Chronic hypobaric hypoxia mediated skeletal muscle atrophy: role of ubiquitin–proteasome pathway and calpains

The most frequently reported symptom of exposure to high altitude is loss of body mass and decreased performance which has been attributed to altered protein metabolism affecting skeletal muscles mass. The present study explores the mechanism of chronic hypobaric hypoxia mediated skeletal muscle wasting by evaluating changes in protein turnover and various proteolytic pathways. Male Sprague-Dawley rats weighing about 200 g were exposed to hypobaric hypoxia (7,620 m) for different durations of exposure. Physical performance of rats was measured by treadmill running experiments. Protein synthesis, protein degradation rates were determined by (14)C-Leucine incorporation and tyrosine release, respectively. Chymotrypsin-like enzyme activity of the ubiquitin-proteasome pathway and calpains were studied fluorimetrically as well as using western blots. Declined physical performance by more than 20%, in terms of time taken in exhaustion on treadmill, following chronic hypobaric hypoxia was observed. Compared to 1.5-fold increase in protein synthesis, the increase in protein degradation was much higher (five-folds), which consequently resulted in skeletal muscle mass loss. Myofibrillar protein level declined from 46.79 ± 1.49 mg/g tissue at sea level to 37.36 ± 1.153 (P < 0.05) at high altitude. However, the reduction in sarcoplasmic proteins was less as compared to myofibrillar protein. Upregulation of Ub-proteasome pathway (five-fold over control) and calpains (three-fold) has been found to be important factors for the enhanced protein degradation rate. The study provided strong evidences suggesting that elevated protein turnover rate lead to skeletal muscle atrophy under chronic hypobaric hypoxia via ubiquitin-proteasome pathway and calpains.     

Impact of low and high fluence rates of UV-B radiation on growth and oxidative stress in Phormidium foveolarum and Nostoc muscorum under copper toxicity: differential display of antioxidants system

In the present study, impact of low (UV-B_L) and high (UV-B_H) fluence rates of UV-B on growth, oxidative stress and antioxidant system was studied in two cyanobacteria i.e. Phormidium foveolarum and Nostoc muscorum under Cu (2 and 5???M) toxicity after 24 and 72?h of experiments. UV-B_H and Cu treatment decreased growth of both the cyanobacteria and Cu induced decrease in growth was accompanied by a significant increase in Cu accumulation. Levels of reactive oxygen species (ROS), i.e. superoxide radicals (SOR; $ \text O_{2}^{\cdot\,-} $ ) and hydrogen peroxide (H₂O₂) were significantly increased by Cu and UV-B_H exposure which in turn accelerated lipid peroxidation (malondialdehyde: MDA) and protein oxidation (reactive carbonyl groups: RCG). Activities of enzymatic antioxidants, such as superoxide dismutase (SOD), peroxidase (POD) and glutathione-S-transferase (GST) were increased by both doses of Cu as well as UV-B. Conversely, Cu and UV-B_H drastically decreased catalase (CAT) activity. After the commencement of 24?h of treatment with Cu alone and together with UV-B_H, non-protein thiols (NP-SH) contents were decreased while after 72?h, a reverse trend was noticed. Unlike NP-SH, cysteine content decreased appreciably during the treatments. In contrast to this, low dose (UV-B_L) of UV-B did not influence growth, SOR, H₂O₂, MDA and RCG contents. An improvement in CAT activity and NP-SH content was observed under Cu and UV-B_L treatment; hence, UV-B_L treatment resulted into certain degree of protection against Cu toxicity in both the organisms. Thus, the results showed that UV-B_H and UV-B_L exerted differential effects on both the organisms under Cu toxicity, and compared to N. muscorum, P. foveolarum was less affected by Cu and UV-B_H.     

The Conformational Ensembles of α-Synuclein and Tau: Combining Single-Molecule FRET and Simulations

Intrinsically disordered proteins (IDPs) are increasingly recognized for their important roles in a range of biological contexts, both in normal physiological function and in a variety of devastating human diseases. However, their structural characterization by traditional biophysical methods, for the purposes of understanding their function and dysfunction, has proved challenging. Here, we investigate the model IDPs α-Synuclein (αS) and tau, that are involved in major neurodegenerative conditions including Parkinson’s and Alzheimer’s diseases, using excluded volume Monte Carlo simulations constrained by pairwise distance distributions from single-molecule fluorescence measurements. Using this, to our knowledge, novel approach we find that a relatively small number of intermolecular distance constraints are sufficient to accurately determine the dimensions and polymer conformational statistics of αS and tau in solution. Moreover, this method can detect local changes in αS and tau conformations that correlate with enhanced aggregation. Constrained Monte Carlo simulations produce ensembles that are in excellent agreement both with experimental measurements on αS and tau and with all-atom, explicit solvent molecular dynamics simulations of αS, with much lower configurational sampling requirements and computational expense.Abbreviations used: AAMD, all-atom molecular dynamics; ECMC, experimentally constrained Monte Carlo; ET_eff, energy transfer efficiency; (sm)FRET, (single molecule) Förster resonance energy transfer; IDP, intrinsically disordered protein; LJ, Lennard-Jones; MC, Monte Carlo; MD, molecular dynamics; PRE, paramagnetic relaxation enhancement; SAX(N)S, small-angle x-ray (neutron) scattering; UMC, unconstrained Monte Carlo     

Assessing the utility of direct and indirect methods for estimating tropical tree age in the Western Ghats, India

The knowledge of tree age is important for understanding tree growth and forest dynamics. It may be estimated by ‘direct’ methods involving growth ring counts, or by ‘indirect’ methods involving field measurements of growth rates. Direct methods are considered more accurate, but it is not clear if they are appropriate for all species, notably from the humid tropics. In this paper we assess the occurrence of annual growth rings and their utility for age estimation in three tropical tree species, Acrocarpus fraxinifolius, Dalbergia latifolia (Fabaceae) and Syzygium cumini (Myrtaceae), growing in traditional shade coffee plantations of the southern Western Ghats, India. These species previously were described as having “indistinct or absent” growth rings. We used anatomical studies, field measurements and computational methods to characterise growth rings and assess similarities between directly and indirectly estimated tree ages. Our study revealed that annual growth rings were characterised by different sets of anatomical features per species and were most distinct in the fast-growing deciduous A. fraxinifolius. Growth rates measured in the field showed annual periodicity in all three species, and reflected annual rainfall-drought cycles in D. latifolia and S. cumini. Direct age estimates were most similar to indirect estimates in D. latifolia, and least so in S. cumini. The results of direct age estimation by counting rings are consistent with them being annual in nature in tropical species with distinct and reliable annual growth ring formation. However, for species with poorly defined growth rings, indirect age estimation methods might be more useful.     

A study on neuroinflammatory marker in brain areas of okadaic acid (ICV) induced memory impaired rats

AimsThe aim of the present study is to investigate the status of proinflammatory cytokine in the brain of intracerebroventricular (ICV) okadaic acid (OKA) induced memory impaired rat.Main methodsOKA (200 ng) intracerebroventricular (ICV) was administered in rats. Memory was assessed by Morris water maze test. Biochemical marker of neuroinflammation (TNF-α, IL-β), total nitrite, mRNA (RT PCR) and protein expression (WB) of iNOS and nNOS were estimated in rat brain areas.Key findingsOKA caused memory-impairment in rats with increased expression of proinflammatory cytokine TNF-α and IL-1β and total nitrite in brain regions hippocampus and cortex. The expression of mRNA and protein of iNOS was increased while; the expressions were decreased in case of nNOS. Pretreatment with antidementic drugs donepezil (5 mg/kg, p.o.) and memantine (10 mg/kg, p.o) for 13 days protected ICV OKA induced memory impairment and changes in level of TNF-α, IL-β, total nitrite and expressions of iNOS and nNOS in OKA treated rat.SignificanceThis study suggests that neuroinflammation may play a vital role in OKA induced memory impairment.     

Physiological changes induced by chromium stress in plants: an overview

This article presents an overview of the mechanism of chromium (Cr) stress in plants. Toxic effects of Cr on plant growth and development depend primarily on its valence state. Cr(VI) is highly toxic and mobile whereas Cr(III) is less toxic. Cr-induced oxidative stress involves induction of lipid peroxidation in plants that cause severe damage to cell membranes which includes degradation of photosynthetic pigments causing deterioration in growth. The potential of plants with the adequacy to accumulate or to stabilize Cr compounds for bioremediation of Cr contamination has gained engrossment in recent years.     

Evaluation of Fermentation Efficiency of Yeast Strains and their Effect on Quality of Young Wines

The yeast has important role in fermentation of wine grapes and wine quality. The fermentation of wine grapes affect by efficiency of particular yeast strain, sugar content, pH, available temperature, etc. To evaluate the efficiency of yeast strains (Premier Cuvee, RS-1, RS-2, RS-3 and natural), present study was conducted on two wine grape varieties viz.; Sauvignon Blanc (White) and Cabernet Sauvignon (Red). Efficiency of yeast strains was evaluated in terms of conversion rate of sugar into alcohol. As per recorded data, strain RS-3 (Pichia kudriavzevii) was found more efficient than other strains in fermentation of Cabernet Sauvignon with efficiency of 84.4 per cent but in case of Sauvignon Blanc, the commercial culture Premier Cuevee was found superior over RS-3. The quality parameters of young wines of both the varieties were also affected by the used strains. Considering the efficiency and impact on various parameters of wines, local strain, i.e., RS-3 was found at par with commercial culture (Premier Cuvee). The RS-3 strain has potential to produce quality wines. However, studies on effects of RS-3 strain on some specific quality parameters of wines like varietal aroma compounds, flavours etc. are needed.     

Homologous Recombination is Activated at Early Time Points Following Exposure to Cobalt Chloride Induced Hypoxic Conditions in Saccharomyces cerevisiae

DNA repair functions are essential for the maintenance of genetic integrity and are regulated in response to both environmental and chemical stressors in mammalian and yeast cells in culture. The inhibitory effect of limited O₂ availability on DNA repair functions in general and on homologous recombination (HR) in particular, correlates with increased chromosomal abnormalities in hypoxic cancer cells. Given the above, we have investigated the effects of CoCl₂,––a hypoxia mimetic agent on HR and genetic aberrations in Saccharomyces cerevisiae. Our studies demonstrate that both acute and chronic exposure to CoCl₂ activated HR and increased genetic aberrations in S. cerevisiae D7 cells. At early time points following addition of CoCl₂ to the growth media, cells were briefly arrested in the G1-S boundary concomitant with a transient increase in Rad52-GFP foci formation and induction of low levels of DNA damage. The mode of action of CoCl₂ is thus similar to that of DNA synthesis inhibitors, the later are known to induce HR and cause G1-S arrest. We propose that the activation of HR in the presence of the hypoxia mimetic agent may be attributed to the replication stress and/or DNA damage induced by the stressor.     

Factors associated with physician agreement and coding choices of cause of death using verbal autopsies for 1130 maternal deaths in India

Background

The Indian Sample Registration System (SRS) with verbal autopsy methods provides estimations of cause specific mortality for maternal deaths, where the majority of deaths occur at home, unregistered. We aim to examine factors that influence physician agreement and coding choices in assigning causes of death from verbal autopsies.

Methodology/Principal Findings

Among adult deaths identified in the SRS, pregnancy-related deaths recorded in 2001–2003 were assigned ICD-10 codes by two independent physicians. Inter-rater reliability was estimated using Landis Koch Kappa classification – poor to fair agreement; > – moderate agreement; > – substantial agreement; >– high agreement. We identified factors associated with physician agreement using multivariate logistic regression. A central consensus panel reviewed cases for errors and reclassified as needed based on 2011 ICD-10 coding guidelines. Of 1130 pregnancy-related deaths, 1040 were assigned ICD-10 codes by two physicians. We found substantial agreement regardless of the woman''s residence, whether the death was registered, religion, respondent''s or deceased''s education, age, hospital admission or gestational age. Physician agreement was not influenced by the above variables, with the exception of greater agreement in cases where the respondent did not live with the deceased, or early gestational age at the time of death. A central consensus panel reviewed all cases and recoded 10% of cases due to insufficient use of information in the verbal autopsy by the coding physicians and rationale for this reclassification are discussed.

Conclusion

In the absence of complete vital registration and universal healthcare services, physician coded verbal autopsies continues to be heavily relied upon to ascertain pregnancy-related death. From this study, two independent physicians had good inter-rater reliability for assigning pregnancy-related causes of death in a nationally-represented sample, and physician coding does not appear to be heavily influenced by case characteristics or demographics.     

Generation of long insert pairs using a Cre-LoxP Inverse PCR approach

Large insert mate pair reads have a major impact on the overall success of de novo assembly and the discovery of inherited and acquired structural variants. The positional information of mate pair reads generally improves genome assembly by resolving repeat elements and/or ordering contigs. Currently available methods for building such libraries have one or more of limitations, such as relatively small insert size; unable to distinguish the junction of two ends; and/or low throughput. We developed a new approach, Cre-LoxP Inverse PCR Paired-End (CLIP-PE), which exploits the advantages of (1) Cre-LoxP recombination system to efficiently circularize large DNA fragments, (2) inverse PCR to enrich for the desired products that contain both ends of the large DNA fragments, and (3) the use of restriction enzymes to introduce a recognizable junction site between ligated fragment ends and to improve the self-ligation efficiency. We have successfully created CLIP-PE libraries up to 22 kb that are rich in informative read pairs and low in small fragment background. These libraries have demonstrated the ability to improve genome assemblies. The CLIP-PE methodology can be implemented with existing and future next-generation sequencing platforms.