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PubMed2003

Characterization of eight Y-STR loci and haplotypes in a Chinese Han population.

In this study we analyzed the eight Y-STR loci, DYS443, DYS444, DYS448, DYS453, DYS455, DYS456, DYS457 (DYS437) and DYS458, investigated haplotype distributions of these Y-STR loci in a Chinese Han population, and sequenced alleles of the eight loci for clarifying the structure. Extracted DNA was amplified by PCR and the PCR products were analyzed by non-denaturing horizontal polyacrylamide gel electrophoresis with a discontinuous buffer system. Alleles were sequenced on an ABI 3700 using a Dye Terminator Cycle sequencing kit. DYS443, DYS453, DYS455 and DYS456 were found to be simple repeat systems, while DYS444, DYS448, DYS457 (DYS437) and DYS458 were complex repeat systems. The gene diversities of DYS443, DYS444, DYS448, DYS453, DYS455, DYS456, DYS457 (DYS437) and DYS458 were 0.7742, 0.7671, 0.7453, 0.3545, 0.0549, 0.6988, 0.6148 and 0.8213, respectively. The haplotype diversity for 8 Y-STR loci was 0.9996, and the discrimination capacity was 0.9815. The results indicate that these eight loci are useful Y-linked markers for forensic applications.

Alleles↗

PubMed2000

Mannose binding lectin (MBL) genotype distributions with relation to serum levels in UK Caucasoids.

Mannose binding lectin (MBL) gene and promoter-region polymorphisms contribute to a reduction in the levels of circulating MBL in a number of ways. Promoter polymorphisms affect the levels of MBL produced, whilst structurally encoding mutations cause non-functional protein to be assembled and subsequently degraded. MBL is important as a protein of the innate immune system in both the clearance of potential pathogens and the activation of the complement cascade. Using variations of SSP-PCR amplifications and SSO probing techniques, we have produced MBL-polymorphism haplotype and genotype profiles of a series of high-level MBL-producing, low-level MBL-producing and random individuals taken from a population of 800 UK Caucasoid controls. Structurally encoding mutant alleles were more frequent within the low-level producing cohort when compared to both high-level producers and the randomly selected sample. However, not all low-level producers could be accounted for by the possession of low-level encoding haplotypes. This may be due to the presence of additional, undetected polymorphisms governing MBL production, or another external factor that may influence the transcriptional regulation of the gene.

Alleles↗

PubMed1999

[Mitochondrial DNA genetic polymorphism of Drosophila immigrans in China].

This article uses RFLP to analyze the mitochondrial DNA(mtDNA) variation in geographic populations of Drosophila immigrans from 6 regions of mainland of China. With the use of fourteen restriction endonucleases, we only discoveried a total of 11 mtDNA haplotypes among 46 isofemale lines. The mean value of I is 0.833, the mean value of J is 0.797, and the estimated Gst value is only 16.8%. We recognized that the genetic structures among the geographic populations of D. immigrans are highly uniform, and the genetic differentiation rate is low. The UPGMA analysis of nucleotide diversity of the 6 populations shows specific characteristics of mtDNA variation in population of Huayang, Qinling Mountains Regions. From the haplotypes special included in each population, the event that the population spread into the high altitute localities of Yunnan perhaps happened more recently. Referring other references, we inferred the population of D. immigrans distributed in mainland of China is more original than that in Chinese Taiwan and Japan.

Animals↗

PubMed2000

Deficiencies of human complement component C4A and C4B and heterozygosity in length variants of RP-C4-CYP21-TNX (RCCX) modules in caucasians. The load of RCCX genetic diversity on major histocompatibility complex-associated disease.

The complement component C4 genes located in the major histocompatibility complex (MHC) class III region exhibit an unusually complex pattern of variations in gene number, gene size, and nucleotide polymorphism. Duplication or deletion of a C4 gene always concurs with its neighboring genes serine/threonine nuclear protein kinase RP, steroid 21-hydroxylase (CYP21), and tenascin (TNX), which together form a genetic unit termed the RCCX module. A detailed molecular genetic analysis of C4A and C4B and RCCX modular arrangements was correlated with immunochemical studies of C4A and C4B protein polymorphism in 150 normal Caucasians. The results show that bimodular RCCX has a frequency of 69%, whereas monomodular and trimodular RCCX structures account for 17.0 and 14.0%, respectively. Three quarters of C4 genes harbor the endogenous retrovirus HERV-K(C4). Partial deficiencies of C4A and C4B, primarily due to gene deletions and homoexpression of C4A proteins, have a combined frequency of 31.6%. This is probably the most common variation of gene dosage and gene size in human genomes. The seven RCCX physical variants create a great repertoire of haplotypes and diploid combinations, and a heterozygosity frequency of 69.4%. This phenomenon promotes the exchange of genetic information among RCCX constituents that is important in homogenizing the structural and functional diversities of C4A and C4B proteins. However, such length variants may cause unequal, interchromosomal crossovers leading to MHC-associated diseases. An analyses of the RCCX structures in 22 salt-losing, congenital adrenal hyperplasia patients revealed a significant increase in the monomodular structure with a long C4 gene linked to the pseudogene CYP21A, and bimodular structures with two CYP21A, which are likely generated by recombinations between heterozygous RCCX length variants.

Adrenal Hyperplasia, Congenital↗

PubMed1995

Epitopes for human CD4+ cells on diphtheria toxin: structural features of sequence segments forming epitopes recognized by most subjects.

The sequence regions of diphtheria toxin (DTX) recognized by CD4+ T cells of seven healthy humans of different major histocompatibility complex haplotypes were identified. Overlapping synthetic peptides, screening the DTX sequence, were used to test in proliferation assays unselected blood CD4+ cells, or DTX-specific CD4+ lines propagated by stimulation with DTX of blood mononuclear cells. Blood CD4+ cells and DTX-specific CD4+ lines gave consistent results. Although each subject had an individual pattern of peptide recognition, six peptide sequences (residues 271-290, 321-340, 331-350, 351-370, 411-430 and 431-450) were recognized by all subjects. In the native DTX molecule, these sequence regions are flanked by sequence loops exposed on the DTX surface. They overlap uncharged segments of the DTX sequence. These structural properties may be general requirements for immunodominance in CD4+ cell sensitization in humans.

Adult↗

PubMed1996

Population structure and genetic differentiation among 16 tribal populations of central India.

Genetic polymorphisms for six blood groups, three red cell enzymes, three serum proteins, and hemoglobin were examined in sixteen central Indian tribal populations. Nine of the tribes belonged to Orissa, five to Madhya Pradesh, and two to Maharashtra. Eleven tribes spoke the Dravidian language, three Indo-Ayran, and two the language of the Austro-Asiatic families. The population structure of these tribal populations was analyzed at the inter- and intrastate and linguistic levels, using data for 13 genetic systems (38 alleles or haplotypes). Nine of the 13 loci showed significant heterogeneity in the 16 tribes, and the pattern of heterogeneity was also discernible in the different states and in the Dravidian-speaking tribes. As expected, the extent of genetic differentiation or gene diversity was the highest so far reported from central India. The mean FIS and HS for each locus in the different state, linguistic, and total tribal groups were consistently higher than the FST and GST values, respectively, showing that the genetic structure of each tribe is highly influenced by inbreeding. In a genetic affinity analysis by genetic distance the Indo-Aryan and Austro-Asiatic language groups showed little affinity with each other, although there was some tendency toward geographic affinity. The present analysis indicates that, in addition to genetic drift, gene flow, and selection, the genetic structure of the populations of central India is also highly influenced by sociocultural adaptation and inbreeding.

Ethnicity↗

PubMedDate not supplied

The effect of differential reproductive success on population genetic structure: correlations of life history with matrilines in humpback whales of the gulf of maine.

