BristolBridge: Bridging the Gaps between the Engineering and Physical Sciences and Antimicrobial Resistance

Lead Research Organisation: University of Bristol
Department Name: Chemistry

Abstract

Antimicrobial (antibiotic) resistance (AMR) is a major and growing problem in many areas of medicine. AMR has been recognised as one of the most important challenges facing the UK. The availability of effective antimicrobial compounds underpins much of modern health care, making possible invasive surgical procedures and aggressive chemotherapeutic regimes that would otherwise be compromised by unacceptable risk of bacterial infection. Within this broad area, the increasing prevalence of resistant Gram-negative bacteria as causes of healthcare associated infections, the lack of new agents effective against these organisms, and the consequent requirement to stimulate antibiotic development, are all highlighted in the recent report of the UK Chief Medical Officer.

Physical scientists, engineers and mathematicians can make potentially transformative contributions to tackling AMR. Unleashing this potential requires new ways of interdisciplinary working, and bringing together researchers from these disciplines with counterparts from biology and human and animal medicine. We will achieve this by the following specific objectives:
(1) A wide range of networking activities to build new interdisciplinary research communities
(2) Pump-priming projects in, and across, three distinct strands we have identified, building on EPS research strengths, aligned with AMR strategy, to foster transformative research to combat AMR
(3) Training activities (training EPS researchers in biomedical methods and models and vice versa), to aid EPS researchers in understanding AMR and equip biomedical researchers to apply EPS methods, effectively training a new generation of researchers to tackle the problems of AMR

The University of Bristol is exceptionally well placed to build and deliver new engineering and physical science research into AMR, combining as it does international excellence across all of these fields. The University of Bristol houses world-leading research in the physical sciences, mathematics, computer science and engineering, much of which is EPSRC-funded. Bristol is also a thriving centre for basic biomedical, clinical, veterinary and community health research, with studies into AMR as a key strength. AMR is a strategic priority at the University of Bristol through our Infection and Immunity research theme and with support from the Elizabeth Blackwell Institute (EBI) for Health Research, we have already begun building connections across these interdisciplinary communities. This Bridging the Gaps project will exploit the potential opportunities that exist across a wide range of outstanding EPS researchers, including those who have never previously felt their research was relevant to AMR. By ensuring that EPS researchers are core members of interdisciplinary research activity, we will identify and seed new approaches to analyse, mitigate and ultimately overcome AMR. UoB houses world-leading research in materials science, engineering, synthetic biology, physics, maths/statistics, nanoscience and chemistry, all with significant EPSRC funding. UoB currently has the 6th largest EPSRC portfolio of any UK University, with in excess of £200M in live grants. Bristol is also a thriving centre for biomedical, clinical and community health research (within Clinical Sciences, Veterinary Sciences, Cellular and Molecular Medicine and in our NHS Trust partners, UoB has the fifth largest active portfolio of grants classified by EPSRC as relevant to the Healthcare sector, totalling approx £30M), in which studies of AMR form a key part. UoB has an outstanding track record of success in developing new interdisciplinary collaborations to address major societal challenges with the EBI, which was formed in 2012 for this express purpose. The EBI is ideally placed to help building interdisciplinary capacity in AMR, and has an existing governance mechanism for open and transparent deployment of this type of funding.

Planned Impact

Benefit of the activities on the future of collaborative research addressing AMR at the institution: UoB hosts considerable experience in the AMR field and EPS departments with huge potential for developing solutions, but the two are disconnected by structural and administrative barriers. The overriding objective of this Bridging the Gaps project is to equip engineers and physical scientists (EPS) at the University of Bristol (UoB) with the knowledge and resources necessary to make future substantive discoveries that will tackle the problem of Antimicrobial Resistance (AMR). We will use specific mechanisms to break these down and forge collaborations as described in the Pathways to Impact. By its very nature, the primary impact of this project will be an increase in collaborative research between UoB EPS and biomedical sciences academics in AMR.

Potential External Beneficiaries: Whilst the primary impact of this project will be to generate collaborations within UoB, advances in AMR research may be transformative beyond the lifetime of this project. Our proposed activities encompass novel antimicrobial discovery (research theme 1) to replenish the supply of drugs; improving antimicrobial delivery (research theme 2) to minimise systemic and environmental exposure, reduce selection for resistance and revitalise existing antibiotics; and health research and surveillance interventions (research theme 3) to reduce antibiotic prescribing and slow resistance development. These may impact upon:
The UK Population: AMR is a significant detriment to UK population health, with resulting increases in morbidity and mortality affecting tens of thousands of people each year. Advances in any of the three research areas would have significant impact on the health of the nation. AMR is also a significant veterinary issue and a threat to global food security.
The UK Health and Social Care systems: AMR cost the UK economy £1 billion per year in 1998, (House of Lords report), and £10 blion per year today (Chief Medical Officer). Greater decline in patient well being prolongs recovery, increases cost, and may result in long term complications that increase cost to outpatient, GP and social care, and potentially reduce the working lifetime of the patient. Any outcome arising from this work that reduces disease severity and time to cure, has the potential to save society money.

Industry/UK Economic Activity: AMR is a global problem. UK research council led research such as this offers potential for direct economic benefit from the research, development and sale of novel antimicrobial drugs, diagnostic tests and drug delivery systems to overseas healthcare systems. There is also potential for job creation in the UK and economic flow from the rest of the world into the UK during the R&D phase.

Increasing impact by learning from Industry: Academics can misunderstand the requirements for achieving successful therapeutic/diagnostics. Accordingly, during the project lifetime, we will use specific events as described in the Pathways to Impact to improve translation of UoB EPS research in the AMR area. This will increase the likelihood of delivering impact to external beneficiaries as set out above.

Public and Educational Engagement: AMR is primarily driven by actions of people. One way to slow the rate of AMR development is public education about the problem, its causes and potential solutions, including the value of taxpayer-funded research. Public interest in this subject, and recognition of its importance, is evidenced by the vote to set the Longitude Prize in the AMR area. Similarly, engaging with schools and young people will enhance awareness, inspire the next generation about research and possible careers in STEM, and highlight opportunities and advances in interdisciplinary research in the AMR field in particular. We see these types of engagements as important impacts and describe events and activities to deliver them.

Publications

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Byrne MJ (2016) The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail. in Journal of the American Chemical Society

 
Title BristolBridge AMR CrossFire video series • Public engagement: consultants for Surgeon X AMR comic (http://surgeonx.co.uk/), school talks, Schools Conference on Antibiotics and Antibiotic Resistance Science and BristolBridge AMR CrossFire hosted on YouT 
Description BristolBridge AMR CrossFire video series • Public engagement: consultants for Surgeon X AMR comic (http://surgeonx.co.uk/), school talks, Schools Conference on Antibiotics and Antibiotic Resistance Science and BristolBridge AMR CrossFire hosted on YouTube https://www.youtube.com/channel/UCjZ6fYNvw_8Mhr4OSWCvsSw • Media engagement - TV and radio (Avison & Seddon) • Media training by BBC Radio as part of Royal Society of Chemistry funded workshop & training for Surgeon X comic (Mulholland, Hughes - 'plus' funded postdoctoral research assistant & Walker - PhD student) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
Impact BristolBridge AMR CrossFire video series • Public engagement: consultants for Surgeon X AMR comic (http://surgeonx.co.uk/), school talks, Schools Conference on Antibiotics and Antibiotic Resistance Science and BristolBridge AMR CrossFire hosted on YouTube https://www.youtube.com/channel/UCjZ6fYNvw_8Mhr4OSWCvsSw • Media engagement - TV and radio (Avison & Seddon) • Media training by BBC Radio as part of Royal Society of Chemistry funded workshop & training for Surgeon X comic (Mulholland, Hughes - 'plus' funded postdoctoral research assistant & Walker - PhD student) 
URL http://www.bristol.ac.uk/bristolbridge/
 
Title Surgeon X Special 'Trial and Error' 
Description Surgeon X comic special edition. Written by Sara Kenney and based on a chemistry storyline developed in consultation with Prof. Adrian Mulholland, Dr Robert Hughes and PhD student Mr Paul Walker (all University of Bristol). Dr Matthew Avison (BristolBridge Co-I) is also Key Science Consultant for the Surgeon X team. 
Type Of Art Creative Writing 
Year Produced 2017 
Impact This is available in print (sold in comic shops) and available online. Sara Kenney has widely exhibited Surgeon X at AMR conferences, exhibitions and many public engagement events. 
URL http://surgeonx.co.uk/
 
Description Details of our Bridging the Gaps activities in AMR are available at: http://www.bris.ac.uk/bristolbridge/ Antimicrobial (antibiotic) resistance (AMR) is a major and growing problem in many areas of medicine. AMR has been recognised as one of the most important challenges facing the UK. The availability of effective antimicrobial compounds underpins much of modern health care, making possible invasive surgical procedures and aggressive chemotherapeutic regimes that would otherwise be compromised by unacceptable risk of bacterial infection. Within this broad area, the increasing prevalence of resistant Gram-negative bacteria as causes of healthcare associated infections, the lack of new agents effective against these organisms, and the consequent requirement to stimulate antibiotic development, are all highlighted in the recent report of the UK Chief Medical Officer. Physical scientists, engineers and mathematicians can make potentially transformative contributions to tackling AMR. Unleashing this potential requires new ways of interdisciplinary working, and bringing together researchers from these disciplines with counterparts from biology and human and animal medicine. We will achieve this by the following specific objectives: (1) A wide range of networking activities to build new interdisciplinary research communities (2) Pump-priming projects in, and across, three distinct strands we have identified, building on EPS research strengths, aligned with AMR strategy, to foster transformative research to combat AMR (3) Training activities (training EPS researchers in biomedical methods and models and vice versa), to aid EPS researchers in understanding AMR and equip biomedical researchers to apply EPS methods, effectively training a new generation of researchers to tackle the problems of AMR The University of Bristol is exceptionally well placed to build and deliver new engineering and physical science research into AMR, combining as it does international excellence across all of these fields. The University of Bristol houses world-leading research in the physical sciences, mathematics, computer science and engineering, much of which is EPSRC-funded. Bristol is also a thriving centre for basic biomedical, clinical, veterinary and community health research, with studies into AMR as a key strength. AMR is a strategic priority at the University of Bristol through our Infection and Immunity research theme and with support from the Elizabeth Blackwell Institute (EBI) for Health Research, we have already begun building connections across these interdisciplinary communities. This Bridging the Gaps project will exploit the potential opportunities that exist across a wide range of outstanding EPS researchers, including those who have never previously felt their research was relevant to AMR. By ensuring that EPS researchers are core members of interdisciplinary research activity, we will identify and seed new approaches to analyse, mitigate and ultimately overcome AMR. UoB houses world-leading research in materials science, engineering, synthetic biology, physics, maths/statistics, nanoscience and chemistry, all with significant EPSRC funding. UoB currently has the 6th largest EPSRC portfolio of any UK University, with in excess of £200M in live grants. Bristol is also a thriving centre for biomedical, clinical and community health research (within Clinical Sciences, Veterinary Sciences, Cellular and Molecular Medicine and in our NHS Trust partners, UoB has the fifth largest active portfolio of grants classified by EPSRC as relevant to the Healthcare sector, totalling approx £30M), in which studies of AMR form a key part. UoB has an outstanding track record of success in developing new interdisciplinary collaborations to address major societal challenges with the EBI, which was formed in 2012 for this express purpose. The EBI is ideally placed to help building interdisciplinary capacity in AMR, and has an existing governance mechanism for open and transparent deployment of this type of funding. BristolBridge: a multidisciplinary approach to tackling antimicrobial resistance. Antimicrobial resistance (AMR) is an escalating global threat. BristolBridge aims to provide exciting new research opportunities for outstanding engineering and physical sciences researchers, including those who have never previously felt their work was relevant to AMR. The antimicrobial resistance (AMR) challenge is part of a cross-Research Council initiative to encourage researchers to work collaboratively to tackle the emergence and spread of infections caused by bacteria that are resistant to treatment by current antibiotics. BristolBridge supports multiple pump-priming projects across the University to generate data for future research proposals. The University of Bristol is committed to fighting the global challenge posed by the increasing problem of antimicrobial resistance (AMR), and has received £10.25 million of research funding from the UKRI 'Tackling AMR - A Cross-Council Initiative' to find effective and sustainable solutions to this urgent problem. Antibiotics transformed healthcare in the 20th century and are still considered one of the greatest medical achievements of the era. Today, we still rely on antibiotics to treat everything from minor cuts to life-threatening bacterial infections and to prevent infection after surgery. These drugs drastically improved our quality of life and increased lifespan. In the 21st century, antibiotic overuse and misuse has led to antibiotics rapidly becoming ineffective resulting in a fall in life expectancy. Antimicrobial resistance, specifically antibacterial resistance, now poses a global threat to human life. Resistance occurs when antibiotics are rendered ineffective against the bacteria they are engineered to fight. We need urgent action to halt resistance and to accelerate new treatments for bacterial infection. The University of Bristol has a number of research projects, programmes and initiatives that are working towards understanding AMR better and finding solutions for this escalating global issue. The AMR research community at Bristol ('Bristol AMR') is a cross-faculty research network supported by the University's Elizabeth Blackwell Institute for Health Research as one of their four Research Strands, which are funded through the Wellcome Trust Institutional Strategic Support Fund (ISSF). This is further funding to which BristolBridge contributed, but as part of a Wellcome Trust ISSF Award (PI Professor Rachael Gooberman-Hill, EBI Director) apparently is not included in the ResearchFish database of awards. BristolBridge was highlighted in an Institute of Physics eBook on research collaboration
First Year Of Impact 2015
Sector Agriculture, Food and Drink,Chemicals,Communities and Social Services/Policy,Creative Economy,Digital/Communication/Information Technologies (including Software),Education,Healthcare,Government, Democracy and Justice,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic,Policy & public services

 
Description Featured in UKRI AMR House of Commons Event
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description AMR Global Development Award 2017
Amount £88,000 (GBP)
Funding ID MR/R014922/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 03/2018
 
Description Biophysical stimulation-enhanced antimicrobial surfaces to combat implant-associated infections
Amount £53,991 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 05/2018
 
Description BristolBridge has contributed to the University of Bristol being the UK's largest recipient of RCUK AMR cross-council funding awards both in number (7) and value (£5.268M). 6 related AMR grants awarded with BristolBridge PIs/Co-Is include MRC-led AMR.
Amount £5,268,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2019
 
Description Carbapenem Antibiotic Resistance in Enterobacteriaceae: Understanding Interactions of KPC Carbapenemases with Substrates and Inhibitors
Amount £668,396 (GBP)
Funding ID MR/T016035/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 01/2020 
End 01/2023
 
Description Confidence in Concept 'Developing a mobile device for rapid antimicrobial resistance detection in primary care'
Amount £74,685 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 06/2017 
End 05/2018
 
Description EPSRC co-funding Innovate UK
Amount £220,245 (GBP)
Funding ID EP/R043361/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 02/2019
 
Description In vitro and in vivo studies of 3D orthopaedic implants with cell-instructive nanotopographies
Amount £699,713 (GBP)
Funding ID MR/S010343/1 
Organisation University of Bristol 
Sector Academic/University
Country United Kingdom
Start 06/2019 
End 05/2022
 
Description One Health Drivers of Antibacterial Resistance in Thailand
Amount £70,825 (GBP)
Funding ID MR/R014922/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 04/2018
 
