Name: determination of mitochondrial respiration and glycolysis in ex vivo retinal tissue samples
Uploaded: 2021-08-04T14:45:00
Description: Watch this Scientific Journal Video about Determination of Mitochondrial Respiration and Glycolysis in Ex Vivo Retinal Tissue Samples at JoVE.com

This work is supported by the Intramural Research Program of the National Eye Institute (ZIAEY000450 and ZIAEY000546).

All mouse protocols were approved by the Animal Care and Use Committee of the National Eye Institute (NEI ASP# 650). Mice were housed in 12 h light-dark conditions and cared for by following the recommendations of the Guide for the Care and Use of Laboratory Animals, the Institute of Laboratory Animal Resources, and the Public Health Service Policy on Humane Care and Use of Laboratory Animals.
1. Hydrating sensor cartridge and preparation of the assay medium
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	<li>The day before the expe...

<ol>
	<li>Nunnari, J., Suomalainen, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondria:+In+sickness+and+in+health.">Mitochondria: In sickness and in health.</a> Cell. 148 (6), 1145-1159 (2012).</li><li>Wong-Riley, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Energy+metabolism+of+the+visual+system.">Energy metabolism of the visual system.</a> Eye Brain. 2, 99-116 (2010).</li><li>Yu, D. Y., Cringle, S. 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H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retinal+energy+demands+control+vascular+supply+of+the+retina+in+development+and+disease:+The+role+of+neuronal+lipid+and+glucose+metabolism.">Retinal energy demands control vascular supply of the retina in development and disease: The role of neuronal lipid and glucose metabolism.</a> Progress in Retina and Eye Research. 64, 131-156 (2018).</li><li>Hurley, J. B., Lindsay, K. J., Du, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glucose,+lactate,+and+shuttling+of+metabolites+in+vertebrate+retinas.">Glucose, lactate, and shuttling of metabolites in vertebrate retinas.</a> Journal of Neuroscience Research. 93 (7), 1079-1092 (2015).</li><li>Haydinger, C. D., Kittipassorn, T., Peet, D. 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S. A. 116 (9), 3530-3535 (2019).</li><li>Wright, A. F., Chakarova, C. F., Abd El-Aziz, M. M., Bhattacharya, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Photoreceptor+degeneration:+genetic+and+mechanistic+dissection+of+a+complex+trait.">Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait.</a> Nature Reviews in Genetics. 11 (4), 273-284 (2010).</li><li>Jarrett, S. G., Boulton, M. 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P., Ibrahim, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolic+dysregulation+and+neurovascular+dysfunction+in+diabetic+retinopathy.">Metabolic dysregulation and neurovascular dysfunction in diabetic retinopathy.</a> Antioxidants. 9 (12), (2020).</li><li>Futterman, S., Kinoshita, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolism+of+the+retina.+I.+Respiration+of+cattle+retina.">Metabolism of the retina. I. Respiration of cattle retina.</a> Journal of Biological Chemistry. 234 (4), 723-726 (1959).</li><li>Linsenmeier, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+light+and+darkness+on+oxygen+distribution+and+consumption+in+the+cat+retina.">Effects of light and darkness on oxygen distribution and consumption in the cat retina.</a> Journal of General Physiology. 88 (4), 521-542 (1986).</li><li>Medrano, C. J., Fox, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oxygen+consumption+in+the+rat+outer+and+inner+retina:+light-+and+pharmacologically-induced+inhibition.">Oxygen consumption in the rat outer and inner retina: light- and pharmacologically-induced inhibition.</a> Experiments in Eye Research. 61 (3), 273-284 (1995).</li><li>Kooragayala, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantification+of+oxygen+consumption+in+retina+ex+vivo+demonstrates+limited+reserve+capacity+of+photoreceptor+mitochondria.">Quantification of oxygen consumption in retina ex vivo demonstrates limited reserve capacity of photoreceptor mitochondria.</a> Investigative Ophthalmology and Visual Science. 56 (13), 8428-8436 (2015).</li><li>Adlakha, Y. K., Swaroop, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+mitochondrial+oxygen+consumption+in+the+retina+ex+vivo:+applications+for+retinal+disease.">Determination of mitochondrial oxygen consumption in the retina ex vivo: applications for retinal disease.