Impact of ambient and supplemental ultraviolet-B stress on kidney bean plants: an insight into oxidative stress management

In the present study, the response of kidney bean (Phaseolus vulgaris L. cv. Pusa Komal) plants was evaluated under three different levels of ultraviolet-B (UV-B), i.e., excluded UV-B (eUV-B), ambient UV-B (aUV-B; 5.8 kJ m^?2 day^?1), and supplemental UV-B (sUV-B; 280–315 nm; ambient?+?7.2 kJ m^?2 day^?1), under near-natural conditions. eUV-B treatment clearly demonstrated that both aUV-B and sUV-B are capable of causing significant changes in the plant’s growth, metabolism, economic yield, genome template stability, total protein, and antioxidative enzyme profiles. The experimental findings showed maximum plant height at eUV-B, but biomass accumulation was minimum. Significant reductions in quantum yield (Fv/Fm) were observed under both aUV-B and sUV-B, as compared to eUV-B. UV-B-absorbing flavonoids increased under higher UV-B exposures with consequent increments in phenylalanine ammonia lyase (PAL) activities. The final yield was significantly higher in plants grown under eUV-B, compared to those under aUV-B and sUV-B. Total protein profile through sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and analysis of isoenzymes, like superoxide dismutase (SOD), peroxidase (POX), catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GPX), and glutathione reductase (GR), through native PAGE revealed major changes in the leaf proteome under aUV-B and sUV-B, depicting induction of some major stress-related proteins. The random amplified polymorphic DNA (RAPD) profile of genomic DNA also indicated a significant reduction of genome template stability under UV-B exposure. Thus, it can be inferred that more energy is diverted for inducing protection mechanisms rather than utilizing it for growth under high UV-B level.     

Spatio‐temporal patterns of genome evolution in allotetraploid species of the genus Oryza

Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct ‘genome types’ (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1–Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels provided several insights into the spatio‐temporal dynamics of genome organization and evolution of this region in ‘natural’ polyploids of Oryza. The major findings of this study are that: (i) homoeologous genomic regions within the same nucleus experience both independent and parallel evolution, (ii) differential lineage‐specific selection pressures do not occur between polyploids and their diploid progenitors, (iii) there have been no dramatic structural changes relative to the diploid ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the BC complex species even though the BC and CD polyploid species appear to have arisen <2 million years ago, and (v) there are no clear distinctions in the patterns of genome evolution in the diploid versus polyploid species.     

A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli

MOTIVATION: Inclusion body formation has been a major deterrent for overexpression studies since a large number of proteins form insoluble inclusion bodies when overexpressed in Escherichia coli. The formation of inclusion bodies is known to be an outcome of improper protein folding; thus the composition and arrangement of amino acids in the proteins would be a major influencing factor in deciding its aggregation propensity. There is a significant need for a prediction algorithm that would enable the rational identification of both mutants and also the ideal protein candidates for mutations that would confer higher solubility-on-overexpression instead of the presently used trial-and-error procedures. RESULTS: Six physicochemical properties together with residue and dipeptide-compositions have been used to develop a support vector machine-based classifier to predict the overexpression status in E.coli. The prediction accuracy is approximately 72% suggesting that it performs reasonably well in predicting the propensity of a protein to be soluble or to form inclusion bodies. The algorithm could also correctly predict the change in solubility for most of the point mutations reported in literature. This algorithm can be a useful tool in screening protein libraries to identify soluble variants of proteins.     

Vascular changes precede tomographic changes in diabetic eyes without retinopathy and improve artificial intelligence diagnostics

The purpose of this study was to evaluate early vascular and tomographic changes in the retina of diabetic patients using artificial intelligence (AI). The study included 74 age‐matched normal eyes, 171 diabetic eyes without retinopathy (DWR) eyes and 69 mild non‐proliferative diabetic retinopathy (NPDR) eyes. All patients underwent optical coherence tomography angiography (OCTA) imaging. Tomographic features (thickness and volume) were derived from the OCTA B‐scans. These features were used in AI models. Both OCT and OCTA features showed significant differences between the groups (P < .05). However, the OCTA features indicated early retinal changes in DWR eyes better than OCT (P < .05). In the AI model using both OCT and OCTA features simultaneously, the best area under the curve of 0.91 ± 0.02 was obtained (P < .05). Thus, the combined use of AI, OCT and OCTA significantly improved the early diagnosis of diabetic changes in the retina.     

Generation of a tissue-specific transgenic model for K8 phosphomutants: A tool to investigate the role of K8 phosphorylation during skin carcinogenesis in vivo

Keratin 8/18, the predominant keratin pair of simple epithelia, is known to be aberrantly expressed in several squamous cell carcinomas (SCCs), where its expression is often correlated with increased invasion, neoplastic progression, and poor prognosis. The majority of keratin 8/18 structural and regulatory functions are governed by posttranslational modifications, particularly phosphorylation. Apart from filament reorganization, cellular processes including cell cycle, cell growth, cellular stress, and apoptosis are known to be orchestrated by K8 phosphorylation at specific residues in the head and tail domains. Even though deregulation of K8 phosphorylation at two significant sites (Serine⁷³/Serine⁴³¹) has been implicated in neoplastic progression of SCCs by various in vitro studies, including ours, it is reported to be highly context-dependent. Therefore, to delineate the precise role of Kereatin 8 phosphorylation in cancer initiation and progression, we have developed the tissue-specific transgenic mouse model expressing Keratin 8 wild type and phosphodead mutants under Keratin 14 promoter. Subjecting these mice to 7,12-dimethylbenz(a)anthracene/12-O-tetradecanoylphorbol-13-acetate-mediated skin carcinogenesis revealed that Keratin 8 phosphorylation may lead to an early onset of tumors compared to Keratin 8 wild-type expressing mice. Conclusively, the transgenic mouse model developed in the present study ascertained a positive impact of Keratin 8 phosphorylation on the neoplastic transformation of skin-squamous cells.