Dr Andrew T Lloyd

PhD, BA
Lecturer in Molecular Evolution
e: andrew.lloyd@itcarlow.ie t: 059 9175518

 
  • Research Interests
  • Publications
  • Research Supervision

Research Interests

Formerly Director of the Irish National Centre for Bioinformatics INCBI, I have spent the last 25 years staring at biological sequences – DNA and proteins – to make sense of their evolution. Early work in software development for high throughput analysis of protein coding DNA sequences grew into whole genome analysis investigating the constraints imposed by genomic location on gene expression. Whole genome analysis, including Next Generation Sequence data, focussed on novel gene discovery particularly in genes related to the innate immune response.  Numerous antimicrobial peptides and an avian specific toll-like receptor TLR15 were among those discoveries.

Collaborations in IT Carlow have led to in interest in hydrogeology; in particular the distribution of metal ions in groundwater, surface water, soils and plants. This is creating a map of the invisible chemical world beneath the skin of County Carlow.  This is an important benchmark against which to set the imminent mining of Mt Leinster for lithium-rich minerals.

Publications

Microbial Biochemistry

Oteino N, Lally RD, Kiwanuka S, Lloyd A, Ryan D, Germaine KJ, Dowling DN. Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Front Microbiol. 2015 Jul 22;6:745. PubMed PMID: 26257721.

Rathore DS, Lopez-Vernaza MA, Doohan F, Connell DO, Lloyd A, Mullins E. Profiling antibiotic resistance and electrotransformation potential of Ensifer adhaerens OV14; a non-Agrobacterium species capable of efficient rates of plant transformation. FEMS Microbiol Lett. 2015 Sep;362(17). PubMed PMID: 26253576.

Innate Immunity


Johnson GP, Lloyd AT, O'Farrelly C, Meade KG, Fair S. Comparative genomic identification and expression profiling of a novel β-defensin gene cluster in the equine reproductive tract. Reprod Fertil Dev. 2015 Apr 30. PubMed PMID: 25924226.

Whelehan CJ, Barry-Reidy A, Meade KG, Eckersall PD, Chapwanya A, Narciandi F,  Lloyd AT, O'Farrelly C. Characterisation and expression profile of the bovine cathelicidin gene repertoire in mammary tissue. BMC Genomics. 2014 Feb 13;15:128. PMID: 24524771.

Meade KG, Cormican P, Narciandi F, Lloyd A, O'Farrelly C. Bovine β-defensin gene family: opportunities to improve animal health? Physiol Genomics. 2014 Jan 1;46(1):17-28. PubMed  PMID: 24220329.

Narciandi F, Lloyd A, Meade KG, O'Farrelly C. A novel subclass of bovine beta-defensins links reproduction and immunology. Reprod Fertil Dev. 2013 Jul 22. doi: 10.1071/RD13153. PMID: 23870162.

Collins AS, McCoy CE, Lloyd AT, O'Farrelly C, Stevenson NJ. miR-19a: an effective regulator of SOCS3 and enhancer of JAK-STAT signalling. PLoS One. 2013  Jul 22;8(7):e69090. doi: 10.1371/journal.pone.0069090. Print 2013. PMID: 23894411.

Connell S, Meade KG, Allan B, Lloyd AT, Downing T, O'Farrelly C, Bradley DG. Genome-wide association analysis of avian resistance to Campylobacter jejuni colonization identifies risk locus spanning the CDH13 gene. G3 (Bethesda). 2013 May 20;3(5):881-90. PMID: 23550144.

Connell S, Meade KG, Allan B, Lloyd AT, Kenny E, Cormican P, Morris DW, Bradley DG, O'Farrelly C. Avian resistance to Campylobacter jejuni colonization is associated with an intestinal immunogene expression signature identified by mRNA sequencing. PLoS One. 2012;7(8):e40409. doi: 10.1371/journal.pone.0040409. PMID: 22870198.

Narciandi F, Lloyd AT, Chapwanya A, O' Farrelly C, Meade KG. Reproductive tissue-specific expression profiling and genetic variation across a 19 gene bovine β-defensin cluster. Immunogenetics. 2011 Oct;63(10):641-51. PMID: 21713586.

Downing T, Lloyd AT, O'Farrelly C, Bradley DG. The differential evolutionary dynamics of avian cytokine and TLR gene classes. J Immunol. 2010 Jun 15;184(12):6993-7000. PMID: 20483729.

Downing T, Cormican P, O'Farrelly C, Bradley DG, Lloyd AT. Evidence of the adaptive evolution of immune genes in chicken. BMC Res Notes. 2009 Dec 15;2:254.  PMID: 20003477.

Cormican P, Lloyd AT, Downing T, Connell SJ, Bradley D, O'Farrelly C. The avian Toll-Like receptor pathway--subtle differences amidst general conformity. Dev Comp Immunol. 2009 Sep;33(9):967-73. PMID: 19539094.

Downing T, Lynn DJ, Connell S, Lloyd AT, Bhuiyan AK, Silva P, Naqvi AN, Sanfo  R, Sow RS, Podisi B, Hanotte O, O'Farrelly C, Bradley DG. Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus. BMC Evol Biol. 2009 Jun 15;9:136. PMID: 19527513.

Downing T, Lynn DJ, Connell S, Lloyd AT, Bhuiyan AK, Silva P, Naqvi AN, Sanfo R, Sow RS, Podisi B, O'Farrelly C, Hanotte O, Bradley DG. Contrasting evolution of diversity at two disease-associated chicken genes. Immunogenetics. 2009 Apr;61(4):303-14. PMID: 19247647.

Meade KG, Cahalane S, Narciandi F, Cormican P, Lloyd AT, O'Farrelly C. Directed alteration of a novel bovine beta-defensin to improve antimicrobial efficacy against methicillin-resistant Staphylococcus aureus (MRSA). Int J Antimicrob Agents. 2008 Nov;32(5):392-7. PMID: 18775651.

Cormican P, Meade KG, Cahalane S, Narciandi F, Chapwanya A, Lloyd AT, O'Farrelly C. Evolution, expression and effectiveness in a cluster of novel bovine beta-defensins. Immunogenetics. 2008 Apr;60(3-4):147-56. doi: 10.1007/s00251-007-0269-8. PMID: 18369613.

Higgs R, Lynn DJ, Cahalane S, Alaña I, Hewage CM, James T, Lloyd AT, O'Farrelly C. Modification of chicken avian beta-defensin-8 at positively selected amino acid sites enhances specific antimicrobial activity. Immunogenetics. 2007 Jul;59(7):573-80. PMID: 17483936.

Lynn DJ, Higgs R, Lloyd AT, O'Farrelly C, Hervé-Grépinet V, Nys Y, Brinkman FS, Yu PL, Soulier A, Kaiser P, Zhang G, Lehrer RI. Avian beta-defensin nomenclature: a community proposed update. Immunol Lett. 2007 May 15;110(1):86-9. PMID: 17467809.

Higgs R, Cormican P, Cahalane S, Allan B, Lloyd AT, Meade K, James T, Lynn DJ, Babiuk LA, O'farrelly C. Induction of a novel chicken Toll-like receptor following Salmonella enterica serovar Typhimurium infection. Infect Immun. 2006 Mar;74(3):1692-8. PMID: 16495540; PubMed Central PMCID: PMC1418683.

Higgs R, Lynn DJ, Gaines S, McMahon J, Tierney J, James T, Lloyd AT, Mulcahy  G, O'Farrelly C. The synthetic form of a novel chicken beta-defensin identified in silico is predominantly active against intestinal pathogens. Immunogenetics. 2005 Apr;57(1-2):90-8. Epub 2005 Mar 3. PMID: 15744537.

Lynn DJ, Higgs R, Gaines S, Tierney J, James T, Lloyd AT, Fares MA, Mulcahy G, O'Farrelly C. Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken. Immunogenetics. 2004 Jun;56(3):170-7. PMID: 15148642.

Lynn DJ, Lloyd AT, Fares MA, O'Farrelly C. Evidence of positively selected sites in mammalian alpha-defensins. Mol Biol Evol. 2004 May;21(5):819-27. PMID: 14963090.

Lynn DJ, Lloyd AT, O'Farrelly C. In silico identification of components of the Toll-like receptor (TLR) signaling pathway in clustered chicken expressed sequence tags (ESTs). Vet Immunol Immunopathol. 2003 Jun 20;93(3-4):177-84. PMID: 12814703.


