Selected publications from groups involved in Synthetic Biology research at Birmingham
Professor Steve Busby
D Lee, S Busby (2012) Repression by cAMP receptor protein at a distance. mBio 3 e00289-12 doi 10 1128/mBio00289-12
M Elrobh, C Webster, S Samarasinghe, D Durose, S Busby (2013) Two DNA sites for MelR in the same orientation are sufficient for optimal MelR-dependent repression at the Escherichia coli melR promoter. FEMS Letters 338 62-67
Professor Mark Cobbold
CA MacLennan et al (2010) Dysregulated Humoral Immunity to Nontyphoidal Salmonella in HIV-Infected African Adults. Science. 328 508-12
F* Mohammed, M* Cobbold et al (2008) Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self. Nature Immunology. 9 1236-43
Professor Jeff Cole
S Alfasi, YR Sevastsyanovich, L Griffiths, R Hall, J Cole (2011) Use of GFP Fusions for the isolation of Escherichia coli strains for improved recombinant protein production. Journal of Biotechnology 156 11-21
Y Sevastsyanovich, S Alfasi, T Overton, R Hall, J Jones, C Hewitt, J Cole (2009) Exploitation of GFP fusion proteins and stress avoidance as a generic strategy for the production of high quality recombinant proteins. FEMS Microbiology Letters 299 86-94.
Dr Phil Cox
KA Littlejohn, P Hooley, PW Cox (2012) Bioinformatics predicts diverse Aspergillus hydrophobins with novel properties. Food Hydrocoll 27 503–16.
Image – Tcoffee alignment of Class II hydrophobins
GS Tucker, HM Brown, PJ Fryer, PW Cox, FL Poole, H-S Lee, MW Adams (2007) A sterilisation time-temperature integrator based on amylase from the hyperthermophilic organism Pyrococcus furiosus. Innovative Food Science and Emerging Technologies (IFSET) 8 63-72.
Dr Liam Cox
PJ Jervis, P Polzella, J Wojno, J-P Jukes, H Ghadbane, YR Garcia Diaz, GS Besra, V Cerundolo, LR Cox (2013) Design, Synthesis and Functional Activity of Labeled CD1d Glycolipid Agonists. Bioconjugate Chem. 24 586–594.
Image – Synthetic glycolipids for binding at the TCR-CD1d interface
PJ Jervis, M Moulis, J-P Jukes, H Ghadbane, LR Cox, V Cerundolo, GS Besra (2012) Towards Multivalent CD1d Ligands: Synthesis and Biological Activity of Homodimeric a-Galactosyl Ceramide Analogues. Carbohydr. Res. 356 152–162.
Image – Synthetic dimeric CD1d ligands containing two a-galactosyl ceramide linkers
Professor Tim Dafforn
R Pacheco-Gomez, J Kraemer, S Stokoe, HJ England, CW Penn, E Stanley, A Rodger, J Ward, MR Hicks, TR Dafforn (2012) Detection of Pathogenic Bacteria Using a Homogeneous Immunoassay Based on Shear Alignment of Virus Particles and Linear Dichroism. Analytical Chemistry 84 91-97.
Image – Biomolecular detection coupling flow and linear dichroism
DJ Turner, I Portman, TR Dafforn, A Rodger, DI Roper, CJ Smith, MS Turner (2012) The Mechanics of FtsZ Fibers. Biophysical Journal 102 731-8.
Professor Heather Draper
H Kirkby, M Calvert, H Draper, T Keeley, S Wilson (2012) What patients want to know about research: a systematic review, BMJOpen 2:e000509
Dr Rosemary Dyson
RJ Dyson, LR Band OE Jensen (2012) A model of crosslink kinetics in the expanding plant cell wall: Yield stress and enzyme action Journal of Theoretical Biology 307, 125–136
LR Band, S Ubeda-Tomas, RJ Dyson, AM Middleton, TC Hodgman, MR Owen, OE Jensen, MJ Bennett JR King (2012) Growth-induced hormone dilution can explain the dynamics of plant root cell elongation Proceedings of the National Academy of Science 109 7577-7582
Dr Francisco Fernández-Trillo
X Xue, G Pasparakis, N Halliday, K Winzer, SM Howdle, CJ Cramphorn, NR Cameron, PM Gardner, BG Davis, F Fernández-Trillo, C Alexander (2011) Synthetic Polymers for Simultaneous Bacterial Sequestration and Quorum Sense Interference, Angew. Chem., Int. Ed. 50 9852–9856.
Image – Designed polymers which can both sequester Vibrio harveyi bacteria from suspensions and quench quorum sense signals.
J Smaldon, FJ Romero-Campero, F Fernández-Trillo, M Gheorghe, C Alexander, N Krasnogor (2010) A computational study of liposome logic: towards cellular computing from the bottom up., Syst Synth Biol. 4 157–179.
Professor Liam Grover
DC Bassett, LM Grover, FA Mueller, MD McKee, JE Barralet (2011) Serum Protein Controlled Nanoparticle Synthesis. Advanced Functional Materials, 21 2968-77.
NC Hunt, LM Grover (2010) Cell encapsulation using biopolymer gels for regenerative medicine. Biotechnology Letters 32 733-42.
Dr Sara Jabbari
S Jabbari, E Steiner, JT Heap, K Winzer, NP Minton, JR King (2013) The putative influence of the agr operon upon survival mechanisms used by Clostridium acetobutylicum. Math. Biosci. 243 223-239.
GJ Thorn, JR King, S Jabbari (2013) pH-induced gene regulation of solvent production by Clostridium acetobutylicum in continuous culture: Parameter estimation and sporulation modelling. Math. biosci. 241 149-166.
Professor Roy Johnston
MT Oakley, DJ Wales, RL Johnston (2011) Energy Landscape and Global Optimisation for a Frustrated Model Protein, J. Phys. Chem. B 115 11525-11529.
Image – Disconnectivity graph representing the energy landscape of a three-color (BLN) 69-residue model protein
MT Oakley, E Oheix, AFA Peacock, RL Johnston (2013) Computational and Experimental Investigations into the Conformations of Cyclic Tetra-alpha/beta-Peptides, J. Chem. Phys. B, DOI: 10.1021/jp4043039.
Image – Disconnectivity graph representing the energy landscape of a cyclic tetrapeptide
Dr Jan-Ulrich Kreft
LA Lardon, BV Merkey, S Martins, A Dötsch, C Picioreanu, JU Kreft, BF Smets (2011) iDynoMiCS: next-generation individual-based modelling of biofilms. Environmental Microbiology 13 2416-2434
CM Costello, JU Kreft, CM Thomas, DM Hammes, P Bao, SD Evans, PM Mendes (2012) Exploiting additive and subtractive patterning for spatially controlled and robust bacterial co-cultures. Soft Matter 8 9147-9155
Dr Peter Lund
NA Burton, MD Johnson, P Antczak, A Robinson, PA Lund (2010) Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics. J Mol Biol. 401 726-42
A Stincone, N Daudi, AS Rahman, P Antczak, IR Henderson, JA Cole, PA Lund, F Falciani (2011) A systems biology approach sheds new light on Escherichia coli acid resistance. Nucleic Acids Res, 39 7512-28
Professor Lynne Macaskie
K Deplanche, MMerroun, T Casadesus, T Tran, IP Mikheenko, JA Bennett, JZhu, J Wood, IP Jones, GA Attard, SSelenska-Pobell, LE Macaskie (2012) Microbial synthesis of core/shell gold/palladium nanoparticles and applications in green chemistry. J. Roy. Soc. Interface 9 1705-12
Image - Electron microscopy of metallized E. coli cells
JA Bennett, IP Mikheenko, K Deplanche, IJ Shannon, J Wood, LE Macaskie (2013) Nanoparticles of palladium supported on bacterial biomass: new re-usable heterogeneous catalyst with comparable activity to homogeneous colloidal palladium in the Heck reaction Appl Catal B: Environmental 140-141 700-707
Image – Palladium nanoparticles supported on bacterial biomass capable of catalysing the Heck reaction
Dr Paula Mendes
FJ Rawson, CL Yeung, SK Jackson, PM Mendes (2013) Tailoring 3D Single-Walled Carbon Nanotubes Anchored to Indium Tin Oxide for Natural Cellular Uptake and Intracellular Sensing Nano Lett.13 1-8
Image – Journal cover illustrating vertically aligned single walled carbon nanotubes for sensing of eukaryotic cells
A Pranzetti, S Mieszkin, P Iqbal, FJ Rawson, ME Callow, JA Callow, P Koelsch, JA Preece, PM Mendes (2013) An Electrically Reversible Switchable Surface to Control and Study Early Bacterial Adhesion Dynamics in Real-Time, Adv. Mat.25 2181-2185.
Image – Design and study of an electrical switchable bacterial adhesion surface
Dr Tim Overton
M Winn, JM Foulkes, S Perni, MJH Simmons, TW Overton, RJM Goss (2012) Biofilms and their Engineered Counterparts: a new Generation of Immobilised Biocatalysts. Catalysis Science and Technology 2 1544-1547
Image – Single species biofilms for specific biotransformations
AN Tsoligkas, M Winn, J Bowen, TW Overton, MJH Simmons, RJM Goss (2011) Engineering Biofilms for Biocatalysis. ChemBioChem 12 1391-1395
Image – Single species biofilms for specific biotransformations
Dr Anna Peacock
AFA Peacock, GA Bullen, L Gethings, JP Williams, FH Kriel, J Coates (2012) Gold-Phosphine Binding to De Novo Designed Coiled Coil Peptides, J. Inorg. Biochem. 117 298-305.
Image - Gold triethylphosphine, analogous to the antiarthrtic drug auranofin, coupled to a de novo designed coiled coil through a single cysteine
M Zastrow, AFA Peacock, J Stuckey, VL Pecoraro (2012) Hydrolytic Catalysis and Structural Stabilization in a Designed Metalloprotein, Nature Chem. 4 118-123.
Image - First de novo designed hydrolytic metalloenzyme
Dr Zoe Pikramenou
A Davies, DJ Lewis, SP Watson, SG Thomas, Z Pikramenou (2012) pH-controlled delivery of luminescent europium coated nanoparticles into platelets, Proceedings of the National Academy of Sciences of the United States of America 109 1862-1867.
Image - Luminescent europium and pH low inserting peptide coated nanoparticles for pH controlled delivery into platelets
DJ Lewis, C Bruce, S Bohic, P Cloetens, SP Hammond, D ARBON, S Blair-Reid, Z Pikramenou, B Kysela (2010) Intracellular synchrotron nanoimaging and DNA damage/genotoxicity screening of novel lanthanide-coated nanovectors, Nanomedicine, 5 1547-1557
Professor Jon Preece
M Soliman, R Nasanit, SR Abdulateefeh, S Allen, MC Davies, SS Briggs, LW Seymour, JA Preece, AM Grabowska, SA Watson, CA Alexander (2012) Multicomponent Synthetic Polymers with Viral-Mimetic Chemistry for Nucleic Acids, Molecular Pharmaceutics, 9 1-13.
Image – Synthetic multicomponent materials developed for gene delivery
M Soliman, RNasanit, M Davies, S Allen, JA Preece, C Alexander (2010) Interaction of Reducible Polypeptide Gene Delivery Vectors with Supported Lipid Bilayers: Pore Formationand Structure Function Relationships, Soft Matter,6 2517-2524.
Image - interactions of synthetic disulfide-linked polypeptide gene delivery vectors with supported phospholipid bilayers probed by AFM.
Professor Mark Simmons
AN Tsoligkas, J Bowen, M Winn, RJM Goss, TW Overton, MJH Simmons (2012) Characterisation of spin coated engineered Escherichia coli biofilms using atomic force microscopy. Colloids and Surfaces B: Biointerfaces 89 152-160
Image - surface properties and adhesive strength of biofilms studied by AFM
AN Tsoligkas, M Winn, J Bowen, TW Overton, MJH Simmons, RJM Goss (2011) Engineering Biofilms for Biocatalysis. ChemBioChem 12 1391-1395
Image – Single species biofilms for conversion of serine and haloindoles to halotryptophans
Dr Dave Smith
JRA McLachlan, DJ Smith, NP Chmel, A Rodger (2013) Calculations of flow-induced orientation distributions for analysis of linear dichroism spectroscopy. Soft Matt. 9 4977-4984
Image – Calculated and experimental linear dichroism orientation of M13 bacteriophage under flow conditions.
W Arlt, M Biehl, AE Taylor, S Hahner, R Libé, BA Hughes, P Schneider, DJ Smith, H Stiekema, N Krone, E Porfiri, G Opocher, J Bertherat, F Mantero, B Alliolio, M Terzolo, P Nightingale, CHL Shackleton, X Bertagna, M Fassnacht, PM Stewart (2011) Urine steroidobolomics – combining mass spectrometry-based steroid profiling and machine learning for detecting adrenal malignancy. J. Clin. Endocrinol. Metab. 96 3775-3784
Professor Chris Thomas
AC Murphy, D Fukuda, Z Song, J Hothersall, RJ Cox, CL Willis, CM Thomas, TJ Simpson (2011) Novel Thiomarinol antibiotics active against MRSA are generated by mutagenesis and mutasynthesis of Pseudoalteromonas SANK73390. Angewandte Chemie International Edition 50 3271–3274.
J Hothersall, J Wu, A Murphy, J Shields, E Stephens, H Cooper, G Campbell, P Williams, CL Willis, TJ Simpson, CM Thomas (2011) Manipulation of quorum sensing regulation in Pseudomonas fluorescens NCIMB 10586 to increase mupirocin production. Applied Microbiology and Biotechnology 90 1017-1026.
Professor James Tucker
HV Nguyen, Z-Y Zhao, A Sallustrau, SL Horswell, L Male, A Mulas, JHR Tucker (2012) A ferrocene nucleic acid oligomer as an organometallic structural mimic of DNA, Chem. Commun. 48 12165-12167
Image – Synthetic ferrocene nucleic acid oligomer
Dr Peter Winn
DB Kokh, S Corni, PJ Winn, M Höfling, RR Gabdoulline, KE Gottschalk, RC Wade (2010) ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent. J. Chem. Theory and Comp. 6 1753-1768.
AS Haines, X Dong, Z Song, R Farmer, C Williams, J Hothersall, E Ploskon, P Wattana-amorn, ER Stephens, E Yamada, R Gurney, Y Takebayashi, J Masschelein, RJ Cox, R Lavigne, CL Willis, TJ Simpson, J Crosby, PJ Winn, CM Thomas, MP Crump, A conserved motif flags Acyl Carrier Proteins for ß-branch insertion during type-I polyketide synthesis, Nature Chemical Biology Biology 9, 685–692 (2013) doi:10.1038/nchembio.1342