Title Annual report to EPSRC; details below 
Description HECBioSim, the UK HEC Biomolecular Simulation Consortium, was established in March 2013, and works closely with and complements CCP-BioSim (the UK Collaborative Computational Project for Biomolecular Simulation at the Life Sciences Interface). Most of the members of the Consortium are experienced users of high end computing. Biomolecular simulations are now making significant contributions to a wide variety of problems in drug design and development, biocatalysis, bio and nano-technology, chemical biology and medicine. The UK has a strong and growing community in this field, recognized by the establishment in 2011 by the EPSRC of CCP-BioSim (ccpbiosim.ac.uk), and its renewal in 2015. There is a clear, growing and demonstrable need for HEC in this field. Members of the Consortium have, for example, served on the HECToR and ARCHER Resource Allocation Panel. The Consortium welcomes members across the whole biomolecular sciences community, and we are currently (and will remain) open to new members (unlike some consortia). Since establishing the Consortium, several new members (FLG, DH, ER) have joined the Management Group. Many of the projects awarded ARCHER time under the Consortium do not involve CCP-BioSim or HECBioSim Management Group members, demonstrating the openness of HECBioSim and its support of the biomolecular simulation community in the UK. A number of other researchers have joined and it is our expectation that other researchers will join HECBioSim in the future. We actively engage with structural and chemical biologists and industrial researchers. We foster interactions between computational, experimental and industrial scientists (see the example case studies; members of the Consortium have excellent links with many pharmaceutical, chemical and biotechnology companies). Details of HECBioSim are available via our webpages at: http://www.hecbiosim.ac.uk Applications are made through the website http://www.hecbiosim.ac.uk and reviewed at one of the series of regular panel meetings. A list of successful HECtime allocations on ARCHER is available at:http://www.hecbiosim.ac.uk/applications/successfulprojects All proposals are of course subject to scientific and technical review, but we have the philosophy of supporting the best science to deliver the highest impact, rather than focusing on supporting development of a couple of codes. An allocation panel (with changing membership) meets twice yearly to judge proposals and requests for AUs; projects are assessed competitively: any groups in the UK can apply. All submitted proposals receive constructive feedback from the allocation panel. The HECBioSim website also provides forums for the biomolecular simulation community, a wiki hosting useful how-tos and user guides, and software downloads (currently FESetup and Longbow). Our lead software development project between Nottingham (Charlie Laughton and Gareth Shannon) and Daresbury (James Gebbie), we have developed a remote job submission tool, 'Longbow' (see below). The tool is designed to reproduce the look and feel of local MD packages, but to stage data and submit jobs to a large HPC resource, such as ARCHER, in a manner invisible to the user. Workshops and New Opportunities No more than half a page detailing upcoming workshops and meetings. Also include discussion of other areas which are potentially of interest to other HEC Consortia and opportunities for cross CCP /HEC working. Workshops are listed below and can be found on the HECBioSim Website We work closely with CCP-BioSim, for example in organizing training workshops and meetings. Our activities are outlined at www.hecbiosim.ac.uk Examples of forthcoming meetings include: Computational Molecular Science 2017 - on Sunday 19 March 2017 17th European Seminar on Computational Methods in Quantum Chemistry - on Tuesday 11 July 2017 Frontiers of Biomolecular Simulation Southampton, September 2016 Issues and Problems Short discussion of any issues or problems that the HEC Consortium faces including issues with the ARCHER service, funding, management of allocation and staffing. This is also a good opportunity to highlight to the SLA committee any issues that the Consortium may have experienced with their SLA support during the reporting period. Details of SLA activities are given in the SLA report. Dr. James Gebbie provides support to HECBioSIm through the SLA. He has been very helpful in the construction of the HECBioSim webpages (hecbiosim.ac.uk). James also worked with Dr. Gareth Shannon on the development of Longbow (See above). In the past year, members of the Consortium faced some queuing problems; close to the end of the first allocation period in particular, there were long queuing times, which led to problems in completing jobs and using allocated time. Throughput has been a real problem in the past few months. Membership Please provide a full list of existing members and their institutions, highlighting any new members that have joined the consortium during the reporting period. If available please provide information on the number of distinct users that have accessed ARCHER via the Consortium during this reporting period. Below is a list of PIs with HECBioSim projects in the current reporting period: Agnes Noy, University of York - new to this reporting period Alessandro Pandini, Brunel University London Arianna Fornili, Queen Mary University of London Cait MacPhee, University of Edinbrurgh - new to this reporting period Charlie Laughton, University of Nottingham Clare-Louise Towse, University of Bradford - new to this reporting period D Flemming Hansen, University College London - new to this reporting period David Huggins, Aston University Edina Rosta, King's College London Francesco Gervasio, University College London Ian Collinson, University of Bristol - new to this reporting period Irina Tikhonova, Queen's University Belfast Jiayun Pang, University of Greenwich Jonathan Doye, University of Oxford Julien Michel, University of Edinburgh Mario Orsi, UWE Bristol Michele Vendruscolo, University of Cambridge Michelle Sahai, University of Roehampton Philip Biggin, University of Oxford Richard Sessions, University of Bristol Stephen Euston, Heriot-Watt University Syma Khalid, University of Southampton PIs in HECBioSIm outside of current allocation period Peter Bond, University of Cambridge Richard Bryce, University of Manchester Juan Antonio Bueren-Calabuig, University of Edinburgh Christo Christov, Northumbria University Anna K Croft, University of Nottingham Jonathan Essex, University of Southampton Robert Glen, University of Cambridge Sarah A Harris, University of Leeds Jonathan Hirst, University of Nottingham Douglas Houston, University of Edinburgh Dmitry Nerukh, Aston University Andrei Pisliakov, University of Dundee Mark Sansom, University of Oxford Marieke Schor, University of Edinburgh Gareth Shannon, University of Nottingham Tatyana Karabencheva-Christova, Northumbria University There are currently 164 members of HECBioSim (i.e. users of HECBioSIm ARCHER time), included the above PIs. 20 new users have been added since January 2016. World class and world leading scientific output: ARCHER should enable high quality and world-leading science to be delivered. This should generate high impact outputs and outcomes that increase the UK's position in world science. • If all the publications relating to the work of the Consortium for this reporting period have been added to ResearchFish / will be added to ResearchFish by the end of the ResearchFish reporting exercise, please indicate this below. • If submission of a full list of publications to the Consortium record/s in ResearchFish has not been possible for this reporting period please provide a list of publications that have resulted from work performed on ARCHER by the Consortium during this reporting period (this can be included as a separate attachment). • For the reporting period please provide a bullet pointed list of key / important research findings that has resulted from work performed on ARCHER by the Consortium. Please reference any related publications. • For the reporting period please include a bullet pointed list of any relevant press announcements and other communications of significance to an international community. All publications can be found in ResearchFish, and have been added by individual researchers. A selection of illustrative highlights are provided below: Julien Michel (University of Edinburgh) New molecular simulation methods have enabled for the first time a complete description of the interactions of several drug-like small molecules with an intrinsically disordered region of the oncoprotein MDM2, as well as the effect of post-translational modifications on the dynamics of this protein. The results obtained suggest new medicinal chemistry strategies to achieve potent and selective inhibition of MDM2 for cancer therapies. Publication: Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004282 Impact of Ser17 Phosphorylation on the Conformational Dynamics of the Oncoprotein MDM2 http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00127 An outreach document is being prepared by EPCC to showcase a lab project on isoform selective inhibition that has benefited from both HECBioSim and EPCC ARCHER allocations. Syma Khalid (Chemistry, Southampton) Publication: OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment Samsudin F, Ortiz-Suarez ML, Piggot TJ, Bond PJ, Khalid S (2016). "OmpA: a Flexible Clamp for Bacterial Cell Wall Attachment", Structure, 24(12):2227-2235 With Singapore National Center for Biotechnology. Sarah Harris (Physics, Leeds) In collaboration with the experimental biochemistry group lead by Radford at Leeds, Sarah Harris used ARCHER time to show how chaperones help outer membrane proteins to fold, see: Schiffrin B, Calabrese AN, Devine PWA, Harris SA, Ashcroft AE, Brockwell DJ, Radford SE "Skp is a multivalent chaperone of outer-membrane proteins" Nature Structural and Molecular Biology 23 786-793, 2016. DOI:10.1038/nsmb.3266 Michelle Sahai (Department of Life Sciences, Roehampton) Publication: Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB. Progress in Neuro-Psychopharmacology and Biological Psychiatry 75, Pages 1-9 (2017) https://www.ncbi.nlm.nih.gov/pubmed/27890676 Phil Biggin (Biochemistry, Oxford) Outputs that have used HECBioSim time: 1. Steered Molecular Dynamics Simulations Predict Conformational Stability of Glutamate Receptors. Musgaard M, Biggin PC. J Chem Inf Model. 2016 Sep 26;56(9):1787-97. doi: 10.1021/acs.jcim.6b00297. 2. Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism. Brown PM, Aurousseau MR, Musgaard M, Biggin PC, Bowie D. J Physiol. 2016 Apr 1;594(7):1821-40. doi: 10.1113/JP271690. 3. Role of an Absolutely Conserved Tryptophan Pair in the Extracellular Domain of Cys-Loop Receptors. Braun N, Lynagh T, Yu R, Biggin PC, Pless SA. ACS Chem Neurosci. 2016 Mar 16;7(3):339-48. doi: 10.1021/acschemneuro.5b00298. 4. Distinct Structural Pathways Coordinate the Activation of AMPA Receptor-Auxiliary Subunit Complexes. Dawe GB, Musgaard M, Aurousseau MR, Nayeem N, Green T, Biggin PC, Bowie D. Neuron. 2016 Mar 16;89(6):1264-76. doi: 10.1016/j.neuron.2016.01.038. Covered by 7 news outlets: I. Health Canal (http://www.healthcanal.com/brain-nerves/70646-what-makes-the-brain-tick-so-fast.html) II. Health Medicine Network (http://healthmedicinet.com/i/scientists-reveal-how-the-brain-processes-information-with-lightning-speed/) III. News Medical (http://www.news-medical.net/news/20160227/Scientists-reveal-how-the-brain-processes-information-with-lightning-speed.aspx) IV. Wired (http://www.wired.co.uk/article/what-we-learned-about-the-brain-this-week-3) V. Alpha Galileo (http://www.alphagalileo.org/ViewItem.aspx?ItemId=161473&CultureCode=en) VI. Science Daily (https://www.sciencedaily.com/releases/2016/02/160225140254.htm) VII. Eureka Alert (https://www.eurekalert.org/pub_releases/2016-02/mu-wmt022516.php) Recommended by F1000 Prime: http://f1000.com/prime/726180600. 5. Accurate calculation of the absolute free energy of binding for drug molecules. Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC. Chem Sci. 2016 Jan 14;7(1):207-218. Arianna Fornili (Biological and Chemical Sciences, Queen Mary University of London) Publication: Fornili, E. Rostkova, F. Fraternali, M. Pfuhl: Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin. Biophysical J. 110 (2016) 297A. More in preparation. Dmitry Nerukh (Engineering and Applied Science, Aston University) Important research findings: Distribution of ions inside a viral capsids influences the stability of the capsid Edina Rosta (Computational Chemistry, Kings College London) Highlighted publication: We have a joint experimental paper with the Vertessy group in JACS where we identified a novel arginine finger residue in dUTPase enzymes, and described the mechanism of action for this residue using crystallographic data, biochemical experiments, MD and QM/MM simulations thanks to HECBioSim. http://pubs.acs.org/doi/abs/10.1021/jacs.6b09012 Press release: Our joint paper with Jeremy Baumberg's group in Cambridge was published in Nature. http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_13-6-2016-16-52-4 Greater scientific productivity: As well as speed increases, the optimisation of codes for the ARCHER machine will enable problems to be solved in less time using fewer compute resources. • For the reporting period please provide a brief update on the progress of software development activities associated with the Consortium and the impact this has had on Consortium members and the broader research community. Our lead software development project between Nottingham (Charlie Laughton and Gareth Shannon) and Daresbury (James Gebbie), we have developed a remote job submission tool, 'Longbow' (see below). The tool is designed to reproduce the look and feel of local MD packages, but to stage data and submit jobs to a large HPC resource such as ARCHER in a manner invisible to the user. An open beta version was released unrestricted to the community in March 2015 (http://www.hecbiosim.ac.uk/longbow and via PyPI https://pypi.python.org ) with ~100 downloads. Functionality includes native support for biosimulation packages AMBER, CHARMM, GROMACS, LAMMPS and NAMD, native support for jobs on ARCHER, native support for jobs running on PBS and LSF schedulers, and support for three different job types (single, ensembles and multiple jobs). The software is written both as an application for users and an API for developers. CCP-EM have integrated Longbow into their developmental GUI, and shortly FESetup will ship with native support for job submission using Longbow. We are currently in talks with ClusterVision with respect to them distributing Longbow to their user base as a user friendly way for novices to interact with their systems. Longbow Longbow has been growing in popularity both amongst researchers within the biosimulation field and those in other fields. In this reporting period there have been five new releases of Longbow delivering a plethora of user requested features and bug fixes. Some of the key developments are summarised below: • Implemented a Recovery mode - Should the event happen that Longbow crashes or the system in which Longbow is controlling jobs from powers down. The user can now reconnect to the crashed session and carry on as if nothing happened. • Sub-Queuing - More and more system administrators are setting limits not just on the number of simulations that can run, but also on the number of jobs that can go into the queue. Longbow can now automatically detect this and implement its own queue feeding jobs into the system queue as slots open up. • Dis-connectible/Re-connectible Longbow sessions - A user can now launch Longbow to fire off all jobs and then disconnect, at a later date the user can re-establish the connection and download all results (no need for persistent connections anymore) • Ability to include scripts in the Longbow generated submit files. • Numerous stability, performance and bug fixes Longbow continues to be the submission engine that is used under the hood of the CCP-EM toolkit FLEX-EM. There are several other interesting projects that are making use of Longbow. A project by the energy efficient computing group (Hartree Center) are currently integrating Longbow with CK, a crowd sourced compilation optimisation tool aimed at finding efficient compilation configuration. A project by the Applications performance engineering group (Hartree Center) are currently integrating longbow into Melody, a runtime optimisation tool aimed at optimising runtime configuration of simulations. A project by the computational biology group (Hartree Center) an automated setup, launch and analysis platform for MD on protein-membrane simulations. Metrics Downloads (HECBioSim) 985 Downloads (PyPi) 3456 Increasing the UK's CSE skills base (including graduate and post doctorate training and support): This builds on the skills sets of trained people in HPC, both in terms of capacity and raising the overall skill level available to the sector. • For the reporting period please provide information on the number of PhDs and Post-Docs that have been trained in the use of ARCHER as a result of work relating to the Consortium. • For the reporting period please provide a bullet pointed list of training activities undertaken by the Consortium, providing information on the target audience and level of attendance. 125 PhD and PDRAs have been trained and have used ARCHER through HECBioSim. In the past 6 months alone that has included: PhD students: Marc Dämgen, University of Oxford Laura Domicevica, University of Oxford Matteo Aldeghi, University of Oxford Shaima Hashem, Queen Mary University of London Ruth Dingle, University College London Lucas Siemons, University College London Elvira Tarasova, Aston University Vladimiras Oleinikovas, University College London Havva Yalinca, University College London Daniel Moore, Queen's University Belfast Aaron Maguire, Queen's University Belfast Maxime Tortora, University of Oxford Michail Palaiokostas, UWE Bristol Wei Ding, UWE Bristol Ganesh Shahane, UWE Bristol Pin-Chia Hsu, University of Southampton Damien Jefferies, University of Southampton PDRA: Maria Musgaard, University of Oxford Teresa Paramo, University of Oxford Marieke Schor, University of Edinbrurgh Antonia Mey, University of Edinbrurgh Ioanna Styliari, University of Nottingham Ivan Korotkin, Aston University Silvia Gomez Coca, King's College London Giorgio Saladino, University College London Federico Comitani, University College London Robin Corey, University of Bristol Jordi Juarez-Jimenez, University of Edinburgh Predrag Kukic, University of Cambridge Giulia Tomba, University of Cambridge Deborah Shoemark, University of Bristol Georgios Dalkas, Heriot-Watt University Robin Westacott, Heriot-Watt University Firdaus Samsudin, University of Southampton Agnes Noy, University of Leeds (now EPSRC fellow at York). Please see below details of the training week held in June 2016 at the University of Bristol. 170 delegates attending the training which ran over 5 days. There is course content available on the HECBioSim Workshop Page CCPBioSim Training Week - Day 5: QM/MM enzyme reaction modelling - on Friday 10 June 2016 CCPBioSim Training Week - Day 4: Monte Carlo Methods for Biomodelling - on Thursday 09 June 2016 CCPBioSim Training Week - Day 3: Python for Biomodellers and FESetup - on Wednesday 08 June 2016 CCPBioSim Training Week - Day 2: Running and analysing MD simulations - on Tuesday 07 June 2016 CCPBioSim Training Week - Day 1: Enlighten: Tools for enzyme-ligand modelling - on Monday 06 June 2016 Past Workshops and Conferences: AMOEBA advanced potential energies workshop - on Friday 09 December 2016 Intel Training Workshop (Parallel programming and optimisation for Intel architecture) - on Wednesday 30 November 2016 3rd Workshop on High-Throughput Molecular Dynamics (HTMD) 2016 - on Thursday 10 November 2016 Free Energy Calculation and Molecular Kinetics Workshop - on Tuesday 13 September 2016 Going Large: tools to simplify running and analysing large-scale MD simulations on HPC resources - HECBioSim - on Wednesday 16 December 2015 This 1 day workshop dealt with Longbow, a Python tool created by HECBioSim consortium that allows use of molecular dynamics packages (AMBER, GROMACS, LAMMPS, NAMD) with ease from the comfort of the desktop, and pyPcazip, a flexible Python-based package for the analysis of large molecular dynamics trajectory data sets. Richard Henchman ( Chemistry, Manchester) I lectured on the CCP5 Summer School in 2015 in Manchester and 2016 in Lancaster for the Advanced Topic Biomolecular Simulation drawing on CCPBiosim training materials. Sarah Harris (Physics, Leeds) Agnes Noy Agnes Noy was trained to use ARCHER independently which helped her to obtain an Early-career EPSRC fellowship. The fellowship grant follows the study of supercoiling DNA by modelling (further funding) and introduces a new member to the community (grant is EPSRC (EP/N027639/1)). Increased impact and collaboration with industry: ARCHER does not operate in isolation and the 'impact' of ARCHER's science is converted to economic growth through the interfaces with business and industry. In order to capture the impacts, which may be economic, social, environmental, scientific or political, various metrics may be utilised. • For the reporting period please provide where possible information on Consortium projects that have been performed in collaboration with industry, this should include: o Details of the companies involved. o Information on the part ARCHER and the Consortium played. o A statement on the impact that the work has / is making. o If relevant, details of any in kind or cash contributions that have been associated with this work. • For the reporting period include a list of Consortium publications that have industrial co-authorship. • For the reporting period please provide details of the any other activities involving industrial participation e.g. activities involving any Industrial Advisory panels, attendance / participation in workshops and Consortium based activities. Examples of industrial engagement through HECBioSim include: Syma Khalid (Computational Biophysics, Southampton) Collaboration with Siewert-Jan Marrink (Netherlands) and Wonpil Im(USA) - paper is being written at the moment - also we have developed and tested the following computational tool as part of this project: http://www.charmm-gui.org/?doc=input/membrane We have signed an NDA with a company developing antibiotics (Auspherix) based on work published in Samsudin et al, Structure, 2016. The company provide us with experimental data and crucially the structures of their potential drug molecules, and we work out how they interact with the bacterial membrane. Press releases https://www.sciencedaily.com/releases/2016/11/161121094122.htm ARCHER time we got from HECBioSim was essential for this project. These are large simulations that are very computationally demanding. Julien Michel (Chemistry, Edinburgh) Industrial collaborations that have benefited from HECBioSim UCB was a project partner of EPSRC-funded research in the Michel lab on modelling binding of ligands to flexible proteins. HECBioSim supported the research via allocation of computing time on ARCHER. The work has been published. Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2 Bueren-Calabuig, J. A. ; Michel, J. Biochemistry, 55 (17), 2500-2509, 2016 Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2 Bueren-Calabuig, J. A. ; Michel, J. PLoS Comput. Biol. , 11(6): e1004282, 2015 International activities I represented HECBioSim at the MolSSI conceptualisation workshop in Houston (October 2016). Arianna Fornili (School of Biological and Chemical Sciences, Queen Mary University of London) This project is done in collaboration with experimental (NMR and SAXS) partners at King's College London (Dr. Mark Pfuhl and Dr. Elena Rostkova), with the final aim of providing a complete molecular model of how muscle contraction is regulated in the heart. Francesco Gervasio (Chemistry, UCL) A new collaboration with UCB on developing new approaches to sample cryptic binding sites of pharmaceutical interest was started. UCB co-sponsored a BBSRC-CASE PhD studentships. The code development and its application to interesting targets was made possible by the access to Archer. Phil Biggin (Biochemistry, Oxford) The following has industrial partners as co-authors: Accurate calculation of the absolute free energy of binding for drug molecules, Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC. Chem. Sci., 2016,7, 207-218 doi: 10.1039/C5SC02678D. The GLAS scoring module for gromacs has yet to be implemented but that would also constitute industrial activity. Richard Henchman (Chemistry, Manchester) Industrial Collaboration I have one publication with an industrial co-author (Evotec), which Julien Michel is part of as well. Assessment of hydration thermodynamics at protein interfaces with grid cell theory, G. Gerogiokas, M. W. Y. Southey, M. P. Mazanetz, A. Heifetz, M. Bodkin, R. J. Law, R. H. Henchman and J. Michel, J. Phys. Chem. B, 2016, 120, 10442-10452. Strengthening of UK's international position: The impacts of ARCHER's science extend beyond national borders and most science is delivered through partnerships on a national or international level. • For the reporting period please provide a bullet pointed list of projects that have involved international collaboration. For each example please provide a brief summary of the part that ARCHER and the Consortium have played. • For the reporting period please provide a list of consortium publications with international co-authorship. • For the reporting period please detail any other international activities that the Consortium might be involved in (workshops, EU projects etc.). Examples of HECBioSim international engagement include: Michelle Sahai (Department of Life Sciences, Roehampton) Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB. Sahai MA, Davidson C, Khelashvili G, Barrese V, Dutta N, Weinstein H, Opacka-Juffry J. Prog Neuropsychopharmacol Biol Psychiatry. (2016) 75:1-9. doi: 10.1016/j.pnpbp.2016.11.004. co-authors affiliations include: Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY, 10065, USA and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. Author contribution: CD, MAS, HW and JOJ were responsible for the study concept and design. CD and VB collected and interpreted the voltammetry data. JOJ and ND conducted the ligand binding experiments and ND analysed the data. MAS (ARCHER user) and GK performed the molecular modelling studies and interpreted the findings. CD, MAS, GK and JOJ drafted the manuscript. All authors critically reviewed the content and approved the final version for publication. Dmitry Nerukh (Engineering and Applied Science, Aston University) Collaborations: • Prof. Makoto Taiji group (K-computer, MDGRAPE), Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC), Kobe, Japan • Prof. Reza Khayat group, City College of New York, United States • Prof. Artyom Yurov group, Immanuel Kant Baltic Federal University, Russian Federation • Prof. Nikolay Mchedlov-Petrosyan group, V.N. Karazin Kharkiv National University, Ukraine • Prof. Natalya Vaysfeld group, Odessa I.I.Mechnikov National University, Ukraine International activities: • International Workshop - Engineering bacteriophages for treating antimicrobial resistance using computational models. Dec. 2016, Aston University, UK Dmitry Nerukh group at Aston University collaborates with the group of Prof. Makoto Taiji (the deputy director of RIKEN Quantitative Biology Institute). Prof. Taiji group is the author and implementer of the fastest machine in the world for molecular dynamics simulations, MDGRAPE, as well as part of the team designing the K-computer and working on it (several times the fastest computer in the world). We are currently preparing a joint manuscript for publication where the results obtained on ARCHER will be used alongside with the results obtained on MDGRAPE-4. Julien Michel (Chemistry, Edinburgh) Free Energy Reproducibility Project Free energy reproducibility project between the Michel, Mobley, Roux groups and STFC. This makes use of FESetup which is CCPBioSim, but calculations have been executed on various HPC platforms, Hannes can clarify whether any of the systems used is within the remit of HECBioSim. Sarah Harris (Physics, Leeds), Charlie Laughton (Pharmacy, Nottingham) and Agnes Noy (Physics, York) In an international collaboration with the Institute for Research in Biomedicine in Barcelona, Noy, Harris and Laughton used ARCHER time obtained through the HecBioSim consortium to perform multiple 100ns molecular dynamics (MD) simulations of DNA minicircles containing ~100 base pairs as part of the validation suite for the new BSC1 nucleic acid forcefield, see: Ivani I., Dans P. D., Noy A., Perez A., Faustino I., Hospital A., Walther J., Andrio P., Goni R., Portella G., Battistini F.,Gelpi J. L. Gonzalez C., Vendruscolo M., Laughton C. A., Harris S. A. Case D. A. & Orozco M. "Parmbsc1: a refined force field for DNA simulations" Nat. Methods 13, 55, 2015, doi:10.1038/nmeth.3658 Jon Essex (Chemistry, Southampton) Development and testing of hybrid coarse-grain/atomistic model of membrane systems. ARCHER and the consortium were instrumental in providing the computing time necessary to complete this work. The work was performed by a research fellow in my group, who has subsequently taken up an academic post in Sweden, where he is continuing to develop this methodology. Publication: All-atom/coarse-grained hybrid predictions of distributioncoefficients in SAMPL5 Samuel Genheden1, Jonathan W. Essex, J Comput Aided Mol Des (2016) 30:969-976 DOI 10.1007/s10822-016-9926-z IP and other industrial engagement, or translation, which has benefited from HECBioSim international collaborations Collaboration Dr Samuel Genheden, University of Gothenburg - see above International activities (e.g. workshops) that have benefited from HECBioSim The work performed with Sam resulted in an successful eCSE application for development work on the LAMMPS software. This is an international simulation package run out of Sandia labs in the US. Through this eCSE application we were able to update the rotational integrator and improve the load balancing for our hybrid simulation methodology. These developments have been incorporated in the latest release versions of the code. An ARCHER training webinar resulted from this work. Training activities see above - ARCHER training webinar on our developments within LAMMPS Software development see above - code modifications in LAMMPS which either have been, or will be, in the release version of the code Advantages you see of the consortium (e.g. could be ability to pursue project quickly; develop collaborations) resources to run the sort of large-scale calculations we need Michelle Sahai (Department of life Sciences, Roehampton) The publication I added on ResearchFish has international co-authors. Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB. Sahai MA, Davidson C, Khelashvili G, Barrese V, Dutta N, Weinstein H, Opacka-Juffry J. Prog Neuropsychopharmacol Biol Psychiatry. (2016) 75:1-9. doi: 10.1016/j.pnpbp.2016.11.004. co-authors affiliations include: Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY, 10065, USA and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. Author contribution: CD, MAS, HW and JOJ were responsible for the study concept and design. CD and VB collected and interpreted the voltammetry data. JOJ and ND conducted the ligand binding experiments and ND analysed the data. MAS (ARCHER user) and GK performed the molecular modelling studies and interpreted the findings. CD, MAS, GK and JOJ drafted the manuscript. All authors critically reviewed the content and approved the final version for publication. Edina Rosta (Computational Chemistry, Kings College London) International collaborations I have several international collaborators with joint computational/experimental projects. For their success the HECBioSim computer time was essential: • Prof. Beata Vertessy, Budapest Technical University, Hungary JACS 2016 138 (45), 15035-15045 • Profs. Walter Kolch, Vio Buchete and Boris Kholodenko, UCD, Ireland Angewandte 55 (3), 983-986, 2016 (this may have been reported previously) PLOS Computational Biology 12 (10), e1005051, 2016 J Phys Chem Letters 7 (14), 2676-2682, 2016 • Jose Maria Lluch, Angels Gonzalez, Autonomous University of Barcelona, Spain JCTC 12 (4), 2079-2090, 2016 Other international activities Free energy and molecular kinetics workshop with Frank Noe's group (Free University of Berlin) and Vio Buchete (UCD, Dublin). Maybe this should be for training activities? Following the workshop, Erasmus students apply to visit my group. Phil Biggin (Biochemistry, Oxford) 2 and 4 were with colleagues from McGill (Brown PM, Aurousseau MR and Bowie) and 3 was with colleagues from Denmark (Braun and Pless) 2. Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism. Brown PM, Aurousseau MR, Musgaard M, Biggin PC, Bowie D. J Physiol. 2016 Apr 1;594(7):1821-40. doi: 10.1113/JP271690. 3. Role of an Absolutely Conserved Tryptophan Pair in the Extracellular Domain of Cys-Loop Receptors. Braun N, Lynagh T, Yu R, Biggin PC, Pless SA. ACS Chem Neurosci. 2016 Mar 16;7(3):339-48. doi: 10.1021/acschemneuro.5b00298. 4. Distinct Structural Pathways Coordinate the Activation of AMPA Receptor-Auxiliary Subunit Complexes. Dawe GB, Musgaard M, Aurousseau MR, Nayeem N, Green T, Biggin PC, Bowie D. Neuron. 2016 Mar 16;89(6):1264-76. doi: 10.1016/j.neuron.2016.01.038. Richard Henchman I have an international collaboration with Professor Franke Grater at the University of Heidelberg on entropy theory for biomolecular systems. Syma Khalid (Chemistry, Southampton) Collaboration with Singapore National Center for Biotechnology. Contributions to CECAM workshops Other Highlights for the Current Reporting Period: Please provide details of any other significant highlights from the reporting period that are not captured elsewhere in the report. Professor Adrian Mullholland organised and chaired the Computational Chemistry, Gordon Research Conference, Girona, Spain 24th - 29th July 2016. The theme of the 2016 Computational Chemistry GRC was "Theory and Simulation Across Scales in Molecular Science". It focused on method development and state-of-the-art applications across computational molecular science, and encouraged cross-fertilization between areas. The conference was oversubscribed, with attendees from industry and academia. The meeting received a High-Performance Rating, and was commended for the assessment that 95% of conferees rated this meeting "above average" on all evaluation areas (science, discussion, management, atmosphere and suitability). HEC Consortia Model: Over the coming months EPSRC will be looking at the future of the HEC Consortia model and potential future funding. We would like to use this opportunity to ask the Consortia Chairs for input: • What are the key benefits that your community have experienced through the existence of the HEC Consortia? • What elements of the financial support provided by the HEC Consortium's grant have worked well and what could be improved in the future? We aim to expand the breadth of the work of the Consortium focusing on cutting-edge applications, and building collaborations with experiments and industry, to achieve maximum impact from ARCHER use. We discussed Grand Challenges at our most recent Management Group meeting. In December 2015, and have identified several to follow up as strategic priorities. We aim to tackle and support large-scale grand challenge applications in biomolecular science, in areas such as antimicrobial resistance, membrane dynamics, drug design and synthetic biology. One specific theme with potentially high impact in drug discovery is large -scale comparative investigation of allosteric regulation in different superfamilies of proteins (e.g. PAS domain containing proteins, tyrosine kinases, etc.). The major impact will be in the identification of novel selective therapeutic molecules with limited adverse side effects. As a Consortium, we intend to develop and apply novel computational approaches for the rational design of allosteric regulators of hitherto 'undruggable' targets. Many of the targets emerging from large-scale genetic screening are deemed undruggable due to the difficulty of designing drug-like modulators that bind to their catalytic sites. It is increasingly clear that these targets might be effectively targeted by designing drugs that bind to protein-protein interfaces and allosteric sites. To do that, however, new rational design strategies, based on an in-depth knowledge of protein dynamics and advanced modelling and new simulation techniques are required. Other challenging frontier areas include dynamics of motor proteins; prediction of the effects of pathogenic mutations on protein function. The accurate prediction of free energy of binding is still in its infancy and needs much further investigation. Finally, kinetics of biomolecular reactions will become the next big topic. It is clear that high end computing resource can provide the necessary power and capability to provide inroads into this vital area. This is important because it is becoming increasingly apparent that kinetics of drug binding is a key factor that the pharmaceutical sector should really be looking at in terms of a major dictator of potency. HECBioSim is now well established, supporting work of many groups across the UK in the growing field of biomolecular simulation. We benefit from an Advisory Group containing members from industry, as we as international biomolecular simulation experts and experimental scientists. The Advisory Board was expanded and refreshed for the renewal and consists of: Dr. Nicolas Foloppe (Vernalis plc, Chair); Dr. Colin Edge (GlaxoSmithKline); Dr. Mike King (UCB Pharmaceuticals); Dr. Mike Mazanetz (Evotec AG); Dr. Garrett Morris (Crysalin Ltd.); Dr. Gary Tresadern (Johnson and Johnson Pharmaceuticals); Dr. Richard Ward (AstraZeneca); Prof. Modesto Orozco (IRB, Barcelona); Prof. Tony Watts, (Oxford, NMR); Dr. Pete Bond (A*STAR Bioinformatics Institute Singapore). We aim to foster industrial collaborations and collaborations with experimentalists (e.g. joint workshops with CCPN, Institute of Physics (Sarah Harris, Leeds Physics); see e.g. case studies. A particular theme for strategic development will be multiscale modelling, building on collaborations between several groups in the Consortium and the other CCPs. This theme reflects the inclusive and forward looking philosophy of HecBioSim, which is a community open to new ideas, keen to develop new methods, and ultimately to use HEC to drive exciting new science. The Consortium model allows new collaborations to develop. The recent reduction in time allocated to HECBioSim has meant that we can support fewer projects. There is significantly more demand for computer time than we can accommodate through our current allocation. We intend to work with Tier 2 Centres to explore possibilities for applications, and e.g. to test emerging architectures for biomolecular simulation. Edina Rosta (Computational Chemistry, Kings College London) comments: "HECBioSim enables my group to perform biomolecular simulations at the high standards required for JACS, Angewandte, etc. Without this consortium I would not be able to perform the necessary calculations leading to publishable work in top journals as our local university resources are limited and the hpc systems are not well maintained". Regarding financial support: the administrative support provided via the consortium grant is essential to the functioning of HECBioSim. This role is currently undertaken by Simone Breckell who not only administers, allocates time to projects and arranges panel meetings but has also done a fantastic job collating the extensive information for this EPSRC report. 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact HECBioSim, the UK HEC Biomolecular Simulation Consortium, was established in March 2013, and works closely with and complements CCP-BioSim (the UK Collaborative Computational Project for Biomolecular Simulation at the Life Sciences Interface). Most of the members of the Consortium are experienced users of high end computing. Biomolecular simulations are now making significant contributions to a wide variety of problems in drug design and development, biocatalysis, bio and nano-technology, chemical biology and medicine. The UK has a strong and growing community in this field, recognized by the establishment in 2011 by the EPSRC of CCP-BioSim (ccpbiosim.ac.uk), and its renewal in 2015. There is a clear, growing and demonstrable need for HEC in this field. Members of the Consortium have, for example, served on the HECToR and ARCHER Resource Allocation Panel. The Consortium welcomes members across the whole biomolecular sciences community, and we are currently (and will remain) open to new members (unlike some consortia). Since establishing the Consortium, several new members (FLG, DH, ER) have joined the Management Group. Many of the projects awarded ARCHER time under the Consortium do not involve CCP-BioSim or HECBioSim Management Group members, demonstrating the openness of HECBioSim and its support of the biomolecular simulation community in the UK. A number of other researchers have joined and it is our expectation that other researchers will join HECBioSim in the future. We actively engage with structural and chemical biologists and industrial researchers. We foster interactions between computational, experimental and industrial scientists (see the example case studies; members of the Consortium have excellent links with many pharmaceutical, chemical and biotechnology companies). Details of HECBioSim are available via our webpages at: http://www.hecbiosim.ac.uk Applications are made through the website http://www.hecbiosim.ac.uk and reviewed at one of the series of regular panel meetings. A list of successful HECtime allocations on ARCHER is available at:http://www.hecbiosim.ac.uk/applications/successfulprojects All proposals are of course subject to scientific and technical review, but we have the philosophy of supporting the best science to deliver the highest impact, rather than focusing on supporting development of a couple of codes. An allocation panel (with changing membership) meets twice yearly to judge proposals and requests for AUs; projects are assessed competitively: any groups in the UK can apply. All submitted proposals receive constructive feedback from the allocation panel. The HECBioSim website also provides forums for the biomolecular simulation community, a wiki hosting useful how-tos and user guides, and software downloads (currently FESetup and Longbow). Our lead software development project between Nottingham (Charlie Laughton and Gareth Shannon) and Daresbury (James Gebbie), we have developed a remote job submission tool, 'Longbow' (see below). The tool is designed to reproduce the look and feel of local MD packages, but to stage data and submit jobs to a large HPC resource, such as ARCHER, in a manner invisible to the user. Workshops and New Opportunities No more than half a page detailing upcoming workshops and meetings. Also include discussion of other areas which are potentially of interest to other HEC Consortia and opportunities for cross CCP /HEC working. Workshops are listed below and can be found on the HECBioSim Website We work closely with CCP-BioSim, for example in organizing training workshops and meetings. Our activities are outlined at www.hecbiosim.ac.uk Examples of forthcoming meetings include: Computational Molecular Science 2017 - on Sunday 19 March 2017 17th European Seminar on Computational Methods in Quantum Chemistry - on Tuesday 11 July 2017 Frontiers of Biomolecular Simulation Southampton, September 2016 Issues and Problems Short discussion of any issues or problems that the HEC Consortium faces including issues with the ARCHER service, funding, management of allocation and staffing. This is also a good opportunity to highlight to the SLA committee any issues that the Consortium may have experienced with their SLA support during the reporting period. Details of SLA activities are given in the SLA report. Dr. James Gebbie provides support to HECBioSIm through the SLA. He has been very helpful in the construction of the HECBioSim webpages (hecbiosim.ac.uk). James also worked with Dr. Gareth Shannon on the development of Longbow (See above). In the past year, members of the Consortium faced some queuing problems; close to the end of the first allocation period in particular, there were long queuing times, which led to problems in completing jobs and using allocated time. Throughput has been a real problem in the past few months. Membership Please provide a full list of existing members and their institutions, highlighting any new members that have joined the consortium during the reporting period. If available please provide information on the number of distinct users that have accessed ARCHER via the Consortium during this reporting period. Below is a list of PIs with HECBioSim projects in the current reporting period: Agnes Noy, University of York - new to this reporting period Alessandro Pandini, Brunel University London Arianna Fornili, Queen Mary University of London Cait MacPhee, University of Edinbrurgh - new to this reporting period Charlie Laughton, University of Nottingham Clare-Louise Towse, University of Bradford - new to this reporting period D Flemming Hansen, University College London - new to this reporting period David Huggins, Aston University Edina Rosta, King's College London Francesco Gervasio, University College London Ian Collinson, University of Bristol - new to this reporting period Irina Tikhonova, Queen's University Belfast Jiayun Pang, University of Greenwich Jonathan Doye, University of Oxford Julien Michel, University of Edinburgh Mario Orsi, UWE Bristol Michele Vendruscolo, University of Cambridge Michelle Sahai, University of Roehampton Philip Biggin, University of Oxford Richard Sessions, University of Bristol Stephen Euston, Heriot-Watt University Syma Khalid, University of Southampton PIs in HECBioSIm outside of current allocation period Peter Bond, University of Cambridge Richard Bryce, University of Manchester Juan Antonio Bueren-Calabuig, University of Edinburgh Christo Christov, Northumbria University Anna K Croft, University of Nottingham Jonathan Essex, University of Southampton Robert Glen, University of Cambridge Sarah A Harris, University of Leeds Jonathan Hirst, University of Nottingham Douglas Houston, University of Edinburgh Dmitry Nerukh, Aston University Andrei Pisliakov, University of Dundee Mark Sansom, University of Oxford Marieke Schor, University of Edinburgh Gareth Shannon, University of Nottingham Tatyana Karabencheva-Christova, Northumbria University There are currently 164 members of HECBioSim (i.e. users of HECBioSIm ARCHER time), included the above PIs. 20 new users have been added since January 2016. World class and world leading scientific output: ARCHER should enable high quality and world-leading science to be delivered. This should generate high impact outputs and outcomes that increase the UK's position in world science. • If all the publications relating to the work of the Consortium for this reporting period have been added to ResearchFish / will be added to ResearchFish by the end of the ResearchFish reporting exercise, please indicate this below. • If submission of a full list of publications to the Consortium record/s in ResearchFish has not been possible for this reporting period please provide a list of publications that have resulted from work performed on ARCHER by the Consortium during this reporting period (this can be included as a separate attachment). • For the reporting period please provide a bullet pointed list of key / important research findings that has resulted from work performed on ARCHER by the Consortium. Please reference any related publications. • For the reporting period please include a bullet pointed list of any relevant press announcements and other communications of significance to an international community. All publications can be found in ResearchFish, and have been added by individual researchers. A selection of illustrative highlights are provided below: Julien Michel (University of Edinburgh) New molecular simulation methods have enabled for the first time a complete description of the interactions of several drug-like small molecules with an intrinsically disordered region of the oncoprotein MDM2, as well as the effect of post-translational modifications on the dynamics of this protein. The results obtained suggest new medicinal chemistry strategies to achieve potent and selective inhibition of MDM2 for cancer therapies. Publication: Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004282 Impact of Ser17 Phosphorylation on the Conformational Dynamics of the Oncoprotein MDM2 http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00127 An outreach document is being prepared by EPCC to showcase a lab project on isoform selective inhibition that has benefited from both HECBioSim and EPCC ARCHER allocations. Syma Khalid (Chemistry, Southampton) Publication: OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment Samsudin F, Ortiz-Suarez ML, Piggot TJ, Bond PJ, Khalid S (2016). "OmpA: a Flexible Clamp for Bacterial Cell Wall Attachment", Structure, 24(12):2227-2235 With Singapore National Center for Biotechnology. Sarah Harris (Physics, Leeds) In collaboration with the experimental biochemistry group lead by Radford at Leeds, Sarah Harris used ARCHER time to show how chaperones help outer membrane proteins to fold, see: Schiffrin B, Calabrese AN, Devine PWA, Harris SA, Ashcroft AE, Brockwell DJ, Radford SE "Skp is a multivalent chaperone of outer-membrane proteins" Nature Structural and Molecular Biology 23 786-793, 2016. DOI:10.1038/nsmb.3266 Michelle Sahai (Department of Life Sciences, Roehampton) Publication: Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB. Progress in Neuro-Psychopharmacology and Biological Psychiatry 75, Pages 1-9 (2017) https://www.ncbi.nlm.nih.gov/pubmed/27890676 Phil Biggin (Biochemistry, Oxford) Outputs that have used HECBioSim time: 1. Steered Molecular Dynamics Simulations Predict Conformational Stability of Glutamate Receptors. Musgaard M, Biggin PC. J Chem Inf Model. 2016 Sep 26;56(9):1787-97. doi: 10.1021/acs.jcim.6b00297. 2. Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism. Brown PM, Aurousseau MR, Musgaard M, Biggin PC, Bowie D. J Physiol. 2016 Apr 1;594(7):1821-40. doi: 10.1113/JP271690. 3. Role of an Absolutely Conserved Tryptophan Pair in the Extracellular Domain of Cys-Loop Receptors. Braun N, Lynagh T, Yu R, Biggin PC, Pless SA. ACS Chem Neurosci. 2016 Mar 16;7(3):339-48. doi: 10.1021/acschemneuro.5b00298. 4. Distinct Structural Pathways Coordinate the Activation of AMPA Receptor-Auxiliary Subunit Complexes. Dawe GB, Musgaard M, Aurousseau MR, Nayeem N, Green T, Biggin PC, Bowie D. Neuron. 2016 Mar 16;89(6):1264-76. doi: 10.1016/j.neuron.2016.01.038. Covered by 7 news outlets: I. Health Canal (http://www.healthcanal.com/brain-nerves/70646-what-makes-the-brain-tick-so-fast.html) II. Health Medicine Network (http://healthmedicinet.com/i/scientists-reveal-how-the-brain-processes-information-with-lightning-speed/) III. News Medical (http://www.news-medical.net/news/20160227/Scientists-reveal-how-the-brain-processes-information-with-lightning-speed.aspx) IV. Wired (http://www.wired.co.uk/article/what-we-learned-about-the-brain-this-week-3) V. Alpha Galileo (http://www.alphagalileo.org/ViewItem.aspx?ItemId=161473&CultureCode=en) VI. Science Daily (https://www.sciencedaily.com/releases/2016/02/160225140254.htm) VII. Eureka Alert (https://www.eurekalert.org/pub_releases/2016-02/mu-wmt022516.php) Recommended by F1000 Prime: http://f1000.com/prime/726180600. 5. Accurate calculation of the absolute free energy of binding for drug molecules. Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC. Chem Sci. 2016 Jan 14;7(1):207-218. Arianna Fornili (Biological and Chemical Sciences, Queen Mary University of London) Publication: Fornili, E. Rostkova, F. Fraternali, M. Pfuhl: Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin. Biophysical J. 110 (2016) 297A. More in preparation. Dmitry Nerukh (Engineering and Applied Science, Aston University) Important research findings: Distribution of ions inside a viral capsids influences the stability of the capsid Edina Rosta (Computational Chemistry, Kings College London) Highlighted publication: We have a joint experimental paper with the Vertessy group in JACS where we identified a novel arginine finger residue in dUTPase enzymes, and described the mechanism of action for this residue using crystallographic data, biochemical experiments, MD and QM/MM simulations thanks to HECBioSim. http://pubs.acs.org/doi/abs/10.1021/jacs.6b09012 Press release: Our joint paper with Jeremy Baumberg's group in Cambridge was published in Nature. http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_13-6-2016-16-52-4 Greater scientific productivity: As well as speed increases, the optimisation of codes for the ARCHER machine will enable problems to be solved in less time using fewer compute resources. • For the reporting period please provide a brief update on the progress of software development activities associated with the Consortium and the impact this has had on Consortium members and the broader research community. Our lead software development project between Nottingham (Charlie Laughton and Gareth Shannon) and Daresbury (James Gebbie), we have developed a remote job submission tool, 'Longbow' (see below). The tool is designed to reproduce the look and feel of local MD packages, but to stage data and submit jobs to a large HPC resource such as ARCHER in a manner invisible to the user. An open beta version was released unrestricted to the community in March 2015 (http://www.hecbiosim.ac.uk/longbow and via PyPI https://pypi.python.org ) with ~100 downloads. Functionality includes native support for biosimulation packages AMBER, CHARMM, GROMACS, LAMMPS and NAMD, native support for jobs on ARCHER, native support for jobs running on PBS and LSF schedulers, and support for three different job types (single, ensembles and multiple jobs). The software is written both as an application for users and an API for developers. CCP-EM have integrated Longbow into their developmental GUI, and shortly FESetup will ship with native support for job submission using Longbow. We are currently in talks with ClusterVision with respect to them distributing Longbow to their user base as a user friendly way for novices to interact with their systems. Longbow Longbow has been growing in popularity both amongst researchers within the biosimulation field and those in other fields. In this reporting period there have been five new releases of Longbow delivering a plethora of user requested features and bug fixes. Some of the key developments are summarised below: • Implemented a Recovery mode - Should the event happen that Longbow crashes or the system in which Longbow is controlling jobs from powers down. The user can now reconnect to the crashed session and carry on as if nothing happened. • Sub-Queuing - More and more system administrators are setting limits not just on the number of simulations that can run, but also on the number of jobs that can go into the queue. Longbow can now automatically detect this and implement its own queue feeding jobs into the system queue as slots open up. • Dis-connectible/Re-connectible Longbow sessions - A user can now launch Longbow to fire off all jobs and then disconnect, at a later date the user can re-establish the connection and download all results (no need for persistent connections anymore) • Ability to include scripts in the Longbow generated submit files. • Numerous stability, performance and bug fixes Longbow continues to be the submission engine that is used under the hood of the CCP-EM toolkit FLEX-EM. There are several other interesting projects that are making use of Longbow. A project by the energy efficient computing group (Hartree Center) are currently integrating Longbow with CK, a crowd sourced compilation optimisation tool aimed at finding efficient compilation configuration. A project by the Applications performance engineering group (Hartree Center) are currently integrating longbow into Melody, a runtime optimisation tool aimed at optimising runtime configuration of simulations. A project by the computational biology group (Hartree Center) an automated setup, launch and analysis platform for MD on protein-membrane simulations. Metrics Downloads (HECBioSim) 985 Downloads (PyPi) 3456 Increasing the UK's CSE skills base (including graduate and post doctorate training and support): This builds on the skills sets of trained people in HPC, both in terms of capacity and raising the overall skill level available to the sector. • For the reporting period please provide information on the number of PhDs and Post-Docs that have been trained in the use of ARCHER as a result of work relating to the Consortium. • For the reporting period please provide a bullet pointed list of training activities undertaken by the Consortium, providing information on the target audience and level of attendance. 125 PhD and PDRAs have been trained and have used ARCHER through HECBioSim. In the past 6 months alone that has included: PhD students: Marc Dämgen, University of Oxford Laura Domicevica, University of Oxford Matteo Aldeghi, University of Oxford Shaima Hashem, Queen Mary University of London Ruth Dingle, University College London Lucas Siemons, University College London Elvira Tarasova, Aston University Vladimiras Oleinikovas, University College London Havva Yalinca, University College London Daniel Moore, Queen's University Belfast Aaron Maguire, Queen's University Belfast Maxime Tortora, University of Oxford Michail Palaiokostas, UWE Bristol Wei Ding, UWE Bristol Ganesh Shahane, UWE Bristol Pin-Chia Hsu, University of Southampton Damien Jefferies, University of Southampton PDRA: Maria Musgaard, University of Oxford Teresa Paramo, University of Oxford Marieke Schor, University of Edinbrurgh Antonia Mey, University of Edinbrurgh Ioanna Styliari, University of Nottingham Ivan Korotkin, Aston University Silvia Gomez Coca, King's College London Giorgio Saladino, University College London Federico Comitani, University College London Robin Corey, University of Bristol Jordi Juarez-Jimenez, University of Edinburgh Predrag Kukic, University of Cambridge Giulia Tomba, University of Cambridge Deborah Shoemark, University of Bristol Georgios Dalkas, Heriot-Watt University Robin Westacott, Heriot-Watt University Firdaus Samsudin, University of Southampton Agnes Noy, University of Leeds (now EPSRC fellow at York). Please see below details of the training week held in June 2016 at the University of Bristol. 170 delegates attending the training which ran over 5 days. There is course content available on the HECBioSim Workshop Page CCPBioSim Training Week - Day 5: QM/MM enzyme reaction modelling - on Friday 10 June 2016 CCPBioSim Training Week - Day 4: Monte Carlo Methods for Biomodelling - on Thursday 09 June 2016 CCPBioSim Training Week - Day 3: Python for Biomodellers and FESetup - on Wednesday 08 June 2016 CCPBioSim Training Week - Day 2: Running and analysing MD simulations - on Tuesday 07 June 2016 CCPBioSim Training Week - Day 1: Enlighten: Tools for enzyme-ligand modelling - on Monday 06 June 2016 Past Workshops and Conferences: AMOEBA advanced potential energies workshop - on Friday 09 December 2016 Intel Training Workshop (Parallel programming and optimisation for Intel architecture) - on Wednesday 30 November 2016 3rd Workshop on High-Throughput Molecular Dynamics (HTMD) 2016 - on Thursday 10 November 2016 Free Energy Calculation and Molecular Kinetics Workshop - on Tuesday 13 September 2016 Going Large: tools to simplify running and analysing large-scale MD simulations on HPC resources - HECBioSim - on Wednesday 16 December 2015 This 1 day workshop dealt with Longbow, a Python tool created by HECBioSim consortium that allows use of molecular dynamics packages (AMBER, GROMACS, LAMMPS, NAMD) with ease from the comfort of the desktop, and pyPcazip, a flexible Python-based package for the analysis of large molecular dynamics trajectory data sets. Richard Henchman ( Chemistry, Manchester) I lectured on the CCP5 Summer School in 2015 in Manchester and 2016 in Lancaster for the Advanced Topic Biomolecular Simulation drawing on CCPBiosim training materials. Sarah Harris (Physics, Leeds) Agnes Noy Agnes Noy was trained to use ARCHER independently which helped her to obtain an Early-career EPSRC fellowship. The fellowship grant follows the study of supercoiling DNA by modelling (further funding) and introduces a new member to the community (grant is EPSRC (EP/N027639/1)). Increased impact and collaboration with industry: ARCHER does not operate in isolation and the 'impact' of ARCHER's science is converted to economic growth through the interfaces with business and industry. In order to capture the impacts, which may be economic, social, environmental, scientific or political, various metrics may be utilised. • For the reporting period please provide where possible information on Consortium projects that have been performed in collaboration with industry, this should include: o Details of the companies involved. o Information on the part ARCHER and the Consortium played. o A statement on the impact that the work has / is making. o If relevant, details of any in kind or cash contributions that have been associated with this work. • For the reporting period include a list of Consortium publications that have industrial co-authorship. • For the reporting period please provide details of the any other activities involving industrial participation e.g. activities involving any Industrial Advisory panels, attendance / participation in workshops and Consortium based activities. Examples of industrial engagement through HECBioSim include: Syma Khalid (Computational Biophysics, Southampton) Collaboration with Siewert-Jan Marrink (Netherlands) and Wonpil Im(USA) - paper is being written at the moment - also we have developed and tested the following computational tool as part of this project: http://www.charmm-gui.org/?doc=input/membrane We have signed an NDA with a company developing antibiotics (Auspherix) based on work published in Samsudin et al, Structure, 2016. The company provide us with experimental data and crucially the structures of their potential drug molecules, and we work out how they interact with the bacterial membrane. Press releases https://www.sciencedaily.com/releases/2016/11/161121094122.htm ARCHER time we got from HECBioSim was essential for this project. These are large simulations that are very computationally demanding. Julien Michel (Chemistry, Edinburgh) Industrial collaborations that have benefited from HECBioSim UCB was a project partner of EPSRC-funded research in the Michel lab on modelling binding of ligands to flexible proteins. HECBioSim supported the research via allocation of computing time on ARCHER. The work has been published. Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2 Bueren-Calabuig, J. A. ; Michel, J. Biochemistry, 55 (17), 2500-2509, 2016 Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2 Bueren-Calabuig, J. A. ; Michel, J. PLoS Comput. Biol. , 11(6): e1004282, 2015 International activities I represented HECBioSim at the MolSSI conceptualisation workshop in Houston (October 2016). Arianna Fornili (School of Biological and Chemical Sciences, Queen Mary University of London) This project is done in collaboration with experimental (NMR and SAXS) partners at King's College London (Dr. Mark Pfuhl and Dr. Elena Rostkova), with the final aim of providing a complete molecular model of how muscle contraction is regulated in the heart. Francesco Gervasio (Chemistry, UCL) A new collaboration with UCB on developing new approaches to sample cryptic binding sites of pharmaceutical interest was started. UCB co-sponsored a BBSRC-CASE PhD studentships. The code development and its application to interesting targets was made possible by the access to Archer. Phil Biggin (Biochemistry, Oxford) The following has industrial partners as co-authors: Accurate calculation of the absolute free energy of binding for drug molecules, Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC. Chem. Sci., 2016,7, 207-218 doi: 10.1039/C5SC02678D. The GLAS scoring module for gromacs has yet to be implemented but that would also constitute industrial activity. Richard Henchman (Chemistry, Manchester) Industrial Collaboration I have one publication with an industrial co-author (Evotec), which Julien Michel is part of as well. Assessment of hydration thermodynamics at protein interfaces with grid cell theory, G. Gerogiokas, M. W. Y. Southey, M. P. Mazanetz, A. Heifetz, M. Bodkin, R. J. Law, R. H. Henchman and J. Michel, J. Phys. Chem. B, 2016, 120, 10442-10452. Strengthening of UK's international position: The impacts of ARCHER's science extend beyond national borders and most science is delivered through partnerships on a national or international level. • For the reporting period please provide a bullet pointed list of projects that have involved international collaboration. For each example please provide a brief summary of the part that ARCHER and the Consortium have played. • For the reporting period please provide a list of consortium publications with international co-authorship. • For the reporting period please detail any other international activities that the Consortium might be involved in (workshops, EU projects etc.). Examples of HECBioSim international engagement include: Michelle Sahai (Department of Life Sciences, Roehampton) Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB. Sahai MA, Davidson C, Khelashvili G, Barrese V, Dutta N, Weinstein H, Opacka-Juffry J. Prog Neuropsychopharmacol Biol Psychiatry. (2016) 75:1-9. doi: 10.1016/j.pnpbp.2016.11.004. co-authors affiliations include: Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY, 10065, USA and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. Author contribution: CD, MAS, HW and JOJ were responsible for the study concept and design. CD and VB collected and interpreted the voltammetry data. JOJ and ND conducted the ligand binding experiments and ND analysed the data. MAS (ARCHER user) and GK performed the molecular modelling studies and interpreted the findings. CD, MAS, GK and JOJ drafted the manuscript. All authors critically reviewed the content and approved the final version for publication. Dmitry Nerukh (Engineering and Applied Science, Aston University) Collaborations: • Prof. Makoto Taiji group (K-computer, MDGRAPE), Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC), Kobe, Japan • Prof. Reza Khayat group, City College of New York, United States • Prof. Artyom Yurov group, Immanuel Kant Baltic Federal University, Russian Federation • Prof. Nikolay Mchedlov-Petrosyan group, V.N. Karazin Kharkiv National University, Ukraine • Prof. Natalya Vaysfeld group, Odessa I.I.Mechnikov National University, Ukraine International activities: • International Workshop - Engineering bacteriophages for treating antimicrobial resistance using computational models. Dec. 2016, Aston University, UK Dmitry Nerukh group at Aston University collaborates with the group of Prof. Makoto Taiji (the deputy director of RIKEN Quantitative Biology Institute). Prof. Taiji group is the author and implementer of the fastest machine in the world for molecular dynamics simulations, MDGRAPE, as well as part of the team designing the K-computer and working on it (several times the fastest computer in the world). We are currently preparing a joint manuscript for publication where the results obtained on ARCHER will be used alongside with the results obtained on MDGRAPE-4. Julien Michel (Chemistry, Edinburgh) Free Energy Reproducibility Project Free energy reproducibility project between the Michel, Mobley, Roux groups and STFC. This makes use of FESetup which is CCPBioSim, but calculations have been executed on various HPC platforms, Hannes can clarify whether any of the systems used is within the remit of HECBioSim. Sarah Harris (Physics, Leeds), Charlie Laughton (Pharmacy, Nottingham) and Agnes Noy (Physics, York) In an international collaboration with the Institute for Research in Biomedicine in Barcelona, Noy, Harris and Laughton used ARCHER time obtained through the HecBioSim consortium to perform multiple 100ns molecular dynamics (MD) simulations of DNA minicircles containing ~100 base pairs as part of the validation suite for the new BSC1 nucleic acid forcefield, see: Ivani I., Dans P. D., Noy A., Perez A., Faustino I., Hospital A., Walther J., Andrio P., Goni R., Portella G., Battistini F.,Gelpi J. L. Gonzalez C., Vendruscolo M., Laughton C. A., Harris S. A. Case D. A. & Orozco M. "Parmbsc1: a refined force field for DNA simulations" Nat. Methods 13, 55, 2015, doi:10.1038/nmeth.3658 Jon Essex (Chemistry, Southampton) Development and testing of hybrid coarse-grain/atomistic model of membrane systems. ARCHER and the consortium were instrumental in providing the computing time necessary to complete this work. The work was performed by a research fellow in my group, who has subsequently taken up an academic post in Sweden, where he is continuing to develop this methodology. Publication: All-atom/coarse-grained hybrid predictions of distributioncoefficients in SAMPL5 Samuel Genheden1, Jonathan W. Essex, J Comput Aided Mol Des (2016) 30:969-976 DOI 10.1007/s10822-016-9926-z IP and other industrial engagement, or translation, which has benefited from HECBioSim international collaborations Collaboration Dr Samuel Genheden, University of Gothenburg - see above International activities (e.g. workshops) that have benefited from HECBioSim The work performed with Sam resulted in an successful eCSE application for development work on the LAMMPS software. This is an international simulation package run out of Sandia labs in the US. Through this eCSE application we were able to update the rotational integrator and improve the load balancing for our hybrid simulation methodology. These developments have been incorporated in the latest release versions of the code. An ARCHER training webinar resulted from this work. Training activities see above - ARCHER training webinar on our developments within LAMMPS Software development see above - code modifications in LAMMPS which either have been, or will be, in the release version of the code Advantages you see of the consortium (e.g. could be ability to pursue project quickly; develop collaborations) resources to run the sort of large-scale calculations we need Michelle Sahai (Department of life Sciences, Roehampton) The publication I added on ResearchFish has international co-authors. Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB. Sahai MA, Davidson C, Khelashvili G, Barrese V, Dutta N, Weinstein H, Opacka-Juffry J. Prog Neuropsychopharmacol Biol Psychiatry. (2016) 75:1-9. doi: 10.1016/j.pnpbp.2016.11.004. co-authors affiliations include: Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY, 10065, USA and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. Author contribution: CD, MAS, HW and JOJ were responsible for the study concept and design. CD and VB collected and interpreted the voltammetry data. JOJ and ND conducted the ligand binding experiments and ND analysed the data. MAS (ARCHER user) and GK performed the molecular modelling studies and interpreted the findings. CD, MAS, GK and JOJ drafted the manuscript. All authors critically reviewed the content and approved the final version for publication. Edina Rosta (Computational Chemistry, Kings College London) International collaborations I have several international collaborators with joint computational/experimental projects. For their success the HECBioSim computer time was essential: • Prof. Beata Vertessy, Budapest Technical University, Hungary JACS 2016 138 (45), 15035-15045 • Profs. Walter Kolch, Vio Buchete and Boris Kholodenko, UCD, Ireland Angewandte 55 (3), 983-986, 2016 (this may have been reported previously) PLOS Computational Biology 12 (10), e1005051, 2016 J Phys Chem Letters 7 (14), 2676-2682, 2016 • Jose Maria Lluch, Angels Gonzalez, Autonomous University of Barcelona, Spain JCTC 12 (4), 2079-2090, 2016 Other international activities Free energy and molecular kinetics workshop with Frank Noe's group (Free University of Berlin) and Vio Buchete (UCD, Dublin). Maybe this should be for training activities? Following the workshop, Erasmus students apply to visit my group. Phil Biggin (Biochemistry, Oxford) 2 and 4 were with colleagues from McGill (Brown PM, Aurousseau MR and Bowie) and 3 was with colleagues from Denmark (Braun and Pless) 2. Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism. Brown PM, Aurousseau MR, Musgaard M, Biggin PC, Bowie D. J Physiol. 2016 Apr 1;594(7):1821-40. doi: 10.1113/JP271690. 3. Role of an Absolutely Conserved Tryptophan Pair in the Extracellular Domain of Cys-Loop Receptors. Braun N, Lynagh T, Yu R, Biggin PC, Pless SA. ACS Chem Neurosci. 2016 Mar 16;7(3):339-48. doi: 10.1021/acschemneuro.5b00298. 4. Distinct Structural Pathways Coordinate the Activation of AMPA Receptor-Auxiliary Subunit Complexes. Dawe GB, Musgaard M, Aurousseau MR, Nayeem N, Green T, Biggin PC, Bowie D. Neuron. 2016 Mar 16;89(6):1264-76. doi: 10.1016/j.neuron.2016.01.038. Richard Henchman I have an international collaboration with Professor Franke Grater at the University of Heidelberg on entropy theory for biomolecular systems. Syma Khalid (Chemistry, Southampton) Collaboration with Singapore National Center for Biotechnology. Contributions to CECAM workshops Other Highlights for the Current Reporting Period: Please provide details of any other significant highlights from the reporting period that are not captured elsewhere in the report. Professor Adrian Mullholland organised and chaired the Computational Chemistry, Gordon Research Conference, Girona, Spain 24th - 29th July 2016. The theme of the 2016 Computational Chemistry GRC was "Theory and Simulation Across Scales in Molecular Science". It focused on method development and state-of-the-art applications across computational molecular science, and encouraged cross-fertilization between areas. The conference was oversubscribed, with attendees from industry and academia. The meeting received a High-Performance Rating, and was commended for the assessment that 95% of conferees rated this meeting "above average" on all evaluation areas (science, discussion, management, atmosphere and suitability). HEC Consortia Model: Over the coming months EPSRC will be looking at the future of the HEC Consortia model and potential future funding. We would like to use this opportunity to ask the Consortia Chairs for input: • What are the key benefits that your community have experienced through the existence of the HEC Consortia? • What elements of the financial support provided by the HEC Consortium's grant have worked well and what could be improved in the future? We aim to expand the breadth of the work of the Consortium focusing on cutting-edge applications, and building collaborations with experiments and industry, to achieve maximum impact from ARCHER use. We discussed Grand Challenges at our most recent Management Group meeting. In December 2015, and have identified several to follow up as strategic priorities. We aim to tackle and support large-scale grand challenge applications in biomolecular science, in areas such as antimicrobial resistance, membrane dynamics, drug design and synthetic biology. One specific theme with potentially high impact in drug discovery is large -scale comparative investigation of allosteric regulation in different superfamilies of proteins (e.g. PAS domain containing proteins, tyrosine kinases, etc.). The major impact will be in the identification of novel selective therapeutic molecules with limited adverse side effects. As a Consortium, we intend to develop and apply novel computational approaches for the rational design of allosteric regulators of hitherto 'undruggable' targets. Many of the targets emerging from large-scale genetic screening are deemed undruggable due to the difficulty of designing drug-like modulators that bind to their catalytic sites. It is increasingly clear that these targets might be effectively targeted by designing drugs that bind to protein-protein interfaces and allosteric sites. To do that, however, new rational design strategies, based on an in-depth knowledge of protein dynamics and advanced modelling and new simulation techniques are required. Other challenging frontier areas include dynamics of motor proteins; prediction of the effects of pathogenic mutations on protein function. The accurate prediction of free energy of binding is still in its infancy and needs much further investigation. Finally, kinetics of biomolecular reactions will become the next big topic. It is clear that high end computing resource can provide the necessary power and capability to provide inroads into this vital area. This is important because it is becoming increasingly apparent that kinetics of drug binding is a key factor that the pharmaceutical sector should really be looking at in terms of a major dictator of potency. HECBioSim is now well established, supporting work of many groups across the UK in the growing field of biomolecular simulation. We benefit from an Advisory Group containing members from industry, as we as international biomolecular simulation experts and experimental scientists. The Advisory Board was expanded and refreshed for the renewal and consists of: Dr. Nicolas Foloppe (Vernalis plc, Chair); Dr. Colin Edge (GlaxoSmithKline); Dr. Mike King (UCB Pharmaceuticals); Dr. Mike Mazanetz (Evotec AG); Dr. Garrett Morris (Crysalin Ltd.); Dr. Gary Tresadern (Johnson and Johnson Pharmaceuticals); Dr. Richard Ward (AstraZeneca); Prof. Modesto Orozco (IRB, Barcelona); Prof. Tony Watts, (Oxford, NMR); Dr. Pete Bond (A*STAR Bioinformatics Institute Singapore). We aim to foster industrial collaborations and collaborations with experimentalists (e.g. joint workshops with CCPN, Institute of Physics (Sarah Harris, Leeds Physics); see e.g. case studies. A particular theme for strategic development will be multiscale modelling, building on collaborations between several groups in the Consortium and the other CCPs. This theme reflects the inclusive and forward looking philosophy of HecBioSim, which is a community open to new ideas, keen to develop new methods, and ultimately to use HEC to drive exciting new science. The Consortium model allows new collaborations to develop. The recent reduction in time allocated to HECBioSim has meant that we can support fewer projects. There is significantly more demand for computer time than we can accommodate through our current allocation. We intend to work with Tier 2 Centres to explore possibilities for applications, and e.g. to test emerging architectures for biomolecular simulation. Edina Rosta (Computational Chemistry, Kings College London) comments: "HECBioSim enables my group to perform biomolecular simulations at the high standards required for JACS, Angewandte, etc. Without this consortium I would not be able to perform the necessary calculations leading to publishable work in top journals as our local university resources are limited and the hpc systems are not well maintained". Regarding financial support: the administrative support provided via the consortium grant is essential to the functioning of HECBioSim. This role is currently undertaken by Simone Breckell who not only administers, allocates time to projects and arranges panel meetings but has also done a fantastic job collating the extensive information for this EPSRC report. 
URL http://www.hecbiosim.ac.uk
 
