Functional assignment to JEV proteins using SVM

Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).     

Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.     

Hemoglobin redox reactions and oxidative stress

Abstract

The role of hemoglobin in transporting oxygen is dependent on the reversible binding of oxygen to Fe(II) hemoglobin with molecular oxygen released at reduced oxygen pressures. The partially oxygenated hemoglobin formed with the release of oxygen from hemoglobin is susceptible to redox reactions where the functional Fe(II) heme is oxidized to Fe(III) and the substrate is reduced. In this article, we review two important redox reactions of hemoglobin and discuss the ramifications of these reactions. The reduction of oxygen to superoxide starts a cascade of oxidative reactions, which are a source for red cell-induced oxidative stress. The reduction of nitrite to nitric oxide produces a labile form of nitric oxide that can be a source for oxidative stress, but can also have important physiological functions.     

Obesity in Older Adults: Technical Review and Position Statement of the American Society for Nutrition and NAASO,The Obesity Society

Obesity causes serious medical complications and impairs quality of life. Moreover, in older persons, obesity can exacerbate the age‐related decline in physical function and lead to frailty. However, appropriate treatment for obesity in older persons is controversial because of the reduction in relative health risks associated with increasing body mass index and the concern that weight loss could have potential harmful effects in the older population. This joint position statement from the American Society for Nutrition and NAASO, The Obesity Society reviews the clinical issues related to obesity in older persons and provides health professionals with appropriate weight‐management guidelines for obese older patients. The current data show that weight‐loss therapy improves physical function, quality of life, and the medical complications associated with obesity in older persons. Therefore, weight‐loss therapy that minimizes muscle and bone losses is recommended for older persons who are obese and who have functional impairments or medical complications that can benefit from weight loss.     

Ecosystem function and species loss – a microcosm study

There are too many kinds of organisms to be able to study and manage each, yet the loss of a single species can sometimes unravel an ecosystem. Such `fusewire species'– critical in the same sense that an electrical fuse can cut out a whole circuit – would be a rewarding focus for research and management effort. However, this approach can only be effective if these `fusewires' represent but a small proportion of the number of species in the system.  

Aim

To demonstrate methods for measuring what proportion of the species in a system are critical to ecosystem function.  

Methods

The prevalence of fusewire species was measured in manipulative experiments on an aquatic microcosm.  

Results

No single genus deletion caused changes in key characteristics of the system.  

Main conclusions

Comparison of these results with other published studies shows that the proportion of critical fusewire species varies amongst different ecosystems. The oxidation pond microcosms were shown to contain no single species indispensable to system function. They appear to be ill-suited to a management strategy which focuses on priority eukaryote species. However, a single study provides no evidence that this result is general or even typical of other kinds of ecosystems; it is presented here as an empirical model. Other methods of investigation are available; they are less experimentally rigorous but more practical. These could provide important guidance in planning an approach to management in a particular ecosystem.     

Distribution of Adult Male and Female Baccharis concinna (Asteraceae) in the Rupestrian Fields of Serra Do Cipó, Brazil

Abstract: This study focuses on the sex ratio and spatial distribution of males and females in three populations of the endemic and restricted tropical dioecious shrub, Baccharis concinna (Asteraceae) in the mountainous region of Serra do Cipó, southeastern Brazil. The proportion of female plants in the population at lower elevation (1000 m a.s.l.) was significantly greater than of male plants. At this elevation of P/N and Ca/Al ratios in the soil were also greater indicating better nutritional status of the soils. The concentration of aluminium increased significantly with the elevation ( p < 0.001), perhaps rendering soils less conducive to female plants at higher elevations. Female plants are possibly adversely affected to a greater extent by soil quality than male plants. The spatial distribution of the populations within habitat was tested by the K(t) function, where the neighbourhood of a given individual was defined by a circle with a radius (t) up to 3 m. Despite the strong tendency for aggregation, the distribution of the sexes within habitats was random and the hypothesis was not supported. The independent distribution of the sexes within habitats may be explained by nutrient homogeneity of the soils, as well as by an absence of antagonism between the sexes. Nevertheless, we found a trend for males and females to be aggregated according to their gender.     

Bayesian Estimation of the Distribution Function of the Poisson Model

This paper presents the Bayes estimators of the Poisson distribution function based on complete and truncated data under a natural conjugate prior. Laplace transform of the incomplete gamma function and the Gauss hypergeometric function have been employed in order to overcome the intractability of the integrals. Numerical examples from biosciences are given to illustrate the results. A Monte Carlo study has been carried out to compare Bayes estimators under complete data with the corresponding maximum liklihood estimators.     

Developmental studies on the loricate choanoflagellateStephanoeca diplocostata Ellis. V. The cytoskeleton and the effects of microtubule poisons

Summary InStephanoeca diplocostata microtubules are located in four positions namely: within the flagellar axoneme; just beneath the plasmalemma; associated with the silica deposition vesicles (SDVs) during early stages of costal strip deposition; and in the mitotic spindle. At the anterior end of the cell the 50–60 peripheral microtubules, which are organized more or less parallel to the long axis of the cell, converge around the base of the emergent flagellum. A short second flagellar base is positioned between the nucleus and the base of the emergent flagellum. Developing costal strips are located individually within SDVs in the peripheral cytoplasm. During the early stages of silica deposition each SDV is curved and subtended longitudinally on its concave side by two microtubules. When a costal strip has achieved sufficient rigidity to withstand bending the SDV-associated microtubules are depolymerized. Treatment of exponentially growing cells with sublethal concentrations of microtubule poisons, such as colchicine, podophyllotoxin, griseofulvin andVinca alkaloids depresses growth. Treatment with these drugs also affects the length and morphology of developing costal strips perhaps by interfering with the shaping and supporting functions of SDV-associated microtubules. Instead of being long and crescentic with a standard radius of curvature, costal strips of treated cells are usually short and misshapen, with irregular bends. After drug treatment, juveniles produced as a result of cell division do not develop flagella but can still assemble a lorica although it is usually misshapen. The role of microtubules and microfilaments in lorica production is discussed.