Publications list

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2008

Lyons M, Cardle L, Rostoks N, Waugh R, Flavell AJ. 2008. Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome. Molecular Genetics and Genomics. 280:275-285. Abstract

Butler A, Glasbey CA. 2008. A latent Gaussian model for compositional data with zeros. Journal of the Royal Statistical Society Series C - Applied Statistics. 57:505-520. Abstract

Selman C, McLaren JS, Mayer CD, Duncan JS, Collins AR, Duthie GG, Redman P, Speakman JR. 2008. Lifelong, . Rejuvenation Research. 11:83-95. Abstract

Stewart D. 2008. Lignin as a base material for materials applications; Chemistry, application and economics (Invited mini review). Industrial Crops and Products. 27:202-207. Abstract

Bishop HO, Grieve IC, Chudek JA, Hopkins DW. 2008. Liming upland grassland: The effects on earthworm communities and the chemical characteristics of carbon in casts. European Journal of Soil Science. 59:526-531. Abstract

Whybrow S, Horgan GW, Stubbs RJ. 2008. Low-energy reporting and duration of recording period. European Journal of Clinical Nutrition. 62:1148-1150. Abstract

Wheaton AD, McKenzie BM, Tisdall JM. 2008. Management to increase the depth of soft soil improves soil conditions and grapevine performance in an irrigated vineyard. Soil and Tillage Research. 98:68-80. Abstract

Comadran J, Russell JR, van Eeuwijk FA, Ceccarelli S, Grando S, Baum M, Stanca AM, Pecchioni N, Mastrangelo AM, Akar T et al.. 2008. Mapping adaptation of barley to droughted environments. Euphytica. 161:35-45. Abstract

Fowler PA, Cassie S, Rhind SM, Brewer MJ, Collinson JM, Lea RG, Baker PJ, Bhattacharya S, O'Shaughnessy PJ. 2008. Maternal smoking during pregnancy specifically reduces human fetal desert hedgehog gene expression during testis development. Journal of Clinical Endocrinology and Metabolism. 93:619-626. Abstract

Solomon-Blackburn RM, Nikan J, Barker H. 2008. Mechanism of strong resistance to Potato leafroll virus infection in a clone of potato (Solanum tuberosum). Annals of Applied Biology. 152:339-347. Abstract

Giuliano G, Tavazza R, Diretto G, Beyer P, Taylor MA. 2008. Metabolic engineering of carotenoid biosynthesis in plants. Trends in Biotechnology. 26:139-145. Abstract

Jiang N, Leach LJ, Hu X, Potokina E, Jia T, Druka A, Waugh R, Kearsey MJ, Luo ZW. 2008. Methods for evaluating gene expression from Affymetrix microarray datasets. BMC Bioinformatics. 9:-284. Abstract

Grzegorczyk M, Husmeier D, Edwards KD, Ghazal P, Millar AJ. 2008. Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. Bioinformatics. 24:2071-2078. Abstract

Morris WL, Ducreux LJM, Bryan GJ, Taylor MA. 2008. Molecular dissection of sensory traits in the potato tuber. American Journal of Potato Research. 85:286-297.

Sharma SK, Millam S, Hedley PE, McNicol JW, Bryan GJ. 2008. Molecular regulation of somatic embryogenesis in potato: an auxin led perspective. Plant Molecular Biology. 68:185-201. Abstract

Simpson CG, Fuller J, Maronova M, Kalyna M, Davidson D, McNicol JW, Barta A, Brown JWS. 2008. Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts. The Plant Journal. 53:1035-1048. Abstract

Nonyane BAS, Theobold CM. 2008. Multiplicative models for combining information from several sensory experiments: A Bayesian analysis. Food Quality and Preference. 19:260-266. Abstract

Raven JA. 2008. Not drowning but photosynthesising probing plant plastrons. New Phytologist. 177:841-845. Abstract

Dennis PG, Miller AJ, Clark IM, Taylor RG, Valsami-Jones E, Hirsch PR. 2008. A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale. Journal of Microbiological Methods. 75:12-18. Abstract

Avrova AO, Boevink P, Young V, Grenville-Briggs LJ, van West P, Birch PRJ, Whisson SC. 2008. A novel Phytophthora infestans haustorium-specific membrane protein is requred for infection of potato. Cellular Microbiology. 10:2271-2284. Abstract

Baccini M, Bachmaier EM, Biggeri A, Boekschoten MV, Bouwman FG, Brennan L, Caesar R, Cinti S, Coort SL, Crosley K et al.. 2008. The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation. Genes and Nutrition. 3:147-151.

Stark LA, Taliansky ME. 2008. Old and new faces of the nucleolus. Workshop on the nucleolus and disease. EMBO Reports. 10:35-40. Abstract

Guilioni L, Jones HG, Leinonen I, Lhomme JP. 2008. On the relationships between stomatal resistance and leaf temperatures in thermography. Agricultural and Forest Meteorology. 148:1908-1912.

Birch PRJ, Boevink P, Gilroy E, Hein I, Pritchard L, Whisson SC. 2008. Oomycete RXLR effectors: delivery, functional redundancy and durable disease resistance. Current Opinion in Plant Biology. 11:373-379. Abstract

Blok VC, Jones JT, Phillips MS, Trudgill DL. 2008. Parasitism genes and host range disparities in biotrophic nematodes: the conundrum of polyphagy versus specialism. Bioessays. 30:249-259. Abstract

Yahiaoui S, Igartua E, Moralejo M, Ramsay L, Molina-Cano J-L, Ciudad FJ, Lasa JM, Gracia MP, Casas AM. 2008. Patterns of genetic and eco-geographical diversity in Spanish barleys. Theoretical and Applied Genetics. 116:271-282. Abstract

Wang J, Zhang X, Bengough AG, Crawford JW. 2008. Performance evaluation of the cell-based algorithms for domain decomposition in flow simulation. International Journal of Numerical Methods for Heat & Fluid Flow. 18:656-672. Abstract

Chapman SN, Faulkner C, Kaiserli E, Garcia-Mata C, Savenkov EI, Roberts AG, Oparka KJ, Christie JM. 2008. The photoreversible fluorescent protein iLOV outperforms GFP as a reporter of plant virus infection. Proceedings of the National Academy of Sciences, USA. 105:20038-20043. Abstract

K SF, Raven JA. 2008. Photosynthetic oscillation in individual cells of the marine diatom Coscinodiscus wailesii (Bacillariophyceae) revealed by microsensor measurements. Photosynthesis Research. 95:37-44. Abstract

Dobson G, Shepherd T, Verrall SR, Conner S, McNicol JW, Ramsay G, Shepherd LVT, Davies HV, Stewart D. 2008. Phytochemical diversity in tubers of potato cultivars and landraces using a GC-MS metabolomics approach. Journal of Agricultural and Food Chemistry. 56:10280-10291. Abstract

van Poppel PMJA, Guo J, van de Vondervoort PJI, Jung MWM, Birch PRJ, Whisson SC, Govers F. 2008. The Phytophthora infestans avirulence gene Avr4 encodes an RXLR-dEER effector. Molecular Plant-Microbe Interactions. 21:1460-1470. Abstract

Mostowfizadeh-Ghalamfarsa R, Cooke DEL, Banihashemi Z. 2008. Phytophthora parsiana sp. nov., a new high-temperature tolerant species. Mycological Research. 112:783-794. Abstract

Lambers H, Raven JA, Shaver GR, Smith SE. 2008. Plant nutrient-acquisition strategies change with soil age. Trends in Ecology and Evolution. 23:94-103. Abstract

Palukaitis P, Carr JP. 2008. Plant resistance responses to viruses. Journal of Plant Pathology. 90:153-171.

Harrison BD. 2008. Plant virology in the 20th century. Phytopathology. 98, Supplement:S193-S194. Abstract

Canetta E, Kim S-H, Kalinina NO, Shaw J, Adya AK, Gillespie T, Brown JWS, Taliansky ME. 2008. A plant virus movement protein forms ringlike complexes with the major nucleolar protein, fibrillarin, in vitro. Journal of Molecular Biology. 376:932-937. Abstract

Grouffaud S, van West P, Avrova AO, Birch PRJ, Whisson SC. 2008. Plasmodium falciparum and Hyaloperonospora parasitica effector translocation motifs are functional in Phytophthora infestans. Microbiology. 154:3743-3751. Abstract

Riepsamen AH, Blok VC, Phillips MS, Gibson T, Dowton M. 2008. Poly(T) variation within mitochondrial protein-coding genes in Globodera (Nematoda : Heteroderidae). Journal of Molecular Evolution. 66:197-209. Abstract

Bradshaw JE, Hackett CA, Pande B, Waugh R, Bryan GJ. 2008. QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Theoretical and Applied Genetics. 116:193-211. Abstract

Bohanec M, Mess A, Scatasta S, Angevin F, Griffiths BS, Krogh PH, Znidars M, Dzeroski S. 2008. A qualitative multi-attribute model for economic and ecological assessment of genetically modified crops. Ecological Modelling. 215:247-261. Abstract

Liu H, Coulthurst SJ, Pritchard L, Hedley PE, Ravensdale M, Humphris SN, Burr T, Takle GW, Brurberg MB, Birch PRJ et al.. 2008. Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum. PLoS Pathogens. 4:-e1000093. Abstract

Carreira JA, Vi B, Garc R, Ochoa V, Hinojosa MB. 2008. Recovery of biochemical functionality in polluted flood-plain soils: The role of microhabitat differentiation through revegetation and rehabilitation of the river dynamics. Soil Biology & Biochemistry. 40:2088-2097. Abstract

Hopkins DW, Sparrow AD, Gregorich EG, Novis P, Elberling B, Greenfield LG. 2008. Redistributed lacustrine detritus as a spatial subsidy of biological resources for soils in an Antarctic dry valley. Geoderma. 144:86-92. Abstract

Debeljak M, Squire GR, Demsar D, Young MW, Dzeroski S. 2008. Relations between the oilseed rape volunteer seedbank, and soil factors, weed functional groups and geographical location in the UK. Ecological Modelling. 212:138-146. Abstract

Singh BK, Nunan N, Ridgway KP, McNicol JW, Young JPW, Daniell TJ, Prosser JI, Millard P. 2008. Relationship between assemblages of mycorrhizal fungi and bacteria on grass roots. Environmental Microbiology. 10:534-541. Abstract

Vassilakos N, Bem F, Tzima A, Barker H, Reavy B, Karanastasi E, Robinson DJ. 2008. Resistance of transgenic tobacco plants incorporating the putative 57-kDa polymerase read-through gene of Tobacco rattle virus against rub-inoculated and nematode-transmitted virus. Transgenic Research. 17:929-941. Abstract

Zhan J, Fitt BDL, Pinnschmidt HO, Oxley SJP, Newton AC. 2008. Resistance, epidemiology and sustainable management of Rhynchosporium secalis populations on barley. Plant Pathology. 57:1-14. Abstract

Iglesias-Rodriguez MD, Buitenhuis ET, Raven JA, Schofield O, Poulton AJ, Gibbs S, Halloran PR, de Baar HJW. 2008. Response to comment on 'Phytoplankton calcification in a high CO2 world'. Science. 322:-1466.

