Publications

Peer Reviewed Journals: 2009-

• Ansell, R.J., Tunon, P.G, Wang, Y., Myers, P., Ivory, C.F., Keen, J.N. and Findlay J.B.C., 2009, Electophoretic field gradient focusing with on-column detection by fluorescence quenching, ANALYST, 134, 226-229
• Butler, G., M.D. Rasmussen, M.F. Lin Manuel, A.S. Santos, S. Sakthikumar, C.A. Munro, E. Rheinbay, M. Grabherr, A. Forche, J.L. Reedy, I. Agrafioti, M.B. Arnaud, S. Bates, A.J.P. Brown, S. Brunke, M.C. Costanzo, D.A. Fitzpatrick, P.W.J. de Groot, D. Harris, L.L. Hoyer, B. Hube, F.M. Klis, C. Kodira, N.Lennard, M.E. Logue, R. Martin, A.M. Neiman, E. Nikolaou, M.A. Quail, J. Quinn, M.C. Santos, F.F. Schmitzberger, G. Sherlock, P. Shah, K.A.T. Silverstein, M.S. Skrzypek, D. Soll, R. Staggs, I. Stansfield, M.P.H. Stumpf, P.E. Sudbery, T. Srikantha, Q. Zeng, J. Berman, M. Berriman, J. Heitman, N.A.R. Gow, M.C. Lorenz, B.W. Birren, M. Kellis and C.A. Cuomo, 2009, Evolution of pathogenicity and sexual reproduction in eight Candida genomes, NATURE, 459, May, 657-662
• Coughlan, A., K. Scanlon, B.P. Mahon and M.R. Towler, 2010, Zinc and Silver Glass Polyalkenoate Cement Solutions: An Evaluation of their Antibacterial Nature Through in vitro and in vivo Testing., BIO-MEDICAL MATERIALS AND ENGINEERING, 20, 99-106
• Dalton J.P., Brindley P.J., Donnelly S. and Robinson, M.W., 2009, The enigmatic asparaginyl endopeptidase of Helminth parasites, TRENDS IN PARASITOLOGY, 25, 2, 59-61
• Diekmann, K., Hodkinson, T.R., Wolfe, K.H., Van Den Bekerom, R., Dix, P.J. and Barth, S., 2009, Complete chloroplast genome sequence of a major allogamous forage species, perennial ryegrass (Lolium perenne L.), DNA RESEARCH, 16, 165-176
• Donoghue P., Staunton L., Mullen E., Manning G. and Ohlendieck, K., 2010, DIGE analysis of rat skeletal muscle proteins using nonionic detergent phase extraction of young adult versus aged gastrocnemius tissue, JOURNAL OF PROTEOMICS, 73, 1441-1453
• Doran, P., Wilton, S.D., Fletcher, S., Ohlendieck ,K., 2009, Proteomic profiling of antisense-induced exon skipping reveals reversal of pathobiochemical abnormalities in dystrophic mdx diaphragm, PROTEOMICS, 9, 3, 671-685
• Dowling D.J., Hamilton, C.M., Donnelly, S., La Course, J., Brophy, P.M., Dalton, J. and O'Neill, SM., 2009, Major secretory antigens of the helminth Fasciola hepatica activate a suppressive dendritic cell phenotype that attenuates Th17 cells but fails to activate Th2 immune responses, INFECTION AND IMMUNITY, 78(2):793-801. Epub. Nov 16
• English K., Mahon, B.P. and Woods, K.J., 2011, Mesenchymal Stromal Cells: Role in Tissue Repair, Drug Discovery and Transplantation Tolerance, CURRENT DRUG DELIVERY, in press
• English, K., J.R. Ryan, L. Tobin, M.J. Murphy, F.P. Barry and B.P. Mahon, 2009, Cell Contact, Prostaglandin E2 and Transforming growth factor beta 1 play non redundant roles in Human Mesenchymal Stem Cell Induction of CD4+CD25HighFoxp3+ Regulatory T cells, CLINICAL AND EXPERIMENTAL IMMUNOLOGY, 156, 149-160
• Ennis, D., Dillon, A.B and Griffin, C.T., 2010, Simulated roots and host feeding enhance infection of subterranean insects by the entomopathogenic nematode Steinernema carpocapsae, JOURNAL OF INVERTEBRATE PATHOLOGY, 104, 140-143
• Everard, A., C.T. Griffin and A.B. Dillon, 2009, Competition and intraguild predation between the braconid parasitoid Bracon hylobii and the entomopathogenic nematodes Heterorhabditis downesi, natural enemies of the large pine weevil, Hylobius abietis, BULLETIN OF ENTOMOLOGICAL RESEARCH, 99,  151-161
• Field-Corbett, C., English, K. and O'Dea, S., 2009, Regulation of surfactant protein B gene expression in bone marrow-derived cells, STEM CELLS, 27, 662-669
• Fitzpatrick, D.A., P. O'Gaora, K.P. Byrne and G. Butler, 2010, Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser, BMC GENOMICS, 11, 290, May
• Fitzpatrick D.A, 2009, Lines of evidence for horizontal gene transfer of a phenazine producing operon into multiple bacterial species, JOURNAL OF MOLECULAR EVOLUTION, 68, 2, Feb., 171-185
• Gaffney, M., Carberry, S., Doyle, S. and Murphy, R., 2009, Purification and characterisation of a xylanase from Thermomyces lanuginosus and subsequent expression by Pichia pastoris, ENZYME AND MICROBIAL TECHNOLOGY, 45, 348-354
• Gaffney, M., Doyle, S., and Murphy, R., 2009, Optimisation of xylanase production by Thermomyces lanuginosus in solid state fermentation, BIOSCIENCE, BIOTECHNOLOGY AND BIOCHEMISTRY, 73,   2640-2644
• Gannon, J., Doran, P., Kirwan, A. and Ohlendieck. K., 2009, Drastic increase of myosin light chain MLC-2 in senescent skeletal muscle indicates fast-to-slow fibre transition in sarcopenia of old age, EUROPEAN JOURNAL OF CELL BIOLOGY, 88, 11, 685-700
• Goh, F., Irvine, K.M., Lovelace, E., Donnelly, S, Jones, M.K., Brion, K., Hume, D.A., Kotze, A.C., Dalton, J.P., Ingham, A., Sweet, M.J., 2009, Selective induction of the Notch ligand Jagged-1 in macrophages by soluble egg antigen from Schistosoma mansoni involves ERK signalling, IMMUNOLOGY, 127, 3, 326-327
• Griffin, M.D., Ritter, T., and B.P. Mahon, 2010, Immunological Aspects of Allogeneic Mesenchymal Stem Cell Therapies, HUMAN GENE THERAPY, 21, 12, Dec., 1641-1655
• Guinan, E. and G.W. Jones, 2009, The role of Hsp70 chaperone machinery in yeast prion propagation, PROTEIN AND PEPTIDE LETTERS, 16, 6, March, 583-586
• Haggerty L.S, Martin, F.J, Fitzpatrick, D.A. and McInerney, J.O., 2009, What do we get when we make a tree of genomes? PROCEEDINGS OF THE ROYAL SOCIETY B
• Haggerty, L.S., Martin, F.J., Fitzpatrick, D.A. and McInerney, J.O., 2009, Gene and Genome Trees Conflict at Many Levels., PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON, 364, 2209-2219
• Hatadani, L.M., McInerney, J.O., de Medeiros, H.F., Martins Junqueira, A.C., de Azerdo-Espin, A.M. and Klaczko, L.B., 2009, Molecular Phylogeny of the Drosophila tripunctata and Closely Related Species Groups (Diptera: Drosophilidae), MOLECULAR PHYLOGENETICS AND EVOLUTION, 51, 595-600
• Holton, T.H., and Pisani, D., 2010, Deep genomic-scale analyses of Metazoa rejects Coelomata: evidence from supertree and supermatrix approaches, GENOME BIOLOGY AND EVOLUTION, in press
• Kalverda, A.P., Thompson, G.S., Vogel, A., Schröder, M., Bowie, A.G., Khan, A.R. and Homans. S.W., 2009, Poxvirus K7 protein adopts a Bcl-2 fold: Biochemical mapping of its interactions with human DEAD-box RNA helicase DDX3, JOURNAL OF MOLECULAR BIOLOGY, 385, 3, Jan, 843-853
• Kary, N.E., Niknam, G., Griffin, C.T., Mohammadi, S.A., and Moghaddam, M., 2009, A survey of entomopathogenic nematodes of the families Steinernematidae and Heterorhabditidae (Nematoda: Rhabditida) in the north-west of Iran, NEMATOLOGY, 11, 107-116
• Kavanagh, H., English, K., Locht, C., and B.P. Mahon, 2010, The attenuated Bordetella pertussis vaccine strain BPZE1 prevents exacerbated allergic pathology in a murine model, CLINICAL AND EXPERIMENTAL ALLERGY, 40, 933-941
• Kavanagh, H., and Mahon, B.P, 2010, Allogeneic mesenchymal stem cells prevent allergic airway inflammation by inducing murine regulatory T cells, ALLERGY, 66, 4, 523-531
• Kavanagh, H., and Mahon, B.P., 2010, Adult Mesenchymal Stem Cells - Intelligent therapies for immune reprogramming, INTERNATIONAL DRUG DISCOVERY, 5, 46-51
• Keith, A.M., Griffin, C.T. and Schmidt, O., 2009, Predatory soil nematodes (Nematoda: Mononchida) in major land-use types across Ireland, JOURNAL OF NATURAL HISTORY, 43, 2571-2577
• Lake, J.A., McInerney, J.O. and Ragan, M, 2009, The network of life: genome beginnings and evolution, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON, 364, 2169-2175
• Lewis, C., Jockusch, H., Ohlendieck, K., 2010, Proteomic Profiling of the Dystrophin-Deficient MDX Heart Reveals Drastically Altered Levels of Key Metabolic and Contractile Protein, JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, 2010,  648-501
• Lewis, C., Ohlendieck, K., 2010, Proteomic profiling of naturally protected extraocular muscles from the dystrophin-deficient mdx mouse, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 396, 1024-1029
• Lewis, C. and Ohlendieck, K., 2010, Mass spectrometric identification of dystrophin isoform Dp427 by on-membrane digestion of sarcolemma from skeletal muscle, ANALYTICAL BIOCHEMISTRY, 404, 197-203
• Lowther, J., Robinson, M.W., Donnelly, S.M., Xu, W., Stack, C.M., Matthews, J.M. and Dalton, J.P., 2009, The Importance of pH in Regulating the Function of the Fasciola hepatica Cathepsin L1 Cysteine Protease, PLoS NEGLECTED TROPICAL DISEASES, 3, 1, e369  
• Lynch, E.M., Earley, B., McGee, M., Byrne, W. and Doyle, S., 2010, Characterisation of physiological, haematological and immunological responses in beef cows to abrupt weaning and subsequent housing, BMC VETERINARY RESEARCH, 6, 37, July
•  Lynch, E.M., Earley, B., McGee, M., Byrne, W. and Doyle, S., 2010, Effect of abrupt weaning at housing on leukocyte distribution, functional activity of neutrophils and acute phase protein response of beef calves, BMC VETERINARY RESEARCH, 6, 39, July
• Madsen, D., Cantwell, E.R., O'Brien, T., Johnson, P.A. and Mahon, B.P., 2009, Adeno-associated virus serotype 2 induces cell-mediated immune responses directed against multiple epitopes of the capsid protein VP1, JOURNAL OF GENERAL VIROLOGY, 90, 11, 2622-2633
• Maric, S., Donnelly, S.M., Robinson, M.W., Skinner-Adams, T., Trenholme, K.R., Gardiner, D.L., Dalton, J.P., Stack, C.M., Lowther, J., 2009, The M17 Leucine Aminopeptidase of the Malaria Parasite Plasmodium falciparum: Importance of Active Site Metal Ions in the Binding of Substrates and Inhibitors, BIOCHEMISTRY, 48, 33
• Martin, F.J. and McInerney, J.O., 2009, Recurring cluster and operon assembly for Phenylacetate degradation genes, BMC EVOLUTIONARY BIOLOGY, 9, 36
•  Marusic, C., Vitale, A., Pedrazzini, E., Donini, M., Frigerio, L., Bock, R., Dix, P.J., McCabe, M.S., Belucci, M. and Benvenuto E., 2009, Plant-based strategies aimed at expressing HIV antigens and neutralizing antibodies at high levels. Nef as a case study, TRANSGENIC RESEARCH, 18, 499-512
• McGowan, S., Porter, C.J., Lowther, J., Stack, C.M., Golding, S.J., Skinner-Adams, T.S., Trenholme, K.R., Teuscher, F., Donnelly, S.M., Grembecka, J., Mucha, A., Kafarski, P., Degori, R., Buckle, A.M., Gardiner, D.L., Whisstock, J.C., Dalton, J.P., 2009, Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, USA, 106, 8, Feb., 2537-2542
• Miller, C.M.D., Smith, N.C., Ikin, R.J., Boulter, N.R., Dalton, J.P., Donnelly, S.M., 2009, Immunological Interactions between 2 Common Pathogens, Th1-Inducing Protozoan Toxoplasma gondii and the Th2-Inducing Helminth Fasciola hepatica, PLoS ONE, 4, 5, May, e5692
• Moynagh, P.N., 2009, The Pellino family: IRAK E3 ligases with emerging roles in innate immune signalling, TRENDS IN IMMUNOLOGY, 30, 33-42
• Mullen, E. and Ohlendieck, K., 2010, Proteomic profiling of non-obese type 2 diabetic skeletal muscle, INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, 25, 3, 445-458
• Mullen, E., O'Reilly, E. and Ohlendieck, K., 2011, Skeletal muscle tissue from the Goto-Kakizaki rat model of type-2 diabetes exhibits increased levels of the small heat shock protein Hsp27, MOLECULAR MEDICINE REPORTS, 4, 229-236
• Mullen, E. and Ohlendieck, K., 2011, Proteomic analysis of the mitochondria-enriched fraction from diabetic rat skeletal muscle, JOURNAL OF INTEGRATED OMICS, 1,  108-114
• Naundorf, S., Schröder, M., Hoflich, C., Suman, N., Volk, H.D. and Grutz, G., 2009, IL-10 interferes directly with TCR-induced IFN-gamma but not IL-17 production in memory T cells., EUROPEAN JOURNAL OF IMMUNOLOGY, 39, 4, April, 1066-, 1077
• O'Connell, K. and Ohlendieck, K., 2009, Proteomic DIGE analysis of the mitochondria-enriched fraction from aged rat skeletal muscle, PROTEOMICS, 9, 24, 5509-5524
• Oda, S., Schröder, M. and Khan, A.R., 2009, Structural basis for targeting of human RNA helicase DDX3 by poxvirus protein K7, STRUCTURE, 17, 11, Nov., 1528-1537
• O’Brien, M., Spillane, C., Meade, C. and E. Mullins, E., 2009, An insight into the impact of arable farming on Irish Biodiversity: A Scarcity of studies hinders a rigorous assessment, PROCEEDINGS OF THE ROYAL IRISH ACADEMY, 108B, 2,  , 97-, 108
• Reardon, W., Chakrabortee, S., Campos Pereira, T., Tyson, T., Banton, M.C., Dolan, K.M., Culleton, B.A., Wise, M.J., Burnell, A.M. and Tunnacliffe, A., 2010, Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae, BMC MOLECULAR BIOLOGY, 11, 6 
• Reardon, W., Fitzpatrick, D.A., Fares, M.A. and Nugent, J.M., 2009, Evolution of flower shape in Plantago lanceolata, PLANT MOLECULAR BIOLOGY, 71, 3, Oct., 241-250
• Regeai, S.O., Dolan, K.M., Fitzpatrick, D.A., Browne, J.A., Jones, J.T. and Burnell, A.M., 2009, 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, 9, 421-424
• Robinson, M.W., Menon, R., Donnelly, S.M., Dalton, J.P., Ranganathan, S., 2009, An integrated transcriptomic and proteomic analysis of the secretome of the helminth pathogen, Fasciola hepatica: proteins associated with invasion and infection of the mammalian host, MOLECULAR & CELLULAR PROTEOMICS, 8, 8
• Rowan, R., C. Moran, M. McCann and K. Kavanagh, 2009, Use of Galleria mellonella larvae to evaluate the in vivo anti-fungal activity of [Ag2(mal)(phen)3], BIOMETALS, 22, 3,  , 461-, 467
• Scanlon KM, Hawksworth RJ, Lane SJ and B.P. Mahon., 2011, IL-17A recruits IgE-secreting B cells through the induction of the chemokine CCL28., INTERNATIONAL ARCHIVES OF ALLERGY AND IMMUNOLOGY, in press
• Schrettl, M., Carberry, S., Kavanagh, K., Haas, H., Jones G.W., O'Brien J., Stephens J., Fenelon, O., Nolan, A. and Doyle, S., 2010, Self-Protection against Gliotoxin- A Component of the Gliotoxin Biosynthetic Cluster, GliT, Completely Protects Aspergillus fumigatus Against Exogenous Gliotoxin, PLOS PATHOGENS, 6, 6, June, e1000952  
• Skerry, C.M., and Mahon, B.P., 2011, A live attenuated Bordetella pertussis vaccine provides long term protection against virulent challenge in a murine model, CLINICAL AND VACCINE IMMUNOLOGY, 18, 2, 187-193
• Skerry, C., Cassidy, J., English, K., Fenou-Fenou, P., Locht, C., and Mahon, B.P., 2009, A live attenuated Bordetella pertussis candidate vaccine does not cause disseminating infection in IFN-g receptor knockout mice, Clinical and Vaccine Immunology, CLINICAL AND VACCINE IMMUNOLOGY, 16, 1344-1351
• Sperling, E., Peterson, K.J., and Pisani, D., 2009, Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa, MOLECULAR BIOLOGY AND EVOLUTION, 26, 2261-2274
• Sperling, E.A., Robinson, J.M., Pisani, D. and Peterson, K.J., 2010, Where's the Glass? Biomarkers, Molecular Clocks and microRNAs suggest a 200 Million Year Missing Precambrian Fossil Record of Siliceous Sponge Spicules., GEOBIOLOGY, 8, 1, 24-36
• Stack, D., Frizzell, A., Tomkins, K. and Doyle, S., 2009, Solid Phase 4'-Phosphopantetheinylation- Fungal Thiolation Domains are Targets for Chemoenzymatic Modification, BIOCONJUGATE CHEMISTRY, 20, 8, 1514-1522
• Zhang, H., Loovers, H.M., Xu, L.Q., Wang, M., Rowling, P.J.E., Itzhaki, L.S., Gong, W., Zhou, J.M., Jones, G.W. and Perrett, S., 2009, Alcohol oxidase (AOX1) from Pichia pastoris is a novel inhibitor of prion propagation and a potential ATPase, MOLECULAR MICROBIOLOGY, 71, 3, Feb., 702-716

Book Chapters 2009-

