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UCD Biology & Environmental Science

'Looking for SARS-Coronaviruses underground'. Image by Dr Sebastien Puechmaille.

'Looking for SARS-Coronaviruses underground'. Image by Dr Sebastien Puechmaille.

UCD School of Biology & Environmental Science - Research Publications 2010/11

Below is the list of research publications for the UCD School of Biology & Environmental Science in the academic year 2010/11




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Books
Dr Florence Renou-Wilson
Renou-Wilson, F. (2011) Optimal practices in the afforestation of cutaway peatlands. Saarbrücken, Germany: Lambert Academic Publishing.  
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Book Chapters
Dr Gareth Dyke
Dyke, G.J. and Gardiner, E. (2011) 'The utility of fossil taxa and the evolution of modern birds: commentary and analysis' In: Dyke, G.J. and Kaiser, K.W (eds). Living Dinosaurs: The Evolutionary History of Modern Birds. London: John Wiley & Sons, Inc.  
Dr Paul McCabe
Diamond, M. and McCabe, P.F. (2010) 'Mitochondrial regulation of plant programmed cell death' In: Frank Kempken (eds). Plant Mitochondria, Advances in Plant Biology 1. Verlag: Springer Publishing.  
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Books Edited
Dr Gareth Dyke
Dyke, G.J. and Kaiser, G.W (Ed.). (2011) Living Dinosaurs: The Evolutionary History of Modern Birds. London: Wiley Blackwell.  
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Peer Reviewed Journals
Dr Jan-Robert Baars
Baars, J-R. and Hill, M.P. (2010) 'The phytophagous organisms associated with Lantana L. species in Jamaica and their potential use as biological control candidates of weedy varieties of Lantana camara L. (Verbenaceae) in South Africa'. Entomotropica, 25 (3):99-108.  
Kibichii, S., Baars, J-R., Kelly-Quinn, M., Holmes, M.C. (2010) 'Parastenocaris phyllura, Kiefer, 1938 (Copepoda: Haparticoida: Parastinocarididae) a species new to Ireland with a few notes on possible habitat preferences'. Bulletin of the Irish Biogeographical Society, 34 (15):97-101.  
Baars, J-R. and Caffrey, J.M. (2010) 'The Frond-feeding Weevil (Stenopelmus rufinasus Gyllenhal)(Coleoptera: Erirhinidae) a natural enemy of Azolla filiculoides in Ireland'. Irish Naturalists' Journal, 30 (2):142-143.  
Baars, J-R., Coetzee, J.A., Martin, G., Hill, M. and Caffrey, J.M. (2010) 'Natural enemies from South Africa for biological control of Lagarosiphon major (Ridl.) Moss ex Wager (Hydrocharitaceae) in Europe'. Hydrobiologia, 656 (1):149-158.  
Professor Thomas Bolger
Arroyo, J. and Bolger, T. (2011) 'The mite (Arachnida: Acari) fauna inhabiting Irish machair: a European Union priority coastal habitat'. Journal of Coastal Conservation, 15 (1):181-194.  
Vandewalle, M., de Bello, F., Berg, M.P., Bolger, T., Dolédec, S., Dubs, F., Feld, C.K., Harrington, R., Harrison, P. A., Lavorel, S., Martins da Silva, P., Moretti, M., Niemelä, J., Santos, P., Sattler, T., Sousa, J.P., Sykes, M.T., Vanbergen, A.J. and Woodcock, B.A. (2010) 'Functional traits as indicators of biodiversity response to land use changes across ecosystems and organisms'. Biodiversity and Conservation, 19 (10):2941-2947.  
Dr Emma Boston
Lundy, M., Teeling, E.C., Boston, E.S.M., Scott. D.D., Buckley, D.J., Prodöhl, P.A., Marnell, F. and Montgomery, W.I. (2011) 'The Shape of Sound: Elliptic fourier descriptors (EFD) discriminate the echolocation calls of Myotis bats (M. daubentoni, M. nattereri and M. mystacinus)'. Bioacoustics, 20 (2):101-116.  
Boston, E.S.M., Buckley, D., Bekaert, M., Lundy, M.G., Gager, Y., Scott, D.D., Prodohl, P.A., Montgomery, I., Marnell, F. and Teeling, E. (2010) 'The status of the cryptic species, Myotis mystacinus (Whiskered bat) and Myotis brandtii (Brandt's bat) in Ireland'. Acta Chiropterologica, 12 (2):457-461.  
Professor Nicholas Clipson
deMenezes, A.B., Lewis, W., O'Donovan, M., O'Neill, B.F., Clipson, N. and Doyle, E.M. (2011) 'Microbiome analysis of dairy cows fed pasture or total mixed ration diets'. FEMS Microbiology Ecology, 78 (2):256-265.  
Dr Tasman Crowe
O'Gorman, E.J., Yearsley, J.M., Crowe T.P., Emmerson, M.C., Jacob, U. and Petchey, O.L. (2011) 'Loss of functionally unique species may gradually undermine ecosystems'. Proceedings of the Royal Society B - Biological Sciences, 278 (1713):1886-1893.  
Crowe, T.P., Forst, N.J. and Hawkins, S.J. (2011) 'Interactive effects of losing key grazers and ecosystem engineers vary with environmental context'. Marine Ecology Progress Series, 430 :223-234.  
Fitch, J.E. and Crowe, T.P. (2011) 'Combined effects of temperature, inorganic nutrients and organic matter on ecosystem processes in intertidal sediments'. Journal of Experimental Marine Biology and Ecology, 400 (1-2):257-263.  
Griffin, J.N., Noel, L.M-J., Crowe, T.P., Burrows, M.T., Hawkins, S.J., Thompson, R.C. and Jenkins, S.J. (2010) 'Species composition, not richness determines consumer effects on rockpool community structure and functioning'. Marine Ecology Progress Series, 420 :45-56.  