To examine whether demographic and life-history traits are correlated with genetic structure, we contrasted mtDNA lineages of individual humpback whales (Megaptera novaeangliae) with sighting and reproductive histories of female humpback whales between 1979 and 1995. Maternal lineage haplotypes were obtained for 323 whales, either from direct sequencing of the mtDNA control region (n = 159) or inferred from known relationships along matrilines from the sequenced sample of individuals (n = 164). Sequence variation in the 550 bp of the control region defined a total of 19 maternal lineage haplotypes that formed two main clades. Fecundity increased significantly over the study period among females of several lineages among the two clades. Individual maternal lineages and other clades were characterized by significant variation in fecundity. The detected heterogeneity of reproductive success has the potential to substantially affect the frequency and distribution of maternal lineages found in this population over time. There were significant yearly effects on adult resighting rates and calf survivorship based on examination of sighting histories with varying capture-recapture probability models. These results indicate that population structure can be influenced by interactions or associations between reproductive success, genetic structure, and environmental factors in a natural population of long-lived mammals.

Animals↗

PubMed2004

Differential geographic patterns of mitochondrial DNA variation in two sympatric species of Japanese wood mice, Apodemus speciosus and A. argenteus.

We examined the gene sequences of mitochondrial cytochrome b (cyt b) in two Japanese wood mouse species, Apodemus speciosus (n = 89) and A. argenteus (n = 46), which are distributed on the four main islands of Japan (Hokkaido, Honshu, Shikoku, and Kyushu) and on the small islands surrounding them. Apodemus speciosus, the larger of the two species, showed substantial genetic variation, with a maximum of 3% sequence divergence, and remarkable phylogenetic subdivision with two major clades. One clade represents haplotypes from a central region, including Honshu, Shikoku, Kyushu, and their adjacent islands; the other clade includes haplotypes from Hokkaido and the peripheral islands, forming four subclades: a) Hokkaido, b) Sado Island, c) Satsunan Islands, and d) the Izu Islands. Sequence divergence among the four subclades was 1.0 to 1.5%, implying that A. speciosus colonized these geographic regions 0.2 to 0.3 million years ago, assuming a substitution rate of 2.4% per million years. The population on the Izu Islands has preserved haplotypes that are distinct from those in any other region, providing good evidence for the natural colonization of the volcanic islands of the Izu Islands. The cyt b sequence variation had no relation to the karyotypic dimorphism for the eastern (2n = 48) and western (2n = 46) geographic groups, between which a strict border exists at central Honshu. On the other hand, Apodemus argenteus, the smaller of the two species, showed a similar level of sequence divergence (maximum of 3%) but no substantial geographic differentiation: populations in Hokkaido, Sado, and Yakushima shared similar haplotypes with each of the central populations, suggesting that genetic exchanges occurred among the localities in the last 0.15 million years. The apparent genetic structure of the mitochondrial DNA found in the A. speciosus population might be caused solely by long-term existence in insular regions, presumably due to ecological superiority relative to A. argenteus.

Animals↗

PubMed2001

CORD9 a new locus for arCRD: mapping to 8p11, estimation of frequency, evaluation of a candidate gene.

PURPOSE: To determine the locus of the mutant gene causing autosomal recessive cone-rod dystrophy (arCRD) in a consanguineous pedigree, to evaluate a candidate gene expressed in retina that maps to this locus, and to estimate the percentage of arCRD cases caused by mutations in this gene. METHODS: DNAs from family members were genotyped for markers covering the entire genome at an average spacing of approximately 9 centimorgans (cM). The data were input into a pedigree computer program to produce output files used to calculate lod scores. Significant linkage was revealed at 8cen, prompting the genotyping of a number of additional markers. Exons of a candidate gene were sequenced directly by standard fluorescent dideoxy methods. Haplotype analysis was performed with markers in this locus in 13 multiplex and 2 simplex CRD families in which neither parent had disease. RESULTS: Four-point linkage analysis gave a maximum lod score of approximately 7.6 at both D8S1769 and GATA101H09 in the large consanguineous family. Recombination events defined an interval of 8.7 cM between D8S1820 and D8S532 within which the gene must lie. This 8p11 locus (CORD9) is immediately distal to but distinct from the RP1 autosomal dominant RP (adRP) locus. Two islands of homozygosity were found in this locus: The alleles of 6 of 10 markers in one of the islands and 2 of 4 in the other were homozygous. The UniGene cluster Hs.8719 (UniGene System, provided by the National Center for Biotechnology Information and available at http://www.ncbi.nlm.nih.gov/UniGene), which tags a gene with significant homology to Dual Specificity Phosphatase 3, maps within the CORD9 interval and is highly expressed in the retina. To evaluate this gene as a potential disease candidate, intron-exon structure was determined, and exons were screened in the consanguineous family. No variants were found that could be related to disease. Haplotype analysis of 15 other families with CRD, using markers at CORD9, excluded this locus in 9 of 15. CONCLUSIONS: A new arCRD locus (CORD9) has been identified corresponding to a yet unidentified gene in the 8.7-cM interval D8S1820-D8S532. No mutations were found in one candidate gene in affected members of the primary study family. Haplotype analysis of a cohort of 13 multiplex and 2 simplex families with CRD ruled out the CORD9 gene in 9 of 15 of the families. To date, a total of 126 loci carrying gene mutations causing various forms of retinal degeneration have been mapped, and the mutant gene has been identified in 64 of them. However, only 2 loci for arCRD have been documented. This is the report of a third.

Chromosome Mapping↗

PubMed1996

Molecular definition of red cell Rh haplotypes by tightly linked SphI RFLPs.

The Rh blood group system of human red cells contains five major antigens D, C/c, and E/e (the latter four designated "non-D") that are specified by eight gene complexes known as Rh haplotypes. In this paper, we report on the mapping of RH locus and identification of a set of SphI RFLPs that are tightly linked with the Rh structural genes. Using exon-specific probes, we have localized the SphI cleavage sites resulting in these DNA markers and derived a comprehensive map for the RH locus. It was found that the SphI fragments encompassing exons 4-7 of the Rh genes occur in four banding patterns or frameworks that correspond to the distribution and segregation of the common Rh haplotypes. This linkage disequilibrium allowed a genotype-phenotype correlation and direct determination of Rh zygosity related to the Rh-positive or Rh-negative status (D/D, D/d, and d/d). Studies on the occurrence of SphI RFLPs in a number of rare Rh variants indicated that Rh phenotypic diversity has taken place on different haplotype backgrounds and has arisen by diverse genetic mechanisms. The molecular definition of Rh haplotypes by SphI RFLP frameworks should provide a useful procedure for genetic counseling and prenatal assessment of Rh alloimmunization.

Base Sequence↗

PubMed2004

Molecular population genetics of Cucumber mosaic virus in California: evidence for founder effects and reassortment.

The structure and genetic diversity of a California Cucumber mosaic virus (CMV) population was assessed by single-strand conformation polymorphism and nucleotide sequence analyses of genomic regions 2b, CP, MP, and the 3' nontranslated region of RNA3. The California CMV population exhibited low genetic diversity and was composed of one to three predominant haplotypes and a large number of minor haplotypes for specific genomic regions. Extremely low diversity and close evolutionary relationships among isolates in a subpopulation suggested that founder effects might play a role in shaping the genetic structure. Phylogenetic analysis indicated a naturally occurring reassortant between subgroup IA and IB isolates and potential reassortants between subgroup IA isolates, suggesting that genetic exchange by reassortment contributed to the evolution of the California CMV population. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that different coding regions and even different parts of coding regions were under different evolutionary constraints, including a short region of the 2b gene for which evidence suggests possible positive selection.

California↗

PubMed2005

The silent KIR3DP1 gene (CD158c) is transcribed and might encode a secreted receptor in a minority of humans, in whom the KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1 genes are duplicated.

Killer-cell Ig-like receptors (KIR) are structurally and functionally diverse, and enable human NK cells to survey the expression of individual HLA class I molecules, often altered in infections and tumors. Multiple events of non-reciprocal recombination have contributed to the rapid diversification of KIR. We show that approximately 4.5% of the individuals of a Caucasoid population bear a recombinant allele of KIR3DP1, officially designed KIR3DP1*004, that associates tightly with gene duplications of KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1. The KIR3DP1 gene is normally silent, but the recombinant allele carries a novel promoter sequence and, as a consequence, is transcribed in all tested individuals. Messenger RNA of KIR3DP1*004 is made up of six exons; of these, exons 1-5 are similar to, and spliced like, those encoding the leader peptide and Ig-domains of KIR3D. By contrast, exon 6 is homologous to no other human KIR sequence, but only to possible homologs in chimpanzees and rhesus macaques, and encodes a short hydrophilic tail. The putative KIR3DP1*004 product, like those of the related genes LAIR-2 and LILRA3/ILT6/LIR4, is predicted to be secreted to the extracellular medium rather than anchored to the cell membrane.

Alleles↗

PubMed1997

Preliminary results on the genetic variability of mitochondrial DNA in the signal crayfish, Pacifastacus leniusculus Dana.

This study presents a revised method for the extraction of mitochondrial genome (mtDNA) from crayfish species of aquacultural interest, Pacifastacus leniusculus. The mean size of the mitochondrial genome is approximately 18,000 bp. Restriction fragment length polymorphism (RFLP) analysis performed on the mtDNA has revealed extensive genetic variability within this species. The estimated percentage of nucleotide sequence divergence among the four haplotypes found for P. leniusculus ranges from 1.16 to 3.99%. These data suggest that RFLP analysis of mtDNA may provide greater resolution than protein electrophoresis for population identification among signal crayfish populations. This marker offers new avenues for aquaculture and for understanding the genetic structure and evolutionary history of crayfish populations.

Animals↗

PubMedDate not supplied

The immunoglobulin kappa gene families of human and mouse: a cottage industry approach.

Some aspects of the work of our group on the human and mouse immunoglobulin kappa genes are reviewed. The human kappa locus contains a large duplication: a 600 kb Ckappa-proximal copy with 40 Vkappa genes is found in the close vicinity of a 440 kb Ckappa-distal copy with 36 very similar, but not identical, Vkappa genes. The chimpanzee has only the Ckappa-proximal copy of the locus. The kappa locus of the mouse is close to 3.2 Mb in size, of which 3.1 Mb have been cloned in four contigs, leaving three small gaps of together about 90 kb; 140 Vkappa genes and pseudogenes were localized and sequenced. In parallel to the elucidation of the structure of the kappa loci, the mechanisms of the V-J rearrangement, somatic hypermutation and kappa gene expression were studied. Various polymorphisms were detected in the human population and a number of haplotypes defined. In addition to the Vkappa genes within the loci numerous Vkappa orphons were localized on different chromosomes. Comparing the kappa loci of different species allows some interesting conclusions as to the evolution of this multigene family. Finally our strategy of elucidating the structure and function of the kappa loci, which has been termed a 'cottage industry approach', is discussed in relation to the large-scale genome analysis as pursued today using automated methods.

Animals↗

PubMed1996

Definition of an HLA-A3-like supermotif demonstrates the overlapping peptide-binding repertoires of common HLA molecules.

An HLA-A3-like supertype (minimally comprised of products from the HLA class I alleles A3, A11, A31, A*3301, and A*6801) has been defined on the basis of (a) structural similarities in the antigen-binding groove, (b) shared main anchor peptide-binding motifs, (c) the identification of peptides cross-reacting with most or all of these molecules, and (d) the definition of an A3-like supermotif that efficiently predicts highly cross-reactive peptides. Detailed secondary anchor maps for A3, A11, A31, A*3301, and A*6801 are also described. The biologic relevance of the A3-like supertype is indicated by the fact that high frequencies of the A3-like supertype alleles are conserved in all major ethnic groups. Because A3-like supertype alleles are found in most major HLA evolutionary lineages, possibly a reflection of common ancestry, the A3-like supermotif might in fact represent a primeval human HLA class I peptide-binding specificity. It is also possible that these phenomena might be related to optimal exploitation of the peptide specificity by human TAP molecules. The grouping of HLA alleles into supertypes on the basis of their overlapping peptide-binding repertoires represents an alternative to serologic or phylogenetic classification.

Alleles↗

PubMed1987

The molecular genetics of HLA-related disorders.

The HLA region on the short arm of chromosome 6 contains a set of highly polymorphic loci responsible for regulating the immune response. Particular haplotypes, defined serologically, have been associated with a risk of developing certain autoimmune diseases such as insulin-dependent (juvenile-onset) diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Recent developments in molecular biology have permitted an improved resolution of the locus and of the sequential arrangement of the susceptibility determinants on these haplotypes. Restriction fragment length polymorphisms have allowed subdivisions of serological haplotypes to be made. These correlate with disease susceptibility in some cases. Amplification of specific HLA class II alleles and nucleic acid sequencing have resulted in the identification of the structural determinants in the HLA that underlie some of these diseases.

Arthritis, Rheumatoid↗

PubMed1988

The B-G region genes of the chicken MHC are responsible for lethal graft-versus-host disease in newly hatched chickens.

Using the genetic model of Prague recombinant congenic lines of chickens we found that incompatibility in the B-G region of the major histocompatibility complex (MHC) causes very severe graft-versus-host reaction (GVHR)-associated haemolytic anaemia in newly hatched chickens. Unexpectedly, mild or no signs of this GVH disease are elicited when a recipient chick and an adult donor of lymphocytes are incompatible in the whole B haplotype (B-F/L + B-G regions). On the other hand, the B-G region incompatibility alone (as has been described previously) is not sufficient to produce any GVH splenomegaly in embryos at 14 days of incubation. However, GVH splenomegaly in the donor-recipient combinations with the difference in the whole B haplotype (B-F/L + B-G regions) is significantly greater than in those with the B-F/L region difference only. These results confirm that the B-G region genes of chicken MHC are also involved in the histocompatibility reactions. Furthermore, a new hypothetical model for the structure of the chicken MHC is discussed.

Anemia, Hemolytic, Autoimmune↗

PubMed1989

I-Ad restricted T cell recognition of influenza hemagglutinin. Synthetic peptides identify multiple epitopes corresponding to antibody-binding regions of the HA1 subunit.

In a recent study, we reported extensive diversity in the Iak-restricted T cell repertoire for the hemagglutinin molecule (HA) of influenza A viruses (H3 subtype). Synthetic peptides identified six nonoverlapping epitopes on the HA1 subunit, and CD4+ T cell clones, specific for these regions, discriminated between natural variant viruses that had accumulated amino acid substitutions during antigenic drift. Here, we demonstrate similar specificity and diversity for the Iad haplotype and have identified multiple T cell epitopes within the sequences HA1 56-76, 71-91, 81-97, 177-199, 186-205, and 206-227. These also include recognition sites for neutralizing antibodies and correlations can be made between antigenic drift substitutions in H3 subtype viruses and the specificity of individual CD4+ clones for mutant HA. Moreover, these peptides appear not to exhibit structural homology and fail to compete for Ag presentation, indicating heterogeneity in peptide-Ia interaction. To explain the observation that CD4+ T cells, from two major haplotypes, recognize antibody binding regions of the HA molecule, we propose that surface Ig receptors of the Ag-specific B memory cell exert a direct effect on the processing of HA peptides and subsequent selection of the class II-restricted T cell memory repertoire after natural infection.

Amino Acid Sequence↗