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Benman W, Datta S, Gonzalez-Martinez D, Lee G, Hooper J, Qian G, Leavitt G, Salloum L, Ho G, Mhatre S, Magaraci MS, Patterson M, Mannickarottu SG, Malani S, Avalos JL, Chow BY, Bugaj LJ. High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates. Commun Biol 2023; 6:1192. [PMID: 38001175 PMCID: PMC10673842 DOI: 10.1038/s42003-023-05532-4] [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: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli. We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.
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Affiliation(s)
- William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Saachi Datta
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Gloria Lee
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Juliette Hooper
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Grace Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gabrielle Leavitt
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lana Salloum
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gabrielle Ho
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sharvari Mhatre
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael S Magaraci
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael Patterson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Saurabh Malani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Jose L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
- The Andlinger Center for Energy and the Environment, Princeton, NJ, 08544, USA
- High Meadows Environmental Institute, Princeton, NJ, 08544, USA
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Kumar S, Khammash M. Platforms for Optogenetic Stimulation and Feedback Control. Front Bioeng Biotechnol 2022; 10:918917. [PMID: 35757811 PMCID: PMC9213687 DOI: 10.3389/fbioe.2022.918917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the potential of optogenetics in biology requires methodologies from different disciplines ranging from biology, to mechatronics engineering, to control engineering. Light stimulation of a synthetic optogenetic construct in a given biological species can only be achieved via a suitable light stimulation platform. Emerging optogenetic applications entail a consistent, reproducible, and regulated delivery of light adapted to the application requirement. In this review, we explore the evolution of light-induction hardware-software platforms from simple illumination set-ups to sophisticated microscopy, microtiter plate and bioreactor designs, and discuss their respective advantages and disadvantages. Here, we examine design approaches followed in performing optogenetic experiments spanning different cell types and culture volumes, with induction capabilities ranging from single cell stimulation to entire cell culture illumination. The development of automated measurement and stimulation schemes on these platforms has enabled researchers to implement various in silico feedback control strategies to achieve computer-controlled living systems—a theme we briefly discuss in the last part of this review.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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Lindner F, Diepold A. Optogenetics in bacteria - applications and opportunities. FEMS Microbiol Rev 2021; 46:6427354. [PMID: 34791201 PMCID: PMC8892541 DOI: 10.1093/femsre/fuab055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Optogenetics holds the promise of controlling biological processes with superb temporal and spatial resolution at minimal perturbation. Although many of the light-reactive proteins used in optogenetic systems are derived from prokaryotes, applications were largely limited to eukaryotes for a long time. In recent years, however, an increasing number of microbiologists use optogenetics as a powerful new tool to study and control key aspects of bacterial biology in a fast and often reversible manner. After a brief discussion of optogenetic principles, this review provides an overview of the rapidly growing number of optogenetic applications in bacteria, with a particular focus on studies venturing beyond transcriptional control. To guide future experiments, we highlight helpful tools, provide considerations for successful application of optogenetics in bacterial systems, and identify particular opportunities and challenges that arise when applying these approaches in bacteria.
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Affiliation(s)
- Florian Lindner
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.,SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
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Kumar S, Rullan M, Khammash M. Rapid prototyping and design of cybergenetic single-cell controllers. Nat Commun 2021; 12:5651. [PMID: 34561433 PMCID: PMC8463601 DOI: 10.1038/s41467-021-25754-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
The design and implementation of synthetic circuits that operate robustly in the cellular context is fundamental for the advancement of synthetic biology. However, their practical implementation presents challenges due to low predictability of synthetic circuit design and time-intensive troubleshooting. Here, we present the Cyberloop, a testing framework to accelerate the design process and implementation of biomolecular controllers. Cellular fluorescence measurements are sent in real-time to a computer simulating candidate stochastic controllers, which in turn compute the control inputs and feed them back to the controlled cells via light stimulation. Applying this framework to yeast cells engineered with optogenetic tools, we examine and characterize different biomolecular controllers, test the impact of non-ideal circuit behaviors such as dilution on their operation, and qualitatively demonstrate improvements in controller function with certain network modifications. From this analysis, we derive conditions for desirable biomolecular controller performance, thereby avoiding pitfalls during its biological implementation.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Marc Rullan
- 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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