1
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Denton MR, Murphy NP, Norton-Baker B, Lua M, Steel H, Beckham GT. Integration of pH Control into Chi.Bio Reactors and Demonstration with Small-Scale Enzymatic Poly(ethylene terephthalate) Hydrolysis. Biochemistry 2024; 63:1599-1607. [PMID: 38907702 PMCID: PMC11223484 DOI: 10.1021/acs.biochem.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/24/2024]
Abstract
Small-scale bioreactors that are affordable and accessible would be of major benefit to the research community. In previous work, an open-source, automated bioreactor system was designed to operate up to the 30 mL scale with online optical monitoring, stirring, and temperature control, and this system, dubbed Chi.Bio, is now commercially available at a cost that is typically 1-2 orders of magnitude less than commercial bioreactors. In this work, we further expand the capabilities of the Chi.Bio system by enabling continuous pH monitoring and control through hardware and software modifications. For hardware modifications, we sourced low-cost, commercial pH circuits and made straightforward modifications to the Chi.Bio head plate to enable continuous pH monitoring. For software integration, we introduced closed-loop feedback control of the pH measured inside the Chi.Bio reactors and integrated a pH-control module into the existing Chi.Bio user interface. We demonstrated the utility of pH control through the small-scale depolymerization of the synthetic polyester, poly(ethylene terephthalate) (PET), using a benchmark cutinase enzyme, and compared this to 250 mL bioreactor hydrolysis reactions. The results in terms of PET conversion and rate, measured both by base addition and product release profiles, are statistically equivalent, with the Chi.Bio system allowing for a 20-fold reduction of purified enzyme required relative to the 250 mL bioreactor setup. Through inexpensive modifications, the ability to conduct pH control in Chi.Bio reactors widens the potential slate of biochemical reactions and biological cultivations for study in this system, and may also be adapted for use in other bioreactor platforms.
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Affiliation(s)
- Mackenzie
C. R. Denton
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Natasha P. Murphy
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Brenna Norton-Baker
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Mauro Lua
- Catalytic
Carbon Transformation and Scale-up Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Harrison Steel
- Department
of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K.
| | - Gregg T. Beckham
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
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2
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Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: engineering habitats for modular consortia. J Appl Microbiol 2024; 135:lxae158. [PMID: 38936824 DOI: 10.1093/jambio/lxae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.
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Affiliation(s)
- Yue Casey Chen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Louie Destouches
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alice Cook
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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3
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Jiang S, Evans-Yamamoto D, Bersenev D, Palaniappan SK, Yachie-Kinoshita A. ProtoCode: Leveraging large language models (LLMs) for automated generation of machine-readable PCR protocols from scientific publications. SLAS Technol 2024; 29:100134. [PMID: 38670311 DOI: 10.1016/j.slast.2024.100134] [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: 12/12/2023] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Protocol standardization and sharing are crucial for reproducibility in life sciences. In spite of numerous efforts for standardized protocol description, adherence to these standards in literature remains largely inconsistent. Curation of protocols are especially challenging due to the labor intensive process, requiring expert domain knowledge of each experimental procedure. Recent advancements in Large Language Models (LLMs) offer a promising solution to interpret and curate knowledge from complex scientific literature. In this work, we develop ProtoCode, a tool leveraging fine-tune LLMs to curate protocols into intermediate representation formats which can be interpretable by both human and machine interfaces. Our proof-of-concept, focused on polymerase chain reaction (PCR) protocols, retrieves information from PCR protocols at an accuracy ranging 69-100 % depending on the information content. In all tested protocols, we demonstrate that ProtoCode successfully converts literature-based protocols into correct operational files for multiple thermal cycler systems. In conclusion, ProtoCode can alleviate labor intensive curation and standardization of life science protocols to enhance research reproducibility by providing a reliable, automated means to process and standardize protocols. ProtoCode is freely available as a web server at https://curation.taxila.io/ProtoCode/.