Title Insitute of Physics eBook on research collaboration 
Description BristolBridge was selected as a project to highlight in an Institute of Physics eBook on research collaboration. 
Type Of Material Improvements to research infrastructure 
Year Produced 2020 
Provided To Others? Yes  
Impact This is a transcription of the IoP interview with the research team. This should not be taken as a checked verbatim record and we accept no responsibility for the contents, and nor would IoP. Bristol Bridge 18 December 2019 18:46 What do you think made this collaboration work? • Adrian Mulholland (AM): o The 'right people' ie people that are: ? Able to speak for their discipline and are open to others ? Able to (or learned to?) translate from one discipline to another ? Open to collaboration ? Interested in developing ideas o Clear scientific area, AMR, which was recognised politically and scientifically as being really important so people cared about it; people wanted to make a difference. o Attitude of the team that managed it- people that became involved in the projects had (or adopted?) the same ethos • Matthew Avison (MA): o We had good fun and we got on well, we still do. o We didn't have too many egos in the room [AM:Just me. MA:We massage it every now and again] o When we had meetings we amicably came to decisions. o I wanted it to work because of self- interest (in AMR)- it keeps us (in AMR) all going • Annela Seddon (AS): o Within the management team- people were interested in the success of the project as a whole, rather than the individual successes that it might bring. o Leaders advocated for the project rather than themselves o People were really willing to raise up other people because that was important for them rather than it always being about them. • MA: o It wasn't about suppressing egos for the common good, the management team just didn't have that big egos anyway- and they've shown in other things that they've done that it is generally about the common good (values) o It helped that we just kind of got on with it o It might have been a bit of luck at the time but if I went back and did it again they would always be the people I would choose. • Katy Turner (KT) o Maybe the people that agreed to it maybe were willing to kind of... • MA o And that may be true, there may be an element of self-selection. • AM: o Team was deliberately not the highest profile Professor in every department, it was people who were interested in learning o AMR could be a part of advancing all of our careers o Not saintliness but an openness to learn and I knew that people were willing to learn • MA: o Apart from you (Adrian), all of us were senior lecturer at that point, we've all moved on at least one rung since then so it has helped all of our careers. • Jim Spencer(JS) o I wonder if the fact that we made it clear at the beginning that the funding was available for anyone to bid for, it wasn't, from the point of view of people from outside of the applicant team. I think we succeeded in making it clear that there was something in it for them, that the pot of money we had applied for wasn't going to be carved up between ourselves. o Any perception that we were a closed shop and I think we succeeded in making clear really early on that this something that was inclusive and that anybody could bring an idea and they had as good a chance as anybody else in Bristol and getting some money • AM: o That was important and the other thing that was important was that within the management group we had a structure that was intended to demonstrate that it was collaborative. We were divided into themes and every theme embodied bringing someone from the EPS side and someone from the biomedical side. o So every theme had joint leadership and those people that led the themes were joint leads o That embodied what we wanted to see through the project o Seed funding proposals had to be collaborative- they had to bring people together from different domains. o Strong thrust on these should be new collaborations • Rob Hughes (RH) o Something that was really obvious coming from an external perspective coming into it was how inclusive everyone was and how quickly and effectively they would wrap you in, everything you needed to know, they would get you trained in the areas that you needed, it didn't feel like there were any boundaries to where you could go, who you could go and talk to, what kind of techniques and tools you could use or learn. And that was, at that stage of career that I was, invaluable. It exposed me to a huge wealth of other things, and other fantastic people. o Initially AS was my main point of contact as I quiveringly went up and spoke to her at a conference. I saw a presentation that Annela had spoken at and I thought there was some sort of connection there, so I spoke to her and she immediately leapt on it and gave me lots of time to talk to her about it and develop the idea and then introduced me to JS and other people as well, to continue that and within a few months I found yself in a biology lab being trained how to stain bacteria, and I had never done anything like that since 6th form! o And so I was plunged into this world but there was a lot of positive and optimistic responsibility given to me and so, them trusting me that I would be able to pick it up as I went and not worrying that I was going to, not understand things straight away, just giving me the time to build those skills and knowledge was really helpful for me, not having any knowledge of that really. • AS: o I just remember a hilarious phone call from RH at about 11pm in Thailand, I sent Rob over to Thailand to collect water samples and apply all of the techniques that we were developing in the lab and to see if he could get them to work in real samples. Rob had been in the lab since 8 in the morning and it was 11 at night and you were like "I've done a thousand agar plates today" and only a few months ago you were an engineer! You've probably plated out more samples in a day than most people do in their PhD. It was brilliant! • RH: o I was on someone's grant as a PostDoc in the Engineering department. o They were very supportive, of expanding your horizons and things like that, they paused the work that I was doing at various points so that I could work on these projects. • MA: o Coming back to the point about "allowing you to..." the reason why I think we could do that we didn't feel under any pressure to make the individual projects succeed, it was about making the collaboration and the network building succeed and so the individual projects, many of them did really, really well, but actually we could be a bit risky and thats one of the benefits of this type of funding. • KT: o And it wasn't loads and loads of money. It was short, defined projects, and we spread them around and there was that feeling that- it is risky to do this, lets see what we can get out of it. • AM: o There was much less worry about the outcomes of the projects, more about getting the spending done as it was quite a short project (2 years). o You had to identify someone like Rob whose supervisor was prepared for them to move off a project or be seconded or something and didn't get a job in the meantime o So various things we could have funded didn't happen because someone moved away or something else happened o So the practicalities. • MA: o It was a flexible pot. o Claire did a huge amount of work just to make the finance work, HR, some of the contracts • AS o And getting visas sorted out • Claire Spreadbury (CS) o It's not easy to do that, across the university. • AM: o And that wasn't envisaged in the application, that came up because we got some additional GCRF funding, can you arrange visas for 20 people from Thailand! • MA: o A large part of the success of the project is that we got Claire in, we got someone who can manage multiple tasks, from organising a conference to organising a visa o They are very different skills and we were very fortunate (and thats why we're trying to keep her :-)) o If we hadn't had someone like that we may not have been successful. o CS can remember everybody's names and what everybody does, and she's like that with the students she remembers exactly what they're doing, she remembers them all and she has many skills but that's one of the important things when you are building a network, just remembering who people are is one of the most important parts of it! • CS: o You get good oversight because you've got the paperwork in front of you, its more tangible. • AM: o It's a lot of people, a huge number of people that you've dealt with. • CS: o I know a lot of people in the AMR world, now, across the country! Serendipity vs deliberate? • Bringing people together is important o E.g. Mervyn Miles meeting someone in a lunch queue at a conference that sparked a project o Making the space for luck to happen o Events are really important for that • MA: o Academics are generally quite good at bumping into each other and finding things that are interesting- reasonable common ground o But what we could do with BristolBridge is that we could put some £s in front of it and say "well there's a reason for you to actually do this", and once people saw projects funded and the university were very supportive of the project in terms of advertising its successes and seeing management attending some of our events and then the wider university sees it as a success and then they become more likely to become involved. o And its funny now like the money has kind of gone, that actually we very much worry about it kind of falling apart a little bit. • AM: o And people retreating into their silos • DH: o Now with no £ we have no avenue for it really • AS: o Its funny I had a conversation soon after we launched we did an event, a workshop, we had a series of flash talks, and a very senior academic who I won't name came over and said , "I don't know why you are bothering with these piddling little bits of money, you should just take a big tranche of money and give it to one or two people to solve the problem." o And I thought You. Don't. Get. This. Like, you don't understand the role of what we are trying to do, you don't understand the riskiness of these short term projects, you don't understand the collaboration. o Because their point of view was, "I'm the best in my field. You should give the money to me, and I will make all of this go away and it will all be fine." And I thought "but you haven't done it so far so what makes you think if we gave you the money now you would be able to, that it would be any different?" o And that attitude, kind of, I was quite taken aback by that. I wanted to say (but I couldn't, I was too scared), "look around this room, can you not see the conversations that are happening and the things that are coming out of this, do you not recognise the value in that?" And I thought well if you don't, then maybe this isn't something you should be involved in. o And that person never got involved in anything. And never turned up again, never engaged. And never applied. • AM o Its a very different sort of funding. Much of science funding is, you know, a slogging, long long process of getting funding, a lot about reputation and facing down referees and all the rest of it. This is a very, very different model of funding. o It wasn't a lottery, it was competitive. o But it was, "you've got a good idea, well, OK, we can probably give you money within a few weeks to begin with and take it from there." And lots of things came out of that. o And I think thats a model of funding that lots of universities and Research Councils could usefully use. o And then because its not really worth the mega beasts going after this, £20k, they're not interested, but for someone else, its going to change their career. • AS o That £20k could lead to a slightly bigger pot of money and then you start to look at the -O-Star project which was about £3million- something like that? • MA o The Thailand- O Dart? One? • AS o Yes that one it grew and grew and it was like a snowball • MA o It was KT doing a bit of work and people coming together and a bit of GCRF investment from the university and CS working hard and BristolBridge and it all came together and we got to that point. o And there's been other examples of success and Rob may well have got himself a lectureship anyway, but now he's got himself a lectureship with that bit of knowledge of AMR, that bit of knowledge of microbiology and now going forward in his career he's going to be always thinking "oh, maybe there's something we can do in that area" that is as much, as far as I'm concerned (given he's got another 50 years before he is allowed to retire), that's a really good outcome just a much as a £3million grant. • LO o Importance of intangible- this is the effect that this project has had on me, and this is what I have been able to do. Social value of the collaboration. • DH o About 3 different pump priming projects working with 3 different people who were some involved with the initial Bristol Bridge- some have come on board, some have dropped away a bit, you know. o The initial project was I went to one of the initial world cafe events and I sat down on a table on my own saying I'd like to talk about Gonhorrea and I thought that I would spend the afternoon and I would have a nice day out and I'd have a cup of tea and a bun and that would be me! But actually lots of people were interested and I met lots of people with really cool technologies that you think , wow, I wonder how I could use that and so I had a sort of half idea in mind but it really consolidated and I think there were twelve people on the initial application. o And we got really nice principle data that enabled more funding elsewhere and thats led to confidence in concept award ultimately from MRC, which is now moving forward which is really good. o Different members of the team have come and gone as its gone on. o KT is the only other person at the university who loves Gonhorrea as much as I do... o We've got now a joint PhD student, co-funded by GSK vaccines and maybe more to come. Building quite a nice nucleus around Gonhorrea expertise in Bristol. o With Charlotte (Birmingham) and the company we've got one of the prototype microscopes now that we're going to apply that technology to the problem so again that's an ongoing, and I'm a molecular microbiologist but its been re-engineered (and thats the extent of my knowledge still about engineering!) but to make a heater stage so thats lots of cross disciplinary stuff happening o And we're working with synthetic chemists as part of the CiC award, so there's still lots of clusters and Shaun, who I met through Merv(yn Miles) - a physicist, we've now got a PhD student on atomic force microscopy as well looking at the surface of bacteria and these are all direct results of a cup of tea and a bun and a chat. • CS o Scones, actually, a cream tea. • AM o We spent quite a lot of time choosing the catering actually • CS o It is important- you want to run a good event so people want to come to the next one • DH o Compared to other events, and I've been to a few different things, over the years, because I've been in Bristol quite a while, and what struck me are, what Adrian said, not only the people, first and foremost, but also the set-up in terms of the space, and the tangible hook that there might be some money that you could apply for, but with so many meetings you sit there and there is talk after talk after talk and they overrun and then you get coffee and then you get "we're only going to have 10 minutes for coffee" and then its back into more talks and then everyone goes away. o Having the space to sit with people from other disciplines and be creative, was what led to that initial application. • AM o We had never done World Cafes before, but we'd defined them in the proposal, we'd said, we'll do that. o I'd never run a world cafe and you do, you have to be quite strict with people to let them be free form in their thinking and by giving short talks, it meant moving people around tables, it meant telling people you can't sit next to your friend from your own department you need to sit next to someone else. Anf that took a bit of prodding but it was worth it. • CS o It was quite nice the way we had a GP and a secondary care physician and a vet lay out the problem of AMR from their perspective. o For all the Engineers and the Physical Scientists in the room, they just explained what the problem was as far as they were concerned, and that allowed people to really focus on their needs. • MA o The world cafes were incredibly successful and the key in DH's case, Gomhorrea is a massive problem and yet its a relatively simple problem in many ways, and so you kind of capture the audience with that. And then you use their technology. o So DH's acts as a nucleus to all of that collaboration. At the time, DH didn't have big funding pots or other things so he had time to think and be reactive in that way but also he's the sort of personality that we've talked about who is prepared to talk to people, ask questions and get involved in a social way as well. o Actually, that experience has made me collaborate with other people differently. Because I know how I reacted in that situation to those people so now when I'm collaborating with the medics who I work with a lot, I now use them to tell me the problem. I never used to do that before. And I feel that that's kind of what the microbiologists and the AMR experts in BristolBridge were doing, we were telling them the problem, thinking they're the ones with the massive brains and they'll come up with a solution. Now I'm constantly hounding clinicians saying "Tell me the problem, I want to solve a real problem". o Now I hope that that makes my grant applications better, my impact in my research more significant, because this is not just something I'm vaguely interested in, some esoteric thing, but something that's relevant to an application. o Yes it has changed the way I do research, the way I look at collaboration. • LO o Space the leadership of this project gave you to explore? How important is the leadership in setting the culture? o Like the idea of the co-investigators around themes? • KT o I think AM was really clear right from the beginning that it was collaboration and I think he said "no stupid questions", he probably said that 50 times • MA o Yes that was the motto of BristolBridge • KT o It became a bit of a mantra • AM o I tried to ask some fairly simple questions, I learned a lot from this project and I tried to make clear that I would ask questions that I felt other people might think were stupid, they were quite basic but they were honest questions. So you know, I am the leader of this but I am prepared to ask simple question and prepared to make myself perhaps look silly but I am more interested in the answer. • KT o And that genuine curiosity about understanding o We all felt that we were in, none of us were experts in all of the different areas • AM o We were all out of our comfort zone • MA o We all learned so much, the last 3 years I've learned more than in the rest of my... We've all learned so much and thats party the joy of it. o But we were all kind of equal in our ignorance, lets face it! o Thats the point, thats where the ego thing comes in as well. o The other thing is I think it was tacitly frowned upon for us as a management committee to corner all of the funding as well. Alright we were involved in quite a lot of the projects, because we were kind of the nucleus for a lot of it but it was kind of like "yeah guys I'm feeling a bit uncomfortable because Mulholland has got 17 of these projects funded and you know..." but it may be that that helped it to be broader and bring people in and that was slightly tacit but still a leadership decision to do that. • JS: o I think it goes very early that, MA and AM, you did a really good job made it very clear at the application stage that if we were going to make an application it was going to be run on a decent basis. The university when the call was announced they went down their standard route for how they would deal with all other calls where there is a limit to the number of applications, 1 per institution, and they asked people for EoIs with the idea of making it competitive amongst ourselves and it was down to AM, once we'd had some conversations about who might put something together it was very clear that it was going to be inclusive o You know not everybody took an interest in the final application but there were a lot of people across the university that were aware that this was going on at the application stage and that they would be mentioned during the application where it was hoped that they would participate so right from the word go it was set up as something that would be visibly inclusive. • AS o Although AM was the PI (name above the door), within the meetings that we had it never felt like AM was dictating to us what we shoudl be doing or how things should be run. It was very very collaborative, very equal, it was a flat management structure in a way. What was really nice was that there was always, we always kept coming back to the same thing which was, "We're going to organise a World Cafe. What do we want the outcome to be?" And CS kept us really honest with that. Always asking "whats the purpose of what we're doing? Why are we doing it? What should our outcome be?"- constantly challenging us, reminding us that it's great to have a meeting, it's great to have a workshop, but you actually have to have it for a purpose. • AM o Every one of our events had a purpose. A distinct purpose. • AS o Absolutely. And I think that was instigated by you (AM), very much hit home by CS in the organisation and how she challenged us in the organisation of it, but then brought together by the rest of the team so it felt like a really, it felt like the structure worked in order to make that happen. o It was good leadership, and brilliant facilitation, it sort of all fell into place after that although at the time it probably felt a lot harder than I'm making it sound! o We didn't agree on everything and we'd go round and round on certain things, and go "what is the point of this?" • AM o We were flying by the seat of our pants.... • KT o We were saying like "we're going to have 2 hours for discussion" and we were like "what do you mean? You know we are going to have 5min talks and then we are going to make people talk to each other and then what if it doesn't work???" o It was pretty scary actually we were like, what if nobody's going to come, but once you've done the first one... • CS o The AM/MA double act is quite engaging.... o No question is too stupid was really helpful • AM o No question is too stupid is my motto • MA o Adrian's too stupid is my motto! o The VC came, he did a really nice, we kind of rolled him in and that was good because then people think "ooo, this is and area of strategic importance and therefore I'm going to get along" • CS o And Nishan (PVC-R) came as well • AM o For what was not a really huge grant either. • MA o But boy has it borne fruit for them. You know, now its one of the top 3 priorities for GW4, so its really gone a long way. • AM o I think we are able to say that BristolBridge aligned with the ethos of the university so Bristol likes to see itself as an interdisciplinary university, we are not enormous but what we re is quite strong across the board so we were able to say, we've got a big EPSRC portfolio, a good Medical School, we've got a dental school, a vetinary school and we've got microbiology etc. And we are quite good (relatively speaking) at talking to each other. So it was kind of Bristol is, relatively speaking a kind of friendly academic environment and a fairly collaborative environment. And I think that message chimed at high levels of the university. Places/venues- choice? • CS o Good to get people away from campus • AM o Off campus and into something that was not a university setting where you couldn't just go back to your office and do your email • AM o 2 at the zoo, Engineers' House o Also different scales of events- so the themes did their own events, smaller than the whole BristolBridge, so a bit like cells, designed to have sub-units and layers • MA o Yes it was budget driven too wasn't it- the strand areas tended to do them within the university. • DH? o Every event was very different or felt very different, as well, so there was never any opportunity for you to get comfortable, you know if you expect the same thing every time then that stifles certain things but because every one was different even with people you'd met before you interacted in slightly different way and I think that helped because it kept people constantly on their toes. • MA o I think it helped having people from different disciplines on the management committee because different disciplines have their own specific way of doing things and so if you've got...the input of "we did one of these" and "we did one of these", it helped us think outside the box a bit. o Most of those events it was all down to CS and CS's prior experience of managing these sorts of things. Cs is always down to the catering because she used to run a pub so she knows about these things and I think that helps, and as someone said "if you go in and you give them a nice cream tea, they will think "oh well we're going to go to another one of those events because they are good"." • AM o Its everything, you've got to have a clear structure, a clear goal and within that structure the people have the freedom to be creative and if you didn't have that structure people wouldn't have had that freedom. • CS o You've got to have a hook, you've got to have a reason for someone to go, and I could see how it should move through in terms of an event. • AS o That first world cafe we were sat there- like- what are we going to do, we all know what the concept of a world cafe is but we need to make it actually valuable, whatever we produce at the end of it has got to count, so one of the activities was we gave people the application form after they'd had their chance to network with each other and said "write your proposal" and we gave them half an hour to just write a proposal. o And actually, that forcing people to go "oh- this isn't just a chat, I've got to come up with a thing at the end of it" was brilliant. o And a few of the things that came out of that got funded, but it was the - OK, now you've had your chat, now the work starts. Here's the application form, if you want the money, this is what you're going to have to fill in. • KT o And the deadline was like a week away • AS o Yes so, you might as well do it now. And people were in the same room together and they really threw themselves into it. o I remember because we discussed what we were going to do and we were like "why don't we just get them to write their application?" and we were all like "yes that's great!" and secretly I'm thinking "God almighty!", I was thinking "how would I feel if someone made me write an application on spec?" but actually people just went with it, it was brilliant. • RH o Yes it was very much out of your comfort zone! Because you thought literally you were sitting down for a bit of a discussion and then we would go away and have a think about it and then I thought- I'm giving a talk on this in 15 minutes time! o Yes because there were pitches. • AS o And I remember [Sarah] doing one and me going "WOW, thats really amazing" • AM o The York BtG took that to an extreme, most of their funding was for ideas that were put forward at a cafe, and they had to come directly from that; I didnt want to go to that extreme, I was slightly formed by an EPSRC experience at an Advanced Fellows event. o The fellows were far too disparate (and maybe too drunk) to come up with anything coherent, but that idea of maybe you can write an application in half an hour and if the idea is interesting, it might fly, and then we will develop it. o And it turned out to be effective. • KT o You didn't have to submit it that day • MA o A few people will have drifted away and maybe never come back again, we didn't necessarily know everybody anyway so we didn't miss them, frankly. • AM o The idea wasn't that everybody in the whole university would suddenly do AMR, the idea was to deliver 12-20 projects • MA o If a few people didnt really engage with the process we would still get something done given the numbers of people involved • KT o Most people stayed actually • MA o There were a couple of areas where there was a bit of negativity. There were a few "oh, its the AMR people"- they've created their little enclave and we're not part of it and there were a few people who did feel that they weren't part of it but actually they never came to any of the events either; and then there was a few people that kept submitting applications that weren't quite / nowhere near what we wanted, and that may have led to some internal frictions- I don't know because I didn't know them personally- I don't know if that caused any problems for colleagues? • AM o There were a few... The hardest thing probably was dealing with unsuccessful applicants, CS had to deal with some of that but in the end what we said was "CS is simply the messenger so If there is a problem bring it to me". And I did have a few dissatisfied people. But mostly, the applications weren't for a huge amount of money so Ok, if you spent a few days writing an applications for £20k and you haven't got it, sorry but we can't fund everything. Many of them we went back to and said "this is the feedback, this is what was lacking." • MA/AS o We did try really hard to give feedback, how to change things o Some people listened and really came back with brilliant things o And some people were repeat offenders- you would keep giving them the feedback and they would keep coming back with something that was a tiny bit different, and then eventually, you would have to go, well if you're not prepared to change it.. • AM o Thats your hobby horse, we are not going to fund it, it doesn't fit o Often, it was because its not AMR, they are trying to cram something into AMR thats not really an AMR thing. • MA o We had a lot of interest from people outside EPS communities, and it was difficult managing that and being inclusive given the grant o Some of the interactions caused a few issues in terms of focus. Bristol AMR has expanded it further and we still suffer from some of those problems, but nonetheless o The thing we didnt do as well was the industrial engagement side- we did put industry events on and we have spun out one company and there is another company that was spun out that ius involved so we have had some successes in that area , but I felt that personally, that was the weakest part in what we did. • AM o The mechanisms that we had were not really well set up to stimulate that. We did spend time cultivating an industrial partner who then pulled all their funding for AMR • JS o It did spawn one project where we had a student together and then now we have an EPSRC grant together • KT o Maybe its just a bit more of a slow burn • AM o The projects were more likely to be entrepreneurial scale up projects in the end and a company isn't going to be interested in 3 months of post doc usually o As you say we had the industry day and we got interest there are lots of people that want to associate with AMR in industry but there are not a lot of industrial partners, there is not really big pharma in AMR any more, and the things we were doing- is there industrial value in chlorohexadrine nanoparticle gel- well probably there is but thats really- from the ground up to define theres a market o And we spent most of our time on procedural stuff- how do you get the money spent, how do you recruit people, dealing with visas and so on. o Running the admin on multiple projects with one person to run it was a huge admin effort really • DH o From my perspective the way you did it was the best way to do it and if you then brought in industry partners at that initial stage and then you got tied up with NDAs and contracts and material transfer etc, probably nothing would have happened, nothing would have nucleated. o From the project I was involved in which was very early stage discussions to now a CiC grant the next step is would be- if this is successful to engage with industry. And theres already been a spin-out. So that is going to happen, naturally. o But the remit that you guys set out to establish cross disciplinary collaborations where the focus was on AMR was a huge success looking at it from the outside in. • MA o It would be interesting to know whether Massimo moved down the spin out route through conversations he had at the industry days or whether he did it off his own bat. o I thought we might give people the skills to take it forward themselves... • Charlotte Birmingham (CB) o I don't think it was the intention at the beginning o I think it was more that he always wanted it to have an application, he was quite focussed on the application of it o But I don't think it was the plan to have a spin out, the project was very much that he had built this microscope and we hadn't really found the killer application for it and the project allowed us to throw some bacteria at it and see what happened, basically. o So, there wasn't an expectation at that point that here would be a spin out coming from it but then we got talking to, probably through events relating to Bristol Bridge, I can't remember, but talking to the commercialisation people in Physics, and talking to people who had that link and that led to a CiC grant which is commercialisation based. o So I think the contents right. • MA o MRC CiCs in Bristol are managed by the Elizabeth Blackwell Institute and I think through BristolBridge we did well at interacting with the other research institutes within the university; we did a joint thing with Data Science, the JGI on AMR, and we did EBI, and now EBI with Wellcome Institutional Support, pay for Bristol AMR to exist, so we did link quite well with other interdisciplinary institutes • CS o Actually what really helped was that JGI and the PBI stuff was CS going to RED (Research and Enterprise Development) going to their meetings as like an 'honourary person' as Bristol Bridge was onbiously trying to get grants funded across EPS and Life Sciences, and just CS being in the room and everyone in the room being aware of what BristolBridge was about and AMR, so that the arts and humanities research development managers and the life sciences and the EPSRC, they all got to know about BristolBridge, like everyone knew about it and what we were trying to do. SO having Patti Holley there from JGI and people from all the other research institutes were there and that really helped (my note- also Patti Holley used to manage another big interdisciplinary EPSRC Centre in Bristol so she knew EPSRC and HT and what we were trying to do too.) o We were very well known within the university • LO o And very well known for what you were doing • CS o And then you can start having joint workshops • MA o And leveraging a bit of their funding to help joint events • LO o And so you get the ball rolling and it gathers as the ball • MA o Yes and we put AMR on the agenda for the University and they thought- Aha! • AM o Became involved in steering committee for Bristol Challenges because of AMR • CS o And with Helen Lambert as well it all just nucleated quite • LO o That happened because of linkages, you all brought your networks • AM o Just looking back at our original objectives I think Bristol Bridge what it achieved was interesting because what it achieved was closer to the case for support than almost ALL grant applications that I've ever been involved in! o It actually did what we said we would do! SO we had 3 objectives, ? To develop and facilitate a wide range of networking activities to build new interdisciplinary research communities, focussing on the EPS community and the current and future AMR challenge ? To fund pump priming projects across 3 different and distinct strands building on EPS research strengths and aligned with the AMR strategy ? To fund training activities to help EPS research to understand AMR and to equip biomedical researchers to apply EPS methods to training a new generation of researchers. o Those were our objectives and I think we actually met them and we met them in the way that we said we would meet them. o We did pay lip service to industry but it was really lip service o And it was remerkably close to what we said we would do, but we had a good idea of what we wanted to do in the first Place • CS o We did have - who was that chap who was based in Chemisty and he did a lot of work with... He went to work with InnovateUK? • AM o Colin? • CS o And unfortunately we lost him but he did help • AM o SO that was how we had the Redx thing • MA o It was pretty good wasn't it really- it was pretty good! • LO o It strikes me the importance of clarity in a collaboration like this, it was very clear what you were trying to do and its easy to be part of that and driving it forward when you've got that clarity in objectives and outcomes from whatever networking events you choose to use. • AB o Extent to which BB contributes to REF? • MA o Do you know if Vitamica is going in as its not quite ready? It isn't there yet but its not quite there yet- maybe next REF • AS o It will feature as part of the environment statement for Physics around Interdisciplinarity and how Physics works with other departments and this will feature its this kind of types of activities that BB did that will go into the environment case study • KT o Vet school plan to have AMR but likely to be more around policy and AMR in agriculture • MA o But we are hoping to get a bit of credit there because we did do a little bit of stuff there o And by building the interdisciplinary community we've allowed other interdisciplinary consortia to build in their own right. • KT o Arguably a large part of what is going on now was facilitated by BB but there were things going on separately as well? • MA o Maybe one of mine might have come from BB/would not have happened without BB • AM o Because of the way REF is set up it has a tendency to iniquitous consequences, excluding minority groups, because its so heavily reliant on publications, the first paper coming out of BB probably didn't come out until 2016 so its a bit early for them to demonstrate impact. • MA o But its a slow burner, you know, we're hoping that there will be some more, we have some exciting things coming along and we are feeding into other applications for translation of technologies o Thats another thing- it has allowed that better interaction through people like KT, being ambassadors in certain areas, to the data science, to the healthcare science, and I'm talking to people now that I would never, ever have met at all if it wasn't for BB o And now we're going to potentially be developing clinical applications, and actually, the future is bright and there will be a lot of fall off on that but some of us will make it through if REF still exists.. • AM o The group was not only the right people but it was consciously a diverse group, we struggle with ethnic diversity in our academic body generally, o But we were scientifically diverse, diverse in background, diverse in gender, diverse in personality type... o Miserable yorkshiremen, • MA o Stuck up Mancuians... • AM o Actually we did, as a management team, take that into consideration when we were thinking about who we were going to ask to speak at our events o We were very upfront about this o We all generally believed about the best science coming from different viewpoints and that means different backgrounds and different life experiences. • AS o Coming to BB advisory meetings were one of the very few university meetings I actually looked forward to, that I also felt like when we were considering matters of diversity it come from a very natural, bottom up discussion and it wasn't a chore. o We talked over lunch about shared values, and this was one of the shared values we naturally have which was that we all believed that diversity was important and it was almost inherent in how we worked. Advice for others? • AS o Pick the right people and the right people aren't always going to be super famous professor X or Y o Its actually pick the right people for the job because one of the other things that I think made this work was that everybody put in the legwork. Nobody was too important • AM o That is true. Everybody worked really hard • AS o Everybody worked hard and we never sat round and thought so and so is not pulling their weight o Thats not the same for every collaboration that I've been in, and I know that I've sometimes been that person who hasn't pulled their weight o Definitely picking the right people o The shared values thing I'd go back to again and again, making sure you have the same shared core values • KT o We all had quite clear roles as well, you felt, you were a representative and so you had a responsibility not just for yourself but to turn up and take Bristol Bridge back to wherever. • LO o Importance of this tribe and somebody being able to come and take and translate back to their tribe o Interlocking networking stuff. Neat way of working • MA o I find I have not patience anymore where people don't pull their weight and are always asking for more money- they always want their bit of money or they always want their, you know. I've stopped engaging with that o And its because we were all relatively junior and prepared to do it, and maybe had a bit more time and it just kind of worked! o Partly luck, partly judgement but it worked. o I run a national integration project that NERC fund, they deliberately make you fight against each other to get the funding and then they say oh we are going to give you a bit of extra funding so you can all be nice to each other. Its impossible! o We just got the funding for an Argentina call and they've done the same thing • LO o It doesn't work because its actually contra to collaboration • MA o Exactly! BB one of 11 BtG awards- did that work, was it useful? • AM o On the whole not that useful • AS o I didn't come away feeling like I had learned anything useful- other than reinforcing my views about the way we were doing it being the right way and that we were having a lot more fun than everybody else! o Genuinely • LO o The energy here is amazing • AS o Quite a lot of bitching/complaining at those meetings o It was like the polar opposite of the experience of BB which was challenging and positive and fun and not without complexity o Always a couple of great people where you share values but also people that you don't o Reason nothing came out of that was that there wasn't that set of shared values • AM o They had different values and different structures o Quite good links with Imperial (EMBRACE), one of PDRs exchanged and a joint application. o There is an assumption that they are all the same and they just weren't at all. o DH sitting next to John Crosby and you could actually see the collaboration happening like " so you want to join those molecules together and we could do that by using Click Chemistry" and it sort of clicked! What would you like to tell an incoming PVC-R about this? • AM o There are things for the university to learn o The AMR community in Bristol has done well from a number of activities one of which was BB, and we have an ongoing strong AMR community. o There are a number of things the university could have learned from this and I'm not sure it has happened, o This model could be applied at different scales, doesn't need to be a big scale, very effectively, you could do it with other small pots of funding. o Some of the people within the university still embody it but its a bit frustrating its not been acted upon o Disappointed that the RCs didn't do a bit more- 2 years of funding has paid off enormously • AS o Uni had a good opportunity, because we do brand ourselves as an interdisciplinary environment in Bristol- they ahd a good opportunity to understand how the back room processes that support research needed to adapt for us to truly be an interdisciplinary university o And what it never did was even when we fed back things like contracts and finance and all of these things that CS took a huge burden of, every single one of us at some point had to engage with, and they were getting the same message from a number of different people over a very short time period and they nodded and smiled and then did nothing about it. o That was immensely frustrating and I still see the legacy of that now, I run an interdisciplinary CDT that spans 4 faculties and I am still having the same conversations I was having 9 years ago about how students transfer and where the money goes. o BB was a small prject with relatively small pots of money that should have been, should have been easy, almost like because some of the pots of money were so small it wasn't worth their time to actually deal with it. o OK, £5k, £10k, £15k might not mean much to the university's budget - probably what you find down the back of the VC's sofa, but to a short project like the stuff that we did, that £15k was everything. And there is not always an appreciation from the higher echelons of the university, while they are always very supportive of the work, that the kind of scale of money that they are used to working with is something that we are never going to concern ourselves with because we are never going to be working with £350M, but they've kind of forgotten that £15k matters and £15k can make or break somebody's career. • LO o I really think you are so right, I don't think a lot of VCs really understand the power of small, pump priming seedcorn. • AS o If I was running the university and I wanted to look at how to change the structure of how a university runs to support multiple activities of this type I would have A finance team whose job it was simply to process quick turnaround short pump prime projects. o So instead of having a faculty team you would have a rapid response finance team who would be there entirely for when RCs drop funding at last minute and you have 2 weeks to turn an application round, or you've got a pump prime project where money is handed out throughout the university and you would have a team whose job it was to be fast response (and across the university) and that would take away the barriers. o In our faculty we have a brilliant finance team but trying to move things across faculties is really really tough so why not have a cross faculty finance team to fund interdisciplinary pump prime projects. • AM o The idea that structures are trivial- they're not. Structures define what you do. In universities and research councils. Applications are written to fit the structure of a RC. Its different for another Council and there are gaps and you have to work to bridge those gaps. o This project at a small level exemplifies what interdisciplinary research should be about ? Clear objectives, ? Bringing people together o Universities I hope will move away from that one PI model and look that PI has got a £20M grant clearly its not that one person its loads of people in a team doing it. Science is not done by one person and £20M. Its done by lots of people with small amounts of money or even no money. Can't we move to that model of doing science ? And that would have to be accepted by all sorts of organisations. • AS o Having that flexibility in how we worked. o You would have to put in the same FEC costing form to get some BB money as you would for a whole massive grant. The overhead on our time was huge. The number of times we were like- we've some up with an idea, the deadline's tommorrow, **** we've got to do the FEC costing! Oh god its got to get signed off. Why can't the university understand that we've already got the money, why have we got to cost it again? And they would be like no, this is the procedure, and I would be like why? It was maybe more frustrating for us because we worked so well together and we'd figured out a way of transcending the boundaries, I couldn't understand why everybody else couldn't do it! That really upset me in a way and it was putting so much unnecessary pressure on people like CS, when she had other things to do with her time • JS o One of the things that has been important to the success and why things multiplied why BB is still going is that Bristol is a big enough and successful enough university mean that there have been other small pots of money to bid for and keep things going. o I wonder whether part of the fact that some of the projects went on to bid for other sorts of funding £15k, £20k-£50k is due to like the Elizabeth Blackwell Institute, GCRF things so there have been other mechanisms in place? • MA o That is true- other universities may not have been able to provide that additional support o The GCRF, EPSRC institutional support went a long way o GW4 money that we got, not huge amounts, but because BB existed we gave the university a vehicle to be able to spend some. Universities often find it difficult to spend some of the pots of money that they are given, and the reason that they would give us the money is that we could spend it for them. o When they made it so difficult for us to spend it, we ended up not spending any of it (they actually gave us the money after the deadline!) • KT o With BB we had enough time to have multiple rounds. • AS o Examples of university contracts not liking the contracts that they negotiated and wanting to renegotiate them • KT o We need all sides, not just finance. Its one of the biggest hassle we had, everything else is fine! • AM o The spirit of BB lives on in Bristol AMR • RH o The ethos behind it and the amount of legwork that went on to train and connect people is enormous and thats the legacy • MA o You can tell by the way we interact why it worked. Technology • Only skype- people skyped in to meetings occasionally. Otherwise post its and flip charts. Future of collaboration • RH o Technology that's available now means that you can communicate with people much more readily- it makes things easier, to work with people o the other side of the world but the fundamental cornerstone of it is still those personal relationships which I think requires people in person having conversations and the willingness to stretch across the divides. • CS o PhD students- although they have met physically they keep in touch through WhatsApp- we designed this portal for them, but no-body uses it. They have a whats app for their own cohort and a joint whats app • MA o Maybe we were successful because we used to play out in the street! o We are going to Thailand next week for a project that KT and I are involved with and I will get more out of the 3 hours that we spend with them then than I have out of the last 6-7 skype meetings, I just think there is something, particularly when you are working across cultures as well, • KT o The number of times you get pulled aside and its like "actually, this is the problem, and we couldn't say it in an email". • AS o EPSRC SAT meeting- sustainable science- should people really be flying people across the world? o If EPSRC would fund the tech to do teleconferencing properly,then you could do it but o Industrial teleconferencing facilities that work are basically like an immersive whole room, so you genuinely feel like you are in the room with someone and it takes the whole wall, it costs £1M. o There are ways of doing virtual stuff effectively but you have to make a really committed effort to install the technology widely o Facetime is ok for a 1:1 catch up but it doesn't work for a meeting or for world cafes etc • LO o It ruins the flow of conversations and its not being in the room and seeing what is happening over coffee and over lunch • AM o You miss that is going on in your peripheral vision • LO o And there serendipitous stuff is almost impossible • AM o That's right you can't o We have a project with BP on VR- how you visualise catalysts virtually, where you can be in different locations but in the same physical space, and you could do that, for a specific purpose. • KT o We did do some technological things- like the crossfire thing o Its like live youtube streaming- and people can ask questions and watch them live • MA o Sabine Hauert- had a lot of techy ideas and set up crossfire. • RH o It was quite good for telling people in the AMR sphere in Bristol what you are doing, and you can watch it later if you can't attend live. • KT o The time and space for creatvie thinking and the time in a room with cups of tea is important. Language- was time the major way that you overcame these • MA o Guidance for people giving talks- not using jargon, explaining everything, most people went with that. o Give plenty of chance for Qs o Many of us took one for the team and asked potentially stupid Qs o And thats one thing I have taken forward into future collaborations- I may ask a Q that I know the answer to already just to make sure that everybody knows the answer • AS o Its about not making assumptions- people might think they understand but within their world they do but not across disciplines o One of the courses I run for postgrads- one of the things we do as part of the interdisciplinary team building exercise is we talk about language, I say to them write down, when I say, what is a cell?, write down what you understand a cell to be and most f them will write down its the basic function capable of sustaining life, a couple of the will write down its the american for mobile phone, and then I show them that if you look it up there are 28 different definitions of what a cell is. So depending on where you're coming from you might have a perfect understanding of what a cell is, to you, in your world, but actually that could be completely different to someone else's definition. And unless you have somebody clarifying and removing the assumptions that we all think we are on the same page, but actually we are not. o So we used to start every kick off meeting with a few slides- this is what AMR is, this is what we are talking about when we mean AMR, because there was still the misconception right at the beginning about what was it that was actually resistant, people think its them, no its not you its the bacteria that are resistant and just getting people to understand that, which to one person might be a really simple concept but to others, the antibiotics work on me, so I must be resistant, that totally flies in the face wof what the project was trying to do. o So I think removing assumptions by asking questions is crucial • LO o Common understanding creates common language o Makes it easier for others to come in and join you • KT o When we were facilitating trying not to just talk but to listen and to clarify, what do you mean by that? • MA o Its really helped in aspects of my career that I'd never really though about until today, when I just thought about it! o I gave a talk at Weston College to a group of 6th formers, and I feel that I now give PE talks that are much better than they work because I can think about it from different perspectives and I can think about what the misunderstandings can be for all of us, and you can bring that in to talks. o You can really inspire kids about working together o With social sciences- academic collaborations very difficult because of some of the absolutely fundamental differences in the way we do our jobs as academics and I think we were fortunate in a sense that the management team of BB have a similar way of doing our jobs and a similar way of doing research which is fundamentally- we have ideas with the people in our teams but we have teams, thats the point and if we have another project we have another team member to do that project. If you are in humanities, or an anthropologist, its you, its your research, you might have aPhD student but you almost certainly won't have a team, and so you've got to fit it into everything else that you've got to do, or you're not interested in doing it at all. To try and say, come on , we'll give you £15k and we'll do a project, they'll look at you and go, well, alright, but when am I going to do this thing. o So it doesn't always work and sometimes it can fall apart if you don't understand the culture, now we've learned all that and now in Bristol AMR we are trying to learn to bridge a bigger divide which is how to bring a Professor of English or in Art History or Law into this • CS o And they don't do posters, we've learned that • MA o And if you had a session where people would discuss, they'd spend half the time explaining to you why that particular word shouldn't be used in that context, or why are you talking about combatting AMR • LO o And wanting to get that right before you move on. • MA o You have to get used to their world and work with it, but you can learn so much I think • LO o Its about people and emotional intelligence, EI as well as I- understanding what its like and putting yourself in other people's shoes. • AM o We were all aware of unconscious bias o It taught me that we are unconsciously formed by the structures that we worked within, of your disciplines, how you communicate impact and output within a discipline, some disciplines don't have posters, some disciplines have conference papers, some disciplines have postdocs and some don't, things that you regard as the way the university works, well no this bit of the university doesn't work like that at all, so if you want to work with this bit of the university you are going to have to mish mash two bits of structure together so recognising the structure and how that defines what you do is quite important. SurgeonX- different type of collaboration • AM o RH and I went to the Shard and did character development o They contacted me and AS volunteered RH. • MA o You lot developed the one -off- tria and error. o I was somehow invited to do the videos for the app for the first one. o I'd done stuff in the past with people writing novels and documentaries etc. • CS o She did media training as well for us • MA o She was really great and we had a 3 hour phone call explaining antibiotic drug discovery • CS o Wellcome PE grant • MA o She had done producing and directing drama for BBC (Holby City) o It gives us a bit of a frontage and we get all these weird and wonderful things now • AM o Yes I got approached by local news o Secrets of the skin- RH- JS asked if I knew how to shake a rattlesnake when I passed him in the street- I was just after a beer. • MA o Channel 4 rotting hippos with Anthrax- I put the fear of got into them so they filmed it with remote cameras. It was hideous. o Two young adult novels, sold pretty well, I was a character in the second novel and saved the world. o The Rain, and The Storm. In The Storm, Professor Beardsall, my middle name is Beardsall my character saves the world. • AM o A lot of the media stuff is too apocolyptic • MA o SurgeonX got great reviews as a comic in its own right. • KT o Its been quite nice to reflect as we didn't really have the chance to do that • AM o Too much one-off , things take much longer. 
 
