1
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Grob A, Enrico Bena C, Di Blasi R, Pessina D, Sood M, Yunyue Z, Bosia C, Isalan M, Ceroni F. Mammalian cell growth characterisation by a non-invasive plate reader assay. Nat Commun 2024; 15:57. [PMID: 38167870 PMCID: PMC10761699 DOI: 10.1038/s41467-023-44396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughput non-invasive method for tracking mammalian cell growth and performance based on plate reader measurements. We show the method to be suitable for both suspension and adhesion cell lines, and we demonstrate it can be adopted when cells are grown under different environmental conditions. We establish that the method is suitable to inform on effective drug treatments to be used depending on the cell line considered, and that it can support characterisation of engineered mammalian cells over time. This work provides the scientific community with an innovative approach to mammalian cell screening, also contributing to the current efforts towards high throughput and automated mammalian cell engineering.
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Affiliation(s)
- Alice Grob
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Chiara Enrico Bena
- Italian Institute for Genomic Medicine, Torino, Italy
- Université Paris-Saclay (INRAE), AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Daniele Pessina
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Matthew Sood
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Zhou Yunyue
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Carla Bosia
- Italian Institute for Genomic Medicine, Torino, Italy.
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London, UK.
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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2
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Redwood-Sawyerr C, Aw R, Di Blasi R, Moya-Ramírez I, Kontoravdi C, Ceroni F, Polizzi K. High-Throughput Spectroscopic Analysis of mRNA Capping Level. Methods Mol Biol 2024; 2774:269-278. [PMID: 38441771 DOI: 10.1007/978-1-0716-3718-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Eukaryotic mRNAs are characterized by terminal 5' cap structures and 3' polyadenylation sites, which are essential for posttranscriptional processing, translation initiation, and stability. Here, we describe a novel biosensor method designed to detect the presence of both cap structures and polyadenylation sites on mRNA molecules. This novel biosensor is sensitive to mRNA degradation and can quantitatively determine capping levels of mRNA molecules within a mixture of capped and uncapped mRNA molecules. The biosensor displays a constant dynamic range between 254 nt and 6507 nt with reproducible sensitivity to increases in capping level of at least 20% and a limit of detection of 2.4 pmol of mRNA. Overall, the biosensor can provide key information about mRNA quality before mammalian cell transfection.
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Affiliation(s)
- Chileab Redwood-Sawyerr
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rochelle Aw
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Roberto Di Blasi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Ignacio Moya-Ramírez
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Departamento de Ingeniería Química, Universidad de Granada, Granada, Spain
| | - Cleo Kontoravdi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Francesca Ceroni
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Karen Polizzi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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3
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Di Blasi R, Pisani M, Tedeschi F, Marbiah MM, Polizzi K, Furini S, Siciliano V, Ceroni F. Resource-aware construct design in mammalian cells. Nat Commun 2023; 14:3576. [PMID: 37328476 PMCID: PMC10275982 DOI: 10.1038/s41467-023-39252-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Resource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here we report the quantification of the resource load imposed by different mammalian genetic components and identify construct designs with increased performance and reduced resource footprint. We use these to generate improved synthetic circuits and optimise the co-expression of transfected cassettes, shedding light on how this can be useful for bioproduction and biotherapeutic applications. This work provides the scientific community with a framework to consider resource demand when designing mammalian constructs to achieve robust and optimised gene expression.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Mara Pisani
- Synthetic and Systems Biology lab for Biomedicine, Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
- Open University affiliated centre, Milton Keynes, UK
| | - Fabiana Tedeschi
- Synthetic and Systems Biology lab for Biomedicine, Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
- University of Naples Federico II, Naples, Italy
| | - Masue M Marbiah
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Simone Furini
- Department of Electrical, Electronic and Information Engineering ″Guglielmo Marconi", University of Bologna, Cesena, Italy
| | - Velia Siciliano
- Synthetic and Systems Biology lab for Biomedicine, Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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4
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5
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Celano T, Argiento LU, Ceroni F, Casapulla C. In-Plane Behaviour of Masonry Walls: Numerical Analysis and Design Formulations. Materials (Basel) 2021; 14:ma14195780. [PMID: 34640177 PMCID: PMC8510409 DOI: 10.3390/ma14195780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022]
Abstract
This paper presents the results of several numerical analyses aimed at investigating the in-plane resistance of masonry walls by means of two modelling approaches: a finite element model (FEM) and a discrete macro-element model (DMEM). Non-linear analyses are developed, in both cases, by changing the mechanical properties of masonry (compressive and tensile strengths, fracture energy in compression and tension, shear strength) and the value of the vertical compression stress applied on the walls. The reliability of both numerical models is firstly checked by means of comparisons with experimental tests available in the literature. The analyses show that the numerical results provided by the two modelling approaches are in good agreement, in terms of both failure loads and modes, while some differences are observed in their load-displacement curves, especially in the non-linear field. Finally, the numerical in-plane resistances are compared with the theoretical formulations provided by the Italian building code for both flexural and shear failure modes and an amendment for the shape factor 'b' introduced in the code formulation for squat walls is proposed.
