The 'transporter associated with antigen processing' (TAP) gene products are involved in the processing of endogenous peptides that bind to class I molecules. Polymorphism within these genes could alter the level of the immune response, a phenomenon relevant to the development of autoimmune diseases. In this study, we examined the polymorphism of TAP1 and TAP2 genes in patients with rheumatoid arthritis (RA). TAP1 and TAP2 typing was performed for 138 Caucasian RA patients and 100 healthy controls, all originating from eastern France. TAP1 polymorphic residues at positions 333 and 637 and amino acid variants 379, 565, 651 and 665 in the TAP2 gene were found using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). This method enabled us to determine four TAP1 alleles (TAP1A to TAP1D) and eight TAP2 alleles (TAP2A to TAP2H). All patients and controls had been HLA-DRB1* genotyped. The polymorphic residues TAP1333 and TAP1637 did not show any difference in their distribution between patients and controls. Similar findings were obtained for TAP2379 and TAP2665. However, we found an increased frequency of Thr homozygosity and heterozygosity at position 565 in the TAP2 gene in RA patients (RA vs. controls: 25.3 vs. 14%; P = 0.032; OR = 2.09; CI = 1.01-4.38). Similarly, the prevalence of subjects who were homozygote and heterozygote for Cys651 was increased in the RA group (RA vs. controls: 36.8 vs. 11%; P = 0.02). The dimorphic site TAP2565 defines TAP2D and TAP2E alleles, while the site at position 651 characterizes TAP2F. Thus, we found that TAP2D and TAP2E alleles were more prevalent in RA, but not significantly so (RA vs. controls: TAP2D: 10 vs. 3.6%; P = 0.24; TAP2E: 3.6 vs. 0%; P = 0.19). Similarly, the frequency of TAP2F was higher in RA patients (24.5%) than in controls (11.3%), but this was not significant after correction (P = 0.029; Pcorr = 0.17). Finally, we found no linkage disequilibrium between DRB1* RA-associated alleles and amino acid substitution Thr565 or TAP2D and TAP2E alleles, whereas Cys651 (and TAP2F) was not independent of DRB1*04, a strongly RA-associated allele. Finally, Thr at position 565 in the TAP2 gene was associated with manifestations of disease severity in only a few patients. Examination of TAP1 and TAP2 gene polymorphisms in RA patients revealed an association between a particular amino acid residue, namely Thr565 in the TAP2 gene, and RA. This association was found to be weak and did not seem to be a predictor for the severity of the disease.
Landscape features (e.g., mountains and rivers) can act as barriers to dispersal and gene flow, and therefore impede population connectivity, increasing genetic differentiation between populations. The concave‐eared torrent frog (Odorrana tormota) is a rare, stream‐associated species in eastern China. In this study, we investigated the genetic structure and population demography of this narrowly distributed frog based on mitochondrial Cyt b gene and seven nuclear microsatellite loci. As a result, we found that the rare frog still preserved a relatively high level of genetic diversity compared to some other amphibia. Population structure analyses distinctly identified three or four tentative genetic clusters for the species in the study area. Additionally, by fine‐scale spatial autocorrelation analysis, significant positive genetic structure was uncovered in the shortest distance classes (0–5 km, 5–10 km). Demographic analyses revealed a population expansion (0.075–0.017 Mya) and 15 times population decline (c. 9000 years ago). In conclusion, we supposed that stable montane environments and associated historical population expansion might provide an opportunity for the species to harbor high genetic diversity. The relatively recent population decline might be correlated with climate change as well as genetic differentiation among populations. In addition, our results showed that, on a small landscape scale, dispersal is closely linked to geographic distance and the presence of river systems may not substantially affect the genetic structure for the narrowly distributed O. tormota.
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