Synthetic Biology Publications

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.
 Tcoffee alignment of Class II hydrophobins

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.

Synthetic glycolipids for binding at the TCR-CD1d interfaceImage – 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 α-Galactosyl Ceramide Analogues. Carbohydr. Res. 356 152–162.

Synthetic dimeric CD1d ligands containing two α-galactosyl ceramide linkers

Image – Synthetic dimeric CD1d ligands containing two α-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.

Biomolecular detection coupling flow and linear dichroism

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.

Designed polymers which can both sequester Vibrio harveyi bacteria from suspensions and quench quorum sense signals.

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.

Disconnectivity graph representing the energy landscape of a three-color (BLN) 69-residue model protein

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.

Disconnectivity graph representing the energy landscape of a cyclic tetrapeptide

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

Electron microscopy of metallized E. coli cells

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
 Palladium nanoparticles supported on bacterial biomass capable of catalysing the Heck reactionImage – 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 1-8Journal cover illustrating vertically aligned single walled carbon nanotubes for sensing of eukaryotic cells

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.

Design and study of an electrical switchable bacterial adhesion surface

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

Single species biofilms for specific biotransformations

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

Single species biofilms for conversion of serine and haloindoles to halotryptophans

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.

Gold triethylphosphine, analogous to the antiarthrtic drug auranofin, coupled to a de novo designed coiled coil through a single cysteine

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.

First de novo designed hydrolytic metalloenzymeImage - 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.

Luminescent europium and pH low inserting peptide coated nanoparticles for pH controlled delivery into plateletsImage - 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.

Synthetic multicomponent materials developed for gene delivery

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.

Interactions of synthetic disulfide-linked polypeptide gene delivery vectors with supported phospholipid bilayers probed by AFM.

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

surface properties and adhesive strength of biofilms studied by AFM.

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

Single species biofilms for conversion of serine and haloindoles to halotryptophans

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
 Calculated and experimental linear dichroism orientation of M13 bacteriophage under flow conditions

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 ZhaoA 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

Synthetic ferrocene nucleic acid oligomer

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 Płoskoń, 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 β-branch insertion during type-I polyketide synthesis, Nature Chemical Biology  Biology 9, 685–692 (2013) doi:10.1038/nchembio.1342