• Donoghue, P., Doran, P. and Ohlendieck, K., 2010, Role of chaperones in dystrophic and senescent muscle fibres, Handbook of Nutritional Biochemistry, pp 195-224, Eds: Haugen, S. and Meijer, S., Nova Science Publisher, New York, Chapt.  5 
• Donoghue, P., Doran, P. and Ohlendieck, K., 2010, Biochemical and proteomic profiling of key metabolic enzymes in aging skeletal muscle, Handbook of Nutritional Biochemistry, pp 42- 443, Nova Science Publishers, New York, Chapt. 14
• Doyle S, 2009, Nonribosomal peptide synthesis, Amino acids, Peptides and Proteins in Organic Chemistry.  Vol 2 - Modified Amino Acids, Organocatalysis and Enzymes, 631-656, Ed. A. Hughes, Wiley-VCH, Weinheim,  ISBN 978-3-527-32098-1
• Doyle, S., 2011, The Detection of Parvoviruses, Methods in Molecular Biology- Diagnostic Virology Protocols, 213-231, Humana Press,  Chapt. 13, 1064/3745, doi:10.1007/978-1-60761-817-1_13
• Fitzpatrick, D.A. and Butler, G., 2010, Comparative genomic analysis of pathogenic yeasts and the evolution of virulence, The Yeast Handbook: Pathogenic Yeasts, 1-18, Ed. H. R.  Asbee and E. M. Bignell, Springer, Berlin,  January 
• Guinan, E., Blumlein, A., S.A. Cusack, S.A., Moran, C., Loovers, H.M. and Jones, G.W., 2009, Propagating prions- the role of molecular chaperones, Prokaryotic and Eukaryotic Heat Shock Protein in Infectious Disease, 25-37, Eds. A.G. Pockley, M.G. Santoro and S.K. Calderwood, Springer, Chapt. 2, ISBN 978-90-481-2975-1, November
• Hogg, B.V., Lelivelt, C.L.C., Dunne, A., Nguyen. K.H., Nugent, J.M., 2009, Plastid transformation., Plant Cell Culture: Methods, Eds.  M. Davey and P. Anthony, Scion Publishing Ltd., Chapt. 13
• O'Connell, K., Doran, P., Gannon, J., Donoghue, P., and Ohlendieck, K., 2011, Proteomic and biochemical profiling of aged skeletal muscle, Sarcopenia: Age-related muscle wasting and weakness. Mechanisms and Treatments, 259-287, Ed. G.S. Lynch, Springer, Heidelberg, Chapt. 12
• O'Shaughnessy L and Doyle S., 2011, Purification of proteins from baculovirus-infected insect cells., Methods Mol Biol., 295-309, Eds. D. Walls and S.T. Loughran, Humana Press, Chapt. 16, ISBN 978-1-60761-912-3 
• Ohlendieck, K., 2009, Centrifugation (revised), Principles and Techniques of Biochemistry and Molecular Biology, 73-99, Eds. K. Wilson and J. Walker, Cambridge University Press, Cambridge, UK, Chapt. 3
• Peterson, K.J. Cotton, J.A., Gehling J.G. and Pisani, D., 2009, The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records, Animal Evolution: Genomes, Fossils, and Trees,  Eds. Telford, M.J. and Littlewood, D.T.J., Oxford University Press, Oxford, 2, ISBN 978-0-19-954942-9, doi:10.1093/acprof:oso/9780199549429.003.0002
• Pisani D., 2009, Arthropoda, The Timetree of Life, 251-254, Eds. S.B. Hedges and S. Kumar, Oxford University Press, Oxford
• Siednienko, J. and Miggin, S.M., 2009, Expression Analysis of the Toll-Like Receptors in Human Peripheral Blood Mononuclear Cells, Methods in Molecular Biology, Vol. 517, Eds. C.E. McCoy and L.A.J. O'Neill, Humana Press Inc., New Jersey, in press, ISBN 978-1-934115-72-5

Biology Department , NUI Maynooth
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