Publications

ClohS5HWIAA39voHighlights

SYNBIOCHEM – a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals (2016) Carbonell, P., Currin, A., Dunstan, M., Fellows, D., Jervis, A., Rattray, N. J. W., Robinson, C. J., Swainston, N., Vinaixa, M., Williams, A., Yan, C., Barran, P., Breitling, R., Chen, G. G., Faulon, J-L., Goble, C., Goodacre, R., Kell, D. B., Le Feuvre, R., Micklefield, J., Scrutton, N. S., Shapira, P., Takano, E., & Turner, N. J., Biochemical Society Transactions, 44, 675-677, DOI: 10.1042/BST20160009 Paper. This issue of Biochem.Soc.Trans. also features spotlights on the other UK SBRCs and UK SynBio – Weblink

Bioinformatics for the synthetic biology of natural products: Integrating across the Design–Build–Test cycle Pablo Carbonell1, Andrew Currin1, Adrian Jervis1, Nicholas J. W. Rattray1, Neil Swainston1, Cunyu Yan1, Eriko Takano1, Rainer Breitling1 – Nat. Prod. Rep., 2016, Advance Article DOI: 10.1039/C6NP00018E. This review highlights how powerful bioinformatics tools are progressing synthetic biology by allowing the integration of design, build and test stages of the biological engineering cycle. The article illustrates how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted and discussed Paper.

Mapping the patent landscape of synthetic biology for fine chemical production pathways. Carbonell, P., A. Gok, et al. (2016). Microb Biotechnol. Synthetic biology bio-foundries aim to innovate through an iterative design/build/test/learn pipeline. In assessing the value of new chemical production routes, the intellectual property (IP) novelty of targets is important.  We performed an assessment of pathways as potential targets for chemical production across the full catalogue of reachable chemicals in the extended metabolic space of chassis organisms, as computed by the retrosynthesis-based algorithm RetroPath.  This large-scale computational study provides useful insights into the IP landscape of synthetic biology for fine and specialty chemicals production. 

SensiPath: computer-aided design of sensing-enabling metabolic pathways. Delepine, B., V. Libis, et al. (2016). Nucleic Acids Res 44(W1): W226-231. Here we present the SensiPath web server (http://sensipath.micalis.fr ) that implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. It explores sensing-enabling metabolic pathways to identify putative biochemical transformations of the target compound and thus enlarges the design space by broadening the possible use of biosensors in synthetic biology applications.

Synthetic Biology’s Second World by Dr Andrew Balmer. Discusses the closed doors meeting at Harvard on the prospect of synthesising the human genome, which has caused something of a stir. See PlosBlog weblink

Natural Product Biosynthesis in Escherichia coli: Mentha Monoterpenoids. Toogood, H. S., S. Tait, et al. (2016). Methods Enzymol 575: 247-270. Synthetic biology heralds in a new, “greener” approach to fine chemical and pharmaceutical drug production taking knowledge of natural metabolic pathways to build new routes to chemicals, nonnatural chemical production, and/or allowing the rapid production of chemicals in alternative, high performing organisms. This route is particularly useful in the production of monoterpenoids in microorganisms, which are naturally sourced from plant essential oils. Successful pathway construction takes into consideration factors such as gene selection, regulatory elements, host selection and optimization, and metabolism of the host organism. Seamless pathway construction techniques enable a “plug-and-play” switching of genes and regulatory parts to optimize the metabolic functioning in vivo. These synthetic biology approaches to microbial monoterpenoid production may ultimately revolutionize “natural” compound formation.

Integrating natural and synthetic catalysts opens new reaction pathways: For over one billion years, nature has evolved catalysts called enzymes to mediate the reactions that we call life. In the last few years, scientists have developed non-natural catalysts, which often include metals, that can be used to prepare pharmaceuticals and other valuable products. The integration of enzymes with synthetic catalysts could potentially deliver many new compounds and materials. However, the natural and synthetic catalysts are often incompatible and require very different operating conditions. Scientists led by Jason Micklefield and Michael Greaney have developed methods whereby enzymes and synthetic metallo-catalysts can be brought together in tandem to catalyse reactions that were previously inaccessible using existing methods. The team used halogenase enzymes to introduce halogen substituents into selected positions of aromatic compounds typically found in drug molecules. A synthetic palladium catalyst then exchanges the halogen for a variety of other substituents, creating a wide range of new structures that would be difficult to access using conventional means. To overcome the issue of catalyst incompatibility, a special membrane was used to separate the two catalytic systems. Whilst the catalysts cannot penetrate the membrane, other components of the reaction, including the halogenated intermediates, can pass through from the enzyme to the palladium catalyst. It is envisaged that the team’s integrated catalysis approach could open the way to more elaborate cascade reactions, with simple starting molecules passing through membranes from one catalyst to the next, to rapidly deliver complex products with no need to isolate any reaction intermediates.  Integrated Catalysis Opens New Arylation Pathways via Regiodivergent Enzymatic C-H Activation Jonathan Latham, Jean-Marc Henry, Humera H. Sharif, Binuraj R. K. Menon, Sarah A. Shepherd, Michael F. Greaney & Jason Micklefield Nature Communications 2016, 7, 11873 Paper.

The Micklefield Lab has engineered catechol-O-methyltransferase (COMT) to improve its regioselectivity and activity with a range of co-factor analogues. See the “Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase,” in Angew. Chem. Int. Ed. 2016, 55, 2683–2687 http://onlinelibrary.wiley.com/doi/10.1002/anie.201508287/abstract

An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins” Struck A-W, Bennet MR, Shepherd SA, Law BJC, Zhuo Y, Wong LS & Micklefield J. (2016) Am. Chem Soc.,  138 (9), pp 3038–3045 http://pubs.acs.org/doi/abs/10.1021/jacs.5b10928. An enzyme cascade including catechol-O-methyltransferase and tyrosinase (an hydroxylase enzyme) that enables the regioselective derivatisation of tyrosine residues in peptides and proteins. Methods for the regioselective modification of specific amino acid residues in peptides and proteins are important in labelling, imaging, diagnostic and therapeutic applications.

2016 Publications

  1. Aslan, A. S., Birmingham, W. R., Karaguler, N. G., Turner, N. J. & Binay, B. Semi-Rational Design of Geobacillus stearothermophilus L-Lactate Dehydrogenase to Access Various Chiral alpha-Hydroxy Acids. Applied biochemistry and biotechnology 179, 474-484, doi:10.1007/s12010-016-2007-x (2016).
  2. Bajhaiya, A. K. et al. High-throughput metabolic screening of microalgae genetic variation in response to nutrient limitation. Metabolomics: Official journal of the Metabolomic Society 12, 9, doi:10.1007/s11306-015-0878-4 (2016).
  3. Balmer, A. The secretive ‘second world’ of human synthetic biology. News Article in the Guardian   (2016).
  4. Beveridge, R. et al. Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding. Nature communications 7, 12163, doi:10.1038/ncomms12163 (2016).
  5. Biarnes-Carrera, M., Breitling, R. & Takano, E. Butyrolactone signalling circuits for synthetic biology. Current opinion in chemical biology 28, 91-98, doi:10.1016/j.cbpa.2015.06.024 (2015).
  6. Birt, J. et al. Lack of evidence for the efficacy of enhanced surveillance compared to other specific interventions to control neonatal healthcare-associated infection outbreaks. Transactions of the Royal Society of Tropical Medicine and Hygiene 110, 98-106, doi:10.1093/trstmh/trv116 (2016).
  7. Both, P. et al. Whole-Cell Biocatalysts for Stereoselective C-H Amination Reactions. Angewandte Chemie 55, 1511-1513, doi:10.1002/anie.201510028 (2016).
  8. Breitling, R. & Takano, E. Synthetic biology advances for pharmaceutical production. Current opinion in biotechnology 35, 46-51, doi:10.1016/j.copbio.2015.02.004 (2015).
  9. Breitling, R. & Takano, E. Synthetic Biology of Natural Products. Cold Spring Harbor perspectives in biology, doi:10.1101/cshperspect.a023994 (2016).
  10. Breitling, R., Takano, E. & Gardner, T. S. Judging synthetic biology risks. Science 347, 107, doi:10.1126/science.aaa5253 (2015).
  11. Carbonell, P. et al. SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. Biochemical Society transactions 44, 675-677, doi:10.1042/BST20160009 (2016)
  12. Carbonell, P. et al. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. Natural product reports 33, 925-932, doi:10.1039/c6np00018e (2016).
  13. Carbonell, P., Gok, A., Shapira, P. & Faulon, J. L. Mapping the patent landscape of synthetic biology for fine chemical production pathways. Microbial biotechnology, doi:10.1111/1751-7915.12401 (2016).
  14. Ceroni, F., Carbonell, P., Francois, J. M. & Haynes, K. A. Editorial – Synthetic Biology: Engineering Complexity and Refactoring Cell Capabilities. Frontiers in bioengineering and biotechnology 3, 120, doi:10.3389/fbioe.2015.00120 (2015).
  15. Chenge, J. et al. Structural characterization of CYP144A1 – a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis. Scientific reports 6, 26628, doi:10.1038/srep26628 (2016).
  16. Delepine, B., Libis, V., Carbonell, P. & Faulon, J. L. SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic acids research 44, W226-231, doi:10.1093/nar/gkw305 (2016).
  17. Eichler, A. et al. Enantioselective Benzylic Hydroxylation Catalysed by P450 Monooxygenases: Characterisation of a P450cam Mutant Library and Molecular Modelling. Chembiochem : a European journal of chemical biology 17, 426-432, doi:10.1002/cbic.201500536 (2016).
  18. Feher, T., Libis, V., Carbonell, P. & Faulon, J. L. A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli. Frontiers in bioengineering and biotechnology 3, 46, doi:10.3389/fbioe.2015.00046 (2015).
  19. Formisano, N. et al. Inexpensive and fast pathogenic bacteria screening using field-effect transistors. Biosensors & bioelectronics 85, 103-109, doi:10.1016/j.bios.2016.04.063 (2016).
  20. Girvan, H. M. & Munro, A. W. Applications of microbial cytochrome P450 enzymes in biotechnology and synthetic biology. Current opinion in chemical biology 31, 136-145, doi:10.1016/j.cbpa.2016.02.018 (2016).
  21. Gray, C. J. et al. Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochimica et biophysica acta 1860, 1688-1709, doi:10.1016/j.bbagen.2016.02.003 (2016).
  22. Grogan, G. & Turner, N. J. InspIRED by Nature: NADPH-Dependent Imine Reductases (IREDs) as Catalysts for the Preparation of Chiral Amines. Chemistry 22, 1900-1907, doi:10.1002/chem.201503954 (2016).
  23. Hastings, J. et al. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic acids research 44, D1214-1219, doi:10.1093/nar/gkv1031 (2016).
  24. Heath, R. S., Pontini, M., Hussain, S. & Turner, N. J. Combined Imine Reductase and Amine Oxidase Catalyzed Deracemization of Nitrogen Heterocycles. Chemcatchem 8, 117-120, doi:10.1002/cctc.201500822 (2016).
  25. Hoeven, R., Hardman, S. J., Heyes, D. J. & Scrutton, N. S. Cross-Species Analysis of Protein Dynamics Associated with Hydride and Proton Transfer in the Catalytic Cycle of the Light-Driven Enzyme Protochlorophyllide Oxidoreductase. Biochemistry 55, 903-913, doi:10.1021/acs.biochem.5b01355 (2016).
  26. Hugentobler, K. G., Sharif, H., Rasparini, M., Heath, R. S. & Turner, N. J. Biocatalytic approaches to a key building block for the anti-thrombotic agent ticagrelor. Organic & biomolecular chemistry, doi:10.1039/c6ob01382a (2016).
  27. Johannissen, L. O., Hay, S. & Scrutton, N. S. Nuclear quantum tunnelling in enzymatic reactions–an enzymologist’s perspective. Physical chemistry chemical physics : PCCP 17, 30775-30782, doi:10.1039/c5cp00614g (2015).
  28. Kavanagh, M. E. et al. Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. Journal of medicinal chemistry 59, 3272-3302, doi:10.1021/acs.jmedchem.6b00007 (2016).
  29. Kavanagh, M. E. et al. Substrate Fragmentation for the Design of M. tuberculosis CYP121 Inhibitors. ChemMedChem, doi:10.1002/cmdc.201600248 (2016).
  30. Kell, D. B. Implications of endogenous roles of transporters for drug discovery: hitchhiking and metabolite-likeness. Nature reviews. Drug discovery 15, 143, doi:10.1038/nrd.2015.44 (2016).
  31. Kell, D. B., Swainston, N., Pir, P. & Oliver, S. G. Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. Trends in biotechnology 33, 237-246, doi:10.1016/j.tibtech.2015.02.001 (2015).
  32. Kent, A. et al. Schedules for Pneumococcal Vaccination of Preterm Infants: An RCT. Pediatrics, doi:10.1542/peds.2015-3945 (2016).
  33. Kent, A. et al. Lymphocyte subpopulations in premature infants: an observational study. Archives of disease in childhood. Fetal and neonatal edition, doi:10.1136/archdischild-2015-309246 (2016).
  34. Knaus, T. et al. Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes. Journal of the American Chemical Society 138, 1033-1039, doi:10.1021/jacs.5b12252 (2016).
  35. Kutta, R. J. et al. The photochemical mechanism of a B12-dependent photoreceptor protein. Nature communications 6, 7907, doi:10.1038/ncomms8907 (2015).
  36. Latham, J. et al. Integrated catalysis opens new arylation pathways via regiodivergent enzymatic C-H activation. Nature communications 7, 11873, doi:10.1038/ncomms11873 (2016).
  37. Law, B. J. et al. Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase. Angewandte Chemie 55, 2683-2687, doi:10.1002/anie.201508287 (2016).
  38. Leys, D. & Scrutton, N. S. Sweating the assets of flavin cofactors: new insight of chemical versatility from knowledge of structure and mechanism. Current opinion in structural biology 41, 19-26, doi:10.1016/j.sbi.2016.05.014 (2016).
  39. Libis, V., Delepine, B. & Faulon, J. L. Sensing new chemicals with bacterial transcription factors. Current opinion in microbiology 33, 105-112, doi:10.1016/j.mib.2016.07.006 (2016).
  40. Libis, V., Delepine, B. & Faulon, J. L. Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways. ACS synthetic biology, doi:10.1021/acssynbio.5b00225 (2016).
  41. Longbotham, J. E. et al. Structure and Mechanism of a Viral Collagen Prolyl Hydroxylase. Biochemistry 54, 6093-6105, doi:10.1021/acs.biochem.5b00789 (2015).
  42. Lygidakis, A. et al. Pinpointing a Mechanistic Switch Between Ketoreduction and “Ene” Reduction in Short-Chain Dehydrogenases/Reductases. Angewandte Chemie 55, 9596-9600, doi:10.1002/anie.201603785 (2016).
  43. Mellor, J., Grigoras, I., Carbonell, P. & Faulon, J. L. Semisupervised Gaussian Process for Automated Enzyme Search. ACS synthetic biology 5, 518-528, doi:10.1021/acssynbio.5b00294 (2016).
  44. Mendes, P., Oliver, S. G. & Kell, D. B. Response to ‘The Need for Speed’, by Matsson et al. Trends in pharmacological sciences 37, 245-246, doi:10.1016/j.tips.2016.02.004 (2016).
  45. Menon, B. R., Hardman, S. J., Scrutton, N. S. & Heyes, D. J. Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR). Journal of photochemistry and photobiology. B, Biology 161, 236-243, doi:10.1016/j.jphotobiol.2016.05.029 (2016).
  46. Morra, R. et al. Dual transcriptional-translational cascade permits cellular level tuneable expression control. Nucleic acids research 44, e21, doi:10.1093/nar/gkv912 (2016).
  47. Muhamadali, H. et al. Metabolomic analysis of riboswitch containing E. coli recombinant expression system. Molecular bioSystems 12, 350-361, doi:10.1039/c5mb00624d (2016).
  48. Peers, M. K. et al. Light-driven biocatalytic reduction of alpha,beta-unsaturated compounds by ene reductases employing transition metal complexes as photosensitizers. Catal Sci Technol 6, 169-177, doi:10.1039/c5cy01642h (2016).
  49. Randles, S. & Laasch, O. Theorising the Normative Business Model. Organ Environ 29, 53-73, doi:10.1177/1086026615592934 (2016).
  50. Rattray, N. J. Analytical medicine: Citizen scientists can aid diagnostics. Nature 528, 193, doi:10.1038/528193c (2015).
  51. Robinson, C. J., Medina-Stacey, D., Wu, M. C., Vincent, H. A. & Micklefield, J. Rewiring Riboswitches to Create New Genetic Circuits in Bacteria. Methods in enzymology 575, 319-348, doi:10.1016/bs.mie.2016.02.022 (2016).
  52. Ruscoe, R. E., Fazakerley, N. J., Huang, H. M., Flitsch, S. & Procter, D. J. Copper-Catalyzed Double Additions and Radical Cyclization Cascades in the Re-Engineering of the Antibacterial Pleuromutilin. Chem-Eur J 22, 116-119, doi:10.1002/chem.201504343 (2016).
  53. S, O. H., Swainston, N., Handl, J. & Kell, D. B. A ‘rule of 0.5’ for the metabolite-likeness of approved pharmaceutical drugs. Metabolomics : Official journal of the Metabolomic Society 11, 323-339, doi:10.1007/s11306-014-0733-z (2015).
  54. Shepherd, S. A. et al. A Structure-Guided Switch in the Regioselectivity of a Tryptophan Halogenase. Chembiochem : a European journal of chemical biology 17, 821-824, doi:10.1002/cbic.201600051 (2016).
  55. Simpson, J. E. et al. Neuronal DNA damage response-associated dysregulation of signalling pathways and cholesterol metabolism at the earliest stages of Alzheimer-type pathology. Neuropathology and applied neurobiology 42, 167-179, doi:10.1111/nan.12252 (2016).
  56. Staniland, S. et al. Biocatalytic Dynamic Kinetic Resolution for the Synthesis of Atropisomeric Biaryl N-Oxide Lewis Base Catalysts. Angewandte Chemie, doi:10.1002/anie.201605486 (2016).
  57. Struck, A. W. et al. An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins. Journal of the American Chemical Society 138, 3038-3045, doi:10.1021/jacs.5b10928 (2016).
  58. Surman, A. J. et al. Sizing and Discovery of Nanosized Polyoxometalate Clusters by Mass Spectrometry. Journal of the American Chemical Society 138, 3824-3830, doi:10.1021/jacs.6b00070 (2016).
  59. Swainston, N. et al. libChEBI: an API for accessing the ChEBI database. Journal of cheminformatics 8, 11, doi:10.1186/s13321-016-0123-9 (2016).
  60. Swainston, N. et al. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics : Official journal of the Metabolomic Society 12, 109, doi:10.1007/s11306-016-1051-4 (2016).
  61. Toogood, H. S. et al. Natural Product Biosynthesis in Escherichia coli: Mentha Monoterpenoids. Methods in enzymology 575, 247-270, doi:10.1016/bs.mie.2016.02.020 (2016).
  62. van Oosterwijk, N. et al. Structural Basis of the Substrate Range and Enantioselectivity of Two (S)-Selective omega-Transaminases. Biochemistry 55, 4422-4431, doi:10.1021/acs.biochem.6b00370 (2016).
  63. Weissenborn, M. J. et al. Whole-cell microtiter plate screening assay for terminal hydroxylation of fatty acids by P450s. Chemical communications 52, 6158-6161, doi:10.1039/c6cc01749e (2016).
  64. Westley, C., Xu, Y., Carnell, A. J., Turner, N. J. & Goodacre, R. Label-Free Surface Enhanced Raman Scattering Approach for High-Throughput Screening of Biocatalysts. Analytical chemistry 88, 5898-5903, doi:10.1021/acs.analchem.6b00813 (2016).
  65. Willies, S. C., Galman, J. L., Slabu, I. & Turner, N. J. A stereospecific solid-phase screening assay for colonies expressing both (R)- and (S)-selective omega-aminotransferases. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 374, doi:10.1098/rsta.2015.0084 (2016).
  66. Yan, C. et al. Rapid and sensitive monitoring of biocatalytic reactions using ion mobility mass spectrometry. The Analyst 141, 2351-2355, doi:10.1039/c6an00617e (2016).
  67. Zebec, Z. et al. Towards synthesis of monoterpenes and derivatives using synthetic biology. Current opinion in chemical biology 34, 37-43, doi:10.1016/j.cbpa.2016.06.002 (2016).

Publications from SYNBIOCHEM Year 1

  1. Ahmed ST, Parmeggiani F, Weise NJ, Flitsch SL, Turner NJ. (2015). Chemo-Enzymatic Synthesis of Optically Pure L-and D-Biarylalanines through Biocatalytic Asymmetric Amination and Palladium-Catalysed Arylation. ACS Catalysis, 5: 5410-5413.
  2. Balmer AS, Marris C, Calvert J, Molyneux-Hodgson S, Kearnes M, Bulpin K, Frow E, Schyfter P, Mackenzie A, and Martin P. (2015). Taking Roles in Interdisciplinary Collaborations: Reflections on Working in Post-ELSI Spaces in the UK Synthetic Biology Community.  Science and Technology Studies, 28(3).
  3. Barran P, and Ruotolo B. (2015). Ion Mobility Mass Spectrometry. Analyst, 14(20): 6772-6774.
  4. Barran P, Cooper H, and Eyers C. (2015). Protein Structure. Proteomics, 15(16): p. 2731-2732.
  5. Berezovskaya Y, Porrini M, Nortcliffe C, and Barran PE. (2015). The use of ion mobility mass spectrometry to assist protein design: a case study on zinc finger fold versus coiled coil interactions. Analyst, 140(8): 2847-2856.
  6. Beveridge R, Phillips AS, Denbigh L, Saleem HM, MacPhee CE and Barran PE. (2015). Relating gas phase to solution conformations: Lessons from disordered proteins. Proteomics, 15(16): 2872-2883.
  7. Biarnes-Carrera M, Breitling R, Takano E, Micklefield J. (2015). Butyrolactone signalling circuits for synthetic biology. Curr. Opin. Chem. Biol. 28: 91-98.
  8. Breitling R, Takano E, Gardner TS. (2015). Judging synthetic biology risks. Science, 347: 107.
  9. Breitling R, Takano E. (2015). Synthetic biology advances for pharmaceutical production. Curr. Opin. Biotechnol. 35: 46-51.
  10. Ceroni F, Carbonell P, François JM, Haynes KA. (2015). Editorial – Synthetic Biology: engineering complexity and refactoring cell capabilities. Frontiers in Synthetic Biology. 3: 120.
  11. Chessher A, Breitling R, Takano E. (2015). Bacterial microcompartments: biomaterials for synthetic biology-based compartmentalization strategies. ACS Biomater. Sci. Eng. 1: 463-616.
  12. Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA. (2014). Insights into secondary metabolism from a global analysis of bacterial biosynthetic gene clusters. Cell, 158: 412-21. Highlighted in Nature Chemical Biology, 10: 798-800.
  13. Cole H, Porrini M, Morris R, Smith T, Kalapothakis J, Weidt S, Mackay CL, MacPhee CE and Barran PE. (2015). Early stages of insulin fibrillogenesis examined with ion mobility mass spectrometry and molecular modelling. Analyst, 14(20): 7000-7011.
  14. Creek DJ, Mazet M, Achcar F, Anderson J, Kim DH, Kamour R, Morand P, Millerioux Y, Biran M, Kerkhoven EJ, Chokkathukalam A, Weidt S, Burgess KEV, Breitling R, Watson DG, Bringaud F, Barrett MP. (2015). Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose. PLoS Pathogens, 11(3):e1004689.
  15. Cummings M, Breitling R, Takano E. (2014). Steps towards the synthetic biology of polyketide biosynthesis FEMS Microbiol. Lett. 351: 116-125.
  16. Currin A, Swainston N, Day PJ, Kell DB. (2014). SpeedyGenes: a novel approach for the efficient production of error-corrected, synthetic gene libraries. Protein Eng. Design Sel. 27: 273-280.
  17. Currin A, Swainston N, Day PJ, Kell DB. (2015). Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem. Soc. Rev. 44: 1172-1239.
