Centre for Synthetic Biology and Biotechnology
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Meet Our Team
Mark Tangney, Director (PhD, MBA, Univeristy College Cork). Mark is the Director of the Synbiocentre and is also a Principal Investigator within the Cork Cancer Research Centre where he head a research team investigating cancer therapies and diagnostics. Interests include Synthetic Biology; development of microbes as cancer therapeutics; associations between bacteria and cancer; and entrepreneurship. Mark has previously worked at various international institutions (Los Angeles, Boston, Copenhagen) and published extensively in the fields of cancer and molecular biology. Mark also serves as Vice Secretary General of the International Society for Cell and Gene Therapy of Cancer (ISCGT); council member of the Irish Association for Cancer Research (IACR); scientific committee member of the European Society for Gene & Cell Therapy (ESGCT),  Vice-President of the Irish Society for Gene and Cell Therapy (ISGCT), and member of the editorial board of several international journals (Scientific Reports; Human Gene Therapy, Current Gene Therapy, Molecular Therapy - Oncolytics, Bioengineered, Biomarkers in Cancer). Tommie McCarthy, Deputy Director (PhD, Cancer Research UK / UCL, University of London). Tommie is a Deputy Director of the Synbiocentre and is also a Professor in Biochemistry in the School of Biochemistry and Cell Biology. Tommie’s main research expertise and interests lie in the broad human molecular genetics area and in the development and application of DNA repair enzyme based DNA analysis technologies. Tommie has extensive knowledge in innovation and experience in commercialisation. His fundamental and applied research on DNA repair enzymes led to development of a novel platform for detection of mutations and polymorphisms in DNA including several patents in the area. Tommie has extensive experience in leadership and strategic planning and served as Head of Department for several years. Tommie also has a long record in mentoring and training of early stage researchers and students, programme development and project management. Tommie is currently the Director of the Masters in Biotechnology programme.  John Morrissey Deputy Director (PhD, EMBL, Heidelberg). John is a Deputy Director of the Synbiocentre and is also a Senior Lecturer in the School of Microbiology.  The major focus of John’s research is in the application of yeasts in food and industrial biotechnology. His work ranges from improving fundamental understanding of metabolism, gene regulation and stress tolerance to selecting and engineering strains for specific biotechnological applications. His current work employs both systems biology and synthetic biology approaches to facilitate design and construct strains for use in industrial biotechnology. John is currently a member of the editorial board of FEMS Yeast Research, represents Ireland on the International Commission for Yeasts (ICY), is a Board member of the Microbial Physiology Section of the European Federation of Biotechnology, and is chair (2016-2017) of the Eukaryotic Division of the Microbiology Society. John is a Principal Investigator and Co-ordinator of CHASSY (2016-2020) - a multipartner Horizon 2020 European project funded. The aim of CHASSY is to deliver a suite of yeast strains that can serve as versatile platforms for the production of high value oleochemicals and aromatic molecules. John Atkins (PhD, Trinity College Dublin). John is a Research Professor at University College Cork and a member of both the Biochemistry and Microbiology. John’s research investigates codes within the genetic code with a focus on signals buried within the coding sequence of mRNAs that stimulate non-standard decoding events in translation. These events include a local redefinition of codon meaning, a shift of reading register or the bypassing of a block of nucleotides present in the mature mRNA. John’s research group also investigate the potential of manipulating recoding and related aspects of protein synthesis for clinical and veterinary purposes and have an interest in exploiting knowledge gained from recoding and related studies for the amelioration of genetic disease and optimisation of protein synthesis under different conditions. John is an Honorary Professor in the Deprtment of Genetics, Trinity College, Dublin, and a member of EMBO, the Royal Irish Academy and the RNA Society. Pasha (Pavel Baranov) (PhD, Moscow State University). Pavel Baranov (Павел Баранов) aka “Pasha” (Паша), is a Lecturer in the School of Biochemistry and Cell Biology and Director of The Laboratory of Post-Transcriptional Control and BioInformatics (LAPTI). The main theme of Pasha’s research is the understanding of how genetic information is decoded from DNA into RNA and proteins with a main focus on "non-standard" decoding events, translational recoding and RNA editing.  LAPTI also develops algorithms and computer programs for identification, analysis and annotation of those genes that utilize recoding. To understand how recoding works, LAPTI researchers compare sequences of these genes and disseminate the sequence features associated with recoding and test these associations experimentally. LAPTI also maintains the Recode database, a public Internet resource dedicated to the genes in which recoding events occur. David Clarke (PhD, Dublin City University). David is a Lecturer in Microbiology at University College Cork. David’s research is aimed at understanding the molecular mechanisms and genes that underpin bacteria-host interactions using a variety of different model systems and how metabolism influences such interactions. This research makes extensive use of the Gram negative bacterium Photorhabdus and also focuses on adherent and invasive E. coli (AIEC) which have been implicated in Crohn’s Disease. Work in this area is ultimately targeted at identifying potential drug targets for novel IBD therapies. A related aspect of David’s research focuses on bioprospecting and biomining in the human gut microbiome for novel functions and bioactive molecules. David is currently programme Director of the BSc in Biotecnology. Eamon Curtin (BEng, Univeristy of Limerick; MBA University College Cork). Eamon is the Director of the IGNITE Graduate Business Innovation Programme at University College Cork. Eamon has worked with early stage and start-up companies as a consultant, mentor and trainer since 2001. In 2003, he founded HJM Business Development to provide business development consultancy and training services to the SME sector. In that time, he has worked extensively on training and development programmes for start-up and early stage businesses. Eamon developed his engineering and management skills with a number of US multinational companies. He spent 5 years in Research and Development at Digital Equipment (Ireland) Ltd. in Clonmel and then joined Burle Industries Ltd. where he was initially based in Cork before taking a long-term assignment in Lancaster, Pennsylvania, USA. He joined MOOG Ltd. in 1992 where he spent 10 years in a number of management roles including long-term assignments in Copenhagen, Denmark and Milan, Italy. Alan Dobson (PhD, National University of Ireland, Galway; DSc, National University of Ireland). Alan is Professor of Environmental Microbiology in the School of Microbiology at University College Cork. Alan was Director of the Environmental Research Institute at UCC from 2006 to 2014. The Institute is one of Ireland’s leading research centres in the areas of Marine, Environmental and Energy research. Alan has served on a several scientific boards and advisory committees for the European Union, and various other funding agencies. Alan’s research programme is focused on the study of microorganisms in both natural or artificial environments, and their potential biotechnological exploitation. The overall goal is the identification of novel bioactive compounds with potential biopharmaceutical applications and enzymes with novel bioprocessing applications. He is a Board member of the International Marine Biotechnology Association, a Fellow of the Royal Society of Biology, UK (FRSB), a member of the Royal Irish Academy MRIA and is a member of the Board of the Marine Institute. Ruslan Dmitriev (PhD, Russian Academy of Sciences, Moscow). Ruslan is SFI Investigator Research Fellow in the School of Biochemistry and Cell Biology at University College Cork. Ruslan’s research is at the interface of biosensor research, multi-parametric quantitative FLIM microscopy and cancer and stem cell-based tissue engineering and is focused on three related areas namely a) measurement and roles of localized O2 gradients in biological systems; hypoxia and cell metabolism in cancer and neuronal cells, O2 and related gradients in 3D tissue models - multicellular aggregates, spheroids, organ explants, b) design of new chemical and biosensor constructs, cell-penetrating O2 and phosphorescent porphyrin probes; new probe, methods and application development; time-resolved fluorescence, live cell imaging and c) function of membrane ion-transporting (Ca-ATPases, X,K-ATPases, H-transporting transhydrogenase NNT) and nuclear proteins including components of MYST1 histone acetylase complex. Eoin Fleming (PhD, University of Aberdeen). Eoin is a Lecturer in Biochemistry and Pharmacy at University College Cork. Research in Eoin’s laboratory is focussed on the expression, function and degradation of ER associated proteins. Our published findings relate to two proteins in particular, the histidine decarboxylase (HDC) enzyme that catalyzes the formation of histamine, and HFE, which is involved in regulating cellular iron metabolism. Mutations in HFE are responsible for the most common inherited disease in Ireland, hereditary haemachromatosis. The Fleming laboratory are particularly interested in characterising the manner in which these two proteins are degraded with the aim of providing new insights into how they are regulated physiologically and how they can potentially be regulated pharmacologically. Cormac Gahan (PhD, University College Cork). Cormac is a Senior Lecturer in Microbiolgy and Pharmacy at University College Cork.  