Dr Lee Coffey
PhD
Adjunct Senior Research Fellow (PMBRC, WIT)
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- Phone +353 51 845514
- ORCID NUMBER 0000-0002-6499-8987
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Biography
Dr Lee Coffey is a Lecturer in Molecular Biology with Biopharmaceutical Science at the Department of Science, WIT and is a Principal Investigator at the PMBRC where he is leading the Molecular Biotechnology and Biopharmaceutical Research Group, with over €1.2 million research funding secured to date.
He received a BSc (Hons) Degree in Applied Biology with Quality Management (first class honours) and a PhD in Molecular Biotechnology from WIT in 2002 and 2007, respectively. In this time Dr Coffey gained experience in industry in both microbiological and pharmaceutical laboratories.
Dr Coffey conducted his postdoctoral research at the PMBRC from 2007 to 2011, expanding the biotechnology research while also serving as manager of the Molecular Biology research lab, overseeing >€1.5M of research projects and commercial activities.
Dr Coffey is currently mentoring two research staff and is lead supervisor for three and co-supervisor for five postgraduate students, with two more positions in recruitment. He received the WIT Postgraduate Supervision Excellence Award in 2016. He has presented at numerous national and international conferences and 13 peer-reviewed publications. The research group follows a strong commercialization focus, with four Invention Disclosures filed to date; detailing biological solutions to biopharmaceutical processes, Patent Co-operation Treaty applications; three filed to date, detailing territories of the above, a Technology License Agreement secured with a global multi-billion $ pharmaceutical company, sharing biotechnology technology products (enzymes/cells) on an ongoing basis on a royalty agreement including an upfront payment. Dr Coffey has established collaborations with various academic and medical institutions and also global biotechnology companies.
Current research interests and projects include rare disease therapy enhancement through directed evolution of gene therapy products, the use of genome editing to enhance protein performance and the development of proprietary biological technology for protein discovery. Dr Coffey is also an affiliate member of the TSSG where he is involved in molecular communications research; the use of DNA for data storage, security and networking.
Department of Science, WIT (2005-current)
Previous module development and/or delivery (2005 –):
B.A. in Culinary Arts Year 3 – Food Product Development –shelf life analysis practicals (2009-2013)
N.C. Science with GMP Year 1 - Biology - lectures and practicals (2005-2013)
BSc. Applied Biology with QM Year 4 - DNA Technology & Bioinformatics, lectures and practicals (2012)
N.D. Applied Biotechnology Year 3 - Molecular Biology lectures (2012)
BSc. Agriculture Year 4 - Research Methods lectures (2012)
BSc. Forestry/Horticulture Year 4 - Research Methods lectures (2012)
N.C Professional Cookery Year 2 - Nutrition and Menu Planning Lectures (2012)
BSc. Applied Biology with QM (full & part-time) Year 4 – Project supervision (2006-2010)
N.C. Science Year 1 - Cell Biology & Biochemistry practicals (2005-2007)
N.C. Applied Biology Year 2 - Biotechnology practicals (2005, 2006)
N.C. Applied Biology Year 2 - Microbiology/Food Microbiology practicals (2006, 2007)
N.D. Applied Biotechnology Year 3 – Molecular Biology practicals (2007)
N.D. Applied Biotech/Chemistry Year 3 – Pharmaceutical Biotechnology practicals (2007)
BSc. Applied Biology with QM (part-time) Year 4 – Biological Analysis practicals (2007)
N.D. Applied Biotechnology Year 3 – Project supervision (2006)
BSc. Applied Biology with QM Year 4 – Biological Analysis lectures and practicals (2006)
Cell Biology & Biochemistry practicals Year 1
Introduction to Food Science practicals Year 1
Microbiology 1 practicals Year 2
Food microbiology practicals Year 2
Current module development and/or delivery (2013 – present):
Bioanalytical Methods for the Food Industry lectures and practicals Year 2
Pharmaceutical Biotechnology lectures & practicals Year 3
Literature Review & Research projects Year 3 & 4
Biopharmaceutical Technology lectures & practicals Year 4
Applications in Microbiology with Biostatistics lectures Year 4
Molecular Biology & Medicine lectures Year 4
DNA Technology & Bioinformatics lectures & Practicals Year 4
Current research interests and projects include rare disease therapy enhancement through directed evolution of gene therapy products, the use of genome editing to enhance protein performance and the development of proprietary biological technology for protein discovery.
Research interests:
Molecular Biology
Genome editing
Biotechnology
Gene therapy
Directed evolution
Microbiology
Biocatalysis
Recombinant DNA technology
Horizontal gene transfer
Enzyme expression
Therapeutic enzymes and enzyme platform technologies
Molecular Communications
Current postgraduate students/research projects:
Student: Erica Owens; Thesis: Purification and analysis of mixed bacterial cultures containing genes associated with nitrile metabolism; Degree type; MSc; Expected year of completion: 2015.
Role – Co-supervisor
Student: Tríona Dooley Cullinane; Thesis: The identification and application of genes and enzymes as biocatalysts towards the production of pharmaceutical intermediates; Degree type; PhD; Expected year of completion: 2016.
Role – PI
Student: Caio Bragança; Thesis: Recombinant enzymes towards the production of pharmaceutical intermediates using biotransformations; Degree type; PhD; Expected year of completion: 2016.
Role – PI
Student: Hazal Yilmaz; Thesis: Characterisation and improvement of microbial enzymes using directed evolution towards bio-pharmaceutical applications; Degree type; PhD; Expected year of completion: 2017.
Role - PI
Student: Evelyn Joyce; Thesis: In-situ bioremediation and molecular microbiological monitoring of ammonia contamination in shallow groundwater.; Degree type; PhD; Expected year of completion: 2017.
Role – Co-supervisor
Student: Tatenda Mereya; Thesis: Enantioselective biocatalytic synthesis of ß-amino acids and amines; Degree type; PhD; Expected year fo completion: 2018
Role - Co-supervisor
Student: Mariana Gavendova; Thesis: Design, synthesis and evaluation of novel organocatalysts towards the synthesis of biologically active oxindoles: Degree type; PhD; Expected year of completion: 2019.
Role – Co-supervisor
Grant History:
WIT Co-fund PhD scholarship 1 (2018)
WIT Co-fund PhD scholarship 1 (2018)
WIT Co-fund PhD scholarship 1 (2018)
Enterprise Ireland Commercialisation Fund (2015), Lee Coffey (Principal Investigator), Catherine O'Reilly, Claire Lennon, Mike Kinsella (Collaborators). Development of an Enzyme Discovery Platform kit towards Biocatalysis – (BIOENZ) –- €541,550
WIT PhD Scholarship Programme (2014), Lee Coffey, Orla O’Donovan, Catherine O’Reilly. Characterisation and improvement of microbial enzymes using directed evolution towards bio-pharmaceutical applications. €48,000
CAPES Science Without Borders Postgraduate Scholarship (2013), Lee Coffey, Catherine O’Reilly. Development of recombinant enzymes towards the production of pharmaceutical intermediates using biotransformations. €82,800
WIT PhD Scholarship Programme (2013), Lee Coffey, Catherine O’Reilly. The identification and application of genes and enzymes as biocatalysts towards the production of pharmaceutical intermediates. €48,000
EI-CFF (2013), Lee Coffey. High throughput platform to generate enzyme banks for industrial applications. €15,000
EI-CFF(2012), Lee Coffey. Production of enantiopure pharmaceutical intermediates using biocatalysis. €12,500
RIA mobility grant (2010), Lee Coffey. Purification and characterisation of nitrilase enzymes from Burkholderia sp. expressed in E.coli. €2,500
SGM Presidents Fund for Research Visits (2010), Lee Coffey. Cloning, expression and characterisation of isonitrile hydratase from Arthrobacter sp. expressed in E.coli. €3,500
SGM summer Vacation Scholarship (2008 -2010), Lee Coffey, Catherine O’Reilly. Screening and characterisation of nitrilase genes from environmental microbes. €2,200 x3
IRCSET PhD scholarship (2002), Lee Coffey. Molecular analysis of genes involved in nitrile metabolism in Microbacterium sp. AJ115, Rhodococcus erythropolis AJ270, AJ300 and ITCBP. €87,000
Other activities:
Certificate in Perl Programming for Bioinformatics, Oxford University, 2008
Certified training in mammalian cell culture handling and aseptic processing, NIBRT, 2018
Expert Reviewer for:
Accounts of Chemical Research, Antonie Van Leeuwenhoek, PLos One, Appl Biochem and Biotech, Appl Envir Microbiol, Biodegradation, Enzyme & Microbial Technol, BMC Biotech, Appl Microbiol Biotech, Lett Appl Microbiol).
Editorial board member (Microbiology) for the Global Journal of Biochemistry (2009-2011)
PhD Internal Examiner, WIT on two occasions; 2016 and 2018
Journal articles
Soares Bragança CR, Dooley-Cullinane TM, O’Reilly C and Coffey L (2017) Applying functional metagenomics to search for novel nitrile-hydrolyzing enzymes using environmental samples. Biomater Tissue Technol: 1(2): 1-5.doi: 10.15761/BTT.1000108
Dooley-Cullinane TM, O’Reilly C, Coffey L (2016) Real-time PCR detection of aldoxime dehydratase genes in nitrile-degrading microorganisms. Antonie van Leeuwenhoek, (2017) 110: 271. doi:10.1007/s10482-016-0786-2
Coady Tracey M, Coffey Lee V, O‘Reilly Catherine, Owens Erica B, Lennon Claire M. (2015) Substrate evaluation of Rhodococcus erythropolis SET1, a nitrile hydrolysing bacterium, demonstrating dual activity strongly dependent on nitrile sub-structure. Europ J Org Chem DOI: 10.1002/ejoc.201403201
Coady Tracey M, Coffey Lee V, O‘Reilly Catherine, Owens Erica B, Lennon Claire M. (2013) A high throughput screening strategy for the assessment of nitrile-hydrolyzing activity towards the production of enantiopure β-hydroxy acids. J Mol Cat B: Enzymatic 97: 150-155
O'Neill, D., Turner, P. D., O'Meara, D. B., Chadwick, E. A., Coffey, L. and O'Reilly, C. (2013) Development of novel real-time TaqMan® PCR assays for the species and sex identification of otter (Lutra lutra) and their application to non-invasive genetic monitoring. Molecular Ecology Resources. 13, 5: 877-883.
O’Meara D, Turner P, Coffey L, O’Reilly C (2012) TaqMan assays for species identification of the red squirrel (Sciurus vulgaris) and the grey squirrel (Sciurus carolinensis). Conserv Genet 4, 3: 603-604.
McCarthy, G., Lawlor, P.G., Coffey, L., Nolan, T., Gutierrez, M., and Gardiner, G.E. (2011) An assessment of pathogen removal during composting of the separated solid fraction of pigmanure. Bioresour Technol 102, 19: 9059-67.
O’Connor L, O’Leary M, Leonard N, Godinho M, O’Reilly C, Coffey L, J.Egan and O’Mahony R (2010) The characterisation of Listeria sp. isolated from food products and the food-processing environment. Lett Appl Microbiol 51, 5: 490-498.
Coffey L, Owens E, Tambling K, O’Neill D, O’Connor L, O’Reilly C (2010) Real-time PCR detection of Fe-type nitrile hydratase genes from environmental isolates suggests horizontal gene transfer between multiple genera. Antonie van Leeuwenhoek 98, 4: 455-463.
Coffey L, Clarke A, Duggan P, Tambling K, Horgan S, Dowling D, O’Reilly C (2009) Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer. Arch Microbiol 10: 761-771.
Song LY, Yuan HJ, Coffey L, Doran J, Wang MX, Qian SJ, O’Reilly C (2008) Efficient expression in E. coli of an enantioselective nitrile hydratase from Rhodococcus erythropolis. Biotechnol Lett 30: 755-762.
O’Mahony R, Doran J, Coffey L, Cahill OJ, Black GW, O’Reilly C (2005) Characterisation of the nitrile hydratase gene clusters of Rhodococcus erythropolis strains AJ270 and AJ300 and Microbacterium sp. AJ115 indicates horizontal gene transfer and reveals an insertion of IS1166. Antonie van Leeuwenhoek 87: 221-232.
Patent applications:
A Process for Producing Amides and Acids using a Nitrile-metabolising Strain/Enzyme, P120817GB01.
A Process for Producing Amides and Acids using a Nitrile-metabolising Strain/Enzyme, P120818GB01.
A Process for Producing Amides and Acids using a Nitrile-metabolising Strain/Enzyme, P120820GB01.
Patent Co-operation Treaty applications:
Filed three Patent Cooperation Treaty applications in July 2012 based on previous patent applications:
A Nitrile-Metabolising Enzyme and a Process for Producing an Acid using SS-4 (PCT/EP2012/063315).
A Nitrile-Metabolising Enzyme and a Process for Producing an Acid using SS-17 (PCT/EP2012/063321).
A Nitrile-Metabolising Enzyme and a Process for Producing an Acid using SS-24 (PCT/EP2012/063323).
Book Chapters:
O’Meara DB, Turner PD, O'Neill D, Coffey L, Harrington A, O'Reilly C (2012) “DNA toolbox for squirrel surveys” Mammal News - Autumn 2012
Conference Proceedings:
30th European Mustelid Colloquium, Dublin, 2012: “Non-invasive genetic monitoring of otter (Lutra lutra) populations”, David O’Neill, Denise O’Meara, Andrew Harrington, Peter Turner, Ceri Morris, Jenny Macpherson, Bernie Guest, Liz Halliwell, Henry Schofield, Lee Coffey and Catherine O’Reilly
AIMS 2012 Conference, Dublin 2012: “Non-invasive genetic tools for squirrel surveys”, Denise O’Meara, Peter Turner, David O’Neill, Lee Coffey, Andrew Harrington and Catherine O’Reilly
Biocatalysis Conference, December 2010: “Gene cloning, overexpression and characterisation of the nitrilases from Burkholderia sp. LC8 and LC9”, Pat Duggan, Lee Coffey, Eoghan O’Dwyer, Sarah Duggan, David O’Neill and Catherine O’Reilly
Annual IT Colloquium, Waterford I.T., 2004: “Localisation of the nitrile hydratase genes in a number of novel Rhodococcal strains”, Lee Coffey, Catherine O’Reilly
Poster Presentations:
35 posters have been presented at national and international conferences to date