Mycobacterial PE_PGRS Proteins Contain Calcium-Binding Motifs with Parallel β-roll Folds

The PE_PGRS family of proteins unique to mycobacteria is demonstrated to con- rain multiple calcium-binding and glycine-rich sequence motifs GGXGXD/NXUX. This sequence repeat constitutes a calcium-binding parallel/3-roll or parallel β-helix structure and is found in RTX toxins secreted by many Gram-negative bacteria. It is predicted that the highly homologous PE_PGRS proteins containing multiple copies of the nona-peptide motif could fold into similar calcium-binding structures. The implication of the predicted calcium-binding property of PE_PGRS proteins in the Ught of macrophage-pathogen interaction and pathogenesis is presented.     

The use of solid waste of a nylon-6 plant as a nutrient for bacterial decolourisation of dyes

Three caprolactam-degrading bacterial isolates grew in liquid synthetic medium containing solubilised solid waste of a nylon-6 production plant as the sole source of carbon and nitrogen. Typically, the caprolactam content of solid waste was decreased by 95% in 72 h by Alcaligenes faecalis. A. faecalis was the most potent caprolactam-degrading bacterium out of the three isolates. The biomass of the bacteria obtained by growth in the solubilised solid waste medium had the ability to decolourise some synthetic azo and triphenylmethane dyes. Decolourisation of dyes was obtained in static condition, in synthetic medium which contained only the components of the solid waste as the sole sources of carbon and nitrogen and also in nutritionally rich medium. The supplementation of yeast extract to solid waste medium did not increase the efficiency of decolourisation in case of two of the bacterial cultures. Depending on the dye, medium and bacteria used, decolourisation in the range of 35–94% was achieved in 48–96 h. The decolourisation was not due to the adsorption of the dyes by the bacterial biomass except in case of Procion Blue MR and Black B. Based on these observations, the simultaneous biological treatment of the solid waste of nylon-6 plant and the decolourisation of synthetic dyes present in wastewater or solid waste is envisaged.     

Thermal Stress Impacts on Reproductive Development and Grain Yield in Grain Legumes

Temperature stress (cold, heat) during reproductive development is one of the serious constraints to the productivity of grain legumes as their cultivation is expanding to warmer environments and temperature variability is increasing due to climate change. Grain legumes exposed to temperature below 10-15°C or above 30°C show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to substantial reduction in grain yield. For managing these effects of temperature extremes, it is important to improve the resistance of grain legumes by using improved breeding and genetic engineering tools. In this review article, the impact of both high and low temperature stress on different phases of the reproductive stage, from meiosis to grain filling, and the sensitivity of different reproductive organs to temperature extremes are discussed. The review also covers the management options to improve resistance to temperature stress in grain legumes. Furthermore, innovative breeding, genetic and molecular strategies in grain legumes against temperature stress are also discussed.     

Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population of Drosophila melanogaster (DGRP) allowed us to rediscover three known cases of adaptation at the loci Ace, Cyp6g1, and CHKov1 known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harris et al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and that instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps in D. melanogaster are first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that most demographic models employed in such analyses are necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require a large number of free parameters.     

Soil carbon sequestration: an innovative strategy for reducing atmospheric carbon dioxide concentration

Global warming due to increasing greenhouse gases emission and the subsequent climatic changes are the most serious environmental challenges faced by environmental scientists, academicians, regulatory agencies and policy makers worldwide. Among the various greenhouse gases, CO₂ constitutes a major share and its concentration is increasing rapidly. Therefore, there is perhaps an urgent need to formulate suitable policies and programs that can firmly reduce and sequester CO₂ emissions in a sustainable way. In order to combat the predicted disaster due to rising CO₂ level, several CO₂ capture and storage technologies and medium are being widely pursued and deliberated. Among them soil carbon sequestration (SCS) is gaining global attention because of its stability and role in long-term surface reservoir, natural low cost and eco-friendly means to combat climate change. Apart from the carbon capturing, the process of soil carbon stabilization also provides other tangible benefits that includes achieving food security, by improving soil quality, wasteland reclamation and preventing soil erosion. The present article aimed to address all these concerns and provide strategies and critical research needs to implement SCS as a mitigation option for increasing atmospheric CO₂ level and its future directions.     

Mycobacterial PE_PGRS Proteins Contain Calcium-Binding Motifs with Parallel β-roll Folds

The PE_PGRS family of proteins unique to mycobacteria is demonstrated to con- rain multiple calcium-binding and glycine-rich sequence motifs GGXGXD/NXUX. This sequence repeat constitutes a calcium-binding parallel/3-roll or parallel β-helix structure and is found in RTX toxins secreted by many Gram-negative bacteria. It is predicted that the highly homologous PE_PGRS proteins containing multiple copies of the nona-peptide motif could fold into similar calcium-binding structures. The implication of the predicted calcium-binding property of PE_PGRS proteins in the Ught of macrophage-pathogen interaction and pathogenesis is presented.     

Effect of poly(vinyl alcohol) treatment of the dyematrix on the chromatography of pyruvate kinase

Summary The utility of poly(vinyl alcohol) as a shielding polymer in dye-affinity chromatography was studied. Difference spectroscopy was used to estimate the strength of the polymer-dye complex. The target enzyme, pyruvate kinase (E.C. 2.7.1.40) from porcine muscle was purified on a Red HE3B-Sepharose column with 95% recovery by salt elution and 85% recovery with specific eluent.