Cormac’s research is dedicated to understanding the molecular interactions between bacteria and the host in the gastrointestinal tract. Cormac led the Infectious Disease programme with Prof. Colin Hill within the Alimentary Pharmabiotic Centre (http://apc.ucc.ie ) from 2003-2013 and now leads the Bile Research Group within the APC Microbiome Institute with Dr. Susan Joyce. His research interests focus upon host-microbe signalling in the gut mediated via microbial bile acid metabolism. Cormac also has a long history of research work on the foodborne pathogen Listeria monocytogenes resulting in key findings in the area. Recent work from the Gahan laboratory has also examined the use of live L. monocytogenes and L. lactis vectors as gene and protein delivery platforms for novel vaccination and therapeutic approaches. Paul Galvin (PhD, University College Cork). Paul is Head of the ICT for Health Strategic Programmes and Head of the Life Sciences Interface Group at the Tyndall National Institute (www.tyndall.ie). Paul’s research interests are in the nanobiotechnology and nanomedicine area and Paul has a strong track record of multidisciplinary research, leveraging nano, photonic and ICT enabled platforms to provide novel solutions for healthcare applications. Paul is a funded investigator in the SFI Insight Centre for Big Data Analytics. He is currently Interim Chair of the Medical Devices Working Group for the European Technology Platform for Nanomedicine and leader of the Working Group on Health Monitoring Sensors within the European Sensor Systems Cluster. He is also a member of the ESTHER (Emerging and Strategic Technologies for HEalthcaRe) Task Force and is a member of the Research Board for DOCTRID. Paddy Harrison (PhD, University of Glasgow). Paddy is a Senior Lecturer in Physiology at University College Cork. The research focus of the Harrison Lab is the development of gene editing to repair disease-causing mutations in the human genome. Paddy’s earlier work pioneered the use of ZFNs and Cas9 to correct the most common Cystic Fibrosis mutation, F508del, by homology- directed repair (HDR) in cell culture. The current focus is the use of CRISPR Cas9 and Cpf1 gene editing as research tools and potential therapeutic agents for genetic diseases including Cystic Fibrosis, Cystinosis, Epidermylosis Bullosa and Atopic Dermatitis. Paddy is a principal investigator in the CF Trust’s Gene Editing Strategic Research Centre (London/Cork), with additional active collaborations in Paris, Lisbon, Auckland and Boston. Paddy is also Associate Editor (Europe) for Gene Therapy. Gary Loughran (D.Phil, University of Oxford). Gary is a Research Fellow in the School of Biochemistry and Cell Biology at University College Cork. Gary’s is the Senior Fellow in Atkins Recoding lab where he works with John Atkins on several aspects of protein synthesis including the control of start codon selection in eukaryotes, overlapping genes in cardioviruses and screening for antivirals against Foot and Mouth disease virus by targeting the unusual virus-specific translation event termed StopGo or Stop Carry-on. Gary and John have an interest in exploiting knowledge gained from recoding and related studies for the amelioration of genetic disease and optimisation of protein synthesis under different conditions. Susan Joyce (PhD, National University of Ireland, Maynooth). Susan is a Lecturer in Biochemistry and Cell Biology at University College Cork and a principal Investigator in the APC Microbiome Institute in the Bile Research Group.Susan’s research focuses on microbial bile acid modification systems and the resulting impact on host signaling to influence host health and disease status. The microbe generated bile acid complexity can influence host processes (either locally or systemically) by interaction with cellular receptors including FXR, TGR5, VDR, LXR, PPAR and SIP2- to impact on host metabolic processes such as circadian rhythm, lipid metabolism, energy metabolism, immune and intestinal homeostasis. Susan’s group characterise bile salt and bile acid altering enzymes, their impact/s on the gut microbiota, their effects on host signaling and how these may be utilized to intervene in the disease state. John MacSharry (PhD, University College Cork). John is a Lecturer in Molecular Microbiology and Assistant director of the GEM programme with the School of Medicine in Microbiology at University College Cork and a principal Investigator in the APC Microbiome Institute. John’s main research interest is in the role mucosal immune sampling plays in systemic immune processes, with particular focus on the areas of host commensal/pathogen interactions. The focus of John’s resaerch is in the interactions of the microbes with human host and the engagement with the immune system with particular interest in the interactions of commensal and pathogenic microbes with the mucosal immune system of both the gut and lung. Justin McCarthy (PhD, University College Cork). Justin is a Senior Lecturer, Associate Dean of Graduate Studies and Science Foundation Ireland Investigator in the School of Biochemistry & Cell Biology at University College Cork. Justin’s research is aimed at  delineating the physiological importance of the presenilin proteins in neurodegeneration. His laboratory focuses on the gamma- secretase protease and its physiological role in growth factor and innate immune signalling, and involvement