Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.     

Structure of an As(III) S-Adenosylmethionine Methyltransferase: Insights into the Mechanism of Arsenic Biotransformation

Enzymatic methylation of arsenic is a detoxification process in microorganisms but in humans may activate the metalloid to more carcinogenic species. We describe the first structure of an As(III) S-adenosylmethionine methyltransferase by X-ray crystallography that reveals a novel As(III) binding domain. The structure of the methyltransferase from the thermophilic eukaryotic alga Cyanidioschyzon merolae reveals the relationship between the arsenic and S-adenosylmethionine binding sites to a final resolution of ～1.6 ?. As(III) binding causes little change in conformation, but binding of SAM reorients helix α4 and a loop (residues 49-80) toward the As(III) binding domain, positioning the methyl group for transfer to the metalloid. There is no evidence of a reductase domain. These results are consistent with previous suggestions that arsenic remains trivalent during the catalytic cycle. A homology model of human As(III) S-adenosylmethionine methyltransferase with the location of known polymorphisms was constructed. The structure provides insights into the mechanism of substrate binding and catalysis.     

The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities

We developed a broad-ranging method for identifying key hydrogen-producing and consuming microorganisms through analysis of hydrogenase gene content and expression in complex anaerobic microbial communities. The method is based on a tiling hydrogenase gene oligonucleotide DNA microarray (Hydrogenase Chip), which implements a high number of probes per gene by tiling probe sequences across genes of interest at 1.67 × –2 × coverage. This design favors the avoidance of false positive gene identification in samples of DNA or RNA extracted from complex microbial communities. We applied this technique to interrogate interspecies hydrogen transfer in complex communities in (i) lab-scale reductive dehalogenating microcosms enabling us to delineate key H₂-consuming microorganisms, and (ii) hydrogen-generating microbial mats where we found evidence for significant H₂ production by cyanobacteria. Independent quantitative PCR analysis on selected hydrogenase genes showed that this Hydrogenase Chip technique is semiquantitative. We also determined that as microbial community complexity increases, specificity must be traded for sensitivity in analyzing data from tiling DNA microarrays.     

Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo

The mammalian Polycomblike protein PHF1 was previously shown to interact with the Polycomb group (PcG) protein Ezh2, a histone methyltransferase whose activity is pivotal in sustaining gene repression during development and in adulthood. As Ezh2 is active only when part of the Polycomb Repressive Complexes (PRC2-PRC4), we examined the functional role of its interaction with PHF1. Chromatin immunoprecipitation experiments revealed that PHF1 resides along with Ezh2 at Ezh2-regulated genes such as the HoxA loci and the non-Hox MYT1 and WNT1 genes. Knockdown of PHF1 or of Ezh2 led to up-regulated HoxA gene expression. Interestingly, depletion of PHF1 did correlate with reduced occupancy of Bmi-1, a PRC1 component. As expected, knockdown of Ezh2 led to reduced levels of its catalytic products H3K27me2/H3K27me3. However, reduced levels of PHF1 also led to decreased global levels of H3K27me3. Notably, the levels of H3K27me3 decreased while those of H3K27me2 increased at the up-regulated HoxA loci tested. Consistent with this, the addition of PHF1 specifically stimulated the ability of Ezh2 to catalyze H3K27me3 but not H3K27me1/H3K27me2 in vitro. We conclude that PHF1 modulates the activity of Ezh2 in favor of the repressive H3K27me3 mark. Thus, we propose that PHF1 is a determinant in PcG-mediated gene repression.     

