Alu-Sx related repeat immediately upstream of the proximal promoter region. This repeat was not present in the DQA2 (DXA) genes analyzed, confirming that DQ locus duplication probably occurred before integration of the Alu repeat into the primordial DQA1 locus, some 31-43 million years (myr) ago. The DQA2 promoter region is highly conserved between DR4 and DR3 haplotypes, with the degree of conservation exceeding that expected from the neutral mutation rate.

Alleles↗

PubMed1998

High-resolution mapping of sperm function defects in the t complex fourth inversion.

Structural variants of the mouse Chr 17-specific t complex, known as t haplotypes, express factors that alter the ability of sperm to carry out their roles in the normal fertilization process. In previous studies of males carrying heterospecific combinations of the t complex, we discovered a unique M. spretus/t haplotype phenotype of male sterility. In additional studies with mice carrying a series of M. spretus-M. m. domesticus recombinant Chr 17 homologs and a complete t haplotype (S-+/t), we monitored physiological aspects of sperm function to map a locus (Hst6) responsible for expression of the t-specific "curlicue" sperm flagellar curvature phenotype to 1 cM within the fourth inversion of the t complex. In the present report, we quantitatively analyze the in vitro capability of sperm from mice with similar S-+/t Chr 17 genotypes to fertilize zona pellucida-free mouse eggs. The results identify a locus, Stop1, mapping distal to Pim1, with acute effects on the ability of sperm to penetrate the oolemma. The data suggest that Stop1 is a complex locus consisting of at least two genetic elements, a proximal one overlapping the Hst6 locus, and another, distal to the Hst6 locus. Further quantitative analyses of the "curlicue" phenotype produced by sperm derived from these same animals indicate that expression of this chronic flagellar curvature phenotype also derives from at least two elements, both mapping within the Hst6 locus. Thus, these studies provide higher resolution mapping of the molecular basis of t haplotype-specific sperm dysfunction emanating from In(17)4.

Animals↗

PubMed2003

Proteus mirabilis and rheumatoid arthritis: no association with the disease.

Proteus mirabilis(PM) is implicated in different studies in the pathogenesis of rheumatoid arthritis (RA) because of the structural homogeneity of its haemolysin B precursor with EQRRAA sequences in DRB 1 haplotype. The aim of the study was to compare the levels of antibodies specific to PM in the sera of patients with RA and healthy controls in our population. Serum samples from 78 consecutive RA patients and 75 healthy controls were analysed for the presence of IgG isotype and total immunoglobulins (IgG+IgA+IgM) against PM using enzyme-linked immunosorbent assay (ELISA) with two kinds of antigen preparation, whole bacteria and SDS-lysed bacterial extract. There was no significant increase in the concentrations of anti- Proteus antibodies (APA) in patients with RA compared to healthy controls in our population, when SDS-lysed bacterial extract or whole bacteria were used as antigen. The APA levels did not correlate with serum CRP levels. Infection with P. mirabilis is found to have no pathological or aggravating role in RA.

Adult↗

PubMed2003

Proteus mirabilis and rheumatoid arthritis: no association with the disease.

Proteus mirabilis (PM) is implicated in different studies in the pathogenesis of rheumatoid arthritis (RA) because of the structural homogeneity of its haemolysin B precursor with EQRRAA sequences in DRB 1 haplotype. The aim of the study was to compare the levels of antibodies specific to PM in the sera of patients with RA and healthy controls in our population. Serum samples from 78 consecutive RA patients and 75 healthy controls were analysed for the presence of IgG isotype and total immunoglobulins (IgG + IgA + IgM) against PM using enzyme-linked immunosorbent assay (ELISA) with two kinds of antigen preparations, whole bacteria and SDS-lysed bacterial extract. There was no significant increase in the concentrations of anti- Proteus antibodies (APA) in patients with RA compared to healthy controls in our population, when SDS-lysed bacterial extract or whole bacteria were used as antigen. The APA levels did not correlate with serum CRP levels. We conclude that P. mirabilis has no pathological or aggravating role in RA.

Adult↗

PubMed1997

Gene organization of human NOTCH4 and (CTG)n polymorphism in this human counterpart gene of mouse proto-oncogene Int3.

