SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment

We describe a suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes. LPC/CSU software provides a common definition of inter-atomic contacts and complementarity of contacting surfaces to analyze protein structure and complexes. In the current version of LPC/CSU, analyses of water molecules and nucleic acids have been added, together with improved and expanded visualization options using Chime or Java based Jmol. The SPACE suite includes servers and programs for: structural analysis of point mutations (MutaProt); side chain modeling based on surface complementarity (SCCOMP); building a crystal environment and analysis of crystal contacts (CryCo); construction and analysis of protein contact maps (CMA) and molecular docking software (LIGIN). The SPACE suite is accessed at

The marketing potential of corporate social responsibility activities : the case of the alcohol industry in Latin America and the Caribbean

This research was supported by the International Development Research Centre, funding number 107 203–001. The authors would like to thank the Uruguayan National Drug Secretariat, Diego Rodríguez Sendoya and Gustavo Sóñora from the Tobacco Investigation Center in Uruguay for all their support during this research. This is one of a series of papers published in a Supplement to Addiction entitled: The Regulation of Alcohol Marketing: From Research to Public Health Policy. This supplement was published with financial support from Alcohol Research UK and the Institute of Alcohol Studies. Preliminary versions of themajority of these manuscripts were first presented at ameeting organized by the Pan American Health Organization.The aims were to: (1) identify, monitor and analyse the Corporate Social Responsibility (CSR) practices of the alcohol industry in Latin America and the Caribbean (LAC) and (2) examine whether the alcohol industry is using these actions tomarket their products and brands

Delivering alcohol identification and brief advice (IBA) in housing settings: a step too far or opening doors?

Within the UK, there is a drive to encourage the delivery of alcohol screening (or identification) and brief advice (IBA) in a range of contexts beyond primary care and hospitals where the evidence is strongest. However, the evidence base for effectiveness in non-health contexts is not currently established. This paper considers the case of housing provided by social landlords, drawing on two research studies which were conducted concurrently. One study examined the feasibility of delivering alcohol IBA in housing settings and the other the role of training in delivering IBA in non-health contexts including housing. This paper draws mainly on the qualitative data collected for both studies to examine the appropriateness and feasibility of delivering IBA in a range of social housing settings by the housing workforce. Findings suggest that while it is feasible to deliver IBA in housing settings, there are similar challenges and barriers to those already identified in relation to primary care. These include issues around role inadequacy, role legitimacy and the lack of support to work with people with alcohol problems. Results indicate that the potential may lie in focusing training efforts on specific roles to deliver IBA rather than it being expected of all staff

Host Transcriptomics as a Tool to Identify Diagnostic and Mechanistic Immune Signatures of Tuberculosis

Tuberculosis (TB) is a major infectious disease worldwide, and is associated with several challenges for control and eradication. First, more accurate diagnostic tools that better represent the spectrum of infection states are required; in particular, identify the latent TB infected individuals with high risk of developing active TB. Second, we need to better understand, from a mechanistic point of view, why the immune system is unsuccessful in some cases for control and elimination of the pathogen. Host transcriptomics is a powerful approach to identify both diagnostic and mechanistic immune signatures of diseases. We have recently reported that optimal study design for these two purposes should be guided by different sets of criteria. Here, based on already published transcriptomics signatures of tuberculosis, we further develop these guidelines and identify additional factors to consider for obtaining diagnostic vs. mechanistic signatures in terms of cohorts, samples, data generation and analysis. Diagnostic studies should aim to identify small disease signatures with high discriminatory power across all affected populations, and against similar pathologies to TB. Specific focus should be made on improving the diagnosis of infected individuals at risk of developing active disease. Conversely, mechanistic studies should focus on tissues biopsies, immune relevant cell subsets, state of the art transcriptomic techniques and bioinformatics tools to understand the biological meaning of identified gene signatures that could facilitate therapeutic interventions. Finally, investigators should ensure their data are made publicly available along with complete annotations to facilitate metadata and cross-study analyses

A reference map of the human binary protein interactome.

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships(1,2). Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome(3), transcriptome(4) and proteome(5) data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes

Clonado de un potencial cofactor capaz de interactuar con el LBD de RXR y VDR

El receptor de vitamina D (VDR) y el receptor de ácido retinoico X (RXR) son factores de transcripción regulados por Iigando, que al unirse al DNAmodulan los niveles de expresión génica. Estudios recientes han demostrado que en ciertos casos estos receptores necesitan factores adicionales para potenciar o reprimir la expresión génica. Con el propósito de encontrar nuevos cofactores involucrados en esta regulación, el Dr. P. N. MacDonald de la Universidad de Saint Louis rastreó una genoteca utilizando el sistema funcional de dos híbridos y aisló el clon 2601 de aproximadamente 1,1Kb capaz de interaccionar con VDR y RXR; y secuenció sus primeros 250 pb. El trabajo presentado en este Seminario de Licenciatura se realizó con el propósito de obtener mayor información sobre este potencial cofactor. Para ello, se rastreó una genoteca y se aislaron varios clones independientes cuya porción 3' es idéntica al clon 2601, entre los que se encuentra el clon 12d de aproximadamente 1,8 Kb. Se analizó en detalle la secuencia aminoacídica de la proteína codificada en el clón 12d y se Ia comparó con proteínas disponibles en las bases de datos. Los resultados obtenidos en este trabajo muestran que esta nueva proteina tiene características comunes a factores de transcripción conocidos. Su capacidad de interaccionar con el LBD de RXR y VDR, la existencia de dos potenciales dedos de zinc y una región rica en prolinas son evidencias muy fuertes que sugieren que esta nueva proteína podría estar involucrada en la regulación de Ia transcripción mediada por miembros de la familia de receptores nucleares.Fil: Babor, Samha Mariana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina