Newcastle University

Publications

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• Holt SA, Le Brun AP, Nelson ARJ, Lakey JH. In situ study of the impact of acidic and neutral deposition pH on alkane phosphate film formation and stability on TiO₂. RSC Advances 2013, 3(8), 2581-2589.
• Blanco B, Prado V, Lence E, Otero JM, Garcia-Doval C, van Raaij MJ, Llamas-Saiz AL, Lamb H, Hawkins AR, Gonzalez-Bello C. Mycobacterium tuberculosis Shikimate Kinase Inhibitors: Design and Simulation Studies of the Catalytic Turnover. Journal of the American Chemical Society 2013, 135(33), 12366-12376.
• Hirt RP. Trichomonas vaginalis virulence factors: an integrative overview. Sexually Transmitted Infections 2013, 89, 439-443.
• Dean P, Kenny B. A bacterial encoded protein induces extreme multinucleation and cell-cell internalization in intestinal cells. Tissue Barriers 2013, 1(1), e22639.
• Boeynaems J-M, Canivet C, Chan A, Clark MJ, Cornu C, Daemen E, Demotes J, De Nys K, Hirst B, Hundt F, Kassai B, Kerpel-Fronius S, Kiessig L, Klech H, Kraehenbuhl J-P, Lafolie P, Lucht M, Niese D, Pauli-Magnus C, Peters B, Schaltenbrand R, Stockis A, Stykova M, Verheus N, Klingmann I. A European approach to clinical investigator training. Frontiers in Pharmacology 2013, 4, 112.
• Keith BJ, Jozwiakowski SK, Connolly BA. A plasmid-based lacZα gene assay for DNA polymerase fidelity measurement. Analytical Biochemistry 2013, 433(2), 153-161.
• FenollarFerrer C, Patti M, Forster I, Werner A, Forrest L. A structural model for the Na/phosphate transporter type II (SLC34A1). PNAS 2013. Submitted.
• Fairhall EA, Wallace K, White SA, Huang GC, Shaw JA, Wright SC, Charlton KA, Burt AD, Wright MC. Adult human exocrine pancreas differentiation to hepatocytes – potential source of a human hepatocyte progenitor for use in toxicology research. Toxicology Research 2013, 2(1), 80-87.
• Bosomworth HJ, Adlard PA, Ford D, Valentine RA. Altered Expression of ZnT10 in Alzheimer's Disease Brain. PLoS One 2013, 8(5), e65475.
• Flanagan MD, Whitehall SK, Morgan BA. An Atg10-like E2 enzyme is essential for cell cycle progression but not autophagy in Schizosaccharomyces pombe. Cell Cycle 2013, 12(2), 271-277.
• Odon V, Luke GA, Roulston C, de Felipe P, Ruan L, Escuin-Ordinas H, Brown JD, Ryan MD, Sukhodub A. APE-Type Non-LTR Retrotransposons of Multicellular Organisms Encode Virus-Like 2A Oligopeptide Sequences, Which Mediate Translational Recoding during Protein Synthesis. Molecular Biology and Evolution 2013, [Epub ahead of print].
• Parikh S, Brownlee IA, Robertson AG, Manning NT, Johnson GE, Brodlie M, Corris PA, Ward C, Pearson JP. Are the enzymatic methods currently being used to measure bronchoalveolar lavage bile salt levels fit for purpose?. Journal of Heart and Lung Transplantation 2013, 32(4), 418-423.
• Robertson AGN, Griffin SM, Bredenoord AJ, Brownlee I, Aseeri A, Stovold R, Brodlie M, Forrest IA, Dark JH, Corris PA, Pearson JP, Ward C. Aspiration and allograft injury secondary to gastro-oesophageal reflux occurs in the immediate post-lung transplantation period. Annals of Surgery 2013, (Accepted for publication). Submitted.
• Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan J. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Journal of Integrative Bioinformatics 2013, 10(2), 224.
• Ali MS, Parikh S, Chater P, Pearson JP. Bile acids in laryngopharyngeal refluxate: Will they enhance or attenuate the action of pepsin?. The Laryngoscope 2013, 123(2), 434-439.
• Werner A. Biological functions of natural antisense transcripts. BMC Biology 2013, 11, 31.
• Sloan KE, Mattijssen S, Lebaron S, Tollervey D, Pruijn GJ, Watkins NJ. Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing. Journal of Cell Biology 2013, 200(5), 577-588.
• Hill CR, Jamieson D, Thomas HD, Brown CDA, Boddy AV, Veal GJ. Characterisation of the roles of ABCB1, ABCC1, ABCC2 and ABCG2 in the transport and pharmacokinetics of actinomycin D in vitro and in vivo. Biochemical Pharmacology 2013, 85(1), 29-37.
• Heaps SE, Boys RJ, Farrow M. Computation of marginal likelihoods with data–dependent support for latent variables. Computational Statistics and Data Analysis 2013, n/a(epub ahead of print), n/a.
• Amo-Ochoa P, Alexandre SS, Hribesh S, Galindo MA, Castillo O, Gómez-García CJ, Pike AR, Soler JM, Houlton A, Zamora F. Coordination Chemistry of 6-Thioguanine Derivatives with Cobalt: Toward Formation of Electrical Conductive One-Dimensional Coordination Polymers. Inorganic Chemistry 2013, 52(9), 5290-5299.
• Nichols CE, Lamb HK, Thompson P, Omari KE, Lockyer M, Charles I, Hawkins AR, Stammers DK. Crystal structure of the dimer of two essential Salmonella typhimurium proteins, YgjD and YeaZ and calorimetric evidence for the formation of a ternary YgjD-YeaZ-YjeE complex. Protein Science 2013, (epub ahead of print).
• Fenton AK, Gerdes K. Direct interaction of FtsZ and MreB is required for septum synthesis and cell division in Escherichia coli. EMBO Journal 2013, 32(13), 1953-1965.
• Ions LJ, Wakeling LA, Bosomworth HJ, Hardyman JEJ, Escolme SM, Swan DC, Valentine RA, Mathers JC, Ford D. Effects of Sirt1 on DNA methylation and expression of genes affected by dietary restriction. Age 2013, (epub ahead of print).
• Judák L, Hegyi P, Rakonczay ZJr, Maléth J, Gray MA, Venglovecz V. Ethanol and its non-oxidative metabolites profoundly inhibit CFTR function in pancreatic epithelial cells which is prevented by ATP supplementation. Pfluegers Archiv 2013, (epub ahead of print).
• Mercier R, Kawai Y, Errington J. Excess Membrane Synthesis Drives a Primitive Mode of Cell Proliferation. Cell 2013, 152(5), 997-1007.
• Albrechtsen A, Grarup N, Li Y, Sparso T, Tian G, Cao H, Jiang T, Kim SY, Korneliussen T, Li Q, Nie C, Wu R, Skotte L, Morris AP, Ladenvall C, Cauchi S, Stancakova A, Andersen G, Astrup A, Banasik K, Bennett AJ, Bolund L, Charpentier G, Chen Y, Dekker JM, Doney ASF, Dorkhan M, Forsen T, Frayling TM, Groves CJ, Gui Y, Hallmans G, Hattersley AT, He K, Hitman GA, Holmkvist J, Huang S, Jiang H, Jin X, Justesen JM, Kristiansen K, Kuusisto J, Lajer M, Lantieri O, Li W, Liang H, Liao Q, Liu X, Ma T, Ma X, Manijak MP, Marre M, Mokrosinski J, Morris AD, Mu B, Nielsen AA, Nijpels G, Nilsson P, Palmer CNA, Rayner NW, Renstrom F, Ribel-Madsen R, Robertson N, Rolandsson O, Rossing P, Schwartz TW, Slagboom PE, Sterner M, Tang M, Tarnow L, Tuomi T, van't Riet E, van Leeuwen N, Varga TV, Vestmar MA, Walker M, Wang B, Wang Y, Wu H, Xi F, Yengo L, Yu C, Zhang X, Zhang J, Zhang Q, Zhang W, Zheng H, Zhou Y, Altshuler D, 't Hart LM, Franks PW, Balkau B, Froguel P, McCarthy MI, Laakso M, Groop L, Christensen C, Brandslund I, Lauritzen T, Witte DR, Linneberg A, Jorgensen T, Hansen T, Wang J, Nielsen R, Pedersen O, DESIR Study Grp, DIAGRAM Consortium. Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes. Diabetologia 2013, 56(2), 298-310.
• White MG, Marshall HL, Rigby R, Huang GC, Amar A, Booth T, White SA, Shaw JAM. Expression of mesenchymal and alpha-cell phenotypic markers in islet beta-cells in recently diagnosed diabetes. Diabetes Care 2013. In Press.
• Best AJ, Dalgleish C, Ehrmann I, Kheirollahi-Kouhestani M, Tyson-Capper AJ, Elliott DJ. Expression of Tra2ß in cancer cells as a potential contributory factor to neoplasia and metastasis. International Journal of Cell Biology 2013, 2013, 843781.
• Krishnappa L, Dreisbach A, Otto A, Goosens VJ, Cranenburgh RM, Harwood CR, Becher D, Maarten van Dijl J. Extracytoplasmic Proteases Determining the Cleavage and Release of Secreted Proteins, Lipoproteins, and Membrane Proteins in Bacillus subtilis. Journal of Proteome Research 2013, 12(9), 4101-4110.
• Singh A, Panting RJ, Varma A, Saijo T, Waldron KJ, Jong A, Ngamskurungroj P, Chang YC, Rutherford JC, Kwon-Chung KJ. Factors required for Activation of Urease as a Virulence Determinant in Cryptococcus neoformans. mBio 2013, 4(3), e00220-13.
• Xie W, Wood AR, Lyssenko V, Weedon MN, Knowles JW, Alkayyali S, Assimes TL, Quertermous T, Abbasi F, Paananen J, Häring H, Hansen T, Pedersen O, Smith U, Laakso M, MAGIC Investigators, DIAGRAM Consortium, RISC Consortium, Dekker JM, Nolon JJ, Groop L, Ferrannini E, Adam KP, Gall WE, Frayling TM, Walker M. Genetic Variants Associated with Glycine Metabolism and their Role in Insulin Sensitivity and Type 2 Diabetes. Diabetes 2013, 62(6), 2141-2150.
• Harun NA, Benning MJ, Horrocks BR, Fulton DA. Gold nanoparticle-enhanced luminescence of silicon quantum dots co-encapsulated in polymer nanoparticles. Nanoscale 2013, (epub ahead of print).
• Jourdain AA, Koppen M, Wydro M, Rodley CD, Lightowlers RN, Chrzanowska-Lightowlers ZM, Martinou JC. GRSF1 Regulates RNA Processing in Mitochondrial RNA Granules. Cell Metabolism 2013, 7(3), 399-410.
• Lightowlers RN, Chrzanowska-Lightowlers ZM. Human pentatricopeptide proteins: Only a few and what do they do?. RNA Biology 2013, 10(9).
• Yamada K, Ono M, Perkins ND, Rocha S, Lamond AI. Identification and Functional Characterization of FMN2, a Regulator of the Cyclin-Dependent Kinase Inhibitor p21. Molecular Cell 2013, 49(5), 922-933.
• Penn L, White M, Lindstrom L, den Boer A, Blaak E, Eriksson JG, Feskens E, Ilanne-Parikka P, Keinänen-Kiukaanniemi SM, Walker M, Mathers JC, Uusitupa M, Tuomilehto J. Importance of Weight Loss Maintenance and Risk Prediction in the Prevention of Type 2 Diabetes: Analysis of European Diabetes Prevention Study RCT. PLoS One 2013, 8(2), e57143.
