PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing ‘global views’ of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein–protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein–protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V–b, for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Behavioral economics: Reunifying psychology and economics

“Behavioral economics” improves the realism of the psychological assumptions underlying economic theory, promising to reunify psychology and economics in the process. Reunification should lead to better predictions about economic behavior and better policy prescriptions.

Human protein Sam68 relocalization and interaction with poliovirus RNA polymerase in infected cells.

A HeLa cDNA expression library was screened for human polypeptides that interacted with the poliovirus RNA-dependent RNA polymerase, 3D, using the two-hybrid system in the yeast Saccharomyces cerevisiae. Sam68 (Src-associated in mitosis, 68 kDa) emerged as the human cDNA that, when fused to a transcriptional activation domain, gave the strongest 3D interaction signal with a LexA-3D hybrid protein. 3D polymerase and Sam68 coimmunoprecipitated from infected human cell lysates with antibodies that recognized either protein. Upon poliovirus infection, Sam68 relocalized from the nucleus to the cytoplasm, where poliovirus replication occurs. Sam68 was isolated from infected cell lysates with an antibody that recognizes poliovirus protein 2C, suggesting that it is found on poliovirus-induced membranes upon which viral RNA synthesis occurs. These data, in combination with the known RNA- and protein-binding properties of Sam68, make Sam68 a strong candidate for a host protein with a functional role in poliovirus replication.

Determinants of the phagocytic signal mediated by the type IIIA Fc gamma receptor, Fc gamma RIIIA: sequence requirements and interaction with protein-tyrosine kinases.

The Fc gamma receptor-associated gamma and zeta subunits contain a conserved cytoplasmic motif, termed the immunoglobulin gene tyrosine activation motif, which contains a pair of YXXL sequences. The tyrosine residues within these YXXL sequences have been shown to be required for transduction of a phagocytic signal. We have previously reported that the gamma subunit of the type IIIA Fc gamma receptor (Fc gamma RIIIA) is approximately 6 times more efficient in mediating phagocytosis than the zeta subunit of Fc gamma RIIIA. By exchanging regions of the cytoplasmic domains of the homologous gamma and zeta chains, we observed that the cytoplasmic area of the gamma chain bearing a pair of the conserved YXXL sequences is important in phagocytic signaling. Further specificity of phagocytic signaling is largely determined by the two internal XX amino acids in the YXXL sequences. In contrast, the flanking amino acids of the YXXL sequences including the seven intervening amino acids between the two YXXL sequences do not significantly affect the phagocytic signal. Furthermore, the protein-tyrosine kinase Syk, but not the related kinase ZAP-70, stimulated Fc gamma RIIIA-mediated phagocytosis. ZAP-70, however, increased phagocytosis when coexpressed with the Src family kinase Fyn. These data demonstrate the importance of the two specific amino acids within the gamma subunit YXXL cytoplasmic sequences in phagocytic signaling and explain the difference in phagocytic efficiency of the gamma and zeta chains. These results indicate the importance of Syk in Fc gamma RIIIA-mediated phagocytosis and demonstrate that ZAP-70 and syk differ in their requirement for a Src-related kinase in signal transduction.

The Impact of Shyness on Loneliness, Social Anxiety, and School Liking in Late Childhood

Author: Charity M. Walker Title: THE IMPACT OF SHYNESS ON LONELINESS, SOCIAL ANXIETY, AND SCHOOL LIKING IN LATE CHILDHOOD Advisor: Maria T. Riva, Ph.D. Degree Date: August 2011 ABSTRACT Shyness is associated with several emotional, social, and academic problems. While there are multiple difficulties that often accompany shyness, there appear to be some factors that can moderate negative effects of shyness. Research has demonstrated that certain parenting factors affect the adjustment of shy children in early childhood, but there is minimal research illuminating the effect of parenting factors in older age groups. The first purpose of this study was to examine relationships between shyness and loneliness, social anxiety, and school liking. The second purpose was to investigate whether the quality of the relationship between a parent and a 10- to 15-year-olds child influences the amount of loneliness or social anxiety a shy child experiences or how the child feels about school. Parent-child dyads served as participants and were recruited from public and private middle schools and church youth groups in Colorado and Indiana. Child participants completed several self-report surveys regarding their relationship with a parent, shyness, loneliness, social anxiety, and their attitude toward school. Parents completed a survey about their relationship with their child and responded to questions related to their perceptions of their child's shyness. Data was analyzed with a series of correlation and regression analyses. Greater degrees of self-reported shyness were found to be associated with higher levels of loneliness and social anxiety and less positive feelings about school. Due to a problem with multicollinearity during data analysis, this study was not able to explore the effect of the parent-child relationship quality on the associations between shyness and adjustment factors. Overall, these findings imply that shyness remains an important issue as children approach adolescence. Further research is needed to continue learning about the potential importance of parent-child interactions in reducing maladjustment for shy children during late childhood.

The Relationship Between Social Support and Self-Advocacy in College Students With Disabilities

This study explored the connection between social support and self-advocacy in college students with disabilities. The College Students with Disabilities Campus Climate Survey (Lombardi, Gerdes, & Murray, 2011) was used to gather data from undergraduate students at a midsize western private university. Social support was found to be a significant predictor of self-advocacy in college students with disabilities. Peer support, family support, and faculty teaching practices made up the construct of social support. Peer support and faculty teaching practices were found to be significant predictors of student self-advocacy. Family support was not found to be significant. The data was examined for group differences between genders, disability types, and disability status (high incidence disabilities versus low incidence disabilities). No significant group differences were found. These findings suggest helping students build social support will increase their level of self-advocacy, which in turn may increase academic success.

Social Inequity and Globalization: Understanding Violent and Nonviolent Responses

Globalization generates economic growth that is dominated by the free market dynamics of liberalization, deregulation, and privatization. The benefits of this growth are not distributed equally. The resulting inequities cause poverty, marginalization, exclusion, and instability. People respond to these inequities in both positive/nonviolent and negative/violent ways. This capstone project investigates the reasons for divergent responses to globalization by contrasting the underlying social factors in two case studies: peace communities in Colombia and piracy in Somalia. By measuring the level of vulnerability, considering security in a variety of domains, and examining stress on socio-cultural norms, this project develops a social factors framework for understanding the reasons for negative/violent versus positive/nonviolent responses to globalization.

Social determinants and health effects of low and high severity intimate partner violence

PURPOSE: We sought to analyze whether the sociodemographic profile of battered women varies according to the level of severity of intimate partner violence (IPV), and to identify possible associations between IPV and different health problems taking into account the severity of these acts. METHODS: A cross-sectional study of 8,974 women (18-70 years) attending primary healthcare centers in Spain (2006-2007) was performed. A compound index was calculated based on frequency, types (physical, psychological, or both), and duration of IPV. Descriptive and multivariate procedures using logistic regression models were fitted. RESULTS: Women affected by low severity IPV and those affected by high severity IPV were found to have a similar sociodemographic profile. However, divorced women (odds ratio [OR], 8.1; 95% confidence interval [CI], 3.2-20.3), those without tangible support (OR, 6.6; 95% CI, 3.3-13.2), and retired women (OR, 2.7; 95% CI, 1.2-6.0) were more likely to report high severity IPV. Women experiencing high severity IPV were also more likely to suffer from poor health than were those who experienced low severity IPV. CONCLUSIONS: The distribution of low and high severity IPV seems to be influenced by the social characteristics of the women involved and may be an important indicator for estimating health effects. This evidence may contribute to the design of more effective interventions.

Social anxiety and self-concept in adolescence

This study analyzes the relationships between social anxiety and dimensions of self-concept in a sample of 2022 (50.1% males) Spanish adolescents, ranging in age from 12 to 16 year-olds. The social anxiety was assessed by the Social Phobia and Anxiety Inventory (SPAI), and self-concept was measured with the Self-Description Questionnaire II (SDQ-II). Logistic regression analyses show that adolescents with social anxiety are more likely to negatively perceive their relationship with opposite sex peers and have lower scores in self-esteem than students without social anxiety. Furthermore, in most logistic models, students with social anxiety also show a higher probability of perceiving their relation with peers of the same sex in a negative way, considering worse student, less attractive and athletic, and more emotional instable than students without social anxiety. The relevance of sex and grade in the relationship between social anxiety and self-concept in adolescence is discussed.

A guide to reading in social ethics and allied subjects: lists of books and articles selected and described for the use of general readers

by teachers in Harvard University.