CAGO: A Software Tool for Dynamic Visual Comparison and Correlation Measurement of Genome Organization

CAGO (Comparative Analysis of Genome Organization) is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG) format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago

Social capital, social participation and life satisfaction among Chilean older adults

OBJECTIVE To examine factors associated with social participation and their relationship with self-perceived well-being in older adults. METHODS This study was based on data obtained from the National Socioeconomic Characterization (CASEN) Survey conducted in Chile, in 2011, on a probability sample of households. We examined information of 31,428 older adults living in these households. Descriptive and explanatory analyses were performed using linear and multivariate logistic regression models. We assessed the respondents’ participation in different types of associations: egotropic, sociotropic, and religious. RESULTS Social participation increased with advancing age and then declined after the age of 80. The main finding of this study was that family social capital is a major determinant of social participation of older adults. Their involvement was associated with high levels of self-perceived subjective well-being. We identified four settings as sources of social participation: home-based; rural community-based; social policy programs; and religious. Older adults were significantly more likely to participate when other members of the household were also involved in social activities evidencing an intergenerational transmission of social participation. Rural communities, especially territorial associations, were the most favorable setting for participation. There has been a steady increase in the rates of involvement of older adults in social groups in Chile, especially after retirement. Religiosity remains a major determinant of associativism. The proportion of participation was higher among older women than men but these proportions equaled after the age of 80. CONCLUSIONS Self-perceived subjective well-being is not only dependent upon objective factors such as health and income, but is also dependent upon active participation in social life, measured as participation in associations, though its effects are moderate

Operons

Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function