DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.

Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon static structures. Here we present DynaMut, a web server implementing two distinct, well established normal mode approaches, which can be used to analyze and visualize protein dynamics by sampling conformations and assess the impact of mutations on protein dynamics and stability resulting from vibrational entropy changes. DynaMut integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability. We demonstrate our approach outperforms alternative approaches to predict the effects of mutations on protein stability and flexibility (P-value < 0.001), achieving a correlation of up to 0.70 on blind tests. DynaMut also provides a comprehensive suite for protein motion and flexibility analysis and visualization via a freely available, user friendly web server at http://biosig.unimelb.edu.au/dynamut/

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predict the effects of missense mutations on protein-protein interaction binding affinity. mCSM-PPI2 uses graph-based structural signatures to model effects of variations on the inter-residue interaction network, evolutionary information, complex network metrics and energetic terms to generate an optimised predictor. We demonstrate that our method outperforms previous methods, ranking first among 26 others on CAPRI blind tests. mCSM-PPI2 is freely available as a user friendly webserver at http://biosig.unimelb.edu.au/mcsm_ppi2/.This work was supported by the Australian Government Research Training Program Scholarship [to C.H.M.R and Y.M.]; the Jack Brockhoff Foundation [JBF 4186, 2016 to D.B.A.]; a Newton Fund RCUK-CONFAP Grant awarded by The Medical Research Council (MRC) and Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) [MR/M026302/1 to D.B.A. and D.E.V.P.]; the National Health and Medical Research Council of Australia [APP1072476 to D.B.A.]; the Victorian Life Sciences Computation Initiative (VLSCI), an initiative of the Victorian Government, Australia, on its Facility hosted at the University of Melbourne [UOM0017]; the Instituto René Rachou (IRR/FIOCRUZ Minas), Brazil and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [to D.E.V.P.] and the Department of Biochemistry and Molecular Biology, University of Melbourne [to D.B.A.]. Supported in part by the Victorian Government's OIS Program

Agricultural climate change mitigation : Carbon calculators as a guide for decision making

This is an Accepted Manuscript of an article published by Taylor & Francis Group in International Journal of Agricultural Sustainability on 9 November 2017, available online: https://doi.org/10.1080/14735903.2017.1398628. Under embargo. Embargo end date: 9 November 2018.The dairy industry is receiving considerable attention in relation to both its significant greenhouse gas (GHG) emissions, and it’s potential for reducing those emissions, contributing towards meeting national targets and driving the industry towards sustainable intensification. However, the extent to which improvements can be made is dependent on the decision making processes of individual producers, so there has been a proliferation of carbon accounting tools seeking to influence those processes. This paper evaluates the suitability of such tools for driving environmental change by influencing on-farm management decisions. Seven tools suitable for the European dairy industry were identified, their characteristics evaluated, and used to process data relating to six scenario farms, emulating process undertaken in real farm management situations. As a result of the range of approaches taken by the tools, there was limited agreement between them as to GHG emissions magnitude, and no consistent pattern as to which tools resulted in the highest/lowest results. Despite this it is argued, that as there was agreement as to the farm activities responsible for the greatest emissions, the more complex tools were still capable of performing a ‘decision support’ role, and guiding management decisions, whilst others could merely focus attention on key issues.Peer reviewe

(Correcting) misdiagnoses of asthma: A cost effectiveness analysis

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: The prevalence of physician-diagnosed-asthma has risen over the past three decades and misdiagnosis of asthma is potentially common. Objective: to determine whether a secondary-screening-program to establish a correct diagnosis of asthma in those who report a physician diagnosis of asthma is cost effective.Method: Randomly selected physician-diagnosed-asthmatic subjects from 8 Canadian cities were studied with an extensive diagnostic algorithm to rule-in, or rule-out, a correct diagnosis of asthma. Subjects in whom the diagnosis of asthma was excluded were followed up for 6-months and data on asthma medications and heath care utilization was obtained. Economic analysis was performed to estimate the incremental lifetime costs associated with secondary screening of previously diagnosed asthmatic subjects. Analysis was from the perspective of the Canadian healthcare system and is reported in Canadian dollars.Results: Of 540 randomly selected patients with physician diagnosed asthma 150 (28%; 95%CI 19-37%) did not have asthma when objectively studied. 71% of these misdiagnosed patients were on some asthma medications. Incorporating the incremental cost of secondary-screening for the diagnosis of asthma, we found that the average cost savings per 100 individuals screened was $35,141 (95$4,588-$69,278).Conclusion: Cost savings primarily resulted from lifetime costs of medication use averted in those who had been misdiagnosed.This work was funded by the Canadian Institute of Health Research, Canada and the University Of Ottawa Division Of Respiratory Medicine

