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Results for “Haplotype structures”

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PubMed2004

Evidence for a central role for PfCRT in conferring Plasmodium falciparum resistance to diverse antimalarial agents.

Chloroquine resistance in Plasmodium falciparum is primarily conferred by mutations in pfcrt. Parasites resistant to chloroquine can display hypersensitivity to other antimalarials; however, the patterns of crossresistance are complex, and the genetic basis has remained elusive. We show that stepwise selection for resistance to amantadine or halofantrine produced previously unknown pfcrt mutations (including S163R), which were associated with a loss of verapamil-reversible chloroquine resistance. This was accompanied by restoration of efficient chloroquine binding to hematin in these selected lines. This S163R mutation provides insight into a mechanism by which PfCRT could gate the transport of protonated chloroquine through the digestive vacuole membrane. Evidence for the presence of this mutation in a Southeast Asian isolate supports the argument for a broad role for PfCRT in determining levels of susceptibility to structurally diverse antimalarials.

Alanine↗

PubMed2004

Effects of geographic origin on captive Macaca mulatta mitochondrial DNA variation.

Partial sequences from mitochondrial (mt) 12S and 16S rRNA genes were analyzed to characterize diversity among captive rhesus macaques (Macaca mulatta) originating from various geographic regions. Several nested clades, defined by closely related haplotypes, were identified, suggesting considerable genetic subdivision, probably relics from heterogeneous origins, founder effects, and genetic drift, followed by breeding isolation. The rhesus matrilineages from India differed discretely and markedly from Chinese matrilineages; approximately 90% of the genetic heterogeneity among the combined samples of Indian and Chinese rhesus macaques studied here was due to country of origin. In addition, mtDNA sequences from macaques of China were more diverse than those from rhesus macaques of India, an outcome consistent with China's greater subspecies diversity and with nuclear genotype distributions. Otherwise, the distribution of mtDNA variation within rhesus macaques of China, and especially within those of India, exhibited far less structure and did not conform to a simple isolation-by-distance model. As the demand for genetically heterogeneous and well-characterized rhesus macaques for biomedical-based research increases, mtDNA haplotypes can be useful for genetically defining, preserving maximal levels of genetic diversity within, and confirming the geographic origin of captive breeding groups of rhesus macaques.

Animals↗

PubMed2005

Population genetics and identity of an introduced terrestrial slug: Arion subfuscus s.l. in the North-East USA (Gastropoda, Pulmonata, Arionidae).

Several European species of the terrestrial slug genus Arion have been introduced into North America. A case in point is the species complex A. subfuscus s.l. which has become one of the most abundant slug taxa in North America. In Europe this complex consists of at least two cryptic species, viz. A. fuscus and A. subfuscus s.s., the latter of which is further subdivided in five strongly divergent mtDNA lineages (A. subfuscus S1-S5). In order to determine which of these A. subfsucus s.l. taxa are present in the NE USA and in order to assess their population genetic structure, we compared mtDNA, nDNA and allozyme variation between populations from the NE USA and Europe. Our results show that (1) at least A. subfuscus S1 has become successfully established in the NE USA, (2) founder effects are the most likely explanation for the loss of a large amount of molecular genetic variation in populations from the NE USA (i.e. a loss of 96% of the 16S rDNA haplotypes, 67% of the ITS1 alleles and 46% of the alleles at polymorphic allozyme loci), and (3) part of the remaining genetic variation in NE USA populations was probably due to multiple introductions from the British Isles and the European mainland, and the hybrid structure of most of these source populations. Apparently, the extreme loss of molecular genetic variation in this introduced species has not prevented it from successfully establishing and spreading in novel environments.

Alleles↗

PubMed2000

Matrilineal genetic structure and female-mediated gene flow in red grouse (Lagopus lagopus scoticus): an analysis using mitochondrial DNA.

DNA sequence variation at the hypervariable 5' end of the mitochondrial control region was examined in 247 individuals to detect genetic divergence among 14 populations of red grouse (Lagopus lagopus scoticus) in northeastern Scotland. Ten haplotypes were resolved, several of which were shared among populations. Analysis of molecular variance, Nei's gamma ST, and a cladistic estimate of the amount of gene flow indicated a lack of overall population differentiation. Patterns of overall panmixia are in stark contrast to previous reports of localized subdivision among the same set of populations detected using hypervariable microsatellite markers. Because grouse cocks are territorial and show extreme natal philopatry and females are the dispersing sex, such discordance could be explained by sex-biased dispersal, with extensive female-mediated gene flow preventing mitochondrial DNA divergence. However, it is difficult to reconcile how effective dispersal of females would not homogenize both mitochondrial and nuclear structure simultaneously. We use a model that examines the spatial and temporal dynamics of diparentally and uniparentally inherited genes to show that, under realistic ecological scenarios and with specific differences in the dispersal of males and females, the local effective size of the nuclear genome can be less than that of the mitochondrial and the patterns of structuring we observe are meaningful.

