Publications list

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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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

Hartley IP, Hopkins DW, Garnett MH, Sommerkorn M, Wookey PA. 2009. No evidence for compensatory thermal adaptation of soil microbial respiration in the study of Bradford et al. (2008). Ecology Letters. 12:E12-E14.

Cummings SP, Gyaneshwar P, Vinuesa P, Farruggia FT, Andrews M, Humphry D, Elliott GN, Nelson A, Orr C, Pettitt D et al.. 2009. Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other Rhizobia. Environmental Microbiology. 11:2510-2525.

Regeai SO, Dolan KM, Fitzpatrick DA, Browne JA, Jones JT, Burnell AM. 2009. Novel primers for the amplification of nuclear DNA introns in the entomopathogenic nematode Heterorhabditis bacteriophora and their cross-amplification in seven other Heterorhabditis species. Molecular Ecology Resources. 9:421-424.

Garnett MH, Hartley IP, Hopkins DW, Sommerkorn M, Wookey PA. 2009. A passive sampling method for radiocarbon analysis of soil respiration using molecular sieve. Soil Biology & Biochemistry. 41:1450-1456. Abstract

Comadran J, Thomas WTB, van Eeuwijk FA, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A et al.. 2009. Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theoretical and Applied Genetics. 119:175-187.

Raven JA, Beardall J, Flynn KJ, Maberly SC. 2009. Phagotrophy in the origins of photosynthesis in eukaryotes and as a complementary mode of nutrition in phototrophs: relation to Darwin's insectivorous plants. Journal of Experimental Botany. 60:3975-3987.

Richardson AE, Hocking PJ, Simpson RJ, George TS. 2009. Plant mechanisms to optimise access to soil phosphorus. Crop and Pasture Science. 60:124-143.

Bradshaw JE. 2009. Potato breeding at the Scottish Plant Breeding Station and the Scottish Crop Research Institute: 1920-2008 (Invited Review). Potato Research. 52:141-172.

Debeljak M, Kocev D, Towers W, Jones M, Griffiths BS, Hallett PD. 2009. Potential of multi-objective models for risk-based mapping of the resilience characteristics of soils: demonstration at a national level. Soil Use and Management. 25:66-77.

Granum E, Roberts K, Raven JA, Leegood RC. 2009. Primary carbon and nitrogen metabolic gene expression in the diatom Thalassiosira pseudonana (Bacillariophyceae): Diel periodicity and effects of inorganic carbon and nitrogen. Journal of Phycology. 45:1083-1092.

Brierley JL, Stewart JA, Lees AK. 2009. Quantifying potato pathogen DNA in soil. Applied Soil Ecology. 41:234-238.

Marshall B, Newton AC, Zhan J. 2009. Quantitative evolution of aggressiveness of powdery mildew under two-cultivar barley mixtures. Plant Pathology. 58:378-388. Abstract

Barnett CM, Bengough AG, McKenzie BM. 2009. Quantitative image analysis of earthworm-mediated soil displacement. Biology and Fertility of Soils. 45:821-828.

Lees AK, Sullivan L, Cullen DW. 2009. A quantitative polymerase chain reaction assay for the detection of Polyscytalum pustulans, the cause of skin spot disease of potato. Journal of Phytopathology. 157:154-158. Abstract

Johnson SN, Hawes C, Karley AJ. 2009. Reappraising the role of plant nutrients as mediators of interactions between root- and foliar-feeding insects. Functional Ecology. 23:699-706. Abstract

Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C. 2009. Reconstruction of monocotyledonous proto-chromosomes reveals faster evolution in plants than in animals. Proceedings of the National Academy of Sciences, USA. 106:14908-14913.

White PJ, Bradshaw JE, Dale MFB, Ramsay G, Hammond JP, Broadley MR. 2009. Relationships between yield and mineral concentrations in potato tubers. Hortscience. 44:6-11. Abstract

Spezia L. 2009. Reversible jump and the label switching problem in hidden Markov models. Journal of Statistical Planning and Inference. 139:2305-2315.

Barr P, Hallett PD. 2009. Rheological stabilisation of wet soils by model root and fungal exudates depends on clay mineralogy. European Journal of Soil Science. 60:525-538. Abstract

Hinsinger P, Bengough AG, Vetterlein D, Young IM. 2009. Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant and Soil. 321:117-152.