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Affiliation(s)
- Shuo Jiang
- SBX BioSciences, Inc. 1600 - 925 West Georgia Street, Vancouver, BC, V6C 3L2, Canada
| | - Daniel Evans-Yamamoto
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Dennis Bersenev
- SBX BioSciences, Inc. 1600 - 925 West Georgia Street, Vancouver, BC, V6C 3L2, Canada
| | - Sucheendra K Palaniappan
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan.
| | - Ayako Yachie-Kinoshita
- SBX BioSciences, Inc. 1600 - 925 West Georgia Street, Vancouver, BC, V6C 3L2, Canada; The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan.
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4
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Harmer Z, Thompson JC, Cole DL, Venturelli OS, Zavala VM, McClean MN. Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro. ACS Synth Biol 2024; 13:1424-1433. [PMID: 38684225 PMCID: PMC11106771 DOI: 10.1021/acssynbio.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/31/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation, we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive split transcription factors in the budding yeast, Saccharomyces cerevisiae. We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering.
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Affiliation(s)
- Zachary
P. Harmer
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Jaron C. Thompson
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - David L. Cole
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ophelia S. Venturelli
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Bacteriology, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Victor M. Zavala
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Mathematics
and Computer Science Division, Argonne National
Laboratory, Lemont, Illinois 60439. United States
| | - Megan N. McClean
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
- University
of Wisconsin Carbone Cancer Center, University
of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, United States
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5
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Kinet R, Richelle A, Colle M, Demaegd D, von Stosch M, Sanders M, Sehrt H, Delvigne F, Goffin P. Giving the cells what they need when they need it: Biosensor-based feeding control. Biotechnol Bioeng 2024; 121:1271-1283. [PMID: 38258490 DOI: 10.1002/bit.28657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
"Giving the cells exactly what they need, when they need it" is the core idea behind the proposed bioprocess control strategy: operating bioprocess based on the physiological behavior of the microbial population rather than exclusive monitoring of environmental parameters. We are envisioning to achieve this through the use of genetically encoded biosensors combined with online flow cytometry (FCM) to obtain a time-dependent "physiological fingerprint" of the population. We developed a biosensor based on the glnA promoter (glnAp) and applied it for monitoring the nitrogen-related nutritional state of Escherichia coli. The functionality of the biosensor was demonstrated through multiple cultivation runs performed at various scales-from microplate to 20 L bioreactor. We also developed a fully automated bioreactor-FCM interface for on-line monitoring of the microbial population. Finally, we validated the proposed strategy by performing a fed-batch experiment where the biosensor signal is used as the actuator for a nitrogen feeding feedback control. This new generation of process control, -based on the specific needs of the cells, -opens the possibility of improving process development on a short timescale and therewith, the robustness and performance of fermentation processes.