in the pathogenesis of neurodegenerative disease and cancer. A more precise understanding of the regulation of presenilin functions and their contribution to disease is of major interest, not only for biologists seeking an understanding of fundamental biological processes, but also with potential long-term significance for the development of novel disease therapeutics and human healthcare. Tom Moore (PhD, University of London). Tom is a Senior Lecturer in the School of Biochemistry & Cell Biology at University College Cork. Tom’s research focuses on the genetic control of embryonic development during pregnancy in the following areas a) the evolution and mechanisms of action of the pregnancy-specific glycoproteins during pregnancy, and their therapeutic potential. b) the regulation and function of the imprinted human pseudoautosomal region-2 (PAR2) gene SPRY3 and c) the development of new methods for making transgenic mice using TARGATTTM and CRISPR technologies. Tom is a founding member of Khonsutherapeutics (www.khonsutherapeutics.com) which focuses on novel therapeutics for autoimmune and inflammatory disease.   Rosemary O’Connor (PhD, National University of Ireland, Maynooth). Rosemary O'Connor is Professor of Cell Biology in the School of Biochemistry & Cell Biology at University College Cork. Rosemary is Director of the Cell Biology Laboratory which focuses on Insulin like Growth Factor actions particularly in cancer and neurodegeneration, and on applications of this research in other branches of biology. Rosemary was a founding Investigator of the Biosciences Institute and Director of UCCs first structured PhD training programme in Cancer Biology. Rosemary has served on a several scientific boards and advisory committees for the European Union, Science Foundation Ireland, the Breast Cancer Campaign (UK), and Irish Cancer Society and has Chaired the Gordon Research Conference on Insulin-like Growth Factors in Physiology and Disease. Rosemary’s research programme is focused on the molecular mechanisms that regulate the IGF signalling pathway, how insulin and IGF actions are different, and how they may be manipulated in cancer, neurodegeneration, and tissue regeneration. Dmitri Papkovsky (PhD, Russian Academy of Sciences). Dmitri is a Professor in Biochemistry at University College Cork and Head of the Biophysics and Bioanalysis laboratory. Dmitri is also a founding member and principal investigator of the SFI funded Irish Photonics Integration Centre and the UCC. He is also co-founder and Chief Scientific Officer of the Irish biotech company Luxcel Biosciences Ltd. Dmitri’s current research interests include investigation of the roles of oxygen in biological systems, cell metabolism and hypoxia research, development of phosphorescence based oxygen sensing probes and measurement methodologies, new applications of optical oxygen sensing and imaging. Dmitri has has extensive experience in innovation and commercialisation. His fundamental and applied research in the oxygen sensing area has led to development of a novel platforms for oxygen sensing and several patents. Mike Prentice (PhD, QMW, University of London, FRCPath Royal College of Pathologists). Mike is a Professor in Medical Microbiology at University College Cork, Head of the Department of Pathology and an investigator in the UCC-based Alimentary Pharmabiotic Centre. Research in Mike’s laboratory is centred on Bacterial Genomics, (particularly the Yersinia pestis and Yersinia enterocolitica genomes) and the role of horizontally transmitted genes in bacterial pathogenicity and evolution. A focus of Mike’s reserarch is on a horizontally-transferred metabolosome-specifying (microcompartment) operon in Y. enterocolitica that was absent from other Yersinia, and which are present in approximately 20% of bacterial genome sequences. Current work investigates microcompartment operon gene expression and their relationship to clinical infections. Roy Sleator (MA Ed, PhD, University College Cork, DSc National University of Ireland). Roy is a Professor at the Department of Biological Sciences, and a PI at Cork Institute of Technology’s Centre for Research in Advanced Therapeutic Engineering (CREATE) and a Funded Investigator at the APC Microbiome Institute. Roy is also the founding Editor-in-Chief of the scientific journal Bioengineered published by Taylor and Francis. Roy’s research work is focused on the design and development of improved bacterial chassis as effective vaccine and drug delivery vehicles. Paul Young (PhD, EMBL, ). Paul is a Lecturer in the School of Biochemistry & Cell Biology at University College Cork. Paul’s research focuses on the mechanisms underlying neural circuit formation and function through the development of novel techniques   label and manipulate neurons in transgenic mice, the roles of the alpha-actinin family of actin-crosslinking proteins at sysnapses ancell biological processes relevant to cancer such as cell migration and the physiological functions of the LNX family of proteins in the nervous system and their putative involvement in colorectal and brain cancer. Paul is a founding member of Milisbio (www.milisbio.com) which is focused on generation of flavoured proteins.