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The Fly! Image by Karl Gaff.

The Fly! Image by Karl Gaff.

UCD Biology & Environmental Science

UCD School of Biology & Environmental Science - Research Publications 2012/13

Below is the list of research publications for the UCD School of Biology & Environmental Science in the academic year 2012/13.




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Books

Dr Jan-Robert Baars
Kelly-Quinn M & Baars J-R (2012). The Remarkable Rye Water. Kileen: Hudson.  
Dr Mary Kelly-Quinn  
Kelly-Quinn M & Baars J-R (2012). The Remarkable Rye Water. Kileen: Hudson.  
Dr Stefano Mariani  
SX Cadrin, L Kerr, Mariani S (2013). Stock Identification Methods. Amsterdam, London, New York, San Diego: Elsevier.  


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Book Chapters

Professor Nicholas Clipson  
Deirdre C Rooney, Nabla M Kennedy, Deirdre B Gleeson & Nicholas JW Clipson (2013). Bacterial Communities Response to Nitrogen, Lime, and Plants In: Sustainable Soil Management. New York: Apple Academic Press.  
Dr Wieland Fricke  
Fricke W. (2013) Single-cell sampling & analysis (SiCSA) In: Plant Mineral Nutrients - Methods in Molecular Biology. Berlin Heidelberg: Springer Verlag.  
Dr Allan McDevitt  
McDevitt AD & Zachos FE (2012). Genetic analyses of natural and anthropogenic movements in deer In: Sykes N, Baker K & Carden RF (eds). Deer and People: Past, Present and Future. Oxford: Windgather Press.  
Dr Anika Mostaert  
Higgins L & Mostaert AS (2013). Qualitative and Quantitative Study of Spiny Starfish (Marthasterias glacialis). Footprints Using Atomic Force Microscopy In: Biological and Biomimetic Adhesives. Challenges and Opportunities. London, UK: RSC Publishing.  
Dr Carl Khee-Yew Ng  
McAinsh MR, Ng CKY (2012). Measurement of Cytosolic-free Ca2+ in Plant Tissue In: DG Lambert (eds). Calcium Signaling Protocols, 3rd Edition. New York: Humana Press.  
Dr Kay Nolan  
Nolan CM (2013). Igf2r Locus. In: Maloy S, Hughes K (eds) Brenner's Encyclopedia of Genetics (Second Edition). Academic Press, San Diego, pp 15-17.  
Professor Bruce Arthur Osborne
Nicolau M, Saunders M, O’Neill M, Osborne B &, Brabazon A (2012). Evolving Interpolating Models of Net Ecosystem CO2 Exchange Using Grammatical Evolution. In: Genetic Programming. 7244: 134-145. Edited by Moraglio A, Silva S, Krawiec K, Machado P, Cotta C: Springer Berlin Heidelberg.  
Dr Tom Wilkinson
Will T, Carolan JC & Wilkinson TL (2013). Breaching the sieve element: the role of saliva as the molecular interface between aphids and the phloem In: Thompson GA & van Bel A. (eds). Biochemistry of Phloem. USA: John Wiley.  


