Natural and Unanticipated Modifiers of RNAi Activity in Caenorhabditis elegans

Organisms used as model genomics systems are maintained as isogenic strains, yet evidence of sequence differences between independently maintained wild-type stocks has been substantiated by whole-genome resequencing data and strain-specific phenotypes. Sequence differences may arise from replication errors, transposon mobilization, meiotic gene conversion, or environmental or chemical assault on the genome. Low frequency alleles or mutations with modest effects on phenotypes can contribute to natural variation, and it has proven possible for such sequences to become fixed by adapted evolutionary enrichment and identified by resequencing. Our objective was to identify and analyze single locus genetic defects leading to RNAi resistance in isogenic strains of Caenorhabditis elegans. In so doing, we uncovered a mutation that arose de novo in an existing strain, which initially frustrated our phenotypic analysis. We also report experimental, environmental, and genetic conditions that can complicate phenotypic analysis of RNAi pathway defects. These observations highlight the potential for unanticipated mutations, coupled with genetic and environmental phenomena, to enhance or suppress the effects of known mutations and cause variation between wild-type strains.     

Insight from γC1 protein model for implication in cotton leaf curl disease

DNA γ is approximately half of the size of Begomovirus DNA. It encodes a γC1 gene that is conserved in position and size. This gene has the capacity to encode a 13 to 14 kDa protein comprising 118 amino acid residues. It has been shown earlier that γC1 protein is necessary for inducing symptoms of cotton leaf curl disease. The structure for γC1 (CLCuDγ01-Pakistan) is still unknown. Therefore, a model of γC1 (CLCuDγ01-Pakistan) was developed using DoBo and I-TASSER servers followed by validation by PROCHECK and VERIFY 3D servers. The developed model provides an insight in a role for this multifunctional protein in causing Cotton Leaf Curl Disease (CLCuD). A possible function of this protein might be the suppression of RNAsilencing in cotton plants.     

An Optimal Au Grating Structure for Light Absorption in Amorphous Silicon Thin Film Solar Cell

Plasmonics - Effect of different gold (Au) grating structures on light absorption in solar cell is investigated by finite elemental analysis using COMSOL multiphysics-RF module. The geometry of the...     

Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage

Molecular Biology Reports - Sesame is an ancient oilseed crop, known for its high oil content and quality. Its sensitivity to drought at early seedling stage is one of the limiting factors...     

Changes in Gut Microbiota in Rats Fed a High Fat Diet Correlate with Obesity-Associated Metabolic Parameters

The gut microbiota is emerging as a new factor in the development of obesity. Many studies have described changes in microbiota composition in response to obesity and high fat diet (HFD) at the phylum level. In this study we used 16s RNA high throughput sequencing on faecal samples from rats chronically fed HFD or control chow (n = 10 per group, 16 weeks) to investigate changes in gut microbiota composition at the species level. 53.17% dissimilarity between groups was observed at the species level. Lactobacillus intestinalis dominated the microbiota in rats under the chow diet. However this species was considerably less abundant in rats fed HFD (P<0.0001), this being compensated by an increase in abundance of propionate/acetate producing species. To further understand the influence of these species on the development of the obese phenotype, we correlated their abundance with metabolic parameters associated with obesity. Of the taxa contributing the most to dissimilarity between groups, 10 presented significant correlations with at least one of the tested parameters, three of them correlated positively with all metabolic parameters: Phascolarctobacterium, Proteus mirabilis and Veillonellaceae, all propionate/acetate producers. Lactobacillus intestinalis was the only species whose abundance was negatively correlated with change in body weight and fat mass. This species decreased drastically in response to HFD, favouring propionate/acetate producing bacterial species whose abundance was strongly correlated with adiposity and deterioration of metabolic factors. Our observations suggest that these species may play a key role in the development of obesity in response to a HFD.     

Mechanisms of Human Erythrocytic Bioactivation of Nitrite

Nitrite signaling likely occurs through its reduction to nitric oxide (NO). Several reports support a role of erythrocytes and hemoglobin in nitrite reduction, but this remains controversial, and alternative reductive pathways have been proposed. In this work we determined whether the primary human erythrocytic nitrite reductase is hemoglobin as opposed to other erythrocytic proteins that have been suggested to be the major source of nitrite reduction. We employed several different assays to determine NO production from nitrite in erythrocytes including electron paramagnetic resonance detection of nitrosyl hemoglobin, chemiluminescent detection of NO, and inhibition of platelet activation and aggregation. Our studies show that NO is formed by red blood cells and inhibits platelet activation. Nitric oxide formation and signaling can be recapitulated with isolated deoxyhemoglobin. Importantly, there is limited NO production from erythrocytic xanthine oxidoreductase and nitric-oxide synthase. Under certain conditions we find dorzolamide (an inhibitor of carbonic anhydrase) results in diminished nitrite bioactivation, but the role of carbonic anhydrase is abrogated when physiological concentrations of CO₂ are present. Importantly, carbon monoxide, which inhibits hemoglobin function as a nitrite reductase, abolishes nitrite bioactivation. Overall our data suggest that deoxyhemoglobin is the primary erythrocytic nitrite reductase operating under physiological conditions and accounts for nitrite-mediated NO signaling in blood.     

Awareness and Acceptance of Evolution and Evolutionary Medicine Among Medical Students in Pakistan

Evolutionary medicine is a perspective on medical sciences derived through application of theory of evolution to aid in therapeutics. This study sought to determine the level of knowledge and acceptance of evolutionary theory in medical students along with their attitude toward teaching evolutionary medicine as a part of their undergraduate course. Factors that are likely to cause difficulty in teaching evolutionary medicine were also identified. A cross-sectional study was carried out at Army Medical College, National University of Sciences and Technology, Pakistan in which 299 medical students were selected by nonprobability convenient sampling technique to participate in the study. Participants’ views were obtained by a structured questionnaire comprised of three sections: appreciation of evolutionary medicine, acceptance of evolutionary theory, knowledge of evolutionary theory. Medical students had a low acceptance [mean measure of acceptance of theory of evolution (MATE) = 58.32] and a low knowledge (mean score of 5.20 out of a total ten marks). Students believed that religious beliefs, lack of resources, and an existent extensive medical curriculum would cause difficulty in imparting such an education despite its potential to improve medical research and clinical practice. Only 37.2% agreed that the subject should be taught in medical schools as an individual subject.     

A Two-Level Computation Model Based on Deep Learning Algorithm for Identification of piRNA and Their Functions via Chou’s 5-Steps Rule

International Journal of Peptide Research and Therapeutics - Piwi interacting RNA (piRNA) molecules belong to a largest class of small non coding RNA molecules which are originally discovered in...