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Synthetic Biology underpins advances in the bioeconomy

Biological systems - including the simplest cells - exhibit a broad range of functions to thrive in their environment. Research in the Imperial College Centre for Synthetic Biology is focused on the possibility of engineering the underlying biochemical processes to solve many of the challenges facing society, from healthcare to sustainable energy. In particular, we model, analyse, design and build biological and biochemical systems in living cells and/or in cell extracts, both exploring and enhancing the engineering potential of biology. 

As part of our research we develop novel methods to accelerate the celebrated Design-Build-Test-Learn synthetic biology cycle. As such research in the Centre for Synthetic Biology highly multi- and interdisciplinary covering computational modelling and machine learning approaches; automated platform development and genetic circuit engineering ; multi-cellular and multi-organismal interactions, including gene drive and genome engineering; metabolic engineering; in vitro/cell-free synthetic biology; engineered phages and directed evolution; and biomimetics, biomaterials and biological engineering.

Publications

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  • Conference paper
    Sootla A, Oyarzun DA, Angeli D, Stan GBet al., 2015,

    Shaping Pulses to Control Bi-Stable Biological Systems

    , American Control Conference 2015, Publisher: IEEE, Pages: 3138-3143

    In this paper, we present a framework for shaping pulses to control biological systems, and specifically systems in synthetic biology. By shaping we mean computing the magnitude and the length of a pulse, application of which results in reaching the desired control objective. Hence the control signals have only two parameters, which makes these signals amenable to wetlab implementations. We focus on the problem of switching between steady states in a bistable system. We show how to estimate the set of the switching pulses, if the trajectories of the controlled system can be bounded from above and below by the trajectories of monotone systems. We then generalise this result to systems with parametric uncertainty under some mild assumptions on the set of admissible parameters, thus providing some robustness guarantees. We illustrate the results on some example genetic circuits.

  • Journal article
    Kopniczky M, freemont P, Moore S,

    Multilevel regulation and translational switches in synthetic biology

    , IEEE Transactions on Biomedical Circuits and Systems, ISSN: 1940-9990

    In contrast to the versatility of regulatory mechanisms in natural systems, synthetic genetic circuits have been so far predominantly composed of transcriptionally regulated modules. This is about to change as the repertoire of foundational tools for post-transcriptional regulation is quickly expanding. We provide an overview of the different types of translational regulators: protein, small molecule and RNA responsive and we describe the new emerging circuit designs utilizing these tools. There are several advantages of achieving multilevel regulation via translational switches and it is likely that such designs will have the greatest and earliest impact in mammalian synthetic biology for regenerative medicine and gene therapy applications.

  • Journal article
    Kopniczky M, freemont P, moore S, 2015,

    Multilevel regulation and translational switches in synthetic biology

    , IEEE Transactions on Biomedical Circuits and Systems, ISSN: 1940-9990
  • Journal article
    Casini A, Storch M, Baldwin GS, Ellis Tet al., 2015,

    Bricks and blueprints: methods and standards for DNA assembly

    , Nature Reviews Molecular Cell Biology, Vol: 16, Pages: 568-576, ISSN: 1471-0080

    DNA assembly is a key part of constructing gene expression systems and even whole chromosomes. In the past decade, a plethora of powerful new DNA assembly methods — including Gibson Assembly, Golden Gate and ligase cycling reaction (LCR) — have been developed. In this Innovation article, we discuss these methods as well as standards such as the modular cloning (MoClo) system, GoldenBraid, modular overlap-directed assembly with linkers (MODAL) and PaperClip, which have been developed to facilitate a streamlined assembly workflow, to aid the exchange of material between research groups and to create modular reusable DNA parts.

  • Journal article
    Hancock E, Stan G-B, Arpino J, Papachristodoulou Aet al., 2015,

    Simplified mechanistic models of gene regulation for analysis and design

    , Journal of the Royal Society Interface, Vol: 12, ISSN: 1742-5689

    Simplified mechanistic models of gene regulation are fundamental to systems biology and essential for synthetic biology. However, conventional simplified models typically have outputs that are not directly measurable and are based on assumptions that do not often hold under experimental conditions. To resolve these issues, we propose a ‘model reduction’ methodology and simplified kinetic models of total mRNA and total protein concentration, which link measurements, models and biochemical mechanisms. The proposed approach is based on assumptions that hold generally and include typical cases in systems and synthetic biology where conventional models do not hold. We use novel assumptions regarding the ‘speed of reactions’, which are required for the methodology to be consistent with experimental data. We also apply the methodology to propose simplified models of gene regulation in the presence of multiple protein binding sites, providing both biological insights and an illustration of the generality of the methodology. Lastly, we show that modelling total protein concentration allows us to address key questions on gene regulation, such as efficiency, burden, competition and modularity.

  • Journal article
    Ceroni F, Algar R, Stan G-B, Ellis Tet al., 2015,

    Quantifying cellular capacity identifies gene expression designs with reduced burden

    , Nature Methods, Vol: 12, Pages: 415-418, ISSN: 1548-7105

    Heterologous gene expression can be a significant burden forcells. Here we describe an in vivo monitor that tracks changesin the capacity of Escherichia coli in real time and can be usedto assay the burden imposed by synthetic constructs and theirparts. We identify construct designs with reduced burden thatpredictably outperformed less efficient designs, despite havingequivalent output.

  • Journal article
    Storch M, Casini A, Mackrow B, Fleming T, Trewhitt H, Ellis T, Baldwin GSet al., 2015,

    BASIC: a new Biopart Assembly Standard for Idempotent Cloning provides accurate, single-tier DNA assembly for synthetic biology

    , ACS Synthetic Biology

    The ability to quickly and reliably assemble DNA constructs is one of the key enabling technologies for synthetic biology. Here we define a new Biopart Assembly Standard for Idempotent Cloning (BASIC), which exploits the principle of orthogonal linker based DNA assembly to define a new physical standard for DNA parts. Further, we demonstrate a new robust method for assembly, based on type IIs restriction cleavage and ligation of oligonucleotides with single stranded overhangs that determine the assembly order. It allows for efficient, parallel assembly with great accuracy: 4 part assemblies achieved 93% accuracy with single antibiotic selection and 99.7% accuracy with double antibiotic selection, while 7 part assemblies achieved 90% accuracy with double antibiotic selection. The linkers themselves may also be used as composable parts for RBS tuning or the creation of fusion proteins. The standard has one forbidden restriction site and provides for an idempotent, single tier organisation, allowing all parts and composite constructs to be maintained in the same format. This makes the BASIC standard conceptually simple at both the design and experimental levels.

  • Journal article
    Wright O, Delmans M, Stan G-B, Elis Tet al., 2015,

    Gene Guard: A Modular Plasnnid System Designed for Biosafety

    , ACS SYNTHETIC BIOLOGY, Vol: 4, Pages: 307-316, ISSN: 2161-5063
  • Journal article
    Kelwick R, Kopniczky M, Bower I, Chi W, Chin MHW, Fan S, Pilcher J, Strutt J, Webb AJ, Jensen K, Stan G-B, Kitney R, Freemont Pet al., 2015,

    A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli

    , PLOS ONE, Vol: 10, ISSN: 1932-6203
  • Journal article
    Pan W, Yuan Y, Ljung L, Goncalves J, Stan G-Bet al., 2015,

    Identifying Biochemical Reaction Networks From Heterogeneous Datasets

    , 2015 54TH IEEE CONFERENCE ON DECISION AND CONTROL (CDC), Pages: 2525-2530, ISSN: 0743-1546
  • Journal article
    Robinson T, Valluri P, Kennedy G, Sardini A, Dunsby C, Neil MAA, Baldwin GS, French PMW, de Mello AJet al., 2014,

    Analysis of DNA Binding and Nucleotide Flipping Kinetics Using Two-Color Two-Photon Fluorescence Lifetime Imaging Microscopy

    , Analytical Chemistry, Vol: 86, Pages: 10732-10740, ISSN: 0003-2700

    Uracil DNA glycosylase plays a key role in DNA maintenance via base excision repair. Its role is to bind to DNA, locate unwanted uracil, and remove it using a base flipping mechanism. To date, kinetic analysis of this complex process has been achieved using stopped-flow analysis but, due to limitations in instrumental dead-times, discrimination of the “binding” and “base flipping” steps is compromised. Herein we present a novel approach for analyzing base flipping using a microfluidic mixer and two-color two-photon (2c2p) fluorescence lifetime imaging microscopy (FLIM). We demonstrate that 2c2p FLIM can simultaneously monitor binding and base flipping kinetics within the continuous flow microfluidic mixer, with results showing good agreement with computational fluid dynamics simulations.

  • Journal article
    Rivadeneira PS, Moog CH, Stan G-B, Brunet C, Raffi F, Ferré V, Costanza V, Mhawej MJ, Biafore F, Ouattara DA, Ernst D, Fonteneau R, Xia Xet al., 2014,

    Mathematical Modeling of HIV Dynamics After Antiretroviral Therapy Initiation: A Review.

    , Biores Open Access, Vol: 3, Pages: 233-241, ISSN: 2164-7844

    This review shows the potential ground-breaking impact that mathematical tools may have in the analysis and the understanding of the HIV dynamics. In the first part, early diagnosis of immunological failure is inferred from the estimation of certain parameters of a mathematical model of the HIV infection dynamics. This method is supported by clinical research results from an original clinical trial: data just after 1 month following therapy initiation are used to carry out the model identification. The diagnosis is shown to be consistent with results from monitoring of the patients after 6 months. In the second part of this review, prospective research results are given for the design of individual anti-HIV treatments optimizing the recovery of the immune system and minimizing side effects. In this respect, two methods are discussed. The first one combines HIV population dynamics with pharmacokinetics and pharmacodynamics models to generate drug treatments using impulsive control systems. The second one is based on optimal control theory and uses a recently published differential equation to model the side effects produced by highly active antiretroviral therapy therapies. The main advantage of these revisited methods is that the drug treatment is computed directly in amounts of drugs, which is easier to interpret by physicians and patients.

  • Journal article
    Rivadeneira PS, Moog CH, Stan G-B, Costanza V, Brunet C, Raffi F, Ferre V, Mhawej M-J, Biafore F, Ouattara DA, Ernst D, Fonteneau R, Xia Xet al., 2014,

    Mathematical Modeling of HIV Dynamics After Antiretroviral Therapy Initiation: A Clinical Research Study

    , AIDS RESEARCH AND HUMAN RETROVIRUSES, Vol: 30, Pages: 831-834, ISSN: 0889-2229
  • Journal article
    Casini A, Christodoulou G, Freemont PS, Baldwin GS, Ellis T, MacDonald JTet al., 2014,

    R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences

    , ACS SYNTHETIC BIOLOGY, Vol: 3, Pages: 525-528, ISSN: 2161-5063
  • Journal article
    Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Gruenberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan G-B, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HMet al., 2014,

    The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

    , NATURE BIOTECHNOLOGY, Vol: 32, Pages: 545-550, ISSN: 1087-0156
  • Journal article
    Oyarzun DA, Lugagne J-B, Stan G-B, 2014,

    Noise propagation in synthetic gene circuits for metabolic control

    , ACS Synthetic Biology, Vol: 4, Pages: 116-125, ISSN: 2161-5063

    Dynamic control of enzyme expression can be an effective strategy to engineer robust metabolic pathways. It allows a synthetic pathway to self-regulate in response to changes in bioreactor conditions or the metabolic state of the host. The implementation of this regulatory strategy requires gene circuits that couple metabolic signals with the genetic machinery, which is known to be noisy and one of the main sources of cell-to-cell variability. One of the unexplored design aspects of these circuits is the propagation of biochemical noise between enzyme expression and pathway activity. In this article, we quantify the impact of a synthetic feedback circuit on the noise in a metabolic product in order to propose design criteria to reduce cell-to-cell variability. We consider a stochastic model of a catalytic reaction under negative feedback from the product to enzyme expression. On the basis of stochastic simulations and analysis, we show that, depending on the repression strength and promoter strength, transcriptional repression of enzyme expression can amplify or attenuate the noise in the number of product molecules. We obtain analytic estimates for the metabolic noise as a function of the model parameters and show that noise amplification/attenuation is a structural property of the model. We derive an analytic condition on the parameters that lead to attenuation of metabolic noise, suggesting that a higher promoter sensitivity enlarges the parameter design space. In the theoretical case of a switch-like promoter, our analysis reveals that the ability of the circuit to attenuate noise is subject to a trade-off between the repression strength and promoter strength.

  • Journal article
    Pothoulakis G, Ceroni F, Reeve B, Ellis Tet al., 2014,

    The spinach RNA aptamer as a characterization tool for synthetic biology

    , ACS Synthetic Biology, Vol: 3, Pages: 182-187, ISSN: 2161-5063

    Characterization of genetic control elements is essential for the predictable engineering of synthetic biology systems. The current standard for in vivo characterization of control elements is through the use of fluorescent reporter proteins such as green fluorescent protein (GFP). Gene expression, however, involves not only protein production but also the production of mRNA. Here, we present the use of the Spinach aptamer sequence, an RNA mimic of GFP, as a tool to characterize mRNA expression in Escherichia coli. We show how the aptamer can be incorporated into gene expression cassettes and how co-expressing it with a red fluorescent protein (mRFP1) allows, for the first time, simultaneous measurement of mRNA and protein levels from engineered constructs. Using flow cytometry, we apply this tool here to evaluate ribosome binding site sequences and promoters and use it to highlight the differences in the temporal behavior of transcription and translation.

  • Journal article
    Pan W, Sootla A, Stan G-B, 2014,

    Distributed Reconstruction of Nonlinear Networks: An ADMM Approach

    , IFAC PAPERSONLINE, Vol: 47, Pages: 3208-3213, ISSN: 2405-8963
  • Journal article
    Casini A, MacDonald JT, De Jonghe J, Christodoulou G, Freemont PS, Baldwin GS, Ellis Tet al., 2013,

    One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

    , Nucleic Acids Research, Vol: 42, ISSN: 1362-4962

    Overlap-directed DNA assembly methods allowmultiple DNA parts to be assembled together inone reaction. These methods, which rely onsequence homology between the ends of DNAparts, have become widely adopted in syntheticbiology, despite being incompatible with a key principleof engineering: modularity. To answer this, wepresent MODAL: a Modular Overlap-DirectedAssembly with Linkers strategy that brings modularityto overlap-directed methods, allowing assemblyof an initial set of DNA parts into a variety ofarrangements in one-pot reactions. MODAL isaccompanied by a custom software tool thatdesigns overlap linkers to guide assembly,allowing parts to be assembled in any specifiedorder and orientation. The in silico design of syntheticorthogonal overlapping junctions allows formuch greater efficiency in DNA assembly for avariety of different methods compared with usingnon-designed sequence. In tests with three differentassembly technologies, the MODAL strategy givesassembly of both yeast and bacterial plasmids,composed of up to five DNA parts in the kilobaserange with efficiencies of between 75 and 100%.It also seamlessly allows mutagenesis to beperformed on any specified DNA parts duringthe process, allowing the one-step creation of constructlibraries valuable for synthetic biologyapplications.

  • Journal article
    O'Clery N, Yuan Y, Stan G-B, Barahona Met al., 2013,

    Observability and coarse graining of consensus dynamics through the external equitable partition

    , PHYSICAL REVIEW E, Vol: 88, ISSN: 1539-3755

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