A Storm in a Tea-Cup? 'Making a Difference' in Two Sure Start Children's Centres

Sure Start Children's Centres were central to the last UK Labour government in improving outcomes for children and families. Yet, participation by those who 'ought' to attend was and remains a focus of concern. Using the work of Foucault, this paper explores parental participation in two Centres to examine how 'government operates at a distance', through the everyday interactions of those who inhabit these spaces. In exploring micro-practices, the humble cup of tea can be seen, not only as a small act of caring but a site of power and struggle over what these spaces meant to parents and practitioners

Public attitudes towards alcohol control policies in Scotland and England: Results from a mixed-methods study

The harmful effects of heavy drinking on health have been widely reported, yet public opinion on governmental responsibility for alcohol control remains divided. This study examines UK public attitudes towards alcohol policies, identifies underlying dimensions that inform these, and relationships with perceived effectiveness. A cross-sectional mixed methods study involving a telephone survey of 3477 adult drinkers aged 16-65 and sixteen focus groups with 89 adult drinkers in Scotland and England was conducted between September 2012 and February 2013. Principal components analysis (PCA) was used to reduce twelve policy statements into underlying dimensions. These dimensions were used in linear regression models examining alcohol policy support by demographics, drinking behaviour and perceptions of UK drinking and government responsibility. Findings were supplemented with a thematic analysis of focus group transcripts. A majority of survey respondents supported all alcohol policies, although the level of support varied by type of policy. Greater enforcement of laws on under-age sales and more police patrolling the streets were strongly supported while support for pricing policies and restricting access to alcohol was more divided. PCA identified four main dimensions underlying support on policies: alcohol availability, provision of health information and treatment services, alcohol pricing, and greater law enforcement. Being female, older, a moderate drinker, and holding a belief that government should do more to reduce alcohol harms were associated with higher support on all policy dimensions. Focus group data revealed findings from the survey may have presented an overly positive level of support on all policies due to differences in perceived policy effectiveness. Perceived effectiveness can help inform underlying patterns of policy support and should be considered in conjunction with standard measures of support in future research on alcohol control policies

Wolbachia in the flesh: symbiont intensities in germ-line and somatic tissues challenge the conventional view of Wolbachia transmission routes

Symbionts can substantially affect the evolution and ecology of their hosts. The investigation of the tissue-specific distribution of symbionts (tissue tropism) can provide important insight into host-symbiont interactions. Among other things, it can help to discern the importance of specific transmission routes and potential phenotypic effects. The intracellular bacterial symbiont Wolbachia has been described as the greatest ever panzootic, due to the wide array of arthropods that it infects. Being primarily vertically transmitted, it is expected that the transmission of Wolbachia would be enhanced by focusing infection in the reproductive tissues. In social insect hosts, this tropism would logically extend to reproductive rather than sterile castes, since the latter constitute a dead-end for vertically transmission. Here, we show that Wolbachia are not focused on reproductive tissues of eusocial insects, and that non-reproductive tissues of queens and workers of the ant Acromyrmex echinatior, harbour substantial infections. In particular, the comparatively high intensities of Wolbachia in the haemolymph, fat body, and faeces, suggest potential for horizontal transmission via parasitoids and the faecal-oral route, or a role for Wolbachia modulating the immune response of this host. It may be that somatic tissues and castes are not the evolutionary dead-end for Wolbachia that is commonly thought