The genetic structure of south Asian populations as revealed by 650 000 SNPs

The analyses of dense marker sets covering the whole genome has revolutionised the field of (human) population genetics. Driven largely by the needs of biomedical research, these new data are helping to unveil our demographic past, exemplified by the study of mtDNA and Y-chromosome variation during the past ∼20 years. We have analysed (Illumina 650K SNPs) over 320 new samples from South and Central Asia and the Caucasus, together with the publicly available databases (HGDP panel and our published data set of ∼600 Eurasian samples) and illustrated the power of full genome analyses by addressing two specific questions. (i) What is the nature of genetic continuity and discontinuity between South Asia, Middle East and Central Asia? (ii) What are the genetic origins of the Munda speakers of India? We use principal component and structure-like analyses to reveal the structure in the genome wide SNP data. The most striking feature of the genetic structure of South Asian populations is the clear separation of the Indus valley and southern India populations. The genetic component prevalent in the latter region is marginal in the former and absent outside South Asia. By contrast, the component ubiquitous to Indus valley is also present (∼30-40 %) among Indo-European speakers from Ganges valley and Dravidic speakers in southern India. Furthermore, this component can also be found in Central Asia and the Caucasus as well as in Middle East. We explored possibilities to identify the source region for this genetic component. Alternative models put the origins of Munda languages speakers either in South Asia (the Munda speakers sport exclusively autochthonous South Asian mtDNA variants) or in Southeast Asia, where the other Austro Asiatic languages have spread. Y-chromosome variation supports the latter model through sharing of hg O2a in both regions. We show that in addition to the dominant ancestry component being shared between the Indian Dravidic and Munda speakers, up to 30% of Munda speakers retain an ancestry component otherwise prevalent in East Asia. There is no widespread sign of South Asian ancestry component in Southeast Asia. This provides genomic support to the model by which Indian Austro-Asiatic populations derive from dispersal from Southeast/East Asia, followed by an extensive admixture with local Indian populations

Reducing the Activity and Secretion of Microbial Antioxidants Enhances the Immunogenicity of BCG

BACKGROUND:In early clinical studies, the live tuberculosis vaccine Mycobacterium bovis BCG exhibited 80% protective efficacy against pulmonary tuberculosis (TB). Although BCG still exhibits reliable protection against TB meningitis and miliary TB in early childhood it has become less reliable in protecting against pulmonary TB. During decades of in vitro cultivation BCG not only lost some genes due to deletions of regions of the chromosome but also underwent gene duplication and other mutations resulting in increased antioxidant production. METHODOLOGY/PRINCIPAL FINDINGS:To determine whether microbial antioxidants influence vaccine immunogenicity, we eliminated duplicated alleles encoding the oxidative stress sigma factor SigH in BCG Tice and reduced the activity and secretion of iron co-factored superoxide dismutase. We then used assays of gene expression and flow cytometry with intracellular cytokine staining to compare BCG-specific immune responses in mice after vaccination with BCG Tice or the modified BCG vaccine. Compared to BCG, the modified vaccine induced greater IL-12p40, RANTES, and IL-21 mRNA in the spleens of mice at three days post-immunization, more cytokine-producing CD8+ lymphocytes at the peak of the primary immune response, and more IL-2-producing CD4+ lymphocytes during the memory phase. The modified vaccine also induced stronger secondary CD4+ lymphocyte responses and greater clearance of challenge bacilli. CONCLUSIONS/SIGNIFICANCE:We conclude that antioxidants produced by BCG suppress host immune responses. These findings challenge the hypothesis that the failure of extensively cultivated BCG vaccines to prevent pulmonary tuberculosis is due to over-attenuation and suggest instead a new model in which BCG evolved to produce more immunity-suppressing antioxidants. By targeting these antioxidants it may be possible to restore BCG's ability to protect against pulmonary TB

Expansion and Exhaustion of T-Cell Responses during Mutational Escape from Long-Term Viral Control in Two DNA/Modified Vaccinia Virus Ankara-Vaccinated and Simian-Human Immunodeficiency Virus SHIV-89.6P-Challenged Macaques▿