• Martin S, Lamb HK, Brady C, Lefkove B, Bonner MY, Thompson P, Lovat PE, Arbiser JL, Hawkins AR, Redfern CPF. Inducing apoptosis of cancer cells using small-molecule plant compounds that bind to GRP78. British Journal of Cancer 2013, 109(2), 433-443.
• Moles A, Sanchez AM, Banks PS, Murphy LB, Luli S, Borthwick L, Fisher A, O'Reilly S, van Laar JM, White SA, Perkins ND, Burt AD, Mann DA, Oakley F. Inhibition of RelA-Ser536 phosphorylation by a competing peptide reduces mouse liver fibrosis without blocking the innate immune response. Hepatology 2013, 57(2), 817-828.
• Balasubramaniam V, Mustar S, Mustafa Khalid N, Abd Rashed A, Mohd Noh MF, Wilcox MD, Chater PI, Brownlee IA, Pearson JP. Inhibitory activities of three Malaysian edible seaweeds on lipase and α-amylase. Journal of Applied Phycology 2013, 1-8. In Press.
• Dean P, Young L, Quitard S, Kenny B. Insights into the Pathogenesis of Enteropathogenic E. coli Using an Improved Intestinal Enterocyte Model. PLoS One 2013, 8(1), e55284.
• Errington J. L-form bacteria, cell walls and the origins of life. Open Biology 2013, 3, 120143.
• Campbell MD, Walker M, Trenell MI, Jakovljevic DG, Stevenson EJ, Bracken RM, Bain SC, West DJ. Large pre- and postexercise rapid-acting insulin reductions preserves glycemia and prevents early- but not late-onset hypoglycemia in patients with type 1 diabetes. Diabetes Care 2013, (epub ahead of print).
• Jans R, Mottram L, Johnson DL, Brown AM, Sikkink S, Ross K, Reynolds NJ. Lysophosphatidic Acid Promotes Cell Migration through STIM1- and Orai1-Mediated Ca²⁺i Mobilization and NFAT2 Activation. Journal of Investigative Dermatology 2013, 133(3), 793-802.
• Nielsen S, Yuzenkova Y, Zenkin N. Mechanism of Eukaryotic RNA Polymerase III Transcription Termination. Science 2013, 340(6140), 1577-1580.
• Kuzmenko A, Atkinson GC, Levitskii S, Zenkin N, Tenson T, Hauryliuk V, Kamenski P. Mitochondrial translation initiation machinery: Conservation and diversification. Biochimie 2013, (epub ahead of print).
• Newman JA, Rodrigues CA, Lewis RJ. Molecular Basis of the Activity of SinR Protein, the Master Regulator of Biofilm Formation in Bacillus subtilis. Journal of Biological Chemistry 2013, 288(15), 10766-10778.
• Richardson TT, Gilroy L, Ishino Y, Connolly BA, Heneneke G. Novel inhibition of archaeal family-D DNA polymerase by uracil. Nucleic Acids Research 2013, 41(7), 4207-4218.
• Dang TS, Walker M, Ford D, Valentine R. Nutrigenetics and Nutrigenomics; the role of nutrition in gene expression. Periodontology 2000 2013. In Press.
• Venditto I, Basle A, Luis AS, Temple MJ, Ferreira LMA, Fontes CMGA, Gilbert HJ, Najmudin S. Overproduction, purification, crystallization and preliminary X-ray characterization of the C-terminal family 65 carbohydrate-binding module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens. Acta Crystallographica. Section F: Structural Biology and Crystallization Communications 2013, 69, 191-194.
• Karavolos MH, Winzer K, Williams P, Khan CM. Pathogen espionage: multiple bacterial adrenergic sensors eavesdrop on host communication systems. Molecular Microbiology 2013, 87(3), 455-465.
• Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biology 2013, 14(2), R19.
• Andrew EJ, Merchan S, Lawless C, Banks AP, Wilkinson DJ, Lydall D. Pentose Phosphate Pathway Function Affects Tolerance to the G-Quadruplex Binder TMPyP4. PLoS One 2013, 8(6), e66242.
• Werner Andreas, Cockell Simon, Falconer Jane, Alnumeir Sammer, Robinson John. Production of small genic RNAs and endogenous siRNAs from sense/antisense transcripts in human cells. Genome Biology 2013. Submitted.
• Townes CL, Ali A, Gross N, Pal D, Williamson SC, Heer R, Robson CN, Pickard R, Hall J. Prostate specific antigen enhances the innate defence of prostatic epithelium against Escherichia coli infection. The Prostate 2013. In Press.
• Kuzmenko AV, Levitskii SA, Vinogradova EN, Atkinson GC, Hauryliuk V, Zenkin N, Kamenski PA. Protein biosynthesis in mitochondria. Biochemistry (Moscow) 2013, 78(8), 855-866.
• Garnett JP, Hickman E, Tunkamnerdthai O, Cuthbert AW, Gray MA. Protein phosphatase 1 coordinates CFTR-dependent airway epithelial HCO₃^- secretion by reciprocal regulation of apical and basolateral membrane Cl^--HCO₃^- exchangers. British Journal of Pharmacology 2013, 168(8), 1946-1960.
• Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM. Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins. Proteomics 2013. In Press.
• Alsharif NH, Al-Said SAF, Birch MA, Horrocks BR, Datta HK. Real-time activity bioassay of single osteoclasts using a silicon nanocrystal-impregnated artificial matrix. Small 2013, (epub ahead of print). In Press.
• Sohal SS, Ward C, Danial W, Wood-Baker R, Walters EH. Recent advances in understanding inflammation and remodeling in the airways in chronic obstructive pulmonary disease. Expert Review of Respiratory Medicine 2013, 7(3), 275-288.
• van Wonderen JH, Kostrz DN, Dennison C, MacMillan F. Refined Distances Between Paramagnetic Centers of a Multi-Copper Nitrite Reductase Determined by Pulsed EPR (iDEER) Spectroscopy. Angewandte Chemie: International Edition 2013, 52(7), 1990-1993.
• Kisielewska J, Whitaker M. Regulation of DNA synthesis at the first cell cycle in the sea urchin in vivo. In: Methods in Molecular Biology. Humana Press, Inc, 2013. In Press.
• Bruni F, Gramegna P, Oliveira JM, Lightowlers RN, Chrzanowska-Lightowlers ZMA. REXO2 is an oligoribonuclease active in human mitochondria. PLoS One 2013, 8(5), e64670.
• Siller L, Lemloh M-L, Piticharoenphun S, Mendis BG, Horrocks BR, Brummer F, Medakovic D. Silver nanoparticle toxicity in sea urchin Paracentrotus lividus. Environmental Pollution 2013, 178, 498-502.
• Liebal UW, Millat T, Marles-Wright J, Lewis RJ, Wolkenhauer O. Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. BMC Systems Biology 2013, 7(1), 3.
• Weatherhead SC, Farr PM, Reynolds NJ. Spectral effects of UV on psoriasis. Photochemical & Photobiological Sciences 2013, 12(1), 47-53.
• Boonstra M, de Jong IG, Scholefield G, Murray H, Kuipers OP, Veening JW. Spo0A regulates chromosome copy number during sporulation by directly binding to the origin of replication in Bacillus subtilis. Molecular Microbiology 2013, 87(4), 925-938.
• Bell N, Hann V, Redfern CPF, Cheek TR. Store-operated Ca²⁺ entry in proliferating and retinoic acid-differentiated N- and S-type neuroblastoma cells. Biochimica et Biophysica Acta: Molecular Cell Research 2013, 1833(3), 643-651.
• Werner A, Mattick JS. Strategies for enhanced evolvability of complex organisms: transpositional shuffling and screening in male germ cell development. Molecular Biology and Evolution 2013. Submitted.
• Le Brun AP, Clifton LA, Halbert CE, Lin B, Meron M, Holden PJ, Lakey JH, Holt SA. Structural Characterization of a Model Gram-Negative Bacterial Surface Using Lipopolysaccharides from Rough Strains of Escherichia coli. Biomacromolecules 2013, 14(6), 2014-2022.
• Rytkonen KT, Akbarzadeh A, Miandare HK, Kamei H, Duan CM, Leder EH, Williams TA, Nikinmaa M. Subfunctionalization of cyprinid hypoxia-inducible factors in development and oxygen sensing. Evolution 2013, 67(3), 873-882.
• Davies OR, Lin C-Y, Radzisheuskaya A, Zhou X, Taube J, Blin G, Waterhouse A, Smith AJH, Lowell S. Tcf15 primes pluripotent cells for differentiation. Cell Reports 2013, 3, 472-484.
• Fullard N, Moles A, O'Reilly S, van Laar JM, Faini D, Diboll J, Reynolds NJ, Mann DA, Reichelt J, Oakley F. The c-Rel Subunit of NF-κB Regulates Epidermal Homeostasis and Promotes Skin Fibrosis in Mice. American Journal of Pathology 2013, 182(6), 2109-2120.
• CastroRoa D, GarciaPino A, vanNuland NAJ, Loris R, Zenkin N. The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu. Nature Chemical Biology 2013. In Press.
• Castro-Roa D, Garcia-Pino A, De Geiter S, van Nuland NAJ, Loris R, Zenkin N. The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu. Nature Chemical Biology 2013, Accepted. Submitted.
• Wight M, Werner A. The functions of natural antisense transcripts. Essays in Biochemistry 2013, 54, 91-102.
• Allen S, Badarau A, Dennison C. The influence of protein folding on the copper affinities of trafficking and target sites. Dalton Transactions 2013, 42(9), 3233-3239.
• Ehrmann I, Dalgliesh C, Liu Y, Danilenko M, Crosier M, Overman L, Arthur HM, Lindsay S, Clowry GJ, Venables JP, Fort P, Elliott DJ. The Tissue-Specific RNA Binding Protein T-STAR Controls Regional Splicing Patterns of Neurexin Pre-mRNAs in the Brain. PLoS Genetics 2013, 9(4), e1003474.
• Dong K, Addinall S, Lydall D, Rutherford JC. The yeast copper response is regulated by DNA damage. Molecular and Cellular Biology 2013, n/a(epub ahead of print), n/a.
• Borthwick LA, Corris PA, Mahida R, Walker A, Gardner A, Suwara M, Johnson GE, Moisey EJ, Brodlie M, Ward C, Perry JD, de Soyza A, Mann DA, Fisher AJ. TNFα From Classically Activated Macrophages Accentuates Epithelial to Mesenchymal Transition in Obliterative Bronchiolitis. American Journal of Transplantation 2013, 13(3), 621-633.
• Luis AS, Venditto I, Temple MJ, Rogowski A, Basle A, Xue J, Knox JP, Prates JAM, Ferreira LMA, Fontes CMGA, Najmudin S, Gilbert HJ. Understanding How Noncatalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan. Journal of Biological Chemistry 2013, 288(7), 4799-4809.
• Richardson TT, Xu W, Keith BJ, Heslop P, Jones AC, Connolly BA. Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil. Nucleic Acids Research 2013, 41(4), 2466-2478.
• Patterson M, McKenzie C, Smith D, da Silva Dantas A, Sherston S, Veal EA, Morgan B, MacCallum D, Erwig LP, Quinn J. Ybp1 and Gpx3 signalling in Candida albicans govern hydrogen peroxide-induced oxidation of the Cap1 transcription factor and macrophage escape. Antioxidants & Redox Signaling 2013, Epub ahead of print.