Biophysical and electrochemical studies of protein-nucleic acid interactions

This review is devoted to biophysical and electrochemical methods used for studying protein-nucleic acid (NA) interactions. The importance of NA structure and protein-NA recognition for essential cellular processes, such as replication or transcription, is discussed to provide background for description of a range of biophysical chemistry methods that are applied to study a wide scope of protein-DNA and protein-RNA complexes. These techniques employ different detection principles with specific advantages and limitations and are often combined as mutually complementary approaches to provide a complete description of the interactions. Electrochemical methods have proven to be of great utility in such studies because they provide sensitive measurements and can be combined with other approaches that facilitate the protein-NA interactions. Recent applications of electrochemical methods in studies of protein-NA interactions are discussed in detail

Enzymatic Preparation of 2 5 ,3 5 Cyclic Dinucleotides, Their Binding Properties to Stimulator of Interferon Genes Adaptor Protein, and Structure Activity Correlations

Cyclic dinucleotides are second messengers in the cyclic GMP AMP synthase cGAS stimulator of interferon genes STING pathway, which plays an important role in recognizing tumor cells and viral or bacterial infections. They bind to the STING adaptor protein and trigger expression of cytokines via TANK binding kinase 1 TBK1 interferon regulatory factor 3 IRF3 and inhibitor of nuclear factor amp; 954;B I amp; 954;B kinase IKK nuclear factor amp; 954;B NF amp; 954;B signaling cascades. In this work, we describe an enzymatic preparation of 2 amp; 8242; 5 amp; 8242;,3 amp; 8242; 5 amp; 8242; cyclic dinucleotides 2 amp; 8242;3 amp; 8242;CDNs with use of cyclic GMP AMP synthases cGAS from human, mouse, and chicken. We profile substrate specificity of these enzymes by employing a small library of nucleotide 5 amp; 8242; triphosphate NTP analogues and use them to prepare 33 2 amp; 8242;3 amp; 8242;CDNs. We also determine affinity of these CDNs to five different STING haplotypes in cell based and biochemical assays and describe properties needed for their optimal activity toward all STING haplotypes. Next, we study their effect on cytokine and chemokine induction by human peripheral blood mononuclear cells PBMCs and evaluate their cytotoxic effect on monocytes. Additionally, we report X ray crystal structures of two new CDNs bound to STING protein and discuss structure activity relationship by using quantum and molecular mechanical QM MM computational modelin

Measuring the food and built environments in urban centres: Reliability and validity of the EURO-PREVOB Community Questionnaire

Objectives: The authors designed an instrument to measure objectively aspects of the built and food environments in urban areas, the EURO-PREVOB Community Questionnaire, within the EU-funded project 'Tackling the social and economic determinants of nutrition and physical activity for the prevention of obesity across Europe' (EURO-PREVOB). This paper describes its development, reliability, validity, feasibility and relevance to public health and obesity research. Study design: The Community Questionnaire is designed to measure key aspects of the food and built environments in urban areas of varying levels of affluence or deprivation, within different countries. The questionnaire assesses (1) the food environment and (2) the built environment. Methods: Pilot tests of the EURO-PREVOB Community Questionnaire were conducted in five to 10 purposively sampled urban areas of different socio-economic status in each of Ankara, Brno, Marseille, Riga, and Sarajevo. Inter-rater reliability was compared between two pairs of fieldworkers in each city centre using three methods: inter-observer agreement (IOA), kappa statistics, and intraclass correlation coefficients (ICCs). Results: Data were collected successfully in all five cities. Overall reliability of the EURO-PREVOB Community Questionnaire was excellent (inter-observer agreement (IOA) > 0.87; intraclass correlation coefficients (ICC)s > 0.91 and kappa statistics > 0.7. However, assessment of certain aspects of the quality of the built environment yielded slightly lower IOA coefficients than the quantitative aspects. Conclusions: The EURO-PREVOB Community Questionnaire was found to be a reliable and practical observational tool for measuring differences in community-level data on environmental factors that can impact on dietary intake and physical activity. The next step is to evaluate its predictive power by collecting behavioural and anthropometric data relevant to obesity and its determinants. © 2013 The Royal Society for Public Health

Measuring the food and built environments in urban centres: Reliability and validity of the EURO-PREVOB Community Questionnaire

Objectives: The authors designed an instrument to measure objectively aspects of the built and food environments in urban areas, the EURO-PREVOB Community Questionnaire, within the EU-funded project ‘Tackling the social and economic determinants of nutrition and physical activity for the prevention of obesity across Europe’ (EURO-PREVOB). This paper describes its development, reliability, validity, feasibility and relevance to public health and obesity research. Study design: The Community Questionnaire is designed to measure key aspects of the food and built environments in urban areas of varying levels of affluence or deprivation, within different countries. The questionnaire assesses (1) the food environment and (2) the built environment. Methods: Pilot tests of the EURO-PREVOB Community Questionnaire were conducted in five to 10 purposively sampled urban areas of different socio-economic status in each of Ankara, Brno, Marseille, Riga, and Sarajevo. Inter-rater reliability was compared between two pairs of fieldworkers in each city centre using three methods: inter-observer agreement (IOA), kappa statistics, and intraclass correlation coefficients (ICCs). Results: Data were collected successfully in all five cities. Overall reliability of the EURO-PREVOB Community Questionnaire was excellent (inter-observer agreement (IOA) > 0.87; intraclass correlation coefficients (ICC)s > 0.91 and kappa statistics > 0.7. However, assessment of certain aspects of the quality of the built environment yielded slightly lower IOA coefficients than the quantitative aspects. Conclusions: The EURO-PREVOB Community Questionnaire was found to be a reliable and practical observational tool for measuring differences in community-level data on environmental factors that can impact on dietary intake and physical activity. The next step is to evaluate its predictive power by collecting behavioural and anthropometric data relevant to obesity and its determinants

Roma coronary heart disease patients have more medical risk factors and greater severity of coronary heart disease than non-Roma

<p>Coronary heart disease (CHD) is the most common cause of mortality and morbidity world-wide. Evidence on ethnic differences between the Roma and non-Roma regarding medical risk factors is scarce. The aim of this study was to assess differences in medical risk factors and the severity of CHD in Roma compared with non-Roma CHD patients, adjusted for gender, age and education.</p><p>Six hundred seventy four patients were included in this cross-sectional study (132 Roma, 542 non-Roma). Data on medical risk factors, symptoms, medication and severity of CHD were obtained from medical records. After matching Roma and non-Roma according to education, linear and logistic regression analyses with adjustments for gender and age were used.</p><p>Compared with non-Roma, Roma patients had significantly more risk factors and more severe types of CHD. They were treated less frequently with statins and beta-blockers, were more frequently left on pharmacotherapy and surgically revascularised. These differences remained after controlling for education, gender and age.</p><p>Roma CHD patients have a worse risk profile at entry of care and seem to be undertreated compared with non-Roma CHD patients.</p>