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Results for “Haplotype structures”

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PubMed2005

Coding SNP in tenascin-C Fn-III-D domain associates with adult asthma.

The extracellular matrix glycoprotein tenascin-C (TNC) has been accepted as a valuable histopathological subepithelial marker for evaluating the severity of asthmatic disease and the therapeutic response to drugs. We found an association between an adult asthma and an SNP encoding TNC fibronectin type III-D (Fn-III-D) domain in a case-control study between a Japanese population including 446 adult asthmatic patients and 658 normal healthy controls. The SNP (44513A/T in exon 17) strongly associates with adult bronchial asthma (chi2 test, P=0.00019, Odds ratio=1.76, 95% confidence interval=1.31-2.36). This coding SNP induces an amino acid substitution (Leu1677Ile) within the Fn-III-D domain of the alternative splicing region. Computer-assisted protein structure modeling suggests that the substituted amino acid locates at the outer edge of the beta-sheet in Fn-III-D domain and causes instability of this beta-sheet. As the TNC fibronectin-III domain has molecular elasticity, the structural change may affect the integrity and stiffness of asthmatic airways. In addition, TNC expression in lung fibroblasts increases with Th2 immune cytokine stimulation. Thus, Leu1677Ile may be valuable marker for evaluating the risk for developing asthma and plays a role in its pathogenesis.

Adult↗

PubMed1989

Structural analysis of peptides capable of binding to more than one Ia antigen.

The Ia binding regions were analyzed for three unrelated peptide Ag (sperm whale myoglobin 106-118, influenza hemagglutinin 130-142, and lambda repressor protein 12-26) for which binding to more than one Ia molecule has previously been demonstrated. By determining the binding profile of three separate series of truncated synthetic peptides, it was found that in all three cases the different Ia reactivities mapped to largely overlapping regions of the peptides; although, for two of the peptides, the regions involved in binding the different Ia specificities were distinct. Moreover, subtle differences were found to dramatically influence some, but not other, Ia reactivities. Using a large panel of synthetic peptides it was found that a significant correlation exists between the capacity of peptides to interact with different alleles of the same molecule (i.e., IAd and IAk), but no correlation was found with the capacity of peptides to interact with different isotypes within the same haplotype (i.e., IAd and IEd). These data suggest that different alleles of the same MHC molecule may actually recognize closely related structures, whereas different isotypes may recognize unrelated, albeit non-mutually exclusive, structures on an Ag molecule.

Amino Acid Sequence↗

PubMed2026

Movi 2: fast and space-efficient queries on pangenomes.

SUMMARY: Space-efficient compressed indexing methods are critical for pangenomics and for avoiding reference bias. In the Movi study, we implemented the move-structure index, highlighting its locality-of-reference and speed. However, Movi had a high memory footprint compared to other compressed indexes. Here, we introduce Movi 2 and describe new methods that greatly reduce size and memory footprint of move structure-based indexes. The most compressed version of Movi 2 reduces the Movi index's space footprint more than five-fold. We also introduce sampling approaches that enable trade-offs between query and space efficiency. To demonstrate, we show that Movi 2 achieves advantageous time and space tradeoffs when applied to large pangenome collections, including both the first and second releases of the Human Pangenome Reference Consortium (HPRC) collection, the latter of which spans over 460 human haplotypes. We show that Movi 2 dominates prior methods on both speed and memory footprint, including both r-index-based and our previous move-structure-based method. AVAILABILITY AND IMPLEMENTATION: The methods we developed for Movi 2 are publicly available at https://github.com/mohsenzakeri/Movi.

Humans↗

PubMed2005

The Atlantic-Mediterranean transition: discordant genetic patterns in two seabream species, Diplodus puntazzo (Cetti) and Diplodus sargus (L.).

Sparids are a group of demersal perciform fish of high commercial value, which have experienced an extensive radiation, particularly in the Mediterranean, where they occupy a variety of different niches. The present study focuses on two species: Diplodus sargus and D. puntazzo, presenting a wide distribution from the Mediterranean to the eastern Atlantic coasts. They display similar ecological behaviour and are evolutionary closely related. Both are highly appreciated in fisheries and D. puntazzo is currently under domestication process. However, little is know on their population structure and it is an open question whether any genetic differentiation exists at the geographic level. To address this issue we examined sequence variation of a portion of the mitochondrial DNA (mtDNA) control region in population samples of each of the two species collected over a wide geographic range. In addition to the mtDNA, analysis of nuclear loci (allozymes) was included in the study to compare patterns revealed by nuclear and mitochondrial markers. The studied samples covered an area from the eastern Mediterranean to the Portuguese coasts immediately outside the Gibraltar Strait. The two species revealed a level of sequence polymorphism remarkably different for the control region with the D. puntazzo and D. sargus showing 111 and 28 haplotypes, respectively. Such a difference was not detected with allozyme markers. The two species also showed large differences in their population structure. While D. puntazzo presented a marked genetic divergence between the Atlantic and Mediterranean samples, D. sargus showed little intraspecific differentiation. These results were supported using both mtDNA and allozyme markers, and were interpreted as the consequence of differences in the history of the two species such as fluctuations in the effective population size due to bottlenecks and expansions, possibly combined with present-day differences in levels of gene flow.