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Peer Reviewed Journals

Dr Jan-Robert Baars
Arroyo J, Baars J-R, O'Driscoll L, Blackmore M & Bolger T (2012). First records of Heminothrus (Capillonothrus) thori (Berlese, 1904) and Perlohmannia (Perlohmannia) dissimilis (Hewitt, 1908) (Arachnida: Acari: Oribatida) in Ireland. Bulletin of the Irish Biogeographical Society, 36:  
Baars J-R, Lyons R & Mary Kelly-Quinn M (2012).  The first records of Ameletus inopinatus Eaton, 1887 (Ephemeroptera: Ameletidae) in upland streams in Co. Kerry, Ireland. Bulletin of the Irish Biogeographical Society, 36: 308-311.  
Earle W, Mangan R, O'Brien M & Baars J-R (2013). Biology of Polypedilum n. sp. (Diptera: Chironomidae), a promising candidate agent for the biological control of the aquatic weed Lagarosiphon major (Hydrocharitaceae) in Ireland. Biocontrol Science and Technology, 23: 1267-1283.  
Kibichii S,  Baars J-R, Kelly-Quinn M and  Holmes JMC (2012). Parastenocaris phyllura, Kiefer, 1938 (Copepoda: Harpacticoida: Parastinocarididae), a species new to Ireland with a few notes on possible habitat preferences. Bulletin of the Irish Biogeographical Society, 36: 97-101.  
Martin, GD, Coetzee J & Baars J-R (2013). Hydrellia lagarosiphon Deeming (Diptera: Ephydridae) a potential biological control agent for the submerged aquatic weed, Lagarosiphon major (Ridl.) Moss ex Wager (Hydrocharitaceae). African Entomology, 21: 151-160.  
Mangan R &, Baars J-R (2012). Use of life table statistics and degree day values to predict the colonisation success of Hydrellia lagarosiphon Deeming (Diptera: Ephydridae), a leaf mining fly of Lagarosiphon major (Ridley) Moss (Hydrocharitaceae), in Ireland and the rest of Europe. Biological Control, 64: 143-151.  
Feeley HB, Bruen M, Blacklocke S, Baars J-R & Kelly-Quinn M (2012) Significant changes in the hydrochemistry and drivers of episodic acidity in headwater streams draining plantation forest in Ireland: increasing role of organic acidity with the reduction of anthropogenic deposition. Science of the Total Environment, 443:  173-183.  
Dr Chiara Benvenuto
Benvenuto C, Cheyppe-Buchmann S, Bermond G, Ris N & Fauvergue X (2012). Intraspecific hybridization, life history strategies and potential invasion success in a parasitoid wasp. Evolutionary Ecology, 26: 1311-1329.  
Professor Thomas Bolger
Andriuzzi WS, Bolger T & Schmidt O (2013). The drilosphere concept: Fine-scale incorporation of surface residue derived N and C around natural Lumbricus terrestris burrows. Soil Biology and Biochemistry, 64: 136-138.  
Arroyo J,  Kenny J & Thomas Bolger T (2012). A survey of the Oribatida and Mesostigmata (Acarina) of Irish forests. Bulletin of the Irish Biogeographical Society, 36: 33-59.  
Arroyo J, Baars J-R, O'Driscoll L, Blackmore M & Bolger T (2013). First records of Heminothrus (Capillonothrus) thori (Berlese, 1904) and Perlohmannia (Perlohmannia) dissimilis (Hewitt, 1908) (Arachnida: Acari: Oribatida) in Ireland. Bulletin of the Irish Biogeographical Society, 36: 212-215.  
Arroyo J, Kenny J & Bolger T (2013). Oribatid and gamasid mite assemblages occurring in aerial and floor habitats of native forestry at Killarney National Park (Ireland). Irish Naturalists' Journal, 32: 121-131.  
Connolly J, Bell T, Bolger T, Brophy C, Carnus T, Finn JA, Kirwan L, Isbell F, Levine J, Loscher A, Picasso V, Roscher C, Sebastia MT, Suter M & Weigelt A (2013). An improved model to predict the effects of changing biodiversity levels on ecosystem function. Journal of Ecology, 101: 344-355.  
Bolger T, Arroyo J, Kenny J & Caplice M (2013). Hierarchical analysis of mite community structures in Irish forests - a study of the relative contribution of location, forest type and microhabitat. Applied Soil Ecology   
Bolger T, Coll M & Anderson R (2013). The arrival of Leistus rufomarginatus (Duftschmid, 1812). (Coleoptera: Carabidae). in Ireland earlier than previously recorded. Irish Naturalists' Journal, 32: 151-151.  
Bolger T, Kenny J & Arroyo J (2013). The Collembola fauna of Irish forests - a comparison between forest type and microhabitat with the forests. Soil Organisms, 85: 61-67.  
Piotrowska K, Connolly J, Finn J, Black A & Bolger T (2013). Evenness and plant species identity affect earthworm diversity and community structure in grassland soils. Soil Biology and Biochemistry, 57: 713-719.  
Wisdom R, Arroyo J & Bolger T. A survey of the Oribatida and Mesostigmata (Acarina) of Irish peatlands. Bulletin of the Irish Biogeographical Society, 36: 130-149  
Dr Jens Carlsson
Collins PC, Croot P, Carlsson J, Colaço A, Grehan A, Hyeong K, Kennedy R, Mohn C, Smith S, Yamamoto H & Rowden A (2013). A primer for the Environmental Impact Assessment of mining at seafloor massive sulfide deposits. Marine Policy, 42: 198-209.  
Lynch SA, Dillane E, Carlsson J & Culloty SC (2013). Development and assessment of a sensitive and cost effective cPCR to detect ostreid herpes virus 1 (OsHV-1) and variants. Journal of Shellfish Research.  
Collins PC, Kennedy R, Copley J, Boschen R, Forde J, Flemming N, Ju SJ, Lindsay D, Marsh L, Nye V, Patterson A, Watanabe H, Yamamoto H, Carlsson J & Thaler AD (2013). Ventbase: Developing a consensus among stakeholders in the deep-sea regarding environmental impact assessment for deep-sea mining. Marine Policy, 42: 334-336.  
Gauthier DT, Audemard CA, Carlsson, JEL, Darden TL, Denson M, Reece KS & Carlsson J (2013). Genetic population structure of U.S. Atlantic coastal striped bass (Morone saxatilis). Journal of Heredity, 104: 510-520.  
Carlsson J, Gauthier D, Carlsson JEL, Coughlan JP, Dillane E, FitzGerald RD, Keating FU, McGinnity P, Mirimin L & Cross TF (2013). Rapid, economical SNP and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua. Journal of Fish Biology, 82: 944-958.  
O'Farrell B, Dennis C, Benzie J, McGinnity P, Carlsson, J, de Eyto E, Coughlan J, Igoe F, Meehan, R & Cross T (2012). Balancing selection on MHC class I in wild brown trout (Salmo trutta). Journal of Fish Biology, 81: 1357-1374.  
Kochmann J, Carlsson J, Crowe TP & Mariani S (2012). Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species - a case study of Pacific oysters (Crassostrea gigas). Journal of Heredity, 103: 661-671.  
Professor Nicholas Clipson
Boots B & Clipson N (2013). Linking ecosystem modification by the yellow meadow ant (Lasius flavus) to microbial assemblages in different soil environments. European Journal of Soil Biology, 55: 100-106.  
Boots B, Lillis L, Clipson N, Petrie K, Kenny DA, Boland TM & Doyle E (2013). Responses of anaerobic rumen fungal diversity (phylum Neocallimastigomycota) to changes in bovine diet. Journal of Applied Microbiology, 114: 626-635.  
Corrigan A, Horgan K, Clipson, N & Murphy RA (2012). Effect of dietary rebiotic (mannan oligosaccharide) supplementation on the cecal bacterial community structure of turkeys. Microbial Ecology, 64: 826-836.  
deMenezes A, Clipson N & Doyle E (2012). Comparative transcriptomics reveals widespread community responses during phenanthrene degradation in soil. Environmental Microbiology, 14: 2577-2588.  
Dr Tasman Crowe
Green DS, Rocha C & Crowe TP (2013). Effects of non-indigenous oysters on ecosystem processes vary with abundance and context. Ecosystems, 16: 881-893.  
Crowe TP, Cusson M, Bulleri F, Davoult D, Arenas F, Aspden R, Benedetti-Cecchi L, Bevilacqua S, Davidson I, Defew E, Fraschetti S, Golléty C, Griffin JN, Herkül K, Kotta J, Migné A, Molis M, Nicol SK, Noël LM LJ, Sousa, Pinto I, Valdivia N, Vaselli S & Jenkins SR (2013). Large-scale variation in combined impacts of canopy loss and disturbance on community structure and ecosystem functioning. PLoS ONE, 8(6):  e66238.  
Callier, MD, Lefebvre, S, Dunagan, M K, Bataille, M-P, Coughlan, J & Crowe, TP (2013). Shift in benthic assemblages and organisms diet under salmon farms: community structure and stable isotope analyses. Marine Ecology Progress Series, 483: 153-167.  
Golléty, C & Crowe, TP (2013). Contributions of biofilm to ecosystem functioning in rock pools with different macroalgal assemblages. Marine Ecology Progress Series, 482: 69-79.  
Green DS & Crowe TP (2013). Physical and biological effects of introduced oysters on biodiversity in an intertidal boulder-field. Marine Ecology Progress Series, 482: 119-132.  
Salvaterra T, Green DS, Crowe TP & O'Gorman EJ (2013). Impacts of the invasive alga Sargassum muticum on ecosystem functioning and food web structure. Biological Invasions, 15: 2563-2567.  
Kochmann J, O'Beirn F, Yearsley J & Crowe TP (2013). Environmental factors associated with invasion: modelling occurrence data from a coordinated sampling programme for Pacific oysters. Biological Invasions, 15: 2265-2279.  
O'Connor NE, Donohue I, Crowe TP & Emmerson M (2012). Distinguishing between direct and indirect effects of predators in complex ecosystems. Journal of Animal Ecology, 82: 438-448.  
Bulleri FL, Benedetti-Cecchi M, Cusson E, Maggi F, Arenas R, Aspden I, Bertocci  Crowe TP, Davoult D, Eriksson BK, Fraschetti S, Golléty C, Griffin J, Jenkins SR,  Kotta J, Kraufvelin P, Molis M, Sousa Pinto I, Terlizzi A,Valdivia N & Paterson DM (2012). The temporal stability of European rocky shore assemblages: variation across a latitudinal gradient and the role of habitat-formers. Oikos, 121: 1801-1809.  
Jochum M, Schneider FD, Crowe TP, Brose U & O'Gorman EJ (2012). Climate-induced changes in bottom-up and top-down processes independently alter a marine ecosystem. Philosophical Transactions of the Royal Society B, 367: 2962-2970.  
Twomey M, Brodte E, Jacob U, Crowe TP & Emmerson MC (2012). Idiosyncratic species effects confound size-based predictions of responses to climate change. Philosophical Transactions of the Royal Society B, 367: 2971-2978.  
Green DS, Boots B & Crowe TP (2012). Effects of non-indigenous oysters on microbial diversity and ecosystem functioning. PLoS ONE, 7 (10): e48410.  
Kochmann, J, Carlsson, J, Crowe, TP & Mariani, S (2012). Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species: a case study of Pacific oysters (Crassostrea gigas). Journal of Heredity, 103: 661-671.  
Dr Fiona Doohan
Arunachalam C & Doohan FM (2013). Trichothecene toxicity in eukaryotes: Cellular and molecular mechanisms in plants and animals. Toxicology Letters, 217: 149-158.  
Hazard C, Gosling P, van der Gast CJ, Mitchell DT, Doohan FM & Bending GD (2013). The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale. Isme Journal, 7: 498-508.  
Ali SS, Nugent B, Mullins E & Doohan FM (2013). Insights from the fungus Fusarium oxysporum point to high affinity glucose transporters as targets for enhancing ethanol production from lignocellulose. PLoS ONE, 8(1): e54701.    
Petti C, Reiber K, Ali S, Berney M & Doohan F (2012). Auxin as a player in the biocontrol of Fusarium head blight disease of barley and its potential as a disease control agent. BMC Plant Biology, 12: 224.  
Dr Evelyn Doyle
Boots B, Lillis L, Clipson N, Petrie K, Kenny DA, Boland TM, and Doyle E (2013). Responses of anaerobic rumen fungal diversity (phylum Neocallimastigomycota) to changes in bovine diet. Journal of Applied Microbiology, 114: 626-635.  
Lynch JP, O'Kiely P & Doyle EM (2013). Yield, nutritive value and ensilage characteristics of whole-crop maize, and of the separated cob and stover components - nitrogen, harvest date and cultivar effects. Journal of Agricultural Science, 151: 347-367.  
Brooks SJ, Nikodinovic J, Martin L, Doyle EM, O'Sullivan T, Guiry PJ, Coulombel L, Li Z & O'Connor KE (2013). Production of a chiral alcohol, 1-(3,4-dihydroxyphenyl). ethanol, by mushroom tyrosinase. Biotechnology Letters, 35: 779-783.  
Lynch JP, O'Kiely P & Doyle, EM (2012).  Yield, quality and ensilage characteristics of whole-crop maize, and of the cob and stover components - Harvest date and hybrid effects. Grass and Forage Science, 67: 472-487.  
deMenezes A, Clipson N & Doyle E (2012). Comparative transcriptomics reveals widespread community responses during phenanthrene degradation in soil. Environmental Microbiology, 14: 2577-2588.  
Dr John Finarelli  
Badgley C & Finarelli JA (2013). Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America. Paleobiology, 39: 373-399.  
Dr Wieland Fricke  
Suku S, Knipfer T & Fricke W (2013). Do root hydraulic properties change during the early vegetative stage of plant development in barley (Hordeum vulgare)? Annals of Botany     
Visnovitz T, Touati M, Miller A & Fricke W (2013). Apoplast Acidification in Growing Barley (Hordeum vulgare L.) Leaves. Journal of Plant Growth Regulation, 32: 131-139.  
Dr Thomas F Gallagher  
Fennell M, Murphy J, Gallagher T & Osborne B (2013). Simulating the effects of climate change on the distribution of an invasive plant, using a high resolution, local scale, mechanistic approach: challenges and insights. Global Change Biology, 19: 1262-12174.     
Dalton E, Griffin D, Gallagher TF Vetten N & Milbourne D (2013). The effect of pyramiding two potato cyst nematode resistance loci to Globodera pallida Pa2/3 in potato. Molecular Breeding, 31: 921-930.     
Professor Thomas Hayden  
Naulty F, Harty H & Hayden TJ (2013). Freedom to choose: Unconstrained mate-searching behaviour by female fallow deer (Dama dama). Folia Zoologica, 62: 143-154.  
Kent JP, Murphy KJ, Salamon A, Hayden TJ & Möstl E (2013). Hormone levels in the outer layer of domestic goose (Anser anser domesticus) eggs change over the laying season. Avian Biology Research, 6: 221-226.  
Jennings DJ, Elwood RW, Carlin CM, Hayden TJ & Gammell MP (2013). Vocal rate as an assessment process during fallow deer contests. Behavioural Processes, 91: 152-158.  
Dr Tamara Hochstrasser  
Burkart D, Finnan, J, Hochstrasser T & Müller C (2013). The greenhouse gas balance of a dairy farm as influenced by the uptake of biogas production. BioEnergy Research, :1-15.  10.1007/s12155-013-9350-3.    
Dr Mary Kelly-Quinn  
Cocchiglia L, Purcell P & Kelly-Quinn M (2012). A critical review of the effects of motorway river crossing construction on the aquatic environment. Freshwater Reviews, 5: 141-168.  
Elsaholi MS & Kelly-Quinn M (2013). The effect of nutrient concentrations and ratios on periphyton biomass in low conductivity streams: implications for determination of nutrient limitation. Inland Waters, 3: 451-458.  
Feeley HB, Bruen M, Blacklocke S & Kelly-Quinn M (2013). A regional examination of episodic acidification response to reduced acidic deposition and the influence of plantation forests in Irish headwater streams. Science of the Total Environment, 443: 173-183.    
Hannigan E & Kelly-Quinn M (2012). Composition and structure of macroinvertebrate communities in contrasting open-water habitats in Irish peatlands: implications for biodiversity conservation. Hydrobiologia, 692: 19-28.  
O’Callaghan P & Kelly-Quinn M (2013). Performance of selected macroinvertebrate-based biotic indices for rivers draining the Merendon Mountains region of Honduras. Cuadernos de Investigación UNED, 5: 45-54.  
Shore M, Murphy PNC, Jordan P, Mellander PE, Kelly-Quinn M, Cushen M, Mechan S, Shine O & Melland AR (2013). Evaluation of a surface hydrological connectivity index in agricultural catchments. Environmental Modelling & Software, 47: 7-15.  
Dr Mohammad Khalil  
MI Khalil G,  Kiely P, O'Brien & Müller C (2013). Estimation of organic carbon stocks in agricultural soils in Ireland using combined empirical and GIS approaches. Geoderma, 193-194: 222-235.    
Jahangir MMR, Johnston P, MI. Khalil G, Grant J Somers C & Richards KG (2012). Evaluation of headspace equilibration methods for quantifying greenhouse gases in groundwater. Journal of Environmental Management, 111: 208-212.    
Dr Stefano Mariani  
Coscia I, McDevitt AD, King JJ, Roche WK, McLoughlin C & Mariani S (2013). A species-to-be? The genetic status and colonization history of the critically endangered Killarney shad. Molecular Phylogenetics and Evolution, 69: 1190-1195.    
Cunha RL, Coscia I, Madeira C, Mariani S, Stefanni S & Castilho R (2012). Ancient Divergence in the trans-oceanic deep-sea Shark Centroscymnus crepidater. PLoS ONE, 7(11): e49196.  
Mariani S, Sala-Bozano M, Chopelet J & Benvenuto C (2013). Spatial and temporal patterns of size-at-sex-change in two exploited coastal fish. Environmental Biology of Fishes, 96: 535-541.    
Coscia I, Vogiatzi E, Kotoulas G, Tsigenopoulos CS & Mariani S (2012). Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L, in the North-East Atlantic. Heredity, 108: 537-546.     
Griffiths AM, Miller DD, Egan A, Fox J, Greenfield A & Mariani S (2013). DNA barcoding unveils skate (Chondrichthyes: Rajidae) species diversity in ‘ray’products
sold across Ireland and the UK. PeerJ, 1: e129.
 