Nart P, Naylor SW, Huntley JF, McKendrick IJ, Gally DL, Low JC. 2008. Responses of cattle to gastrointestinal colonization by Escherichia coli O157:H7. Infection and Immunity. 76:5366-5372. Abstract

Griffiths BS, Liu Q, Wang H, Zhang B, Kuan HL, McKenzie BM, Hallett PD, Neilson R, Daniell TJ. 2008. Restoration of soil physical and biological stability are not coupled in response to plants and earthworms. Ecological Restoration. 26:102-104. Abstract

Chen S, Hajirezaei MR, Zanor MI, Hornyik C, Debast S, Lacomme C, Fernie AR, Sonnewald U, Bornke F. 2008. RNA interference-mediated repression of sucrose-phosphatase in transgenic potato tubers (Solanum tuberosum) strongly affects the hexose-to-sucrose ratio upon cold storage with only minor effects on total soluble carbohydrate accumulation. Plant Cell and Environment. 31:165-176.

Hancock RD, Roberts AG, Viola R. 2008. A role for symplastic gating in the control of the potato tuber life cycle. Plant Signaling and Behaviour. 3:27-29. Abstract

Ingram JSI, Gregory PJ, Izac AM. 2008. The role of agronomic research in climate change and food security policy. Agriculture, Ecosystems and Environment. 126:4-12. Abstract

Mahmood-ul-Hassan M, Gregory PJ. 2008. The role of rainfall intensity and soil in determining rates of flow through cryoturbated chalk. Pakistan Journal of Science and Industrial Research. 51:235-241.

Brown JWS, Shaw PJ. 2008. The role of the plant nucleolus in pre-mRNA processing. Current Topics in Microbiology and Immunology. 326:291-311.

Bahar B, Schmidt O, Moloney AP, Scrimgeour CM, Begley IS, Monahan FJ. 2008. Seasonal variation in the C, N and S stable isotope composition of retail organic and conventional Irish beef. Food Chemistry. 106:1299-1305. Abstract

Phillips MS, Blok VC. 2008. Selection for reproductive ability in Globodera pallida populations in relation to quantitative resistance form Solanum vernei and S.tuberosum ssp. andigena CPC2802. Plant Pathology. 57:573-580. Abstract

Holeva RC, Brown DJF, Curtis RHC, Neilson R. 2008. Selective recovery of the virus-vector trichodorid nematode Paratrichodorus anemones from soil samples by immunomagnetic capture. European Journal of Plant Pathology. 120:85-89. Abstract

Broadley MR, Hammond JP, King GJ, Astley D, Bowen HC, Meacham MC, Mead A, Pink DAC, Teakle G, Hayden R et al.. 2008. Shoot calcium and magnesium concentrations differ between subtaxa, are highly heritable, and associate with potentially pleiotropic loci in Brassica oleracea. Plant Physiology. 146:1707-1720. Abstract

Jones MR, Raven JA, Leith ID, Cape JN, Smith RI, Fowler D. 2008. Short-term flux chamber experiment to quantify the deposition of gaseous 15N-NH3 to Calluna vulgaris. Agricultural and Forest Meteorology. 148:893-901. Abstract

Peter KA, Liang D, Palukaitis P, Gray SM. 2008. Small deletions in the potato leafroll virus readthrough protein affect particle morphology, aphid transmission, virus movement and accumulation. Journal of General Virology. 89:2037-2045. Abstract

Griffiths BS, Caul S, Thompson J, Hackett CA, Cortet J, Pernin C, Krogh PH. 2008. Soil microbial and faunal responses to herbicide tolerant maize and herbicide in two soils. Plant and Soil. 308:93-103. Abstract

Hartley IP, Hopkins DW, Garnett MH, Sommerkorn M, Wookey PA. 2008. Soil microbial respiration in arctic soil does not acclimate to temperature. Ecology Letters. 11:1092-1100. Abstract

Mahmood-ul-Hassan M, Akhtar MS, Gregory PJ. 2008. Solute movement through intact columns of cryoturbated Upper Chalk. Hydrological Processes. 22:2086-2093. Abstract

Kasprowicz L, Malloch G, Pickup J, Fenton B. 2008. Spatial and temporal dynamics of Myzus persicae clones in fields and suction traps. Agricultural and Forest Entomology. 10:91-100. Abstract

Orfanus T, Bedrna Z, Lichner L, Hallett PD, Knava K, Sebin M. 2008. Spatial variability of water repellency in pine forest soil. Soil and Water. 3:S123-S129. Abstract

Glasbey CA, Allcroft DJ. 2008. A spatiotemporal auto-regressive moving average model for solar radiation. Journal of the Royal Statistical Society Series C - Applied Statistics. 57:343-355. Abstract

Nisbet AJ, Redmond DL, Matthews JB, Watkins C, Yaga R, Jones JT, Nath M, Knox DP. 2008. Stage-specific gene expression in Teladorsagia circumcincta (Nematoda: Strongylida) infective larvae and early parasitic stages. International Journal for Parasitology. 38:829-838. Abstract

Brueggeman R, Druka A, Nirmala J, Cavileer T, Drader T, Rostoks N, Mirlohi A, Bennypaul H, Gill U, Kudrna D et al.. 2008. The stem rust resistance gene Rpg5 encodes a protein with nucleotide binding site, leucine-rich and protein kinase domains. Proceedings of the National Academy of Sciences, USA. 105:14970-14975. Abstract

Shillam LL, Hopkins DW, Badalucco L, Laudicina VA. 2008. Structural diversity and enzyme activity of volcanic soils at different stages of development and response to experimental disturbance. Soil Biology & Biochemistry. 40:2182-2185. Abstract

Hammond JP, White PJ. 2008. Sucrose transport in the phloem; integrating root responses to phosphorus starvation. Journal of Experimental Botany. 59:93-109. Abstract