In this study, we monitored the temporal breadths, frequencies, and functions of antiviral CD4 and CD8 T cells in 2 of 22 DNA/modified vaccinia virus Ankara-vaccinated macaques that lost control of a simian-human immunodeficiency virus 89.6P challenge by 196 weeks postchallenge. Our results show that both mutation and exhaustion contributed to escape. With the reappearance of viremia, responding CD8 and CD4 T cells underwent an initial increase and then loss of breadth and frequency. Antiviral gamma interferon (IFN-γ)- and interleukin 2-coproducing cells were lost before IFN-γ-producing cells and CD4 cells before CD8 cells. At euthanasia, all CD8, but no CD4, Gag epitopes detected during long-term control contained mutations

Signature for Long-Term Vaccine-Mediated Control of a Simian and Human Immunodeficiency Virus 89.6P Challenge: Stable Low-Breadth and Low-Frequency T-Cell Response Capable of Coproducing Gamma Interferon and Interleukin-2

In 2001, we reported 20 weeks of control of challenge with the virulent 89.6P chimera of simian and human immunodeficiency viruses (SHIV-89.6P) by a Gag-Pol-Env vaccine consisting of DNA priming and modified vaccinia virus Ankara boosting. Here we report that 22 out of 23 of these animals successfully controlled their viremia until their time of euthanasia at 200 weeks postchallenge. At euthanasia, all animals had low to undetectable viral loads and normal CD4 counts. During the long period of viral control, gamma interferon (IFN-γ)-producing antiviral T cells were present at unexpectedly low breadths and frequencies. Most animals recognized two CD8 and one CD4 epitope and had frequencies of IFN-γ-responding T cells from 0.01 to 0.3% of total CD8 or CD4 T cells. T-cell responses were remarkably stable over time and, unlike responses in most immunodeficiency virus infections, maintained good functional characteristics, as evidenced by coproduction of IFN-γ and interleukin-2. Overall, high titers of binding and neutralizing antibody persisted throughout the postchallenge period. Encouragingly, long-term control was effective in macaques of diverse histocompatibility types

Change in CD25 expression on B and CD4+ T cells negatively correlates with viral load.

<p>PBMCs were cultured overnight with or without anti-CD3 stimulation. Change in CD25 or CD86 expression was determined by subtracting the frequency of expression before stimulation from the frequency of expression after stimulation. (<b>A</b>) Representative plots of CD25 expression on CD4+ T cells and B cells with (bottom) and without (top) anti-CD3 stimulation. CD4+ T cell population shown is CD3+CD4+CD19- and B cell population shown is CD3-CD4-CD19+. (<b>B</b>-<b>D</b>) Change in expression of CD25 on CD4+ T cells (r= -.53; p= .056) (B), CD25 on B cells (r= -.63; p= .018) (C), and CD86 on B cells (r= -.44; p= .11) (D) correlates negatively with viral load. </p

Frequency of PD-1 surface expression on lymphocytes is elevated during HIV infection.

<p>Expression of PD-1 on B cells, CD4+ T cells, and CD8+ cells was measured directly <i>ex </i><i>vivo</i>. (<b>A</b>) In HIV-infected individuals, PD-1 expression on CD4+ is not correlated with viral load (r=.33; p=.17). (B) In HIV-infected individuals PD-1 expression on CD8+ T cells correlated positively with viral load (r= .56; p=.01). (<b>C</b>) PD-1 expression is higher on B cells from HIV+ (closed circles) compared to HIV- (open circles) subjects (p=.04). (<b>D</b>) The frequency of PD-1 surface expression is significantly lower on B cells compared to CD4 (p< .0001) and CD8 T cells (p<.0001) in HIV infection.</p

CD86+ B cells are more frequent in HIV+ than HIV- subjects and correlate with viremia.

<p>PBMCs from HIV- (open circles) or HIV+ (closed circles) subjects were incubated overnight without stimulation and evaluated for surface level CD86 expression on B cells. HIV+ subjects had a higher frequency of CD86+ B cells compared to HIV- subjects (unpaired t-test not shown on graph, p=0.03). The frequency of CD19+CD86+ B cells in HIV+ individuals correlates with the level of viremia (r=.63; p=.003). Correlation statistics shown are derived from HIV+ subject data only and do not include data from HIV- subjects. </p