Research Profile

David Clarke

Biography

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 returned to Ireland in February 2007 and he is a Senior Lecturer in the School of Microbiology at UCC. 

Dr Clarke is currently Head of the School of Microbiology, Director of the BSc Biotechnology programme and he is  a Funded Investigator in APC Microbiome Ireland (http://apc.ucc.ie).

Research Interests

My research is interested in understanding the molecular biology of bacteria-host interactions i.e. symbiosis. Recent studies have shown that the complex interactions between bacteria and hosts (such as humans) are essential for the well-being of the host. However these interactions when inappropriate can also cause disease. Research in my laboratory is focused on understanding the molecular consequences associated with the change from beneficial bacteria to pathogen. To address this question we are using a number of model bacterial species including Escherichia coli and Bacteroides (important inhabitants of the human gut) and Photorhabdus (a bacterium that inhabits the gut of soil-dwelling nematodes and is a potent pathogen of insects).

Research Grants

 ProjectFunding
Body
Start DateEnd DateAward
Moleacular Mechanisms of Adherent Invasive Escherichia Coli (AIEC) Persistance in Macronphag...Health Research Board30-AUG-0830-SEP-11€152,800.00
A systems level approach to understanding the role and regulation of phenotypicEnterprise Irl29-AUG-1828-MAY-19€3,444.00
Trainign Network to Deliver a Systems-level Understanding of Entomopathogenic Nematode Production.Enterprise Irl04-AUG-1704-MAY-18€5,650.00
Role of Photorhabdus DNAIrish Research Council01-JAN-1831-DEC-18€1,588.00
Marine Biodiversity as Sustainable Resource of Disease-Suppressive Microbes and Bioprotectants for Aquaculture and Crop DiseasesHorizon 202001-APR-2031-MAR-25€606,505.00
SFI-Integrating metabolism and genomics: aromatic amino acid metabolism in photorhabus luminescenceScience Foundation of Ireland01-AUG-0731-DEC-10€178,932.00
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
Stilbene and Entomopathogenic Nematodes: Unlocking the PotentialHorizon 202001-JAN-1731-DEC-18€175,866.00
individual consumable budget.Higher Education authority01-MAR-1130-SEP-15€38,260.00
Characterisation of choA, a gene encoding a novel cholesterol-degrading activity in the human gut.Science Foundation of Ireland01-APR-1331-JUL-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
Molecular characterization of a novel invasion produced by adherent-invasive Escherichia coli.Foreign Research Institute01-JUN-1323-AUG-13€2,200.00
Biofilm formation by E Coli in the gastrointestinal tract.Irish Research Council01-OCT-1430-SEP-18€96,000.00

Publications

Peer Reviewed Journals

 YearPublication
(2024)'Microbial metabolites as modulators of host physiology'
Joyce SA;Clarke DJ; (2024) 'Microbial metabolites as modulators of host physiology'. Advances In Microbial Physiology, 84 [DOI] [Details]
(2024)'Identification and expression of MarCE, a marine carboxylesterase with synthetic ester-degrading activity'
Carr CM;Göttsch F;de Oliveira BFR;Murcia PAS;Jackson SA;Wei R;Clarke DJ;Bornscheuer UT;Dobson ADW; (2024) 'Identification and expression of MarCE, a marine carboxylesterase with synthetic ester-degrading activity'. Microbial Biotechnology, 17 (6) [DOI] [Details]
(2023)'Purification and biochemical characterization of SM14est, a PET-hydrolyzing enzyme from the marine sponge-derived Streptomyces sp. SM14'
Carr CM;Keller MB;Paul B;Schubert SW;Clausen KSR;Jensen K;Clarke DJ;Westh P;Dobson ADW; (2023) 'Purification and biochemical characterization of SM14est, a PET-hydrolyzing enzyme from the marine sponge-derived Streptomyces sp. SM14'. Frontiers In Microbiology, 14 [DOI] [Details]
(2023)'Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules'
Ryan E;Joyce SA;Clarke DJ; (2023) 'Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules'. Microbiology-SGM, 169 (3) [DOI] [Details]
(2023)'Lipidomic analysis reveals differences in Bacteroides species driven largely by plasmalogens, glycerophosphoinositols and certain sphingolipids'
Ryan, E.; Gonzalez Pastor, B.; Gethings, L.A.; Clarke, D.J.; Joyce, S.A. (2023) 'Lipidomic analysis reveals differences in Bacteroides species driven largely by plasmalogens, glycerophosphoinositols and certain sphingolipids'. Metabolites, 13 (13):360-400   [Details]
(2022)'Identification of BgP, a cutinase-like polyesterase from a deep-sea sponge-derived actinobacterium'
Carr, Clodagh M.; Rodrigues de Oliveira, Bruno Francesco; Jackson, Stephen A.; Laport, Marinella Silva; Clarke, David J.; Dobson, Alan D. W. (2022) 'Identification of BgP, a cutinase-like polyesterase from a deep-sea sponge-derived actinobacterium'. Frontiers In Microbiology, 13 :1-16 [DOI] [Full Text] [Details]
(2021)'In Vitro and In Vivo Assessment of the Potential of Escherichia coli Phages to Treat Infections and Survive Gastric Conditions'
Kaczorowska, J;Casey, E;Lugli, GA;Ventura, M;Clarke, DJ;van Sinderen, D;Mahony, J (2021) 'In Vitro and In Vivo Assessment of the Potential of Escherichia coli Phages to Treat Infections and Survive Gastric Conditions'. Microorganisms, 9 [DOI] [Details]
(2020)'Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria'
Li J.H.;Oh J.;Kienesberger S.;Kim N.Y.;Clarke D.J.;Zechner E.L.;Crawford J.M. (2020) 'Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria'. Angewandte Chemie International Edition, [DOI] [Details]
(2020)'Photorhabdus: a tale of contrasting interactions'
Clarke, DJ (2020) 'Photorhabdus: a tale of contrasting interactions'. Microbiology-SGM, 166 :335-348 [DOI] [Details]
(2020)'Microbial Polyethylene Terephthalate Hydrolases: Current and Future Perspectives'
Carr CM;Clarke DJ;Dobson ADW; (2020) 'Microbial Polyethylene Terephthalate Hydrolases: Current and Future Perspectives'. Frontiers In Microbiology, 11 [DOI] [Details]
(2020)'Nigral overexpression of alpha-synuclein in a rat Parkinson's disease model indicates alterations in the enteric nervous system and the gut microbiome'
O'Donovan, SM;Crowley, EK;Brown, JRM;O'Sullivan, O;O'Leary, OF;Timmons, S;Nolan, YM;Clarke, DJ;Hyland, NP;Joyce, SA;Sullivan, AM;O'Neill, C (2020) 'Nigral overexpression of alpha-synuclein in a rat Parkinson's disease model indicates alterations in the enteric nervous system and the gut microbiome'. Neurogastroenterology and Motility, 32 [DOI] [Details]
(2019)'Iso-propyl stilbene: a life cycle signal?'
Hapeshi, A;Benarroch, JM;Clarke, DJ;Waterfield, NR (2019) 'Iso-propyl stilbene: a life cycle signal?'. Microbiology-SGM, 165 :516-526 [DOI] [Details]
(2019)'The glycine lipids of Bacteroides thetoiotaomicron are important for fitness during growth in vivo and in vitro'
Lynch, A;Tammireddy, SR;Doherty, MK;Whitfield, PD;Clarke, DJ (2019) 'The glycine lipids of Bacteroides thetoiotaomicron are important for fitness during growth in vivo and in vitro'. Applied and Environmental Microbiology, 85 [DOI] [Details]
(2019)'Microbial Population Changes in Decaying Ascophyllum nodosum Result in Macroalgal-Polysaccharide-Degrading Bacteria with Potential Applicability in Enzyme-Assisted Extraction Technologies'
Ihua, MW;Guiheneuf, F;Mohammed, H;Margassery, LM;Jackson, SA;Stengel, DB;Clarke, DJ;Dobson, ADW (2019) 'Microbial Population Changes in Decaying Ascophyllum nodosum Result in Macroalgal-Polysaccharide-Degrading Bacteria with Potential Applicability in Enzyme-Assisted Extraction Technologies'. Marine Drugs, 17 [DOI] [Details]
(2019)'Role of the Photorhabdus Dam methyltransferase during interactions with its invertebrate hosts'
