This work was supported by National Institutes of Health grant R35GM128873 and National Science Foundation grant 2045493 (awarded to M.N.M.). Megan Nicole McClean, Ph.D. holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund. Z.P.H. was supported by an NHGRI training grant to the Genomic Sciences Training Program 5T32HG002760. We acknowledge fruitful discussions with McClean lab members, and in particular, we are grateful to Kieran Sweeney for providing comments on the manuscript.

The yeast strains utilized in this study are documented in the Table of Materials. These strains exhibit robust growth within the temperature range of 22 &#176;C to 30 &#176;C and can be cultivated in various standard yeast media.
1. Setting up the automation workstation
<ol>
	<li>Equip the automated workstation with a Robotic Gripper Arm (RGA, see Table of Materials) capable of moving microwell plates (Figure 1...

Yeast Optogenetic Response Analysis Using the Lustro Automation Technique

<ol>
	<li>P&#233;rez, A. L. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+strategies+for+the+control+of+gene+expression+in+yeasts.">Optogenetic strategies for the control of gene expression in yeasts.</a> Biotechnology Advances. 54, 107839 (2022).</li><li>Lan, T. -. H., He, L., Huang, Y., Zhou, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetics+for+transcriptional+programming+and+genetic+engineering.">Optogenetics for transcriptional programming and genetic engineering.</a> Trends in Genetics. 38 (12), 1253-1270 (2022).</li><li>Olson, E. J., Tabor, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+characterization+methods+overcome+key+challenges+in+synthetic+and+systems+biology.">Optogenetic characterization methods overcome key challenges in synthetic and systems biology.</a> Nature Chemical Biology. 10, 502-511 (2014).</li><li>Hallett, R. A., Zimmerman, S. P., Yumerefendi, H., Bear, J. E., Kuhlman, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Correlating+in+vitro+and+in+vivo+Activities+of+Light+Inducible+Dimers:+a+Cellular+Optogenetics+Guide.">Correlating in vitro and in vivo Activities of Light Inducible Dimers: a Cellular Optogenetics Guide.</a> ACS Synthetic Biology. 5 (1), 53-64 (2016).</li><li>Scott, T. D., Sweeney, K., McClean, M. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biological+signal+generators:+integrating+synthetic+biology+tools+and+in+silico+control.">Biological signal generators: integrating synthetic biology tools and in silico control.</a> Current Opinion in Systems Biology. 14, 58-65 (2019).</li><li>Harmer, Z. P., McClean, M. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lustro:+High-throughput+optogenetic+experiments+enabled+by+automation+and+a+yeast+optogenetic+toolkit.">Lustro: High-throughput optogenetic experiments enabled by automation and a yeast optogenetic toolkit.</a> ACS Synthetic Biology. 12 (7), 1943-1951 (2023).</li><li>Bindels, D. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mScarlet:+a+bright+monomeric+red+fluorescent+protein+for+cellular+imaging.">mScarlet: a bright monomeric red fluorescent protein for cellular imaging.</a> Nature Methods. 14 (1), 53-56 (2017).</li><li>Bugaj, L. J., Lim, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+multicolor+optogenetics+in+microwell+plates.">High-throughput multicolor optogenetics in microwell plates.</a> Nature Protocols. 14 (7), 2205-2228 (2019).</li><li>H&#246;hener, T. C., Landolt, A. E., Dessauges, C., Hinderling, L., Gagliardi, P. A., Pertz, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=LITOS:+a+versatile+LED+illumination+tool+for+optogenetic+stimulation.">LITOS: a versatile LED illumination tool for optogenetic stimulation.</a> Scientific Reports. 12 (1), 13139 (2022).</li><li>Gr&#248;dem, E. O., Sweeney, K., McClean, M. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+calibration+of+optoPlate+LEDs+to+reduce+light+dose+variation+in+optogenetic+experiments.">Automated calibration of optoPlate LEDs to reduce light dose variation in optogenetic experiments.</a> BioTechniques. 69 (4), 313-316 (2020).</li><li>Dunlop, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> A supplemental guide to building the optoPlate-96. , (2021).</li><li>Thomas, O. S., H&#246;rner, M., Weber, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+graphical+user+interface+to+design+high-throughput+optogenetic+experiments+with+the+optoPlate-96.">A graphical user interface to design high-throughput optogenetic experiments with the optoPlate-96.</a> Nature Protocols. 15 (9), 2785-2787 (2020).</li><li>Robertson, J. B., Davis, C. R., Johnson, C. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visible+light+alters+yeast+metabolic+rhythms+by+inhibiting+respiration.">Visible light alters yeast metabolic rhythms by inhibiting respiration.</a> Proceedings of the National Academy of Sciences of the United States of America. 110 (52), 21130-21135 (2013).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthetic+Complete+(SC)+Medium.">Synthetic Complete (SC) Medium.</a> 2016 (11), (2016).</li><li>Lambert, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FPbase:+a+community-editable+fluorescent+protein+database.">FPbase: a community-editable fluorescent protein database.</a> Nature Methods. 16 (4), 277-278 (2019).</li><li>Hecht, A., Endy, D., Salit, M., Munson, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=When+wavelengths+collide:+bias+in+cell+abundance+measurements+due+to+expressed+fluorescent+proteins.">When wavelengths collide: bias in cell abundance measurements due to expressed fluorescent proteins.</a> ACS Synthetic Biology. 5 (9), 1024-1027 (2016).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=YPD+media.">YPD media.</a> 2010 (9), (2010).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Low-Fluorescence Yeast Nitrogen Base without Riboflavin and Folic Acid Medium (LFM). 2016 (11), (2016).</li><li>Csibra, E., Stan, G. -. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Parsley:+a+web+app+for+parsing+data+from+plate+readers.">Parsley: a web app for parsing data from plate readers.</a> Zenodo. , (2023).</li><li>Gerhardt, K. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+open-hardware+platform+for+optogenetics+and+photobiology.">An open-hardware platform for optogenetics and photobiology.</a> Scientific Reports. 6 (1), 35363 (2016).</li><li>Guti&#233;rrez Mena, J., Kumar, S., Khammash, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+cybergenetic+control+of+bacterial+co-culture+composition+via+optogenetic+feedback.">Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback.</a> Nature Communications. 13, 4808 (2022).</li><li>Milias-Argeitis, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+silico+feedback+for+in+vivo+regulation+of+a+gene+expression+circuit.">In silico feedback for in vivo regulation of a gene expression circuit.</a> Nature Biotechnology. 29 (12), 1114-1116 (2011).</li><li>Milias-Argeitis, A., Rullan, M., Aoki, S. K., Buchmann, P., Khammash, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+optogenetic+feedback+control+for+precise+and+robust+regulation+of+gene+expression+and+cell+growth.">Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth.</a> Nature Communications. 7, 12546 (2016).</li><li>Bertaux, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancing+bioreactor+arrays+for+automated+measurements+and+reactive+control+with+ReacSight.">Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight.</a> Nature Communications. 13 (1), 3363 (2022).</li><li>Benisch, M., Benzinger, D., Kumar, S., Hu, H., Khammash, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+closed-loop+feedback+control+of+the+unfolded+protein+response+optimizes+protein+production.">Optogenetic closed-loop feedback control of the unfolded protein response optimizes protein production.</a> Metabolic Engineering. 77, 32-40 (2023).</li><li>Melendez, J., Patel, M., Oakes, B. L., Xu, P., Morton, P., McClean, M. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+optogenetic+control+of+intracellular+protein+concentration+in+microbial+cell+cultures.">Real-time optogenetic control of intracellular protein concentration in microbial cell cultures.</a> Integrative Biology. 6 (3), 366-372 (2014).</li><li>Datta, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+feedback-enabled+optogenetic+stimulation+and+spectroscopy+in+microwell+plates.">High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates.</a> bioRxiv. , (2022).</li><li>Pouzet, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+control+of+beta-carotene+bioproduction+in+yeast+across+multiple+lab-scales.">Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales.</a> Frontiers in Bioengineering and Biotechnology. 11, 1085268 (2023).</li><li>Pouzet, S., Banderas, A., Le Bec, M., Lautier, T., Truan, G., Hersen, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+promise+of+optogenetics+for+bioproduction:+dynamic+control+strategies+and+scale-up+instruments.">The promise of optogenetics for bioproduction: dynamic control strategies and scale-up instruments.</a> Bioengineering. 7 (4), 151 (2020).</li></ol>

The authors have nothing to disclose.

The Lustro protocol presented here automates the culturing, illumination, and measurement processes, enabling high-throughput screening and characterization of optogenetic systems6. This is achieved by integrating an illumination device, microplate reader, and shaking device into an automation workstation. This protocol specifically demonstrates Lustro&#39;s utility for screening different optogenetic constructs integrated into the yeast S. cerevisiae and comparing light induction program...

Optogenetics is a powerful technique that utilizes light-sensitive proteins to control the behavior of cells with high precision1,2,3. However, prototyping optogenetic constructs and identifying optimal illumination conditions can be time-consuming, making it difficult to optimize optogenetic systems4,5. High-throughput methods to rapidly screen and characterize the activity of optogenetic systems can accelerate the design-build-test cycle for prototyping constructs and exploring their function.
The Lustro platform was developed as a laboratory automation technique designed for high-throughput screening and characterization of optogenetic systems. It integrates a microplate reader, illumination device, and shaking device with an automation workstation6. Lustro combines automated culturing and light stimulation of cells in microwell plates (Figure 1 and Supplementary Figure 1), enabling the rapid screening and comparison of different optogenetic systems. The Lustro platform is highly adaptable and can be generalized to work with other laboratory automation robots, illumination devices, plate readers, cell types, and optogenetic systems, including those responsive to different wavelengths of light.
This protocol demonstrates the setup and use of Lustro for characterizing an optogenetic system. Optogenetic control of split transcription factors in yeast is used as an example system to illustrate the function and utility of the platform by probing the relationship between light inputs and the expression of a fluorescent reporter gene, mScarlet-I7. By following this protocol, researchers can streamline the optimization of optogenetic systems and accelerate the discovery of new strategies for the dynamic control of biological systems.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>96-well glass bottom plate with&#160; #1.5 cover glass</td>
			<td>Cellvis</td>
			<td>P96-1.5H-N</td>
			<td></td>
		</tr>
		<tr>
			<td>BioShake 3000-T elm (heater shaker)</td>
			<td>QINSTRUMENTS</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fluent Automation Workstation</td>
			<td>Tecan</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>LITOS (alternative illumination device)</td>
			<td>Hohener, et al. Scientific Reports. 2022</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>optoPlate-96 (illumination device)</td>
			<td>Bugaj, et al. Nature Protocols. 2019</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Robotic Gripper Arm</td>
			<td>Tecan</td>
			<td></td>
			<td>Standard or long Z axes; regular gripper head or automatic Finger Exchange System gripper head, both with a choice of gripper fingers &#8211; eccentric, long eccentric, centric, tube; barcode reader option</td>
		</tr>
		<tr>
			<td>Spark (plate reader)</td>
			<td>Tecan</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Synthetic Complete media</td>
			<td>SigmaAldrich</td>
			<td>Y1250</td>
			<td></td>
		</tr>
		<tr>
			<td>Tecan Connect (user alert app)</td>
			<td>Tecan</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>yMM1734 (BY4741 Mat&#945; ura3&#916;0::5&#39; Ura3 homology, pRPL18B-Gal4DBD-eMagA-tENO1, pRPL18B-eMagB-Gal4AD-tENO1, pGAL1-mScarlet-I-tENO1, Ura3, Ura 3&#39; homology&#160; his3D1 leu2D0 lys2D0 gal80::KANMX gal4::spHIS5)</td>
			<td>Harmer, et al. ACS Syn Bio. 2023</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>yMM1763 (BY4741 Mat&#945; ura3&#916;0::5&#39; Ura3 homology, pRPL18B-Gal4DBD-CRY2(535)-tENO1, pRPL18B-Gal4AD-CIB1-tENO1, pGAL1-mScarlet-I-tENO1, Ura3, Ura 3&#39; homology&#160; his3D1 leu2D0 lys2D0 gal80::KANMX gal4::spHIS5)</td>
			<td>Harmer, et al. ACS Syn Bio. 2023</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>yMM1765 (BY4741 Mat&#945; ura3&#916;0::5&#39; Ura3 homology, pRPL18B-Gal4DBD-eMagA-tENO1, pRPL18B-eMagBM-Gal4AD-tENO1, pGAL1-mScarlet-I-tENO1, Ura3, Ura 3&#39; homology&#160; his3D1 leu2D0 lys2D0 gal80::KANMX gal4::spHIS5)</td>
			<td>Harmer, et al. ACS Syn Bio. 2023</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>YPD Agar</td>
			<td>SigmaAldrich</td>
			<td>Y1500</td>
			<td></td>
		</tr>
	</tbody>
</table>

high-throughput optogenetics experiments in yeast using the automated platform lustro

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&#160;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&#39;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.

Author Spotlight: Advancing Optogenetics Research Using Lustro 

High-Throughput Optogenetics Experiments in Yeast Using the Automated Platform Lustro

Different devices such as bioreactors and microwell plate illuminators are currently available. Bioreactors offer fine temporal resolution but are limited in throughput. Microwell plate devices offer higher throughput, but lack automation for reliable recording of outputs over time.Lustro offers reliable and high throughput characterization of optogenetic systems in real time. It can also interface with assays that can be performed by liqui-handling robots. Optogenetic systems are an attractive tool due to the fine spatial and temporal control they offer over cellular behavior.The ability to design, build, and test optogenetic systems more rapidly will pave the way for better understanding and control of biological behavior.

Figure 4A shows the fluorescence values over time for an optogenetic strain expressing a fluorescent reporter controlled by a light-inducible split transcription factor. The different light conditions used in the experiment are reflected by variations in the duty cycle, which represents the percentage of time the light is on. The overall fluorescence level is observed to be proportional to the duty cycle of the light stimulation. Figure 4B displays the correspon...

Watch this Scientific Journal Video about Advancing Optogenetics Research Using Lustro at JoVE.com

This protocol outlines the steps for utilizing the automated platform Lustro to perform high-throughput characterization of optogenetic systems in yeast.

Optogenetics offers precise control over cellular behavior by utilizing genetically encoded light-sensitive proteins. However, optimizing these systems to ...

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Using Lustro for Automated High-Throughput Optogenetic Characterization of Yeast

Start by setting up the automation workstation. Incorporate a microplate illumination device, such as an optoPlate, that allows convenient robot gripper arm access. Next, process a spreadsheet with the available MATLAB script to program the optoPlate.Execute the light stimulation program by flashing onto the optoPlate. To program the robot, troubleshoot any potential errors to ensure the proper functioning of the carrier and LabWare definitions. Run an empty plate through the script loop multiple times to verify the robot gripper arm's ability to pick up and place the plate accurately.Next, select colonies from the plates to set up the sample plate. Then inoculate them into three milliliters of synthetic complete media in glass culture tubes. Incubate these cultures overnight at 30 degrees Celsius on a roller drum in the dark.In cuvette, dilute 200 microliters of the culture in one milliliter of synthetic complete medium. Record its optical density using a spectrophotometer. Next, dilute each overnight culture to an optical density of 0.1 in glass culture tubes.Pipette the diluted cultures into a 96-well plate. Include wells with blank media and non-fluorescent cells as negative controls. Incubate the sample plate in a shaker incubator at 30 degrees Celsius for five hours.Now, place the sample plate on the heater shaker. Initiate the automation script by clicking on Run. Once the initial measurement has been recorded on the plate reader, start the light stimulation program by switching on the power strip of the illumination device.The fluorescence values over time for an optogenetic strain showed that the overall fluorescence level was proportional to the duty cycle of the light stimulation. The corresponding optical density values were consistent, suggesting that growth remained unaffected by varying light conditions. Different optogenetic strains employed different responses to light pulse intensity, period, and duty cycle variations.

493 Views.  University of Wisconsin-Madison.  This protocol outlines the steps for utilizing the automated platform Lustro to perform high-throughput characterization of optogenetic systems in yeast.

Yeast Optogenetic Response Analysis Using the Lustro Automation Technique

Summary