1
|
Nadra AD. Navigating tensions between public and commercial interests: a case study of open source biosensors for detecting water contaminants in Argentina. Front Med (Lausanne) 2024; 11:1268950. [PMID: 38283621 PMCID: PMC10810021 DOI: 10.3389/fmed.2024.1268950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Affiliation(s)
- Alejandro D. Nadra
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biología Traslacional, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
2
|
Wang L, Zhao J, Xiong X, Li L, Zhu T, Pei H. Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection. Chempluschem 2023; 88:e202300083. [PMID: 37005227 DOI: 10.1002/cplu.202300083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/04/2023]
Abstract
Fold-change detection is widespread in sensory systems of various organisms. Dynamic DNA nanotechnology provides an important toolbox for reproducing structures and responses of cellular circuits. In this work, we construct an enzyme-free nucleic acid circuit based on the incoherent feed-forward loop using toehold-mediated DNA strand displacement reactions and explore its dynamic behaviors. The mathematical model based on ordinary differential equations is used to evaluate the parameter regime required for fold-change detection. After selecting appropriate parameters, the constructed synthetic circuit exhibits approximate fold-change detection for multiple rounds of inputs with different initial concentrations. This work is anticipated to shed new light on the design of DNA dynamic circuits in the enzyme-free environment.
Collapse
Affiliation(s)
- Likun Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Jiayan Zhao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Xiewei Xiong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Tong Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241 (P. R., China
| |
Collapse
|
3
|
Gomez-Hinostroza ES, Gurdo N, Alvan Vargas MVG, Nikel PI, Guazzaroni ME, Guaman LP, Castillo Cornejo DJ, Platero R, Barba-Ostria C. Current landscape and future directions of synthetic biology in South America. Front Bioeng Biotechnol 2023; 11:1069628. [PMID: 36845183 PMCID: PMC9950111 DOI: 10.3389/fbioe.2023.1069628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Synthetic biology (SynBio) is a rapidly advancing multidisciplinary field in which South American countries such as Chile, Argentina, and Brazil have made notable contributions and have established leadership positions in the region. In recent years, efforts have strengthened SynBio in the rest of the countries, and although progress is significant, growth has not matched that of the aforementioned countries. Initiatives such as iGEM and TECNOx have introduced students and researchers from various countries to the foundations of SynBio. Several factors have hindered progress in the field, including scarce funding from both public and private sources for synthetic biology projects, an underdeveloped biotech industry, and a lack of policies to promote bio-innovation. However, open science initiatives such as the DIY movement and OSHW have helped to alleviate some of these challenges. Similarly, the abundance of natural resources and biodiversity make South America an attractive location to invest in and develop SynBio projects.
Collapse
Affiliation(s)
- E. Sebastian Gomez-Hinostroza
- Laboratorio de Investigación en Citogenética y Biomoléculas de Anfibios (LICBA), Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Linda P. Guaman
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | | | - Raúl Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito, Ecuador,Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador,*Correspondence: Carlos Barba-Ostria,
| |
Collapse
|
4
|
Juhas M. Synthetic Biology in Microbiology. BRIEF LESSONS IN MICROBIOLOGY 2023:79-91. [DOI: 10.1007/978-3-031-29544-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
5
|
Ryan J, Hong S, Foo M, Kim J, Tang X. Model-Based Investigation of the Relationship between Regulation Level and Pulse Property of I1-FFL Gene Circuits. ACS Synth Biol 2022; 11:2417-2428. [PMID: 35729788 PMCID: PMC9295143 DOI: 10.1021/acssynbio.2c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mathematical models are powerful tools in guiding the construction of synthetic biological circuits, given their capability of accurately capturing and predicting circuit dynamics. Recent innovations in RNA technology have enabled the development of a variety of new tools for regulating gene expression at both the transcription and translation levels. However, the effects of different regulation levels on the circuit dynamics remain largely unexplored. In this study, we focus on the type 1 incoherent feed-forward loop (I1-FFL) gene circuit with four different variations (TX, TL, HY-1, HY-2), to investigate how regulation at the transcription and translation levels affect the circuit dynamics. We develop a mechanistic model for each of the four circuits and deploy sensitivity analysis to investigate the circuits' dynamics in terms of pulse generation. Based on the analysis, we observe that the repression regulation mechanism dominates the characteristics of the pulse as compared to the activation regulation mechanism and find that the I1-FFL with transcription repression has a higher chance of generating a pulse meeting the desired criteria. The experimental results in Escherichia coli also confirm our findings from the computational analysis. We expect our findings to facilitate future experimental construction of gene circuits with insights on the selection of appropriate transcription and translation regulation tools.
Collapse
Affiliation(s)
- Jordan Ryan
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Seongho Hong
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Mathias Foo
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Xun Tang
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
6
|
|
7
|
Mante J, Roehner N, Keating K, McLaughlin JA, Young E, Beal J, Myers CJ. Curation Principles Derived from the Analysis of the SBOL iGEM Data Set. ACS Synth Biol 2021; 10:2592-2606. [PMID: 34546707 DOI: 10.1021/acssynbio.1c00225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
As an engineering endeavor, synthetic biology requires effective sharing of genetic design information that can be reused in the construction of new designs. While there are a number of large community repositories of design information, curation of this information has been limited. This in turn limits the ways in which design information can be put to use. The aim of this work was to improve this situation by creating a curated library of parts from the International Genetically Engineered Machines (iGEM) registry data set. To this end, an analysis of the Synthetic Biology Open Language (SBOL) version of the iGEM registry was carried out using four different approaches-simple statistics, SnapGene autoannotation, SYNBICT autoannotation, and expert analysis-the results of which are presented herein. Key challenges encountered include the use of free text, insufficient part provenance, part duplication, lack of part removal, and insufficient continuous curation. On the basis of these analyses, the focus has shifted from the creation of a curated iGEM part library to instead the extraction of a set of lessons, which are presented here. These lessons can be exploited to facilitate the creation and curation of other part libraries using a simpler and less labor intensive process.
Collapse
Affiliation(s)
- Jeanet Mante
- University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Nicholas Roehner
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Kevin Keating
- Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | | | - Eric Young
- Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Chris J. Myers
- University of Colorado Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
8
|
Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits. Biomolecules 2021; 11:biom11081182. [PMID: 34439849 PMCID: PMC8391864 DOI: 10.3390/biom11081182] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization.
Collapse
|
9
|
Nadra AD, Rodríguez PE, Grunberg R, Olalde LG, Sánchez IE. Developing synthetic biology in Argentina: the Latin American TECNOx community as an alternative way for growth of the field. Crit Rev Biotechnol 2020; 40:357-364. [PMID: 32075446 DOI: 10.1080/07388551.2020.1712322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Synthetic biology emerged in the USA and Europe twenty years ago and quickly developed innovative research and technology as a result of continued funding. Synthetic biology is also growing in many developing countries of Africa, Asia and Latin America, where it could have a large economic impact by helping its use of genetic biodiversity in order to boost existing industries. Starting in 2011, Argentine synthetic biology developed along an idiosyncratic path. In 2011-2012, the main focus was not exclusively research but also on community building through teaching and participation in iGEM, following the template of the early "MIT school" of synthetic biology. In 2013-2015, activities diversified and included society-centered projects, social science studies on synthetic biology and bioart. Standard research outputs such as articles and industrial applications helped consolidate several academic working groups. Since 2016, the lack of a critical mass of researchers and a funding crisis were partially compensated by establishing links with Latin American synthetic biologists and with other socially oriented open technology collectives. The TECNOx community is a central node in this growing research and technology network. The first four annual TECNOx meetings brought together synthetic biologists with other open science and engineering platforms and explored the relationship of Latin American technologies with entrepreneurship, open hardware, ethics and human rights. In sum, the socioeconomic context encouraged Latin American synthetic biology to develop in a meandering and diversifying manner. This revealed alternative ways for growth of the field that may be relevant to other developing countries.
Collapse
Affiliation(s)
- Alejandro D Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo E Rodríguez
- Facultad de Ciencias Sociales, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones "Gino Germani", Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Raik Grunberg
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Laura G Olalde
- Protein Physiology Laboratory, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignacio E Sánchez
- Protein Physiology Laboratory, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
10
|
Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J, Agrawal DK, Dunlop MJ, Noireaux V, Beisel CL, Lucks J, Franco E. Distinct timescales of RNA regulators enable the construction of a genetic pulse generator. Biotechnol Bioeng 2019; 116:1139-1151. [DOI: 10.1002/bit.26918] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/25/2018] [Accepted: 01/06/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Alexandra Westbrook
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York
| | - Xun Tang
- Department of Mechanical Engineering University of California at Riverside Riverside California
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota Minneapolis Minnesota
| | - Colin S. Maxwell
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
| | | | - Deepak K. Agrawal
- Biomedical Engineering Department Boston University Boston Massachusetts
| | - Mary J. Dunlop
- Biomedical Engineering Department Boston University Boston Massachusetts
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota Minneapolis Minnesota
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
- Helmholtz Institute for RNA‐based Infection Research (HIRI) Helmholtz‐Centre for Infection Research (HZI), Würzburg Germany
- Faculty of Medicine, University of Würzburg Würzburg Germany
| | - Julius Lucks
- Department of Chemical and Biological Engineering Northwestern University Evanston Illinois
| | - Elisa Franco
- Department of Mechanical Engineering University of California at Riverside Riverside California
| |
Collapse
|