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
| Project | Funding Body | Start Date | End Date | Award | |
|---|---|---|---|---|---|
| Marine Biodiversity as Sustainable Resource of Disease-Suppressive Microbes and Bioprotectants for Aquaculture and Crop Diseases | Horizon 2020 | 01-APR-20 | 31-MAR-25 | €606,505.00 | |
| A systems level approach to understanding the role and regulation of phenotypic | Enterprise Irl | 29-AUG-18 | 28-MAY-19 | €3,444.00 | |
| Trainign Network to Deliver a Systems-level Understanding of Entomopathogenic Nematode Production. | Enterprise Irl | 04-AUG-17 | 04-MAY-18 | €5,650.00 | |
| Role of Photorhabdus DNA | Irish Research Council | 01-JAN-18 | 31-DEC-18 | €1,588.00 | |
| Stilbene and Entomopathogenic Nematodes: Unlocking the Potential | Horizon 2020 | 01-JAN-17 | 31-DEC-18 | €175,866.00 | |
| Biofilm formation by E Coli in the gastrointestinal tract. | Irish Research Council | 01-OCT-14 | 30-SEP-18 | €96,000.00 | |
| Characterisation of choA, a gene encoding a novel cholesterol-degrading activity in the human gut. | Science Foundation of Ireland | 01-APR-13 | 31-JUL-17 | €244,318.00 | |
| individual consumable budget. | Higher Education authority | 01-MAR-11 | 30-SEP-15 | €38,260.00 | |
| SFI CSET Programme 2 - High Throughput Analysis Platform B | Science Foundation of Ireland | 01-NOV-08 | 31-OCT-13 | €215,751.00 | |
| SFI CSET Programme 2 - Genomics & Metagenomics Core 4c | Science Foundation of Ireland | 01-NOV-08 | 31-OCT-13 | €214,279.00 | |
| Molecular characterization of a novel invasion produced by adherent-invasive Escherichia coli. | Foreign Research Institute | 01-JUN-13 | 23-AUG-13 | €2,200.00 | |
| Regulation of a DNA switch that controls pathogenicity and mutualism in Photorhabdus luminescens. | Foreign Research Institute | 31-MAY-12 | 12-AUG-12 | €1,761.00 | |
| Moleacular Mechanisms of Adherent Invasive Escherichia Coli (AIEC) Persistance in Macronphag... | Health Research Board | 30-AUG-08 | 30-SEP-11 | €152,800.00 | |
| SFI-Integrating metabolism and genomics: aromatic amino acid metabolism in photorhabus luminescence | Science Foundation of Ireland | 01-AUG-07 | 31-DEC-10 | €178,932.00 |
Contract Researchers
| Researcher Name | Project | Role | Funding Body | |
|---|---|---|---|---|
| John Cathcpole | TNF and macrophages | Research Assistant | Science Foundation Ireland | |
| Marc McCarthy | Microbiome metagenomics | Research Assistant | Science Foundation Ireland | |
| Eoghan Casey | Microbiome metagenomics | Research Assistant | Science Foundation Ireland | |
| Elaine Crowley | Microbiome metagenomics | Research Assistant | Science Foundation Ireland | |
| Emma Smith | Invasion mechanisms of adherent-invasive Escherichia coli | Postdoctoral Researcher | Science Foundation Ireland | |
| Susan Joyce | Bioluminescence in Photorhabdus | Senior Postdoctoral Researcher | ||
| Tanishka Talekar | Functional Genomics in Bacteroides | Research Assistant | ||
| Belen Gonzales-Pastor | Functional Gemomic in Baceroides | Research Assistant | ||
| Alli Lynch | Glycine lipids in Bacteroides | Postdoctoral Researcher | ||
| Jane Williams | Photorhabdus functional genomics | Postdoctoral Researcher | ||
| Lionel Ferrieres | Biofilm formation in Escherichia coli | Postdoctoral Researcher | ||
| Dana Blackburn | STEPN-UP: stilbene and entomopathogenic nematodes-unlocking the potential | Research Fellow | EU Marie Sklodowska-Curie Actions (MSCA) Individual Fellowship |
Publications
Peer Reviewed Journals
| Year | Publication | |
|---|---|---|
| (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] | |
| (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] | |
| (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) | '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] | |
| (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) | '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] | |
| (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) | '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] | |
| (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) | '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] | |
| (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) | '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] | |
| (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] | |
| (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) | '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] | |
| (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] | |
| (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] | |
| (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] | |
| (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] | |
| (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, 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] | |
| (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) | '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 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) | '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) | '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 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) | '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) | '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] | |
| (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) | '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] | |
| (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) | '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) | '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) | '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) | '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] | |
| (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] | |
| (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) | '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] | |
| (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) | '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) | '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] | |
| (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) | 'Pathogenicity of Xenorhabdus luminescens' Clarke, D. J.,Dowds, B. C.; (1992) 'Pathogenicity of Xenorhabdus luminescens'. Biochem Soc Trans, 20 (1) [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] |
Book Chapters
| Year | Publication | |
|---|---|---|
| (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
| Year | Publication | |
|---|---|---|
| (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
| Association | Function | From / To | |
|---|---|---|---|
| Microbiology Society (previously Society for General Microbiolopgy) | Member | / | |
| American Society for Microbiology | Member | / |
Committees
| Committee | Function | From / To | |
|---|---|---|---|
| Microbiology Society Governing Council | Elected member | 2022 / 2024 | |
| Academic Council, UCC | Elected member | 2021 / | |
| Academic Council Graduate Studies Committee | Vice-Dean Graduate Studies, SEFS | 2021 / 2022 | |
| SEFS Graduate Studies Committee | Chair | 2021 / 2022 | |
| Academic Council Graduate Studies Committee | SEFS representative | 2018 / 2020 | |
| SEFS Graduate Studies Committee | Member | 2013 / 2019 | |
| Academic Council Student Experience Committee | Member | 2013 / 2015 | |
| Student Financial Concerns and Support Committee | Member | 2012 / 2015 | |
| SEFS Teaching, Learning and Student Experience Committee | Member | 2011 / 2013 | |
| Microbiology Society Irish Division committee | Chair | 2018 / 2019 | |
| Society for General Microbiology Prokaryotic Division | Committee member | 2010 / 2014 | |
| Microbiology Society Irish Division committee | Member | 2016 / 2019 |
Employment
| Employer | Position | From / To | |
|---|---|---|---|
| University College Cork | Lecturer | 01-FEB-07 / | |
| University College Cork | Head of School | 01-AUG-22 / | |
| University College Cork | Senior Lecturer | 01-JUL-19 / | |
| University College Cork | SEFS Vice Dean for Graduate Affairs | 01-AUG-21 / 31-JUL-22 | |
| University of Bath, UK | Senior Lecturer | 01-APR-04 / 31-JAN-07 | |
| University of Bath, UK | Lecturer | 01-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 fellow | 02-MAY-94 / 30-SEP-98 |
Education
| Year | Institution | Qualification | Subject | |
|---|---|---|---|---|
| 1994 | NUI Maynooth | PHD | Microbiology | |
| 1989 | Dublin City University | BSC (HONS) | Biotechnology |
Consultancy
| Client | Description | |
|---|---|---|
| Ad hoc reviewer for international funding agencies and journals | ||
| Merlion |
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
| Journal | Role | To / From | |
|---|---|---|---|
| Microbiology | Editor | 01-JUN-21 - | |
| Fems Microbiology Letters | Member of Editorial Board | 01-JAN-04 - 31-DEC-14 |