Garc R, Ochoa V, Hinojosa MB, Carreira JA. 2008. Suitability of enzyme activities for the monitoring of soil quality improvement in organic agricultural systems. Soil Biology & Biochemistry. 40:2137-2145. Abstract

Tilston EL, Halpin C, Hopkins DW. 2008. Tissue culture propagation alters plant-microbe interactions in tobacco rhizosphere. Biology and Fertility of Soils. 44:897-901. Abstract

Chichkova NV, Galiullina RA, Taliansky ME, Vartapetian AB. 2008. Tissue disruption activates a plant caspase-like protease with TATD cleavage specificity. Plant Stress. 2:89-95. Abstract

Potokina E, Druka A, Luo ZW, Moscou M, Wise R, Waugh R, Kearsey MJ. 2008. Tissue-dependent limited pleiotropy affects gene expression in barley. Plant Journal. 56:287-296.

McDougall GJ, Martinussen I, Stewart D. 2008. Towards fruitful metabolomics: High throughput analyses of polyphenol composition in berries using direct infusion mass spectrometry. Journal of Chromatography B. 871:362-369. Abstract

Druka A, Druka I, Centeno AG, Li H, Sun Z, Thomas WTB, Bonar N, Steffenson BJ, Ullrich SE, Kleinhofs A et al.. 2008. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genetics. 9:-73. Abstract

Raven JA. 2008. Transpiration: how many functions? New Phytologist. 179:905-908. Abstract

Simpson CG, Brown JWS. 2008. U12-dependent intron splicing in plants. Current Topics in Microbiology and Immunology. 326:61-82.

Schena L, Cardle L, Cooke DEL. 2008. Use of genome sequence data in the design and testing of SSR markers for Phytophthora species. BMC Genomics. 9:620-643. Abstract

Lacomme C, Chapman S. 2008. Use of potato virus X (PVX)-based vectors for gene expression and virus induced gene silencing (VIGS). Current Protocols in Microbiology. 8:16I.1.1-16I.1.13. Abstract

George TS, Gregory PJ, Hocking P, Richardson AE. 2008. Variation in root-associated phosphatase activities in wheat contributes to the utilisation of organic P substrates in vitro, but does not explain differences in the P-nutrition of plants when grown in different soils. Environmental and Experimental Botany. 64:239-249.

Johnson SN, Anderson EA, Dawson G, Griffiths DW. 2008. Varietal susceptibility of potatoes to wireworm herbivory. Agricultural and Forest Entomology. 10:167-174. Abstract

Titlyanov EA, Kiyashko SI, Titlyanova TV, Kalita TL, Raven JA. 2008. δ13C and δ15N values in reef corals Porites lutea and P. cylindrica and in their epilithic and endolithic algae. Marine Biology. 155:353-361. Abstract

2009

Song BK, Hein I, Druka A, Waugh R, Marshall DF, Nadarajah K, Yap SJ, Ratnam W. 2009. The 172 kb genomic DNA region of the O. rufipogon ylg1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica. Functional & Integrative Genomics. 9:97-108.

Kim S-H, Koroleva OA, Lewandowska D, Pendle AF, Clark GP, Simpson CG, Shaw PJ, Brown JWS. 2009. Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. Plant Cell. 21:2045-2057.

Russell JR, Kadu CAC, Jamnadass R, Booth A, Cordeiro NJ, Woodhead M, Dawson IK. 2009. AFLP and SSR diversity in the African fruit tree Allanblackia: implications for management of a genus newly subject to domestication for the edible oil industry. Tree Genetics and Genomes. 5:517-527.

Beardall J, Allen D, Bragg J, Finkel ZV, Flynn KJ, Quigg A, Rees TAV, Richardson A, Raven JA. 2009. Allometry and stoichiometry of unicellular, colonial and multicellular phytoplankton. New Phytologist. 181:295-309.

Karim N, Jones JT, Okada H, Kikuchi T. 2009. Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae. BMC Genomics. 10:-525.

Terzi LC, Simpson GG. 2009. Arabidopsis RNA immunoprecipitation. Plant Journal. 59:163-168.

Antunez-Lamas M, Cabrera E, Lopez-Solanilla E, Solano R, Gonzalez-Melendi P, Chico JM, Toth IK, Birch PRJ, Pritchard L, Liu H et al.. 2009. Bacterial chemoattraction towards jasmonate plays a role in the entry of Dickeya dadantii through wounded tissues. Molecular Microbiology. 74:662-671.

Lewis FI, Gunn GJ, McKendrick IJ, Murray FM. 2009. Bayesian inference for within-herd prevalence of Leptospira interrogans serovar Hardjo using bulk milk antibody testing. Biostatistics. 10:719-728.

McDougall GJ, Kulkarni NN, Stewart D. 2009. Berry polyphenols inhbit pancreatic lipase actvity in vitro. Food Chemistry. 115:193-199. Abstract

Bowen SR, Gregorich EG, Hopkins DW. 2009. Biochemical properties and biodegradation of dissolved organic matter from soils. Biology and Fertility of Soils. 45:733-742. Abstract

White PJ, Broadley MR. 2009. Biofortification of crops with seven mineral elements often lacking in human diets - iron, zinc, copper, calcium, magnesium, selenium and iodine (Review). New Phytologist. 182:49-84. Abstract

Woodward FI, Bardgett RD, Raven JA, Hetherington AM. 2009. Biological approaches to global environmental change: mitigation and remediation. Current Biology. 19:R615-R623.

Subbarao GV, Kishii M, Nakahara K, Ishikawa T, Ban T, Tsujimoto H, George TS, Berry WL, Hash CT, Ito O. 2009. Biological nitrification inhibition (BNI) - Is there potential for genetic interventions in Triticeae? Breeding Science. 59:529-545.