Animals↗

PubMed2006

The genetic structure of Australasian green turtles (Chelonia mydas): exploring the geographical scale of genetic exchange.

Ecological and genetic studies of marine turtles generally support the hypothesis of natal homing, but leave open the question of the geographical scale of genetic exchange and the capacity of turtles to shift breeding sites. Here we combine analyses of mitochondrial DNA (mtDNA) variation and recapture data to assess the geographical scale of individual breeding populations and the distribution of such populations through Australasia. We conducted multiscale assessments of mtDNA variation among 714 samples from 27 green turtle rookeries and of adult female dispersal among nesting sites in eastern Australia. Many of these rookeries are on shelves that were flooded by rising sea levels less than 10 000 years (c. 450 generations) ago. Analyses of sequence variation among the mtDNA control region revealed 25 haplotypes, and their frequency distributions indicated 17 genetically distinct breeding stocks (Management Units) consisting either of individual rookeries or groups of rookeries in general that are separated by more than 500 km. The population structure inferred from mtDNA was consistent with the scale of movements observed in long-term mark-recapture studies of east Australian rookeries. Phylogenetic analysis of the haplotypes revealed five clades with significant partitioning of sequence diversity (Phi = 68.4) between Pacific Ocean and Southeast Asian/Indian Ocean rookeries. Isolation by distance was indicated for rookeries separated by up to 2000 km but explained only 12% of the genetic structure. The emerging general picture is one of dynamic population structure influenced by the capacity of females to relocate among proximal breeding sites, although this may be conditional on large population sizes as existed historically across this region.

Animal Migration↗

PubMed1995

Von Hippel-Lindau (VHL) disease with pheochromocytoma in the Black Forest region of Germany: evidence for a founder effect.

We identified a germline missense mutation at nucleotide 505 (T to C) of the VHL tumor suppressor gene in 14, apparently unrelated, VHL type 2A families from the Black Forest region of Germany. This mutation was previously identified in two VHL 2A families living in Pennsylvania (USA). All affected individuals in the 16 families shared the same VHL haplotype indicating a founder effect. This missense mutation at codon 169 (Tyr to His) would probably cause an alteration in the structure of the putative VHL protein. The association of this distinct mutation with the pheochromocytoma phenotype in VHL may help to elucidate the genetic mechanism of carcinogenesis in this multi tumor cancer syndrome.

Adrenal Gland Neoplasms↗

PubMed2002

Two Y-chromosome-specific polymorphisms 12f2 and DFFRY in the Japanese population and their relations to other Y-polymorphisms.

This study of male-specific genetic markers in the Japanese population was carried out in an attempt to refine the existing theories concerning its population genetics and migration events. We examined the relation between the constructed haplotypes of three biallelic Y-chromosome-specific markers (YAP, 47z and SRY) and the results of studying two other Y-specific polymorphisms of both 12f2 and DFFRY markers. The 12f2 marker was completely absent in 14.7% of Japanese males; all of them were haplotype II males. None of the Japanese males from other haplotypes or other East Asian populations showed any deletion of 12f2. In all haplotype II Japanese men, we found that DFFRY gene harbors a (C-->T) substitution polymorphism that was not found in any other population of this study. These results suggested that although haplotype II Japanese males share with the other haplotype II men from different geographical areas in having the YAP insertion on their Y-chromosomes, their Y-chromosomal structure is somewhat characteristically different. They are probably descendants of the ancestral Jomonese population who lived in Japan before the Yayoi immigrants entered Japan approximately 2300 years ago. These findings suggested that linkage studies between Y-specific markers are helpful in understanding the migratory patterns in East Asia. We also suggested that Japanese males have characteristically different Y-chromosomes compared with other populations.

Alleles↗

PubMed1981

Immunochemical evidence in two haplotypes for at least three D region-encoded molecules, D, L, and R.

Sequential immunoprecipitation analyses have defined a new transplantation antigen, designated R, which in addition to the 2 previously isolated D and L molecules is encoded in the D region. All 3 of these gene products are 45,000 m.w. glycoprotein, and each bears a unique combination of specificities as recognized by monoclonal and/or conventional anti-H-2 sera. Three D region products, D, L, and R, have now been isolated from soluble antigens of both the H-2d and H-2q haplotypes. The resulted reported here also indicate that the loss-mutant BALB/c-H-2dm2 fails to express both Ld and Rd antigens. Further chemical comparisons of the primary structure of R molecules with D and L molecules will now be necessary to determine whether R antigens are the products of a unique gene, as opposed to a glycosylation or conformational variant of D and/or L molecules. In either case, the discovery of 3 D region-encoded gene products in certain haplotypes raises new questions about the evolution and regulation of expression of H-2 loci.

Animals↗

PubMed2006

Spatial patterns of genetic diversity across European subspecies of the mountain hare, Lepus timidus L.

Fossil evidence shows that populations of species that currently inhabit arctic and boreal regions were not isolated in refugia during glacial periods, but instead maintained populations across large areas of central Europe. These species commonly display little reduction in genetic diversity in northern areas of their range, in contrast to many temperate species. The mountain hare currently inhabits both temperate and arctic-boreal regions. We used nuclear microsatellite and mtDNA sequence data to examine population structure and alternate phylogeographic hypotheses for the mountain hare, that is, temperate type (lower genetic diversity in northern areas) and arctic-boreal type (high northern genetic diversity). Both data sets revealed concordant patterns. Highest allelic richness, expected heterozygosity and mtDNA haplotype diversity were identified in the most northerly subspecies, indicating that this species more closely maps to phylogeographic patterns observed in arctic-boreal rather than temperate species. With regard to population structure, the Alpine and Fennoscandian subspecies were most genetically similar (F(ST) approximately 0.1). These subspecies also clustered together on the mtDNA tree and were assigned with highest likelihood to a common Bayesian cluster. This is consistent with fossil evidence for intermediate populations in the central European plain, persisting well into the postglacial period. In contrast, the geographically close Scottish and Irish populations occupied separate Bayesian clusters, distinct clades on the mtDNA maximum likelihood tree and were genetically divergent from each other (F(ST) > 0.4) indicating the influence of genetic drift, long isolation (possibly dating from the late glacial era) and/or separate postglacial colonisation routes.

Animals↗

PubMed2005

Presence of alanine-to-valine substitutions in myofibrillogenesis regulator 1 in paroxysmal nonkinesigenic dyskinesia: confirmation in 2 kindreds.

BACKGROUND: Paroxysmal nonkinesigenic dyskinesia (PNKD) is a rare disorder characterized by attacks of involuntary movements brought on by stress, alcohol, or caffeine, but not by movement. An autosomal dominant form of this disorder was mapped to chromosome 2q33-36, and different missense mutations in exon 1 of the myofibrillogenesis regulator 1 (MR1) gene were identified recently in 2 kindreds. OBJECTIVES: To describe studies on a new pedigree with PNKD, to explore the possibility of locus heterogeneity, and to further delineate the spectrum of mutations in MR1 in 2 families with PNKD. DESIGN, SETTING, AND PATIENTS: All 10 exons of MR1 were sequenced in DNA from members of 2 pedigrees with autosomal dominant PNKD. RESULTS: Different missense mutations in exon 1 of MR1 that cosegregate with disease were identified in each multiplex family. These single-nucleotide mutations predicted substitution of valine for alanine in residue 7 in one family and residue 9 in the other. The same mutations were found in the only 2 families previously published. Family history and haplotype analysis make it unlikely that the families with the same mutations are related. CONCLUSIONS: The function of MR1 is unknown, but the 2 mutations identified in the 4 families with PNKD studied to date are predicted to disrupt the amino terminal alpha-helix suggesting that this region of the gene is critical for proper gene function under stressful conditions. Study of additional families will be important to determine whether analysis of a single exon (MR1 exon 1) is sufficient for genetic testing purposes.

Alanine↗

PubMed1992

Recurrent transverse myelitis, myasthenia gravis, and autoantibodies.

A 45-year-old man with a longstanding diagnosis of myasthenia gravis presented with four episodes of transverse myelitis in 5 years. Each episode improved after treatment with steroids. Laboratory studies revealed no evidence of multiple sclerosis or a structural spinal lesion. He had antinuclear and anti-DNA antibodies and the HLA-A1, B8, DR3 haplotype known to be associated with certain autoimmune diseases. We propose an autoimmune cause for the recurrent episodes of myelitis.

Antibodies, Antinuclear↗

PubMed1987

Class I H-2Db determinants are not involved in hybrid resistance to parental H-2b/Hh-1b bone marrow allograft.

Hybrid resistance to parental H-2b bone marrow grafts is directed to a cell surface structure controlled by the Hh-1 locus in or near the H-2D region. The nature of this surface structure is not known. Since homozygosity at the class I H-2D locus or loci in this haplotype would seem a necessary but not sufficient condition for the grafts' susceptibility to resistance, we tested whether the expression of this phenotype is dependent on the expression of class I H-2Db determinants. Cloned variants of H-2b tumor RBL-5 were obtained by immunoselection for the absence of H-2Db expression, as determined by the inability to bind specific antibody and to induce or react with alloreactive cytotoxic T lymphocytes. The three clones used in this study were H-2Db negative but H-2Kb positive and were natural killer cell resistant. When tested in vivo as competitive inhibitors the variant cells were capable of blocking hybrid resistance to parental H-2b bone marrow grafts as were unselected H-2Db-positive parental line cells. Therefore, H-2Db expression is irrelevant for Hh-1b expression. An incidental observation was that YAC-1 cells, a non-H-2b tumor with pronounced susceptibility to natural killing, were able to block hybrid resistance. This reactivity, not observed in our previous studies, raises the possibility that at least some of the effector cells are cross-reactive or capable of dual recognition.

Animals↗

PubMed2026

Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley.

Barley (Hordeum vulgare L.) is an important crop in the world, and its seed dormancy is primarily controlled by a mitogen-activated protein kinase kinase 3 (MKK3) gene. Although kinase activity of MKK3 and its roles in barley post-domestication have been widely studied, the pre-domestication evolution of MKK3 and the spread of nondormant alleles among global barley varieties remain largely unexplored. In this study, we analyzed MKK3 sequences in barley and its wild progenitor (Hordeum spontaneum K. Koch) and identified two polymorphic miniature inverted-repeat transposable elements (MITEs). Comparative analyses indicated that the insertions/excision of the MITEs predated the current estimates of barley domestication. Examination of the barley pangenomes coupled with droplet digital polymerase chain reaction revealed extensive copy number variation of MKK3 and suggested that transposons likely contributed to tandem amplification of the MKK3 gene on chromosome 5H. Additionally, approximately 1-Kb MKK3 sequences were found on chromosomes 1H and 6H. Further analysis indicated that these short MKK3 sequences were captured by a CACTA transposon that also contained fragments from four other expressed genes. The acquisition of MKK3 was estimated to be between 1.9 and 2.5 million years ago. Together, these findings illuminate the dynamic pre-domestication evolution of the MKK3 gene and identify three divergent MKK3 haplotype groups including a unique lineage predominant in Ethiopian germplasm. This study highlights the contribution of transposons to structural diversification and evolutionary differentiation of the MKK3 locus and provides helpful information for understanding the complex history of MKK3 gene in barley and also for improving preharvest sprouting tolerant varieties under distinct natural conditions.

Hordeum↗

PubMed1995

Mitochondrial DNA variation in North American oedipodinae.

Restriction fragment analysis of mitochondrial DNA (mtDNA) was used to examine genetic variation and population structure in 13 species of banded-winged grasshoppers (subfamily Oedipodinae). Total DNA of 246 individuals was digested with 11 restriction enzymes and probed with three cloned EcoRI fragments representing the entire mitochondrial genome of Melanoplus sanguinipes. On average, members of this subfamily were five times more variable than those in another subfamily, Melanoplinae, previously examined. This would appear to lend support to Vickery's claim that the time of origin of Nearctic oedipodines is more ancient than that of melanoplines. With respect to population structure, a few different patterns were exhibited. Species such as Camnula pellucida had populations containing a mixture of haplotypes, some widespread and some geographically restricted. In contrast, Chortophaga viridifasciata populations were characterized by unique assemblages of diverse haplotypes. Phylogeographic hypotheses are advanced to account for these observations.

Animals↗

PubMed1988

A unique alpha chain in hemoglobin of "Skive" Danish Mus musculus.

The primary structures of the alpha chains in hemoglobins from three stocks of mice with the Hbaw2, Hbaw3, and Hbaw4 haplotypes were determined to establish whether the tentative alpha-chain assignments based on the results of isoelectric focusing patterns were correct. These Hba haplotypes were identified in laboratory descendants of feral mice captured in different parts of the world. Hemoglobin from "Centreville", Maryland, Mus musculus domesticus (Hbaw2) contains equal amounts of alpha chains 1 and 3. Hemoglobin from "Czech" Mus musculus musculus (Hbaw4) contains equal amounts of alpha chains 3 and 4. Amino acid analysis of the alpha-globins of "Skive" Danish Mus musculus musculus (Hbaw3) establishes that its hemoglobin is comprised of about one-third alpha chain 2 as expected plus a greater amount of a unique alpha chain that has not been described previously. This unique alpha chain has glycine at position 25, isoleucine at position 62, and serine at position 68; it is called chain 7. It may represent an intermediate in the evolution of genes that code for chain 2 (which has glycine, valine, and serine at positions 25, 62, and 68, respectively) and chain 4 (which has valine, isoleucine, and serine at positions 25, 62, and 62, respectively).

Amino Acids↗

PubMed1986

Close linkage of human chromosomal pepsinogen A genes.

We have obtained a clone containing two pepsinogen A genes in a single insert by screening a recombinant cosmid library for human genomic DNA. Restriction endonuclease mappings of this cloned DNA showed that these two genes are very similar, but distinct in structure, and that they are closely linked to one another in the human chromosome DNA. The close arrangement of the genes with very similar structures could facilitate the homologous recombination or the unequal crossing-over which accounts for high frequency of haplotype variation in copy number of pepsinogen A genes as reported by Taggart et al.

Cloning, Molecular↗

PubMed1985

Specificity of monoclonal antibodies directed against human and murine class II histocompatibility antigens as analyzed by binding to HLA-deletion mutant cell lines.

The specificity of 70 monoclonal anti-Ia monoclonal antibodies (MoAbs) (18 mouse allo-induced and 52 rodent anti-human) was studied with a panel of 17 HLA-deletion mutants that were derived from a single parent line and vary in expression of Ia antigens due to deletion of different subregions of HLA. MoAb binding was analyzed both by ELISA and flow microfluorometry. Characterization of the MoAbs with respect to specificity for products of subregions of a DR1-DC1-SB2 haplotype revealed great complexity. Many antibodies were quite specific for DR-linked determinants (26 MoAbs), DC-linked determinants (5 MoAbs), or determinants indistinguishable from SB (4 MoAbs). However, many MoAbs bound to products of more than one subregion: DR + SB (+/- weak DC) (22 MoAbs); DR + DC (3 MoAbs); or DR + DC + SB (1 MoAb). Furthermore, a number of the MoAbs bound unequally to products of the two HLA haplotypes analyzed, particularly among those recognizing DC1-linked determinants and the murine alloinduced MoAbs. Finally, despite strong structural homologies of murine I-A to human DC and murine I-E to human DR, the intraspecies cross-reactions of MoAbs do not closely follow that pattern. These data: (1) illustrate the usefulness of HLA-deletion mutant cell lines for analysis of the specificity of MoAbs and for delineation of HLA subregions; (2) demonstrate the great diversity of MoAbs specific for class II molecules and the high frequency of MoAbs that bind to products of more than one Ia subregion, particularly DR and SB. In view of such complexity, many (perhaps most) MoAbs cannot be relied on to unambiguously identify products of a particular Ia subregion, without extensive characterization.

Animals↗

PubMed1989

The human alpha-amylase multigene family consists of haplotypes with variable numbers of genes.

Polymorphic amylase protein patterns have suggested the presence in the human genome of various haplotypes encoding these allozymes. To investigate the genomic organization of the human alpha-amylase genes, we isolated the pertinent genes from a cosmid library constructed of DNA from an individual expressing three different salivary amylase allozymes. From the restriction maps of the overlapping cosmids and a comparison of these maps with the restriction enzyme patterns of DNA from the donor and family members, we were able to identify two haplotypes consisting of very different numbers of salivary amylase genes. The short haplotype contains two pancreatic genes (AMY2A and AMY2B) and one salivary amylase gene (AMY1C), arranged in the order 2B-2A-1C, encompassing a total length of approximately 100 kb. The long haplotype spans about 300 kb and contains six additional genes arranged in two repeats, each one consisting of two salivary amylase genes (AMY1A and AMY1B) and a pseudogene lacking the first three exons (AMYP1). The order of the amylase genes within the repeat is 1A-1B-P1. All genes are in a head-to-tail orientation except AMY1B, which has the reverse orientation with respect to the other genes. Analysis of somatic cell hybrids confirmed the presence of these short and long haplotypes. Furthermore, we present evidence for the existence of additional haplotypes in the human population and propose a general model for the evolution of the human alpha-amylase multigene family. A general designation 2B-2A-(1A-1B-P)n-1C can describe these haplotypes, n being 0 and 2 for the short and the long haplotypes presented in this paper, respectively.

Biological Evolution↗