  18. de Graaff C, Bensch L, Boersma SJ, Cioc RC, van Lint MJ, Janssen E, Turner NJ, Orru RVA and Ruijter E. (2015). Asymmetric Synthesis of Tetracyclic Pyrroloindolines and Constrained Tryptamines by a Switchable Cascade Reaction. Angew. Chem. Int. Ed. 54: 14133-14136.
  19. Dickinson ER, Jurneczko E, Nicholson J, Hupp TR, Zawacka-Pankau J, Selivanova G, Barran PE. (2015). The use of ion mobility mass spectrometry to probe modulation of the structure of p53 and of MDM2 by small molecule inhibitors. Front Mol Biosci. 2: 39.
  20. Dickinson ER, Jurneczko E, Pacholarz KJ, Clarke DJ, Reeves M, Ball KL, Hupp T, Campopiano D, Nikolova PV, Barran PE. (2015). Insights into the Conformations of Three Structurally Diverse Proteins: Cytochrome c, p53, and MDM2, Provided by Variable-Temperature Ion Mobility Mass Spectrometry. Analytical Chemistry. 87(6): 3231-3238.
  21. Diez V, Loznik M, Taylor S, Winn M, Rattray NJ, Podmore H, Micklefield J, Goodacre R, Medema MH, Müller U, Bovenberg R, Janssen DB, & Takano E. (2015). Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block. ACS Synth. Biol. 4(7): 796-807.
  22. Fehér T, Libis V, Carbonell P, Faulon JL. (2015). A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli. Front Bioeng. Biotechnol. 3: 46.
  23. Gromski PS, Xu Y, Kotze KL, Correa E, Ellis DI, Armitage EG, Turner ML. & Goodacre R. (2014). Influence of missing values substitutes on multivariate analysis of metabolomics data. Metabolites, 4: 433-452.
  24. Hardman SJ, Hauck AF, Clark IP, Heyes DJ, Scrutton NS. (2014). Comprehensive analysis of the green-to-blue photoconversion of full-length Cyanobacteriochrome Tlr0924. Biophys. J. 107(9): 2195-203.
  25. Harvey SR, et al., Barran PE. (2015). Electron capture dissociation and drift tube ion mobility-mass spectrometry coupled with site directed mutations provide insights into the conformational diversity of a metamorphic protein. Physical Chemistry Chemical Physics. 17(16): 10538-10550.
  26. Herter S, McKenna SM, Frazer AR, Leimkühler S, Carnell AJ, and Turner NJ. (2015). Galactose Oxidase Variants for the Oxidation of Amino Alcohols in Enzyme Cascade Synthesis. Chem. Cat. Chem. 7: 2313-2317.
  27. Hussain S, Leipold F, Man H, Wells E, France SP, Mulholland KR, Grogan G and Turner NJ. (2015). An (R)-Imine Reductase [(R)-IRED biocatalyst] for the Asymmetric Reduction of Cyclic Imines. Chem. Cat. Chem. 7: 579-583.
  28. Jankevics A, Breitling R. (2015). Chapter 6: Advanced LC–MS applications for identification and quantification of the metabolome. In: Advanced LC-MS applications for metabolomics. 84–93. Future Science Group, London, UK.
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Blogs and Media

  1. Balmer A, Choosing an iGEM Project Weblink
  2. Balmer A. Public Perceptions, Knowledge Deficit and Expertise in Synthetic Biology. Weblink
  3. Gök A, Shapira P. “Tracking Synthetic Biology.” Blog post, Nesta. January 22, 2015. Weblink
  4. Li Y, and Shapira P. “Synthetic biology in China: An update from the field.” Blog – Rising Powers and Interdependent Futures, July 3, 2015. Weblink
  5. Shapira P. “Why synthetic biology has the potential to reshape our lives,” Blog, Policy@Manchester, October 28, 2015. Weblink
  6. Shapira P, and Gök A. “UK Synthetic Biology Centres tasked with addressing public concerns,” Science Political Science, The Guardian, January 30, 2015. Weblink