Kochmann J, Carlsson J, Crowe TP & Mariani S (2012).Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species - a case study of pacific oysters (Crassostrea gigas). Journal of Heredity, 103: 661-671.     
Miller D, Jessel A & Mariani S (2012). Seafood mislabelling: comparisons of two western European case studies assist in defining influencing factors, mechanisms and motives. Fish and Fisheries, 13: 345-358.     
Miller DD & Mariani S (2013). Irish fish, Irish people: roles and responsibilities for an emptying ocean. Environment, Development and Sustainability, 15: 529-546.  
Russo T, Pulcini D, Costantini D, Pedreschi D, Palamara E, Boglione C, Cataudella S, Scardi M & Mariani S (2013) “Right” or “wrong”? insights into the ecology of sidedness in european flounder, Platichthys flesus. Journal of Morphology 273: 337-346.  
Dr Paul McCabe  
Diamond M, Reape TJ, Rocha O, Doyle SM, Kacprzyk J, Doohan FM & McCabe PF (2013). The Fusarium mycotoxin deoxynivalenol can inhibit plant apoptosis-like programmed cell death. PLoS ONE, 8(7): e69542.     
Reape TJ & McCabe PF (2013). The cellular condensation of dying plant cells: Programmed retraction or necrotic collapse? Plant Science, 207: 135-139.     
Dr Allan McDevitt  
Coscia I, McDevitt AD, King JJ, Roche WK, McLoughlin C & Mariani S (2013). A species-to-be? The genetic status and colonization history of the critically endangered Killarney shad. Molecular Phylogenetics and Evolution, 69: 1190-1195.    
McDevitt, AD, Oliver MK, Piertney SB, Szafra?ska PA, Konarzewski M & Zub K (2013). Individual variation in dispersal associated with phenotype influences fine-scale genetic structure in weasels. Conservation Genetics, 14: 499-509.     
Sommer S, McDevitt AD, Balkenhol N (2013). Landscape genetic approaches in conservation biology and management. Conservation Genetics, 14: 249-251.    
Zachos FE, Apollonio M, Barmann EV, Festa-Bianchet M, Gohlich U, Habel JC, Haring E, Kruckenhauser L, Lovari S, McDevitt AD, Pertoldi C, Rossner GE, Sanchez-Villagra MR, Scandura M & Suchentrunk F (2013). Species inflation and taxanomic artefacts - a critical comment on recent trends in mammalian classification. Mammalian Biology, 78: 1-6.     
Ciuti S, Muhly TB, Patton DG, McDevitt AD, Musiani M & Boyce MS (2012). Human selection of elk behavioural traits in a landscape of fear. Proceedings of the Royal Society B - Biological Sciences, 279: 4407-4416.    
Professor Jenny McElwain  
Bacon KL, Belcher CM, Haworth, M & McElwain JC (2013). Increased atmospheric SO2 detected from changes in leaf physiognomy across the Triassic-Jurassic boundary interval of East Greenland. PLoS ONE, 8(4): e60614.    
Haworth M, Elliott-Kingston C & McElwain JC (2013). Co-ordination of physiological and morphological responses of stomata to elevated [CO2] in vascular plants. Oecologia, 171: 71-82.    
Mander L, Kurschner WM & McElwain JC (2013). Palynostratigraphy and vegetation history of the Triassic-Jurassic transition in East Greenland. Journal of the Geological Society, 170: 37-46.    
Mander L, Wesseln CJ, McElwain JC & Punyasena SW (2012). Tracking taphonomic regimes using chemical and mechanical damage of pollen and spores: an example from the triassic–jurassic mass extinction. PLoS ONE 7(11): e49153.  
Steinthorsdottir M, Woodward FI, Surlyk F & McElwain JC (2012). Deep-time evidence of a link between elevated CO2 concentrations and perturbations in the hydrological cycle via drop in plant transpiration. Geology, 40: 815-818.     
Professor Christoph Mueller  
Khalil MI, Kiely G, O'Brien P & Mueller, C (2013). Organic carbon stocks in agricultural soils in Ireland using combined empirical and GIS approaches. Geoderma, 193-194: 222-235.     
Inselsbacher E, Wanek W, Strauss J, Zechmeister-Boltenstern S & Müller C (2013). A novel 15N tracer model reveals: plant nitrate uptake governs nitrogen transformation rates in agricultural soils. Soil Biology and Biochemistry, 57: 301-310.    
Clough TJ, Condron LM, Kammann C & Müller C (2013). A review of biochar and soil nitrogen dynamics. Agronomy Journal, 3: 275-293.    
Clough TJ, Müller C & Laughlin RJ (2013). Using stable isotopes to follow excreta N dynamics and N2O emissions in animal production systems. Animal, 7: 418-426.    
Dieterich B, Finnan J, Hochstrasser T & Müller C (2013). The greenhouse gas balance of a dairy farm as influenced by the uptake of biogas production. Bioenergy Research, 1-15.    
Zhang Y, Zhang J, Meng T, Zhu T, Müller C, Cai Z (2013). Heterotorophic nitrification is the predominant NO3- production pathway in acid coniferous forest soil in subtropical China. Biology and Fertility of Soils, 49: 955-957.    
Zhang J, Zhu T, Meng T, Zhang Y, Yang J, Yang W, Müller C & Cai Z (2013). Agricultural land use affects nitrate production and conservation in humid subtropical soils in China. Soil Biology and Biochemistry, 62: 107-114.    
Zhang J, Cai Z, Zhu T-B, YangW-Y & Müller C (2013). Mechanisms for the retention of inorganic N in acidic forest soils of southern China. Scientific Reports, 3: 2342-2342.    