Ma'shum M, Tisdall JM, Borrell AK, McKenzie BM, Gill JS, Kusnarta IGM, Sukartono M, Van Cooten DE. 2009. Rice responses to soil management in rice-based cropping system in the semi-arid tropics of southern Lombok, Eastern Indonesia. Field Crops Research. 110:197-206. Abstract

Rosso MN, Jones JT, Abad P. 2009. RNAi and functional genomics in plant parasitic nematodes. Annual Review of Phytopathology. 47:207-232.

Wang MH, Hu XH, Li G, Leach LJ, Potokina E, Druka A, Waugh R, Kearsey MJ, Luo ZW. 2009. Robust detection and genotyping of single feature polymorphisms from gene expression data. PLoS Computational Biology. 5:-e1000317.

Lewsey M, Surette M, Robertson FC, Ziebell H, Choi SH, Ryu KH, Canto T, Palukaitis P, Payne T, Walsh JA et al.. 2009. The role of the Cucumber mosaic virus 2b protein in viral movement and symptom induction. Molecular Plant-Microbe Interactions. 22:642-654. Abstract

Lawson DJ, Jensen HJ. 2009. The role of weak selection and high mutation rates in nearly neutral evolution. Journal of Theoretical Biology. 257:696-703.

Gregory PJ, Bengough AG, Grinev DV, Schmidt S, Thomas WTB, Wojciechowski T, Young IM. 2009. Root phenomics of crops - opportunities and challenges. Functional Plant Biology. 36:922-929.

McGavin WJ, MacFarlane SA. 2009. Rubus chlorotic mottle virus, a new Sobemovirus infecting raspberry and bramble. Virus Research. 139:10-13. Abstract

Crampton BG, Hein I, Berger DK. 2009. Salicylic acid confers resistance to a biotrophic rust pathogen, Puccinia substriata, in pearl millet (Pennisetum glaucum). Molecular Plant Pathology. 10:291-304.

Lehrach WP, Husmeier D. 2009. Segmenting bacterial and viral DNA sequence alignments with a trans-dimensional phylogenetic factorial hidden Markov model. Journal of the Royal Statistical Society Series C - Applied Statistics. 58:307-327.

Hammond JP, Broadley MR, White PJ, King GJ, Bowen HC, Hayden R, Meacham MC, Mead A, Overs T, Spracklen WP et al.. 2009. Shoot yield drives phosphorus use efficiency in Brassica oleracea and correlates with root architecture traits. Journal of Experimental Botany. 60:1953-1965.

Maestre FT, Bowker M, Puche MD, Bowker M, Hinojosa MB, Mart I, Garc P, Castillo AP, Soliveres S, Luzuriaga AL et al.. 2009. Shrub encroachment can reverse desertification in semi-arid Mediterranean grasslands. Ecology Letters. 12:930-941. Abstract

Bradshaw JE, Titley M, Wilson RN. 2009. Single seed descent as a breeding method for swedes (Brassica napus L. var. napobrassica Peterm). Euphytica. 169:387-401.

McKenzie BM, K S, MacKenzie K, Peth S, Horn R. 2009. Soil compaction by uniaxial loading and the survival of the earthworm Aporrectodea caliginosa. Soil and Tillage Research. 104:320-323.

Garc R, Ochoa V, Vi B, Hinojosa MB, Pe R, Li G, Linares JC, Carreira JA. 2009. Soil enzymes, nematode community and selected physico-chemical properties as soil quality indicators in organic and conventional olive oil farming: influence of seasonality and site features. Applied Soil Ecology. 41:305-314. Abstract

Hopkins DW, Waite IS, McNicol JW, Poulton PR, MacDonald AJ, O'Donnell AG. 2009. Soil organic carbon contents in long-term experimental grassland plots in the UK (Palace Leas and Park Grass) have not changed consistently in recent decades. Global Change Biology. 15:1739-1754. Abstract

White PJ, Hammond JP. 2009. The sources of phosphorus in the waters of Great Britain. Journal of Environmental Quality. 38:13-26. Abstract

Polechov J, Barton N, Marion G. 2009. Species' range: adaptation in space and time. American Naturalist. 174:E186-E204.

Ki LP, Felber F, Flavell AJ, Guadagnuolo R, Guiatti D, Hauser TP, Olivieri AM, Scotti I, Syed NH, Vischi M et al.. 2009. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L.. Genetic Resources and Crop Evolution. 56:405-419.