Animals↗

PubMed1992

HLA haplotype segregation and ultrastructural study in familial immotile-cilia syndrome.

The immotile-cilia syndrome (ICS) is a congenital disorder characterized by dysmotility or even complete immotility of the cilia in the ciliated epithelia. The most frequent consequences include recurrent airway infections from early childhood. Neonatal asphyxia often occurs. Males are usually sterile, whereas females may be fertile or infertile. The disease is inherited as an autosomal recessive trait, but previous attempts to localize the ICS susceptibility gene have so far been unsuccessful. Here, we present the case of two sib pairs affected by ICS from two unrelated families. The electron microscopic investigation of nasal biopsies showed structural anomalies of the cilia, characterized by single microtubules or doublets, arranged randomly in the axoneme. Histocompatibility antigen (HLA)-genotyping of all family members revealed: 1) a significant association of ICS with the HLA-DR7; DQW2 haplotype, which is shared by all the affected sibs (P = 0.0099; RR = 25.94); 2) a possible linkage of the ICS susceptibility gene with HLA, both the affected sibs being HLA-identical, the healthy brother in family B being HLA-different (sib-pair analysis: P less than 0.001).

Child, Preschool↗

PubMed2006

High non-protective, long-lasting antibody levels in malaria are associated with haplotype shifting in MHC-peptide-TCR complex formation: a new mechanism for immune evasion.

An effective malarial vaccine must contain multiple immunogenic, protection-inducing epitopes able to block and destroy the P. falciparum malaria parasite, the most lethal form of this disease in the world. Our strategy has consisted in using conserved peptides blocking parasite binding to red blood cells; however, these peptides are non-immunogenic and non-protection-inducing. Modifying their critical residues can make them immunogenic. Such peptides induced antibody titers (determined by immunofluorescence antibody test, IFA) and made the latter reactive (determined by Western blot) and protection inducing against experimental challenge with a highly infective Aotus monkey adapted P. falciparum strain. Modified peptides also induce highly non-protective long-lasting antibody levels. Modifications performed might allow them to bind specifically to different HLA-DRbeta purified molecules. These immunological and biological activities are associated with modifications in their three-dimensional structure as determined by (1)H-NMR. It was found that modified, high non-protective long-lasting antibody level peptides bound to HLA-DR molecules from a different haplotype (to which immunogenic, protection-inducers bind) and had 4.6 +/- 1.4 A shorter distances between residues fitting into these molecules' Pocket 1 to Pocket 9, suggesting fitting into an inappropriate HLA-DR molecule. A multi-component, subunit-based, malarial vaccine is therefore feasible if modified peptides are suitably modified for an appropriate fit into the correct HLA-DRbeta1* molecule in order to form a proper MHC-II-peptide-TCR complex.

Amino Acid Sequence↗

PubMed1987

[Structural analysis of the class II gene region of rat MHC (RT1)--a novel beta-chain gene mapped to RT1. B region].

In the present study, genomic DNAs obtained from intra-RT1 recombinant rats were subjected to restriction fragment length polymorphism (RELP) analysis, using HLA-DP beta cDNA as a probe. Out of 8 strains of rats whose haplotypes were evaluated serologically, 3 strains (NIG-III, LEJ, and DA. 1I (BI)), including 1 congenic strain, had RT1. A/B recombinant haplotypes (RT1. AqB1D1, AuBbDb, and AnBaDa, respectively). After digestion with BglII or HincII, RFLP analysis of these strains with HLA-DP beta probe showed strong bands associated with RT 1. A haplotypes, in addition to some weaker cross-hybridizing bands. That is, after BglII digestion, 4.2kb band was detected associated with RT 1. Aq, 2.1 kb band with A1 and Ab, 4.3 kb band with Au, respectively. After HincII digestion, 1.2 kb band was detected in association with RT1. Aa and 13.0 kb band with An, respectively. From these results I conclude that the recombination events have occurred within the class II region of RT1, especially between B beta gene and a novel class II beta gene which is proposed to be mapped near RT1. A region. The novel gene seems to be a candidate for DP beta-like gene in RT1, because it strongly hybridized with HLA-DP beta cDNA. As in the mouse or the man, a recombinational hotspot might be generated around this novel gene, which provides another evidence for the structural homology among the MHCs of these three species.

Animals↗

PubMed2001

Evidence for population sub-structuring in São Tomé e Príncipe as inferred from Y-chromosome STR analysis.

Seven Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 have been analysed in population samples of Angolares, Forros and Tongas, three ethnic groups from the African archipelago of São Tomé e Príncipe (Gulf of Guinea). Complete typings were obtained for 103 chromosomes, which belonged to 79 different haplotypes. The mean heterozygosity per locus in the overall São Tomean sample was 0.566, with the highest value found among Forros and the lowest among Angolares. Angolares also showed the lowest level of haplotype diversity. On average, the mean pairwise difference between two random haplotypes from Angolares, Forros and Tongas was 4.69, 6.74 and 6.23 repeats, respectively. The genetic distances were found to be statistically significant between Angolares and Forros or Tongas. In accordance, AMOVA revealed that the percentage of variation attributable to differences among groups was only significant when we distinguished between Angolares and non-Angolares. Globally, these results indicate that, with respect to the pool of male lineages of São Tomé e Príncipe, some genetic sub-structuring does exist, basically determined by the Angolares ethnic group.

Emigration and Immigration↗

PubMed1996

Inadequate function of sterile tw5/tw32 spermatozoa overcome by intracytoplasmic sperm injection.

Mice carrying two t complementary haplotypes (tw5/tw32) are totally sterile. Their spermatozoa have poor motility and fertilize neither zona-intact nor zona-free oocytes, even though they are structurally indistinguishable from control (wild-type) spermatozoa. However, when injected directly into oocytes, these infertile spermatozoa are able to participate in normal development. This suggests that infertility of tw5/tw32 male (spermatozoa) is more likely to be due to poor sperm-oocyte interaction than to genetic incompetence of sperm nuclei.

Animals↗

PubMed2001

Family-based association study of serotonin transporter promoter in suicidal adolescents: no association with suicidality but possible role in violence traits.

The serotonin transporter-linked promoter region polymorphism (5-HTTLPR) is thought to be associated with some serotonin dysfunction-related psychopathologies such as depression and anxiety disorders. Suicide and suicide-related behaviors such as violence, aggression, and impulsivity have been reproducibly associated with serotonin dysfunction and are partially genetic. This study examined the association of 5-HTTLPR with suicidal behavior and related traits in Israeli suicidal adolescent inpatients using the haplotype relative risk (HRR) method that controls for artifacts caused by population stratification. Forty-eight inpatient adolescents who recently attempted suicide were assessed by structured interviews for detailed clinical history, diagnoses, suicide intent, suicide risk, impulsivity, violence, and depression. Blood samples were collected and DNA extracted from patients and their biological parents. The 5-HTTLPR allele frequencies were tested for association with suicidality by the HRR method. In addition, the relationship between genotypes and phenotypic severity of several clinical parameters was analyzed. No significant allelic association of the 5-HTTLPR polymorphism with suicidal behavior was found (chi square = 0.023; P = 0.88). Analysis of variance of the suicide-related trait measures for the three genotypes demonstrated a significant difference in violence measures between patients carrying the LL and LS genotypes (9.50+/-4.04 vs. 5.36+/-4.03; P = 0.029). This study suggests that the 5-HTTLPR polymorphism is unlikely to have major relevance to the pathogenesis of suicidal behavior in adolescence but may contribute to violent behavior in this population.

Adolescent↗

PubMed1987

Genetic control of the target structures recognized in hybrid resistance.

Hybrid resistance of lethally irradiated (C57BL/6 X DBA/2)F1 and (C57BL/10 X C3H)F1 hybrid mice to the engraftment of parental C57BL/6 or C57BL/10 bone marrow cells is controlled by the H-2-linked Hh-1 locus. This resistance can be specifically blocked or inhibited by the injection of irradiated spleen cells from lethally irradiated, marrow reconstituted donor mice of certain strains. By testing the ability of regenerating spleen cells from various donor strains to block the resistance, we studied the genetic requirements for the expression of putative cell-surface structures recognized in hybrid resistance to H-2b marrow cells. Strains of mice bearing informative intra-H-2 or H-2/Qa-Tla recombinant haplotypes provided evidence that the Hh-1 locus is located telomeric to the H-2S region complement loci and centromeric to the H-2D region class I locus in the H-2b chromosome. Two mutations that affect the class I H-2Db gene have no effect on Hh-1b gene expression. The H-2D region of the H-2s haplotype contains an allele of the Hh-1 locus indistinguishable from that of the H-2Db region, as judged by the phenotypes of relevant strains and F1 hybrids. Collectively these data indicate that the Hh-1 locus is distinct from the class I H-2D (L) locus in the H-2b or H-2s genome, and favor the view that the expression or recognition of the relevant determinants is not associated with class I gene products.

Alleles↗

PubMed1987

Immunochemistry of the HLA class II molecules isolated from a mouse cell transfected with DQ alpha and beta genes from a DR4 haplotype.

Cells from a mouse B lymphoma were transfected by DQ alpha and DQ beta genes derived from a DR4 haplotype. Quantitatively, the resulting expression of human class II molecules was similar to that of human B lymphoblastoid cell lines. Qualitatively, the transformant class II molecules differed from "normal" class II molecules in their carbohydrate moiety. As for their antigenic specificity, they were shown to carry two determinants previously identified on DQ molecules controlled by DR4 haplotypes, i.e., DQw3 and DCHON. The transformant molecules did not carry a third DR4-associated specificity, DC5 (equivalent to TA10), and must possess a structure allelic to DC5. However, no corresponding alloantigenic specificity was detected by a screening of relevant alloantisera.

Animals↗

PubMed1987

Definitive RFLPs to distinguish between the human complement C4A/C4B isotypes and the major Rodgers/Chido determinants: application to the study of C4 null alleles.

Definitive restriction fragment length polymorphisms (RFLPs) representing the exact locations responsible for isotypicity between the human complement components C4A and C4B, and their generally associated major Rodgers (Rg1) and Chido (Ch1) antigenic determinants, have been designed. By means of C4d-specific genomic probe for Southern blot analysis, a C4A gene can be defined by the presence of the 276 bp and 191 bp N1a IV fragments, while a C4B gene can be defined by a single 467 bp N1aIV fragment. In addition, an Rg1-expressing C4 gene can be represented by a 565 bp EcoO 109 fragment, and a Ch1-expressing C4 gene by a 458 bp EcoO 109 fragment, under the same conditions. All these polymorphic restriction fragments can be unambiguously and conveniently detected. In combination with the Taq I polymorphic patterns specific for the C4 loci and for the neighboring 21-hydroxylase genes, the nature and structure of the tandem C4,21-hydroxylase gene complex can be elucidated. In this study, it is inferred that the null allele of the HLA haplotype B44 DR6 C4A3 C4BQO is not a C4B allele, but probably encodes another C4A 3 allotype at the second C4 locus.

Alleles↗

PubMed1983

A cytotoxic monoclonal antibody specific for the private alloantigenic determinant of the HLA-B 13 molecule.

A murine monoclonal antibody (TU 110) prepared against blast cells of a patient with acute "undifferentiated" leukemia was tested in the microcytotoxicity assay on peripheral blood lymphocytes of 122 normal Caucasian donors. The TU 110 reactivity was found to show a correlation coefficient of 1.0 in population analysis for the presence of the HLA-B locus specificity B 13 as defined by alloantisera. Family segregation studies confirmed MHC linked inheritance of the TU 110 antigenic determinant strictly on HLA-B 13 positive haplotypes. As the first monoclonal reagent against the private specificity of this HLA-B locus antigen, TU 110 provides the possibility to study the structural relationships of sub- and supertypic determinants on this allotype and may help to correlate antigenic domains of HLA-B 13 with definable functional properties.

Animals↗

PubMed1992

Maturation of the filaria Litomosoides sigmodontis in BALB/c mice; comparative susceptibility of nine other inbred strains.

When inoculated subcutaneously, the infective larvae of L. sigmodontis undergo complete development and produce a patent microfilaraemia in mice of the BALB background (BALB/c, BALB/K and BALB/B, with respectively the H-2d, H-2k et H-2b haplotypes). The most susceptible strain is BALB/c with all mice harbouring adult filariae and 47% of mice presenting with a patent microfilaraemia. Mice with the B10 background (B10, B10Br and B10D2, with respectively the H-2b, H-2k et H-2d haplotypes) are almost completely resistant to infection. Adult filariae were recovered from all mice of the CBA/Ca, CBA/HN, C3H/HeN, DBA/2N strains. However, the site and structural development of the parasite varied in each strain. Absence of microfilaraemia is associated with absent or abnormal spicules, reduced number of female filariae and small size of female filariae. These results show that the Major Histocompatibility Complex only modulates the developmental pattern of filariae within the limits imposed by background genes. Male CBA/HN and C3H/HeN were more susceptible to infection than female mice. Inverse phenomenon was observed with strains BALB/c; and, no host sex effect was seen in DBA/D2N.

Animals↗

PubMed1986

Cotransfer of the Ed alpha and Ad beta genes into L cells results in the surface expression of a functional mixed-isotype Ia molecule.

Ia molecules play a key role in antigen recognition by T lymphocytes. To analyze the structural features of the individual alpha and beta chains relevant to the assembly of intact Ia molecules, mouse fibroblasts were cotransfected with various combinations of haplotype- and isotype-mismatched Ia alpha/beta gene pairs. Two important points emerged. First, the level of surface expression of a given haplotype-mismatched A alpha A beta pair appears to depend upon the alpha and beta chain alleles involved. Second, transfection with some isotype-mismatched combinations such as Ed alpha Ad beta results in a significant level of surface expression of a stable mixed-isotype dimer, which also appears to be normally expressed at a low level by an Iad-positive B lymphoma. Moreover, a T-cell hybridoma specific for human gamma globulin and restricted by the Ed molecule was found to be efficiently stimulated by the Ed alpha Ad beta-positive transfectant in the presence of antigen. The stimulation was specifically inhibited by monoclonal antibodies directed to either the Ia or the L3T4 molecule. These findings suggest that the estimates of the potential number of Ia molecules available in an animal for restricting T-lymphocyte recognition of antigens must be revised.

Animals↗

PubMed2004

Mutation history of the roma/gypsies.

The 8-10 million European Roma/Gypsies are a founder population of common origins that has subsequently split into multiple socially divergent and geographically dispersed Gypsy groups. Unlike other founder populations, whose genealogy has been extensively documented, the demographic history of the Gypsies is not fully understood and, given the lack of written records, has to be inferred from current genetic data. In this study, we have used five disease loci harboring private Gypsy mutations to examine some missing historical parameters and current structure. We analyzed the frequency distribution of the five mutations in 832-1,363 unrelated controls, representing 14 Gypsy populations, and the diversification of chromosomal haplotypes in 501 members of affected families. Sharing of mutations and high carrier rates supported a strong founder effect, and the identity of the congenital myasthenia 1267delG mutation in Gypsy and Indian/Pakistani chromosomes provided the best evidence yet of the Indian origins of the Gypsies. However, dramatic differences in mutation frequencies and haplotype divergence and very limited haplotype sharing pointed to strong internal differentiation and characterized the Gypsies as a founder population comprising multiple subisolates. Using disease haplotype coalescence times at the different loci, we estimated that the entire Gypsy population was founded approximately 32-40 generations ago, with secondary and tertiary founder events occurring approximately 16-25 generations ago. The existence of multiple subisolates, with endogamy maintained to the present day, suggests a general approach to complex disorders in which initial gene mapping could be performed in large families from a single Gypsy group, whereas fine mapping would rely on the informed sampling of the divergent subisolates and searching for the shared genomic region that displays the strongest linkage disequilibrium with the disease.

Chromosome Mapping↗

PubMed1993

Unusual variability of the Drosophila melanogaster ref(2)P protein which controls the multiplication of sigma rhabdovirus.

The ref(2)P gene of Drosophila melanogaster was identified by the discovery of two alleles, Po and Pp, respectively, permissive and restrictive for sigma rhabdovirus multiplication. A surprising variability of this gene was first noticed by the observation of size differences between the transcripts of permissive and restrictive alleles. In this paper, another restrictive allele, Pn, clearly distinct from Pp, is described: it exhibits a weaker antiviral effect than Pp and differs from Pp by its molecular structure. Five types of alleles were distinguished on the basis of their molecular structure, as revealed by S1 nuclease analysis of 17 D. melanogaster strains; three alleles were permissive and two restrictive. Comparison of the sequences of four haplotypes revealed numerous point mutations, two deletions (21 and 24 bp) and a complex event involving a 3-bp deletion, all affected the coding region. The unusual variability of the ref(2)P locus was confirmed by the high ratio of amino acid replacements to synonymous mutations (7:1), as compared to that of other genes, such as the Adh (2:42). Nevertheless, nucleotide sequence comparison with the Drosophila erecta ref(2)P gene shows that selective pressures are exerted to maintain the existence of a functional protein. The effects of this high variability on the ref(2)P protein are discussed in relation to its specific antiviral properties and to its function in D. melanogaster, where it is required for male fertility.

Alleles↗