Dr Evelyn Doyle
deMenezes, A.B., Lewis, W., O'Donovan, M., O'Neill, B.F., Clipson, N. and Doyle, E.M. (2011) 'Microbiome analysis of dairy cows fed pasture or total mixed ration diets'. FEMS Microbiology Ecology, 78 (2):256-265.  
Coulumbel, L., Nolan, L.C., Nikodinovic, J., Doyle, E.M. and O'Connor, K.E. (2011) 'Biotransformation of 4-halophenols to 4-halocatechols using Escherichia coli expressing 4-hydroxyphenylacetate 3-hydroxylase'. Applied Microbiology and Biotechnology, 89 (6):1867-1875.  
Dr Gareth Dyke
Naish, D., Dyke. G.J., Cau, A., Escuillie, F. and Godefroit, P. (2011) 'A gigantic bird from the Upper Cretaceous of Central Asia'. Biology Letters, Published online before print . Available Online  
Kurochkin, E.N. and Dyke, G.J. (2011) 'The first fossil owls (Aves: Strigiformes) from the Paleogene of Asia and a review of the fossil record of Strigiformes'. Paleontological Journal, 45 (4):85-97.  
Dyke, G.J. and Naish, D.W. (2011) 'What about European alvarezsauroids?'. Proceedings of the National Academy of Sciences of the United States of America, 108(22) E147 .  
Belevedere, M., Dyke, G.J., Hadri, M., and Ishigaki, S. (2011) 'The oldest evidence for birds in Northern Gondwana?: Small tridactyl footprints from the Middle Jurassic of Msemrir (Morocco)'. Gondwana Research, 19 (2):542-549.  
Nudds, R.L., Kaiser, G.W. and Dyke, G.J. (2011) 'Scaling of primary feather length in birds'. PLoS ONE, 6(2) e15665 .  
Dyke, G.J., Benton, M.J., Posmosanu, E. and Naish, D.W. (2011) 'Early Cretaceous (Berriasian) birds and pterosaurs from the Cornet bauxite mine, Romania'. Palaeontology, 54 (1):79-95.  
Wang, X., Csiki, Z., ?si, A., and Dyke, G.J. (2011) 'The first definitive record of a fossil bird from the Upper Cretaceous (Maastrichtian) of the Ha?eg Basin, Romania'. Journal of Vertebrate Paleontology, 31 (1):227-230.  
Wilson, L.E., Chin, K., Cumbaa, S. and Dyke, G.J. (2010) 'A high latitude hesperornithiform (Aves) from Devon Island: palaeobiogeography and size distribution of North American hesperornithiforms'. Journal of Systematic Palaeontology, 9 (1):9-23.  
Dr Wieland Fricke
Knipfer, T., Besse, M., Verdeil, J-L. and Fricke, W. (2011) 'Aquaporin-facilitated water uptake in barley (Hordeum vulgare L.) roots'. Journal of Experimental Botany, 62 (12):4115-4126.  
Besse, M., Knipfer, T., Miller, A.J., Verdeil, J-L, Jahn, T.P. and Fricke, W. (2011) 'Developmental pattern of aquaporin expression in barley (Hordeum vulgare L.) leaves'. Journal of Experimental Botany, 62 (12):4127-4142.  
Lehmann, S., Gumy, C., Blatter, E., Boeffel, S., Fricke, W. and Rentsch, D. (2011) 'In planta function of compatible solute transporters of the AtProT family'. Journal of Experimental Botany, 62 (2):787-796.  
Knipfer, T. and Fricke, W. (2011) 'Water uptake by seminal and adventitious roots in relation to whole-plant water flow in barley (Hordeum vulgare L.)'. Journal of Experimental Botany, 62 (2):717-730.  
Mr Hubert Fuller
Puechmaille, S.J., Wibbelt, G., Korn, V., Fuller, H., Forget, F., Muhldorfer, K., Kurth, A., Bogdanowicz, W., Borel, C., Bosch, T., Cherezy, T., Drebet, M., Gorfol, T., Haarsma, A.J., Herhaus, F., Hallart, G., Hammer, M., Jungmann, C., Le Bris, Y., Lutsar, L., Masing, M., Mulkens, B., Passior, K., Starrach, M., Wojtaszewski, A., Zophel, U. and Teeling, E.C. (2011) 'Pan-European Distribution of White-Nose Syndrome Fungus (Geomyces destructans) Not Associated with Mass Mortality'. PLoS ONE, 6(4) e19167 .  
Puechmaille, S.J.,Fuller, H. andTeeling, E.C. (2011) 'Effect of sample preservation methods on the viability of Geomyces destructans, the fungus associated with white-nose syndrome in bats'. Acta Chiropterologica, 13 :217-221.  
Dr Thomas F Gallagher
Fennell, M., Gallagher, T., and Osborne, B. (2010) 'Patterns of genetic variation in invasive populations of Gunnera tinctoria: an analysis at three spatial scales'. Biological Invasions, 12 (12):3973-3987.  
Professor Thomas J Hayden
Jennings, D.J., Carlin, C.M., Hayden, T.J., Gammell, M.P. (2011) 'Third-party intervention behaviour during fallow deer fights: the role of dominance, age, fighting and body size'. Animal Behaviour, 81 (6):1217-1222.  
Dr Tamara Hochstrasser
Brennan, M., Shahumyan, H. and Hochstrasser, T. (2010) 'Simulated future development of the Greater Dublin Area: consequences for protected areas and coastal flooding risk'. Journal of Irish Urban Studies, 9 :31-51.  
Dr David Hone
Hone, D.W.E., Wang, K., Sullivan, C., Zhao, X., Chen, S., Li, D., Ji, S., Ji, Q. and Xu, X. (2011) 'A new, large tyrannosaurine theropod from the Upper Cretaceous of China'. Cretaceous Research, 32 (4):495-503.  
Taylor, M.P., Hone, D.W.E., Wedel, M.J. and Naish, D. (2011) 'The long necks of sauropods did not evolve primarily through sexual selection'. Journal of Zoology, 258 (2):150-161.  