Title Individual-based gonorrhoea transmission model 
Description This repository contains the following MATLAB files, which define and simulate an individual-based dynamic transmission model of gonorrhoea infection and treatment in MSM. The model incorporates ciprofloxacin-sensitive and resistant strains, a time-dependent sexual contact network, and allows a flexible choice of complex (individual-based) treatment, testing and tracing options, including strain-sensitive diagnostic tests with variable time delays. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
 
Description A sustained delivery chlorhexidine gel (Barbour/van Duijenvelt/Spencer) 
Organisation Quaid-i-Azam University
Country Pakistan 
Sector Academic/University 
PI Contribution Barbour (PI) - intellectual input, project design and expertise in antimicrobial biomaterials and oral nanoscience.
Collaborator Contribution Expertise from a physical chemist (specialising in soft condensed matter) to help develop a sustained release antimicrobial gel formulation. Expertise from a microbiologist and training of the research assistant undertaking the project in microbiological techniques
Impact Project funded by BristolBridge. New research collaboration: Dr Rabaab Zahra at Quaid-i-Azam University in Pakistan. Follow-on funding via Elizabeth Blackwell Institute/Wellcome Trust Translational Acceleration and Knowledge Transfer (TRACK) award in July 2016 to further the initial work funded by BristolBridge. "A novel, emulsion gel formulation of sustained release chlorhexidine to prevent umbilical cord infection and improve outcomes for neonates in developing countries". Follow-on funding by EPSRC GCRF Institutional Sponsorship "Saving neonates' lives by preventing umbilical cord infection: Cheap and effective spray delivery of sustained efficacy chlorhexidine" Barbour (PI), van Duijneveldt (Co-I) and Spencer (Co-I) (BristolBridge Co-I) Related iCASE BBSRC SWBio DTP studentship that evolved after conversation between Barbour and Barrett (Veterinary Sciences) at the BristolBridge AMR World Cafe in January 2016. "A novel, sustained efficacy, biocide-based treatment for bacterial foot disease in ruminants". Supervisor, David Barrett, Co-supervisor Jim Spencer (BristolBridge Co-I); industry supervisor Michele Barbour; CASE partner. Pertinax Pharma Ltd. This is a multi-disciplinary collaboration involving biomaterials, oral nanoscience, chemistry and microbiology.
Start Year 2015
 
Description A sustained delivery chlorhexidine gel (Barbour/van Duijenvelt/Spencer) 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution Barbour (PI) - intellectual input, project design and expertise in antimicrobial biomaterials and oral nanoscience.
Collaborator Contribution Expertise from a physical chemist (specialising in soft condensed matter) to help develop a sustained release antimicrobial gel formulation. Expertise from a microbiologist and training of the research assistant undertaking the project in microbiological techniques
Impact Project funded by BristolBridge. New research collaboration: Dr Rabaab Zahra at Quaid-i-Azam University in Pakistan. Follow-on funding via Elizabeth Blackwell Institute/Wellcome Trust Translational Acceleration and Knowledge Transfer (TRACK) award in July 2016 to further the initial work funded by BristolBridge. "A novel, emulsion gel formulation of sustained release chlorhexidine to prevent umbilical cord infection and improve outcomes for neonates in developing countries". Follow-on funding by EPSRC GCRF Institutional Sponsorship "Saving neonates' lives by preventing umbilical cord infection: Cheap and effective spray delivery of sustained efficacy chlorhexidine" Barbour (PI), van Duijneveldt (Co-I) and Spencer (Co-I) (BristolBridge Co-I) Related iCASE BBSRC SWBio DTP studentship that evolved after conversation between Barbour and Barrett (Veterinary Sciences) at the BristolBridge AMR World Cafe in January 2016. "A novel, sustained efficacy, biocide-based treatment for bacterial foot disease in ruminants". Supervisor, David Barrett, Co-supervisor Jim Spencer (BristolBridge Co-I); industry supervisor Michele Barbour; CASE partner. Pertinax Pharma Ltd. This is a multi-disciplinary collaboration involving biomaterials, oral nanoscience, chemistry and microbiology.
Start Year 2015
 
