1
|
Beal J, Selvarajah V, Chambonnier G, Haddock T, Vignoni A, Vidal G, Roehner N. Standardized Representation of Parts and Assembly for Build Planning. ACS Synth Biol 2023; 12:3646-3655. [PMID: 37956262 DOI: 10.1021/acssynbio.3c00418] [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: 11/15/2023]
Abstract
The design and construction of genetic systems, in silico, in vitro, or in vivo, often involve the handling of various pieces of DNA that exist in different forms across an assembly process: as a standalone "part" sequence, as an insert into a carrier vector, as a digested fragment, etc. Communication about these different forms of a part and their relationships is often confusing, however, because of a lack of standardized terms. Here, we present a systematic terminology and an associated set of practices for representing genetic parts at various stages of design, synthesis, and assembly. These practices are intended to represent any of the wide array of approaches based on embedding parts in carrier vectors, such as BioBricks or Type IIS methods (e.g., GoldenGate, MoClo, GoldenBraid, and PhytoBricks), and have been successfully used as a basis for cross-institutional coordination and software tooling in the iGEM Engineering Committee.
Collapse
Affiliation(s)
- Jacob Beal
- Intelligent Software & Systems, Raytheon BBN Technologies, 10 Moulton Street, Cambridge, Massachusetts 02138, United States
| | - Vinoo Selvarajah
- iGEM Foundation, 45 Prospect Street, Cambridge, Massachusetts 02139, United States
| | - Gaël Chambonnier
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Traci Haddock
- Asimov, Inc., 201 Brookline Avenue, Suite 1201, Boston, Massachusetts 02215, United States
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, Institut d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camino de Vera s/n, Valencia 46022, Spain
| | - Gonzalo Vidal
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Nicholas Roehner
- Intelligent Software & Systems, Raytheon BBN Technologies, 10 Moulton Street, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
2
|
Arboleda-García A, Alarcon-Ruiz I, Boada-Acosta L, Boada Y, Vignoni A, Jantus-Lewintre E. Advancements in synthetic biology-based bacterial cancer therapy: A modular design approach. Crit Rev Oncol Hematol 2023; 190:104088. [PMID: 37541537 DOI: 10.1016/j.critrevonc.2023.104088] [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] [Received: 06/10/2023] [Revised: 07/18/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023] Open
Abstract
Synthetic biology aims to program living bacteria cells with artificial genetic circuits for user-defined functions, transforming them into powerful tools with numerous applications in various fields, including oncology. Cancer treatments have serious side effects on patients due to the systemic action of the drugs involved. To address this, new systems that provide localized antitumoral action while minimizing damage to healthy tissues are required. Bacteria, often considered pathogenic agents, have been used as cancer treatments since the early 20th century. Advances in genetic engineering, synthetic biology, microbiology, and oncology have improved bacterial therapies, making them safer and more effective. Here we propose six modules for a successful synthetic biology-based bacterial cancer therapy, the modules include Payload, Release, Tumor-targeting, Biocontainment, Memory, and Genetic Circuit Stability Module. These will ensure antitumor activity, safety for the environment and patient, prevent bacterial colonization, maintain cell stability, and prevent loss or defunctionalization of the genetic circuit.
Collapse
Affiliation(s)
- Andrés Arboleda-García
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain
| | - Ivan Alarcon-Ruiz
- Gene Regulation in Cardiovascular Remodeling and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lissette Boada-Acosta
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Molecular Oncology Laboratory, Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain
| | - Yadira Boada
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain
| | - Alejandro Vignoni
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain.
| | - Eloisa Jantus-Lewintre
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Molecular Oncology Laboratory, Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Department of Biotechnology, Universitat Politècnica de València, Valencia, Spain
| |
Collapse
|
3
|
González-Cebrián A, Borràs-Ferrís J, Boada Y, Vignoni A, Ferrer A, Picó J. PLATERO: A calibration protocol for plate reader green fluorescence measurements. Front Bioeng Biotechnol 2023; 11:1104445. [PMID: 36741754 PMCID: PMC9895789 DOI: 10.3389/fbioe.2023.1104445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
One of the most common sources of information in Synthetic Biology is the data coming from plate reader fluorescence measurements. These experiments provide a measure of the light emitted by a certain fluorescent molecule, such as the Green Fluorescent Protein (GFP). However, these measurements are generally expressed in arbitrary units and are affected by the measurement device gain. This limits the range of measurements in a single experiment and hampers the comparison of results among experiments. In this work, we describe PLATERO, a calibration protocol to express fluorescence measures in concentration units of a reference fluorophore. The protocol removes the gain effect of the measurement device on the acquired data. In addition, the fluorescence intensity values are transformed into units of concentration using a Fluorescein calibration model. Both steps are expressed in a single mathematical expression that returns normalized, gain-independent, and comparable data, even if the acquisition was done at different device gain levels. Most important, the PLATERO embeds a Linearity and Bias Analysis that provides an assessment of the uncertainty of the model estimations, and a Reproducibility and Repeatability analysis that evaluates the sources of variability originating from the measurements and the equipment. All the functions used to build the model, exploit it with new data, and perform the uncertainty and variability assessment are available in an open access repository.
Collapse
Affiliation(s)
- Alba González-Cebrián
- Multivariate Statistical Engineering Group, Department of Applied Statistics and O.R. and Quality, Universitat Politècnica de València, València, Spain
| | - Joan Borràs-Ferrís
- Multivariate Statistical Engineering Group, Department of Applied Statistics and O.R. and Quality, Universitat Politècnica de València, València, Spain
| | - Yadira Boada
- Synthetic Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, València, Spain
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, València, Spain,*Correspondence: Alejandro Vignoni,
| | - Alberto Ferrer
- Multivariate Statistical Engineering Group, Department of Applied Statistics and O.R. and Quality, Universitat Politècnica de València, València, Spain
| | - Jesús Picó
- Synthetic Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, València, Spain
| |
Collapse
|
4
|
Aldulijan I, Beal J, Billerbeck S, Bouffard J, Chambonnier G, Ntelkis N, Guerreiro I, Holub M, Ross P, Selvarajah V, Sprent N, Vidal G, Vignoni A. Functional Synthetic Biology. Synth Biol (Oxf) 2023; 8:ysad006. [PMID: 37073284 PMCID: PMC10105873 DOI: 10.1093/synbio/ysad006] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.
Collapse
Affiliation(s)
- Ibrahim Aldulijan
- Systems Engineering, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, 07030, NJ, USA
| | | | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jeff Bouffard
- Centre for Applied Synthetic Biology, and Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, H4B 1R6, Québec, Canada
| | - Gaël Chambonnier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
| | - Nikolaos Ntelkis
- Specialized Metabolism research group, Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
| | - Isaac Guerreiro
- iGEM Foundation, 45 Prospect Street, Cambridge, 02139, MA, USA
| | - Martin Holub
- Delft University of Technology, Van der Maasweg 9, 2629 HZ, The Netherlands
| | - Paul Ross
- BioStrat Marketing, 9965 Harbour Lake Circle, Boynton Beach, FL, 33437, USA
| | | | - Noah Sprent
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, SW7 2AZ, UK
| | - Gonzalo Vidal
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing, Newcastle University, Devonshire Building, Devonshire Terrace, NE1 7RU, Newcastle Upon Tyne, UK
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, Instituto de Automatica e Informatica Industrial, Universitat Politecnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain
| |
Collapse
|
5
|
Beal J, Telmer CA, Vignoni A, Boada Y, Baldwin GS, Hallett L, Lee T, Selvarajah V, Billerbeck S, Brown B, Cai GN, Cai L, Eisenstein E, Kiga D, Ross D, Alperovich N, Sprent N, Thompson J, Young EM, Endy D, Haddock-Angelli T. Multicolor Plate Reader Fluorescence Calibration. Synth Biol (Oxf) 2022; 7:ysac010. [PMID: 35949424 PMCID: PMC9357555 DOI: 10.1093/synbio/ysac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/15/2021] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Plate readers are commonly used to measure cell growth and fluorescence, yet the utility and reproducibility of plate reader data is limited by the fact that it is typically reported in arbitrary or relative units. We have previously established a robust serial dilution protocol for calibration of plate reader measurements of absorbance to estimated bacterial cell count and for green fluorescence from proteins expressed in bacterial cells to molecules of equivalent fluorescein. We now extend these protocols to calibration of red fluorescence to the sulforhodamine-101 fluorescent dye and blue fluorescence to Cascade Blue. Evaluating calibration efficacy via an interlaboratory study, we find that these calibrants do indeed provide comparable precision to the prior calibrants and that they enable effective cross-laboratory comparison of measurements of red and blue fluorescence from proteins expressed in bacterial cells.