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Affiliation(s)
- Thomas Celano
- Department of Engineering, University of Naples Parthenope, Centro Direzionale Is. C4, 80143 Napoli, Italy;
| | - Luca Umberto Argiento
- Department of Structure for Engineering and Architecture, University of Naples Federico II, Via Forno Vecchio, 80134 Napoli, Italy; (L.U.A.); (C.C.)
| | - Francesca Ceroni
- Department of Engineering, University of Naples Parthenope, Centro Direzionale Is. C4, 80143 Napoli, Italy;
- Correspondence:
| | - Claudia Casapulla
- Department of Structure for Engineering and Architecture, University of Naples Federico II, Via Forno Vecchio, 80134 Napoli, Italy; (L.U.A.); (C.C.)
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6
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Celano T, Argiento LU, Ceroni F, Casapulla C. Literature Review of the In-Plane Behavior of Masonry Walls: Theoretical vs. Experimental Results. Materials (Basel) 2021; 14:3063. [PMID: 34205221 PMCID: PMC8200034 DOI: 10.3390/ma14113063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
In-plane strength of masonry walls is affected by the resistant mechanisms activated in the walls, i.e., related to flexural or shear behavior. The latter one can occur in the walls according to different failure modes depending on both mortar and unit strengths and on the type of assembling, i.e., 'regular' or 'irregular' texture. In this paper, a critical review of the existing design formulations for the in-plane strength of masonry walls is firstly presented, with important information on the achievable failure modes depending on the geometrical and mechanical features of the masonry fabric. Then, experimental tests are collected from the literature and a comparison between theoretical and experimental results is carried out. The presented analyses are aimed to highlight the differences between the existing formulations and to identify the most suitable ones.
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Affiliation(s)
- Thomas Celano
- Department of Engineering, University of Naples Parthenope, Centro Direzionale Is. C4, 80143 Napoli, Italy;
| | - Luca Umberto Argiento
- Department of Structure for Engineering and Architecture, University of Naples Federico II, Via Forno Vecchio, 80134 Napoli, Italy; (L.U.A.); (C.C.)
| | - Francesca Ceroni
- Department of Engineering, University of Naples Parthenope, Centro Direzionale Is. C4, 80143 Napoli, Italy;
| | - Claudia Casapulla
- Department of Structure for Engineering and Architecture, University of Naples Federico II, Via Forno Vecchio, 80134 Napoli, Italy; (L.U.A.); (C.C.)
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7
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Di Blasi R, Marbiah MM, Siciliano V, Polizzi K, Ceroni F. A call for caution in analysing mammalian co-transfection experiments and implications of resource competition in data misinterpretation. Nat Commun 2021; 12:2545. [PMID: 33953169 PMCID: PMC8099865 DOI: 10.1038/s41467-021-22795-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 02/08/2023] Open
Abstract
Transient transfections are routinely used in basic and synthetic biology studies to unravel pathway regulation and to probe and characterise circuit designs. As each experiment has a component of intrinsic variability, reporter gene expression is usually normalized with co-delivered genes that act as transfection controls. Recent reports in mammalian cells highlight how resource competition for gene expression leads to biases in data interpretation, with a direct impact on co-transfection experiments. Here we define the connection between resource competition and transient transfection experiments and discuss possible alternatives. Our aim is to raise awareness within the community and stimulate discussion to include such considerations in future experimental designs, for the development of better transfection controls.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Masue M Marbiah
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Velia Siciliano
- Synthetic and Systems Biology lab for Biomedicine, Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples (ITA), Italy
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK. .,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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8
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Enrico Bena C, Del Giudice M, Grob A, Gueudré T, Miotto M, Gialama D, Osella M, Turco E, Ceroni F, De Martino A, Bosia C. Initial cell density encodes proliferative potential in cancer cell populations. Sci Rep 2021; 11:6101. [PMID: 33731745 PMCID: PMC7969775 DOI: 10.1038/s41598-021-85406-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/26/2021] [Indexed: 01/18/2023] Open
Abstract
Individual cells exhibit specific proliferative responses to changes in microenvironmental conditions. Whether such potential is constrained by the cell density throughout the growth process is however unclear. Here, we identify a theoretical framework that captures how the information encoded in the initial density of cancer cell populations impacts their growth profile. By following the growth of hundreds of populations of cancer cells, we found that the time they need to adapt to the environment decreases as the initial cell density increases. Moreover, the population growth rate shows a maximum at intermediate initial densities. With the support of a mathematical model, we show that the observed interdependence of adaptation time and growth rate is significantly at odds both with standard logistic growth models and with the Monod-like function that governs the dependence of the growth rate on nutrient levels. Our results (i) uncover and quantify a previously unnoticed heterogeneity in the growth dynamics of cancer cell populations; (ii) unveil how population growth may be affected by single-cell adaptation times; (iii) contribute to our understanding of the clinically-observed dependence of the primary and metastatic tumor take rates on the initial density of implanted cancer cells.
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Affiliation(s)
- Chiara Enrico Bena
- CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Sorbonne Université, 75005, Paris, France.,IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060, Candiolo, Italy
| | - Marco Del Giudice
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060, Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Str. Prov.le 142, km 3.95, 10060, Candiolo, Italy
| | - Alice Grob
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, London, UK
| | - Thomas Gueudré
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060, Candiolo, Italy
| | - Mattia Miotto
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Dimitra Gialama
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Matteo Osella
- Physics Department and INFN, University of Turin, Via P. Giuria 1, 10125, Turin, Italy
| | - Emilia Turco
- Molecular Biotechnology Center, University of Turin, Via Nizza 52, 10126, Turin, Italy
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, London, UK
| | - Andrea De Martino
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060, Candiolo, Italy.,Soft and Living Matter Lab, CNR-NANOTEC, Rome, Italy
| | - Carla Bosia
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060, Candiolo, Italy. .,Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy.
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9
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Di Blasi R, Blyuss O, Timms JF, Conole D, Ceroni F, Whitwell HJ. Non-Histone Protein Methylation: Biological Significance and Bioengineering Potential. ACS Chem Biol 2021; 16:238-250. [PMID: 33411495 DOI: 10.1021/acschembio.0c00771] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in regulating important cellular processes and the activity of many proteins, including transcription factors, enzymes, and structural complexes. The extensive and dynamic role that protein methylation plays within the cell also highlights its potential for bioengineering applications. Indeed, while synthetic histone protein methylation has been extensively used to engineer gene expression, engineering of non-histone protein methylation has not been fully explored yet. Here, we report the latest findings, highlighting how non-histone protein methylation is fundamental for certain cellular functions and is implicated in disease, and review recent efforts in the engineering of protein methylation.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, U.K
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - John F Timms
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, U.K
| | - Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, U.K
| | - Francesca Ceroni
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Harry J Whitwell
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, U.K
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Sir Alexander Fleming Building, Imperial College London, Hammersmith Campus, London, SW7 2AZ, U.K
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10
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Ciampa E, Ceroni F, Pecce MR. Finite Element Modeling of Bond Behavior of FRP and Steel Plates. Materials (Basel) 2021; 14:ma14040757. [PMID: 33562779 PMCID: PMC7915636 DOI: 10.3390/ma14040757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 11/29/2022]
Abstract
Strengthening systems for existing reinforced concrete (RC) structures are increasingly needed due to several problems such as degradation of materials over the time, underdesign, serviceability or seismic upgrading, or new code requirements. In the last decades, strengthening by fibers composite materials applied with various techniques (FRP, FRCM, NSM) were largely investigated and theoretical formulations have been introduced in national and international design guidelines. Although they are an excellent strengthening solution, steel plates may represent still a valid traditional alternative, due to low costs, ductile stress-strain behavior, simple and fast mounting with possibility of reusing the material. Guidelines for a correct design are still lack and, therefore, detailed models and design formulas are needed. In this paper, the bond behavior at the plate-concrete interface, which plays a key role for the effectiveness of the strengthening system, is analyzed by means of 3D finite element models calibrated on experimental results available in literature. Parametric analyses were carried out by changing some meaningful parameters.
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Affiliation(s)
- Elena Ciampa
- Department of Engineering, University of Sannio, Piazza Roma, 82100 Benevento, Italy;
- Correspondence:
| | - Francesca Ceroni
- Department of Engineering, University of Napoli Parthenope, Centro Direzionale, 80143 Naples, Italy;
| | - Maria Rosaria Pecce
- Department of Engineering, University of Sannio, Piazza Roma, 82100 Benevento, Italy;
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11
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Di Blasi R, Zouein A, Ellis T, Ceroni F. Genetic Toolkits to Design and Build Mammalian Synthetic Systems. Trends Biotechnol 2021; 39:1004-1018. [PMID: 33526300 DOI: 10.1016/j.tibtech.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022]
Abstract
Construction of DNA-encoded programs is central to synthetic biology and the chosen method often determines the time required to design and build constructs for testing. Here, we describe and summarise key features of the available toolkits for DNA construction for mammalian cells. We compare the different cloning strategies based on their complexity and the time needed to generate constructs of different sizes, and we reflect on why Golden Gate toolkits now dominate due to their modular design. We look forward to future advances, including accessory packs for cloning toolkits that can facilitate editing, orthogonality, advanced regulation, and integration into synthetic chromosome construction.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Annalise Zouein
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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12
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Boo A, Ceroni F. Engineering Sensors for Gene Expression Burden. Methods Mol Biol 2021; 2229:313-330. [PMID: 33405229 DOI: 10.1007/978-1-0716-1032-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RNA-seq enables the analysis of gene expression profiles across different conditions and organisms. Gene expression burden slows down growth, which results in poor predictability of gene constructs and product yields. Here, we describe how we applied RNA-seq to study the transcriptional profiles of Escherichia coli when burden is elicited during heterologous gene expression. We then present how we selected early responsive promoters from our RNA-seq results to design sensors for gene expression burden. Finally, we describe how we used one of these sensors to develop a burden-driven feedback regulator to improve cellular fitness in engineered E. coli.
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Affiliation(s)
- Alice Boo
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Francesca Ceroni
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Department of Chemical Engineering, Imperial College London, London, UK.
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13
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Evans SW, Beal J, Berger K, Bleijs DA, Cagnetti A, Ceroni F, Epstein GL, Garcia-Reyero N, Gillum DR, Harkess G, Hillson NJ, Hogervorst PAM, Jordan JL, Lacroix G, Moritz R, ÓhÉigeartaigh SS, Palmer MJ, van Passel MWJ. Embrace experimentation in biosecurity governance. Science 2020; 368:138-140. [PMID: 32273459 DOI: 10.1126/science.aba2932] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Sam Weiss Evans
- Program on Science, Technology, and Society, Harvard University, Cambridge, MA, USA. .,Program on Emerging Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Centre for the Study of Existential Risk, University of Cambridge, Cambridge, UK
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, USA
| | | | - Diederik A Bleijs
- Netherlands Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Alessia Cagnetti
- Polo d'Innovazione Genomica Genetica e Biologia (PoloGGB), Terni, Italy
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, London, UK
| | - Gerald L Epstein
- Center for the Study of Weapons of Mass Destruction, National Defense University, Washington, DC, USA
| | | | | | | | - Nathan J Hillson
- Joint Genome Institute, U.S. Department of Energy, Berkeley, CA, USA
| | - Petra A M Hogervorst
- Netherlands Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | | | - Geneviève Lacroix
- Centre for Biosecurity, Public Health Agency of Canada, Ottawa, Canada
| | | | - Seán S ÓhÉigeartaigh
- Centre for the Study of Existential Risk, University of Cambridge, Cambridge, UK
| | - Megan J Palmer
- Center for International Security and Cooperation, Stanford University, Stanford, CA, USA
| | - Mark W J van Passel
- Netherlands Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
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14
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Ledesma-Amaro R, Nikel PI, Ceroni F. Editorial: Synthetic Biology-Guided Metabolic Engineering. Front Bioeng Biotechnol 2020; 8:221. [PMID: 32266245 PMCID: PMC7099041 DOI: 10.3389/fbioe.2020.00221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/04/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College London, London, United Kingdom.,Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Francesca Ceroni
- Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.,Department of Chemical Engineering, Imperial College London, London, United Kingdom
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15
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Abstract
Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts the equilibrium of resource allocation in the host, leading to slow growth and reduced biosynthesis. Here we built integrated host-circuit models to quantify growth defects caused by synthetic gene circuits. Simulations reveal a complex relation between circuit output and cellular capacity for gene expression. For weak induction of heterologous genes, protein output can be increased at the expense of growth defects. Yet for stronger induction, cellular capacity reaches a tipping point, beyond which both gene expression and growth rate drop sharply. Extensive simulations across various growth conditions and large regions of the design space suggest that the critical capacity is a result of ribosomal scarcity. We studied the impact of growth defects on various gene circuits and transcriptional logic gates, which highlights the extent to which cellular burden can limit, shape, and even break down circuit function. Our approach offers a comprehensive framework to assess the impact of host-circuit interactions in silico, with wide-ranging implications for the design and optimization of bacterial gene circuits.
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Affiliation(s)
| | - Andrea Y. Weiße
- Department of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Diego A. Oyarzún
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
- SynthSys − Centre for Synthetic & Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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16
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Enrico Bena C, Grob A, Isalan M, Bosia C, Ceroni F. Commentary: Synthetic Addiction Extends the Productive Life Time of Engineered Escherichia coli Populations. Front Bioeng Biotechnol 2018; 6:77. [PMID: 29946542 PMCID: PMC6005837 DOI: 10.3389/fbioe.2018.00077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/24/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Chiara Enrico Bena
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.,Italian Institute for Genomic Medicine, Torino, Italy
| | - Alice Grob
- Department of Life Sciences, Imperial College London, London, United Kingdom.,Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, United Kingdom.,Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Carla Bosia
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.,Italian Institute for Genomic Medicine, Torino, Italy
| | - Francesca Ceroni
- Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.,Department of Chemical Engineering, Imperial College London, London, United Kingdom
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17
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Ceroni F, Boo A, Furini S, Gorochowski TE, Borkowski O, Ladak YN, Awan AR, Gilbert C, Stan GB, Ellis T. Burden-driven feedback control of gene expression. Nat Methods 2018; 15:387-393. [PMID: 29578536 DOI: 10.1038/nmeth.4635] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 02/01/2018] [Indexed: 12/21/2022]
Abstract
Cells use feedback regulation to ensure robust growth despite fluctuating demands for resources and differing environmental conditions. However, the expression of foreign proteins from engineered constructs is an unnatural burden that cells are not adapted for. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed. We observed that native promoters related to the heat-shock response activated expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a dCas9-based feedback-regulation system that automatically adjusts the expression of a synthetic construct in response to burden. Cells equipped with this general-use controller maintained their capacity for native gene expression to ensure robust growth and thus outperformed unregulated cells in terms of protein yield in batch production. This engineered feedback is to our knowledge the first example of a universal, burden-based biomolecular control system and is modular, tunable and portable.
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Affiliation(s)
- Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Alice Boo
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Olivier Borkowski
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Yaseen N Ladak
- ITMAT Data Science Group, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Ali R Awan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Charlie Gilbert
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
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18
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Holt R, Ceroni F, Bax DA, Broadgate S, Diaz DG, Santos C, Gerrelli D, Ragge NK. New variant and expression studies provide further insight into the genotype-phenotype correlation in YAP1-related developmental eye disorders. Sci Rep 2017; 7:7975. [PMID: 28801591 PMCID: PMC5554234 DOI: 10.1038/s41598-017-08397-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/07/2017] [Indexed: 01/06/2023] Open
Abstract
YAP1, which encodes the Yes-associated protein 1, is part of the Hippo pathway involved in development, growth, repair and homeostasis. Nonsense YAP1 mutations have been shown to co-segregate with autosomal dominantly inherited coloboma. Therefore, we screened YAP1 for variants in a cohort of 258 undiagnosed UK patients with developmental eye disorders, including anophthalmia, microphthalmia and coloboma. We identified a novel 1 bp deletion in YAP1 in a boy with bilateral microphthalmia and bilateral chorioretinal coloboma. This variant is located in the coding region of all nine YAP1 spliceforms, and results in a frameshift and subsequent premature termination codon in each. The variant is predicted to result in the loss of part of the transactivation domain of YAP1, and sequencing of cDNA from the patient shows it does not result in nonsense mediated decay. To investigate the role of YAP1 in human eye development, we performed in situ hybridisation utilising human embryonic tissue, and observed expression in the developing eye, neural tube, brain and kidney. These findings help confirm the role of YAP1 and the Hippo developmental pathway in human eye development and its associated anomalies and demonstrate its expression during development in affected organ systems.
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Affiliation(s)
- R Holt
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - F Ceroni
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - D A Bax
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - S Broadgate
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - D Gold Diaz
- Institute of Child Health, University College London, London, UK
| | - C Santos
- Institute of Child Health, University College London, London, UK
| | - D Gerrelli
- Institute of Child Health, University College London, London, UK
| | - N K Ragge
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK. .,Clinical Genetics Unit, West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.
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19
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Borkowski O, Ceroni F, Stan GB, Ellis T. Overloaded and stressed: whole-cell considerations for bacterial synthetic biology. Curr Opin Microbiol 2016; 33:123-130. [PMID: 27494248 DOI: 10.1016/j.mib.2016.07.009] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 12/27/2022]
Abstract
The predictability and robustness of engineered bacteria depend on the many interactions between synthetic constructs and their host cells. Expression from synthetic constructs is an unnatural load for the host that typically reduces growth, triggers stresses and leads to decrease in performance or failure of engineered cells. Work in systems and synthetic biology has now begun to address this through new tools, methods and strategies that characterise and exploit host-construct interactions in bacteria. Focusing on work in E. coli, we review here a selection of the recent developments in this area, highlighting the emerging issues and describing the new solutions that are now making the synthetic biology community consider the cell just as much as they consider the construct.
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Affiliation(s)
- Olivier Borkowski
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Francesca Ceroni
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Guy-Bart Stan
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK.
| | - Tom Ellis
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK.
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20
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21
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Ceroni F, Carbonell P, François JM, Haynes KA. Editorial - Synthetic Biology: Engineering Complexity and Refactoring Cell Capabilities. Front Bioeng Biotechnol 2015; 3:120. [PMID: 26347864 PMCID: PMC4543857 DOI: 10.3389/fbioe.2015.00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/06/2015] [Indexed: 01/04/2023] Open
Affiliation(s)
- Francesca Ceroni
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Bioengineering, Imperial College London , London , UK
| | - Pablo Carbonell
- SYNBIOCHEM, Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , Manchester , UK
| | - Jean-Marie François
- LISBP, INSA, INP, UPS, Université de Toulouse , Toulouse , France ; MR792, Ingénierie des Systèmes Biologiques et des Bioprocédés, INRA , Toulouse , France ; UMR 5504, CNRS , Toulouse , France
| | - Karmella A Haynes
- Ira A. Fulton School of Biological and Health Systems Engineering, Arizona State University , Tempe, AZ , USA
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22
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Ceroni F, Algar R, Stan GB, Ellis T. Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat Methods 2015; 12:415-8. [PMID: 25849635 DOI: 10.1038/nmeth.3339] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 02/20/2015] [Indexed: 12/29/2022]
Abstract
Heterologous gene expression can be a significant burden for cells. Here we describe an in vivo monitor that tracks changes in the capacity of Escherichia coli in real time and can be used to assay the burden imposed by synthetic constructs and their parts. We identify construct designs with reduced burden that predictably outperformed less efficient designs, despite having equivalent output.
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Affiliation(s)
- Francesca Ceroni
- 1] Centre for Synthetic Biology and Innovation, Imperial College London, London, UK. [2] Department of Bioengineering, Imperial College London, London, UK
| | - Rhys Algar
- 1] Centre for Synthetic Biology and Innovation, Imperial College London, London, UK. [2] Department of Bioengineering, Imperial College London, London, UK
| | - Guy-Bart Stan
- 1] Centre for Synthetic Biology and Innovation, Imperial College London, London, UK. [2] Department of Bioengineering, Imperial College London, London, UK
| | - Tom Ellis
- 1] Centre for Synthetic Biology and Innovation, Imperial College London, London, UK. [2] Department of Bioengineering, Imperial College London, London, UK
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23
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Abstract
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.
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Affiliation(s)
- Georgios Pothoulakis
- Centre for Synthetic
Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
- Department
of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
| | - Francesca Ceroni
- Centre for Synthetic
Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
- Department
of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
| | - Benjamin Reeve
- Centre for Synthetic
Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
- Department
of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
| | - Tom Ellis
- Centre for Synthetic
Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
- Department
of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Rd, London SW7 2AZ, United Kingdom
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24
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Ceroni F, Furini S, Stefan A, Hochkoeppler A, Giordano E. A synthetic post-transcriptional controller to explore the modular design of gene circuits. ACS Synth Biol 2012; 1:163-71. [PMID: 23651154 DOI: 10.1021/sb200021s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly from modular parts is an efficient approach for creating new devices in Synthetic Biology. In the "bottom-up" designing strategy, modular parts are characterized in advance, and then mathematical modeling is used to predict the outcome of the final device. A prerequisite for bottom-up design is that the biological parts behave in a modular way when assembled together. We designed a new synthetic device for post-transcriptional regulation of gene expression and tested if the outcome of the device could be described from the features of its components. Modular parts showed unpredictable behavior when assembled in different complex circuits. This prevented a modular description of the device that was possible only under specific conditions. Our findings shed doubts into the feasibility of a pure bottom-up approach in synthetic biology, highlighting the urgency for new strategies for the rational design of synthetic devices.
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Affiliation(s)
- Francesca Ceroni
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
| | - Simone Furini
- Department of Medical Surgery and Bioengineering, University of Siena, I-53100 Siena, Italy
| | - Alessandra Stefan
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Alejandro Hochkoeppler
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Emanuele Giordano
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
- Department of Biochemistry “G. Moruzzi”, University of Bologna, I-40126 Bologna, Italy
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25
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Abstract
RNA interference is a natural gene expression silencing system that appears throughout the tree of life. As the list of cellular processes linked to RNAi grows, so does the demand for tools to accurately measure RNAi dynamics in living cells. We engineered a synthetic RNAi sensor that converts this negative regulatory signal into a positive output in living mammalian cells, thereby allowing increased sensitivity and activation. Furthermore, the circuit's modular design allows potentially any microRNA of interest to be detected. We demonstrated that the circuit responds to an artificial microRNA and becomes activated when the RNAi target is replaced by a natural microRNA target (miR-34) in U2OS osteosarcoma cells. Our studies extend the application of rationally designed synthetic switches to RNAi, providing a sensitive way to visualize the dynamics of RNAi activity rather than just the presence of miRNA molecules.
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Affiliation(s)
- Karmella A. Haynes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United
States
| | - Francesca Ceroni
- Laboratory of Cellular
and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
| | - Daniel Flicker
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115,
United States
| | - Andrew Younger
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115,
United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115,
United States
- The Wyss
Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts 02115, United
States
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26
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Ceroni F, Furini S, Giordano E, Cavalcanti S. Rational design of modular circuits for gene transcription: A test of the bottom-up approach. J Biol Eng 2010; 4:14. [PMID: 21070658 PMCID: PMC2993646 DOI: 10.1186/1754-1611-4-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 11/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR) and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. RESULTS We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. CONCLUSIONS This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.
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Affiliation(s)
- Francesca Ceroni
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy.,Department of Electronics, Computer Science and Systems, University of Bologna, I-47521 Cesena, Italy
| | - Simone Furini
- Department of Medical Surgery and Bioengineering, University of Siena, I-53100 Siena, Italy
| | - Emanuele Giordano
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy.,Department of Biochemistry "G. Moruzzi", University of Bologna, I-40126 Bologna, Italy
| | - Silvio Cavalcanti
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy.,Department of Electronics, Computer Science and Systems, University of Bologna, I-47521 Cesena, Italy
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