Shi B-J, Symons RH, Palukaitis P. 2009. Stability and competitiveness of interviral recombinant RNAs derived from a chimeric cucumovirus. Virus Research. 140:216-221. Abstract

Neumann G, George TS, Plassard C. 2009. Strategies and methods for studying the rhizosphere - the plant science toolbox. Plant and SoilPlant and Soil. 321:431-456.

Weaver J, Briscoe T, Hou M, Goodman C, Kata S, Ross HA, McDougall GJ, Stewart D, Riches A. 2009. Strawberry polyphenols are equally cytotoxic to tumourigenic and normal human breast and prostate cell lines. International Journal of Oncology. 34:777-786.

Mess A, Squire GR, Perry JN, Angevin F, Gomez M, Townend P, Sausse C, Breckling B, Langrell S, Dzeroski S et al.. 2009. Sustainable introduction of GM crops into European agriculture: a summary report of the FP6 SIGMEA research project. Ol. 16:37-51.

Wright HW, Bartley K, Nisbet AJ, McDevitt RM, Sparks NHC, Brocklehurst S, Huntley JF. 2009. The testing of antibodies raised against poultry red mite antigens in an in vitro feeding assay; preliminary screen for vaccine candidates. Experimental and Applied Acarology. 48:81-91.

Jones HG, Serraj R, Loveys BR, Xiong LH, Wheaton A, Price AH. 2009. Thermal infrared imaging of crop canopies for the remote diagnosis and quantification of plant responses to water stress in the field.. Functional Plant Biology. 36:978-989.

Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F. 2009. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics. 25:126-127.

Birch PRJ, Armstrong MR, Bos J, Boevink P, Gilroy EM, Taylor RM, Wawra S, Pritchard L, Conti L, Ewan R et al.. 2009. Towards understanding the virulence functions of RXLR effectors of the oomycete plant pathogen Phytophthora infestans (Review). Journal of Experimental Botany. 60:1133-1140.

Margaritopoulos JT, Kasprowicz L, Malloch GL, Fenton B. 2009. Tracking the global dispersal of a cosmopolitan insect pest, the peach potato aphid. BMC Ecology. 9:-13. Abstract

Foito A, Byrne SL, Shepherd T, Stewart D, Barth S. 2009. Transcriptional and metabolic profiles of Lolium perenne L. genotypes in response to a PEG induced water stress. Plant Biotechnology Journal. 7:719-732.

Potokina E, Druka A, Luo ZW, Waugh R, Kearsey MJ. 2009. The transcriptome analysis of barley (Hordeum vulgare L.) using the Affymetrix Barley1 GeneChip. Russian Journal of Genetics. 45:1317-1328.

van Dijk JP, Cankar K, Scheffer SJ, Beenen HGJ, Shepherd LVT, Stewart D, Davies HV, Wilcockson SJ, Leifert C, Gruden K et al.. 2009. Transcriptome analysis of potato tubers - effects of different agricultural practices. Journal of Agricultural and Food Chemistry. 57:1612-1623. Abstract

Bahar B, Moloney AP, Monahan FJ, Harrison SM, Zazzo A, Scrimgeour CM, Begley IS, Schmidt O. 2009. Turnover of carbon, nitrogen and sulfur in bovine longissimus dorsi and psoas major muscles: Implications for isotopic authentication of meat. Journal of Animal Science. 87:905-913.

Glasbey CA. 2009. Two-dimensional generalisations of dynamic programming for image analysis. Statistics and Computing. 19:49-56.

Torrance L, Lukhovitskaya NI, Schepetilnikov MV, Cowan GH, Ziegler A, Savenkov EI. 2009. Unusual long-distance movement strategies of Potato mop-top virus RNAs in Nicotiana benthamiana. Molecular Plant-Microbe Interactions. 22:381-390.

Davidson RS, Marion G, White PCL, Hutchings MR. 2009. Use of host population reduction to control wildlife infection: rabbits and paratuberculosis. Epidemiology and Infection. 137:131-138.

Crosley LK, Duthie SJ, Polley AC, Bouwman FG, Heim C, Mulholland F, Horgan GW, Johnson IT, Mariman EC, Elliott RM et al.. 2009. Variation in protein levels obtained from human blood cells and biofluids for platelet, peripheral blood mononuclear cell, plasma, urine and saliva proteomics. Genes and Nutrition. 4:95-102.

Swanson MM, Fraser G, Daniell TJ, Torrance L, Gregory PJ, Taliansky ME. 2009. Viruses in soils: morphological diversity and abundance in the rhizosphere. Annals of Applied Biology. 155:51-60. Abstract

Hein I, Gilroy EM, Armstrong MR, Birch PRJ. 2009. The zig-zag-zig in oomycete-plant interactions. Molecular Plant Pathology. 10:547-562.

