Investigating the DNA-Binding Site for VirB, a Key Transcriptional Regulator of Shigella Virulence Genes, Using an In Vivo Binding Tool

The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood. While a 7-8 bp VirB-binding site has been proposed, it was derived from studies at a single VirB-dependent promoter, icsB. Our previous in vivo studies at a different VirB-dependent promoter, icsP, found that the proposed VirB-binding site was insufficient for regulation. Instead, the required site was found to be organized as a near-perfect inverted repeat separated by a single nucleotide spacer. Thus, the proposed 7-8 bp VirB-binding site needed to be re-evaluated. Here, we engineer and validate a molecular tool to capture protein-DNA binding interactions in vivo. Our data show that a sequence organized as a near-perfect inverted repeat is required for VirB-DNA binding interactions in vivo at both the icsB and icsP promoters. Furthermore, the previously proposed VirB-binding site and multiple sites found as a result of its description (i.e., sites located at the virB, virF, spa15, and virA promoters) are not sufficient for VirB to bind in vivo using this tool. The implications of these findings are discussed

Operationalising a real-time research ethics approach: supporting ethical mindfulness in agriculture-nutrition-health research in Malawi

BACKGROUND: There have been notable investments in large multi-partner research programmes across the agriculture-nutrition-health (ANH) nexus. These studies often involve human participants and commonly require research ethics review. These ANH studies are complex and can raise ethical issues that need pre-field work, ethical oversight and also need an embedded process that can identify, characterise and manage ethical issues as the research work develops, as such more embedded and dynamic ethics processes are needed. This work builds on notions of 'ethics in practice' by developing an approach to facilitate ethical reflection within large research programmes. This study explores the application of a novel 'real-time research ethics approach' (RTREA) and how this can support ethical mindfulness. This involves embedding ethical analysis and decision-making within research implementation, with a continuous dialogue between participants and researchers. The aim is to improve ethical responsiveness and participant experience, which in turn may ethically support adherence and retention. In this case study, a bioethics team (BT) was embedded in a community-based randomised, controlled trial conducted in rural Malawi, titled the 'Addressing Hidden Hunger with Agronomy'. To identify ethical issues, the researchers conducted ten focus group discussions, fourteen in-depth interviews with key informants, two workshops, observed two sensitisation and three activity meetings conducted by the trial team, and analysed fifteen reports from pre-trial to trial implementation. RESULTS: The RTREA facilitated the identification of social and ethical concerns and made researchers aware of participants' 'lived research experience'. To address concerns and experiences, the BT worked with researchers to facilitate conversation spaces where social and ethical issues were discussed. Conversation spaces were designed to create partnerships and promote participatory methods to capture trial participants' (TPs) perspectives and experiences. CONCLUSIONS: The use of RTREA showed the value of real-time and continuous engagement between TPs and researchers. These real-time processes could be embedded to complement traditional ethical guidance and expert opinions. A deeper engagement appeared to support greater operationalising of principles of inclusion, empowerment, and participant autonomy and supported researchers 'ethical mindfulness' which in turn may support instrumental outcomes of high recruitment, retention, and adherence levels

Can selenium deficiency in Malawi be alleviated through consumption of agro-biofortified maize flour? Study protocol for a randomised, double-blind, controlled trial

Micronutrient deficiencies including selenium (Se) are widespread in Malawi and potentially underlie a substantial disease burden, particularly among poorer and marginalised populations. Concentrations of Se in staple cereal crops can be increased through application of Se fertilisers – a process known as agronomic biofortification (agro-biofortification) – and this may contribute to alleviating deficiencies. The Addressing Hidden Hunger with Agronomy (AHHA) trial aims to establish the efficacy of this approach for improving Se status in rural Malawi

Biofortified Maize Improves Selenium Status of Women and Children in a Rural Community in Malawi: Results of the Addressing Hidden Hunger With Agronomy Randomized Controlled Trial