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Affiliation(s)
| | | | | | | | | | | | - Hannah Sehrt
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Philippe Goffin
- Molecular and Cellular Biology, University of Brussels, Brussels, Belgium
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6
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De Marchi D, Shaposhnikov R, Gobaa S, Pastorelli D, Batt G, Magni P, Pasotti L. Design and Model-Driven Analysis of Synthetic Circuits with the Staphylococcus aureus Dead-Cas9 (sadCas9) as a Programmable Transcriptional Regulator in Bacteria. ACS Synth Biol 2024; 13:763-780. [PMID: 38374729 DOI: 10.1021/acssynbio.3c00541] [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] [Indexed: 02/21/2024]
Abstract
Synthetic circuit design is crucial for engineering microbes that process environmental cues and provide biologically relevant outputs. To reliably scale-up circuit complexity, the availability of parts toolkits is central. Streptococcus pyogenes (sp)-derived CRISPR interference/dead-Cas9 (CRISPRi/spdCas9) is widely adopted for implementing programmable regulations in synthetic circuits, and alternative CRISPRi systems will further expand our toolkits of orthogonal components. Here, we showcase the potential of CRISPRi using the engineered dCas9 from Staphylococcus aureus (sadCas9), not previously used in bacterial circuits, that is attractive for its low size and high specificity. We designed a collection of ∼20 increasingly complex circuits and variants in Escherichia coli, including circuits with static function like one-/two-input logic gates (NOT, NAND), circuits with dynamic behavior like incoherent feedforward loops (iFFLs), and applied sadCas9 to fix a T7 polymerase-based cascade. Data demonstrated specific and efficient target repression (100-fold) and qualitatively successful functioning for all circuits. Other advantageous features included low sadCas9-borne cell load and orthogonality with spdCas9. However, different circuit variants showed quantitatively unexpected and previously unreported steady-state responses: the dynamic range, switch point, and slope of NOT/NAND gates changed for different output promoters, and a multiphasic behavior was observed in iFFLs, differing from the expected bell-shaped or sigmoidal curves. Model analysis explained the observed curves by complex interplays among components, due to reporter gene-borne cell load and regulator competition. Overall, CRISPRi/sadCas9 successfully expanded the available toolkit for bacterial engineering. Analysis of our circuit collection depicted the impact of generally neglected effects modulating the shape of component dose-response curves, to avoid drawing wrong conclusions on circuit functioning.
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Affiliation(s)
- Davide De Marchi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Roman Shaposhnikov
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Samy Gobaa
- Institut Pasteur, Université Paris Cité, Biomaterials and Microfluidics Core Facility, 28 Rue du Docteur Roux, 75015 Paris, France
| | - Daniele Pastorelli
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
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7
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Harmer ZP, Thompson JC, Cole DL, Zavala VM, McClean MN. Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572411. [PMID: 38187522 PMCID: PMC10769237 DOI: 10.1101/2023.12.19.572411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive spit transcription factors in the budding yeast, Saccharomyces cerevisiae . We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering. Graphical abstract
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8
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Ruess J, Ballif G, Aditya C. Stochastic chemical kinetics of cell fate decision systems: From single cells to populations and back. J Chem Phys 2023; 159:184103. [PMID: 37937934 DOI: 10.1063/5.0160529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/14/2023] [Indexed: 11/09/2023] Open
Abstract
Stochastic chemical kinetics is a widely used formalism for studying stochasticity of chemical reactions inside single cells. Experimental studies of reaction networks are generally performed with cells that are part of a growing population, yet the population context is rarely taken into account when models are developed. Models that neglect the population context lose their validity whenever the studied system influences traits of cells that can be selected in the population, a property that naturally arises in the complex interplay between single-cell and population dynamics of cell fate decision systems. Here, we represent such systems as absorbing continuous-time Markov chains. We show that conditioning on non-absorption allows one to derive a modified master equation that tracks the time evolution of the expected population composition within a growing population. This allows us to derive consistent population dynamics models from a specification of the single-cell process. We use this approach to classify cell fate decision systems into two types that lead to different characteristic phases in emerging population dynamics. Subsequently, we deploy the gained insights to experimentally study a recurrent problem in biology: how to link plasmid copy number fluctuations and plasmid loss events inside single cells to growth of cell populations in dynamically changing environments.
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Affiliation(s)
- Jakob Ruess
- Inria Saclay, 91120 Palaiseau, France
- Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | | | - Chetan Aditya
- Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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9
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Henrion L, Martinez JA, Vandenbroucke V, Delvenne M, Telek S, Zicler A, Grünberger A, Delvigne F. Fitness cost associated with cell phenotypic switching drives population diversification dynamics and controllability. Nat Commun 2023; 14:6128. [PMID: 37783690 PMCID: PMC10545768 DOI: 10.1038/s41467-023-41917-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
Isogenic cell populations can cope with stress conditions by switching to alternative phenotypes. Even if it can lead to increased fitness in a natural context, this feature is typically unwanted for a range of applications (e.g., bioproduction, synthetic biology, and biomedicine) where it tends to make cellular response unpredictable. However, little is known about the diversification profiles that can be adopted by a cell population. Here, we characterize the diversification dynamics for various systems (bacteria and yeast) and for different phenotypes (utilization of alternative carbon sources, general stress response and more complex development patterns). Our results suggest that the diversification dynamics and the fitness cost associated with cell switching are coupled. To quantify the contribution of the switching cost on population dynamics, we design a stochastic model that let us reproduce the dynamics observed experimentally and identify three diversification regimes, i.e., constrained (at low switching cost), dispersed (at medium and high switching cost), and bursty (for very high switching cost). Furthermore, we use a cell-machine interface called Segregostat to demonstrate that different levels of control can be applied to these diversification regimes, enabling applications involving more precise cellular responses.
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Affiliation(s)
- Lucas Henrion
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Juan Andres Martinez
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Vincent Vandenbroucke
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Mathéo Delvenne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Samuel Telek
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Andrew Zicler
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Alexander Grünberger
- Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
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10
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Delvigne F, Martinez JA. Advances in automated and reactive flow cytometry for synthetic biotechnology. Curr Opin Biotechnol 2023; 83:102974. [PMID: 37515938 DOI: 10.1016/j.copbio.2023.102974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/31/2023]
Abstract
Automated flow cytometry (FC) has been initially considered for bioprocess monitoring and optimization. More recently, new physical and software interfaces have been made available, facilitating the access to this technology for labs and industries. It also comes with new capabilities, such as being able to act on the cultivation conditions based on population data. This approach, known as reactive FC, extended the range of applications of automated FC to bioprocess control and the stabilization of cocultures, but also to the broad field of synthetic and systems biology for the characterization of gene circuits. However, several issues must be addressed before automated and reactive FC can be considered standard and modular technologies.
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Affiliation(s)
- Frank Delvigne
- Terra Research and Teaching Center, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
| | - Juan A Martinez
- Terra Research and Teaching Center, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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11
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Harmer ZP, McClean MN. High-Throughput Optogenetics Experiments in Yeast Using the Automated Platform Lustro. J Vis Exp 2023:10.3791/65686. [PMID: 37590537 PMCID: PMC11085938 DOI: 10.3791/65686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Abstract
Optogenetics offers precise control over cellular behavior by utilizing genetically encoded light-sensitive proteins. However, optimizing these systems to achieve the desired functionality often requires multiple design-build-test cycles, which can be time-consuming and labor-intensive. To address this challenge, we have developed Lustro, a platform that combines light stimulation with laboratory automation, enabling efficient high-throughput screening and characterization of optogenetic systems. Lustro utilizes an automation workstation equipped with an illumination device, a shaking device, and a plate reader. By employing a robotic arm, Lustro automates the movement of a microwell plate between these devices, allowing for the stimulation of optogenetic strains and the measurement of their response. This protocol provides a step-by-step guide on using Lustro to characterize optogenetic systems for gene expression control in the budding yeast Saccharomyces cerevisiae. The protocol covers the setup of Lustro's components, including the integration of the illumination device with the automation workstation. It also provides detailed instructions for programming the illumination device, plate reader, and robot, ensuring smooth operation and data acquisition throughout the experimental process.
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Affiliation(s)
- Zachary P Harmer
- Department of Biomedical Engineering, University of Wisconsin-Madison
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health;
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12
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Harmer Z, McClean MN. Lustro: High-Throughput Optogenetic Experiments Enabled by Automation and a Yeast Optogenetic Toolkit. ACS Synth Biol 2023; 12:1943-1951. [PMID: 37434272 PMCID: PMC10368012 DOI: 10.1021/acssynbio.3c00215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Indexed: 07/13/2023]
Abstract
Optogenetic systems use genetically encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light; however, these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae. We expand the yeast optogenetic toolkit to include variants of the cryptochromes and enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to the high-throughput characterization of optogenetic systems across a range of biological systems and applications.
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Affiliation(s)
- Zachary
P. Harmer
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Megan N. McClean
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
- University
of Wisconsin Carbone Cancer Center, University
of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, United States
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13
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Sosa-Carrillo S, Galez H, Napolitano S, Bertaux F, Batt G. Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches. Nat Commun 2023; 14:3028. [PMID: 37231013 DOI: 10.1038/s41467-023-38807-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
Optimizing the production of recombinant proteins is a problem of major industrial and pharmaceutical importance. Secretion of the protein by the host cell considerably simplifies downstream purification processes. However, for many proteins, this is also the limiting production step. Current solutions involve extensive engineering of the chassis cell to facilitate protein trafficking and limit protein degradation triggered by excessive secretion-associated stress. Here, we propose instead a regulation-based strategy in which induction is dynamically adjusted to an optimal strength based on the current stress level of the cells. Using a small collection of hard-to-secrete proteins, a bioreactor-based platform with automated cytometry measurements, and a systematic assay to quantify secreted protein levels, we demonstrate that the secretion sweet spot is indicated by the appearance of a subpopulation of cells that accumulate high amounts of proteins, decrease growth, and face significant stress, that is, experience a secretion burnout. In these cells, adaptations capabilities are overwhelmed by a too strong production. Using these notions, we show for a single-chain antibody variable fragment that secretion levels can be improved by 70% by dynamically keeping the cell population at optimal stress levels using real-time closed-loop control.
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Affiliation(s)
| | - Henri Galez
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - Sara Napolitano
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - François Bertaux
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
- Lesaffre International, 101 rue de Menin, Marcq-en-Baroeul, France
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France.
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14
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Harmer ZP, McClean MN. Lustro: High-throughput optogenetic experiments enabled by automation and a yeast optogenetic toolkit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536078. [PMID: 37066312 PMCID: PMC10104134 DOI: 10.1101/2023.04.07.536078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Optogenetic systems use genetically-encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light, however these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae . We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to high-throughput characterization of optogenetic systems across a range of biological systems and applications.
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15
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Naseri G. A roadmap to establish a comprehensive platform for sustainable manufacturing of natural products in yeast. Nat Commun 2023; 14:1916. [PMID: 37024483 PMCID: PMC10079933 DOI: 10.1038/s41467-023-37627-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Secondary natural products (NPs) are a rich source for drug discovery. However, the low abundance of NPs makes their extraction from nature inefficient, while chemical synthesis is challenging and unsustainable. Saccharomyces cerevisiae and Pichia pastoris are excellent manufacturing systems for the production of NPs. This Perspective discusses a comprehensive platform for sustainable production of NPs in the two yeasts through system-associated optimization at four levels: genetics, temporal controllers, productivity screening, and scalability. Additionally, it is pointed out critical metabolic building blocks in NP bioengineering can be identified through connecting multilevel data of the optimized system using deep learning.
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Affiliation(s)
- Gita Naseri
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
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16
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Caringella G, Bandiera L, Menolascina F. Recent advances, opportunities and challenges in cybergenetic identification and control of biomolecular networks. Curr Opin Biotechnol 2023; 80:102893. [PMID: 36706519 DOI: 10.1016/j.copbio.2023.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Cybergenetics is a new area of research aimed at developing digital and biological controllers for living systems. Synthetic biologists have begun exploiting cybergenetic tools and platforms to both accelerate the development of mathematical models and develop control strategies for complex biological phenomena. Here, we review the state of the art in cybergenetic identification and control. Our aim is to lower the entry barrier to this field and foster the adoption of methods and technologies that will accelerate the pace at which Synthetic Biology progresses toward applications.
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Affiliation(s)
- Gianpio Caringella
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Lucia Bandiera
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Filippo Menolascina
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK.
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17
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Taguchi S, Suda Y, Irie K, Ozaki H. Automation of yeast spot assays using an affordable liquid handling robot. SLAS Technol 2022; 28:55-62. [PMID: 36503082 DOI: 10.1016/j.slast.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022]
Abstract
The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time points a posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.
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18
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Lee TA, Steel H. Cybergenetic control of microbial community composition. Front Bioeng Biotechnol 2022; 10:957140. [PMID: 36277404 PMCID: PMC9582452 DOI: 10.3389/fbioe.2022.957140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The use of bacterial communities in bioproduction instead of monocultures has potential advantages including increased productivity through division of labour, ability to utilise cheaper substrates, and robustness against perturbations. A key challenge in the application of engineered bacterial communities is the ability to reliably control the composition of the community in terms of its constituent species. This is crucial to prevent faster growing species from outcompeting others with a lower relative fitness, and to ensure that all species are present at an optimal ratio during different steps in a biotechnological process. In contrast to purely biological approaches such as synthetic quorum sensing circuits or paired auxotrophies, cybergenetic control techniques - those in which computers interface with living cells-are emerging as an alternative approach with many advantages. The community composition is measured through methods such as fluorescence intensity or flow cytometry, with measured data fed real-time into a computer. A control action is computed using a variety of possible control algorithms and then applied to the system, with actuation taking the form of chemical (e.g., inducers, nutrients) or physical (e.g., optogenetic, mechanical) inputs. Subsequent changes in composition are then measured and the cycle repeated, maintaining or driving the system to a desired state. This review discusses recent and future developments in methods for implementing cybergenetic control systems, contrasts their capabilities with those of traditional biological methods of population control, and discusses future directions and outstanding challenges for the field.
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19
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Gutiérrez Mena J, Kumar S, Khammash M. Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback. Nat Commun 2022; 13:4808. [PMID: 35973993 PMCID: PMC9381578 DOI: 10.1038/s41467-022-32392-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/29/2022] [Indexed: 12/19/2022] Open
Abstract
Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. However, the difficulty of controlling the composition of microbial consortia over time hinders their optimal use in many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements and computer-controlled optogenetic modulation of bacterial growth to implement precise and robust compositional control of a two-strain E. coli community. In addition, we develop a general framework for dynamic modeling of synthetic genetic circuits in the physiological context of E. coli and use a host-aware model to determine the optimal control parameters of our closed-loop compositional control system. Our platform succeeds in stabilizing the strain ratio of multiple parallel co-cultures at arbitrary levels and in changing these targets over time, opening the door for the implementation of dynamic compositional programs in synthetic bacterial communities.
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Affiliation(s)
- Joaquín Gutiérrez Mena
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
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20
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Salzano D, Fiore D, di Bernardo M. Ratiometric control of cell phenotypes in monostrain microbial consortia. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220335. [PMID: 35858050 PMCID: PMC9277296 DOI: 10.1098/rsif.2022.0335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We address the problem of regulating and keeping at a desired balance the relative numbers between cells exhibiting a different phenotype within a monostrain microbial consortium. We propose a strategy based on the use of external control inputs, assuming each cell in the community is endowed with a reversible, bistable memory mechanism. Specifically, we provide a general analytical framework to guide the design of external feedback control strategies aimed at balancing the ratio between cells whose memory is stabilized at either one of two equilibria associated with different cell phenotypes. We demonstrate the stability and robustness properties of the control laws proposed and validate them in silico, implementing the memory element via a genetic toggle-switch. The proposed control framework may be used to allow long-term coexistence of different populations, with both industrial and biotechnological applications. As a representative example, we consider the realistic agent-based implementation of our control strategy to enable cooperative bioproduction of a dimer in a monostrain microbial consortium.
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Affiliation(s)
- Davide Salzano
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
| | - Davide Fiore
- Department of Mathematics and Applications 'R. Caccioppoli', University of Naples Federico II, Via Cintia, Monte S. Angelo, 80126 Naples, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy.,Scuola Superiore Meridionale, Largo S. Marcellino 10, 80138 Naples, Italy
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