2018 Babraham Institute Annual Research Report Facilities 442-53 Facilities 42 MT101112131415161718192021226789XY X=Chr3:102.3 Mbp-Chr6:10.1 Mbp Y=Chr3:104.3 Mbp-Chr6:8.2 Mbp 5 4 Bioinformatics Biological Chemistry Biological Support Unit Flow Cytometry Gene Targeting 3 12312 4 5 678910111213141516171819202122MTXY Imaging Lipidomics Mass Spectrometry Sequencing 43 Facilities Bioinformatics Research increasingly includes the creation of large amounts of data and the use of computers to manage and process that information. The Bioinformatics facility provides Simon Andrews infrastructure to support the analysis Facility head of biological data. We provide guidance and training in data analysis, statistics Facility members and data management to both internal Biological statistician: and external groups. We also develop Anne Segonds-Pichon novel tools, and administer the Institute’s computing cluster. Bioinformaticians: Laura Biggins Capabilities Christel Krueger n An 800 node compute cluster with an Felix Krueger extensive collection of bioinformatics Steven Wingett software and pipelines. Training developer: n Jo Montgomery A range of custom software often focused on next generation sequencing, data visualisation and quality control. n Experience in the processing, This year, we expanded our toolsets to management and analysis of large support technologies such as NMT-Seq biological data sets. and single-cell RNA-Seq, BS-Seq, and RNA– interaction data. n An extensive modular portfolio of bioinformatics training courses targeted at biologists. Progress in 2018 Selected Impact Activities In 2018 the Bioinformatics group has n We established a new set of bioinformaticians from around greatly expanded its training programme. bioinformatics training bootcamps, Cambridge and the surrounding We have established a set of larger training covering next generation sequencing, areas. bootcamps running over several days R programming and Linux systems n Two members of the group undertook that provide an in-depth introduction administration. to a number of relevant topics covering an extended trip to the Hunter n sequence analysis, programming and We organised the Second Cambridge Medical Research Institute, Australia, technical skills. As well as running these Bioinformatics Hackathon at the to run a series of bioinformatics on site at the Babraham Research Campus, Centre for Computing History, and statistics training courses and we have also run training courses for bringing together over 50 establish a longer term relationship academic and commercial groups in the between our institutes. UK, Germany, Spain and Australia. Publications www.bioinformatics.babraham.ac.uk @babraham_bioinf n Clark, S.J. et al. (2018) scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat. Commun. 9(1):781 n Chovanec, P. et al. (2018). Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq. Nat. Protoc. 13(6):1232-1252 n Wingett, S.W. et al. (2018) FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 7:1338 44 Biological Chemistry The Biological Chemistry group provides investigating the chemical changes n Development of new reagents and support for scientists working at the which occur in connective tissues as analytical methods. interface between chemistry and we age. n Help and advice on any aspect of the biology. We bring an understanding of Capabilities application of chemistry/biochemistry to chemistry and its application to solving Jonathan Clark n Chemical synthesis of standards and the exploration of biological problems. biological problems along with the Facility head reagents which are not commercially capability to implement our suggestions Progress in 2018 available. using chemical and analytical tools. Facility members During 2018 we have supported groups n Analysis of biological molecules by mass throughout the Institute on a wide range In addition to our collaborations with Postdoctoral research spectroscopy. of varied projects. These have ranged the Institute’s research groups we are scientists: from synthetic chemistry projects to make Izabella Niewczas compounds which are not commercially Mel Stammers available through to developing new analytical methods to analyse lipids in cell extracts. In addition to these activities we have also continued to run routine lipid analysis for a number of groups, both within the Institute and externally. Separately in the connective tissue project, we have shown for the first time that the chemistry of collagen dynamically changes in response to stretching. In this work we have been able to describe the changes that occur to this chemistry with age and provide an explanation for the changes in the physical properties of tendons observed in ageing and in diabetes. Selected Impact Activities n Through 2018 we have run many commercial PIP3 analysis samples for a number of pharmaceutical companies studying the action of PI 3-kinase inhibitors in a clinical setting. n We have provided lipid analysis for a number of external academic groups throughout 2018. Publications www.babraham.ac.uk/science-services/biological-chemistry n Stark, A. K. et al. (2018) PI3Kδ hyper-activation promotes development of B cells that exacerbate Streptococcus pneumoniae infection in an antibody-independent manner. Nat. Commun. 