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Researchers and One Health professionals who deal with data generation, data integration and data analysis tasks, for example during disease surveillance, outbreak investigation, or risk assessments, need to be continuously informed about new digital solutions that support these activities and also promote the One Health -compliant exchange of information across sectors. The online software fair was organised to inform researchers and One Health professionals of new digital solutions and tools that support data generation, data integration and data analysis tasks. It is the intention that these tools could be utilised in the future for disease surveillance, outbreak investigation, and/or risk assessment. The tools presented are being or have already been developed for application across all pillars of One Health, including human health, animal health, environmental health, and food safety. To read more about the tools presented, download the abstract book here. The online software fair was split into two sessions. In the morning session, eight digital solutions and software tools were presented in the form of pitch presentations by members of our consortium from INIA (Spain), NIPH (Norway), NVI (Norway) and BfR (Germany). In the afternoon session, each software tool was presented in a breakout room. Delegates could join up to three breakout rooms to learn more and take part in discussions, interactive exercises and gain hands-on experience using these tools and innovative solutions, and applying them to their area of expertise.All delegates were given access to the slides and recordings after the workshop, so they continue to be inspired and benefit from the content presented. Over 70 delegates across 29 countries worldwide registered to attend – including PhD students, junior and senior researchers, bioinformaticians, epidemiologists, and other One Health professionals. The workshop was a big success and an exemplary demonstration in how using training opportunities is an effective way to facilitate One Health-compliant exchange of information across sectors. The event highlights the One Health EJP’s ability to bring together experts from across our European network and share tools to promote a sustainable One Health approach in the future.

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The One Health EJP has funded 17PhDs, and the research focus of the individual PhD projects falls within at least one of the three research domains of the OHEJP: foodborne zoonoses, antimicrobial resistance and emerging threats. The PhD projects provide excellent added value to the OHEJP, including improved integration (both geographical and interdisciplinary), and an opportunity to develop the next generation of scientists in One Health contributing to the sustainability of the One Health approach. Each year, the PhD projects report on the research activities, progress, results, risks, ethics, and impact for the previous 12-month reporting period. A record of the dissemination activities and soft skills training that took place during this period is also reported. This deliverable report contains the 12-month reports for each PhD project for months 25 to 36 (Jan-Dec 2020) of the One Health EJP. The purpose of this deliverable is to monitor, report and disseminate the progress and results that can be shared publicly.

Short Term Missions (STMs) provide small travel grants with the aim of sharing scientific expertise, methodologies, equipment and facilities to harmonise the existing approaches and methodologies within the large OHEJP network, and to drive the research forward in a collaborative and non-duplicative fashion to strengthen both the scientific capacity within the OHEJP and also future prevention, preparedness, detection and response of the EU to foodborne and other emerging threats across human-animal-environmental sectors. Read the report full report here of the first round of missions that were co-funded and took place in 2019.&nbsp

TheOne Health EJP's Communication and Media workshop was hosted as an online event on 5th-6thOctober 2020. The workshop was organised by the One Health EJP partners- Bulgarian Food Safety Agencyand University of Surrey. The workshop’s main aim was to aid early career researchers and develop their communication skills to disseminate information effectively to the general public and to their key stakeholders. By covering all media distribution formats (television, radio, the internet, social media, direct public events, etc.), our goal was to equip the participants with the knowledge on how to generate the maximum impact of their research towards their target audiences. The workshop boasted leading communication experts in public health, with a specific focus on food safety and risk assessment, and included training delivered by a former TV News broadcaster, presenter and reporter who is an expert on media performance and media interviews. Read the full report here.

Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 Å. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn(2+) and NAD(P)(+), we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P)(+) cofactor in multiple conformations, including an inactive, compact NAD(+) form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologs.

Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ provides the required reducing power for lipid biosynthesis. Here, we present the X-ray crystal structure of MEZ to 3.6 Å resolution and compare it with known structures of prokaryotic and eukaryotic malic enzymes. We use biochemical assays to determine its oligomeric state and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+ and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually disordered, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that MEZ subunits alternate between open and closed states and that MEZ can stably bind its NAD(P)+ cofactor in multiple conformations, including an inactive, compact NAD+ form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb.

The ASM Satellite Workshop 2019 aimedto provide a platform to discuss digital innovation within and outside the OHEJP consortium, in addition to developing an understanding and interest in data management plans. This proved to be an excellent opportunity to understand how data management plans can be applied to one’s research. Read the full report here.

