Simulation of Finnish Population History,Guided by Empirical Genetic Data,to Assess Power of Rare-Variant Tests in Finland

Finnish samples have been extensively utilized in studying single-gene disorders, where the founder effect has clearly aided in discovery, and more recently in genome-wide association studies of complex traits, where the founder effect has had less obvious impacts. As the field starts to explore rare variants’ contribution to polygenic traits, it is of great importance to characterize and confirm the Finnish founder effect in sequencing data and to assess its implications for rare-variant association studies. Here, we employ forward simulation, guided by empirical deep resequencing data, to model the genetic architecture of quantitative polygenic traits in both the general European and the Finnish populations simultaneously. We demonstrate that power of rare-variant association tests is higher in the Finnish population, especially when variants’ phenotypic effects are tightly coupled with fitness effects and therefore reflect a greater contribution of rarer variants. SKAT-O, variable-threshold tests, and single-variant tests are more powerful than other rare-variant methods in the Finnish population across a range of genetic models. We also compare the relative power and efficiency of exome array genotyping to those of high-coverage exome sequencing. At a fixed cost, less expensive genotyping strategies have far greater power than sequencing; in a fixed number of samples, however, genotyping arrays miss a substantial portion of genetic signals detected in sequencing, even in the Finnish founder population. As genetic studies probe sequence variation at greater depth in more diverse populations, our simulation approach provides a framework for evaluating various study designs for gene discovery.     

Impact of body melanisation on desiccation resistance in montane populations of D. melanogaster: Analysis of seasonal variation

In the montane localities of subtropical regions, winter is the dry season and ectothermic drosophilids are expected to evolve desiccation resistance to cope with drier climatic conditions. An analysis of six montane populations (600–2226 m) of D. melanogaster showed variations for body melanisation (i.e. pigmentation) and desiccation resistance across seasons as well as along altitude. During winter season, plastic changes for melanisation of three posterior abdominal segments (5th + 6th + 7th) correspond with higher desiccation resistance. Thus, we analyzed genetic and plastic effects for these ecophysiological traits by comparing wild-caught and laboratory reared individuals of D. melanogaster for autumn as well as winter season. A ratio of slope values in wild vs. laboratory populations has shown a 1.64-fold plastic effect during autumn; and a two-fold effect during winter. For body melanisation and desiccation resistance, evolutionary response to altitudinal environmental gradient is similar to the phenotypic response across seasons. Thus, our observations are in agreement with the co-gradient hypothesis. Further, we tested the hypothesis whether a thicker cuticle (either due to melanisation or cuticular lipids) leads to lesser cuticular water loss and higher desiccation resistance across seasons as well as according to altitude. Based on within and between population analyses, body melanisation was found to be positively correlated with desiccation resistance but negatively with cuticular water loss. Interestingly, there were no changes in the amount of cuticular lipids per fly across seasons as well as along altitude; and therefore cuticular lipids did not account for desiccation resistance. Cuticular water loss exhibited negative correlation with body melanisation but not with cuticular lipids as well as with changes in body size across seasons. Thus, our data suggest that seasonal changes in body melanisation confer desiccation resistance in montane populations of D. melanogaster.     

Identification of antibodies directed against O-acetylated sialic acids in visceral leishmaniasis: its diagnostic and prognostic role

A significantly increased O-acetylated sialic acid (O-AcSA) binding fraction was purified from serum of visceral leishmaniasis (VL) patients by affinity chromatography on immobilized bovine submaxillary mucin (BSM) and found to be immunoglobulin in origin. The serodiagnostic and prognostic potential of BSM as a capture antigen was established by ELISA with no cross reactivity with coendemic diseases like malaria, tuberculosis, leprosy, chagas disease and cutaneous leishmaniasis; however, a strong cross reactivity was present with trypanosomiasis patients. In 56 clinically diagnosed VL patients, the BSM-ELISA was compared with diagnosis by microscopy using Giemsa stained tissue smears and direct ELISA using crude parasite antigen (parasite-ELISA); 49/56(87.5%) and 5/56(9.0%) were positive and negative respectively by all 3 methods. The BSM-ELISA failed to diagnose 2/56(3.5%) patients which were biopsy and parasite-ELISA positive. The prognostic potential of the BSM-ELISA in 18 longitudinally monitored VL patients before and after conventional antimonial treatment showed a significant decrease in anti O-AcSA titres in drug responsive patients whereas anti O-AcSA levels persisted in drug unresponsive patients. The IgG subclass distribution of antibodies directed against O-AcSA showed increased IgG2 levels in VL patients as compared to healthy controls. The BSM-based ELISA holds great promise as a serodiagnostic and prognostic assay for VL.     

Adaptive associations between total body color dimorphism and climatic stress‐related traits in a stenothermal circumtropical Drosophila species

Abstract Low desiccation resistance of Drosophila ananassae reflects its rarity outside the humid tropics. However, the ability of this sensitive species to evolve under seasonally varying subtropical areas is largely unknown. D. ananassae flies are mostly lighter during the rainy season but darker and lighter flies occur in the autumn season in northern India. We tested the hypothesis whether seasonally varying alternative body color phenotypes of D. ananassae vary in their levels of environmental stress tolerances and mating behavior. Thus, we investigated D. ananassae flies collected during rainy and autumn seasons for changes in body melanization and their genetic basis, desiccation‐related traits, cold tolerance and mating propensity. On the basis of genetic crosses, we found total body color dimorphism consistent with a single gene model in both sexes of D. ananassae. A significant increase in the frequency of the dark morph was observed during the drier autumn season, and body color phenotypes showed significant deviations from Hardy‐Weinberg equilibrium, which suggests climatic selection plays a role. Resistance to desiccation as well as cold stress were two‐ to three‐fold higher in the dark body color strain as compared with the light strain. On the basis of no‐choice mating experiments, we observed significantly higher assortative matings between dark morphs under desiccation or cold stress, and between light morphs under hot or higher humidity conditions. To the best of our knowledge, this is the first report on the ecological significance of seasonally varying total body color dimorphism in a tropical species, D. ananassae.     

Selection of Potential Probiotic Bacteria from Exclusively Breastfed Infant Faeces with Antagonistic Activity Against Multidrug-Resistant ESKAPE Pathogens

The past decade has brought a significant rise in antimicrobial resistance, and the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) have considerably aggravated a threat to public health, causing nosocomial infections worldwide. The objective of the current study was to isolate novel probiotic strain with antimicrobial activity against multidrug-resistant ESKAPE pathogens. For this purpose, eighteen breastfed infant faeces were collected and lactic acid bacteria (LAB) with antagonistic activity were isolated. Out of 102 anaerobic LAB isolated, only nine exhibited inhibitory activity against all ESKAPE pathogens. These selected nine isolates were further characterized for their probiotic attributes such as lysozyme tolerance, simulated gastrointestinal tolerance, cellular auto-aggregation and cell surface hydrophobicity. Bile salt deconjugation and cholesterol-lowering capacity was also determined. Among all nine, isolate LBM220 was found to possess superior probiotic potential. Confirmatory identification of isolate LBM220 was done by both 16S rRNA sequence analysis and mass spectrometric analysis using MALDI-TOF. Based on BLAST result, isolate LBM220 was identified as Lactobacillus gasseri. Phylogenetic analysis of Lactobacillus gasseri LBM220 [accession number MN097539] was performed. Also, detailed safety evaluation study of Lact. gasseri LBM220 showed the presence of intrinsic antibiotic resistance and the absence of hemolytic, DNase, gelatinase and toxic mucinolytic activity. Time kill assay was also performed to confirm the strong kill effect of Lact. gasseri LBM220 on all six multidrug resistant ESKAPE pathogens. Thus, Lact. gasseri LBM220 can be utilized and explored as potential probiotic with therapeutic intervention.