Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction

The A protein of the U1 small nuclear ribonucleoprotein particle, interacting with its stem–loop RNA target (U1hpII), is frequently used as a paradigm for RNA binding by recognition motif domains (RRMs). U1A/U1hpII complex formation has been proposed to consist of at least two steps: electrostatically mediated alignment of both molecules followed by locking into place, based on the establishment of close-range interactions. The sequence of events between alignment and locking remains obscure. Here we examine the roles of three critical residues, Tyr13, Phe56 and Gln54, in complex formation and stability using Biacore. Our mutational and kinetic data suggest that Tyr13 plays a more important role than Phe56 in complex formation. Mutational analysis of Gln54, combined with molecular dynamics studies, points to Arg52 as another key residue in association. Based on our data and previous structural and modeling studies, we propose that electrostatic alignment of the molecules is followed by hydrogen bond formation between the RNA and Arg52, and the sequential establishment of interactions with loop bases (including Tyr13). A quadruple stack, sandwiching two bases between Phe56 and Asp92, would occur last and coincide with the rearrangement of a C-terminal helix that partially occludes the RRM surface in the free protein

Employers' and Employees' Understanding of Occupational Health and Safety Risks in Small Businesses: A Case Study

Many small businesses have hazardous work environments and exposures to significant occupational health and safety risks. Differences in understanding of risks by employers and employees are one of the factors leading to the hazardous work environment and risk exposures in small businesses. Employees generally describe “the tools of the trade” as the sources of risks of accidents and injuries, whereas employers generally identify “bad employees” or “bad luck” as the cause of accidents. It seems that employer and employees having the same or a shared understanding of occupational health and safety problems, their causal relations and the course of action is essential to remedy the work environment problems in the workplace. This paper describes a study that explores owner/managers’ and employees’ understandings of occupational health and safety risks in small business workplaces within the framework of the Local Theory of Work Environment. A case study of an independently operated restaurant and café in New Zealand employing 6­19 employees was undertaken.. Data was collected using participant­as­observer ethnographic observation of the workplace followed by semi structured interviews of the owner, a manager and more than fifty per cent of employees employed in the business. Preliminary findings based on interview data are reported in this paper. The results suggest that the owner/manager and employees mainly consider physical safety problems experienced by employees or food safety problems affecting the customers as the key work environment problems. The owner/manager and employees generally link common sense and breach of norms with the causal relation behind these problems. Social exchange and external certification, among others, are found to be prominent reasons for bringing to attention the perceived problems in the wider work environment context. Implicit individual element of action and explicit organizational element of action are recognised as the two courses of action remedying the occupational health and safety problems. Further studies can be directed at finding how a shared understanding of the OHS risks occurs and what influences this process

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a ‘lure and lock’ model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the ‘lure’ step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on ‘top’ of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein–RNA complexes

Employers' and Employees' Understanding of Occupational Health and Safety Risks in Small Businesses: A Case Study

Many small businesses have hazardous work environments and exposures to significant occupational health and safety risks. Differences in understanding of risks by employers and employees are one of the factors leading to the hazardous work environment and risk exposures in small businesses. Employees generally describe “the tools of the trade” as the sources of risks of accidents and injuries, whereas employers generally identify “bad employees” or “bad luck” as the cause of accidents. It seems that employer and employees having the same or a shared understanding of occupational health and safety problems, their causal relations and the course of action is essential to remedy the work environment problems in the workplace. This paper describes a study that explores owner/managers’ and employees’ understandings of occupational health and safety risks in small business workplaces within the framework of the Local Theory of Work Environment. A case study of an independently operated restaurant and café in New Zealand employing 6­19 employees was undertaken.. Data was collected using participant­as­observer ethnographic observation of the workplace followed by semi structured interviews of the owner, a manager and more than fifty per cent of employees employed in the business. Preliminary findings based on interview data are reported in this paper. The results suggest that the owner/manager and employees mainly consider physical safety problems experienced by employees or food safety problems affecting the customers as the key work environment problems. The owner/manager and employees generally link common sense and breach of norms with the causal relation behind these problems. Social exchange and external certification, among others, are found to be prominent reasons for bringing to attention the perceived problems in the wider work environment context. Implicit individual element of action and explicit organizational element of action are recognised as the two courses of action remedying the occupational health and safety problems. Further studies can be directed at finding how a shared understanding of the OHS risks occurs and what influences this process

Statistical Characterization of the Chandra Source Catalog

The first release of the Chandra Source Catalog (CSC) contains ~95,000 X-ray sources in a total area of ~0.75% of the entire sky, using data from ~3,900 separate ACIS observations of a multitude of different types of X-ray sources. In order to maximize the scientific benefit of such a large, heterogeneous data-set, careful characterization of the statistical properties of the catalog, i.e., completeness, sensitivity, false source rate, and accuracy of source properties, is required. Characterization efforts of other, large Chandra catalogs, such as the ChaMP Point Source Catalog (Kim et al. 2007) or the 2 Mega-second Deep Field Surveys (Alexander et al. 2003), while informative, cannot serve this purpose, since the CSC analysis procedures are significantly different and the range of allowable data is much less restrictive. We describe here the characterization process for the CSC. This process includes both a comparison of real CSC results with those of other, deeper Chandra catalogs of the same targets and extensive simulations of blank-sky and point source populations.Comment: To be published in the Astrophysical Journal Supplement Series (Fig. 52 replaced with a version which astro-ph can convert to PDF without issues.

Body mass index, muscle strength and physical performance in older adults from eight cohort studies: the HALCyon programme.

Objective To investigate the associations of body mass index (BMI) and grip strength with objective measures of physical performance (chair rise time, walking speed and balance) including an assessment of sex differences and non-linearity. Methods Cross-sectional data from eight UK cohort studies (total N = 16 444) participating in the Healthy Ageing across the Life Course (HALCyon) research programme, ranging in age from 50 to 90+ years at the time of physical capability assessment, were used. Regression models were fitted within each study and meta-analysis methods used to pool regression coefficients across studies and to assess the extent of heterogeneity between studies. Results Higher BMI was associated with poorer performance on chair rise (N = 10 773), walking speed (N = 9 761) and standing balance (N = 13 921) tests. Higher BMI was associated with stronger grip strength in men only. Stronger grip strength was associated with better performance on all tests with a tendency for the associations to be stronger in women than men; for example, walking speed was higher by 0.43 cm/s (0.14, 0.71) more per kg in women than men. Both BMI and grip strength remained independently related with performance after mutual adjustment, but there was no evidence of effect modification. Both BMI and grip strength exhibited non-linear relations with performance; those in the lowest fifth of grip strength and highest fifth of BMI having particularly poor performance. Findings were similar when waist circumference was examined in place of BMI. Conclusion Older men and women with weak muscle strength and high BMI have considerably poorer performance than others and associations were observed even in the youngest cohort (age 53). Although causality cannot be inferred from observational cross-sectional studies, our findings suggest the likely benefit of early assessment and interventions to reduce fat mass and improve muscle strength in the prevention of future functional limitations

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts