Use of quantitative membrane proteomics identifies a novel role of mitochondria in healing injured muscles

Skeletal muscles are proficient at healing from a variety of injuries. Healing occurs in two phases, early and late phase. Early phase involves healing the injured sarcolemma and restricting the spread of damage to the injured myofiber. Late phase of healing occurs a few days postinjury and involves interaction of injured myofibers with regenerative and inflammatory cells. Of the two phases, cellular and molecular processes involved in the early phase of healing are poorly understood. We have implemented an improved sarcolemmal proteomics approach together with in vivo labeling of proteins with modified amino acids in mice to study acute changes in the sarcolemmal proteome in early phase of myofiber injury. We find that a notable early phase response to muscle injury is an increased association of mitochondria with the injured sarcolemma. Real-time imaging of live myofibers during injury demonstrated that the increased association of mitochondria with the injured sarcolemma involves translocation of mitochondria to the site of injury, a response that is lacking in cultured myoblasts. Inhibiting mitochondrial function at the time of injury inhibited healing of the injured myofibers. This identifies a novel role of mitochondria in the early phase of healing injured myofibers.     

Cultivation impacts soil microbial dynamics in dry tropical forest ecosystem in India

We studied for two years the seasonal changes in plant available nitrate and ammonium nitrogen (N), nitrification, N-mineralization, microbial biomass carbon (MBC), nitrogen (MBN) and phosphorus (MBP) in two forest and three cropland sites, derived from a tropical forest ecosystem of India. Results indicated that seasonal values of nitrate N, ammonium N and phosphate P ranged from 7.33–12.99, 5.1–10.22 and 4.0–7.8 μg g^?1 in forest and 4.13–9.26, 9.35–14.46 and 2.8–5.8 μg g^?1 in cropland ecosystems, respectively, with maximum values in summer and minimum in rainy seasons. Nitrification and N-mineralization values varied from 6–28 and 4–26 μg g^?1 mo^?1 in forest and 3–14 μg g^?1 mo^?1 and 4–17 μg g^?1 mo^?1 in cropland, with maximum values in rainy season and minimum in summer season.MBC, MBN MBP ranged from 393–753, 34–80 and 16–36 μg g^?1 in forests and 186–414, 21–41 and 11–22 μg g^?1 in croplands, being maximum in summer and minimum in rainy seasons. There was gradual increase in the values of inorganic N, nitrification, N-mineralization and MBC, MBN and MBP along the age of cropland. Analysis of variance indicated significant difference in the concentration of inorganic N, nitrification and N-mineralization and MBC, MBN and MBP due to sites and seasons.Cultivation caused decline in the mean annual organic C, N and P by 42%, 29% and 13%. The values of nitrate N were decreased by 23–38%, while ammonium N was increased by 39–74%. Nitrification and N-mineralization values were reduced by 39–63% and 40–60%, respectively. Microbial C, N and P were reduced by 44–54%, 41–50% and 28–44%, respectively. Nonetheless, the contribution of soil microbial biomass reflected in total N was enhanced from 4.76% in forest to 5.03% in cropland ecosystem. Enhancement of plant available ammonium-N and microbial contribution in total N are an indicator of natural conserving mechanism to check the nitrogen loss from the nutrient poor agro-ecosystem.     

Dose-finding study with nicotine as a proconvulsant agent in PTZ-induced seizure model in mice

The present study was conducted to investigate the possible interaction between low doses of nicotine and pentylenetetrazole (PTZ) in vivo and also to evaluate the influence of nicotine on the antiseizure efficacy of topiramate and sodium valproate in the PTZ-induced seizure model in mice. Graded dose–response study with nicotine showed the CD50 value for nicotine at 6.76 mg/kg. i.p. Subtheshold dose of nicotine (4 mg/kg, i.p.) pretreatment significantly decreased the CD50 value for PTZ from 47.86 mg/kg, i.p. (of PTZ per se) to 31.62 mg/kg, i.p. Sodium valproate but not topiramate, significantly inhibited PTZ-induced seizures in mice with an ED50 value of 177.83 mg/kg, i.p. Nonconvulsive dose of nicotine (1 mg/kg, i.p.) significantly antagonized the protective efficacy of sodium valproate against PTZ-induced seizures and increased the ED50 value to 338.84 mg/kg, i.p. PTZ-induced seizures significantly increased the mouse brain levels of MDA and reduced the level of GSH while sodium valproate reversed such changes. Nicotine pretreatment reversed the anti-lipid peroxidative action of sodium valproate in the PTZ-induced seizure model in mice. The study highlighted the convulsant as well as proconvulsant role of nicotine and established dose discrimination for nicotine as a proconvulsant agent and an anti-antiseizure agent. The study bears significant clinical relevance particularly amongst epileptic smokers who may show failure of efficacy of antiepileptic agents and present with breakthrough seizure attacks on exposure to nicotine.     