The causative agent of TB, Mycobacterium tuberculosis (Mtb) is once again the world’s number one infectious killer. M. tuberculosis resides primarily within macrophages and metabolic reprogramming within this intracellular niche is a crucial determinant of virulence. We previously applied the metabolic modelling-based tool 13C-flux spectral analysis (13C-FSA) to show that intracellular M. tuberculosis co-metabolises multiple gluconeogenic and glycolytic carbon substrates by utilizing the reactions of the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate (OAA) or anaplerotic (ANA) node. However, predicting the metabolic mode of operation required for intracellular survival is chellenging using a metabolic network as the ANA node consists of several apparently functionally redundant bidirectional reactions. Here we use multiple techniques including 13C isotopomer profiling, lipid analysis and fluorescent reporter strains to dissect the role of the ANA node. We show that this node has unexpected roles in the life cycle of M. tuberculosis including lipid biosynthesis, protection from known toxic intracellular carbon sources and redox regulation. Inhibiting enzymes at this node with novel therapeutic compounds restricts the growth of M. tuberculosis and limits the ability of this formidable pathogen to survive within the human host cell identifying the ANA node as a potential druggable pathway for controlling TB.

Nitrogen metabolism of Mycobacterium tuberculosis (Mtb) is crucial for the survival and virulence of this pathogen inside host macrophages but little is known about the nitrogen sources acquired from the host or their route of assimilation. Here we performed a systems-based analysis of nitrogen metabolism in intracellullar Mtb and developed 15N-Flux Spectral Ratio Analysis (FSRA) to probe the metabolic cross-talk between the host cell and Mtb. We demonstrate that intracellular Mtb acquires nitrogen from multiple amino acids in the macrophage including glutamate, glutamine, aspartate, alanine, glycine and valine, with glutamine being the predominant nitrogen donor. Each nitrogen source is uniquely assimilated into specific intracellular pools indicating compartmentalised metabolism. This was not observed for in vitro-grown Mtb indicating that there is a switch in nitrogen metabolism when the pathogen enters the intracellular environment. These results provide clues about the potential metabolic targets for development of innovative anti-tuberculosis therapies.

Enzymes at the phosphoenolpyruvate (PEP)–pyruvate–oxaloacetate or anaplerotic (ANA) node control the metabolic flux to glycolysis, gluconeogenesis, and anaplerosis. Here we used genetic, biochemical, and 13C isotopomer analysis to characterize the role of the enzymes at the ANA node in intracellular survival of the world's most successful bacterial pathogen, Mycobacterium tuberculosis (Mtb). We show that each of the four ANA enzymes, pyruvate carboxylase (PCA), PEP carboxykinase (PCK), malic enzyme (MEZ), and pyruvate phosphate dikinase (PPDK), performs a unique and essential metabolic function during the intracellular survival of Mtb. We show that in addition to PCK, intracellular Mtb requires PPDK as an alternative gateway into gluconeogenesis. Propionate and cholesterol detoxification was also identified as an essential function of PPDK revealing an unexpected role for the ANA node in the metabolism of these physiologically important intracellular substrates and highlighting this enzyme as a tuberculosis (TB)-specific drug target. We show that anaplerotic fixation of CO2 through the ANA node is essential for intracellular survival of Mtb and that Mtb possesses three enzymes (PCA, PCK, and MEZ) capable of fulfilling this function. In addition to providing a back-up role in anaplerosis we show that MEZ also has a role in lipid biosynthesis. MEZ knockout strains have an altered cell wall and were deficient in the initial entry into macrophages. This work reveals that the ANA node is a focal point for controlling the intracellular replication of Mtb, which goes beyond canonical gluconeogenesis and represents a promising target for designing novel anti-TB drugs.

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. This article has been made available through the Brunel Open Access Publishing Fund. Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format. This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources.

An explicit and logically consistent model for the representation of biomedical protocols would enable researchers in the Life Sciences to better record, execute, share, and report experimental procedures and results. The model we propose is based on the ontology of EXperimental ACTions (EXACT). The EXACT model is designed to define typical actions performed by biologists in labs and their essential attributes to enable recording of biomedical protocols in a computer processable form. This oral communication aims to report on the recent progress with the EXACT-based representation of biomedical protocols.