Typing short amplicon binary polymorphisms: supplementary SNP and Indel genetic information in the analysis of highly degraded skeletal remains.

Two sets of short amplicon binary markers (SABs): 50 single nucleotide polymorphisms (SNPs) and 38 insertion/deletion polymorphisms (Indels) were used to genotype bones of 35 years "post-mortem". Typing results of these binary markers were compared with those obtained for standard commercial STR and mini-STR DNA typing kits. We observed SAB marker performance to be better compared with conventional STR and mini-STR genotyping in degraded bone sample analysis. Furthermore, additional genetic information provided by these 88 binary markers, 50 SNPs and 38 Indels, combined with classical markers gave very high discrimination power even in severely degraded specimens, with all tested bone samples showing Random Match Probabilities (RMPs) higher than 1019. Missing person and disaster victim identification by kinship analysis is considerably strengthened by the addition of SAB markers since they can be successfully typed on degraded bone samples while adding considerable extra genetic data when poor or incomplete information is available from conventional forensic markers for the analysis of family pedigrees.

Genetic structure and admixture in urban populations of the Argentine North-West.

BACKGROUND: From the ethnic point of view, the Argentine North-West (ANW) constitutes one of the most noticeable areas in the country due to the cultural peculiarities that integrate it to the Andean world and the ethno-historical and demographic characteristics of how it became populated. AIM: The study analysed the genetic structure and diversity of the ANW urban populations, and the contribution of parental populations to its genetic pool. SUBJECTS AND METHODS: Previously reported data on allele frequencies of HLA-A and HLA-B loci of 1293 individuals from Jujuy, Salta, Tucumán, Santiago del Estero, Catamarca and La Rioja were used. Our estimates include: (a) genetic intra-population diversity; (b) genetic distances between populations; (c) linkage disequilibrium (LD); (d) admixture rates and genetic distances with respect to three parental populations (European, American Indian and African). RESULTS: Low intra-population genetic differentiation and low genetic distances between populations were found. Differential LD distribution varied according to province, with 60% variance due to intra-population differences. The Spanish contribution (50%) predominated in ANW, followed by the American Indian (40%) and African (10%) contributions, and a marked inter-population heterogeneity of genetic admixture rates was observed. The shortest genetic distance was found in the American Indian parental population, and the longest in the African parental population. CONCLUSION: Five hundred years after the Spanish conquest, urban populations at ANW that have probably been subject to the same evolutionary forces present low genetic diversity and a similar genetic structure. Genetic distances and admixture percentages observed agree with census and ethno-historical data on settlement in the region.

Interactions of HLA-B*4801 with peptide and CD8.

Functional properties of the B*4801 allotype were investigated using HLA class I-deficient 221 cells transfected with B*4801 cDNA. From pool sequence analysis of endogenously bound peptides, B*4801 was shown to select for nonamer peptides having glutamine or lysine at position 2 and leucine at the carboxyl-terminus. In an in vitro cell-cell binding assay, B*4801 binds CD8 alpha homodimers weakly due to the presence of a threonine residue at position 245 in the alpha 3 domain. A mutant B*4801 molecule in which alanine replaces threonine 245, binds CD8 alpha homodimers at levels comparable to those of other HLA class I allotypes. Despite the low affinity of B*4801 for CD8 alpha, alloreactive T-cells that recognize B*4801 molecules expressed by the 221 transfectant are inhibited by anti-CD8 monoclonal antibodies. Analysis of 25 B*48-expressing individuals from various populations showed threonine 245 was encoded by every B*48 allele.

Involvement of accessory cells in the Trypanosoma cruzi-induced inhibition of the polyclonal response of T lymphocytes.

Infection with Trypanosoma cruzi is characterized by hyporesponsiveness of the immune system during the acute phase of infection. To better understand the immunological mechanisms affected by T. cruzi, we studied if a reduced T cell proliferative response could originate from an inability of T cells to proliferate or a functional deficiency at the level of accessory cells (AC). The inhibitory effect exerted by T. cruzi was during the induction phase of the lymphoproliferative response, suggesting the participation of AC in the hyporesponse. Then we further investigated the potential of the parasite to interfere with accessory cell-dependent and -independent pathways of human T cell proliferation. Peripheral blood mononuclear cells and peripheral blood lymphocytes from healthy individuals, enriched for T cells, were analysed with regard to their proliferative capacity using: phytohaemagglutinin, immobilized anti-CD3 monoclonal antibody (MoAb) and MoAb to the CD28 antigen, anti-CD3 MoAb and recombinant IL-2 and anti-CD3 MoAb plus phorbol myristate acetate in the presence of parasites. Significant suppression of the proliferative response was caused by the parasite only when AC were present. The parasite markedly reduced the surface expression of HLA-DR and CD11b antigens, key molecules in PHA-induced proliferation. Addition of indomethacin to the culture failed to reverse the inhibitory effect of the parasites, suggesting that prostaglandin E2 was not involved. These data suggest that AC in contact with T. cruzi become incompetent as antigen presenting cell because they are unable to induce a normal proliferative response in T lymphocytes.

Antibody isotypes profiles against Trypanosoma cruzi acidic antigens in two Amerindian populations from a Chagas' disease endemic area.

The isotype distribution of the antibody response against one Trypanosoma cruzi antigenic fraction, FIV, and the putative association to heart disease were analyzed in patients of two apparently genetically distinct Amerindian populations, Mataco (M) and Toba (T), infected with this parasite. The isotypes profiles were analyzed by ELISA, and the antigen specificity of IgG immune response was determined by the immunoblot method. The percentages of infected individuals with abnormal electrocardiograms (GII) were 50% for population M and 10% for population T. Many individuals from both populations had measureable IgG2, IgG3 and IgG4 antibodies to FIV, but the level and frequency (%) of positive sera in population T was considerably higher than in population M (70% vs 15% for IgG2; 75% vs 40% for IgG3; 85% vs 20% for IgG4). The level and frequency of IgG1 reactivity against FIV were similar in the two populations. When the sera were titrated, the most remarkable difference in isotype levels between populations T and M was seen for IgG2 and IgG4, the T population showing the highest titer. No association between clinical state and a particular isotype profile was found by ELISA in any population. When the antigen specificity of antibody response was determined by immunoblot, the antigen patterns recognized by sera from the two clinical groups showed some differences only in population M. All sera assayed from GII of population M fixed more IgG than those with normal electrocardiograms (GI). Two bands of 36 and 43 kD were revealed only in GII of this population. Similar antigenic patterns between the two clinical groups from population T were observed, and they were comparable with those obtained with GI from population M.

Asian affinities and continental radiation of the four founding Native American mtDNAs.

The mtDNA variation of 321 individuals from 17 Native American populations was examined by high-resolution restriction endonuclease analysis. All mtDNAs were amplified from a variety of sources by using PCR. The mtDNA of a subset of 38 of these individuals was also analyzed by D-loop sequencing. The resulting data were combined with previous mtDNA data from five other Native American tribes, as well as with data from a variety of Asian populations, and were used to deduce the phylogenetic relationships between mtDNAs and to estimate sequence divergences. This analysis revealed the presence of four haplotype groups (haplogroups A, B, C, and D) in the Amerind, but only one haplogroup (A) in the Na-Dene, and confirmed the independent origins of the Amerinds and the Na-Dene. Further, each haplogroup appeared to have been founded by a single mtDNA haplotype, a result which is consistent with a hypothesized founder effect. Most of the variation within haplogroups was tribal specific, that is, it occurred as tribal private polymorphisms. These observations suggest that the process of tribalization began early in the history of the Amerinds, with relatively little intertribal genetic exchange occurring subsequently. The sequencing of 341 nucleotides in the mtDNA D-loop revealed that the D-loop sequence variation correlated strongly with the four haplogroups defined by restriction analysis, and it indicated that the D-loop variation, like the haplotype variation, arose predominantly after the migration of the ancestral Amerinds across the Bering land bridge.

HLA polymorphism in a Mataco South American Indian tribe: serology of class I and II antigens. Molecular analysis of class II polymorphic variants.

In the present study, HLA-A, B, C, DR, DQ, and DP loci were analyzed in a group of Mataco Amerindians of Argentina. Using reagents from the 11th International Histocompatibility Workshop (11th IHW), class I specifities such as Bw70, Bw75, and Bw48 were found in this population, other than the HLA determinants commonly described in South American Indians. The class II antigens found were DR4, DRw14, and DRw8 at the DR locus, and DQw4 and DQw7 at the DQ locus. The analysis of DRB1-DR4 related alleles, performed by PCR amplification and oligonucleotide probe hybridization, showed the presence of DRB1*0403, *0404, *0405, and *0411 in individuals from this ethnic group. By the analysis of DRB1-DRw14 related alleles, two variants were found: DRB1*1402 and DRB1*1406, the latter provisionally called DRB1 14.6 in 11th IHW. The DRw8-related allele present was DRB1*0802. The analysis of DRB3 gene revealed only the presence of DRB3*0101 allele in DRw14 individuals. DPB1 locus was also analyzed in unrelated individuals of the same population. Only five DPB1 alleles were found: DPB1*0201, *0301, *0402, *0501, and *1301 over the 19 previously described in the literature. These findings emphasize the restricted HLA class I and II variation observed in this ethnic group as it has been previously shown in other American groups. Some particular haplotypes in this Mataco tribe are described in this work.

Rheumatoid arthritis and its association with HLA-DR antigens. II. Antibodies to native connective tissue antigens detected by enzyme linked immunosorbent assay.

The distribution of frequencies of HLA-DR alloantigens in HLA-DR4 negative subjects was determined in patients with Rheumatoid arthritis (RA) and normal individuals. An increased incidence of HLA-DR1 alloantigen in DR4 negative RA patients (45.9%) compared with DR4 negative healthy controls (23.6%) was found. The difference became significant when the incidence of DR1 was compared between patients with severe disease stages (III-IV) (75%) in contrast to 32% of incidence in patients of the milder stages (I-II) (p less than 0.05). Using Enzyme Linked Immunosorbent Assay we have determined the incidence of serum antibodies to native bovine type I and type II collagens and proteoglycans in patients with RA. Presence of serum antibodies to native type I collagen was detected in 59% of patients with RA, 60% of sera exhibited reactivity to type II collagen and 12% had antibodies to proteoglycans. There was no correlation between the presence of antibodies to type I and II collagens and disease stages, however, the incidence of serum antibodies to proteoglycans was increased in severe disease stages. On the other hand, the presence of high levels of antibodies to type I collagen was associated to HLA-DR1 antigen, (p less than 0.05).

Rheumatoid arthritis and its association with HLA-DR antigens. I. Cell mediated immune response against connective tissue antigens.

HLA-DR antigens and cellular sensitivity to native bovine type I and type II collagen and proteoglycans were examined in patients with classic rheumatoid arthritis (RA) and normal individuals. Fifty eight percent of patients with RA (n = 88) and 28% of normals (n = 52) were DR4+ (pc less than 0.01). DR4 phenotype was significantly increased in patients with severe disease stages (III-IV), as defined by the ARA criteria, in contrast to those showing mild disease stages (I-II) (p less than 0.05). Furthermore, peripheral blood mononuclear cells from 55 patients and 30 controls were evaluated for the in vitro production of leukocyte inhibitory factor in response to native type I and type II collagen and proteoglycans. By using this assay, cells from the arthritic group exhibited a statistically significant response when stimulated with native type I collagen and proteoglycans. The cellular immune response was not associated with any particular HLA-DR antigens, or to the disease stage or severity.

Study of HLA system in a Mataco population: a geographically isolated American Indian tribe.

A search for antigens of the HLA system has been carried out in 53 Mataco Indians of Argentina living in a geographically isolated area in the northeast of the country. Samples were mostly collected from adults of both sexes who were not directly related. Lymphocyte typing was performed using the microcytotoxicity technique of NIH. 118 sera specific for 15 antigens of the first HLA locus, 22 antigens of the second and 6 of the third were used. The most frequently found alleles were HLA-A28, Aw31 and A2 for the first locus; B15 and B40 for the second; and Cw3 and Cw4 for the third. In addition to previously published investigations on South American Indians, our typing work shows a remarkable homogeneous gene pool and a restricted range of polymorphism; therefore, a further set of haplotypes rendered us also restricted. The most frequent haplotypes that showed a significant statistical linkage disequilibrium were: A2-Cw4, A28-Bx, A2-Cw3, Aw31-Bw16, Aw24-Cw3, B15-Cw3, Bw16-Cw3 and A28-B5. Some of these haplotypes have also been found in other indian populations.