Background: Selenium deficiency is widespread in the Malawi population. The selenium concentration in maize, the staple food crop of Malawi, can be increased by applying selenium-enriched fertilizers. It is unknown whether this strategy, called agronomic biofortification, is effective at alleviating selenium deficiency. Objectives: The aim of the Addressing Hidden Hunger with Agronomy (AHHA) trial was to determine whether consumption of maize flour, agronomically-biofortified with selenium, affected the serum selenium concentrations of women, and children in a rural community setting. Design: An individually-randomized, double-blind placebo-controlled trial wasconducted in rural Malawi. Participants were randomly allocated in a 1:1 ratio to receive either intervention maize flour biofortified with selenium through application of selenium fertilizer, or control maize flour not biofortified with selenium. Participant households received enough flour to meet the typical consumption of all household members (330 g capita−1 day−1) for a period of 8 weeks. Baseline and endline serum selenium concentration (the primary outcome) was measured by inductively coupled plasma mass spectrometry (ICP-MS). Results: One woman of reproductive age (WRA) and one school-aged child (SAC) from each of 180 households were recruited and households were randomized to each group. The baseline demographic and socioeconomic status of participants were well-balanced between arms. No serious adverse events were reported. In the intervention arm, mean (standard deviation) serum selenium concentration increased over the intervention period from 57.6 (17.0) μg L−1 (n = 88) to 107.9 (16.4) μg L−1 (n = 88) among WRA and from 46.4 (14.8) μg L−1 (n = 86) to 97.1 (16.0) μg L−1 (n = 88) among SAC. There was no evidence of change in serum selenium concentration in the control groups Conclusion: Consumption of maize flour biofortified through application of selenium-enriched fertilizer increased selenium status in this community providing strong proof of principle that agronomic biofortification could be an effective approach to address selenium deficiency in Malawi and similar settings. Clinical Trial Registration http://www.isrctn.com/ISRCTN85899451, identifier: ISRCTN85899451

ISBS 2018 AUCKLAND CONFERENCE SPRINZ-HPSNZ-AUT MILLENNIUM APPLIED PROGRAMME

An interactive afternoon of sessions delivered by High Performance Sport New Zealand (HPSNZ) and AUT SPRINZ Biomechanists, Performance Analysts and other biomechanics relevant sport facing practitioners. The 11 sessions are at AUT Millennium (AUTM), which is a satellite site of AUT University and the Auckland training hub for many HPSNZ supported sports such as athletics, sailing, and swimming. These sports and others (cycling, rowing, snow sports etc.) will be represented in the line-up. The applied sessions involve practical demonstrations of aspects of analysis and/or tools used to deliver in the field to directly positively impact athletes performances on the world stage. Following these engaging sessions there will be tasting of New Zealand wine, allowing for further discussion and networking. Sir Graeme Avery will be acknowledged for his contribution to sport science. Mike Stanley is AUT Millennium Chief Executive & NZ Olympic Committee President will explain the partners in the facility. AUT Millennium is a charitable trust established to help New Zealanders live longer and healthier lives, and to enjoy and excel in sport through the provision of world-class facilities, services, research and education. Founded in 2002 as Millennium Institute of Sport and Health (MISH) by Sir Stephen Tindall and Sir Graeme Avery as a premium health and fitness facility for both athletes and the public alike. Partnered with AUT University in 2009, forming AUT Millennium, to expand research and education in the sporting sector. Professor Barry Wilson is an Adjunct Professor with SPRINZ at Auckland University of Technology and will be outlining the research and student opportunities. Martin Dowson is the General Manager Athlete Performance Support at High Performance Sport New Zealand and has overall responsibility for the programme. Simon Briscoe, AUT Millennium Applied Session Coordinator, is the head of the Performance and Technique Analysis discipline within HPSNZ. Simon is coordinating the applied sessions along with technical support from Dr Allan Carman, Research Fellow, AUT SPRINZ. Jodi Cossor and Matt Ingram will provide a demonstration of a multidisciplinary approach driven by biomechanical analysis for Paralympic swimmers. Justin Evans and Sarah-Kate Millar will provide a practical session assessing the athletes rowing stroke to assist the coach on technical changes. This session will demonstrate various rowing traits and how the biomechanist and coach can work together to optimise boat speed. Mike Schofield and Kim Hébert-Losier will provide a session looking at shotput and the evidence based approach to coaching. Dr Craig Harrison and Professor John Cronin will provide examples from the AUTM Athlete Development programme. Kim Simperingham and Jamie Douglas who work with high performance rugby athletes will outline sprinting mechanics in practice. Dr Bruce Hamilton, Fiona Mather, Justin Ralph and Rone Thompson will demonstrate the approach of HPSNZ and Cycling NZ performance health teams in the use of some specific tools for prevention of injury and optimisation of performance. Kelly Sheerin, Denny Wells and Associate Professor Thor Besier will provide examples of using IMU and motion capture methods for running and basketball biomechanics research, education and service. Dr Rodrigo Bini and Associate Professor Andrew Kilding will show how linking of biomechanics and physiology improves injury prevention and performance enhancement. Robert Tang, Andre de Jong and Farhan Tinwala discuss select projects developed by Goldmine, HPSNZ’s in-house engineering team, and how these innovations have enabled unprecedented levels of biomechanics feedback. Cameron Ross and Paul McAlpine demonstrate the technology being used at the Snow Sports NZ training centre in Cadrona to enhance load monitoring of athletes. This application allows greater insight into training performances and biomechanical loads than has been previously possible in the training environment. AUT Millennium tour guides are coordinated by Josh McGeown and include Enora Le Flao, Dustin Oranchuk, Erika Ikeda, Jono Neville, Aaron Uthoff, Andrew Pichardo, Farhan Tinwala, Shelley Diewald, Renata Bastos Gottgtroy, Jessica Yeoman, Casey Watkins, Eric Harbour, Anja Zoellner, Alyssa Joy Spence, Victor Lopez Jr, and Albert Chang

