Stereochemical criteria for prediction of the effects of proline mutations on protein stability

When incorporated into a polypeptide chain, proline (Pro) differs from all other naturally occurring amino acid residues in two important respects. The phi dihedral angle of Pro is constrained to values close to -65 degrees and Pro lacks an amide hydrogen. Consequently, mutations which result in introduction of Pro can significantly affect protein stability. In the present work, we describe a procedure to accurately predict the effect of Pro introduction on protein thermodynamic stability. Seventy-seven of the 97 non-Pro amino acid residues in the model protein, CcdB, were individually mutated to Pro, and the in vivo activity of each mutant was characterized. A decision tree to classify the mutation as perturbing or nonperturbing was created by correlating stereochemical properties of mutants to activity data. The stereochemical properties including main chain dihedral angle phi and main chain amide H-bonds (hydrogen bonds) were determined from 3D models of the mutant proteins built using MODELLER. We assessed the performance of the decision tree on a large dataset of 163 single-site Pro mutations of T4 lysozyme, 74 nsSNPs, and 52 other Pro substitutions from the literature. The overall accuracy of this algorithm was found to be 81% in the case of CcdB, 77% in the case of lysozyme, 76% in the case of nsSNPs, and 71% in the case of other Pro substitution data. The accuracy of Pro scanning mutagenesis for secondary structure assignment was also assessed and found to be at best 69%. Our prediction procedure will be useful in annotating uncharacterized nsSNPs of disease-associated proteins and for protein engineering and design.     

Synergy Between Metal Oxide Nanofibers and Graphene Nanoribbons for Rechargeable Lithium‐Oxygen Battery Cathodes

The challenges for rechargeable lithium‐oxygen batteries of low practical capacity and poor round‐trip efficiency urgently demand effective cathode materials to overcome the limitations. However, the synergy between the multiple active materials is not well understood. Here, findings of the synergistic effect between electrospun zinc oxide (ZnO) nanofibers and graphene nanoribbons (GNRs) unzipped from carbon nanotubes (CNTs) as cathode materials in rechargeable lithium‐oxygen batteries are described. Furthermore, the overpotentials and discharge capacities are tuned by the surface defect states of ZnO nanofibers and Pt nanocrytals in GNRs. It is observed that the optimized zinc oxide nanofibers hybridized with GNRs achieved a high reversible capacity of 6300 mAh g^‐1_carbon and enhanced stable cyclability under specific 50% of full discharge capacities. This report demonstrates that the ZnO nanofibers with a high degree of defects and hydrophilicity of the surface may be a promising cathode component for rechargeable lithium‐oxygen batteries and the optimum synergy between ZnO nanofibers and GNRs can balance the discharge capacity and cycle life.     

CIBMAN: Database exploring Citrus biodiversity of Manipur

The rich wealth of Citrus genetic resources makes India to enjoy a remarkable position in the “Citrus belt of the world”. We have developed CIBMAN, a unique database on Citrus biodiversity of Manipur which comprises 33 accessions collected through extensive survey for more than three years. CIBMAN provides integrated access to Citrus species through sophisticated web interface which has following capabilities a) morphological details, b) socio-economic details, c) taxonomic details and d) geographical distribution. Morphological variability among Citrus accessions is due to variance in their genome which contributes to diverse agronomical traits and diverse bioactive compounds of high value. This diverse gene pool can be potential source for genetic improvement of existing cultivars and rootstocks. Systematic collection, characterization and conservation of the underutilized or lesser exploited varieties is required for incorporating in breeding program and conserve the germplasm from ever going on genetic erosion. This database will be useful for scientific validations and updating of traditional wisdom in bioprospecting aspects especially industrialization of Citrus found in the state. Further, the features will be suited for detailed investigation on potential medicinal and edible Citrus that make CIBMAN a powerful tool for sustainable management.

