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Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information.Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.

Metallic nanoparticles are widely used in cosmetics, food products and textile industry. These particles are known to cause respiratory toxicity and epithelial inflammation. They are eventually released to aquatic environment necessitating toxicity studies in cells from respiratory organs of aquatic organisms. Hence, we have developed and characterized a new cell line, WAG, from gill tissue of Wallago attu for toxicity assessment of TiO2 and ZnO nanoparticles. The efficacy of the cell line as an in vitro system for nanoparticles toxicity studies was established using electron microscopy, cytotoxicity assays, genotoxicity assays and oxidative stress biomarkers. Results obtained with MTT assay, neutral red uptake assay and lactate dehydrogenase assay showed acute toxicity to WAG cells with IC50 values of 25.29±0.12, 34.99±0.09 and 35.06±0.09 mg/l for TiO2 and 5.716±0.1, 3.160±0.1 and 5.57±0.12 mg/l for ZnO treatment respectively. The physicochemical properties and size distribution of nanoparticles were characterized using electron microscopy with integrated energy dispersive X-ray spectroscopy and Zetasizer. Dose dependent increase in DNA damage, lipid peroxidation and protein carbonylation along with a significant decrease in activity of Superoxide Dismutase, Catalase, total Glutathione levels and total antioxidant capacity with increasing concentration of exposed nanoparticles indicated that the cells were under oxidative stress. The study established WAG cell line as an in vitro system to study toxicity mechanisms of nanoparticles on aquatic organisms.

Alexithymia, characterized by difficulty in identifying and describing feelings and a deficit in the cognitive modulation of emotions, has been linked with health related problems. Indirect empirical evidences suggest the possibility that alexithymia may potentially also relate with emotion regulation difficulties. However, the exact nature of the relationship between the two constructs has not been fully explored. The relationship between the two constructs may reflect the overlap of the content domains or dependence of one (e.g., emotion regulation difficulties) on the other (e.g., alexithymia). Given the link between the two constructs, it is also likely that alexithymics" health related difficulties may result from their impaired ability to regulate emotions. The present study tested the above theoretical propositions on 27 alexithymic and 26 nonalexithymic participants who were assessed on self-report measures of emotion regulation difficulties and general mental health. The findings revealed that compared to non-alexithymics, the alexithymics showed greater emotion regulation difficulties and such affective difficulties differentiated the two groups with a very high accuracy. Further, the observation of two orthogonal components (emotion regulation difficulties and alexithymia) with a minimum overlap suggests that these constructs represent two independent domains of behavior. Findings also revealed that alexithymics reported more health related problems as compared to non-alexithymics and the health problems of alexithymics are likely to be an outcome of their emotion regulation difficulties (indicated by a non-significant health difference after controlling for emotion regulation difficulties). The findings imply that alexithymia is associated with emotion regulation difficulties and such difficulties largely contribute to health related problems.

Evidently, epigenetics is at forefront in explaining the mechanisms underlying the success of human pathogens and in the identification of pathogen-induced modifications within host plants. However, there is a lack of studies highlighting the role of epigenetics in the modulation of the growth and pathogenicity of fungal plant pathogens. In this review, we attempt to highlight and discuss the role of epigenetics in the regulation of the growth and pathogenicity of fungal phytopathogens using Magnaporthe oryzae, a devastating fungal plant pathogen, as a model system. With the perspective of wide application in the understanding of the development, pathogenesis and control of other fungal pathogens, we attempt to provide a synthesized view of the epigenetic studies conducted on M. oryzae to date. First, we discuss the mechanisms of epigenetic modifications in M. oryzae and their impact on fungal development and pathogenicity. Second, we highlight the unexplored epigenetic mechanisms and areas of research that should be considered in the near future to construct a holistic view of epigenetic functioning in M. oryzae and other fungal plant pathogens. Importantly, the development of a complete understanding of the modulation of epigenetic regulation in fungal pathogens can help in the identification of target points to combat fungal pathogenesis.

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