Xu, X., Sullivan, C., Pittman, M., Choiniere, J.N., Hone, D., Upchurch, P., Tan, Q., Xiao, D., Tan, L. and Han, F. (2011) 'A monodactyl nonavian dinosaur and the complex evolution of the alvarezsauroid hand'. Proceedings of the National Academy of Sciences of the United States of America, 108 (6):2338-2342.  
Elgin, R.A., Hone, D.W.E. and Frey, E. (2010) 'The extent of the pterosaur flight membrane'. Acta Palaeontologica Polonica, 56 (1):99-111.  
Dr Mary Kelly-Quinn
Feeley, H.B., Kerrigan, C., Fanning, P., Hannigan, E. and Kelly-Quinn, M. (2011) 'Longitudinal extent of acidification effects of plantation forest on benthic macroinvertebrate communities in soft water streams: evidence for localised impact and temporal ecological recovery'. Hydrobiologia, 671 (1):217-226.  
Purcell, P., Bruen, M., O'Sullivan, J., Cocchiglia, L. and Kelly-Quinn, M. (2011) 'Water quality monitoring during the construction of the M3 motorway in Ireland'. Water and Environment Journal, Published online before print . Available Online  
Hannigan, E., Mangan, R. and Kelly-Quinn, M. (2011) 'Evaluation of the success of mountain blanket bog pool restoration in terms of aquatic macroinvertebrates'. Biology and Environment-Proceedings of the Royal Irish Academy, 111B (2):95-105.  
Elsaholi, M.S., Hannigan, E. and Kelly-Quinn, M. (2011) 'Nutrient and light limitation of algal biomass in selected streams in Ireland'. Inland Waters, 1 (2):74-80.  
Hayden, B., Massa-Gallucci, A., Caffrey, J., Harrod, C., Mariani, S., O'Grady, M. and Kelly-Quinn, M. (2011) 'Trophic dynamics within a hybrid zone - interactions between an abundant cyprinid hybrid and sympatric parental species'. Freshwater Biology, 56 (9):1723-1735.  
Kibichii, S., Baars, J-R., Kelly-Quinn, M., Holmes, M.C. (2010) 'Parastenocaris phyllura, Kiefer, 1938 (Copepoda: Haparticoida: Parastinocarididae) a species new to Ireland with a few notes on possible habitat preferences'. Bulletin of the Irish Biogeographical Society, 34 (15):97-101.  
Dr Mohammad Khalil
Khalil, M.I. and Richards, K.G. (2011) 'Denitrification enzyme activity and potential of subsoils under grazed grasslands assayed by membrane inlet mass spectrometer'. Soil Biology and Biochemistry, 43 (9):1787-1797.  
Fenton, O., Healy, M.G., Henry, T., Khalil, M.I., Grant, J., Baily, A. and Richards, K.G. (2011) 'Investigating denitrification potential in groundwater over time using δ15N/δ18O Isotopes and Membrane Inlet Mass Spectroscopy'. Ecological Engineering, 37 (9):1304-1313.  
Khalil, M.I., Schmidhalter, U., Gutser, R. and Heuwinkel, H. (2011) 'Fertilizer N movement and recovery by spring wheat associated with urea supergranules point-placed at different soil depths'. Journal of Plant Nutrition, 34 (6):779-797.  
Dr Stefano Mariani
Longmore, C., Trueman, C.N., Neat, F., O'Gorman, E., Milton, J.A. and Mariani, S. (2011) 'Otolith geochemistry indicates life-long spatial population structuring in a deep sea fish, Coryphaenoides rupestris'. Marine Ecology Progress Series, 435 :209-224.  
Cadrin, S.X., Mariani, S., Pampoulie, C., Bernreuther, M., Danielsdottir, A.K., Johanssen, T., Kerr, L., Nedreass, K., Reinert, J., Sigurðsson, Þ., Stransky, C. (2011) 'Counter-comment on: Cadrin et al. (2010) Population structure of beaked redfish, Sebastes mentella: evidence of divergence associated with different habitats. ICES Journal of Marine Science, 67: 1617:1630'. Ices Journal of Marine Science, 68 (10):2016-2018.  
Miller, D.D., Jessel, A. and Mariani, S. (2011) 'Seafood mislabelling: comparisons of two westerns European case studies assist in defining influencing factors, mechanisms and motives'. Fish and Fisheries, Published online before print . Available Online  
Sala-Bozano, M. and Mariani, S. (2011) 'Life-history variation in a marine teleost across a heterogeneous landscape'. Estuarine Coastal and Shelf Science, 92 (4):555-563.  
Hayden, B., Coscia, I. and Mariani, S. (2011) ''Low cytochrome-b variation in bream, Abramis brama L.''. Journal of Fish Biology, 78 (5):1579-1587.  
Andre, C., Larsson, L., Laikre, L., Bekkevold, D., Brigham, J., Carvalho, G.R., Dahlgren, T.G., Hutchinson, W.F., Mariani, S., Mudde, K., Ruzzante, D.E. and Ryman, N. (2011) 'Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral versus putatively selected loci'. Heredity, 106 :270-280.  
Hayden, B., Massa-Gallucci, A., Caffrey, J., Harrod, C., Mariani, S., O'Grady, M. and Kelly-Quinn, M. (2011) 'Trophic dynamics within a hybrid zone - interactions between an abundant cyprinid hybrid and sympatric parental species'. Freshwater Biology, 56 (9):1723-1735.  
Coscia, I. and Mariani, S. (2011) 'Phylogeography and population structure of European sea bass in the north-east Atlantic'. Biological Journal of the Linnean Society, 104 (2):364-377.  
Helyar, S., Coscia, I., Sala-Bozano, M. and Mariani, S. (2011) 'New microsatellite loci for the long-nosed velvet dogfish Centroselachus crepidater (Squaliformes: Somniosidae) and other deep sea sharks'. Conservation Genetics Resources, 3 (1):173-176.  
Miller, D.D. and Mariani, S. (2010) 'Smoke, mirrors and mislabelled cod: poor transparency in the European seafood industry'. Frontiers in Ecology and the Environment, 8 (10):517-521.  