Collapse
Affiliation(s)
- Jacob Beal
- Intelligent Software and Systems, Raytheon BBN Technologies , 10 Moulton Street, Cambridge 02138, MA, USA
| | - Cheryl A Telmer
- Department of Biological Sciences, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, PA, USA
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Group, Instituto de Automatica e Informatica Industrial, Universitat Politecnica de Valencia , Camino de Vera s/n, Valencia 46022, Spain
| | - Yadira Boada
- Synthetic Biology and Biosystems Control Group, Instituto de Automatica e Informatica Industrial, Universitat Politecnica de Valencia , Camino de Vera s/n, Valencia 46022, Spain
| | - Geoff S Baldwin
- Department of Life Sciences, Imperial College London , South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Liam Hallett
- Department of Life Sciences, Imperial College London , South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Taeyang Lee
- Department of Life Sciences, Imperial College London , South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | | | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Bradley Brown
- School of Engineering, Newcastle University , Devonshire Building, Devonshire Terrace, NE1 7RU Newcastle Upon Tyne, UK
| | - Guo-nan Cai
- School of Life Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Liang Cai
- School of Life Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Edward Eisenstein
- Fischell Department of Bioengineering, University of Maryland Institute of Bioscience and Biotechnology Research, , 9600 Gudelsky Drive, Rockville 20850, MD, USA
| | - Daisuke Kiga
- School of Advanced Science and Engineering, Waseda University , 2-2 Wakamatsu Cho, Totsukamachi, Shinjuku City 169-8050, Tokyo, Japan
| | - David Ross
- Material Measurement Laboratory, National Institute of Standards and Technology , 100 Bureau Dr., Gaithersburg 20899, MD, USA
| | - Nina Alperovich
- Material Measurement Laboratory, National Institute of Standards and Technology , 100 Bureau Dr., Gaithersburg 20899, MD, USA
| | - Noah Sprent
- Department of Chemical Engineering, Imperial College London , South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Jaclyn Thompson
- Chemical Engineering, Worcester Polytechnic Institute , 100 Institute Road, Worcester 01609-2280, MA, USA
| | - Eric M Young
- Chemical Engineering, Worcester Polytechnic Institute , 100 Institute Road, Worcester 01609-2280, MA, USA
| | - Drew Endy
- Bioengineering, Stanford University , 443 Via Ortega, Stanford 94305, CA, USA
| | | |
Collapse
|
6
|
Boada Y, Santos-Navarro FN, Picó J, Vignoni A. Modeling and Optimization of a Molecular Biocontroller for the Regulation of Complex Metabolic Pathways. Front Mol Biosci 2022; 9:801032. [PMID: 35425808 PMCID: PMC9001882 DOI: 10.3389/fmolb.2022.801032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
Achieving optimal production in microbial cell factories, robustness against changing intracellular and environmental perturbations requires the dynamic feedback regulation of the pathway of interest. Here, we consider a merging metabolic pathway motif, which appears in a wide range of metabolic engineering applications, including the production of phenylpropanoids among others. We present an approach to use a realistic model that accounts for in vivo implementation and then propose a methodology based on multiobjective optimization for the optimal tuning of the gene circuit parts composing the biomolecular controller and biosensor devices for a dynamic regulation strategy. We show how this approach can deal with the trade-offs between the performance of the regulated pathway, robustness to perturbations, and stability of the feedback loop. Using realistic models, our results suggest that the strategies for fine-tuning the trade-offs among performance, robustness, and stability in dynamic pathway regulation are complex. It is not always possible to infer them by simple inspection. This renders the use of the multiobjective optimization methodology valuable and necessary.
Collapse
|
7
|
Boada Y, Picó J, Vignoni A. Multi-Objective Optimization Tuning Framework for Kinetic Parameter Selection and Estimation. Methods Mol Biol 2022; 2385:65-89. [PMID: 34888716 DOI: 10.1007/978-1-0716-1767-0_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Semi-mechanistic kinetic (i.e., dynamic) models based on first principles are particularly relevant in biology, as they can explain and predict functional behavior that arises from varying concentrations of the cellular components over time. Here, we describe a computational tuning framework to facilitate both the selection of kinetic parameters for these models and its estimation from experimental data. On the one hand, the tuning framework uses multi-objective optimization to generate a model-based set of guidelines for the selection of the kinetic parameters. These parameter values are the required ones to provide a biological system with desired behavior, while fulfilling the design criteria encoded in the optimization problem itself. On the other hand, this framework can also be used to estimate the parameter values of biological systems from experimental data, once the optimization objectives had been defined appropriately. The methodology gives accurate identification results, as it provides clear orientation on the effect of the parameter values over the system's behavior even under different experimental scenarios. It is particularly useful for easily combining time-course-averaged data and steady-state distribution data. This protocol also addresses aspects related to the appropriate description of the kinetic models and the settings of the software tools. Therefore, it supplies for hands-on testing to evaluate the validity of the underlying technical assumptions of the biological kinetic models.
Collapse
Affiliation(s)
- Yadira Boada
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Valencia, Spain
- Centro Universitario EDEM, Escuela de Empresarios, La Marina de València, Valencia, Spain
| | - Jesús Picó
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Valencia, Spain
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Valencia, Spain.
| |
Collapse
|
8
|
Santos-Navarro FN, Vignoni A, Boada Y, Picó J. RBS and Promoter Strengths Determine the Cell-Growth-Dependent Protein Mass Fractions and Their Optimal Synthesis Rates. ACS Synth Biol 2021; 10:3290-3303. [PMID: 34767708 PMCID: PMC8689641 DOI: 10.1021/acssynbio.1c00131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Models of gene expression
considering host–circuit interactions
are relevant for understanding both the strategies and associated
trade-offs that cell endogenous genes have evolved and for the efficient
design of heterologous protein expression systems and synthetic genetic
circuits. Here, we consider a small-size model of gene expression
dynamics in bacterial cells accounting for host–circuit interactions
due to limited cellular resources. We define the cellular resources
recruitment strength as a key functional coefficient that explains
the distribution of resources among the host and the genes of interest
and the relationship between the usage of resources and cell growth.
This functional coefficient explicitly takes into account lab-accessible
gene expression characteristics, such as promoter and ribosome binding
site (RBS) strengths, capturing their interplay with the growth-dependent
flux of available free cell resources. Despite its simplicity, the
model captures the differential role of promoter and RBS strengths
in the distribution of protein mass fractions as a function of growth
rate and the optimal protein synthesis rate with remarkable fit to
the experimental data from the literature for Escherichia
coli. This allows us to explain why endogenous genes
have evolved different strategies in the expression space and also
makes the model suitable for model-based design of exogenous synthetic
gene expression systems with desired characteristics.
Collapse
Affiliation(s)
- Fernando N. Santos-Navarro
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Yadira Boada
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Jesús Picó
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| |
Collapse
|
9
|
Boada Y, Vignoni A, Picó J, Carbonell P. Extended Metabolic Biosensor Design for Dynamic Pathway Regulation of Cell Factories. iScience 2020; 23:101305. [PMID: 32629420 PMCID: PMC7334618 DOI: 10.1016/j.isci.2020.101305] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/05/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Transcription factor-based biosensors naturally occur in metabolic pathways to maintain cell growth and to provide a robust response to environmental fluctuations. Extended metabolic biosensors, i.e., the cascading of a bio-conversion pathway and a transcription factor (TF) responsive to the downstream effector metabolite, provide sensing capabilities beyond natural effectors for implementing context-aware synthetic genetic circuits and bio-observers. However, the engineering of such multi-step circuits is challenged by stability and robustness issues. In order to streamline the design of TF-based biosensors in metabolic pathways, here we investigate the response of a genetic circuit combining a TF-based extended metabolic biosensor with an antithetic integral circuit, a feedback controller that achieves robustness against environmental fluctuations. The dynamic response of an extended biosensor-based regulated flavonoid pathway is analyzed in order to address the issues of biosensor tuning of the regulated pathway under industrial biomanufacturing operating constraints.
Collapse
Affiliation(s)
- Yadira Boada
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain; Centro Universitario EDEM, Escuela de Empresarios, Muelle de la Aduana s/n, La Marina de València, 46024 Valencia, Spain
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Jesús Picó
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Pablo Carbonell
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain.
| |
Collapse
|
10
|
Boada Y, Vignoni A, Alarcon-Ruiz I, Andreu-Vilarroig C, Monfort-Llorens R, Requena A, Picó J. Characterization of Gene Circuit Parts Based on Multiobjective Optimization by Using Standard Calibrated Measurements. Chembiochem 2019; 20:2653-2665. [PMID: 31269324 DOI: 10.1002/cbic.201900272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/12/2019] [Indexed: 01/08/2023]
Abstract
Standardization and characterization of biological parts is necessary for the further development of bottom-up synthetic biology. Herein, an easy-to-use methodology that embodies both a calibration procedure and a multiobjective optimization approach is proposed to characterize biological parts. The calibration procedure generates values for specific fluorescence per cell expressed as standard units of molecules of equivalent fluorescein per particle. The use of absolute standard units enhances the characterization of model parameters for biological parts by bringing measurements and estimations results from different sources into a common domain, so they can be integrated and compared faithfully. The multiobjective optimization procedure exploits these concepts by estimating the values of the model parameters, which represent biological parts of interest, while considering a varied range of experimental and circuit contexts. Thus, multiobjective optimization provides a robust characterization of them. The proposed calibration and characterization methodology can be used as a guide for good practices in dry and wet laboratories; thus allowing not only portability between models, but is also useful for generating libraries of tested and well-characterized biological parts.
Collapse
Affiliation(s)
- Yadira Boada
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain.,Centro Universitario EDEM, Escuela de Empresarios, La Marina de València, Muelle de la Aduana S/N, 46024, Valencia, Spain
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain
| | - Iván Alarcon-Ruiz
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain.,Escuela Tècnica Superior de Ingeniería Agronómica y del Medio Natural, Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain
| | - Carlos Andreu-Vilarroig
- Escuela Técnica Superior de Ingeniería Industrial, Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain
| | - Roger Monfort-Llorens
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain.,Escuela Técnica Superior de Ingeniería Industrial, Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain
| | - Adrián Requena
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain.,Escuela Tècnica Superior de Ingeniería Agronómica y del Medio Natural, Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain
| | - Jesús Picó
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Camino de Vera S/N, 46022, Valencia, Spain
| |
Collapse
|
11
|
Vignoni A, Boada Y, Boada Acosta L, Andreu-Vilarroig C, Alarcón I, Requena A, Picó J. Fluorescence calibration and color equivalence for quantitative synthetic biology. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.ifacol.2019.12.247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
12
|
Boada Y, Vignoni A, Picó J. Engineered Control of Genetic Variability Reveals Interplay among Quorum Sensing, Feedback Regulation, and Biochemical Noise. ACS Synth Biol 2017; 6:1903-1912. [PMID: 28581725 DOI: 10.1021/acssynbio.7b00087] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Stochastic fluctuations in gene expression trigger both beneficial and harmful consequences for cell behavior. Therefore, achieving a desired mean protein expression level while minimizing noise is of interest in many applications, including robust protein production systems in industrial biotechnology. Here, we consider a synthetic gene circuit combining intracellular negative feedback and cell-to-cell communication based on quorum sensing. Accounting for both intrinsic and extrinsic noise, stochastic simulations allow us to analyze the capability of the circuit to reduce noise strength as a function of its parameters. We obtain mean expression levels and noise strengths for all species under different scenarios, showing good agreement with system-wide available experimental data of protein abundance and noise in Escherichia coli. Our in silico experiments, validated by preliminary in vivo results, reveal significant noise attenuation in gene expression through the interplay between quorum sensing and negative feedback and highlight the differential role that they play in regard to intrinsic and extrinsic noise.
Collapse
Affiliation(s)
- Yadira Boada
- Institut
d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Alejandro Vignoni
- Center
for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhaurstr. 108, 01307 Dresden, Germany
| | - Jesús Picó
- Institut
d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| |
Collapse
|
13
|
Boada Y, Reynoso-Meza G, Picó J, Vignoni A. Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case. BMC Syst Biol 2016; 10:27. [PMID: 26968941 PMCID: PMC4788947 DOI: 10.1186/s12918-016-0269-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 10/13/2015] [Accepted: 02/16/2016] [Indexed: 12/22/2022]
Abstract
Background Model based design plays a fundamental role in synthetic biology. Exploiting modularity, i.e. using biological parts and interconnecting them to build new and more complex biological circuits is one of the key issues. In this context, mathematical models have been used to generate predictions of the behavior of the designed device. Designers not only want the ability to predict the circuit behavior once all its components have been determined, but also to help on the design and selection of its biological parts, i.e. to provide guidelines for the experimental implementation. This is tantamount to obtaining proper values of the model parameters, for the circuit behavior results from the interplay between model structure and parameters tuning. However, determining crisp values for parameters of the involved parts is not a realistic approach. Uncertainty is ubiquitous to biology, and the characterization of biological parts is not exempt from it. Moreover, the desired dynamical behavior for the designed circuit usually results from a trade-off among several goals to be optimized. Results We propose the use of a multi-objective optimization tuning framework to get a model-based set of guidelines for the selection of the kinetic parameters required to build a biological device with desired behavior. The design criteria are encoded in the formulation of the objectives and optimization problem itself. As a result, on the one hand the designer obtains qualitative regions/intervals of values of the circuit parameters giving rise to the predefined circuit behavior; on the other hand, he obtains useful information for its guidance in the implementation process. These parameters are chosen so that they can effectively be tuned at the wet-lab, i.e. they are effective biological tuning knobs. To show the proposed approach, the methodology is applied to the design of a well known biological circuit: a genetic incoherent feed-forward circuit showing adaptive behavior. Conclusion The proposed multi-objective optimization design framework is able to provide effective guidelines to tune biological parameters so as to achieve a desired circuit behavior. Moreover, it is easy to analyze the impact of the context on the synthetic device to be designed. That is, one can analyze how the presence of a downstream load influences the performance of the designed circuit, and take it into account. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0269-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yadira Boada
- Institut d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, Valencia, Spain
| | - Gilberto Reynoso-Meza
- Industrial and Systems Engineering Graduate Program (PPGEPS), Pontificial Catholic University of Parana (PUCPR), Curitiba, Brazil
| | - Jesús Picó
- Institut d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, Valencia, Spain
| | - Alejandro Vignoni
- Institut d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, Valencia, Spain. .,Present Address: Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
14
|
Abstract
OBJECTIVE The aim of this study was to assess whether a single noninvasive technique, ultrasonography, is able in vivo: 1) to evaluate the time-related patterns of gallbladder bile storage and emptying, and 2) to quantitate the amount of bile flux through the gallbladder (GB). METHODS Healthy volunteers were submitted to the simultaneous assessment of gallbladder volume variations by frequent serial ultrasonographic (US) measurements and of hepatic bile flow through the GB by quantitative cholescintigraphy (QC) during continuous i.v. infusion of 99 mTc-HIDA. An ad hoc mathematical analysis of US GB volume measurements was used to estimate the amount of bile flux through the GB. The QC-derived measurements of the flux of hepatic bile through the GB was used to substantiate the US-derived estimates. RESULTS The curves expressing the time-related GB handling of hepatic bile obtained independently from US and QC measurements were statistically equivalent, and both techniques showed that the patterns and the amount of hepatic bile handled by the gallbladder after meal ingestion is remarkably different during three successive phases. After meals, hepatic bile was mainly 1) stored in the GB in the first phase; 2) emptied from the GB in a second phase; and 3) stored in the GB in the third phase. The ultrasonographic analysis estimated that 1) 23.8+/-12.5 ml (0.44+/-0.11 ml/min), 5.1+/-3.9 ml (0.15+/-0.10 ml/min), and 33.2+/-10.5 ml (0.53+/-0.16 ml/min) of hepatic bile entered into the GB during the three successive postprandial phases, and 2) the entire amount of bile flowing bidirectionally through the cystic duct, during the observation period (132.6+/-23.3 ml) was about five-fold greater than that estimated by the usually employed variables. CONCLUSION The proposed mathematical analysis of frequent ultrasonographic measurements of the GB volumes enables one to estimate noninvasively the flux of bile through the gallbladder in humans.
Collapse
Affiliation(s)
- N Pallotta
- Cattedra di Gastroenterologia I, Clinica Medica II, DPT Medicina Nucleare, Università degli Studi di Roma La Sapienza, Italy
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Corazziari E, Cicala M, Habib FI, Scopinaro F, Fiocca F, Pallotta N, Viscardi A, Vignoni A, Torsoli A. Hepatoduodenal bile transit in cholecystectomized subjects. Relationship with sphincter of Oddi function and diagnostic value. Dig Dis Sci 1994; 39:1985-93. [PMID: 8082508 DOI: 10.1007/bf02088136] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The hepatic hilum-duodenum transit time (HHDT) was evaluated in cholecystectomized subjects to assess its relationship with the motor function of the sphincter of Oddi (SO) and its diagnostic accuracy in the detection of SO dysfunction. The study was performed in asymptomatic controls and symptomatic patients with SO dysfunction before and after sphincterotomy. HHDT showed a direct correlation with manometric SO maximal basal pressure (r = 0.77; P < 0.001) but not with SO phasic activity. In sphincterotomized subjects HHDT did not differ from that of the asymptomatic subjects, and HHDT, which was prolonged before sphincterotomy, normalized after sphincterotomy. HHDT had a 100% specificity and an 83% sensitivity in diagnosing SO dysfunction when compared to SO manometry. In conclusion, the cholescintigraphic HHDT is mainly related to the SO maximal basal pressure, presenting an elevated specificity and a satisfactory sensitivity in the diagnosis of SO dysfunction in cholecystectomized subjects.
Collapse
Affiliation(s)
- E Corazziari
- Cattedra di Gastroenterologia I, Università La Sapienza, Rome, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Scopinaro F, Cicala M, Vignoni A, Corazziari E. [Effect of spasmodil complex on bile flow. Double-blind controlled study]. Minerva Dietol Gastroenterol 1988; 34:39-41. [PMID: 3386863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
17
|
Lundstam S, Sengupta CH, Timbal Y, Vignoni A. Diclofenac sodium in renal colic. Practitioner 1984; 228:704-705. [PMID: 6473273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
|
18
|
Vignoni A, Fierro A, Moreschini G, Cau M, Agostino A, Daniele E, Foti G, Grossi E. Diclofenac sodium in ureteral colic: a double-blind comparison trial with placebo. J Int Med Res 1983; 11:303-7. [PMID: 6357890 DOI: 10.1177/030006058301100510] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A randomized prospective double blind study of the analgesic effect of 75 mg intramuscular diclofenac sodium (Voltaren), a potent prostaglandin synthetase inhibitor, versus placebo (saline solution) was carried out in 131 consecutive patients with acute ureteral colic. Diclofenac provided complete relief of pain 25 minutes after the injection in 59% of the cases, while placebo provided relief in 29% (p less than 0.01). Forty patients in the placebo group and seventeen patients in the diclofenac group needed an open injection of 75 mg diclofenac intramuscularly after 25 minutes due to persistent pain. Fifty-four of the fifty-seven patients treated with an open injection of diclofenac achieved complete relief of pain after 30 minutes. There were no side-effects of the treatment.
Collapse
|
19
|
De Rosis F, Centi Colella A, Paleani Vettori PG, Vignoni A. [Aspects of the use of a computer in scintiscanning diagnosis]. Minerva Med 1970; 61:5477-81. [PMID: 4923170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
20
|
Bompiani C, Giacco G, Scarpa G, Tomiselli A, Vignoni A. [Experience with the shielded whole body counter of the Instituto di Radiologia of the University of Rome]. Minerva Med 1969; 60:4111-22. [PMID: 5351824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|