Description A systems-based platform for the production of novel antibiotics 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution BristolBridge funded this pump-priming project
Collaborator Contribution Expertise and intellectual input
Impact Outcome: A PhD student is taking this project forward. Multidisciplinary collaboration: Microbiology, chemistry, biochemistry, computer science
Start Year 2016
 
Description Assay Development for Bacterial Phosphoethanolamine Transferases that Confer Resistance to Last Resort Antibiotics 
Organisation University of Bristol
Department School of Chemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution Pump-priming project funded by BristolBridge. Intellectual input by the research team.
Collaborator Contribution Intellectual input and expertise. Access to equipment and facilities.
Impact This is a multi-disciplinary project involving synthetic chemistry and microbiology
Start Year 2017
 
Description Biomimetic antimicrobial surfaces to combat antimicrobial resistant infection (Su/Nobbs/Briscoe/May) 
Organisation University of Bristol
Department School of Oral & Dental Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Su (PI) Intellectual input, project design and expertise in biomaterials engineering.
Collaborator Contribution The collaborators are providing expertise in chemistry and oral microbiology.
Impact Project funded by BristolBridge. Invitation to speak at workshop on Bio-inspired antimicrobial surfaces for medical implants at Sheffield University (EPSRC-funded Sheffield Antimicrobial Resistance Network) 6th April 2016. New research collaboration with University of Southampton (stem cells for nanospikes) Meetings with Renishaw plc to develop a new collaboration on surface nanoengineering of 3D printed titanium scaffolds/devices. MRC Theme 2 Innovation Grant (awarded to Prof. Su in Oct 2015) has taken the BristolBridge funded project further (same Research Associate) A multi-disciplinary collaboration comprising biomaterials engineering, chemistry and oral microbiology .
Start Year 2016
 
Description Biomimetic antimicrobial surfaces to combat antimicrobial resistant infection (Su/Nobbs/Briscoe/May) 
Organisation University of Southampton
Country United Kingdom 
Sector Academic/University 
PI Contribution Su (PI) Intellectual input, project design and expertise in biomaterials engineering.
Collaborator Contribution The collaborators are providing expertise in chemistry and oral microbiology.
Impact Project funded by BristolBridge. Invitation to speak at workshop on Bio-inspired antimicrobial surfaces for medical implants at Sheffield University (EPSRC-funded Sheffield Antimicrobial Resistance Network) 6th April 2016. New research collaboration with University of Southampton (stem cells for nanospikes) Meetings with Renishaw plc to develop a new collaboration on surface nanoengineering of 3D printed titanium scaffolds/devices. MRC Theme 2 Innovation Grant (awarded to Prof. Su in Oct 2015) has taken the BristolBridge funded project further (same Research Associate) A multi-disciplinary collaboration comprising biomaterials engineering, chemistry and oral microbiology .
Start Year 2016
 
Description Developing novel biocompatible and antimicrobial coatings for orthopaedic implants (Tarlton/Scott/Cogan) 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution Tarlton (PI); Intellectual input, design of project, expertise in matrix biology and regenerative medicine
Collaborator Contribution The collaborator in Physics is helping to develop a novel photocatalytic titanium dioxide (TiO2) based antimicrobial surface for use in orthopaedic implants
Impact Project funded by BristolBridge. No outputs or outcomes yet. This is a multi-disciplinary collaboration involving regenerative medicine, matrix biology and physics.
Start Year 2016
 
Description Developing strategies to minimize AMR in territorial wildlife population 
Organisation University of Bristol
Department Faculty of Engineering
Country United Kingdom 
Sector Academic/University 
PI Contribution Project funded by BristolBridge.
Collaborator Contribution Intellectual input and expertise.
Impact This is a multidisciplinary project involving applied mathematics and biology. A paper has been submitted for publication.
Start Year 2017
 
Description Early phase development of a primary care device to detect rapidly antibiotic resistance in common bacteria 
Organisation University of Bristol
Department School of Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution BristolBridge 'Bridging the Gaps between the Engineering and Physical Sciences' funded this pump-priming project
Collaborator Contribution Antognozzi (PI) project design, physics expertise Avison (BristolBridge Co-I and Impact Lead) has contributed his microbiology expertise to this project
Impact Follow on funding via EPSRC Institutional Sponsorship 2016, August 2016 (Validation of a primary care device to rapidly detect antimicrobial drug resistance in common bacteria" Antognozzi (Physics), Avison (Cellular & Molecular Medicine), Baxter (South Gloucestershire & North Somerset Clinical Commissioning Groups and Social & Community Medicine) and Redmond (National Institute for Health Research Collaborations for Leadership in Applied Health Research and Care West [NIHR CLAHRC West] & Social and Community Medicine). University Research Committee Interdisciplinary Research Internship 2016 to Kloucek MSci 2nd year Physics undergraduate. Supervisor Antognozzi, Co-supervisor Avison Follow on funding: Innovation-to-Commercialisation (ICURe) award from the SETsquared Partnership, March 2017 to validate primary care device in the marketplace. Longitude Prize Development Award, August 2017. Innovate UK funding, January 2018. Multidisciplinary collaboration: Physics, microbiology, social science.
Start Year 2016
 
Description Electrostatic capture of bacteria (Schwarzacher/Carreira/Spencer) 
Organisation University of Bristol
Department School of Physics
Country United Kingdom 
Sector Academic/University 
PI Contribution Schwarzacher/Carreira PI's; Intellectual input, planning and designing project
Collaborator Contribution Spencer Co-I; Supervision of microbiological work
Impact Project application to BristolBridge (approved for funding) Multi-disciplinary collaboration involving physics and microbiology
Start Year 2016
 
Description Identifying and Characterising Inhibitors of Essential Enzymes as Routes to New Anti-Tuberculosis Therapies 
Organisation Ubon Ratchathani University
Country Thailand 
Sector Academic/University 
PI Contribution Funded by BristolBridge, Intellectual input and expertise. Training of visiting research staff and access to equipment and facilties.
Collaborator Contribution Intellectual input and expertise.
Impact This is a multi-disciplinary collaboration involving computational chemistry. biochemistry and microbiology. A grant application has been submitted to the MRC.
Start Year 2017
 
Description Investigating AMR gene transfer in the aerosol phase 
Organisation Centre for Ecology & Hydrology (CEH)
Country United Kingdom 
Sector Public 
PI Contribution The research team provided intellectual input, expertise and access to equipment and facilties
Collaborator Contribution The partner provided Intellectual input and expertise.
Impact This collaboration is multi-disciplinary and involves the disciplines of aerosol science/chemistry and microbiology
Start Year 2017
 
Description Mathematical modelling of the impact of novel AMR diagnostics for Neisseria gonorrhoeae 
Organisation University of Bristol
Department School of Clinical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Funded by EPSRC GCRF Institutional Sponsorship award to BristolBridge Turner (BristolBridge Co-I) project design, intellectual input, statistical and economic modelling expertise Homer (BristolBridge Co-), mathematics, data science expertise
Collaborator Contribution Hill (Co-I) Microbiology expertise Christensen (Co-I) economic modelling expertise
Impact Multidisciplinary project: mathematics, data science, computer science, modelling, social medicine
Start Year 2016
 
Description Novel methods for visualising bacteria (GersenAvison) 
Organisation University of Bristol
Department School of Cellular and Molecular Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Gersen (PI); Intellectual input, project design and expertise in imaging
Collaborator Contribution Avison (Co-I); Microbiology expertise and training of postdoctoral research assistant (a physical scientist) in microbiological techniques.
Impact Short project application submitted to BristolBridge (approved for funding) Multidisciplinary collaboration; physics and microbiology
Start Year 2016
 
Description Novel ways of improving antibiotic delivery to promote the direct killing of Neisseria gonorrhoeae 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution BristolBridge funded the project Turner (BristolBridge Co-I) contributed expertise on sexually transmitted infectious diseases and intellectual input to the design of project and potential for impact
Collaborator Contribution Hill (PI) Project design, intellectual input, microbiology expertise Crosby (Co-I) chemistry expertise
Impact Part-funded by EPSRC GCRF Institutional Sponsorship awarded to BristolBridge resulting in project extension EPSRC Bristol Centre for Functional Nanomaterials CDT full-time PhD student researching related aspects of this project. Patent under discussion Multidisciplinary: Microbiology, Chemistry, Physics
Start Year 2016
 
Description Phage based sensitization to fluoroquinolone antibiotics (Avison/Dillingham) 
Organisation University of Bristol
Department School of Cellular and Molecular Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Intellectual input and microbiological expertise
Collaborator Contribution Intellectual input and biochemical expertise.
Impact Funding application made to the BBSRC/EPSRC-funded Bristol Synthetic Biology Research Centre (pending) A multi-disciplinary collaboration involving biochemistry and microbiology
Start Year 2016
 
Description Rapid identification of urinary tract infection bacteria and their antibiotic susceptibility using volatile profile sensing technology 
Organisation University of the West of England
Department Faculty of Health and Applied Science
Country United Kingdom 
Sector Academic/University 
PI Contribution The research team provided microbiological expertise, training of staff and access to facilities.
Collaborator Contribution The partners provided intellectual input and expertise on volatile metabolite profiling.
Impact The collaboration is multi-disciplinary and involves the disciplines of Chemistry and Microbiology
Start Year 2017
 
Description Selcia collaboration (Spencer/Mulholland) 
Organisation Selcia
Country United Kingdom 
Sector Private 
PI Contribution Hosted meetings to build a collaboration. Agreement to look at Selcia material in vitro and in silico at the University of Bristol (pending material transfer agreement MTA)
Collaborator Contribution Selcia to provide materials (once MTA is approved)
Impact Muiti-disciplinary collaboration involving drug discovery, microbiology, chemistry and computer modelling
Start Year 2016
 
Description Selcia collaboration (Spencer/Mulholland) 
Organisation University of Bristol
Department School of Cellular and Molecular Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Hosted meetings to build a collaboration. Agreement to look at Selcia material in vitro and in silico at the University of Bristol (pending material transfer agreement MTA)
Collaborator Contribution Selcia to provide materials (once MTA is approved)
Impact Muiti-disciplinary collaboration involving drug discovery, microbiology, chemistry and computer modelling
Start Year 2016
 
Description Towards a flexible and multi-use databank for veterinary AMR research 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution BristolBridge funded project Homer and Turner (BristolBridge Co-Is) have contributed mathematical and data science expertise, training of staff
Collaborator Contribution Reyher (PI) Project design and management, intellectual input Bullock (Co-I) data science expertise, training of staff
Impact BBSRC Bioinformatics and Biological Resource Fund (BBRF) grant pending (BB/P024491/1). Reyher (PI) Multidisciplinary project: Computer science, data science, engineering maths, veterinary sciences, social science,
Start Year 2016
 
Description Towards devices for detecting antimicrobial resistance in resource-poor settings; on-chip magnetic separation, concentration and detection of bacteria 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution Funded by EPSRC GCRF Insitutional Sponsorship funds awarded to BristolBridge Seddon (BristolBridge Co-I) - project design, intellectual input, physics/diagnostics expertise Spencer (BristolBridge Co-I) - microbiology and diagnostics expertise
Collaborator Contribution Hughes (Co-I) design, engineering and fabrication of devices
Impact New LIMC collaboration with Professor Skorn Mongkolsuk (Chulabhorn Research Institute, Bangkok, Thailand New LIMC collaboration with Dr Cecelia Mbae, Kenya Medical Research Institute, Nairobi Multidisciplinary project involving physics, mechanical engineering and clinical microbiology
Start Year 2016
 
Description cell-instructive surfaces 
Organisation Polytechnic University of Catalonia
Country Spain 
Sector Academic/University 
PI Contribution Nanostructured surfaces: generation and characterisation
Collaborator Contribution Functionalisation of nano-surfaces with cell-binding ligands to improve cell attachment while preventing bacterial growth
Impact A joint publication in Scientific Reports. One more in preparation.
Start Year 2017
 
Title APPARATUS FOR AND METHOD OF PROCESSING BIOLOGICAL SAMPLES 
Description The present invention provides systems, devices, apparatuses and methods for automated bioprocessing. Examples of protocols and bioprocessing procedures suitable for the present invention include but are not limited to: immunoprecipitation, chromatin immunoprecipitation, recombinant protein isolation, nucleic acid separation and isolation, protein labeling, separation and isolation, cell separation and isolation, food safety analysis and automatic bead based separation. In some embodiments, the invention provides automated systems, automated devices, automated cartridges and automated methods of western blot processing. Other embodiments include automated systems, automated devices, automated cartridges and automated methods for separation, preparation and purification of nucleic acids, such as DNA or RNA or fragments thereof, including plasmid DNA, genomic DNA, bacterial DNA, viral DNA and any other DNA, and for automated systems, automated devices, automated cartridges and automated methods for processing, separation and purification of proteins, peptides and the like. 
IP Reference US2018111121 
Protection Patent application published
Year Protection Granted 2018
Licensed Yes
Impact the patent has been instrumental for the incorporation of the spin out company Vitamica Ltd
 
Title METHOD AND APPARATUS FOR BACTERIAL ANALYSIS 
Description An apparatus (10) comprising: a light source (12); to cast light toward a substrate (20) defining a bacteria binding volume to create an evanescent field (22), the bacteria binding volume being within the evanescent field; a detector (32, 34) arranged to receive light from the bacteria binding volume and output data (36, 37); and a processor (38) arranged to determine vibration of bacteria (26) within the bacteria binding volume in three-dimensions from the data. 
IP Reference WO2019025771 
Protection Patent application published
Year Protection Granted 2019
Licensed Yes
Impact The patent has being instrumental for the incorporation of the spin out company Vitamica Ltd.
 