Wilson D, Farrell C, Müller C, Hepp & Renou-Wilson F (2013). Rewetted industrial cutaway peatlands in western Ireland: a prime location for climate change mitigation? Mires and Peatlands, 11: 1-22.    
Müller C & Clough TJ (2013). Advances in understanding nitrogen flows and transformations: gaps and research pathways. Journal of Agricultural Science.    
Augustenborg  C, McBennett L, Connolly L, Priegnitz U, Finnan J & Mueller C (2012). Farmers perspectives for the development of a bioenergy industry in Ireland. Global Change Biology (Bioenergy), 4: 597-610.     
Lenhart K, Bunge M, Ratering S, Neu TR, Schüttmann I, Greule M, Kammann C, Schnell S, Mueller C, Zorn H & Keppler F (2012). Evidence for methane production by saprotrophic fungi. Nature Communications, 3, 1046.    
Meade G, Pierce K, O'Doherty JV, Mueller C, Hepp S, Lanigan G & McCabe, T (2012). Gaseous emissions of methane and carbon dioxide following land application of high and low nitrogen pig manures to winter wheat at three key crop growth stages. Journal of Agricultural Science.    
Dr Carl Khee-Yew Ng  
Shinde S, Shinde R, Downey F & Ng CKY (2013). Abiotic stress-induced oscillations in steady-state transcript levels of Group 3 LEA protein genes in the moss, Physcomitrella patens. Plant Signaling and Behaviour, 8, e22535.     
Chambers JP, Behpouri A, Bird A & Ng CKY (2012). Evaluation of the use of the polyubiquitin genes, Ubi4 and Ubi10 as reference genes for gene expression studies in Brachypodium distachyon. PLoS ONE, 7(11): e49372.     
Dr Kay Nolan  
Williams C, Hoppe HJ, Rezgui D, Strickland M, Forbes BE, Grutzner F, Frago S, Ellis RZ, Wattana-Amorn P, Prince SN, Zaccheo OJ, Nolan CM, Mungall AJ, Jones EY, Crump MP & Hassan AB (2012). An exon splice enhancer primes IGF2:IGF2R binding site structure and function evolution. Science, 338: 1209-1213.    
Terzo E, McConnell JF, Shiel RE, McAllister H, Behr S, Priestnall SL, Smith KC, Nolan CM & Callanan JJ (2012). Unique topographic distribution of greyhound nonsuppurative meningoencephalitis. Veterinary radiology & ultrasound: the official journal of the American College of Veterinary Radiology and the International Veterinary Radiology Association, 53: 636-642.    
Professor Bruce Arthur Osborne  
Don A, Osborne B, Hastings A, Skiba U, Carter M, Drewer J, Flessa H, Freibauer A, Hyvonen N, Jones, MB, Lanigan G, Mander U, Mont, A, Njakou Djomo S, Valentine J, Walter K, Zegada-Lizarazu W & Zenone T (2012). Land-use change to bioenergy production in Europe: implications for the greenhouse gas balance and soil carbon. Global Change Biology Bioenergy, 4: 372-391.  
Fennell M. Murphy JE, Gallagher T & Osborne B (2013). Simulating the effects of climate change on the distribution of an invasive plant, using a high resolution, local scale, mechanistic approach: challenges and insights. Global Change Biology, 19: 1262-1274.    
Abdalla M, Osborne B, Lanigan G, Forristal D, Williams M, Smith P & Jones MB (2013). Conservation tillage systems: a review of its consequences for greenhouse gas emissions. Soil Use and Management 29: 199-209.  
Abdalla M, Rueangritsarakul K, Jones M, Osborne B, Helmy M, Roth B, Burke J, Nolan P, Smith P & Williams M (2012). How Effective is Reduced Tillage-Cover Crop Management in Reducing N2O Fluxes from Arable Crop Soils? Water Air and Soil Pollution 223: 5155-5174.  
Abdalla MS, Hastings A. Williams M. Smith P,. Osborne B, Lanigan  G & Jones MB (2013). Simulating the impacts of land use in northwest Europe on Net Ecosystem Exchange (NEE): the role of arable ecosystems, grasslands and forest plantations in climate change mitigation. The Science of the Total Environment 465: 325-336.  
Saunders M, Tobin B, Black K, Gioria M, Nieuwenhuis M & Osborne BA (2012). Thinning effects on the net ecosystem carbon exchange of a Sitka spruce forest are temperature-dependent. Agriculture and Forest Meteorology 157:1-10.  
Wang T, Brender P, Ciais P, Piao S, Mahecha MD, Chevallier F, Reichstein M, Ottlé C, Maignan F, Arain A, Bohrer G, Cescatti A, Kiely G, Law BE, Lutz M, Montagnani L, Moors E, Osborne B, Panferov O, Papale D & Vaccari FP (2012). State-dependent errors in a land surface model across biomes inferred from eddy covariance observations on multiple timescales. Ecological Modelling 246: 11-25.  
Dr Sebastien Puechmaille  
Walters C. Maltby A, Dietz C, Fenton B, Jones G, Obrist M, Puechmaille SJ, Sattler T, Siemers B, Jones K & Parsons S (2012). A continental-scale tool for acoustic identification of European bats. Journal of Applied Ecology, 49: 1064-1074.    
Thong, VD, Dietz C, Denzinger A, Bates PJJ, Puechmaille SJ, Callou C & Schnitzler H-U (2012). Resolving a mammal mystery: the identity of Paracoelops megalotis (Chiroptera: Hipposideridae). Zootaxa, 3505: 75-85.     
Dr Emmanuel Reynaud  
Page H, Flood P & Reynaud EG (2013). Three-dimensional tissue cultures: current trends and beyond. Cell and Tissue Research 352: 123-131  
Dr Florence Renou-Wilson  
Wilson DC, Farrell C, Mueller C & Renou-Wilson F (2013). Rewetted industrial cutaway peatlands in western Ireland: a prime location for climate change mitigation. Mires and Peatlands, 11: 1-22.     
Professor Jeremy Simpson  
Stadler C, Rexhepaj E, Singan, VR, Murphy RF, Pepperkok R, Uhlen M, Simpson JC &  Lundberg E. (2013). Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. Nature Methods, 10: 315-323.    
Miranda-CasoLuengo AA, Miranda-CasoLuengo R Lieggi NT, Luo H, Simpson JC &  Meijer WG (2013). A real-time impedance based method to assess Rhodococcus equi virulence. PLoS ONE, 8(3): e60612.    
McCarthy JM, Franke M, Resenberger UK, Waldron S, Simpson JC, Tatzelt J, Appelhans D & Rogers MS (2013). Anti-prion drug mPPIg5 inhibits PrPC conversion to PrPSc. PLoS ONE, 8(1): e55282.    
Singan VR, Handzic K & Simpson JC (2012). Quantitative image analysis approaches for probing Rab GTPase localization and function in mammalian cells. Biochemical Society Transactions, 40: 1389-1393.    
Yi P, Higa A, Taouji S, Bexiga MG, Marza E, Arma D, Castain C, Le Bail B, Simpson JC, Rosenbaum J, Balabaud C, Bioulac-Sage P, Blanc JF & Chevet E (2012). Sorafenib-mediated targeting of the AAA+ ATPase p97/VCP leads to disruption of the secretory pathway, rndoplasmic reticulum stress, and hepatocellular cancer cell death. Molecular Cancer Therapeutics, 11: 2610-2620.    
Roth SD, Schüttrumpf J, Milanov P, Abriss D, Ungerer C, Quade-Lyssy P, Simpson JC, Pepperkok R, Seifried E & Tonn T (2012). Chemical Chaperones Improve Protein Secretion and Rescue Mutant Factor VIII in Mice with Hemophilia A. PLoS ONE, 7(9): e44505.    
Varela JA, Bexiga MG, Aberg C, Simpson JC & Dawson KA (2012). Quantifying size-dependent interactions between fluorescently labeled polystyrene nanoparticles and mammalian cells. Journal of Nanobiotechnology, 10: 39.    
Dr Gavin Stewart  
Dix L, Ward DT & Stewart GS (2013). Urea transporter protein UT-B in bovine parotid gland. Journal of Dairy Science, 96: 1685-1690.    
Professor Emma C Teeling  
Buckley DJ, Lundy MG, Boston ESM, Scott DD, Gager Y, Prodohl P, Marnell F,  Montgomery WI & Teeling EC. (2012). The spatial ecology of the whiskered bat (Myotis mystacinus) at the western extreme of its range provides evidence of regional adaptation. Mammalian Biology, 78: 198-204.  
Dool SE,  Puechmaille SJ,  Dietz C, Juste J,  Ibáñez C, Hulva P, Roué SG, Petit EJ, Jones G, Rossiter SJ & Teeling EC (2013). Phylogeography and postglacial recolonisation of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers. Molecular Ecology, 22: 4055-4070.  
Goodman SM, Puechmaille SJ, Friedli-Weyeneth N, Gerlach J, Ruedi M, Schoeman MC, Stanley WT & Teeling EC (2012). Phylogeny of the Emballonurini (Emballonuridae) with descriptions of a new genus and species from Madagascar. Journal of Mammalogy, 93: 1440-1455.  
Hughes GM, Gang L, Murphy WJ, Higgins DG & Teeling EC (2013). Using Illumina Next Generation Sequencing Technologies to Sequence Multigene Families in de novo Species. Molecular Ecology Resources, 13: 510-512.  
Jones G, Teeling EC & Rossiter SJ (2013). From the ultrasonic to the infrared: molecular evolution and the sensory biology of bats. Frontiers in Integrative Physiology, 4.  10.3389/fphys.2013.00117    
Kirwan J, Bekaert M, Commins KT, Davies J, Rossiter SJ & Teeling EC (2013). A Phylomedicine Approach to Understanding the Evolution of Auditory Sensory Perception and Disease in Mammals. Evolutionary Applications, 6: 412-422.  
Lundy MG, Harrison A, Buckley DJ, Boston ES, Scott DD, Teeling EC, Montgomery WI & Houghton JDR (2013). Prey field switching based on preferential behaviour can induce Levy flights. Journal of the Royal Society, Interface / the Royal Society, 10 (78).    
Morgan C, McCartney A, Donoghue M, Loughran N, Spillane C, Teeling E & O'Connell M (2013). Molecular adaptation of telomere associated genes in mammals. BMC Evolutionary Biology 13: 251.  
Scott DD,  Fitzpatrick S, Bailie DA, Boston EM, Lundy MG, Buckley DJ,  Teeling EC  Montgomery WI &  Prodöhl PA (2013). Isolation and characterization of eight polymorphic microsatellite loci for Natterer's bat, Myotis nattereri (Vespertilionidae, Chiroptera). Conservation Genetics Resources, 5: 643-645.    
Springer MS, Meredith RB, Teeling EC & Murphy WJ (2013). Technical comment on the placental mammal ancestor and the post-K-Pg radiation of placentals. Science, 9: 613-603.    
Teeling  EC & Hedges SB (2013). Making the impossible possible: rooting the tree of placental mammals. Molecular Biology and Evolution, 30: 1999-2000.    
Dr Tom Wilkinson  
Rao S, Carolan JC & Wilkinson TL (2013). Proteomic profiling of cereal aphid saliva reveals ubiquitous and adaptative secreted proteins. PLoS ONE 7(1): e57413.    
Dr Jonathan Yearsley  
Broquet T, Viard F & Yearsley JM (2013). Genetic drift and collective dispersal can result in chaotic genetic patchiness. Evolution, 67: 1660-1675.    
Yearsley JM, Viard F, Broquet T (2013). The effect of collective dispersal on the genetic structure of a subdivided population. Evolution, 67: 1649-1659.    
Kochmann J, O'Beirn F, Yearsley JM & Crowe TP (2013). Environmental factors associated with invasion: modelling occurrence data from a coordinated sampling programme for Pacific oysters. Biological Invasions. 15: 2265-2279.    