The cDNA and genomic clones for the human counterpart of the mouse mammary tumor gene Int3 were isolated and sequenced. We designated this human major histocompatibility complex (MHC) class III gene as NOTCH4, since very recently, by sequencing cDNA clones, the complete form of the mouse proto-oncogene Int3 has been clarified and named Notch4. The present human NOTCH4 sequence is the first example of the genomic sequence for the extracellular portion of the mammalian Notch4, and by comparing it with the mouse Notch4 cDNA sequence, the exon/intron organization was clarified. The comparison of the predicted amino acid sequence of human NOTCH4 with those of other Notch homologues of a wide range of species revealed four subfamilies for mammalian Notch. In the protein coding region of human NOTCH4, we found (CTG)n repeats showing a variable number tandem repeat (VNTR) polymorphism for different human leukocyte antigen (HLA) haplotypes. Ten genes mapped on 6p21.3, including NOTCH4, were found to have counterparts structurally and functionally similar to those mostly mapped on 9q33-q34, indicating segmental chromosome duplication during the course of evolution. Similarity of genes on chromosomes 1, 6, 9 and 19 was also discussed.

Amino Acid Sequence↗

PubMed1985

Predicted protein sequence of the murine I-E-beta S-polypeptide chain from cDNA and genomic clones.

Ia antigens are polymorphic cell-surface glycoprotein complexes, encoded within the I region of the mouse major histocompatibility complex, that control the ability of the organism to mount effective antigen-specific immune responses. We have isolated and determined the nucleotide sequences of cDNA and genomic clones for the I-E beta s gene and we present the predicted protein sequence for most of the E beta s polypeptide chain. The E beta s polypeptide shows 95% protein homology to the other cloned E beta alleles. Comparison of the protein sequences of five E beta alleles from haplotypes that differ in responder phenotype to pigeon cytochrome c suggests that the structure of one of the E beta hypervariable regions may determine responsiveness to this antigen.

Alleles↗

PubMed2003

RHD allele distribution in Africans of Mali.

BACKGROUND: Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. RESULTS: We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHDPsi for 7% and Ccdes for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHDPsi. Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated. CONCLUSION: Besides standard RHD and the RHD deletion, DAU-0, RHDPsi and Ccdes are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies.

Alleles↗

PubMed1992

Role of hapten-anchoring peptides in defining hapten-epitopes for MHC-restricted cytotoxic T cells. Cross-reactive TNP-determinants on different peptides.

Synthetic hapten-peptide conjugates selectively modify cell-bound MHC class I molecules in a haplotype-specific way. We investigated the contribution of the carrier peptides to the structural specificity of T cell-antigenic TNP epitopes, using different H-2Kb-binding TNP-peptides and a collection of TNP/Kb-specific CTL clones. Adjustment of peptide sequences to the proposed Kb-specific "motif" (octamers with F or Y and L in positions 5 and 8, respectively) enhanced Kb-binding and antigenicity by many orders of magnitude. Moreover, several clones reacted to peptides, containing the "motif" and TNP-lysine in position 4 but were otherwise unrelated by sequence. TNP in other positions was not recognized by these cells, but other CTL reacted to TNP in position 7. This points to the positioning of hapten determinants within the MHC binding groove as a major role of the anchoring peptide. However, determination of the limiting amounts of TNP peptides that elicit antigenicity or inhibit other Kb-restricted CTL reactions revealed that TCR also recognize variations in the sequences of carrier peptides. This contribution is low for TNP in position 4 but high in position 7, indicating lysine in position 4 as a particularly dominant and cross-reactive hapten-anchoring site in Kb-associated peptides. This implies that cell modification with lysine-reactive TNP reagents results in immunodominant, highly repetitive TNP epitopes, which may explain the strong antigenicity and the allergenic properties of TNP, as well as the restricted TCR repertoire directed against this hapten. Our data further recommend hapten peptides for general studies of TCR-Ag interactions because in contrast to pure protein Ag, hapten epitopes tolerate substantial structural variations in the MHC-anchoring peptide, and can be located by hapten-specific antibodies.

Amino Acid Sequence↗

PubMed1994

Anthropological approach to the heterogeneity of beta-thalassemia mutations in northern Africa.

Results of an epidemiological survey for beta-thalassemic defects involving 239 chromosomes in Algeria are analyzed in relation to the geographic and historical background of the country and are compared with published series for the Tunisian population. Four common mutations account for 81% of the chromosomes, but 13 other defects have been found, illustrating the highly heterogeneous nature of the disease in the northern African countries of the Maghreb. The high frequency of homozygous cases reflects the endogamous social structure of these populations. Distribution of the mutations and linkage to specific RFLP haplotypes provide information concerning their origin and date of introduction in good correlation with the anthropological history of Algeria.

Algeria↗

PubMed1993

[Genetic and phenotypic aspects of the interrelationship between cellular and humoral immune response to sheep erythrocytes in mice].

