Principal Investigator
Alimentary Pharmabotic Centre (Apc)
University College Cork
Cork
Ireland

T: +353 (0)21 4903624
E: david.clarke@ucc.ie
Lecturer
Microbiology
University College Cork
Cork
Ireland

T: +353-21-490-3000
E: david.clarke@ucc.ie

David Clarke graduated with a B.Sc in Biotechnology from Dublin City University in 1989. From here he went to the National University of Ireland in Maynooth to undertake a PhD in Microbiology, graduating in 1993. He then traveled to France where he was awarded an International Traveling Prize Fellowship by the Wellcome Trust to undertake post-doctoral research in the laboratory of Professor Barry Holland who was based at the Institut de Genetique et Microbiologie, Universite Paris-Sud. In September 1998 David briefly returned to the Department of Biology at NUI Maynooth before joining the faculty of the Department of Biology and Biochemistry at the University of Bath, UK as a Lecturer in January 2000. He was promoted to Senior Lecturer in September 2004 before finally returning to Ireland in February 2007 as a College Lecturer in the Department of Microbiology at UCC. Dr Clarke is also a Principal Investigator in the Alimentary Pharmabiotic Centre (APC, http://apc.ucc.ie)

Research Interests

Photorhabdus

Photorhabdus is a Gram negative bacterium that is closely related to Escherichia coli and other important mammalian pathogens. However Photorhabdus does not infect humans but rather this bacterium is a highly virulent pathogen of insects. At the same time Photorhabdus also has a mutualistic (symbiotic) association with nematodes from the family Heterorhabditis. We are interested in understanding the molecular basis of the interactions between Photorhabdus and its different hosts. Key questions that we are asking include: what are the bacterial genes required for ach of these interactions and how is the expression of these gene regulated? We are particularly interested in understanding the role played by primary metabolism in controlling the life cycle of Photorhabdus and also mapping the links between primary metabolism and the production of a range of interesting bioactive secondary metabolites produced by the Photorhabdus genus.


E. coli and Crohn's disease

Inflammatory bowel diseases (IBD) are chronic relapsing disorders of the gastrointestinal tract that include ulcerative colitis (UC) and Crohn¿s disease (CD). Although the cause of CD is not fully understood it is thought to be due to a combination of both host (i.e. genetic) and environmental (i.e. bacteria) factors. Escherichia coli are well-known inhabitants of the human gut where the bacteria occupy a niche in the colon. Although generally considered to be commensal organisms some strains of E. coli have the ability to cause disease, either in the intestine (e.g. E. coli O157::H7) or at other sites (e.g. E. coli are the primary cause of urinary tract infections). Recently a new group of E. coli, called adherent and invasive E. coli (AIEC), has been implicated in CD. Unlike most other strains of E. coli AIEC have the ability to 1) attach to and invade epithelial cells and 2) persist and replicate within macrophages. We are particularly interested in understanding the molecular mechanisms underpinning these phenotypes with the aim of identifying potential drug targets for novel IBD therapies.

 

Bioprospecting the human gut microbiome.

The human gut contains 1013-1015 bacteria (i.e. the microbiome) that contribute a significant metabolic function to their host. The microbiome has been shown to play an important role in maintaining normal gut function, digesting certain nutrients and has also been implicated in obesity and diabetes. Only a small fraction of the microbiome has been cultured suggesting that a significant fraction of the metabolic function associated with the gut microbiome remains to be discovered.  Therefore, using an approach based on functional metagenomic screens, we are undertaking targeted bioprospecting and biomining in the human gut microbiome for novel functions and bioactive molecules. To do this we are taking advantage of metagenomic libraries of the human gut microbiome and a robotics platform both available within the Alimentary Pharmabiotic Centre (APC).



Research Grants

 ProjectFunding
Body
Start DateEnd DateAward
Biofilm formation by E Coli in the gastrointestinal tract.Irish Research Council01-OCT-1430-SEP-18€96,000.00
Molecular characterization of a novel invasion produced by adherent-invasive Escherichia coli.Foreign Research Institute01-JUN-1323-AUG-13€2,200.00
Characterisation of choA, a gene encoding a novel cholesterol-degrading activity in the human gut.Science Foundation of Ireland01-APR-1331-MAR-17€244,318.00
Regulation of a DNA switch that controls pathogenicity and mutualism in Photorhabdus luminescens.Foreign Research Institute31-MAY-1212-AUG-12€1,761.00
individual consumable budget.Higher Education authority01-MAR-1130-SEP-15€31,800.00
SFI CSET Programme 2 - High Throughput Analysis Platform BScience Foundation of Ireland01-NOV-0831-OCT-13€215,751.00
SFI CSET Programme 2 - Genomics & Metagenomics Core 4cScience Foundation of Ireland01-NOV-0831-OCT-13€214,279.00
Moleacular Mechanisms of Adherent Invasive Escherichia Coli (AIEC) Persistance in Macronphag...Health Research Board30-AUG-0830-SEP-11€152,800.00
SFI-Integrating metabolism and genomics: aromatic amino acid metabolism in photorhabus luminescenceScience Foundation of Ireland01-AUG-0731-DEC-10€178,932.00

Book Chapters

YearPublication
(2012)'Nematode parasites and entomopathogens'
Lewis, E. E. and Clarke, D. J. (2012) 'Nematode parasites and entomopathogens' In: Insect Pathology. London, UK: Academic Press. [Details]
(2012)'The Rcs phosphorelay: biofilm formation and virulence in the Enterobacteriaceae'
Clarke, D. J. (2012) 'The Rcs phosphorelay: biofilm formation and virulence in the Enterobacteriaceae' In: Two-component systems in bacteria. Norfolk, UK: Caister Academic Press. [Details]
(2006)'Bacteria-nematode associations'
Clarke, D. J. and L. Eberl ; (2006) 'Bacteria-nematode associations' In: Intestinal microorganisms of termites and other invertebrates (Soil Biology). Springer. [Details]
(2002)'Bacteria-nematode symbiosis'
Forst, S. and D. J. Clarke ; (2002) 'Bacteria-nematode symbiosis' In: Entomopathogenic nematodes. CABI Press. [Details]

Peer Reviewed Journals

YearPublication
(2014)'The Genetic Basis of the Symbiosis Between Photorhabdus and Its Invertebrate Hosts'
Clarke, DJ (2014) 'The Genetic Basis of the Symbiosis Between Photorhabdus and Its Invertebrate Hosts'. Advances In Applied Microbiology, 88 :1-29 [DOI] [Details]
(2013)'Pathogenesis of adherent-invasive Escherichia coli'
Smith, EJ, Thompson, AP, O'Driscoll, A, and Clarke, DJ (2013) 'Pathogenesis of adherent-invasive Escherichia coli'. Future Microbiology, 8 (10):1289-1300 [Details]
(2013)'The expression of stlA in Photorhabdus luminescens is controlled by nutrient limitation'
Lango-Scholey, L, Brachmann, AO, Bode, HB, and Clarke, DJ (2013) 'The expression of stlA in Photorhabdus luminescens is controlled by nutrient limitation'. Plos One, 8 (11) [Details]
(2012)'HdfR is a regulator in Photorhabdus luminescens that modulates metabolism and symbiosis with the nematode Heterorhabditis'
Easom, CA,Clarke, DJ (2012) 'HdfR is a regulator in Photorhabdus luminescens that modulates metabolism and symbiosis with the nematode Heterorhabditis'. Environmental Microbiology, 14 :953-966 [DOI] [Details]
(2011)'The Regulation of Secondary Metabolism and Mutualism in the Insect Pathogenic Bacterium Photorhabdus luminescens'
Joyce SA, Lango L, Clarke DJ (2011) 'The Regulation of Secondary Metabolism and Mutualism in the Insect Pathogenic Bacterium Photorhabdus luminescens'. Advances In Applied Microbiology, 76 :1-25 [DOI] [Details]
(2011)'Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605'
Clarke DJ, Chaudhuri RR, Martin HM, Campbell BJ, Rhodes JM, Constantinidou C, Pallen MJ, Loman NJ, Cunningham AF, Browning DF, Henderson IR (2011) 'Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605'. Journal of Bacteriology, 193 (17) [DOI] [Details]
(2011)'Degradation of the Extracellular Matrix Components by Bacterial-derived Metalloproteases: Implications for Inflammatory Bowel Diseases'
Pruteanu, Mihaela and Hyland, Niall P. and Clarke, David J. and Kiely, Barry and Shanahan, Fergus (2011) 'Degradation of the Extracellular Matrix Components by Bacterial-derived Metalloproteases: Implications for Inflammatory Bowel Diseases'. Inflammatory Bowel Diseases, 17 (5):1189-1200 [Details]
(2010)'Identification of genes involved in the mutualistic colonization of the nematode Heterorhabditis bacteriophora by the bacterium Photorhabdus luminescens'
Easom, CA; Joyce, SA; Clarke, DJ; (2010) 'Identification of genes involved in the mutualistic colonization of the nematode Heterorhabditis bacteriophora by the bacterium Photorhabdus luminescens'. BMC Microbiology, 10 [DOI] [Details]
(2010)'A metabolic switch is involved in lifestyle decisions in Photorhabdus luminescens'
Lango, L; Clarke, DJ; (2010) 'A metabolic switch is involved in lifestyle decisions in Photorhabdus luminescens'. Molecular Microbiology, 77 :1394-1405 [Details]
(2010)'The role of iron uptake in pathogenicity and symbiosis in Photorhabdus luminescens TT01'
Watson, RJ; Millichap, P; Joyce, SA; Reynolds, SE; Clarke, DJ; (2010) 'The role of iron uptake in pathogenicity and symbiosis in Photorhabdus luminescens TT01'. BMC Microbiology, 10 [DOI] [Full Text] [Details]
(2010)'The Rcs phosphorelay: more than just a two-compoent pathway'
Clarke, DJ; (2010) 'The Rcs phosphorelay: more than just a two-compoent pathway'. Future Microbiology, 5 :1173-1184 [Details]
(2010)'Dissecting the immune response to the entomopathogen Photorhabdus'
Eleftherianos I, ffrench-Constant RH, Clarke DJ, Dowling AJ, Reynolds SE (2010) 'Dissecting the immune response to the entomopathogen Photorhabdus'. Trends In Microbiology, 18 (12):552-560 [DOI] [Details]
(2010)'Probing the tritrophic interaction between insects, nematodes and Photorhabdus'
Eleftherianos, I; Joyce, SA; ffrench-Constant, RH; Clarke, DJ; Reynolds, SE ; (2010) 'Probing the tritrophic interaction between insects, nematodes and Photorhabdus'. Parasitology, 26 :1-12 [Details]
(2009)'Comparative functional analysis of the RcsC sensor kinase from different Enterobacteriaceae'
Huang, Y. H.,Ferrieres, L.,Clarke, D. J.; (2009) 'Comparative functional analysis of the RcsC sensor kinase from different Enterobacteriaceae'. FEMS Microbiol Lett, 293 (2):248-54 [Details]
(2009)'Photorhabdus and a host of hosts'
Waterfield, N. R.,Ciche, T.,Clarke, D.; (2009) 'Photorhabdus and a host of hosts'. Annu Rev Microbiol, 63 :557-74 [Details]
(2009)'Comparative functional analysis of the RcsC sensor kinase from different Enterobacteriaceae'
Huang, YH,Ferrieres, L,Clarke, DJ; (2009) 'Comparative functional analysis of the RcsC sensor kinase from different Enterobacteriaceae'. Fems Microbiology Letters, 293 :248-254 [DOI] [Details]
(2009)'Heterorhabditis gerrardi n. sp. (Nematoda: Heterorhabditidae): the hidden host of Photorhabdus asymbiotica (Enterobacteriaceae: gamma-Proteobacteria)'
Plichta, K. L., Joyce, S. A., Clarke, D. J., Waterfield, N. and Stock, S. P. ; (2009) 'Heterorhabditis gerrardi n. sp. (Nematoda: Heterorhabditidae): the hidden host of Photorhabdus asymbiotica (Enterobacteriaceae: gamma-Proteobacteria)'. Journal of Helminthology, 16 :1-12 [Details]
(2009)'Elevated levels of sigma S inhibit biofilm formation in Escherichia coli: a role for the Rcs phosphorelay'
Ferrieres, L; Thompson, A; Clarke, DJ; (2009) 'Elevated levels of sigma S inhibit biofilm formation in Escherichia coli: a role for the Rcs phosphorelay'. Microbiology, 155 (Pt 11):3544-53 [Details]
(2008)'Photorhabdus: a model for the analysis of pathogenicity and mutualism'
Clarke, D. J.; (2008) 'Photorhabdus: a model for the analysis of pathogenicity and mutualism'. Cell Microbiol, 10 (11):2159-67 [Details]
(2008)'The importance of the Rcs phosphorelay in the survival and pathogenesis of the enteropathogenic yersiniae. Microbiology'
Hinchliffe, S. J.,Howard, S. L.,Huang, Y. H.,Clarke, D. J.,Wren, B. W.; (2008) 'The importance of the Rcs phosphorelay in the survival and pathogenesis of the enteropathogenic yersiniae. Microbiology'. Microbiology, 154 (Pt 4):1117-31 [Details]
(2008)'Bacterial biosynthesis of a multipotent stilbene'
Joyce, S. A.,Brachmann, A. O.,Glazer, I.,Lango, L.,Schwar, G.,Clarke, D. J.,Bode, H. B.; (2008) 'Bacterial biosynthesis of a multipotent stilbene'. Angew Chem Int Ed Engl, 47 (10):1942-5 [Details]
(2008)'Motility is required for the competitive fitness of entomopathogenic Photorhabdus luminescens during insect infection. BMC Microbiol'
Easom, C. A.,Clarke, D. J.; (2008) 'Motility is required for the competitive fitness of entomopathogenic Photorhabdus luminescens during insect infection. BMC Microbiol'. BMC Microbiol, 8 [DOI] [Details]
(2007)'A type II polyketide synthase is responsible for anthraquinone biosynthesis in Photorhabdus luminescens'
Brachmann, A. O.,Joyce, S. A.,Jenke-Kodama, H.,Schwar, G.,Clarke, D. J.,Bode, H. B.; (2007) 'A type II polyketide synthase is responsible for anthraquinone biosynthesis in Photorhabdus luminescens'. Chembiochem, 8 (14):1721-8 [Details]
(2007)'The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production'
Ferrieres, L.,Aslam, S. N.,Cooper, R. M.,Clarke, D. J.; (2007) 'The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production'. Microbiology, 153 (Pt 4):1070-80 [Details]
(2007)'Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination'
Goodrich-Blair, H.,Clarke, D. J.; (2007) 'Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination'. Mol Microbiol, 64 (2):260-8 [Details]
(2007)'An antibiotic produced by an insect-pathogenic bacterium suppresses host defenses through phenoloxidase inhibition'
Eleftherianos, I.,Boundy, S.,Joyce, S. A.,Aslam, S.,Marshall, J. W.,Cox, R. J.,Simpson, T. J.,Clarke, D. J.,ffrench-Constant, R. H.,Reynolds, S. E.; (2007) 'An antibiotic produced by an insect-pathogenic bacterium suppresses host defenses through phenoloxidase inhibition'. Proc Natl Acad Sci U S A, 104 (7):2419-24 [Details]
(2006)'The role of the Rcs phosphorelay in Enterobacteriaceae'
Huang, Y. H.,Ferrieres, L.,Clarke, D. J.; (2006) 'The role of the Rcs phosphorelay in Enterobacteriaceae'. Res Microbiol, 157 (3):206-12 [Details]
(2006)'The regulation of pathogenicity and mutualism in Photorhabdus'
Joyce, S. A.,Watson, R. J.,Clarke, D. J.; (2006) 'The regulation of pathogenicity and mutualism in Photorhabdus'. Curr Opin Microbiol, 9 (2):127-32 [Details]
(2005)'The pbgPE operon in Photorhabdus luminescens is required for pathogenicity and symbiosis'
Bennett, H. P.,Clarke, D. J.; (2005) 'The pbgPE operon in Photorhabdus luminescens is required for pathogenicity and symbiosis'. J Bacteriol, 187 (1):77-84 [Details]
(2005)'The exbD gene of Photorhabdus temperata is required for full virulence in insects and symbiosis with the nematode Heterorhabditis'
Watson, R. J.,Joyce, S. A.,Spencer, G. V.,Clarke, D. J.; (2005) 'The exbD gene of Photorhabdus temperata is required for full virulence in insects and symbiosis with the nematode Heterorhabditis'. Mol Microbiol, 56 (3):763-73 [Details]
(2005)'The gene stlA encodes a phenylalanine ammonia-lyase that is involved in the production of a stilbene antibiotic in Photorhabdus luminescens TT01'
Williams, J. S.,Thomas, M.,Clarke, D. J.; (2005) 'The gene stlA encodes a phenylalanine ammonia-lyase that is involved in the production of a stilbene antibiotic in Photorhabdus luminescens TT01'. Microbiology, 151 (Pt 8):2543-50 [Details]
(2004)'Study of the attachment of Pseudomonas aeruginosa on gold and modified gold surfaces using surface plasmon resonance'
Jenkins, A. T.,ffrench-constant, R.,Buckling, A.,Clarke, D. J.,Jarvis, K.; (2004) 'Study of the attachment of Pseudomonas aeruginosa on gold and modified gold surfaces using surface plasmon resonance'. Biotechnol Prog, 20 (4):1233-6 [Details]
(2003)'Photorhabdus: towards a functional genomic analysis of a symbiont and pathogen'
ffrench-Constant, R.,Waterfield, N.,Daborn, P.,Joyce, S.,Bennett, H.,Au, C.,Dowling, A.,Boundy, S.,Reynolds, S.,Clarke, D.; (2003) 'Photorhabdus: towards a functional genomic analysis of a symbiont and pathogen'. FEMS Microbiol Rev, 26 (5):433-56 [Details]
(2003)'The RcsC sensor kinase is required for normal biofilm formation in Escherichia coli K-12 and controls the expression of a regulon in response to growth on a solid surface'
Ferrieres, L.,Clarke, D. J.; (2003) 'The RcsC sensor kinase is required for normal biofilm formation in Escherichia coli K-12 and controls the expression of a regulon in response to growth on a solid surface'. Mol Microbiol, 50 (5):1665-82 [Details]
(2003)'A hexA homologue from Photorhabdus regulates pathogenicity, symbiosis and phenotypic variation'
Joyce, S. A.,Clarke, D. J.; (2003) 'A hexA homologue from Photorhabdus regulates pathogenicity, symbiosis and phenotypic variation'. Mol Microbiol, 47 (5):1445-57 [Details]
(2003)'The transmembrane domain of the DnaJ-like protein DjlA is a dimerisation domain'
Toutain, C. M.,Clarke, D. J.,Leeds, J. A.,Kuhn, J.,Beckwith, J.,Holland, I. B.,Jacq, A.; (2003) 'The transmembrane domain of the DnaJ-like protein DjlA is a dimerisation domain'. Mol Genet Genomics, 268 (6):761-70 [Details]
(2002)'Genetic analysis of the RcsC sensor kinase from Escherichia coli K-12'
Clarke, D. J.,Joyce, S. A.,Toutain, C. M.,Jacq, A.,Holland, I. B.; (2002) 'Genetic analysis of the RcsC sensor kinase from Escherichia coli K-12'. J Bacteriol, 184 (4):1204-8 [Details]
(2002)'The ner gene of Photorhabdus: effects on primary-form-specific phenotypes and outer membrane protein composition'
O'Neill, K. H.,Roche, D. M.,Clarke, D. J.,Dowds, B. C.; (2002) 'The ner gene of Photorhabdus: effects on primary-form-specific phenotypes and outer membrane protein composition'. J Bacteriol, 184 (11):3096-105 [Details]
(1998)'Increased sensitivity of E. coli to novobiocin, EDTA and the anticalmodulin drug W7 following overproduction of DjlA requires a functional transmembrane domain'
Bernard, S.,Clarke, D. J.,Chen, M. X.,Holland, I. B.,Jacq, A.; (1998) 'Increased sensitivity of E. coli to novobiocin, EDTA and the anticalmodulin drug W7 following overproduction of DjlA requires a functional transmembrane domain'. Mol Gen Genet, 259 (6):645-55 [Details]
(1997)'Point mutations in the transmembrane domain of DjlA, a membrane-linked DnaJ-like protein, abolish its function in promoting colanic acid production via the Rcs signal transduction pathway'
Clarke, D. J.,Holland, I. B.,Jacq, A.; (1997) 'Point mutations in the transmembrane domain of DjlA, a membrane-linked DnaJ-like protein, abolish its function in promoting colanic acid production via the Rcs signal transduction pathway'. Mol Microbiol, 25 (5):933-44 [Details]
(1996)'The gram-negative cell envelope 'springs' to life: coiled-coil trans-envelope proteins'
Pimenta, A.,Blight, M.,Clarke, D.,Holland, I. B.; (1996) 'The gram-negative cell envelope 'springs' to life: coiled-coil trans-envelope proteins'. Mol Microbiol, 19 (3):643-5 [Details]
(1996)'A novel DnaJ-like protein in Escherichia coli inserts into the cytoplasmic membrane with a type III topology'
Clarke, D. J.,Jacq, A.,Holland, I. B.; (1996) 'A novel DnaJ-like protein in Escherichia coli inserts into the cytoplasmic membrane with a type III topology'. Mol Microbiol, 20 (6):1273-86 [Details]
(1995)'The relationship between growth rate of Photorhabdus sp. strain K122 and pathogenicity to Galleria mellonella (Waxmoth) larvae: the possible role of extracellular enzymes in pathogenicity'
Clarke, D. J., and B. C. A. Dowds ; (1995) 'The relationship between growth rate of Photorhabdus sp. strain K122 and pathogenicity to Galleria mellonella (Waxmoth) larvae: the possible role of extracellular enzymes in pathogenicity'. J Inver Pathol, 66 :149-155 [Details]
(1994)'The gene coding for polynucleotide phosphorylase in Photorhabdus sp. strain K122 is induced at low temperatures'
Clarke, D. J.,Dowds, B. C.; (1994) 'The gene coding for polynucleotide phosphorylase in Photorhabdus sp. strain K122 is induced at low temperatures'. J Bacteriol, 176 (12):3775-84 [Details]
(1992)'Isolation/generation of cold active strains of Xenorhabdus luminescens, the symbiont of entomopathogenic nematodes of the genus Heterorhabditis'
Clarke, D. J., H. Wang, and B. C. A. Dowds. ; (1992) 'Isolation/generation of cold active strains of Xenorhabdus luminescens, the symbiont of entomopathogenic nematodes of the genus Heterorhabditis'. Nematologica, 32 (404) [Details]
(1992)'Pathogenicity of Xenorhabdus luminescens'
Clarke, D. J.,Dowds, B. C.; (1992) 'Pathogenicity of Xenorhabdus luminescens'. Biochem Soc Trans, 20 (1) [Details]

Conference Publications

YearPublication
(1994)Genetics of Entomopathogenic Nematode - Bacterium Complexes. Proceedings of a COST symposium and workshops
Clarke, D. J., and B. C. A. Dowds; (1994) Cold acclimation in Photorhabdus spp . In: Burnell, A., Ehlers, R. -U., and Masson, J. -P. E eds. Genetics of Entomopathogenic Nematode - Bacterium Complexes. Proceedings of a COST symposium and workshops St. Patricks College, Maynooth, Co. Kildare, Ireland, , 23-OCT-93 - 25-OCT-93 , pp.170-177 [Details]

Professional Associations

 AssociationFunctionFrom / To
Society for General Microbiology Member/
American Society for Microbiology Member/

Committees

 CommitteeFunctionFrom / To
Society for General Microbiology Prokaryotic Division Committee member2010 /
Society for General Microbiology Irish Division Member2014 /

Employment

 EmployerPositionFrom / To
University College Cork Lecturer (full-time, fixed contract)01-FEB-07 /
University of Bath, UK Senior Lecturer01-APR-04 / 31-JAN-07
University of Bath, UK Lecturer01-JAN-00 / 01-MAR-04
NUI Maynooth Lecturer (full-time, fixed contract)01-OCT-98 / 01-DEC-99
Institut de Génétique et Microbiologie, Universite Paris 11 Post-doctoral fellow02-MAY-94 / 30-SEP-98

Education

 YearInstitutionQualificationSubject
1994NUI Maynooth PHDMicrobiology
1989Dublin City University BSC (HONS)Biotechnology

Consultancy

 ClientDescription
Ad hoc reviewer for international funding agencies and journals
BBSRC, Wellcome Trust, NSF, ISME Journal, Molecular Microbiology, Journal of Bacteriology, Cellular Microbiology, Microbiology
Merlion
Offered expert advice and undertook some proof-in-prinicple experiments for Merlion, a pharmaceutical company based in Singapore

Outreach Activities

 Description

Every year, for the past 5 years, I have given 2 x 1h presentations to 5th and 6th class primary school children (>300 students in total, aged 10-12). These talks are on biological related topics such as the Immune system, the Circulatory System and Vaccination and have been in different schools around Cork City including Gaelscoil Ui Riada, Upper Glanmire National School and St Johns National School, Mayfield.

Journal Activities

 JournalRoleTo / From
Fems Microbiol Lett Member of Editorial Board01-JAN-06 -

Other Activities

 Description

Invited speaker at following conferences: 1. Metabolism meets virulence (MMV), Osnabruck, April 2014 2. Society for General Microbiology (SGM) Spring Conference 2013, Manchester, March 2013 3. SGM Irish Division Meeting, March 2013, University College Dublin 4. Current Trends in Biomedicine Workshop on The Biology of Intracellular Bacterial Pathogens, October 2011, Universidad Internacional de Andalucia, Baeza, Spain 5. 50th Anniversary Meeting of the Society of Nematology July 2011, Corvallis, Oregon, USA 6. 3rd Nemasym meeting, July 2011, Corvallis, Oregon, USA 7. 2nd Nemasym meeting, November 2010, Tucson, Arizona, USA 8. SGM Autumn Conference, September 2010, University of Nottingham 9. 41st Annual Meeting of the Society for Invertebrate Pathology (SIP), August 2008, University of Warwick, UK 10. 40th Annual Meeting of the SIP, August 2007, Quebec, Canada 11. Host-pathogen co-evolution: a tale of struggle and affection. International symposium, Wurzburg November 2007 12. COST850, Salzau, Germany June 2006 13. The evolution of symbiosis, Edinburgh April 2006 14. 38th Annual Meeting of the SIP, August 2005, University of Anchorage, Alaska, USA 15. OMIG symposium November 2004, Bristol, UK. 16. SGM Autumn Conference, September 2004, Trinity College, Dublin. 17. Euroconference on Bacterial Neural Networks, May 2004, Barcelona, Spain 18. International workshop on entomopathogenic nematodes and their bacterial symbionts, November 2003, Eilat, Israel. 19. Royal Entomological Society, July 2003, University of Reading, UK. 20. Euroconference on Bacterial Neural Networks, June 2002, Obernai, France. 21. 27th Wellcome Trust Advanced Course in Genetic, Molecular and Informatic Methods for Caenorhabditis elegans. September 2000, Hinxton, Cambridge.

Invited Research seminars 1. Trinity College Dublin, December 2014 2. Institute of Food Research, March 2014 3. University of Glasgow, November 2013 4. University of Cardiff, February 2013 5. University of Dundee, September 2012 6. Institut Pasteur, September 2012 7. Ludwig Maximilians Universitat (LMU) Munich, June 2009 8. Trinity College Dublin, February 2009 9. National University of Ireland, Galway, October 2007 10. Institut Pasteur, February 2006 11. Trinity College Dublin, January 2006 12. University of Birmingham, November 2005 13. University of Oxford, November 2004 14. University College Dublin, November 2004 15. John Innes Centre, June 2004 16. University of Reading, June 2004 17. Dublin City University, February 2003 18. University of Birmingham, May 2002

Recent Postgraduates

 Graduation YearStudent NameInstitutionDegree TypeThesis Title
2013Aoife Thompson UCCPhD
2011Catherine Easom UCCPhD
2012Lea Lango UCCPhD
2012Adam O'Driscoll UCCPhD

Current Postgraduate Students

 StudentDegree Type
O Neill Ian James Doctoral Degree (Structured)
Barrett Kevin Paul Masters Degree by Research
Buttimer Finbarr James Doctoral Degree
Lynch Alli Doctoral Degree

Modules Taught

 Term (ID))TitleLinkSubject
2015Research Frontiers in Food Microbiology MB6027Research Frontiers in Food Microbiology
2015Research Project MB4002Research Project
2015Environmental Systems Microbiology: Themes in microbe-host interactions MB3017Environmental Systems Microbiology: Themes in microbe-host interactions
2015Molecular Genetics and Genomics MB3007Molecular Genetics and Genomics
2015Microbial Diversity and Ecology MB4022Microbial Diversity and Ecology
2015Medical Microbiology MB3001Medical Microbiology
2015Medical Microbiology MB3901Medical Microbiology
2015Literature Project on Genetics GN3002Literature Project on Genetics
2015Research Dissertation MB6303Research Dissertation
2015Environmental Microbial Genomics II: understanding and exploiting microbial communities MB4020Environmental Microbial Genomics II: understanding and exploiting microbial communities
2015Research Frontiers in Microbiology MB4027Research Frontiers in Microbiology
2015Molecular Biology and Physiology of Bacteria MB4026Molecular Biology and Physiology of Bacteria