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Other Journals

Professor Nicholas Clipson
Liliensiek AK,  Thakuria D,  Clipson N & Talukdar NC (2013). Linking phylogeny to abundant ribotypes of community fingerprints: an exercise on the phylotypic responses to plant species, fertilisation and Lolium perenne ingression. SpringerPlus, 2.  
Dr Allan McDevitt
McDevitt AD (2013). Invasions and Expansions: the greater white-toothed shrew in Ireland. Genetics Society News, 68: 51-52.  
McDevitt AD & Carden RF. (2012). Squatters' Rights - The Native Problem. Irish Wildlife, Winter: 22-25.  
McDevitt AD, O'Toole P, Edwards CJ & Carden RF (2012). Landscape genetics of red deer (Cervus elaphus, Linnaeus 1758) in Killarney National Park, County Kerry. Irish Naturalists' Journal : 23-30.  
McDevitt AD & Carden RF (2012). Ireland's ancient deer. Deer, 16: 23-26.  
Dr Jonathan Yearsley
Prat N, Belcher C, Hadden R, Rein G & Yearsley J (2013). A laboratory study of the effect of moisture content on the spread of smouldering fires. FLAMMA, 6: 35-38.  


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Conference Publications

Dr Tasman Crowe
Murphy C, Crowe T, Rocha C, Doyle E & Clipson N (2013). Impacts of changing biodiversity on ecosystem functioning in intertidal sedimentary systems. In: SGM eds. Society for General Microbiology, Dublin, 60.  
Dr Evelyn Doyle
Storey S, deMenezes A, Clipson N & Doyle E (2013). Microbiome analysis of a phenanthrene contaminated soil. In: FEMS eds. FEMS 2013, 5th Congress of European Microbiologists, Leipzig, Germany, 211.  
Ashaari MM, Hutchens E, Benson M, Murphy C, Clipson N & Doyle E (2013). Targeted metagenomic analysis of polycyclic aromatic hydrocarbon (PAH). degradation gene in contaminated soil. In: SGM eds. Society for General Microbiology, Dublin.  
Murphy C, Crowe T, Rocha C, Doyle E & Clipson N (2013). Impacts of changing biodiversity on ecosystem functioning in intertidal sedimentary systems. In: SGM eds. Society for General Microbiology, Dublin, 60.  
Lynch JP, O'Kiely P & Doyle EM (2012). Dry matter recovery and aerobic stability of maize whole-crop, cob and stover silages, harvest date and cultivar effects EUCARPIA 29th Fodder Crops and Amenity Grasses Section Meeting.  
Dr Tamara Hochstrasser
Tamara Hochstrasser (2013). What is needed for the design of adaptive policy appraisal? 33rd Annual Meeting of International Association for Impact Assessment, Calgary, Alberta, Canada.  
Professor Bruce Arthur Osborne  
Mulakupadom S, Otero S, Lanigan G & Osborne B (2013). Photosynthetic Performance of Maize Subjected to Low Temperatures.  In: Proceedings of the International Congress on Photosynthesis - Photosynthesis Research for Food, Fuel and the Future. Springer Berlin Heidelberg, pp 716-721.  


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Other Publications

Dr Jan-Robert Baars
Baars J-R, Mangan R & Earle W (2013). Investigations into the potential use of Biological Control to manage Lagarosiphon major. Reports.  
Baars J-R, Keenan E & Caffrey JM (2013). The effect of an aquatic invasive weed Lagarosiphon major and its management on the flora and fauna of shallow littoral habitats in Lough Corrib, Ireland. Reports.  
Dr Claire Cave
Cave C. (2013). World Heritage: cooperation, communication and capacity building. London, UK: Articles.   
Dr Fiona Doohan
Arunachalam C & Doohan FM (2013). Trichothecene toxicity in eukaryotes: Cellular and molecular mechanisms in plants and animals. Reviews.  
Professor Jenny McElwain
McElwain JC (2013). Ginkgo The Tree That Time Forgot. Book Reviews. Science  340: 812-813.  
Dr Allan McDevitt  
McDevitt AD (2013). Invasions and Expansions: the greater white-toothed shrew in Ireland. Genetics Society News, 68: 51-52.  
   


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