Mapping the interaction site of Rpb4 and Rpb7 subunits of RNA polymerase II in Saccharomyces cerevisiae

Rpb4 and Rpb7, the fourth and the seventh largest subunits of RNA polymerase II, form a heterodimer in Saccharomyces cerevisiae. To identify the site of interaction between these subunits, we constructed truncation mutants of both these proteins and carried out yeast two hybrid analysis. Deletions in the amino and carboxyl terminal domains of Rpb7 abolished its interaction with Rpb4. In comparison, deletion of up to 49 N-terminal amino acids of Rpb4 reduced its interaction with Rpb7. Complete abolishment of interaction between Rpb4 and Rpb7 occurred by truncation of 1-106, 1-142, 108-221, 172-221 or 198-221 amino acids of Rpb4. Use of the yeast two-hybrid analysis in conjunction with computational analysis of the recently reported crystal structure of Rpb4/Rpb7 sub-complex allowed us to identify regions previously not suspected to be involved in the functional interaction of these proteins. Taken together, our results have identified the regions that are involved in interaction between the Rpb4 and Rpb7 subunits of S. cerevisiae RNA polymerase II in vivo.     

Grey Matter Atrophy in Multiple Sclerosis: Clinical Interpretation Depends on Choice of Analysis Method

Background

Studies disagree on the location of grey matter (GM) atrophy in the multiple sclerosis (MS) brain.

Aim

To examine the consistency between FSL, FreeSurfer, SPM for GM atrophy measurement (for volumes, patient/control discrimination, and correlations with cognition).

Materials and Methods

127 MS patients and 50 controls were included and cortical and deep grey matter (DGM) volumetrics were performed. Consistency of volumes was assessed with Intraclass Correlation Coefficient/ICC. Consistency of patients/controls discrimination was assessed with Cohen’s d, t-tests, MANOVA and a penalized double-loop logistic classifier. Consistency of association with cognition was assessed with Pearson correlation coefficient and ANOVA. Voxel-based morphometry (SPM-VBM and FSL-VBM) and vertex-wise FreeSurfer were used for group-level comparisons.

Results

The highest volumetry ICC were between SPM and FreeSurfer for cortical regions, and the lowest between SPM and FreeSurfer for DGM. The caudate nucleus and temporal lobes had high consistency between all software, while amygdala had lowest volumetric consistency. Consistency of patients/controls discrimination was largest in the DGM for all software, especially for thalamus and pallidum. The penalized double-loop logistic classifier most often selected the thalamus, pallidum and amygdala for all software. FSL yielded the largest number of significant correlations. DGM yielded stronger correlations with cognition than cortical volumes. Bilateral putamen and left insula volumes correlated with cognition using all methods.

Conclusion

GM volumes from FreeSurfer, FSL and SPM are different, especially for cortical regions. While group-level separation between MS and controls is comparable, correlations between regional GM volumes and clinical/cognitive variables in MS should be cautiously interpreted.     

Augmentation of a Microbial Consortium for Enhanced Polylactide (PLA) Degradation

Bioplastics are eco-friendly and derived from renewable biomass sources. Innovation in recycling methods will tackle some of the critical issues facing the acceptance of bioplastics. Polylactic acid (PLA) is the commonly used and well-studied bioplastic that is presumed to be biodegradable. Considering their demand and use in near future, exploration for microbes capable of bioplastic degradation has high potential. Four PLA degrading strains were isolated and identified as Penicillium chrysogenum, Cladosporium sphaerospermum, Serratia marcescens and Rhodotorula mucilaginosa. A consortium of above strains degraded 44 % (w/w) PLA in 30 days time in laboratory conditions. Subsequently, the microbial consortium employed effectively for PLA composting.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0559-z) contains supplementary material, which is available to authorized users.     

Diastereoselective synthesis of glycosylated prolines as alpha-glucosidase inhibitors and organocatalyst in asymmetric aldol reaction

1,3-Dipolar cycloaddition of azomethine ylides and glycosyl E-olefins in presence of LDA led to diastereoselective formation of C-glycosylated proline esters. The selected esters on regioselective hydrolysis with LiOH gave C-glycosyl prolines. Few of the proline esters exhibited very good alpha-glucosidase inhibitory activity. The organocatalytic activity of the proline derivatives in a prototype Aldol reaction has also been investigated.     

Human papillomavirus elevated genetic biomarker signature by statistical algorithm

Head and neck squamous cell carcinoma (HNSCC) is the one of the most frequently found cancers in the world. The aim of the study was to find the genes responsible and enriched pathways associated with HNSCC using bioinformatics and survival analysis methods. A total of 646 patients with HNSCC based on clinical information were considered for the study. HNSCC samples were grouped according to the parameters (RFS, DFS, PFS, or OS). The probe ID of these 11 genes was retrieved by Affymetrix using the NetAffx Query algorithm. The protein–protein interaction (PPI) network and Kaplan–Meier curve were used to find associations among the genes' expression data. We found that among these 11 genes, nine genes, CCNA1, MMP3, FLRT3, GJB6, ZFR2, PITX2, SYCP2, MEI1, and UGT8 were significant (p < .05). A survival plot was drawn between the p value and gene expression. This study helped us find the nine significant genes which play vital roles in HNSCC along with their key pathways and their interaction with other genes in the PPI network. Finally, we found the biomarker index for relapse time and risk factors for HNSCC in cancer patients.     

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene’s tolerance to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 autosomal protein coding genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutral de novo mutation (p<10⁻⁴). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases.