Analysis of P-Loop and its Flanking Region Subsequence of Diverse NTPases Reveals Evolutionary Selected Residues

The P-loop NTPases are involved in diverse cellular functions. Members of the P-loop NTPase superfamily are characterized by presence of a highly conserved sequence pattern GxxxxGKS/T, known as Walker A motif. This motif adopts an archetypal P-loop conformation which allows accommodation of the triphosphate moiety of a bound nucleotide. Despite the presence of Walker A as a common sequence motif, P-loop NTPases exhibit extreme sequence divergence which hampers their phylogenetic or evolutionary classification. Here, we show that P-loop and its flanking region subsequence (termed as “extended-WalkerA motif”) contain distinct signatures that can be utilized to classify NTPase domain of functionally diverse proteins. We find a clearly classified group of diverse NTPases of Conserved Domain Database such as G-proteins, Ylqf, RecA like, DExDc, AAA, CPT, NK, ABC transporter and NifH proteins.     

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.Subject terms: Plant genetics, Plant breeding, Agricultural genetics, Quantitative trait

Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a platform for research and development. In this review, we examine three themes covering new developments in crop MPP research: (1) we survey the rapidly expanding variety of crop MPPs, explaining how differences in their design and construction affect their power and precision in mapping quantitative trait loci (QTL), on which we provide a brief primer. (2) We review the use of genomic technologies in MPPs, which have proven particularly suitable for gathering dense genomic information across large populations. We make general recommendations for collecting genotypic resources in MPPs. (3) We discuss successful applications of MPPs, particularly where they have been used for breeding and pre-breeding. This includes the identification of QTL, the application of genomic prediction to MPPs, and the direct use of MPP lines as germplasm for varietal release or pre-breeding. These recent developments have shown the potential of MPPs for crop improvement.     

Mild alkaline pretreatment can achieve high hydrolytic and fermentation efficiencies for rice straw conversion to bioethanol

Abstract

Mild alkaline pretreatment was evaluated as a strategy for effective lignin removal and hydrolysis of rice straw. The pretreatment efficiency of different NaOH concentrations (0.5, 1.0, 1.5 or 2.0% w/w) was assessed. Rice straw (RS) pretreated with 1.5% NaOH achieved better sugar yield compared to other concentrations used. A cellulose conversion efficiency of 91% (45.84?mg/ml glucose release) was attained from 1.5% NaOH pretreated rice straw (PRS), whereas 1% NaOH pretreated rice straw yielded 35.10?mg/ml of glucose corresponding to a cellulose conversion efficiency of 73.81%. The ethanol production from 1% and 1.5% NaOH pretreated RS hydrolysates was similar at ～3.3% (w/v), corresponding to a fermentation efficiency of 86%. The non-detoxified hydrolysate was fermented using the novel yeast strain Saccharomyces cerevisiae RPP-03O without any additional supplementation of nutrients.     

Insights from the docking analysis of biologically active compounds from plant Litsea Genus as potential COX-2 inhibitors

Litsea spp of Laural family are traditionally used as herbal medicine for treating inflammation including gastroenterologia, oedema and rheumatic arthritis. Therefore, it is of interest to investigate and understand the molecular principles for such actions. Here, we have illustrated the binding of thirteen Litsea derived biologically active compounds against the inflammation associated target COX (cyclo-oxygenase) -2 enzymes. We compared the binding information of these compounds with a selected number of already known COX-2 inhibitors. The comparison reflected that some of these compounds such as linderol, catechin, 6''-hydroxy-2'',3'',4'' - trimethoxy-chalcone and litseaone have better or equivalent binding features compared to already known inhibitory compounds namely celecoxib, acetylsalicylic acid, rofecoxib. Therefore, all these small compounds reported from plant Litsea spp were found to possess potential medicinal values with anti-inflammatory properties.     

Comparison of innate immune activation after prolonged feeding of milk fermented with three species of Lactobacilli

The present investigation aimed at identifying the abilities of three different species of probiotic lactobacilli to modulate cellular immune responses in mouse neutrophils and macrophages in vivo over a study period of 60 days. Neutrophil respiratory burst enzymes (cytochrome c reductase and MPO) showed remarkable increased activity (P ≤ 0.01) after consumption of milks fermented by different species of probiotics over 30 and 60 days of feeding trials. Enzyme activities (β‐galactosidase and β‐glucuronidase) and nitric oxide production also increased considerably (P ≤ 0.01) in macrophages, both in peritoneal fluid and in enriched cell cultures. The effects of enhanced enzyme activities were corroborated by simultaneous increases in the phagocytic activities of neutrophils and macrophages. The increases in cellular functions were invariably maximal during the first 30 days of study and were maintained, but did not increase, over the next 30 days. Further, Lactobacillus helveticus‐fed groups were most effective at modulating neutrophil functions whereas Lactobacillus paracasei‐fed groups were more potent at enhancing macrophage functions. Together, our results indicate that probiotics have strain specific effects on stimulating cellular functions while not causing excessive stimulation of the immune system over longer feeding periods, thereby resulting in maximum and stable health benefits.