The presence of the two types of immune reactivity has been shown earlier: 1st--with prevalence of delayed type hypersensitivity reaction over antibody response (in mice of C57Bl/6 strain), 2nd--with prevalence of antibody responses (in mice of CBA strain). These differences first of all have been displayed in case of using by suboptimal doses of antigen. In the present study the character of local and common immune response in mice of BALB/c, DBA/2, CC57BR, C3H strains and (CBA x C57Bl/6)F1 hybrid on different sheep erythrocyte doses has been investigated. It has been revealed, that DBA/2, BALB/c and CC57BR mice react according to the first type and mice of C3H strain--according to the second. It has been concluded, that the relationship between cellular and humoral immune response depends on the structure of H-2 complex and in F1 hybrid mice any of parents' haplotypes can predominate, depending on phenotypical factors.

Animals↗

PubMed1981

Polymorphism of germ-line immunoglobulin VH genes correlates with allotype and idiotype markers.

The polymorphic nature of the immunoglobulin VH genes was investigated by Southern blot analysis of liver DNA of sixteen different mouse strains and hybridization with VH probes. Differences in restriction enzyme pattern (REP) were observed and six different patterns of restriction fragments were found for the sixteen strains analyzed. No equivalent polymorphism was observed in another multigene family, the actins. The six patterns correlate with immunoglobin constant region allotypes (Igh-1). Experiments with Igh-1-congenic strains suggest that the VH REP is linked to immunoglobulin constant region haplotype. Mouse strains which share inherited idiotypes also share identical VH restriction pattern. This provides a structural basis for the genetic linkage between idiotypes and allotypes. It also indicates that different strains carry different VH gene repertoires, which may be the basis for the expression of different inherited idiotypes in various strains. We propose that a VH group in a set of linked genes that are coinherited as a cluster with the constant region genes and that VH and Ch can be regarded as an extended haplotype.

Animals↗

PubMed2003

Phylogenetic status and matrilineal structure of the biting midge, Culicoides imicola, in Portugal, Rhodes and Israel.

The biting midge Culicoides imicola Kieffer (Diptera: Ceratopogonidae) is the most important Old World vector of African horse sickness (AHS) and bluetongue (BT). Recent increases of BT incidence in the Mediterranean basin are attributed to its increased abundance and distribution. The phylogenetic status and genetic structure of C. imicola in this region are unknown, despite the importance of these aspects for BT epidemiology in the North American BT vector. In this study, analyses of partial mitochondrial cytochrome oxidase subunit I gene (COI) sequences were used to infer phylogenetic relationships among 50 C. imicola from Portugal, Rhodes, Israel, and South Africa and four other species of the Imicola Complex from southern Africa, and to estimate levels of matrilineal subdivision in C. imicola between Portugal and Israel. Eleven haplotypes were detected in C. imicola, and these formed one well-supported clade in maximum likelihood and Bayesian trees implying that the C. imicola samples comprise one phylogenetic species. Molecular variance was distributed mainly between Portugal and Israel, with no haplotypes shared between these countries, suggesting that female-mediated gene flow at this scale has been either limited or non-existent. Our results provide phylogenetic evidence that C. imicola in the study areas are potentially competent AHS and BT vectors. The geographical structure of the C. imicola COI haplotypes was concordant with that of BT virus serotypes in recent BT outbreaks in the Mediterranean basin, suggesting that population subdivision in its vector can impose spatial constraints on BT virus transmission.

African Horse Sickness↗

PubMed2004

Chloroplast DNA variation in the Quercus affinis-Q. laurina complex in Mexico: geographical structure and associations with nuclear and morphological variation.

The geographical distribution of chloroplast DNA (cpDNA) variation in 39 populations of two hybridizing Mexican red oaks, Quercus affinis and Q. laurina, was investigated using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Six haplotypes were identified. Of these, two (H1 and H4), separated by four mutations, had high frequencies (58 and 23% of the individuals, respectively) and were present across the whole geographical range of both species, often co occurring in the same populations. The other four haplotypes were rare, geographically restricted, and are probably derived from the two frequent haplotypes. Latitudinal or other clinal patterns in diversity levels or haplotype composition of populations were not apparent. The pattern of haplotype distribution was characterized by some mosaicism, with contrasting populations often situated in proximity. Average within-population diversity (hS=0.299) and population differentiation (GST=0.499) were, respectively, higher and lower than values reported in previous studies of oak species. There was evidence for phylogeographical structure, as indicated by NST (0.566) being significantly higher than GST. Haplotypic variation was largely species-independent, although some very weak associations were detected between haplotypes H1 and H4 and morphological and nuclear molecular variation correspondingly characterizing Q. affinis and Q. laurina. These oaks probably did not experience a marked restriction to one or a few particular subregions of their present range during the last glacial cycle. It is more likely that substantial populations persisted throughout several episodes of climatic change, but experienced recurrent latitudinal and altitudinal migrations which may have caused the widespread distribution of haplotypes H1 and H4 and frequent intermixing of populations.

DNA, Chloroplast↗

PubMedDate not supplied

SGS--Spatial Genetic Software: a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations.

We have developed a program called Spatial Genetic Software (SGS), which provides a user-friendly Windows tool to analyze both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, or biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers. Data based on any of these markers can be analyzed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits. The program implements various parameters to analyze spatial genetic and phenotypic structure: Moran's index, Geary's index, number of alleles in common, and approaches using genetic distances and F(ST) values. The statistical significance of all measures is verified by the use of a permutation test. The results are assessed by graphics that can be integrated, via the clipboard, to other Windows programs. The details of the computations are given in a table and can be stored as ASCII files.

Demography↗

PubMed2006

Molecular population genetics of the malaria vector Anopheles darlingi in Central and South America.

To analyze the genetic relatedness and phylogeographic structure of Anopheles darlingi from 19 localities throughout Central and South America, we used a minimum spanning network, diversity measures, differentiation, neutrality tests, and mismatch distribution with mitochondrial cytochrome oxidase subunit I (COI) sequences. All the Central American haplotypes were separated by seven mutational steps from the South American haplotypes and the FST distance-based neighbor-joining tree showed a primary division between Central and South America, evidence for a putative gene pool division. More ancestral and diverse haplotypes were found in Amazonian and southern Brazil populations, suggesting that Central American populations may have originated in South America. The patterns of the mtDNA haplotype diversity and five of six tests for equilibrium implicate demographic expansion in the South American populations as the historical structure, but mismatch distribution depicts populations at mutation drift equilibrium (MDE). In South America, the departure from equilibrium was consistent with an expansion that occurred during the Pleistocene.

Animals↗

PubMed1996

N-linked glycans in the CD4-binding domain of human immunodeficiency virus type 1 envelope glycoprotein gp160 are essential for the in vivo priming of T cells recognizing an epitope located in their vicinity.

Deglycosylation of viral glycoproteins has been suggested to influence the number of available T cell determinants and to increase T cell recognition of antigens. In this study, we have investigated whether T cell responses to the HIV-1 envelope glycoprotein gp160 were influenced by deletion of three N-glycans of the protein. Wild type (wt) and a mutated form of gp160 (gp160A123) lacking the three N-glycans in the C-terminal CD4-binding region efficiently induced antigen-specific T cell responses in mice of the H-2b, H-2d, and H-2k haplotypes. Further, T cells primed by either wt gp160 or gp160A123 were stimulated in vitro to a similar extent by the homologous and heterologous protein, indicating that deletion of the glycans did not affect the overall immunogenicity and antigenicity of gp160A123. Wild-type gp160 and gp160A123 induced comparable T cell responses to those of epitopes which with respect to the secondary structure of gp160 were distant from the deleted glycans. However, in mice of the H-2b haplotype, wt gp160 primed T cells which responded in vitro to a peptide containing one of the deleted N-glycosylation sites (Asn448), whereas T cells induced by gp160A123 were unable to recognize this peptide. Thus, deletion of the glycans abrogated the in vivo priming of T cells recognizing an epitope in close proximity to the deletion sites. Furthermore, enzymatically deglycosylated gp160 failed to induce a T cell response to this epitope. These results indicate that the in vivo generation of certain T cell determinants from glycoproteins is dependent on the glycosylation of the protein.

Amino Acid Sequence↗

PubMed2026

Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl.

Sex-linked traits are widespread, but their genetic architecture has been challenging to characterize, due in part to the repetitive and structurally complex nature of sex chromosomes. In swordtails and platyfish of the genus Xiphophorus, diverse melanic pigmentation patterns are thought to be controlled by a region on the sex chromosomes classically referred to as the "macromelanophore determining locus". Despite nearly a century of study, the identity of the causal gene remains controversial, partially due to previous inability to fully sequence the sex chromosomes. Here, we characterize and investigate two melanin-based pigmentation phenotypes in the species X. nezahualcoyotl: "spotted side" and "marmoratus". We generate a gapless near-telomere-to-telomere X. nezahualcoyotl assembly and perform GWAS to identify regions associated with pigmentation pattern variation and sex-determination. We find both patterns map near the sex-determining region and to a narrow interval near the oncogene xmrk. By generating additional long-read assemblies of sex chromosomes derived from individuals with distinct phenotypes, we find haplotypes containing xmrk can be both X- and Y-linked, and vary dramatically in gene content, structure, and accumulation of repetitive elements including a newly described composite satellite. This variability may impact the region's stability and affect recombination between haplotypes associated with each pattern. Our results shed light on a longstanding debate surrounding the genetic architecture of sex-linked phenotypes. More generally, we showcase how long-read sequencing can reveal phenotypic variation linked to complex and dynamic genomic regions, which may contribute to the evolution of diverse sex-linked traits.

Journal Article↗