Longmore, C., Fogarty, K., Neat, F., Brophy, D., Trueman, C., Milton, A. and Mariani, S. (2010) 'A comparison of otolith microchemistry and otolith shape analysis for the study of spatial variation in a deep-sea teleost, Coryphaenoides rupestris'. Environmental Biology of Fishes, 89 (3-4):591-605.  
Farrell, E.D., Mariani, S. and Clarke, M. (2010) 'Reproductive biology of the starry smooth-hound shark Mustelus asterias: geographic variation and implications for sustainable exploitation'. Journal of Fish Biology, 77 (7):1505-1525.  
Coscia, I., Rountree, V., King, J.J., Roche, W.K. and Mariani, S. (2010) 'A highly permeable species boundary between two anadromous fishes'. Journal of Fish Biology, 77 (5):1137-1149.  
Dr Paul McCabe
Alden, K.P., Dhont-Cordelier, S., McDonald, K.L., Reape, T.J., Ng, C.K.Y., McCabe, P.F. and Leaver, C.J. (2011) 'Sphingolipid long chain base phosphates can regulate apoptotic-like programmed cell death in plants'. Biochemical and Biophysical Research Communications, 410 (3):574-580.  
Dr Jenny McElwain
Bacon, K.L., Belcher, C.M., Hesselbo, S.P. and McElwain, J.C. (2011) 'The Triassic-Jurassic boundary carbon-isotope excursions expressed in taxonomically identified leaf cuticles'. Palaios, 26 (8):461-469.  
Steinthorsdottir, M., Jeram, A.J. and McElwain, J.C. (2011) 'Extremely elevated CO2 concentrations at the Triassic/Jurassic boundary'. Palaeogeography Palaeoclimatology Palaeoecology, 308 (3-4):418-432.  
Steinthorsdottir, M., Bacon, K.L., Popa, M.E., Bochner, L. and McElwain, J.C. (2011) 'Bennettitalean leaf cuticle fragments (here Anomozamites and Pterophyllum) can be used interchangeably in stomatal frequency-based palaeo-CO2 reconstructions'. Palaeontology, 54 (4):867-882.  
Haworth, M., Elliott-Kingston, C. and McElwain, J.C. (2011) 'Stomatal control as a driver of plant evolution'. Journal of Experimental Botany, 62 (8):2419-2423.  
Haworth, M., Elliott-Kingston, C., McElwain, J.C. (2011) 'The stomatal CO2 proxy does not saturate at high atmospheric CO2 concentrations: evidence from stomatal index responses of Araucariaceae conifers'. Oecologia, 167 (1):11-19.  
Belcher, C.M., Yearsley, J.M., Hadden, R.M., McElwain, J.C. and Rein, G. (2010) 'Baseline intrinsic flammability of Earth's ecosystems estimated from paleoatmospheric oxygen over the past 350 million years'. Proceedings of the National Academy of Sciences of the United States of America, 107 (52):22448-22453.  
Haworth, M., Gallagher, A., Elliott-Kingston, C., Rashi, A., Marandola, D., McElwain, J.C. (2010) 'Stomatal index responses of Agrostis canina to CO2 and sulphur dioxide: implications for palaeo-[Co2] using the stomatal proxy'. New Phytologist, 188 (3):845-855.  
Taylor, C.T. and McElwain, J.C. (2010) 'Ancient Atmospheres and the Evolution of Oxygen Sensing Via the Hypoxia-Inducible Factor in Metazoans'. Physiology, 25 (5):272-279.  
Professor Christoph Mueller
Zhang, J., Müller, C., Chen, Y. and Cai, Z. (2011) 'Heterotrophic nitrification is the predominant NO3- production mechanism in coniferous but not broad-leaf acid forest soil in subtropical China'. Biology and Fertility of Soils, 47 (5):533-542.  
Rütting, T., Boeckx, P., Müller, C. and Klemedtsson, L. (2011) 'Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle'. Biogeosciences, 8 (7):1779-1791.  
Regan, K., Kammann, C., Hartung, K., Lenhart, K., Müller, C., Philippot, L., Kandeler, E. and Marhan, S. (2011) 'Can differences in microbial abundances help explain enhanced N2O emissions in a permanent grassland under elevated atmospheric CO2 ?'. Global Change Biology, 17 (10):3176-3186.  
Müller, C., Laughlin, R.J., Christie, P. and Watson, C.J. (2011) 'Effects of repeated fertilizer and slurry applications over 38 years on N dynamics in a temperate grassland soil'. Soil Biology and Biochemistry, 43 (6):1362-1371.  
Straelens, J., Rütting, T., Huygens, D., De Schrijver, A., Müller, C., Verheyen, K. and Boeckx, P. (2011) 'In situ gross nitrogen transformations differ between temperate deciduous and coniferous forest soils'. Biogeochemistry, Published online before print . Available Online  
Rütting, T., Huygens, D., Straelens, J., Müller, C. and Boeckx, P. (2011) 'Advances in 15N-tracing experiments: new labelling and data analysis approaches'. Biochemical Society Transactions, 39 :279-283.  
Meade, G., Pierce, K., O'Doherty, J.V., Mueller, C., Lanigan, G. and Mc Cabe, T. (2011) 'Ammonia and nitrous oxide emissions following land application of high and low nitrogen pig manures to winter wheat at three growth stages'. Agriculture, Ecosystems and Environment, 140 (1-2):208-217.  
Rütting, T., Clough, T.J., Müller, C., Lieffering, M., and Newton, P.C.D. (2010) 'Ten years of elevated atmospheric carbon dioxide alters soil nitrogen transformations in a sheep-grazed pasture'. Global Change Biology, 16 (9):2530-2542.  
Dr Carl Khee-Yew Ng
Islam, M.N., Chambers, J.P. and Ng, C.K.Y. (2011) 'Lipid profiling of the model temperate grass, Brachypodium distachyon'. Metabolomics, Published online before print . Available Online  
Alden, K.P., Dhont-Cordelier, S., McDonald, K.L., Reape, T.J., Ng, C.K.Y., McCabe, P.F. and Leaver, C.J. (2011) 'Sphingolipid long chain base phosphates can regulate apoptotic-like programmed cell death in plants'. Biochemical and Biophysical Research Communications, 410 (3):574-580.  
Dr Eoin O'Gorman
Longmore, C., Trueman, C.N., Neat, F., O'Gorman, E., Milton, J.A. and Mariani, S. (2011) 'Otolith geochemistry indicates life-long spatial population structuring in a deep sea fish, Coryphaenoides rupestris'. Marine Ecology Progress Series, 435 :209-224.  
O'Gorman, E.J., Yearsley, J.M., Crowe T.P., Emmerson, M.C., Jacob, U. and Petchey, O.L. (2011) 'Loss of functionally unique species may gradually undermine ecosystems'. Proceedings of the Royal Society B - Biological Sciences, 278 (1713):1886-1893.  
O'Gorman, E.J. and Emmerson, M.C. (2011) 'Body mass-abundance relationships are robust to cascading effects in marine food webs'. Oikos, 120 (4):520-528.  
Professor Bruce Arthur Osborne
Walmsley, D.C., Siemens, J., Kindler, R., Kirwan, L., Kaiser, K., Saunders, M., Kaupenjohann, M. and Osborne, B.A. (2011) 'Dissolved carbon leaching from an Irish cropland soil is increased by reduced tillage and cover cropping'. Agriculture, Ecosystems and Environment, 142 (3-4):393-402.  
Kindler, R., Siemens, J., Kaiser, K., Walmsley, D.C., Bernhofer, C., Buchmann, N., Cellier, P., Eugster, W., Gleixner, G., Grunwald, T., Heim, A., Ibrom, A., Jones, S.K., Jones, M., Klumpp, K., Kutsch, W., Larsen, K.S., Lehuger, S., Loubet, B., McKenzie, R., Moors, E., Osborne, B., Pilegaard, K., Rebmann, C., Saunders, M., Schmidt, M.W.I., Schrumpf, M., Seyfferth, J., Skiba, U., Soussana, J.F., Sutton, M.A., Tefs, C., Vowinckel, B., Zeeman, M.J. and Kaupenjohann, M. (2011) 'Dissolved carbon leaching from soil is a crucial component of the net ecosystem carbon balance'. Global Change Biology, 17 :1167-1185.  
Fennell, M., Gallagher, T. and Osborne, B. (2010) 'Patterns of genetic variation in invasive populations of Gunnera tinctoria'. Biological Invasions, 12 (12):3973-3987.  
Kutsch, W.L., Aubinet, M., Nuchmann, N., Smith, P., Osborne, B., Eugster, W., Wattenbach, M., Schrumpf, M., Schulze, E.D., Tomelleri, E., Ceschia, E., Bernhofer, C., Beziat, P., Carrara, A., Di Tommasi, T., Grunwald, T., Jones, M., Magliulo, V., Marloie, O., Moureaux, C., Olioso, A., Sanz, M.J., Saunders, M., Sogaard, H. and Ziegler, W. (2010) 'The net biome production of full crop rotations in Europe'. Agriculture, Ecosystems and Environment, 139 (3):336-345.  
Smith, P., Lanigan. G., Kutsch, W.L., Buchmann, N., Eugster, W., Aubinet, M., Ceschia, E., Beziat, P., Yeluripati, J.B., Osborne, B., Moors, E.J., Brut, A., Wattenbach, M., Saunders, M. and Jones, M. (2010) 'Measurements necessary for assessing the net ecosystem carbon budget of croplands'. Agriculture, Ecosystems and Environment, 139 (3):302-315.  
Osborne, B., Saunders, M., Walmsley, D., Jones, M.J. and Smith, P. (2010) 'Key Questions and uncertainties associated with the cropland greenhouse gas balance'. Agriculture, Ecosystems and Environment, 139 (3):293-301.  
Wattenbach, M., Sus, O., Vuichard, N., Lehuger, S., Gottschalk, G., Li, L., Leip, A., Williams, M., Tomelleri, E., Kutsch, W.L., Buchmann, N., Eugster, W., Dietiker, D., Aubinet, M., Ceschia, E., Beziat, P., Grunwald, T., Hastings, A., Osborne, B., Ciais, P., Cellier, P. and Smith, P. (2010) 'The carbon balance of European croplands: a cross site comparison of simulation models'. Agriculture, Ecosystems and Environment, 139 (3):419-453.  
Dr Sebastien Puechmaille
Boston, E.S.M., Hanrahan, N., Puechmaille, S.J., Ruedi, M., Buckley, D.J., Lundy, M.G., Scott, D.D., Prodohl, P.A., Montgomery, W.I., Teeling, E.C. (2011) 'A rapid PCR-based assay for identification of cryptic Myotis spp. (M. mystacinus, M. brandtii and M. alcathoe)'. Conservation Genetics Resources, 3 (3):557-563.  
Ar Gouilh, M., Puechmaille, S., Gonzalez, J.P., Teeling, E., Pattamaporn, K. and Manuguerra, J-C. (2011) 'SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory'. Infection, Genetics and Evolution, 11 (7):1690-1702.  
Puechmaille, S., Fuller, H., and Teeling, E.C. (2011) 'Effect of sample preservation methods on the viability of Geomyces destructans, the fungus associated with white-nose syndrome in bats'. Acta Chiropterologica, 13 (1):217-222.  
Puechmaille, S.J., Wibbelt, G., Korn, V., Fuller, H., Forget, F., Muhldorfer, K., Kurth, A., Bogdanowicz, W., Borel, C., Bosch, T., Cherezy, T., Drebet, M., Gorfol, T., Haarsma, A.J., Herhaus, F., Hallart, G., Hammer, M., Jungmann, C., Le Bris, Y., Lutsar, L., Masing, M., Mulkens, B., Passior, K., Starrach, M., Wojtaszewski, A., Zophel, U. and Teeling, E.C. (2011) 'Pan-European Distribution of White-Nose Syndrome Fungus (Geomyces destructans) Not Associated with Mass Mortality'. PLoS ONE, 6(4) e19167 .  
Buckley, D.J., Puechmaille, S.J., Roche, N. and Teeling, E.C. (2011) 'A critical assessment of the presence of Barbastella barbastellus and Nyctalus noctula in Ireland with a description of N. leisleri echolocation calls from Ireland'. Hystrix - Italian Journal of Mammalogy, 22 (11):111-127.  
Saveng, I., Soisook, P., Bumrungsri, S., Kingston, T., Puechmaille, S.J., Struebig, M.J., Hla Bu, S.S., Thong, V.D., Furey, N., Hammond, N., Bates, P.J.J. (2011) 'A taxonomic review of Rhinolophus coelophyllus Peters 1867 and R. shameli Tate 1943 (Chiroptera: Rhinolophidae) in continental Southeast Asia'. Acta Chiropterologica, 13 (1):41-59.  
Dr Theresa Reape
Alden, K.P., Dhont-Cordelier, S., McDonald, K.L., Reape, T.J., Ng, C.K.Y., McCabe, P.F. and Leaver, C.J. (2011) 'Sphingolipid long chain base phosphates can regulate apoptotic-like programmed cell death in plants'. Biochemical and Biophysical Research Communications, 410 (3):574-580.  
Dr Emmanuel Reynaud
Boistel, R., Swoger, J., Krzicz, U., Fernandez, V., Gillet, B. and Reynaud, E.G. (2011) 'The future of three-dimensional microscopic imaging in marine biology'. Marine Ecology, 32 (4):1-15.  
Tängemo, C., Ronchi, P., Colombelli, J., Haselmann, U., Simpson, J.C., Antony, C., Stelzer, E.H.K., Pepperkok, R. and Reynaud, E.G. (2011) 'A Novel Laser Nanosurgery Approach Provides Support for de novo Golgi Biogenesis in Mammalian Cells'. Journal of Cell Science, 124 :978-987.  
Devos, D.P. and Reynaud, E.G. (2010) 'Intermediate steps'. Science, 330 (6008):1187-1188.  
Dr Matthew Saunders
Walmsley, D.C., Siemens, J., Kindler, R., Kirwan, L., Kaiser, K., Saunders, M., Kaupenjohann, M. and Osborne, B.A. (2011) 'Dissolved carbon leaching from an Irish cropland soil is increased by reduced tillage and cover cropping'. Agriculture, Ecosystems and Environment, 142 (3-4):393-402.  
Kindler, R., Siemens, J., Kaiser, K., Walmsley, D.C., Bernhofer, C., Buchmann, N., Cellier, P., Eugster, W., Gleixner, G., Grunwald, T., Heim, A., Ibrom, A., Jones, S.K., Jones, M., Klumpp, K., Kutsch, W., Larsen, K.S., Lehuger, S., Loubet, B., McKenzie, R., Moors, E., Osborne, B., Pilegaard, K., Rebmann, C., Saunders, M., Schmidt, M.W.I., Schrumpf, M., Seyfferth, J., Skiba, U., Soussana, J.F., Sutton, M.A., Tefs, C., Vowinckel, B., Zeeman, M.J. and Kaupenjohann, M. (2011) 'Dissolved carbon leaching from soil is a crucial component of the net ecosystem carbon balance'. Global Change Biology, 17 :1167-1185.  
Smith, P., Lanigan. G., Kutsch, W.L., Buchmann, N., Eugster, W., Aubinet, M., Ceschia, E., Beziat, P., Yeluripati, J.B., Osborne, B., Moors, E.J., Brut, A., Wattenbach, M., Saunders, M. and Jones, M. (2010) 'Measurements necessary for assessing the net ecosystem carbon budget of croplands'. Agriculture, Ecosystems and Environment, 139 (3):302-315.  
Kutsch, W.L., Aubinet, M., Nuchmann, N., Smith, P., Osborne, B., Eugster, W., Wattenbach, M., Schrumpf, M., Schulze, E.D., Tomelleri, E., Ceschia, E., Bernhofer, C., Beziat, P., Carrara, A., Di Tommasi, T., Grunwald, T., Jones, M., Magliulo, V., Marloie, O., Moureaux, C., Olioso, A., Sanz, M.J., Saunders, M., Sogaard, H. and Ziegler, W. (2010) 'The net biome production of full crop rotations in Europe'. Agriculture, Ecosystems and Environment, 139 (3):336-345.  
Osborne, B., Saunders, M., Walmsley, D., Jones, M.J. and Smith, P. (2010) 'Key Questions and uncertainties associated with the cropland greenhouse gas balance'. Agriculture, Ecosystems and Environment, 139 (3):293-301.  
Professor Jeremy Simpson
Tängemo, C., Ronchi, P., Colombelli, J., Haselmann, U., Simpson, J.C., Antony, C., Stelzer, E.H.K., Pepperkok, R. and Reynaud, E.G. (2011) 'A Novel Laser Nanosurgery Approach Provides Support for de novo Golgi Biogenesis in Mammalian Cells'. Journal of Cell Science, 124 :978-987.  
Dr Gavin Stewart
Collins, D., Walpole, C., Ryan, E., Winter, D., Baird, A. and Stewart, G. (2011) 'UT-B1 mediates transepithelial urea flux in the rat gastrointestinal tract'. Journal of Membrane Biology, 239 (3):123-130.  
Dr Emma C Teeling
Ar Gouilh, M., Puechmaille, S., Gonzalez, J.P., Teeling, E., Pattamaporn, K. and Manuguerra, J-C. (2011) 'SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory'. Infection, Genetics and Evolution, 11 (7):1690-1702.  
Puechmaille, S., Fuller, H., and Teeling, E.C. (2011) 'Effect of sample preservation methods on the viability of Geomyces destructans, the fungus associated with white-nose syndrome in bats'. Acta Chiropterologica, 13 (1):217-222.  
Puechmaille, S., Wibbelt, G., Korn, V., Fuller, H., Forget, F., Mühldorfer, K., Kurth, A., Bogdanowicz, W., Borel, C., Bosch, T., Cherezy, T., Drebet, M., Görföl, T., Haarsma, A-J., Herhaus, F., Hallart, G., Hammer, M., Jungmann, C., Le Bris, Y., Lutsar, L., Masing, M., Mulkens, B., Passior, K., Starrach, M., Wojtaszewski, A., Zöphel, U. and Teeling, E.C. (2011) 'Pan-European distribution of white-nose syndrome fungus (Geomyces destructans) not associated with mass mortality'. PLoS ONE, 6(4) e19167 .  
Lundy, M., Teeling, E.C., Boston, E.S.M., Scott. D.D., Buckley, D.J., Prodöhl, P.A., Marnell, F. and Montgomery, W.I. (2011) 'The Shape of Sound: Elliptic fourier descriptors (EFD) discriminate the echolocation calls of Myotis bats (M. daubentoni, M. nattereri and M. mystacinus)'. Bioacoustics, 20 (2):101-116.  
Buckley, D., Puechmaille, S., Roche, N. and Teeling, E. (2011) 'A critical assessment of the presence of Barbastella barbastellus and Nyctalus noctula in Ireland with a description of N. leisleri echolocation calls from Ireland'. Hystrix - Italian Journal of Mammalogy, 22 (1):111-127.  
Boston, E.S.M., Buckley, D., Bekaert, M., Lundy, M.G., Gager, Y., Scott, D.D., Prodohl, P.A., Montgomery, I., Marnell, F. and Teeling, E. (2010) 'The status of the cryptic species, Myotis mystacinus (Whiskered bat) and Myotis brandtii (Brandt's bat) in Ireland'. Acta Chiropterologica, 12 (2):457-461.  
Dr Tom Wilkinson
Carolan, J.C., Caragea, D., Rearson, K.T., Mutti, N.S., Dittmer, N., Pappan, K. Cui, F., Castaneto, M., Poulain, J., Dossat, C., Tagu, D., Reese, J.C., Reeck, G.R., Wilkinson, T.L. and Edwards, O.R. (2011) 'Predicted Effector Molecules in the Salivary Secretome of the Pea Aphid (Acyrthosiphon pisum): a Dual Transcriptomic/Protemic Approach'. Journal of Proteome Research, 10 (4):1505-1518.  
Dr Jonathan Yearsley
Yearsley, J.M. and Sigwart, J.D. (2011) 'Larval transport modelling of deep-sea invertebrates can aid the search for undiscovered populations'. PLoS ONE, 6(8) e23063 .  
O'Gorman, E.J., Yearsley, J.M., Crowe T.P., Emmerson, M.C., Jacob, U. and Petchey, O.L. (2011) 'Loss of functionally unique species may gradually undermine ecosystems'. Proceedings of the Royal Society B - Biological Sciences, 278 (1713):1886-1893.  
Jaquiéry, J., Broquet, T., Hirzel, A.H., Yearsley, J. and Perrin, N. (2011) 'Inferring landscape effects on dispersal from genetic distances: how far can we go?'. Molecular Ecology, 20 (4):692-705.  
Vuilleumier, S., Buttler, A., Perrin, N. and Yearsley, J.M. (2011) 'Invasion and eradication of a competitively superior species in heterogeneous landscapes'. Ecological Modelling, 222 (3):398-406.  
Belcher, C.M., Yearsley, J.M., Hadden, R., McElwain, J.C. and Rein, G. (2010) 'Baseline intrinsic flammability of Earth's ecosystems estimated from paleoatmospheric oxygen over the past 350 million year'. Proceedings of the National Academy of Sciences of the United States of America, 107 (52):22448-22453.  
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Other Journals
Dr Tamara Hochstrasser
Finnan, J. Dietrich, B. and Hochstrasser, T. (2011) 'Grass to energy and back again?' TResearch, 6 (1):18-19.  
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Conference Publications
Professor Nicholas Clipson
Storey, S., McCabe, G., Harty, M., Clipson, N. and Doyle, E. (2011) Informing the design of in-situ bioremediation strategies for PAH contaminated soils . In: McClean, S eds. Society for General Microbiology Meeting, Tallaght, Dublin,  
Storey, S., Clipson, N. and Doyle, E. (2011) Effect of soil structure on bacterial community dynamics in a PAH-contaminated artificial soil . In: Leonid Kulakov eds. Society for General Microbiology, Queens University Belfast, 67 - 68  
Ashaari, M.M., Hutchens, E., Murphy, C., Clipson, N. and Doyle, E.M. (2011) Screening a metagenomic library from a polycyclic aromatic hydrocarbon contaminated soil . In: Leonid Kulakov eds. Society for General Microbiology Meeting, Queen's University Belfast, 67 - 68  
Ashaari, M.M., Hutchens, E., Benson, M., Murphy, C., Clipson, N. and Doyle, E. (2010) Metagenomics of polycyclic aromatic hydrocarbon (PAH) contaminated soil International Conference on Environment 2010 (ICENV 2010), Penang, Malaysia,  
Dr Evelyn Doyle
Storey, S., McCabe, G., Harty, M., Clipson, N. and Doyle, E. (2011) Informing the design of in-situ bioremediation strategies for PAH contaminated soils . In: McClean, S eds. Society for General Microbiology Meeting, Tallaght, Dublin,  
Storey, S., Clipson, N. and Doyle, E. (2011) Effect of soil structure on bacterial community dynamics in a PAH-contaminated artificial soil . In: Leonid Kulakov eds. Society for General Microbiology, Queens University Belfast, 67 - 68  
Ashaari, M.M., Hutchens, E., Murphy, C., Clipson. N. and Doyle, E.M. (2011) Screening a metagenomic library from a polycyclic aromatic hydrocarbon contaminated soil . In: Leonid Kulakov eds. Society for General Microbiology Meeting, Queens University Belfast, 67 - 68  
Ashaari, M.M., Hutchens, E., Benson, M., Murphy, C., Clipson, N. and Doyle, E. (2010) Metagenomics of polycyclic aromatic hydrocarbon (PAH) contaminated soil International Conference on Environment 2010 (ICENV 2010), Penang, Malaysia,  
Dr Tamara Hochstrasser
Fry, J., Carvill, P., Grist, B. and Hochstrasser, T. (2011) Developing IBIA: Legal and administrative issues 31st Annual Meeting of International Association for Impact Assessment, Puebla, Mexico,  
Fry, J., Hochstrasser, T., González, A., Scott, P., Carvill, P. and Shahumyan, H. (2011) Developing IBIA: Process and content? 31st Annual Meeting of International Association for Impact Assessment, Puebla, Mexico,  
González, A., Fry, J., Hochstrasser, T. and Shahumyan, H. (2011) Developing IBIA: Data limitations on GIS-support 31st Annual Meeting of International Association for Impact Assessment, Puebla, Mexico,  
Dr Mary Kelly-Quinn
Cocchiglia, L., Kelly-Quinn, M. and Purcell, P. (2010) Construction impacts of road crossings on watercourses in SACs National Hydrology Conference, Athlone,  
Dr Mohammad Khalil
Khalil, M.I., O'Brien, P., Kiely, G. and Mueller, C. (2011) High spatial resolution data for land use-soil type can reliably estimate baseline organic carbon stocks in agricultural soils International Symposium on Soil organic Matter: Organic Matter Dynamics - from Soils to Oceans, Leuven, Belgium, 107  
Kuhs M., Khalil, M.I. and Byrne, C. (2011) Nitrous oxide emissions and mitigation potentials in Irish agriculture International conference on Nitrogen and Global Change: Key Findings - Future Challenges, Edinburgh,  
Cahalan, E., Ernfors, M., Devaney, D., Khalil, M.I., Müller, C., Laughlin, R., Watson, C., Hennessy, D., McGeough, V. and Richards, K.G. (2011) Use of a nitrification inhibitor to decrease nitrous oxide emissions after application of slurry to Irish grassland International conference on Nitrogen and Global Change: Key Findings - Future Challenges, Edinburgh,  
Khalil, M.I., O'Brien, P., Kiely, G. and Mueller, C. (2011) Empirical estimation of organic carbon stocks fro agricultural soils in the Republic of Ireland European Geosciences General Assembly 2011,  
Barrett, M., Khalil, M.I., Jahangir, M.M.R., Lee, C., Cardenas, L.M., Collins, G., Richards, K.G. and O'Flaherty, V. (2011) Quantitative molecular biology and N2O/N2 flux measurements demonstrate carbon amendment and depth affects on the distrubition and activity of sub-soil denitrifiers International conference on Nitrogen and Global Change: Key Findings - Future Challenges, Edinburgh,  
Cahalan, E., Ernfors, M., Mueller, C., Devaney, D., Khalil, M.I., Lauglin, R., Watson, C., McGeough, K., Hennessy, D. and Richards, K.G. (2011) The effect of dicyandiamide (DCD) amended cattle slurry on herbage production at three Irish grassland sites Agricultural Research Forum 2011, Tullamore,  
Khalil, M.I., O'Brien, P., Kiely, G. and Mueller, C. (2011) Empirical estimation of baseline organic carbon stocks for agricultural soils in the ROI Agricultural Research Forum 2011, Tullamore,  
Professor Christoph Mueller
Khalil, M.I., O'Brien, P., Kiely, G. and Mueller, C. (2011) High spatial resolution data for land use-soil type can reliably estimate baseline organic carbon stocks in agricultural soils International Symposium on Soil organic Matter: Organic Matter Dynamics - from Soils to Oceans, Leuven, Belgium, 107  
Renou-Wilson, F., Wilson, D., Foy, B. and Mueller, C. (2011) CALISTO: CArbon Loss from Histosols . In: Caron, P. and Rochefort, L eds. International Symposium on Responsible Peatland Management, Quebec City, Canada, 77  
Cahalan, E., Ernfors, M., Devaney, D., Khalil, M.I., Müller, C., Laughlin, R., Watson, C., Hennessy, D., McGeough, V. and Richards, K.G. (2011) Use of a nitrification inhibitor to decrease nitrous oxide emissions after application of slurry to Irish grassland . In: Edinburgh eds. International conference on Nitrogen and Global Change: Key Findings - Future Challenges,  
Khalil, M.I., O'Brien, P., Kiely, G. and Mueller, C. (2011) Empirical estimation of organic carbon stocks fro agricultural soils in the Republic of Ireland European Geosciences General Assembly 2011,  
Cahalan, E., Ernfors, M., Mueller, C., Devaney, D., Khalil, M.I., Lauglin, R., Watson, C., McGeough, K., Hennessy, D. and Richards, K.G. (2011) The effect of dicyandiamide (DCD) amended cattle slurry on herbage production at three Irish grassland sites Agricultural Research Forum 2011, Tullamore,  
Khalil, M.I., O'Brien, P., Kiely, G. and Mueller, C. (2011) Empirical estimation of baseline organic carbon stocks for agricultural soils in the ROI Agricultural Research Forum 2011, Tullamore,  
Dr Florence Renou-Wilson
Renou-Wilson, F., Wilson, D., Foy, B. and Mueller, C. (2011) CALISTO: CArbon Loss from Histosols . In: Caron, P. and Rochefort, L eds. International Symposium on Responsible Peatland Management, Quebec City, Canada, 77  
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Published Reports
Dr Tasman Crowe
Crowe, T.P., Fitch, J.E., Somerfield, P.J. and Frid, C.L.J. (2011) A framework for managing sea bed habitats in near shore Special Areas of Conservation. Department of the Environment, Heritage and Local Government, Ireland, Dublin.  
Professor Ken Whelan
Fealy, R., Allott, N., Broderick, C., deEyto, E., Dillane, M., Erdil, R.M., Jennings, E. McCrann, K., Murphy, C., O'Toole, C., Poole, R., Rogan, G., Ryder, L., Taylor, D., Whelan, K. and White, J (2010) RESCALE: Review and Simulate Climate and Catchment Responses at Burrishoole. Marine Institute, Galway.  
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