A lambda = 1.3 mm and 2 mm molecular line survey towards M82

We study the chemical complexity towards the central parts of the starburst galaxy M82, and investigate the role of certain molecules as tracers of the physical processes in the galaxy circumnuclear region. We carried out a spectral line survey with the IRAM-30m telescope towards the northeastern molecular lobe of M82. It covers the frequency range between 129.8 GHz and 175.0 GHz in the 2 mm atmospheric window, and between 241.0 GHz and 260.0 GHz in the 1.3 mm atmospheric window. Sixty-nine spectral features corresponding to 18 different molecular species are identified. In addition, three hydrogen recombination lines are detected. The species NO, H2S, H2CS, NH2CN, and CH3CN are detected for the first time in this galaxy. Assuming local thermodynamic equilibrium, we determine the column densities of all the detected molecules. We also calculated upper limits to the column densities of fourteen other important, but undetected, molecules, such as SiO, HNCO, or OCS. We compare the chemical composition of the two starburst galaxies M82 and NGC253. This comparison enables us to establish the chemical differences between the products of the strong photon-dominated regions (PDRs) driving the heating in M82, and the large-scale shocks that influence the properties of the molecular clouds in the nucleus of NGC253. Overall, both sources have different chemical compositions. Some key molecules highlight the different physical processes dominating both central regions. Examples include CH3CCH, c-C3H2, or CO+, the abundances of which are clearly higher in M82 than in NGC253, pointing at photodissociating regions. On the other hand, species such as CH2NH, NS, SiO, and HOCO+ have abundances of up to one order of magnitude higher in NGC253 than in M82.Comment: Accepted for publication in A&A. 19 pages, 8 figures, 3 table

Preparing for a community-based agriculture-to-nutrition trial in rural Malawi: formative research to assess feasibility and inform design and implementation decisions.

BACKGROUND: This study reports findings from formative research conducted to assess the feasibility and inform the design and implementation of the Addressing Hidden Hunger with Agronomy (AHHA) trial. The AHHA trial was a randomised, controlled trial conducted in rural Malawi, in which participants were given maize flour biofortified with selenium or control flour not biofortified with selenium for a period of 10 weeks, after which blood samples were taken to measure selenium status. METHODS: Formative research was conducted in villages near to the AHHA trial study site 1 year before the planned intervention. A short questionnaire with adult women (n = 50), focus group discussions with male (n groups = 3) and female (n groups = 3) community members, and in-depth key informant interviews (n = 7) were conducted to understand community practices and perceptions. FINDINGS: Meals were typically cooked and eaten at home in this community, while participants reported that maize flour would be less readily sold than maize grain - important considerations for the design of the trial. Regarding intervention delivery, we identified potential concerns around effects on fertility, links between blood sampling and witchcraft, and the potential for social stigma if community members considered participants lazy for receiving free flour. Participants reported that involvement of the Malawi government partners including health extension workers would increase trust. INTERPRETATION: Following the formative research, the AHHA trial appeared feasible. However, community sensitisation would be essential to address potential fears and concerns; effective sensitisation would support recruitment and treatment adherence, and would protect the safety and wellbeing of participants and researchers. People in positions of authority and trust including village headmen, religious leaders, health and agriculture extension workers, and community care groups should be involved in community sensitisation

Tracking genomic cancer evolution for precision medicine: The Lung TRACERx Study

The importance of intratumour genetic and functional heterogeneity is increasingly recognised as a driver of cancer progression and survival outcome. Understanding how tumour clonal heterogeneity impacts upon therapeutic outcome, however, is still an area of unmet clinical and scientific need. TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy [Rx]), a prospective study of patients with primary non-small cell lung cancer (NSCLC), aims to define the evolutionary trajectories of lung cancer in both space and time through multiregion and longitudinal tumour sampling and genetic analysis. By following cancers from diagnosis to relapse, tracking the evolutionary trajectories of tumours in relation to therapeutic interventions, and determining the impact of clonal heterogeneity on clinical outcomes, TRACERx may help to identify novel therapeutic targets for NSCLC and may also serve as a model applicable to other cancer types

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease