111 results found
Boo A, Ellis T, Stan G, Host-Aware Synthetic Biology, Current Opinion in Systems Biology
Kylilis N, Riangrungroj P, Lai H-E, et al., 2019, Whole-Cell Biosensor with Tunable Limit of Detection Enables Low-Cost Agglutination Assays for Medical Diagnostic Applications., ACS Sens, Vol: 4, Pages: 370-378
Whole-cell biosensors can form the basis of affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing, but to date the detection of analytes such as proteins that cannot easily diffuse across the cell membrane has been challenging. Here we developed a novel biosensing platform based on cell agglutination using an E. coli whole-cell biosensor surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design to detect a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations using straightforward design rules and a mathematical model. Finally, we re-engineer our whole-cell biosensor for the detection of a medically relevant biomarker by the display of two different nanobodies against human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for field-testing in the developing world, emergency or disaster relief sites, as well as routine medical testing and personalized medicine.
Kuntz J, Thomas P, Stan G-B, et al., 2019, The exit time finite state projection scheme: bounding exit distributions and occupation measures of continuous-time Markov chains
We introduce the exit time finite state projection (ETFSP) scheme, atruncation-based method that yields approximations to the exit distribution andoccupation measure associated with the time of exit from a domain (i.e., thetime of first passage to the complement of the domain) of time-homogeneouscontinuous-time Markov chains. We prove that: (i) the computed approximationsbound the measures from below; (ii) the total variation distances between theapproximations and the measures decrease monotonically as states are added tothe truncation; and (iii) the scheme converges, in the sense that, as thetruncation tends to the entire state space, the total variation distances tendto zero. Furthermore, we give a computable bound on the total variationdistance between the exit distribution and its approximation, and we delineatethe cases in which the bound is sharp. We also revisit the related finite stateprojection scheme and give a comprehensive account of its theoreticalproperties. We demonstrate the use of the ETFSP scheme by applying it to twobiological examples: the computation of the first passage time associated withthe expression of a gene, and the fixation times of competing species subjectto demographic noise.
Kylilis N, Riangrungroj P, Lai H-E, et al., 2019, A low-cost biological agglutination assay for medical diagnostic applications, ACS Sensors, ISSN: 2379-3694
Affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing are key in addressing challenges in the diagnosis of medical conditions and for improving global health in general. Ideally, POC diagnostic tests should be highly selective for the biomarker, user-friendly, have a flexible design architecture and a low cost of production. Here we developed a novel agglutination assay based on whole E. coli cells surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design as a new diagnostic platform by the detection of a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations supported using straight-forward design rules and a mathematical model. Finally, we re-engineer E. coli cells for the detection of a medically relevant biomarker by the display of two different antibodies against the human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for both field-testing in the developing world, emergency or disaster relief sites as well as routine medical testing and personalized medicine.
Kuntz J, Thomas P, Stan G-B, et al., 2018, Approximation schemes for countably-infinite linear programs with moment bounds
We introduce approximation schemes for a type ofcountably-infinite-dimensional linear programs (CILPs) whose feasible pointsare unsigned measures and whose optimal values are bounds on the averages ofthese measures. In particular, we explain how to approximate the program'soptimal value, optimal points, and minimal point (should one exist) by solvingfinite-dimensional linear programs. We show that the approximations converge tothe CILP's optimal value, optimal points, and minimal point as the size of thefinite-dimensional program approaches that of the CILP. Inbuilt in our schemesis a degree of error control: they yield lower and upper bounds on the optimalvalues and we give a simple bound on the approximation error of the minimalpoint. To motivate our work, we discuss applications of our schemes taken fromthe Markov chain literature: stationary distributions, occupation measures, andexit distributions.
Kylilis N, Tuza ZA, Stan G-B, et al., 2018, Tools for engineering coordinated system behaviour in synthetic microbial consortia, NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723
Pan W, Yuan Y, Ljung L, et al., 2018, Identification of Nonlinear State-Space Systems From Heterogeneous Datasets, IEEE TRANSACTIONS ON CONTROL OF NETWORK SYSTEMS, Vol: 5, Pages: 737-747, ISSN: 2325-5870
Tomazou M, Barahona M, Polizzi KM, et al., 2018, Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation, CELL SYSTEMS, Vol: 6, Pages: 508-+, ISSN: 2405-4712
Borkowski O, Bricio C, Murgiano M, et al., 2018, Cell-free prediction of protein expression costs for growing cells, NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723
Tomazou M, Stan G-B, 2018, Portable gene expression guaranteed, NATURE BIOTECHNOLOGY, Vol: 36, Pages: 313-314, ISSN: 1087-0156
Jonas FRH, Royle KE, Aw R, et al., 2018, Investigating the consequences of asymmetric endoplasmic reticulum inheritance in Saccharomyces cerevisiae under stress using a combination of single cell measurements and mathematical modelling, SYNTHETIC AND SYSTEMS BIOTECHNOLOGY, Vol: 3, Pages: 64-75, ISSN: 1389-0166
Cox RS, Madsen C, McLaughlin J, et al., 2018, Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0, JOURNAL OF INTEGRATIVE BIOINFORMATICS, Vol: 15, ISSN: 1613-4516
Tuza ZA, Stan G-B, 2018, Characterization of Biologically Relevant Network Structures form Time-series Data, Publisher: IEEE
O'Clery N, Yuan Y, Stan G-B, et al., 2018, Global Network Prediction from Local Node Dynamics., CoRR, Vol: abs/1809.00409
Kylilis N, Stan G-B, Polizzi K, 2017, Tools for engineering coordinated system behaviour in synthetic microbial consortia, Publisher: bioRxiv
Advancing synthetic biology to the multicellular level requires the development of multiple orthogonal cell-to-cell communication channels to propagate information with minimal signal interference. The development of quorum sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on reducing signal leakage between systems of cognate AHL/transcription factor pairs. However, the use of non-cognate signals as a design feature has received limited attention so far. Here, we demonstrate the largest library of AHL-receiver devices constructed to date with all cognate and non-cognate chemical signal interactions quantified and we develop a software tool that allows automated selection of orthogonal chemical channels. We use this approach to identify up to four orthogonal channels in silico and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels will facilitate the design of synthetic microbial consortia for novel applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation, and spatial organisation.
Hancock EJ, Ang J, Papachristodoulou A, et al., 2017, The Interplay between Feedback and Buffering in Cellular Homeostasis, CELL SYSTEMS, Vol: 5, Pages: 498-+, ISSN: 2405-4712
Cells use feedback regulation to ensure robust growth despite fluctuating demands on resources and different environmental conditions. Yet the expression of foreign proteins from engineered constructs is an unnatural burden on resources that cells are not adapted for. Here we combined multiplex RNAseq with an in vivo assay to reveal the major transcriptional changes in two E. coli strains when a set of inducible synthetic constructs are expressed. We identified that native promoters related to the heat-shock response activate expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a CRISPR/dCas9-based feedback regulation system that automatically adjusts synthetic construct expression in response to burden. Cells equipped with this general-use controller maintain capacity for native gene expression to ensure robust growth and as such outperform unregulated cells at protein yields in batch production. This engineered feedback is the first example of a universal, burden-based biomolecular control system and is modular, tuneable and portable.
Borkowski O, Bricio Garberi C, Murgiano M, et al., 2017, Cell-free prediction of protein expression costs for growing cells
Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any gene is a major challenge, as multiple processes and factors determine translation efficiency. Here, to enable prediction of the cost of gene expression in bacteria, we describe a standard cell-free lysate assay that determines the relationship between in vivo and cell-free measurements and γ, a relative measure of the resource consumption when a given protein is expressed. When combined with a computational model of translation, this enables prediction of the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.
Mısırlı G, Madsen C, de Murieta IS, et al., 2017, Constructing synthetic biology workflows in the cloud, Engineering Biology, Vol: 1, Pages: 61-65
Walker BJ, Stan G-BV, Polizzi KM, 2017, Intracellular delivery of biologic therapeutics by bacterial secretion systems, EXPERT REVIEWS IN MOLECULAR MEDICINE, Vol: 19, ISSN: 1462-3994
Kuntz J, Thomas P, Stan G-B, et al., 2017, Rigorous bounds on the stationary distributions of the chemical master equation via mathematical programming
The stochastic dynamics of biochemical networks is usually modelled with thechemical master equation (CME). The stationary distributions of CMEs are seldomsolvable analytically, and numerical methods typically produce estimates withuncontrolled errors. To fill this gap, we introduce mathematical programmingapproaches that yield approximations of these distributions with computableerror bounds which enable the verification of their accuracy. First, we usesemidefinite programming to compute increasingly tighter upper and lower boundson the moments of the stationary distributions for networks with rationalpropensities. Second, we use these moment bounds to formulate linear programsthat yield convergent upper and lower bounds on the stationary distributionsthemselves. The bounds obtained provide a computational test for the uniquenessof these distributions. In the unique case, the bounds form an approximation ofthe stationary distribution with a computable bound on its error. In thenon-unique case, our approach yields converging approximations of the ergodicdistributions. We illustrate our methodology through two biochemical networksthat exhibit bifurcations to multimodal behaviour: Schl\"ogl's model and atoggle switch model.
Foo M, Sawlekar R, Kim J, et al., 2017, Biomolecular implementation of nonlinear system theoretic operators, European Control Conference (ECC), Publisher: IEEE, Pages: 1824-1831
Synthesis of biomolecular circuits for controlling molecular-scale processes is an important goal of synthetic biology with a wide range of in vitro and in vivo applications, including biomass maximization, nanoscale drug delivery, and many others. In this paper, we present new results on how abstract chemical reactions can be used to implement commonly used system theoretic operators such as the polynomial functions, rational functions and Hill-type nonlinearity. We first describe how idealised versions of multi-molecular reactions, catalysis, annihilation, and degradation can be combined to implement these operators. We then show how such chemical reactions can be implemented using enzyme-free, entropy-driven DNA reactions. Our results are illustrated through three applications: (1) implementation of a Stan-Sepulchre oscillator, (2) the computation of the ratio of two signals, and (3) a PI+antiwindup controller for regulating the output of a static nonlinear plant.
Tomazou M, Stan GB, 2017, Engineering autoregulation in enzymatic degradation based systems for robust dynamics and improved host capacity, Pages: 161-162
Borkowski O, Ceroni F, Stan G-B, et al., 2016, Overloaded and stressed: whole-cell considerations for bacterial synthetic biology, CURRENT OPINION IN MICROBIOLOGY, Vol: 33, Pages: 123-130, ISSN: 1369-5274
Pan W, Menolascina F, Stan G-B, 2016, Online Model Selection for Synthetic Gene Networks, 55th IEEE Conference on Decision and Control (CDC), Publisher: IEEE, Pages: 776-782, ISSN: 0743-1546
Kuntz J, Ottobre M, Stan G-B, et al., 2016, BOUNDING STATIONARY AVERAGES OF POLYNOMIAL DIFFUSIONS VIA SEMIDEFINITE PROGRAMMING, SIAM JOURNAL ON SCIENTIFIC COMPUTING, Vol: 38, Pages: A3891-A3920, ISSN: 1064-8275
Sootla A, Oyarzun D, Angeli D, et al., 2016, Shaping pulses to control bistable systems: Analysis, computation and counterexamples, AUTOMATICA, Vol: 63, Pages: 254-264, ISSN: 0005-1098
Pan W, Yuan Y, Goncalves J, et al., 2016, A Sparse Bayesian Approach to the Identification of Nonlinear State-Space Systems, IEEE TRANSACTIONS ON AUTOMATIC CONTROL, Vol: 61, Pages: 182-187, ISSN: 0018-9286
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