Availability

http://ibsd.gov.in/cibman     

Predicting sub-cellular localization of tRNA synthetases from their primary structures

Since endo-symbiotic events occur, all genes of mitochondrial aminoacyl tRNA synthetase (AARS) were lost or transferred from ancestral mitochondrial genome into the nucleus. The canonical pattern is that both cytosolic and mitochondrial AARSs coexist in the nuclear genome. In the present scenario all mitochondrial AARSs are nucleus-encoded, synthesized on cytosolic ribosomes and post-translationally imported from the cytosol into the mitochondria in eukaryotic cell. The site-based discrimination between similar types of enzymes is very challenging because they have almost same physico-chemical properties. It is very important to predict the sub-cellular location of AARSs, to understand the mitochondrial protein synthesis. We have analyzed and optimized the distinguishable patterns between cytosolic and mitochondrial AARSs. Firstly, support vector machines (SVM)-based modules have been developed using amino acid and dipeptide compositions and achieved Mathews correlation coefficient (MCC) of 0.82 and 0.73, respectively. Secondly, we have developed SVM modules using position-specific scoring matrix and achieved the maximum MCC of 0.78. Thirdly, we developed SVM modules using N-terminal, intermediate residues, C-terminal and split amino acid composition (SAAC) and achieved MCC of 0.82, 0.70, 0.39 and 0.86, respectively. Finally, a SVM module was developed using selected attributes of split amino acid composition (SA-SAAC) approach and achieved MCC of 0.92 with an accuracy of 96.00%. All modules were trained and tested on a non-redundant data set and evaluated using fivefold cross-validation technique. On the independent data sets, SA-SAAC based prediction model achieved MCC of 0.95 with an accuracy of 97.77%. The web-server 'MARSpred' based on above study is available at http://www.imtech.res.in/raghava/marspred/.     

A limited role for antibody in protective immunity induced by rCPAF and CpG vaccination against primary genital Chlamydia muridarum challenge

Mice deficient in B cells (μmT mice) were used to evaluate the role of antibody in enhanced chlamydial clearance and reduction of pathology afforded by vaccination with recombinant chlamydial protease-like activity factor (rCPAF). Enhanced, but comparable, chlamydial clearance was observed in μmT and wild-type (WT) mice after rCPAF+CpG vaccination. Chlamydia -induced pathology was present in mock-immunized animals, but at significantly greater levels in μmT than WT mice, whereas vaccinated μmT and WT mice exhibited similar reductions in pathology. Thus, antibodies may play a role in protection against chlamydial pathology after primary infection, but were largely dispensable in rCPAF+CpG-induced chlamydial clearance and reduction in pathology.     

Thiazolidinedione derivatives as PTP1B inhibitors with antihyperglycemic and antiobesity effects

Benzylidene-2,4-thiazolidinedione derivatives with substitutions on the phenyl ring at the ortho or para positions of the thiazolidinedione (TZD) group were synthesized as PTP1B inhibitors with IC₅₀ values in a low micromolar range. Compound 3e, the lowest, bore an IC₅₀ of 5.0 μM. In vivo efficacy of 3e as an antiobesity and hypoglycemic agent was evaluated in a mouse model system. Significant improvement of glucose tolerance was observed. This compound also significantly suppressed weight gain and significantly improved blood parameters such as TG, total cholesterol and NEFA. Compound 3e was also found to activate peroxisome proliferator-activated receptors (PPARs) indicating multiple mechanisms of action.     

Enumeration of Escherichia coli Cells on Chicken Carcasses as a Potential Measure of Microbial Process Control in a Random Selection of Slaughter Establishments in the United States

To evaluate whether the number of Escherichia coli bacteria in carcass rinses from chicken slaughter establishments could be monitored for the purpose of microbial process control, we drew a random sample from 20 of 127 large USDA-inspected operations. In 2005, every 3 months, two sets of 10 carcass rinses, 100 ml each, were collected from establishments, netting 80 sample sets from the rehang and postchill stages. E. coli and Campylobacter numbers and Salmonella prevalence were measured. Mixed-effect models were used to estimate variance of mean log₁₀ E. coli cell numbers of 10-carcass rinse sample sets. Relationships between E. coli and Campylobacter and Salmonella were examined. For 10-carcass rinse sets, at both the rehang and postchill stages the mean log₁₀ E. coli CFU/ml fit the logistic distribution better than the normal distribution. The rehang overall mean log₁₀ E. coli was 3.3 CFU/ml, with a within-sample set standard deviation of 0.6 CFU/ml. The overall postchill mean log₁₀ E. coli was 0.8 CFU/ml, with 13 establishments having mean log₁₀ E. coli CFU/ml values of less than 1.0 and 7 having mean values of 1.2 or more. At the midpoint separating these establishments, a mean log₁₀ E. coli CFU/ml of 1.1, the within-sample set standard deviation was 0.5 CFU/ml, with smaller standard deviations as means increased. Postchill sample sets with mean log₁₀ E. coli counts less than or equal to 1.1 CFU/ml had lower overall prevalence of Salmonella and mean log₁₀ Campylobacter CFU/ml than sample sets with higher means. These findings regarding reductions in E. coli numbers provide insight relevant to microbial process control.Regulatory food microbiology standards are defined and enforced with the intent of protecting public health and maintaining consumer confidence in the safety of the food supply. Resource demands (22) and legal constraints (21) have hindered the U.S. Department of Agriculture (USDA) from enforcing its current Salmonella performance standard (3). For this reason, in 2004 the USDA requested guidance from its national scientific advisory committee on the possible use of E. coli numbers to monitor sanitary conditions during poultry slaughter (12). The committee acknowledged that, if valid, such a performance standard could facilitate inspection of slaughter processing establishments. The committee recommended studies to define how E. coli numbers vary in poultry carcass rinses during poultry processing by processing stage, time of year, and geographic region and with respect to food-borne pathogens.The widespread presence and high numbers of generic E. coli bacteria on poultry entering the slaughter establishment (2, 5, 14) are suitable characteristics for an indicator organism used to monitor microbial control processes. The ease and lower cost (5, 13) of E. coli enumeration also allow more observations than can be made when comparable resources are allocated for Campylobacter or Salmonella testing (15).Regulatory agencies and food manufacturers have recognized the potential utility of E. coli numbers as a measure of slaughter process control. For example, USDA''s hazard analysis and critical control point rule (3) specifies two criteria for evaluating process control: establishments are to maintain less than 100 CFU of E. coli per ml in 80% of poultry carcass rinses and never exceed 1,000 CFU/ml. Surveys have been performed to define precise E. coli performance criteria for poultry (5), to monitor microbial reduction during slaughter processing (6), and to validate interventions to reduce microbial numbers on poultry (20).If generic E. coli numbers on poultry carcasses fit a parametric distribution, with a predictable mean and standard deviation, then carcasses could be monitored using a statistical process control plan. For example, if E. coli numbers decrease by an acceptable amount during processing to a reasonable level, then the process could be considered to be under control. Or a plan could be designed to monitor for acceptable occurrences of small, medium, and large deviations above a target E. coli number (7). If relationships were found between E. coli and Campylobacter numbers during chicken slaughter as well as Salmonella prevalence, they would further support the use of E. coli numbers as a measure of process control.This study of a random sample of 20 large chicken slaughter operations located throughout the United States measured microbial numbers at two processing line locations. Once a quarter, 10 carcass rinse samples were collected from both the post-feather-pick (rehang) and postchill locations. Rinses were examined to estimate mean Salmonella prevalence and E. coli and Campylobacter numbers by location within establishments. The primary objective was to assess whether the reduction in E. coli numbers between the rehang and postchill stages or numbers at the postchill location might have utility as a measure of process control during chicken slaughter. A related objective was to estimate values of parameters that could be used to design statistical process control plans (7).