McMenemy LS, Mitchell C, Johnson SN. 2009. Biology of the European large raspberry aphid (Amphorophora idaei); its role in virus transmission and resistance breakdown in red raspberry. Agricultural and Forest Entomology. 11:61-71. Abstract

Raven JA, Giordano M. 2009. Biomineralization by photosynthetic organisms: Evidence of coevolution of the organisms and their environment? Geobiology. 7:140-154.

Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalko A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B et al.. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 25:1422-1423.

Harrison BD. 2009. A brief outline of the development of plant virology in the 20th century. Journal of Plant Pathology. 91:509-520.

Peter KA, Gildow FE, Palukaitis P, Gray SM. 2009. The C-terminus of the Polerovirus P5 readthrough domain limits virus infection to the phloem. Journal of Virology. 83:5419-5429. Abstract

Hillier J, Hawes C, Squire GR, Hilton A, Wale S, Smith P. 2009. The carbon footprints of food crop production. International Journal of Agicultural Sustainability. 7:107-118.

Eaton SL, Anderson MJ, Hamilton S, Gonz L, Sales J, Jeffrey M, Reid HW, Rocchi MA, Chianini F. 2009. CD21 B cell populations are altered following subcutaneous scrapie inoculation in sheep. Veterinary Immunology and Immunopathology. 131:105-109.

Hudacsek P, Bransby MF, Hallett PD, Bengough AG. 2009. Centrifuge modelling of climatic effects on clay embankments. Proceedings of the Institution of Civil Engineers - Engineering Sustainability. 162:91-100.

Koza A, Hallett PD, Moon CD, Spiers AJ. 2009. Characterisation of a novel air-liquid interface biofilm of Pseudomonas fluorescens SBW25. Microbiology. 155:1397-1406.

Adam MAM, Phillips MS, Tzortzakakis M, Blok VC. 2009. Characterisation of mjap genes encoding novel secreted proteins from the root-knot nematode, Meloidogyne javanica. Nematology. 11:253-265.

Canto T, Aranda MA, Fereres A. 2009. Climate change effects on physiology and population processes of hosts and vectors that influence the spread of hemipteran-borne plant viruses. Global Change Biology. 15:1884-1894.

Prashar A, Hocking PM, Erichsen JT, Fan Q, Saw S-M, Guggenheim JA. 2009. Common determinants of body size and eye size in chickens from an advanced intercross line. Experimental Eye Research. 89:42-48.

Ziegler A, Cowan GH, Torrance L. 2009. Comparative sequence analysis and serological and infectivity studies indicate that cocksfoot mild mosaic virus is a member of the genus Panicovirus. Archives of Virology. 154:1545-1549.

Schreiber AWJ, Sutton T, Caldo RA, Kalashyan E, Lovell B, Mayo G, Muehlbauer G, Druka A, Waugh R, Wise RP et al.. 2009. Comparative transcriptomics in the Triticeae. BMC Genomics. 10:-285. Abstract

Barker H, McGeachy KD, Toplak N, Gruden K, Zel J, Browning I. 2009. Comparison of genome sequence of PVY isolates with biological properties. American Journal of Potato Research. 86:227-238.

Van Toor R, Malloch G, Fenton B. 2009. A concept for management of virus-vectors and insecticide resistance in Myzus persicae on potatoes. Redia. XCII:219-221.

Tilston EL, Szili-Kov T, Hopkins DW. 2009. Contributions of labile and resistant organic materials to the immobilization of inorganic soil N when used in the restoration of abandoned agricultural fields. Soil Use and Management. 25:168-174. Abstract

Cockell CS, Kaltenegger L, Raven JA. 2009. Cryptic photosynthesis - extrasolar planetary oxygen without a surface biological signature. Astrobiology. 9:623-636.

Squire GR, Hawes C, Begg GS, Young MW. 2009. Cumulative impact of GM herbicide-tolerant cropping on arable plants assessed through species-based and functional taxonomies. Environmental Science and Pollution Research. 16:85-94. Abstract

Cockell CS, L A, Fridlund M, Herbst TM, Kaltenegger L, Absil O, Beichman C, Benz W, Blanc M, Brack A et al.. 2009. Darwin - a mission to detect and search for life on extrasolar planets. Astrobiology. 9:1-22.

McKenzie BM, Bengough AG, Hallett PD, Thomas WTB, Forster BP, McNicol JW. 2009. Deep rooting and drought screening of cereal crops: A novel field-based method and its application.. Field Crops Research. 112:165-171. Abstract

Newton AC, Begg GS, Swanston JS. 2009. Deployment of diversity for enhanced crop function. Annals of Applied Biology. 154:309-322. Abstract

White PJ. 2009. Depolarisation-activated calcium channels shape the calcium signatures induced by low-temperature stress. New Phytologist. 183:6-8.

Stokes A, Atger C, Bengough AG, Fourcaud T, Sidle RC. 2009. Desirable plant root traits for protecting natural and engineered slopes against landslides (Invited review). Plant and Soil. 324:1-30.

Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S et al.. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics. 10:-582.

Kopecky D, Bartos J, Lukaszewski AJ, Baird JH, Cernoch V, K R, Rognli OA, Blois H, Caig V, Lubberstedt T et al.. 2009. Development and mapping of DArT markers within the Festuca - Lolium complex. BMC Genomics. 10:-473.

Brennan RM, Jorgensen L, Gordon SL, Loades K, Hackett CA, Russell JR. 2009. The development of a PCR-based marker linked to resistance to the blackcurrant gall mite (Cecidophyopsis ribis Acari: Eriophyidae). Theoretical and Applied Genetics. 118:205-211. Abstract

Bartley PM, Wright SE, Maley SW, Buxton D, Nath M, Innes EA. 2009. The development of immune responses in Balb/c mice following inoculation with attenuated or virulent Neospora caninum tachyzoites. Parasite Immunology. 31:392-401.