Other Activities
| Description | |
|---|---|
Conferences 1. Microbiology Society Annual Conference 2019 2. New Horizons Research Conference 2018 3. Beneficial Microbes, University of Wisconsin 2018 4. Society for Invertebrate Pathology Annual meeting July 2016, Tours, France 5. Metabolism meets virulence, April 2014, Osnabruck, Germany 6. Society for General Microbiology (SGM) Spring Conference April 2013, Manchester 7. SGM Irish Division Meeting, March 2013, University College Dublin 8. Current Trends in Biomedicine Workshop on The Biology of Intracellular Bacterial Pathogens, October 2011, Universidad Internacional de Andalucia, Baeza, Spain 9. 50th Anniversary Meeting of the Society of Nematology July 2011, Corvallis, Oregon, USA 10. 3rd Nemasym meeting, July 2011, Corvallis, Oregon, USA 11. 2nd Nemasym meeting, November 2010, Tucson, Arizona, USA 12. SGM Autumn Conference, September 2010, University of Nottingham 13. 41st Annual Meeting of the Society for Invertebrate Pathology (SIP), August 2008, University of Warwick, UK 14. 40th Annual Meeting of the SIP, August 2007, Quebec, Canada 15. International symposium of the SFB479: Host-pathogen co-evolution: a tale of struggle and affection, November 2007, Wurzburg, Germany 16. Workshop on the Evolution of Symbiosis, April 2006, Edinburgh, UK 17. 38th Annual Meeting of the SIP, August 2005, University of Anchorage, Alaska, USA 18. Oral Microbiology and Immunology Group symposium, November 2004, Bristol, UK. 19. SGM Autumn Conference, September 2004, Trinity College, Dublin. 20. Euroconference on Bacterial Neural Networks, May 2004, Barcelona, Spain 21. International workshop on entomopathogenic nematodes and their bacterial symbionts, November 2003, Eilat, Israel. 22. Royal Entomological Society, July 2003, University of Reading, UK. 23. Euroconference on Bacterial Neural Networks, June 2002, Obernai, France. 24. 27th Wellcome Trust Advanced Course in Genetic, Molecular and Informatic Methods for Caenorhabditis elegans. September 2000, Cambridge, UK. Invited research seminars 1. Janssen Biologics, Ringaskiddy; November 2019 2. Institut Paster, October 2017 3. University of Liverpool 3rd November 2015 4. University of Copenhagen, 29th June 2015 5. Trinity College Dublin 11th December 2014 6. Institute of Food Research, March 2014 7. University of Glasgow, October 2013 8. University of Cardiff, February 2013 9. University of Dundee, September 2012 10. Institut Pasteur, September 2012 11. Ludwig Maximilians Universitat (LMU) Munich, June 2009 12. University of Dublin, February 2009 13. National University of Ireland, Galway, October 2007 14. Institut Pasteur, February 2006 15. Trinity College Dublin, January 2006 16. University of Birmingham, November 2005 17. University of Oxford, November 2004 18. University College Dublin, November 2004 19. John Innes Centre, June 2004 20. University of Reading, June 2004 21. Dublin City University, February 2003 22. University of Birmingham, May 2002 |
Teaching Activities
Recent Postgraduates
| Graduation Year | Student Name | Institution | Degree Type | Thesis Title | |
|---|---|---|---|---|---|
| 2023 | Christina Killian | University College Cork | PHD | ||
| 2017 | Kevin Barrett | University College Cork | Msc | ||
| 2018 | Alli Lynch | University College Cork | PHD | ||
| 2019 | Finbarr Buttimer | University College Cork | PHD | ||
| 2013 | Aoife Thompson | UCC | PhD | ||
| 2011 | Hilton McWeeney | NUI Maynooth | PHD | ||
| 2024 | Clodagh Carr | University College Cork | PHD | ||
| 2016 | Ian O'Neill | UCC | PHD | A molecular analysis of the interaction between Escherichia coli and macrophage | |
| 2011 | Catherine Easom | UCC | PhD | ||
| 2012 | Lea Lango | UCC | PhD | ||
| 2012 | Adam O'Driscoll | UCC | PhD |
Current Postgraduate Students
| Student | Degree Type | |
|---|---|---|
| Gzara Fairouz Sarah Hanane | Doctoral Degree |
Research Information
Internal Collaborators
| Name | Institute | Country | |
|---|---|---|---|
| Alan Dobson | UCC | IRELAND | |
| Susan Joyce | UCC | IRELAND |
External Collaborators
| Name | Organisation / Institute | Country | |
|---|---|---|---|
| Prof Helge B. Bode | Goethe Universitat Frankfurt | GERMANY | |
| Ricardo Machado | University of Neuchatel | SWITZERLAND | |
| Philip Aherne | Lerner Research Institute Cleveland Clinic | U.S.A. |