9: 1-16 n Riento, K. et al. (2018) Flotillin proteins recruit sphingosine to membranes and maintain cellular sphingosine-1-phosphate levels. PLoS One 13: 1-18 n Chow, W. Y. et al. (2018) Essential but sparse collagen hydroxylysyl post-translational modifications detected by DNP NMR. Chem. Commun. 54: 12570-12573 45 Facilities Tim Pearce Facility head Biological Support Unit Facility members: 2 Deputy Facility Selected Impact Activities heads n A team of animal technicians and 7 Managers managers attended a LifeLab event held in Peterborough in 7 Supervisors September to promote careers in 3 Deputy Supervisors animal technology and engage 30 Experienced Animal members of the public in line with Technicians our commitment to the Concordat 4 Trainee/Apprentice on Openness on Animals in Animal Technicians Research. 3 Support Service n Facility tours and visits: All Technicians campus staff are invited to take 1 Administrator a virtual tour of the Institute’s animal facility to find out how our facility operates and how The use of animals in research continues researchers. We have a commitment to animals are used in our research. to be key in helping to understand uphold the highest standards of animal The facility ran three tours for biology and disease. The Biological welfare in all aspects of our work. campus staff in 2018. In addition, Support Unit provides state-of-the-art n Our Central Services unit utilises we continued to host visits from housing and care for pathogen-free robotic cage-washing technology and industry representatives, with rodents used in both academic and automated sterilisation processes to respect to animal facility design private company research programmes. provide equipment and consumables to for new builds and refurbishments, Our team of professionally qualified the bio-science units. and to share technical expertise animal technicians provide expert and guidance for their projects. technical support to researchers by Progress in 2018 undertaking regulated procedures, n In 2018, the BSU successfully formed n The 2018 KEC prize (and also the maintaining the animal health barrier a collaboration and partnership with Datesand group’s Janet Wood and undertaking animal husbandry. Agenda Resource Management creating Innovation Award) was awarded to a BSU Manager recognising their an ongoing recruitment initiative for Capabilities invention and development of apprentice animal technicians, with the n The BSU is made up of four bio-science an innovative animal enrichment BSU fast becoming acknowledged as units, each performing a unique role device. in the provision of flexible services to a centre-of-excellence for foundation meet the dynamic requirements of training and beyond. biological research. Our team of highly n The BSU continues to provide rentable trained animal technicians and service space and technical support to technicians perform daily animal commercial companies, with a 12% husbandry duties and provide essential increase in income from this venture services to the facility. compared to 2017. Throughout the year n Our animal technicians hold Home the facility has continued to draw a high Office Personal Licences enabling level of interest from new companies us to provide technical support for wanting to utilise the facility’s services. www.babraham.ac.uk/science-services/biological-support-unit 46 Flow Cytometry Flow cytometry is a powerful Capabilities Progress in 2018 technology allowing cells to be n State-of-the-art analysers: BD In 2018, the facility expanded with the identified, counted, analysed and LSRFortessa and Propel Lab YETI acquision of a new, high-end BD AriaFusion sorted on the basis of specific analysers allowing up to 30 parameters sorter to strengthen our cell sorting to be simultaneously analysed. capabilities. The facility also welcomed Rachael Walker physical or chemical features, two new members of staff to support the Facility head including using fluorescently labelled n Image cytometry: The facility houses sorting service. antibodies. The Flow Cytometry a Merck Millipore Imagestream MkII facility provides a world-class service allowing