2008

Du Z, Chen F, Zhao Z, Liao Q, Palukaitis P, Chen J. 2008. The 2b protein and the C-terminus of the 2a protein of Cucumber mosaic virus subgroup I strains both play a role in the viral RNA accumulation and induction of symptoms. Virology. 380:363-370. Abstract

Davies HV, Bryan GJ, Taylor MA. 2008. Advances in functional genomics and genetic modification of potato (Review). Potato Research. 51:283-299. Abstract

Marion G, Smith LA, Swain DL, Davidson RS, Hutchings MR. 2008. Agent-based modelling of foraging behaviour: the impact of spatial heterogeneity on disease risks from faeces in grazing systems. Journal of Agricultural Science. 146:507-520. Abstract

Pswarayi A, van Eeuwijk FA, Ceccarelli S, Grando S, Comadran J, Russell JR, Francia E, Pecchioni N, Li Destri O, Akar T et al.. 2008. Barley adaptation and improvement in the Mediterranean basin. Plant Breeding. 127:554-560.

Gregory PJ, Ingram JSI. 2008. Climate change and the current 'food crisis'. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 3, 090:1-10. Abstract

Holden N, Pritchard L, Toth IK. 2008. Colonisation outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria. FEMS Microbiology ReviewsFEMS Microbiology Reviews. 33:689-703.

Abecia L, Balcells J, Fondevila M, Belenguer A, Holtrop G, Lobley GE. 2008. Contribution of gut microbial lysine to liver and milk amino acids in lactating does. British Journal of Nutrition. 100:977-983.

White PCL, B M, Marion G, Hutchings MR. 2008. Control of bovine tuberculosis in British livestock: there is no 'silver bullet'. Trends in Microbiology. 16:420-427. Abstract

McDougall GJ, Kulkarni NK, Stewart D. 2008. Current developments on the inhibitory effects of berry polyphenols on digestive enzymes. Biofactors. 34:73-80. Abstract

Cullen DW, Squire GR, McNicol JW, Jacobs JH, Osborne JL, Ford L, Ramsay G, Scrimgeour CM, Young MW. 2008. Development and validation of gas chromatography and real-time quantitative PCR for the quantification of landscape-scale gene flow from varieties of high erucic acid (HEAR) oilseed rape. Journal of the Science of Food and Agriculture. 88:2253-2264. Abstract

Zazzo A, Moloney AP, Monahan FJ, Scrimgeour CM, Schmidt O. 2008. Effect of age and food intake on dietary carbon turnover recorded in sheep wool. Rapid Communications in Mass Spectrometry. 22:2937-2945. Abstract

Broadley MR, White PJ, Hammond JP, Graham NS, Bowen HC, Emmerson ZF, Fray RG, Iannetta PPM, McNicol JW, May ST. 2008. Evidence of neutral transcriptome evolution in plants. New Phytologist. 180:587-593. Abstract

Chatterjee A, Horgan GW, Theobald CM. 2008. Exposure assessment for pesticide intake from multiple food products: a Bayesian latent-variable approach. Risk Analysis. 28:1727-1736. Abstract

Ducreux LJM, Morris WL, Prosser IM, Morris JA, Beale MH, Wright F, Shepherd T, Bryan GJ, Hedley PE, Taylor MA. 2008. Expression profiling of potato germplasm differentiated in quality traits leads to the identification of candidate flavour and texture genes. Journal of Experimental Botany. 59:4219-4231. Abstract

Clayton SJ, Read DB, Murray PJ, Gregory PJ. 2008. Exudation of alcohol and aldehyde sugars from roots of defoliated Lolium perenne L. grown under sterile conditions. Journal of Chemical Ecology. 34:1411-1421. Abstract

Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P, Flint HJ. 2008. Human colonic microbiota associated with diet, obesity and weight loss. International Journal of Obesity. 32:1720-1724.

Hughes V, Bannantine JP, Denham S, Smith S, Garcia-Sanchez A, Sales J, Paustian ML, McLean K, Stevenson K. 2008. Immunogenicity of proteome-determined Mycobacterium avium subsp paratuberculosis-specific proteins in sheep with Paratuberculosis. Clinical and Vaccine Immunology. 15:1824-1833.

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.

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

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

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

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

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

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.

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

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

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.

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

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

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.