Colon Cancer


Coss A, Tosetto M, Fox EJ, Sapetto-Rebow B, Gorman S, Kennedy BN, Lloyd AT, Hyland JM, O'Donoghue DP, Sheahan K, Leahy DT, Mulcahy HE, O'Sullivan JN. Increased topoisomerase IIalpha expression in colorectal cancer is associated with advanced disease and chemotherapeutic resistance via inhibition of apoptosis. Cancer Lett. 2009 Apr 18;276(2):228-38. PMID: 19111388.


Developmental Biology


Meade KG, Higgs R, Lloyd AT, Giles S, O'Farrelly C. Differential antimicrobial peptide gene expression patterns during early chicken embryological development. Dev Comp Immunol. 2009 Apr;33(4):516-24. PMID: 19007808.


Whole Genome Analysis


Singer GA, Lloyd AT, Huminiecki LB, Wolfe KH. Clusters of co-expressed genes  in mammalian genomes are conserved by natural selection. Mol Biol Evol. 2005 Mar;22(3):767-75. Epub 2004 Dec 1. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1160. PMID: 15574806.

Huminiecki L, Lloyd AT, Wolfe KH. Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. BMC Genomics. 2003  Jul 29;4(1):31. PMID: 12885301.

Lynn DJ, Lloyd AT, O'Farrelly C. Bioinformatics: implications for medical research and clinical practice. Clin Invest Med. 2003 Apr;26(2):70-4. PMID: 12722839.

Duffy MJ, Lynn DJ, Lloyd AT, O'Shea CM. The ADAMs family of proteins: from basic studies to potential clinical applications. Thromb Haemost. 2003 Apr;89(4):622-31. Review. PMID: 12669115.

Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res. 1999 Apr 1;27(7):1642-9. PMID: 10075995.


Phylogenetics


Lloyd AT, Sharp PM. Evolution of the recA gene and the molecular phylogeny of bacteria. J Mol Evol. 1993 Oct;37(4):399-407. PMID: 8308907.


Synonymous Codon Usage


Sharp PM, Averof M, Lloyd AT, Matassi G, Peden JF. DNA sequence evolution: the sounds of silence. Philos Trans R Soc Lond B Biol Sci. 1995 Sep 29;349(1329):241-7. Review. PMID: 8577834.

Stenico M, Lloyd AT, Sharp PM. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res.  1994 Jul 11;22(13):2437-46. PMID: 8041603.

Sharp PM, Stenico M, Peden JF, Lloyd AT. Codon usage: mutational bias, translational selection, or both? Biochem Soc Trans. 1993 Nov;21(4):835-41. Review. PMID: 8132077.

Lloyd AT, Sharp PM. Synonymous codon usage in Kluyveromyces lactis. Yeast. 1993 Nov;9(11):1219-28. PMID: 8109171.

Sharp PM, Lloyd AT. Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. Nucleic Acids Res. 1993 Jan 25;21(2):179-83. PMID: 8441625.

Lloyd AT, Sharp PM. Evolution of codon usage patterns: the extent and nature  of divergence between Candida albicans and Saccharomyces cerevisiae. Nucleic Acids Res. 1992 Oct 25;20(20):5289-95. PMID: 1437548.

Lloyd AT, Sharp PM. CODONS: a microcomputer program for codon usage analysis. J Hered. 1992 May-Jun;83(3):239-40. PMID: 1624775.

Lloyd AT, Sharp PM. Codon usage in Aspergillus nidulans. Mol Gen Genet. 1991  Nov;230(1-2):288-94. PMID: 1745237.


Population Genetics


Lloyd AT. Cats from history and history from cats. Endeavour. 1987;11(3):112-5. PMID: 2445554.
Todd NB, Lloyd AT. Mutant allele frequencies in domestic cats of Portugal and the Azores. J Hered. 1984 Nov-Dec;75(6):495-7. PMID: 6512241.


Palaeoanthropology

Blumenberg B, Lloyd AT. Australopithecus and the origin of the genus Homo: aspects of biometry and systematics with accompanying catalog of tooth metric data. Biosystems. 1983;16(2):127-67. Review. PMID: 6416328.

Research Supervision

I have supervised two PhD students to completion of theses on gene discovery and the innate immune system.  Since arriving in IT Carlow,  I have been co-supervising three post-graduate students: one MSc, one transferred to PhD and one in the process of transfer.