David Fitzpatrick, BSc, PhD (NUI)
Head of Laboratory

 

Genome Evolution Laboratory

• Dr. David Fitzpatrick;
  Fax: (353-1) 708 3845;
• david.fitzpatrick@nuim.ie

Research Interests

The research of this laboratory focuses on the evolution of unicellular microorganisms paying special attention to fungal species. We use comparative genomics, phylogenomics, phylogenetics and synteny based tools to elucidate fungal gene and genome evolution. We are currently using comparative genomics to perform an analysis of 8 Candida and related species, both pathogenic and non-pathogenic, to identify species-specific metabolic pathways and lineage-specific loss or gain of metabolic genes. The presence or absence of particular pathways or pathway components can be correlated with pathogenesis and species-specific virulence characteristics, which can lead to the development of novel therapeutic strategies. We are also investigating the frequency of horizontal gene transfer within the Candida genus. Acquired genetic material from an external source can lead to increased virulence and can provide novel antifungal drug targets. We are also interested in sequencing and annotating medically / biotechnological important fungal strains.

Current Sources of Funding

Health Research Board of Ireland

Departmental funding

Publications

• Reardon W, Fitzpatrick DA, Fares MA, Nugent JM. Evolution of flower shape in Plantago lanceolata. Plant Mol Biol. 2009 Oct;71(3):241-50.
• Haggerty LS, Martin FJ, Fitzpatrick DA, McInerney JO. Gene and genome trees conflict at many levels. Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2209-19.
• Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 2009 Jun 4;459(7247):657-62.
• Fitzpatrick DA. Lines of evidence for horizontal gene transfer of a phenazine producing operon into multiple bacterial species. J Mol Evol. 2009 Feb;68(2):171-85.
• S. O. Regeai, K. M. Dolan, D.A. Fitzpatrick, J. A. Browne, J. T. Jones and A. M. Burnell. Novel primers for the amplification of nuclear DNA introns in the entomopathogenic nematode Heterorhabditis bacteriophora and their cross-amplification in seven other Heterorhabditis species. Molecular Ecology Notes (In press)
• Fitzpatrick DA, Logue ME, Butler G. Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evol Biol. 2008 Jun 24;8:181.
• Fitzpatrick D.A, Logue ME, Stajich JE, Butler G. A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol. 2006 6(1):99
• Johnston CR, O'dushlaine C, Fitzpatrick D.A., Edwards RJ, Shields DC. Evaluation Of Whether Accelerated Protein Evolution In Chordates Has Occurred Before, After Or Simultaneously With Gene Duplication. Mol Biol Evol. 2006 Oct 25.
• *Fitzpatrick, D.A., O'Halloran, D.M. and Burnell, A.M. Multiple Lineage Specific Expansions in the Guanylyl Cyclase Gene Family. BMC Evolutionary Biology 2006, 6:26.
• O'Halloran, D.M., *Fitzpatrick, D.A., McCormack, G.P., McInerney, J.O. and Burnell, A.M. The Molecular Phylogeny and Functional Significance of a Nematode Specific Clade of Heterotrimeric G-protein α-Subunit Genes. J Mol Evol. 2006 Jul;63(1):87-94
• Fitzpatrick DA, Creevey CJ and McInerney JO (2005). An α-proteobacterial molecular phylogeny using a supertree approach and a place for the mitochondria among the α-proteobacteria. Molecular Biology and Evolution 23(1) 74-85.
• Fitzpatrick DA, Creevey CJ and McInerney JO (2005). Evidence of positive Darwinian selection in putative meningococcal vaccine antigens. Journal of Molecular Evolution 60 (1), 90-98.
• Shannon, A. Browne, JA. Boyd, J. Fitzpatrick, DA and Burnell, AM (2005). The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus Journal of Experimental Biology 208:2433-2445.
• Fitzpatrick DA and McInerney JO (2005). Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability. Journal of Molecular Evolution 60(2) 268-73.
• Creevey, C. J., Fitzpatrick, D. A., Philip, G. K., Kinsella, R. J., O’Connell, M. J., Pentony, M. M., Travers, S. A., Wilkinson, M. and McInerney, J. O. (2004) A tree-like phylogeny only exists at the tips in the prokaryotes. Proceedings of the Royal Society London, B series: Biological Sciences 271 (1557): 2551-8.
• Kinsella RJ, Fitzpatrick DA, Creevey CJ, McInerney JO (2003) Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication. Proceedings of the National Academy of Sciences of the United States of America 100:10320-5

  * Joint first author

Book Chapters

• Comparative genomic analysis of pathogenic yeasts and the evolution of virulence.  D vid A. Fitzpatrick and Geraldine Butler (In press)
• O’Halloran, DM. Fitzpatrick, DA and Burnell, AM. Chemoreception and Chemoreceptor Genes in Nematodes (2006), In: Chemical Communication: from Genes to Ecosystems. Eds Marcel Dicke and Willem Takken (Frontis Publishing).
• McInerney, J.O., Pisani, D., O’Connell, M.J., Fitzpatrick, D.A. and Creevey,C.J. (2006). A Prokaryotic Phylogenetic Tree: Yes or No? In: Towards the Tree of Life: taxonomy and systematics of large and species rich taxa. Eds: Trevor Hodkinson, John Parnell and Steve Waldren. Systematic Association special volume, CRC Press.

Last edited: Monday, 31-Aug-2009 10:29:29 IST

Biology Department , NUI Maynooth
Tel: +353-1-708 3843 | Fax: +353-1-708 3845| Email: terry.roche@nuim.ie