Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages

BACKGROUND: Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India. RESULTS: The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports. CONCLUSION: This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup

Biphasic Effect of Sildenafil on Energy Sensing is Mediated by Phosphodiesterases 2 and 3 in Adipocytes and Hepatocytes

Sirt1 (Sirtuin 1), AMPK (AMP-activated protein kinase), and eNOS (endothelial nitric oxide synthase) modulate hepatic energy metabolism and inflammation and play a major role in the development of NASH. Cyclic nucleotide phosphodiesterases (PDEs) play an important role in signal transduction by modulating intracellular levels of cyclic nucleotides. We previously found the PDE5 inhibitor sildenafil to synergize with leucine and leucine-metformin combinations in preclinical studies of NASH and obesity. However, efficacy is diminished at higher sildenafil concentrations. Herein, we have successfully modeled the U-shaped sildenafil dose-response in vitro and utilized this model to assess potential mechanisms of this dose-response relationship. Adipocytes and liver cells were treated with leucine (0.5 mM) and different concentrations of sildenafil (1 nM to 100 µM). cAMP, cGMP, and P-AMPK protein expression were used to demonstrate the biphasic response for increasing concentrations of sildenafil. The reversal with higher sildenafil levels was blunted by PDE2 inhibition. These data indicate that sildenafil-mediated increases in cGMP inhibits PDE3 at lower concentrations, which increases cAMP. However, further increases in cGMP from higher sildenafil concentrations activate PDE2 and consequently decrease cAMP, which demonstrates crosstalk between cAMP and cGMP via PDE2, PDE3, and PDE5. These changes in cAMP concentration are further reflected in downstream effects, including AMPK activation

A Combination of Leucine, Metformin, and Sildenafil Treats Nonalcoholic Fatty Liver Disease and Steatohepatitis in Mice

Sirt1, AMPK, and eNOS modulate hepatic energy metabolism and inflammation and are key players in the development of NASH. L-leucine, an allosteric Sirt1 activator, synergizes with low doses of metformin or sildenafil on the AMPK-eNOS-Sirt1 pathway to reverse mild NAFLD in preclinical mouse models. Here we tested a possible multicomponent synergy to yield greater therapeutic efficacy in NAFLD/NASH. Liver cells and macrophages or an atherogenic diet induced NASH mouse model was treated with two-way and three-way combinations. The three-way combination Sild-Met-Leu increased hepatic fatty acid oxidation and reduced lipogenic gene expression and inflammatory marker in vitro. In mice, Sild-Met-Leu reduced the diet induced increases of ALT, TGFβ, PAI-1, IL1β, and TNFα, hepatic collagen expression, and nearly completely reversed hepatocyte ballooning and triglyceride accumulation, while all two-way combinations had only modest effects. Therefore, these data provide preclinical evidence for therapeutic efficacy of Sild-Met-Leu in the treatment of NAFLD and NASH

A Linguistically Informed Autosomal STR Survey of Human Populations Residing in the Greater Himalayan Region

The greater Himalayan region demarcates two of the most prominent linguistic phyla in Asia: Tibeto-Burman and IndoEuropean. Previous genetic surveys, mainly using Y-chromosome polymorphisms and/or mitochondrial DNA polymorphisms suggested a substantially reduced geneflow between populations belonging to these two phyla. These studies, however, have mainly focussed on populations residing far to the north and/or south of this mountain range, and have not been able to study geneflow patterns within the greater Himalayan region itself. We now report a detailed, linguistically informed, genetic survey of Tibeto-Burman and Indo-European speakers from the Himalayan countries Nepal and Bhutan based on autosomal microsatellite markers and compare these populations with surrounding regions. The genetic differentiation between populations within the Himalayas seems to be much higher than between populations in the neighbouring countries. We also observe a remarkable genetic differentiation between the Tibeto-Burman speaking populations on the one hand and Indo-European speaking populations on the other, suggesting that language and geography have played an equally large role in defining the genetic composition of present-day populations within the Himalayas

Summary of Mantel tests in zt.

<p>The results of the simple Mantel tests are shown above the diagonal; the results of the partial Mantel tests are shown below the diagonal. r_p: correlation coefficient for Mantel test on population level with 100 thousand randomisations, r_i: correlation coefficient for Mantel test on individual level with 10 thousand randomisations. Corresponding p-values are shown between brackets.</p

Summary of Mantel tests in zt.

<p>The results of the simple Mantel tests are shown above the diagonal; the results of the partial Mantel tests are shown below the diagonal. r_p: correlation coefficient for Mantel test on population level with 100 thousand randomisations, r_i: correlation coefficient for Mantel test on individual level with 10 thousand randomisations. Corresponding p-values are shown between brackets.</p