Do natural container habitats impede invader dominance? Predator-mediated coexistence of invasive and native container-dwelling mosquitoes

Predator-mediated coexistence of competitors occurs when a species that is superior in competition is also more vulnerable to a shared predator compared to a poorer competitor. The invasive mosquito Aedes albopictus is usually competitively superior to Ochlerotatus triseriatus. Among second instar larvae, A. albopictus show a lesser degree of behavioral modification in response to water-borne cues from predation by the larval midge Corethrella appendiculata than do O. triseriatus, rendering A. albopictus more vulnerable to predation by C. appendiculata than O. triseriatus. The hypothesis that C. appendiculata predation favors coexistence of these competitors predicts that C. appendiculata abundances will be negatively and positively correlated with A. albopictus and O. triseriatus abundances, respectively, and that coexistence will occur where C. appendiculata are common. Actual abundances of O. triseriatus, A. albopictus, and C. appendiculata in three habitats fit this prediction. In natural container habitats like tree holes, C. appendiculata were abundant and competitors co-existed at similar densities. In cemeteries and tires, which occur primarily in non-forested, human-dominated habitats, A. albopictus dominated, with abundances twice those found in tree holes, but C. appendiculata and O. triseriatus were rare or absent. We also tested for whether antipredatory behavioral responses of A. albopictus differed among habitats or populations, or were correlated with local C. appendiculata abundances. We could detect no differences in A. albopictus antipredatory behavioral responses to water-borne cues from predation. Tree hole habitats appear to promote co-existence of O. triseriatus and A. albopictus through interactions with predatory C. appendiculata, and this predator effect appears to limit invasion success of A. albopictus in tree holes. There are many studies on predator-mediated coexistence in natural habitats but to our knowledge this is the first study to suggest differential predator-mediated coexistence between natural and man-made habitats. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effect of Extremely Low Power Time-Varying Electromagnetic Field on Germination and Other Characteristics in Foxtail Millet (Setaria italica) Seeds

The ability of extremely low, time-varying electromagnetic field (EMF) to improve germination efficacy was studied in Foxtail millet (Setaria italica) seeds using response surface methodology. An optimal factorial central composite design was chosen to optimize the EMF with three critical factors, viz. frequency, intensity, and duration. The adequacy of the model and fitness was evaluated by analysis of variance and regression coefficients. This model suggested that the factors, frequency, and intensity had a significant impact on germination. Optimal conditions for germination were observed to be 10 Hz frequency, 30,007 nT intensity, and 30-min duration with an observed germination percentage of 93.0, and a predicted germination percentage of 92.92. Magneto-priming was found to increase the germination efficacy (15.66%), shoot length (27.78%), total seedling length (20.30%), seedling dry mass (26.49%), and water uptake (34.48% at 80 min) showing significant output when compared with the control and positive controls. Remarkable improvements were observed in germination parameters such as vigor index-1 (39.14%), vigor index-2 (46.28%), speed of germination (27.52%), and emergence index (12.50%). Magneto-priming was found to reduce the levels of germination-specific enzymes, viz. α-amylase, protease, and dehydrogenase, while it enhanced the levels of antioxidant enzymes, viz. catalase (114.63%) and superoxide dismutase (19.62%), triggering fast germination and early vigor of seedlings. This study clearly showed that EMF priming significantly improved the germination effect and other characteristics of Foxtail millet seeds. Bioelectromagnetics. © 2020 Bioelectromagnetics Society     

Effect of vitamin E and menadione supplementation on riboflavin production and stress parameters in Ashbya gossypii

Ashbya gossypii is a filamentous fungus which overproduces riboflavin as a pseudo-secondary metabolite. Vitamin E supplemented at 1, 2.5 and 5 μM levels in the growth medium of A. gossypii increased the extracellular secretion of riboflavin and at 50, 100 and 240 μM levels reduced the biomass and riboflavin yield. With 2.5 μM vitamin E total riboflavin production and extracellular riboflavin secretion on day 2 was higher than non-supplemented control. By day 3 the production in supplemented was nearly the same as in non-supplemented, but the intracellular riboflavin levels were lower and extracellular levels higher. Supplemented cells showed increased levels of catalase, glutathione peroxidase, lipid peroxides and membrane lipid peroxides, and decreased glutathione indicating that vitamin E, a well-known antioxidant, had acted as a pro-oxidant at low levels of 2.5 μM and had increased the oxidative stress. Menadione, a well known oxidant also increased riboflavin production and secretion at 1.0, 2.5 and 5.0 μM level. This is the first report were vitamin E and menadione effects support the concept that overproduction of riboflavin is a stress induced phenomenon. These findings are not only of scientific interest but also useful for improving the industrial production of riboflavin.