Uibopuu A, Moora M, Saks U, Daniell TJ, Zobel M, Opik M. 2009. Differential effect of arbuscular mycorrhizal fungal communities from ecosystems along management gradient on the growth of forest understorey plant species. Soil Biology & Biochemistry. 41:2141-2146.

Hallett PD, Feeney D, Bengough AG, Rillig MC, Scrimgeour CM, Young IM. 2009. Disentangling the impact of AM fungi versus roots on soil structure and water transport. Plant and Soil. 314:183-196. Abstract

Dawson IK, Hedley PE, Guarino L, Jaenicke H. 2009. Does biotechnology have a role in the promotion of underutilised crops? Food Policy. 34:319-328.

Makarov VV, Rybakova EN, Efimov AV, Dobrov EN, Serebryakova MV, Solovyev AG, Yaminsky IV, Taliansky ME, Morozov SV, Kalinina NO. 2009. Domain organization of the N-terminal portion of hordeivirus movement protein TGBp1. Journal of General Virology. 90:3022-3032.

Koroleva OA, Calder G, Pendle AF, Kim S-H, Lewandowska D, Simpson CG, Jones IM, Brown JWS, Shaw PJ. 2009. Dynamic behaviour of Arabidopsis eIF4A-III, putative core protein of exon junction complex: fast relocation to nucleolus and splicing speckles under hypoxia. Plant Cell. 21:1592-1606.

Barr P, McKenzie BM, Hallett PD. 2009. Earthworms bring compacted and loose soils to a similar mechanical state. Soil Biology & Biochemistry. 41:656-658. Abstract

Yang D, Zhang T, Zhang K, Greenwood DJ, Hammond JP, White PJ. 2009. An easily implemented agro-hydrological procedure with dynamic root simulation for water transfer in the crop-soil system: Validation and application. Journal of Hydrology. 370:177-190. Abstract

Wookey PA, Aerts R, Bardgett RD, Baptist F, Brathan KA, Cornelissen JHC, Gough L, Hartley IP, Hopkins DW, Lavorerl S et al.. 2009. Ecosystem feedbacks and cascade processes: understanding their role in the responses of Arctic and alpine ecosystems to environmental change. Global Change Biology. 15:1153-1172. Abstract

Wypijewski K, Hornyik C, Shaw JA, Stephens J, Goraczniak R, Gunderson SI, Lacomme C. 2009. Ectopic 5' splice sites inhibit gene expression by engaging RNA surveillance and silencing pathways in plants. Plant Physiology. 151:955-965.

Pawlett M, Hopkins DW, Moffett BF, Harris JA. 2009. The effect of earthworms and liming on soil microbial communities. Biology and Fertility of Soils. 45:361-369. Abstract

Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. 2009. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. British Journal of Nutrition. 101:541-550.

Gregory AS, Watts CW, Griffiths BS, Hallett PD, Kuan HL, Whitmore AP. 2009. The effect of long-term soil management on the physical and biological resilience of a range of arable and grassland soils in England. Geoderma. 153:172-185.

Wemelsfelder F, Nevison IM, Lawrence AB. 2009. The effect of perceived environmental background on qualitative assessments of pig behaviour. Animal Behaviour. 78:477-484.

Wojciechowski T, Gooding MJ, Ramsay L, Gregory PJ. 2009. The effects of dwarfing genes on seedling root growth of wheat. Journal of Experimental Botany. 60:2565-2573.

Brown KL, Wathne GJ, Sales J, Bruce ME, Mabbott NA. 2009. The effects of host age on follicular dendritic cell status dramatically impair scrapie agent neuroinvasion in aged mice. Journal of Immunology. 183:5199-5207.

Newton AC, Guy DC. 2009. The effects of uneven patchy cultivar mixtures on disease control and yield in winter barley. Field Crops Research. 110:225-228. Abstract

Glasbey CA, Khondoker MR. 2009. Efficiency of functional regression estimators for combining multiple laser scans of cDNA microarrays. Biometrical Journal. 51:45-55.

Waugh R, Jannink JL, Muehlbauer GJ, Ramsay L. 2009. The emergence of whole genome association scans in barley. Current Opinion in Plant Biology. 12:218-222.

Kassim A, Poette J, Paterson A, Zait D, McCallum S, Woodhead M, Smith K, Hackett CA, Graham J. 2009. Environmental and seasonal influences on red raspberry anthocyanin antioxidant contents and identification of quantitative traits loci (QTL). Molecular Nutrition and Food Research. 53:625-634. Abstract

Le Gall O, Sanfacon H, Ikegami M, Iwanami T, Jones AT, Karasev A, Lehto K, Wellink J, Wetzel T, Yoshikawa N. 2009. Erratum: Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae). Archives of Virology. 154:1019-1019.

Cornulier T, Elston DA, Arcese P, Benton TG, Douglas DJT, Lambin X, Reid J, Robinson RA, Sutherland WJ. 2009. Estimating the annual number of breeding attempts from breeding dates using mixture models. Ecology Letters. 12:1184-1193.

Ashman MR, Hallett PD, Brookes PC, Allen J. 2009. Evaluating soil stabilisation by biological processes using step-wise aggregate fractionation. Soil and Tillage Research. 102:209-215.

Thiel T, Graner A, Waugh R, Grosse I, Close TJ, Stein N. 2009. Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evolutionary Biology. 9:-209.

Lokossou AA, Park TH, van Arkel G, Arens M, Ruyter-Spira C, Morales J, Whisson SC, Birch PRJ, Visser RGF, Jacobsen E et al.. 2009. Exploiting knowledge of R/Avr genes to rapidly clone a new LZ-NBS-LRR family of late blight resistance genes from potato linkage group IV. Molecular Plant-Microbe Interactions. 22:630-641.

George TS, Richardson AE, Li SM, Gregory PJ, Daniell TJ. 2009. Extracellular release of a heterologous phytase from roots of transgenic plants: does manipulation of rhizosphere biochemistry impact microbial community structure? FEMS Microbiology Ecology. 70:433-445. Abstract

Low JC, Chambers J, McKelvey WAC, McKendrick IJ, Jeffrey M. 2009. Failure to transmit scrapie infection by transferring preimplantation embryos from naturally infected donor sheep. Theriogenology. 72:809-816.

Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JWS, Green PJ, Barton GJ, Hutvagner G. 2009. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA. 15:2147-2160.

Osterrieder A, Carvalho CM, Latijnhouwers M, Johansen JN, Stubbs C, Botchway S, Hawes CL. 2009. Fluorescence lifetime imaging of interactions between Golgi tethering factors and small GTPases in plants. Traffic. 10:1034-1046.

Al-Mrabeh A, Ziegler A, Cowan GH, Torrance L. 2009. A fully recombinant ELISA using in vivo biotinylated antibody fragments for the detection of Potato leaf roll virus. Journal of Virological Methods. 159:200-205.

Hawes C, Haughton AJ, Bohan DA, Squire GR. 2009. Functional approaches for assessing plant and invertebrate abundance patterns in arable systems. Basic and Applied Ecology. 10:34-42. Abstract

Raven JA. 2009. Functional evolution of photochemical energy transformations in oxygen-producing organisms. Functional Plant Biology. 36:505-515.

McLellan H, Gilroy EM, Yun BW, Birch PRJ, Loake GJ. 2009. Functional redundancy in the Arabidopsis Cathepsin B gene family contributes to basal defence, the hypersensitive response and senescence. New Phytologist. 183:408-418.

Bradshaw JE. 2009. A genetic perspective on yield plateau in potato (Review). Potato Journal (Indian). 36:79-94.

MacFarlane SA, McGavin WJ. 2009. Genome activation by Raspberry bushy dwarf virus coat protein. Journal of General Virology. 90:747-753.

Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T et al.. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 461:393-398.

Bierman S, Glasbey CA. 2009. A graphical method for dating chicks using bivariate body measurements. Journal of Agricultural, Biological and Environmental Statistics. 14:443-451.

Dimier C, Brunet C, Geider RD, Raven JA. 2009. Growth and photoregulation dynamics of the picoeukaryote Pelagomonas calceolata in fluctuating light. Limnology and Oceanography. 54:823-836.

Raven JA. 2009. Horsetails get the wind up. New Phytologist. 184:6-9.

Caron-Lormier G, Bohan DA, Hawes C, Raybould A, Haughton AJ, Humphry RW. 2009. How might we model an ecosystem? Ecological Modelling. 220:1935-1949.

Kemp HF, Meier-Augenstein W. 2009. Human provenancing of mutilated murder victims through stable isotope profiles (Review). Minerva Medicolegale. 129:219-231.

Madsen CT, Stephens J, Hornyik C, Shaw J, Collinge DB, Lacomme C, Albrechtsen M. 2009. Identification and characterization of barley RNA-directed RNA polymerases. Biochimica et Biophysica Acta. 1789:375-385.

Rehman S, Butterbach P, Popeijus H, Overmars H, Davis EL, Jones JT, Goverse A, Bakker J, Smant G. 2009. Identification and characterization of the most abundant cellulases in stylet secretions from Globodera rostochiensis. Phytopathology. 99:194-202.

Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, Castelli L, Chapman S, Cock PJA, Grenier E, Lilley CJ, Phillips MS et al.. 2009. Identification and functional characterisation of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida. Molecular Plant Pathology. 10:815-828.

Basnayake S, Maclean DJ, Whisson SC, Drenth A. 2009. Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae. Current Genetics. 55:521-536.

Kikuchi T, Li H, Karim N, Kennedy MW, Moens M, Jones JT. 2009. Identification of putative expansin-like genes from the pine wood nematode, Bursaphelenchus xylophilus, and evolution of the expansin gene family within the Nematoda. Nematology. 11:355-364. Abstract

Brennan RM, Graham J. 2009. Improving fruit quality in Rubus and Ribes through breeding (Invited review). Functional Plant Science and Biotechnology. 3 Special Issue 1:22-29.

Rakhshanderhoo F, Takeshita M, Squires J, Palukaitis P. 2009. The influence of RNA-dependent RNA polymerase 1 on Potato virus Y infection and on other antiviral response genes. Molecular Plant-Microbe Interactions. 22:1312-1318.

Maberly SC, Ball LA, Raven JA, S D. 2009. Inorganic carbon acquisition by chrysophytes. Journal of Phycology. 45:1052-1061.

Gregory PJ, Johnson SN, Newton AC, Ingram JSI. 2009. Integrating pests and pathogens into the climate change/food security debate. Journal of Experimental Botany. 60:2827-2838. Abstract

Smith LA, Marion G, Swain DL, White PCL, Hutchings MR. 2009. Inter- and intra-specific exposure to parasites and pathogens via the faecal-oral route: a consequence of behaviour in a patchy environment. Epidemiology and Infection. 137:630-643.

Sprent JI. 2009. An interdisciplinary look at legumes and their bacterial symbionts: some thoughts from Big Sky. New Phytologist. 184:15-17.

Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer GJ, Sato K, Schulman AH, Waugh R, Wise RP et al.. 2009. International Barley Sequencing Consortium - at the threshold of efficient access to the barley genome. Plant Physiology. 149:142-147. Abstract

Mahajan A, Currie CG, Mackie S, Tree J, McAteer S, McKendrick I, McNeilly TN, Roe A, La Ragione RM, Woodward MJ et al.. 2009. An investigation of the expression and adhesin function of H7 flagella in the interaction of Escherichia coli O157:H7 with bovine intestinal epithelium. Cellular Microbiology. 11:121-137.

Hopkins DW, Sparrow AD, Gregorich EG, Elberling B, Novis P, Fraser F, Scrimgeour CM, Dennis PG, Meier-Augenstein W, Greenfield LG. 2009. Isotopic evidence for the provenance and turnover of organic carbon by soil microorganisms in the Antarctic dry valleys. Environmental Microbiology. 11:597-608. Abstract

Cousens C, Thonur L, Imlach S, Crawford J, Sales J, Griffiths DJ. 2009. Jaagsiekte sheep retrovirus is present at high concentration in lung fluid produced by ovine pulmonary adenocarcinoma-affected sheep and can survive for several weeks at ambient temperatures. Research in Veterinary Science. 87:154-156.

Opik M, Metsis M, Daniell TJ, Zobel M, Moora M. 2009. Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist. 184:424-437.

Torres-Ca P, Hinojosa MB, Garcia-Ruiz R, Daniell TJ, Carreira JA. 2009. Linking biogeochemical variability and microbial community structure in forest soils: Abies pinsapo-fir forests as a study case. Ecosistemas. 18:91-102.

Dennis PG, Hirsch PR, Smith SJ, Taylor RG, Valsami-Jones E, Miller AJ. 2009. Linking rhizoplane pH and bacterial density at the microhabitat scale. Journal of Microbiological Methods. 76:101-104.

Braga RA, Dupuy L, Pasqual M, Cardoso RR. 2009. Live biospeckle laser imaging of root tissues. European Biophysics Journal. 38:679-686. Abstract

Smith LA, Marion G, Swain DL, White PCL, Hutchings MR. 2009. Livestock grazing behavior and inter- versus intraspecific disease risk via the fecal-oral route. Behavioral Ecology. 20:426-432.

Koroleva OA, Brown JWS, Shaw PJ. 2009. Localization of eIF4A-III in the nucleolus and splicing speckles is an indicator of plant stress. Plant Signaling & Behavior. 4:1148-1151.

Baggaley NJ, Langan SJ, Futter MN, Potts JM, Dunn SM. 2009. Long-term trends in hydro-climatology of a major Scottish mountain river. Science of the Total Environment. 407:4633-4641.

Wouters J, Raven JA, Minnhagen S, Janson S. 2009. The luggage hypothesis: Comparisons of two phototrophic hosts with nitrogen-fixing cyanobacteria and implications for analogous life strategies for kleptoplastids/secondary symbiosis in dinoflagellates. Symbiosis. 49:61-70.

Graham J, Hackett CA, Smith K, Woodhead M, Hein I, McCallum S. 2009. Mapping QTLs for developmental traits in raspberry from bud break to ripe fruit. Theoretical and Applied Genetics. 118:1143-1155. Abstract

Hargreaves CE, Gregory PJ, Bengough AG. 2009. Measuring root traits in barley (Hordeum vulgare ssp. vulgare and ssp. spontaneum) seedlings using gel chambers, soil sacs and x-ray microtomography. Plant and Soil. 316:285-297.

Mickovski SB, Hallett PD, Bransby MF, Davies MCR, Sonnenberg R, Bengough AG. 2009. Mechanical reinforcement of soil by willow roots: impacts of root properties and root failure mechanism. Soil Science Society of America Journal. 73:1276-1285. Abstract

Pritchard L, Liu H, Booth C, Douglas E, Fran P, Schrenzel J, Hedley PE, Birch PRJ, Toth IK. 2009. Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens. PLoS Computational Biology. 5:-e1000473.

Vinten AJA, Potts JM, Avery L, Strachan NJC. 2009. Microbial pollution of water by livestock: approaches to risk assessment and mitigation. Animal. 3:744-752.

Butler A, Doherty RM, Marion G. 2009. Model averaging to combine simulations of future global vegetation carbon stocks. Environmetrics. 20:791-811.

Karley AJ, White PJ. 2009. Moving cationic minerals to edible tissues: potassium, magnesium, calcium (Review). Current Opinion in Plant Biology. 12:291-298. Abstract

Blower TR, Fineran PC, Johnson MJ, Toth IK, Humphreys DP, Salmond GPC. 2009. Mutagenesis and functional characterisation of the RNA and protein components of the toxIN abortive infection and toxin-antitoxin locus of Erwinia. Journal of Bacteriology. 191:6029-6039.

Meier-Augenstein W, Kemp HF, Lock CM. 2009. N2: A potential pitfall for bulk 2H isotope analysis of explosives and other nitrogen-rich compounds by continuous-flow isotope-ratio mass spectrometry. Rapid Communications in Mass Spectrometry. 23:2011-2016.

Graham J, Woodhead M, Smith K, Russell JR, Marshall B, Ramsay G, Squire GR. 2009. New insight into wild red raspberry populations using simple sequence repeat markers. Journal of the American Society for Horticultural Science. 134:109-119. Abstract

Moir HJ, Gibbins CN, Buffington JM, Webb JH, Soulsby C, Brewer MJ. 2009. A new method to identify the fluvial regimes used by spawning salmonids. Canadian Journal of Fisheries and Aquatic Sciences. 66:1404-1408.

Andrews M, Lea PJ, Raven JA, Azevedo RA. 2009. Nitrogen use efficiency. 3. Nitrogen fixation: genes and costs. Annals of Applied Biology. 155:1-13.