Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network

Computational identification of heme-binding residues is beneficial for predicting and designing novel heme proteins. Here we proposed a novel method for heme-binding residue prediction by exploiting topological properties of these residues in the residue interaction networks derived from three-dimensional structures. Comprehensive analysis showed that key residues located in heme-binding regions are generally associated with the nodes with higher degree, closeness and betweenness, but lower clustering coefficient in the network. HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features. The results showed that incorporation of network-based features significantly improved the prediction performance. We also compared the residue interaction networks of heme proteins before and after heme binding and found that the topological features can well characterize the heme-binding sites of apo structures as well as those of holo structures, which led to reliable performance improvement as we applied HemeNet to predicting the binding residues of proteins in the heme-free state. HemeNet web server is freely accessible at http://mleg.cse.sc.edu/hemeNet/

An anatomy of Turkish football match-fixing

While discussion on corruption in sport is intensifying and football match-fixing in particular is attracting increasing attention, new fixing scandals emerge offering new accounts of actors and corrupt practices within the football industry and the level of the external threat to the sport. The scandal exposure of fixed matches in Turkey in 2011 sheds light on the fixing of 17 matches played in the 2010/11 football season and allowed for insights to the actors, structure and processes behind the fix. Following four criminal and seven disciplinary proceedings, the case is still pending appeal for its final decision, involving a total of 93 suspects and having already resulted in the exclusion of two teams from European competitions. The evidence collected by the authorities points towards a hierarchical criminal organisation led by the President of a football club that arranged and coordinated the fixing in order for his team to win the national Championship. The aim of this article is to provide an account of the organisation and coordination of match-fixing in Turkey, with its actors, specifics and criminal characteristics, while offering an examination of match-fixing for sporting success, the least documented type of match-fixing

Protein supplementation in strength and conditioning adepts: knowledge, dietary behaviour and practice in Palermo, Italy

Background: It is known that supplement use is a widespread and accepted practice by athletes and people who attend commercial gyms. Little is known about protein supplement amongst people undertaking strength training in commercial gyms in Italy when compared to the US. Objective: The purpose of this study was to examine the use of protein supplementation, alone or in association with other supplements, and dietary behavior amongst regular fitness center attendees in Palermo, Italy. Design: Resistance training information have been collected from 800 regular fitness center attendees for the initial analysis. A specific questionnaire was generated for the experimentation. Data were collected using a face-to-face interview method. Supplement users were then compared to the non users and analyzed using a one-way ANOVA, Kruskall-Wallis, chi-square test or exact test of Fisher when appropriate. Results: 30.1% of the respondents use dietary supplements during their training as a believe it is the "way to gain muscles and strength". Whey protein shakes (50.0%) mixed with creatine and amino-acids (48.3%) were the most frequent choices amongst the users. A majority of the subjects (34.0%) appeared to rely on their gym instructors' advice for their intake; a lower proportion (13.0%) consulted physicians, while none of them consulted nutritionists. A high consumption of milk has been noticed in both users (67,7%) and non-users (52,8%); supplement non-users consumed significantly more snacks and bakery products than users per week (P < 0.001), while users consumed significantly more protein-rich foods (P < 0.01) with a particular preference for meat (48.0%). Conclusions: A considerable number of regular strength training adepts consume protein supplements mixed with other products (mainly creatine and amino-acids). Limited numbers consult "dietary specialists" and rely mainly on their instructors. We emphasize on the importance of the dissemination of scientifically based information about supplementation in this environment and the promotion of updated educational programs for the instructors

Translating global recommendations on HIV and infant feeding to the local context: the development of culturally sensitive counselling tools in the Kilimanjaro Region, Tanzania

BACKGROUND: This paper describes the process used to develop an integrated set of culturally sensitive, evidence-based counselling tools (job aids) by using qualitative participatory research. The aim of the intervention was to contribute to improving infant feeding counselling services for HIV positive women in the Kilimanjaro Region of Tanzania. METHODS: Formative research using a combination of qualitative methods preceded the development of the intervention and mapped existing practices, perceptions and attitudes towards HIV and infant feeding (HIV/IF) among mothers, counsellors and community members. Intervention Mapping (IM) protocol guided the development of the overall intervention strategy. Theories of behaviour change, a review of the international HIV/IF guidelines and formative research findings contributed to the definition of performance and learning objectives. Key communication messages and colourful graphic illustrations related to infant feeding in the context of HIV were then developed and/or adapted from existing generic materials. Draft materials were field tested with intended audiences and subjected to stakeholder technical review. RESULTS: An integrated set of infant feeding counselling tools, referred to as 'job aids', was developed and included brochures on feeding methods that were found to be socially and culturally acceptable, a Question and Answer Guide for counsellors, a counselling card on the risk of transmission of HIV, and an infant feeding toolbox for demonstration. Each brochure describes the steps to ensure safer infant feeding using simple language and images based on local ideas and resources. The brochures are meant to serve as both a reference material during infant feeding counselling in the ongoing prevention of mother to child transmission (pMTCT) of HIV programme and as take home material for the mother. CONCLUSION: The study underscores the importance of formative research and a systematic theory based approach to developing an intervention aimed at improving counselling and changing customary feeding practices. The identification of perceived barriers and facilitators for change contributed to developing the key counselling messages and graphics, reflecting the socio-economic reality, cultural beliefs and norms of mothers and their significant others

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

<p>Abstract</p> <p>Background</p> <p>Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues.</p> <p>Results</p> <p>Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM). The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone.</p> <p>Conclusions</p> <p>HemeBIND is the first specialized algorithm used to predict binding residues in protein structures for heme ligands. Extensive experiments indicated that both the structure-based and sequence-based methods have effectively identified heme binding residues while the complementary relationship between them can result in a significant improvement in prediction performance. The value of our method is highlighted through the development of HemeBIND web server that is freely accessible at <url>http://mleg.cse.sc.edu/hemeBIND/</url>.</p

ABHD4-dependent developmental anoikis safeguards the embryonic brain

During embryonic development, neural progenitor cells undergo numerous cell divisions. Here, the authors show that ABHD4-mediated developmental anoikis distinguishes the physiological delamination and the pathological detachment of progenitor cells with relevance to fetal alcohol-induced apoptosis