Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

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Background:The ability of antigen-specific T cells to simultaneously produce multiple cytokines has been associated with control of HIV and tuberculosis (TB). Dual infection with HIV and Mycobacterium tuberculosis (MTB) is thought to increase disease progression of both diseases. The aim of this study was to assess the impact of MTB infection on HIV-specific T cell functionality.Methods: We enrolled 13 HIV positive individuals with active TB, 9 HIV positive individuals with presumed latent MTB infection (LTBI), and 13 HIV positive individuals without evidence of LTBI or active TB. All subjects were chronically HIV infected adults from Durban, South Africa. All subjects were CD4+ matched. TB was identified by a positive sputum culture or positive sputum acid fast bacillus smear. LTBI was defined by a positive IFN-gamma ELISPOT using the RD-1 antigens ESAT-6 and CFP-10, in the absence of signs and symptoms of TB. We assessed T cell functionality by investigating IFNy, IL-2, TNF␣, IL-21 and IL-17 cytokine secretion capacity, using polychromatic flow cytomtery, following antigenspecific stimulation of PBMC.Results: HIV-specific CD4+ T cell polyfunctionality decreased progressively from those with HIV mono-infection, to those coinfected with LTBI, to those co-infected with TB. When compared to HIV mono-infected subjects, HIV positive individuals co-infected with LTBI displayed decreased HIV-specific CD4+ levels of IL-2 (p< 0.001) and IL-17 (p=0.001). When compared to HIV co-infected subjects with LTBI and those with HIV mono-infection, individuals co-infected with TB had decreased HIV-specific CD4+ levels of IFN-␥ (p<0.001) and TNF-␣ (p<0.001). A similar decrease in HIV-specific CD8+ T cell polyfunctionality was observed. When compared to HIV mono-infected subjects, HIV positive individuals co-infected with LTBI displayed decreased HIV-specific CD8+ levels of IFN␥ (p<0.001) and TNF-␣ (p<0.001). Conclusion:Our results indicate that MTB infection is linked to decreased HIV-specific T cell function. HIV-specific T cells were most defective in HIV co-infection with active TB compared to LTBI, suggesting that bacterial load may contribute to the loss of T cell function. This may be a contributing factor to the pathogenesis of co-infection as functionally defective HIV-specific T cells may be less able to control HIV.