Payelleville A.;Blackburn D.;Lanois A.;Pagès S.;Cambon M.;Ginibre N.;Clarke D.;Givaudan A.;Brillard J. (2019) 'Role of the Photorhabdus Dam methyltransferase during interactions with its invertebrate hosts'. Plos One, 14 (10) [DOI] [Details]
(2017)'The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity'
Lynch A;Crowley E;Casey E;Cano R;Shanahan R;McGlacken G;Marchesi JR;Clarke DJ; (2017) 'The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity'. Scientific Reports, 7 (1) [DOI] [Details]
(2017)'Synthesis and characterisation of cross-linked chitosan composites functionalised with silver and gold nanoparticles for antimicrobial applications'
Ryan C;Alcock E;Buttimer F;Schmidt M;Clarke D;Pemble M;Bardosova M; (2017) 'Synthesis and characterisation of cross-linked chitosan composites functionalised with silver and gold nanoparticles for antimicrobial applications'. Science and Technology of Advanced Materials, 18 (1) [DOI] [Details]
(2017)'HexA is a versatile regulator involved in the control of phenotypic heterogeneity of Photorhabdus luminescens'
Langer, Angela; Moldovan, Adriana; Harmath, Christian; Joyce, Susan A.; Clarke, David J.; Heermann, Ralf (2017) 'HexA is a versatile regulator involved in the control of phenotypic heterogeneity of Photorhabdus luminescens'. Plos One, 12 (4):1-23 [DOI] [Full Text] [Details]
(2016)'The Regulation of Secondary Metabolism in Photorhabdus'
Clarke DJ; (2016) 'The Regulation of Secondary Metabolism in Photorhabdus'. Current Topics In Microbiology And Immunology, [DOI] [Details]
(2013)'Pathogenesis of adherent-invasive Escherichia coli'
Smith, EJ;Thompson, AP;O'Driscoll, A;Clarke, DJ (2013) 'Pathogenesis of adherent-invasive Escherichia coli'. Future Microbiology, 8 :1289-1300 [DOI] [Details]
(2012)'Nematode Parasites and Entomopathogens'
Lewis, EE,Clarke, DJ,Vega, FE,Kaya, HK (2012) 'Nematode Parasites and Entomopathogens'. Insect Pathology, 2nd Edition, :395-424 [DOI] [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]
(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 [DOI] [Details]
(2010)'The role of iron uptake in pathogenicity and symbiosis in Photorhabdus luminescens TT01'
Watson, RJ;Millichap, P;Joyce, SA;Reynolds, S;Clarke, DJ (2010) 'The role of iron uptake in pathogenicity and symbiosis in Photorhabdus luminescens TT01'. BMC Microbiology, 10 [DOI] [Details]
(2010)'Probing the tri-trophic interaction between insects, nematodes and Photorhabdus'
Eleftherianos, I;Joyce, S;Ffrench-Constant, RH;Clarke, DJ;Reynolds, SE (2010) 'Probing the tri-trophic interaction between insects, nematodes and Photorhabdus'. Journal Of Parasitology, 137 :1695-1706 [DOI] [Details]
(2009)'Methods in Investigating Nematode-Bacterium-Insect Symbiosis'
Goodrich-Blair, H,Clarke, DJ,Grewal, PS,Ciche, TA,Stock, SP,Vanderberg, J,Boemare, N,Glazer I (2009) 'Methods in Investigating Nematode-Bacterium-Insect Symbiosis'. Insect Pathogens: Molecular Approaches And Techniques, :241-271 [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]
(2016)'Alarmone (p)ppGpp regulates the transition from pathogenicity to mutualism in Photorhabdus luminescens'
Bager R;Roghanian M;Gerdes K;Clarke DJ; (2016) 'Alarmone (p)ppGpp regulates the transition from pathogenicity to mutualism in Photorhabdus luminescens'. Molecular Microbiology, 100 (4) [DOI] [Details]
(2016)'Glycolysis and pyrimidine biosynthesis are required for replication of adherent-invasive Escherichia coli in macrophages'
Thompson AP;O'Neill I;Smith EJ;Catchpole J;Fagan A;Burgess KE;Carmody RJ;Clarke DJ; (2016) 'Glycolysis and pyrimidine biosynthesis are required for replication of adherent-invasive Escherichia coli in macrophages'. Microbiology (Reading, England), 162 (6) [DOI] [Details]
(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]
(2011)'Degradation of the Extracellular Matrix Components by Bacterial-derived Metalloproteases: Implications for Inflammatory Bowel Diseases'
Pruteanu, M;Hyland, NP;Clarke, DJ;Kiely, B;Shanahan, F (2011) 'Degradation of the Extracellular Matrix Components by Bacterial-derived Metalloproteases: Implications for Inflammatory Bowel Diseases'. Inflammatory Bowel Diseases, 17 :1189-1200 [DOI] [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-SGM, 155 :3544-3553 [DOI] [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]
(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]
(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]
(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]
(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, Ioannis; Boundy, Sam; Joyce, Susan A.; Aslam, Shazia; Marshall, James W.; Cox, Russell J.; Simpson, Thomas J.; Clarke, David J.; ffrench-Constant, Richard H.; Reynolds, Stuart E. (2007) 'An antibiotic produced by an insect-pathogenic bacterium suppresses host defenses through phenoloxidase inhibition'. Proceedings of The National Acadamy of Sciences, 104 (7):2419-24   [DOI] [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]

Book Chapters

 YearPublication
(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]

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 Activities

Professional Associations

 AssociationFunctionFrom / To
Microbiology Society (previously Society for General Microbiolopgy) Member/
American Society for Microbiology Member/

Committees

 CommitteeFunctionFrom / To
Microbiology Society Governing Council Elected member2022 / 2024
Microbiology Society Irish Division committee Chair2018 / 2019
Society for General Microbiology Prokaryotic Division Committee member2010 / 2014
Microbiology Society Irish Division committee Member2016 / 2019

Employment

 EmployerPositionFrom / To
University College Cork Lecturer01-FEB-07 /
University College Cork Head of School01-AUG-22 /
University College Cork Senior Lecturer01-JUL-19 /
University College Cork SEFS Vice Dean for Graduate Affairs01-AUG-21 / 31-JUL-22
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
EU, FCT (Portugal), 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
Microbiology Editor01-JUN-21 -
Fems Microbiology Letters Member of Editorial Board01-JAN-04 - 31-DEC-14

Other Activities

 Description

I have been an invited speaker at a number of international conferences and have given invited research seminars at research institutes/universities in 6 different countries since 2007.

Teaching Activities

Recent Postgraduates

 Graduation YearStudent NameInstitutionDegree TypeThesis Title
2013Aoife Thompson UCCPhD
2016Ian O'Neill UCCPHDA molecular analysis of the interaction between Escherichia coli and macrophage
2011Catherine Easom UCCPhD
2012Lea Lango UCCPhD
2012Adam O'Driscoll UCCPhD

Contact details

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School of Microbiology

Scoil na Micribhitheolaíochta

Microbiology Office, Room FSB452, 4th Floor Food Science & Technology Building, University College Cork, Cork T12 Y337

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