Title METHOD FOR DETECTION OF INTESTINAL, AND BLOOD-BRAIN BARRIER PERMEABILITY AND TESTING MATERIALS THERETO 
Description METHOD FOR DETECTION OF INTESTINAL, AND BLOOD-BRAIN BARRIER PERMEABILITY AND TESTING MATERIALS THERETO Methods, assays, and apparatus are disclosed for testing of antigens associated with intestinal and/or blood-brain barrier permeability. For example, blood, saliva or other bodily fluid can be tested for binding (1) to a bacterial toxin (preferably a lipopolysaccharide), and (2) binding to tissue antigens selected from at least one of (a) a gut-related antigen and (b) a blood brain barrier-related antigen. Analysis of test results can be used to assist in detecting and diagnosing diseases associated with leaky gut syndrome (whether due to paracellular or transcellular pathways, and whether due to bacterial toxins or some other cause) and/or to diseases associated with excessive blood brain barrier permeability, which are contemplated herein to include both neuroinflammation and/or neuroautoimmunity conditions, and especially amyotrophic lateral sclerosis, Parkinsons disease, multiple sclerosis, Alzheimer's, or peripheral neuropathy, and major depression. 
IP Reference AU2016259430 
Protection Patent application published
Year Protection Granted 2016
Licensed Yes
Impact the patent has been instrumental for the incorporation of the spin out company Vitamica Ltd
 
Company Name Vitamica Ltd 
Description Vitamica is developing a novel diagnostic technology to test pathogenic bacteria for susceptibility to antibiotics within one hour. The need for more targeted and appropriate use of existing antibiotics grows daily, and healthcare professionals must have the diagnostic tools to support decisions on which antibiotic to use. Rapid antimicrobial susceptibility testing (AST) of patient samples would inform doctors which antibiotics will be effective and to which the bacteria show resistance. Crucially, the test results would be available in time for the first antibiotics to be prescribed, rather than 48 hours later as is typical for current testing methods. Rapid AST enables the timely prescription of appropriate antibiotics leading to better patient outcomes as patients receive effective antibiotics sooner, and also reducing healthcare costs due to faster recovery times and a lower incidence of complications. Importantly, the prescription of more targeted and appropriate antibiotics enabled by rapid AST also reduces the spread of antimicrobial resistance. Current susceptibility testing methods typically take 36-48 hours because they rely on detecting growth of the organism as a phenotypic signal that the bacteria are alive (or not) after treatment with antibiotics. In order to develop rapid susceptibility testing methods, approaches that do not rely on detecting growth of the organism are needed. Vitamica is developing a rapid AST based on a novel technology that detects tiny fluctuations within the individual bacteria, indicating in a few seconds whether the cells are alive or not. This technology will allow us to test pathogenic bacteria for susceptibility to antibiotics within one hour, transforming the way clinicians make decisions on antibiotic choice for the benefit of patients now and in the future. Rapid AST is based on a recently developed imaging technique - Sub-cellular Fluctuation Imaging (SCFI) - that directly detects nanoscale fluctuations that are present in bacteria when they are alive. These fluctuations are too small to be seen using an optical microscope, but the unique optical set up of SCFI allows us to directly image them in real time. Using this technology Vitamica can detect the effects of antibiotics as soon as they have acted on the bacteria - leading to a very rapid susceptibility test. 
Year Established 2018 
Impact One full time equivalent scientific post
Website http://www.bristol.ac.uk/amr/research/development-of-novel-resistance-diagnostics/rapid-amr-detector...
 
Company Name VITAMICA LIMITED 
Description Vitamica was established in early 2018 as a spin-out company from the University of Bristol. Taking optical technology from the School of Physics, the new company is beginning its journey towards commercialisation of a rapid and novel diagnostic method that has high potential for use in antimicrobial susceptibility testing. With a growing IP portfolio and an active approach to identifying opportunities in healthcare, veterinary and pharma sectors, Vitamica fully intends to make its mark as another successful company to originate from the University of Bristol. 
Year Established 2018 
Impact The company is working on the development of a rapid AMR diagnostic device that could be used in healthcare, veterinary and pharma sectors.
Website https://www.vitamica.co.uk
 
Description (Bruce and Reyher) Food Industry Initiative on Antimicrobials R&D group, London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Attending meeting
Year(s) Of Engagement Activity 2019
 
Description (Reyher and Buller) Fieldwork, presentations and meetings in Bangkok, Thailand 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Presentation of DIAL research and engagement with academic and research community through MRC funded OH-DART project
Year(s) Of Engagement Activity 2018
 
Description (Reyher) DARC, Stonleigh 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Attendance at Meeting as member of DIAL project (and other projects)
Year(s) Of Engagement Activity 2018
 
Description (Reyher) Food Industry Initiative on Antimicrobials R&D group, London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation of DIAL project and other engaged AMR research
Year(s) Of Engagement Activity 2018
 
Description (Reyher) RSM AMR Meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Attendance and presentation of DIAL project and related research
Year(s) Of Engagement Activity 2018
 
Description (Reyher) RUMA, Stoneleigh 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Attended meeting as member of DIAL team (and other research teams)
Year(s) Of Engagement Activity 2018
 
Description (Reyher) SEFARI AMR conference, Glasgow 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Presentation as a member of DIAL Research team (and other teams)
Year(s) Of Engagement Activity 2018
 
Description (Reyher) UK AMR Strategy Stakeholder Forum, Surrey 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Attended as member of Forum and as member of DIAL research team (and other research teams)
Year(s) Of Engagement Activity 2018
 
Description (Reyher) UK-Israel AMR workshop, Birmingham 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attended meeting as member of DIAL research team (and others)
Year(s) Of Engagement Activity 2018
 
Description AMR talk at Monkton Coombe School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Matthew Avison visited Monkton Coombe School to give a talk on AMR entitled 'Superbugs: Is Resistance Futile?' Pupils came up with imaginative questions and the school reported increased interest in the subject within the school population.
Year(s) Of Engagement Activity 2017
 
Description Access to Bristol schools event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact About 50 motivated college students came to Bristol from the region to get a taster for microbiology. Matthew gave a talked entitled Superbugs: Is Resistance Futile? Some students reported it had given them an interest in going into the field of microbiology.
Year(s) Of Engagement Activity 2016
 
Description American and Canadian High School visit to UoB 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Pupils from American and Canadian High Schools attended a day at UoB. Matthew gave a talk entitled Superbugs: Is Resistance Futile? Pupils had many challenging questions and some said afterwards that they had no idea you could select for an antibiotic resistance gene by using another antimicrobial like ammonium compounds.
Year(s) Of Engagement Activity 2016
 
Description Antibiotics Unearthed, A school visit and workshop exploring the potential for new soil microbes as producers of antibiotic substances. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact a workshop sponsored by the Microbiology Society, culturing soil bacteria and investigating them to see if any were making antibiotic substances. This event was aimed at Y13 students as St Marys School, Calne, Wilts, taking A-level Biology. It demonstrated good microbiological practice, techniques such as serial dilution, bioassays and the like. The activity is ongoing and will likely be repeated. A presentation was included about the challenges of how to combat AMR, and led top lively debate, particularly from some student s interested in pursuing careers in medicine.
Year(s) Of Engagement Activity 2017
 
Description BBC Radio Bristol Interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Matthew Avison had 30 minute interview with Steve Yabsley on BBC Radio Bristol about AMR research project. Stimulated discussion via phone in comment from members of the public
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/programmes/p04dxl57
 
Description BridgeBridge AMR Schools Outreach Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact 160 students from the region came to a cross-faculty schools conference recently for post-16 biology and chemistry students held within the School of Chemistry to examine why AMR is an escalating global threat. Matthew opened the conference and gave a talk entitled 'Superbugs: Is Resistance Futile?'
Year(s) Of Engagement Activity 2016
URL http://www.bristol.ac.uk/news/2016/december/schools-conference-amr.html
 
Description Bristol Grammar School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Matthew Avison gave a talk entitled 'Superbugs: Is Resistance Futile?' to Bristol Grammar Senior School pupils. Pupils gave feedback such as "I used to think antibiotics were normal when you have a bad cold but I now know it's more likely to be a virus so will only use them if I have to."
Year(s) Of Engagement Activity 2017
 
Description Bristol Health Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Matthew gave a talk to over 100 members of the general public during a session called Bristol Love Bugs. His talk was about the Impact of Antibiotic Use on the Microbiome.
Year(s) Of Engagement Activity 2016
URL http://www.bristolhealthpartners.org.uk/events/view/2016/10/22/bristol-loves-bugs-the-human-microbio...
 
Description Bristol Post newspaper article (Dr Matthew Avison) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Dr Matthew Avison was interviewed by the Bristol Post on his antibiotic resistance research and an article published (print and on line version)
Year(s) Of Engagement Activity 2016
URL http://www.bristolpost.co.uk/Bristol-professor-s-UK-trial-antibiotic/story-28687151-detail/story.htm...
 
Description BristolBridge Press release 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Press release/news story ("BristolBridge: a multidisciplinary approach to tackling antimicrobial resistance") on the BristolBridge grant award. This raised the profile of BristolBridge which helped to engage interdisciplinary research interest across the campus, research institutes and local NHS Trusts.
Year(s) Of Engagement Activity 2015
URL http://www.bristol.ac.uk/news/2015/april/bristolbridge.html
 
Description BristolBridge Schools Conference on Antibiotics and Antibiotic Resistance Science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact 160 students and 15 teachers from nine schools across the south west attended lectures, hands-on displays and discovery-led demonstrations.

The students were invited to comment about what they had learned in the lectures and whether it had changed their attitude to antibiotics and AMR. The views received included: "I realise now how much we need/should reduce the use of antibiotics";"I never realised how close and urgent this whole issue is"; "Antibiotics need to be used less in farming".

After hearing about, and exploring the ways in which the physical sciences, engineering and mathematics research at the University of Bristol is helping to tackle the global problem of AMR, it was very encouraging that one student commented "Not as hopeless as I thought. Excited by the new technology that can help!"

The University's press release can also be read here: http://www.bristol.ac.uk/news/2016/december/schools-conference-amr.html
Year(s) Of Engagement Activity 2016
URL http://www.bristol.ac.uk/bristolbridge/news/schools-conference-on-antibiotics-and-antibiotic-resista...
 
Description Cheltenham Ladies' College - talk on AMR 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Matthew Avison gave a talk called "Superbugs: Is Resistance Futile?" to 90 students at Cheltenham Ladies College. This talk provoked questions and debate about AMR and Matthew was also approached by students afterwards with further queries.
Year(s) Of Engagement Activity 2017
 
Description European Antibiotic Awareness Day Event, Veterinary School, Bristol (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Talk on 'What you really need to know about antibiotic prescribing' to professional practitioners, policy makers and undergraduate and postgraduate students in clinical and veterinary medicine as part of Antibiotic Awareness Week. Feedback received that people's views changed on antibiotic prescribing as a result.
Year(s) Of Engagement Activity 2015
URL http://www.bristol.ac.uk/infection-immunity/seminars/2015/world-antimicrobial-awareness-week.html
 
Description Filton College 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Matthew gave a talk entitled 'Superbugs: Is Resistance Futile?'. Response was good and some students asked about careers in microbiology.
Year(s) Of Engagement Activity 2016
 
Description Gave talk at Sidmouth Science Festival 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact About 100 members of the general public attended my talk, "Superbugs: Is Resistance Futile?". Feedback included surprise at "cross resistance caused by biocides," that "antibiotics occur in soils" and "how long E.coli can live in the body". The audience reported changed views such as "I used to think basically that the more antibiotics you used, the healthier and better prepared you were. Now I'll be more cautious."
Year(s) Of Engagement Activity 2016
 
Description Highlight notice on Diamond Light Source website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I worked with the Diamond Light Source press office to coordinate a press release related to our study of MCR-1 mediated resistance and to produce a highlight notice to feature on their website
Year(s) Of Engagement Activity 2017
URL http://www.diamond.ac.uk/Science/Research/Highlights/2017/MX-resistance.html
 
Description Invited talk in a workshop by The Sheffield Antimicrobial Resistance Network (SHAMROK). 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited talk in a workshop by The Sheffield Antimicrobial Resistance Network (SHAMROK).
Year(s) Of Engagement Activity 2016
 
Description Invited talk in a workshop organised by the Institute for Molecular Science and Engineering (IMSE) at Imperial College London 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Audience from a number of different department at Imperial, including Materials, Medicine, Mathematics, Life Sciences, Chemical Engineering, Chemistry, and the Imperial NHS Trust attended.
Year(s) Of Engagement Activity 2017
 
Description Invited talk in an international conference of Advanced Materials organised by Newcastle University 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact International audience mostly from Europe attended this conference
Year(s) Of Engagement Activity 2016
 
Description Magazine article (Nonesuch biannual magazine) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact BristolBridge lead PI (Professor Adrian Mulholland) and Co-I's (Dr Matthew Avison and Dr Michele Barbour) were interviewed for an article written by Catherine Treble on "Buying time: the fight against antibiotic resistance". The magazine is sent to University alumni and supporters around the world and resulted in shared information from an Italian resident about the research being undertaken by a team member.
Year(s) Of Engagement Activity 2015
URL http://bristol.ac.uk/alumni/news/2015/antibiotic-resistance.html
 
Description Presentation to Chief Scientific Advisor Chris Whitty 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Professor Chris Whitty, Chief Scientific Advisor for the Department of Health visited University of Bristol to hear of our work and latest findings. Matthew Avison and Ashley Bryce gave presentations, and Professor Whitty sent feedback later in the week saying he'd taken our findings on board and had found the visit useful.
Year(s) Of Engagement Activity 2017
 
Description Public Open Day at the University of Bristol (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Members of the general public attended a University of Bristol open day and heard a public engagement talk on 'Antibiotic resistance: We are all in it together'. Feedback since has shown that people changed the way they thought about antibiotics and the problem of antibiotic resistance.
Year(s) Of Engagement Activity 2015
 
Description Research Talk: Chulabhorn Research Institute, Thailand 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk to staff and students of Chulabhorn Research Institute, Thailand as part of my collaboration/network building activities visiting Thailand in January 2017.
Year(s) Of Engagement Activity 2017
 
Description School visit to Clifton College, Bristol (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Outreach presentation to pupils and teachers on antibiotic resistance "We are all in it together"
Year(s) Of Engagement Activity 2015
 
Description School visit to King Edward VI High School, Birmingham (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Outreach presentation to pupils and teachers on antibiotic resistance "We are all in it together"
Year(s) Of Engagement Activity 2015
 
Description School visit to St. Joseph's International Institution, Singapore (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Talk to international school pupils on antibiotic resistance on "We're all in this together".
Year(s) Of Engagement Activity 2016
 
Description School visit to Tanglin Trust School, Singapore (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Presentation to approximately 100 international school pupils on antibiotic resistance on "We're all in this together"
Year(s) Of Engagement Activity 2016
 
Description School visit to Taylors College, Kuala Lumpur, Malaysia (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Talk to up to 100 international school pupils on antibiotic resistance on "We're all in this together".
Year(s) Of Engagement Activity 2016
 
Description School visit to United World College, Dover Campus, Singapore (Dr Matthew Avison) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Talk to international school pupils and teachers on antibiotic resistance "We're all in it together"
Year(s) Of Engagement Activity 2016
 
Description Sheldon School - AMR talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Matthew Avison gave a talk entitled 'Superbugs: Is Resistance Futile?' to 80 secondary school pupils. Students asked questions about antibiotics and resistant bacteria and the school sent good feedback about the talk.
Year(s) Of Engagement Activity 2017
 
Description St Lawrence School talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Matthew gave a talk entitled 'Superbugs: Is Resistance Futile?' There were many interesting questions from pupils and teachers reported the kids felt they had learnt a lot.
Year(s) Of Engagement Activity 2016
 
Description Surgeon X Comic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Matthew Avison was asked to advise and contribute to the Surgeon X comic (Wellcome Trust Funded), which imagines a world beyond the antibiotic age, which was published via Wowbagger Productions. The comic is sold in print form and via an app. There has been significant international impact.
Year(s) Of Engagement Activity 2016
URL http://surgeonx.co.uk/our-team/
 
Description Swindon College AMR talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Matthew Avison gave a talk entitled 'Superbugs: Is Resistance Futile?' This was to inspire a new generation of microbiologists and raise awareness of AMR. Students fed back change in perceptions and increased interest in microbiology.
Year(s) Of Engagement Activity 2017
 
Description Symposium talk: do beta lactams have a future (Oxford University) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited talk at a symposium (Nov 2nd 2016) organised to mark the award of an American Chemical Society Citation for Chemical Breakthrough to the University of Oxford for the development of penicillin.
Year(s) Of Engagement Activity 2016
 
Description Talk at Warwick SWON Alliance Industry day. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Talk at the SWAN industry day to industry and academic representatives. Significant interest generated in methods for determining antibiotic action via proteomics
Year(s) Of Engagement Activity 2016
URL https://www2.warwick.ac.uk/fac/cross_fac/wamic/swon/industry/
 
Description Telephone interview: The Atlantic magazine 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I gave a telephone interview to a journalist from this publication, which resulted in a published article highlighting our research.
Year(s) Of Engagement Activity 2017
URL https://www.theatlantic.com/health/archive/2017/01/colistin-resistance-spread/512705/
 
Description Winterbourne International Academy - school talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Parents and pupils of Winterbourne Academy attended their Festival of Science lectures, one of which was a talk by Matthew entitled "No more drugs for superbugs"
Year(s) Of Engagement Activity 2016
URL http://www.myyate.co.uk/yate/e/18972/festival-of-science-lectures
 
Description invited talk, Naresuan University, Phitsanulok, Thailand 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented our work on MCR-1 to staff and students of Naresuan University as part of my visit to Thailand to build collaborations and research networks.
Year(s) Of Engagement Activity 2017
 
Description presented display at National Fungus Day event at FeedBristol, Sept 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact National Fungus Day is facilitated by the Bristish Mycological Society. We had a locally organized day as part of this national event. It was based at Feed Bristol which is an independent farming/gardening cooperative and was open to the public. It was advertised via a number of supporting organisations including various local conservation groups such as Avon Wildlife Trust. I presented display material relating to approaches for the discovery of useful antibiotics and other pharmaceuticals from fungi.
The event was attended by more than 300 visitors of all ages, and I was kept busy all day with conversations about the beneficial uses of fungi and why their conservation might be important as it allows their exploitation in the future for useful products.
It also severed as a useful platform to talk about antibiotics and the ongoing concerns about their use and many useful conversations were had discussing various aspect of this, including dealing with some major misunderstandings about their use in farming..
Year(s) Of Engagement Activity 2018
URL https://www.avonwildlifetrust.org.uk/events/2018/10/06/uk-fungus-day?instance=0