</a> Methods in Molecular Biology. 1753, 167-177 (2018).</li><li>. Agilent Mitocondrial stress test user guide Available from: <a target="_blank" href="https://www.agilent.com/cs/library/usermanuals/public/XF_Cell_Mito_Stress_Test_Kit_User_Guide.pdf">https://www.agilent.com/cs/library/usermanuals/public/XF_Cell_Mito_Stress_Test_Kit_User_Guide.pdf</a> (2021)</li><li>. Agilent Glycolytic rate assay user guide Available from: <a target="_blank" href="https://www.agilent.com/cs/library/usermanuals/public/103344-400.pdf">https://www.agilent.com/cs/library/usermanuals/public/103344-400.pdf</a> (2021)</li><li>. Agilent wave 2.6 user guide Available from: <a target="_blank" href="https://www.agilent.com/cs/library/usermanuals/public/103344-400.pdf">https://www.agilent.com/cs/library/usermanuals/public/103344-400.pdf</a> (2021)</li><li>. AVMA Guidelines for the Euthanasia of Animals Available from: <a target="_blank" href="https://www.avma.org/sites/default/files/2020-01/2020-Euthanasia-Final-1-17-20.pdf">https://www.avma.org/sites/default/files/2020-01/2020-Euthanasia-Final-1-17-20.pdf</a> (2021)</li><li>. Improving Quantification of Cellular Glycolytic Rate Using Agilent Seahorse XF Technology Available from: <a target="_blank" href="https://www.agilent.com/cs/library/whitepaper/public/whitepaper-improve-quantification-of-cellular-glycolytic-rate-cell-analysis-5991-7894en-agilent.pdf">https://www.agilent.com/cs/library/whitepaper/public/whitepaper-improve-quantification-of-cellular-glycolytic-rate-cell-analysis-5991-7894en-agilent.pdf</a> (2021)</li><li>. 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Agilent sensor cartridges and cell culture microplates Available from: <a target="_blank" href="https://www.agilent.com/cs/library/brochures/5991-8657EN_seahorse_plastics_brochure.pdf">https://www.agilent.com/cs/library/brochures/5991-8657EN_seahorse_plastics_brochure.pdf</a> (2021)</li><li>. Agilent Seahorse XF Glycolysis Stress Test Kit User Guide Available from: <a target="_blank" href="https://www.agilent.com/cs/library/usermanuals/public/XF_Glycolysis_Stress_Test_Kit_User_Guide.pdf">https://www.agilent.com/cs/library/usermanuals/public/XF_Glycolysis_Stress_Test_Kit_User_Guide.pdf</a> (2021)</li><li>Fan, Y. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+bioassay+to+measure+energy+metabolism+in+mouse+colonic+crypts,+organoids,+and+sorted+stem+cells.">A bioassay to measure energy metabolism in mouse colonic crypts, organoids, and sorted stem cells.</a> American Journal of Physiology-Gastrointestinal and Liver Physiology. 309, 1-9 (2015).</li><li>Huang, L., 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=Ductal+pancreatic+cancer+modeling+and+drug+screening+using+human+pluripotent+stem+cell-+and+patient-derived+tumor+organoids.">Ductal pancreatic cancer modeling and drug screening using human pluripotent stem cell- and patient-derived tumor organoids.</a> Nature Medicine. 21 (11), 1364-1371 (2015).</li><li>Jeon, C. J., Strettoi, E., Masland, R. 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M., 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=Identification+of+a+novel+mitochondrial+uncoupler+that+does+not+depolarize+the+plasma+membrane.">Identification of a novel mitochondrial uncoupler that does not depolarize the plasma membrane.</a> Molecular Metabolism. 3 (2), 114-123 (2014).</li><li>Corso-Diaz, X., 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=Genome-wide+profiling+identifies+DNA+methylation+signatures+of+aging+in+rod+photoreceptors+associated+with+alterations+in+energy+metabolism.">Genome-wide profiling identifies DNA methylation signatures of aging in rod photoreceptors associated with alterations in energy metabolism.</a> Cell Reports. 31 (3), 107525 (2020).</li><li>Berkowitz, B. 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Provided here are detailed instructions for performing microplate-based assays of mitochondrial respiration and glycolysis activity using ex vivo, freshly dissected retinal punch disks. The protocol has been optimized to: 1) ensure the use of a suitable assay medium for ex vivo retinal tissue; 2) employ proper size of retinal punch disks to obtain OCR and ECAR readings that fall within the machine&#39;s optimal detecting range; 3) coating mesh inserts to enhance the adhesiveness of retinal punch for sta...

Mitochondria are essential organelle that regulates cellular metabolism, signaling, homeostasis, and apoptosis by coordinating multiple crucial physiological processes1. Mitochondria serve as the powerhouse in the cell to generate adenosine triphosphate (ATP) through oxidative phosphorylation (OXPHOS) and provide energy that supports almost all cellular events. The majority of cellular oxygen is metabolized in mitochondria, where it serves as the final electron acceptor in the electron transport chain (ETC) during aerobic respiration. Low amounts of ATP can also be produced from glycolysis in the cytosol, where glucose is converted to pyruvate, which can be further converted to lactate or be transported into mitochondria and oxidized to acetyl-CoA, a substrate in the tricarboxylic acid cycle (TCA cycle).
The retina is one of the most metabolically active tissues in mammals2, displaying high levels of mitochondrial respiration and extremely high oxygen consumption3. The rod and cone photoreceptors contain a high density of mitochondria4, and OXPHOS generates most ATP in the retina5. In addition, the retina also relies heavily on aerobic glycolysis6,7 by converting glucose to lactate5. Mitochondrial defects are associated with various neurodegenerative diseases8,9; and with its unique high energy demands, the retina is especially vulnerable to metabolic defects, including those affecting mitochondrial OXPHOS4 and glycolysis10. Mitochondrial dysfunction and defects in glycolysis are implicated in retinal11,12 and macular13 degenerative diseases, age-related macular degeneration10,14,15,16, and diabetic retinopathy17,18. Therefore, accurate measurements of mitochondrial respiration and glycolysis can provide important parameters for assessing the integrity and health of the retina.
Mitochondrial respiration can be measured through the determination of oxygen consumption rate (OCR). Given that the conversion of glucose to pyruvate and subsequently to lactate results in extrusion of protons into and acidification of the extracellular environment, measurements of the extracellular acidification rate (ECAR) provide an indication of glycolysis flux. As the retina is composed of multiple cell types with intimate relationships and active synergy, including the exchange of substrates6, it is imperative to analyze mitochondrial function and metabolism in the context of whole retinal tissue with intact lamination and circuitry. For the past several decades, the Clark type O2 electrodes and other oxygen microelectrodes have been used to measure oxygen consumption in the retina19,20,21. These oxygen electrodes have major limitations in sensitivity, requirement of a large sample volume, and the need for continuous stirring of suspending sample, which usually leads to the disruption of cellular and tissue context. The protocol described here was developed using a microplate-based, fluorescence technique to measure mitochondrial energy metabolism in freshly dissected ex vivo mouse retina tissue. It allows mid-throughput real-time measurements of both OCR and ECAR simultaneously using a small sample (1 mm punch) of ex vivo retinal tissue while avoiding the need for suspension and continuous stirring.
Demonstrated here is the experimental procedure for mitochondrial stress assay and glycolytic rate assay on freshly dissected retinal punch disks. This protocol allows the measurement of mitochondria-related metabolic activities in an ex vivo tissue context. Different from the assays performed using cultured cells, the readings obtained here reflect combined energy metabolism at the tissue level and are influenced by interactions between the different cell types within the tissue. The protocol is modified from a previously published version22,23 to adapt to the new generation of the Agilent Seahorse extracellular flux 24-wells (XFe24) analyzer with Islet Capture plate. The assay medium, injection compound concentrations, and number/duration of assay cycles have also been optimized for retinal tissue. A detailed step-by-step protocol is given for the preparation of retinal punch disks. More information on the program setup and data analysis can be obtained from the manufacturer&#39;s user guide24,25,26.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1X PBS</td>
			<td>Thermo Fisher</td>
			<td>14190-144</td>
			<td></td>
		</tr>
		<tr>
			<td>2-Deoxy glucose (2-DG), 500 mM stock solution</td>
			<td>Sigma</td>
			<td>D6134</td>
			<td>Dissolve in Seahorse XF DMEM medium, prepare ahead of time</td>
		</tr>
		<tr>
			<td>30-gauge needle</td>
			<td>BD Precision Glide</td>
			<td>305106</td>
			<td></td>
		</tr>
		<tr>
			<td>Antimycin A, 10 mM stock solution</td>
			<td>Sigma</td>
			<td>A8674</td>
			<td>Dissolve in DMSO, prepare ahead of time</td>
		</tr>
		<tr>
			<td>Bam15, 10 mM stock solution</td>
			<td>TimTec</td>
			<td>ST056388</td>
			<td>Dissolve in DMSO, prepare ahead of time</td>
		</tr>
		<tr>
			<td>Biopsy puncher, 1 mm</td>
			<td>Integra Miltex</td>
			<td>33-31AA</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell-Tak</td>
			<td>Corning Life Sciences</td>
			<td>CB40240</td>
			<td></td>
		</tr>
		<tr>
			<td>CO2 asphyxiation chamber</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Dissection forceps-Dumont #5</td>
			<td>Fine Science Tools</td>
			<td>11251-10</td>
			<td>Stright tip</td>
		</tr>
		<tr>
			<td>Dissection forceps-Dumont #7</td>
			<td>Fine Science Tools</td>
			<td>11274-20</td>
			<td>Curved tip</td>
		</tr>
		<tr>
			<td>Dissection microscope</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Sigma</td>
			<td>D2438</td>
			<td></td>
		</tr>
		<tr>
			<td>Graefe forceps</td>
			<td>Fine Science Tools</td>
			<td>11051-10</td>
			<td>Curved, Serrated tip</td>
		</tr>
		<tr>
			<td>Microscissors</td>
			<td>Fine Science Tools</td>
			<td>15004-08</td>
			<td>Curved tip</td>
		</tr>
		<tr>
			<td>NaOH solution, 1 M</td>
			<td>Sigma-Aldrich</td>
			<td>S8263</td>
			<td>Aqueous solution, prepare ahead of time</td>
		</tr>
		<tr>
			<td>Rotenone, 10 mM stock solution</td>
			<td>Sigma</td>
			<td>R8875</td>
			<td>Dissolve in DMSO, prepare ahead of time</td>
		</tr>
		<tr>
			<td>Seahorse calibration medium</td>
			<td>Agilent</td>
			<td>100840-000</td>
			<td></td>
		</tr>
		<tr>
			<td>Seahorse XF 1.0 M glucose</td>
			<td>Agilent</td>
			<td>103577-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Seahorse XF 100 mM pyruvate</td>
			<td>Agilent</td>
			<td>103578-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Seahorse XF 200 mM glutamine</td>
			<td>Agilent</td>
			<td>103579-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Seahorse XF DMEM medium</td>
			<td>Agilent</td>
			<td>103575-100</td>
			<td>pH 7.4, with 5 mM HEPES</td>
		</tr>
		<tr>
			<td>Seahorse XFe24 Islet Capture FluxPak</td>
			<td>Agilent</td>
			<td>103518-100</td>
			<td>Containing Sensor Cartridge and Islet Capture microplate</td>
		</tr>
		<tr>
			<td>Seahorse XFe24, Extra Cellular Flux Analyzer</td>
			<td>Agilent</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium bicarbonate solution, 0.1 M</td>
			<td>Sigma-Aldrich</td>
			<td>S5761</td>
			<td>Aqueous solution, prepare ahead of time</td>
		</tr>
		<tr>
			<td>Superfine eyelash brush</td>
			<td>Ted Pella</td>
			<td>113</td>
			<td></td>
		</tr>
	</tbody>
</table>

determination of mitochondrial respiration and glycolysis in ex vivo retinal tissue samples

Mitochondrial respiration is a critical energy-generating pathway in all cells, especially retinal photoreceptors that possess a highly active metabolism. In addition, photoreceptors also exhibit high aerobic glycolysis like cancer cells. Precise measurements of these metabolic activities can provide valuable insights into cellular homeostasis under physiological conditions and in disease states. High throughput microplate-based assays have been developed to measure mitochondrial respiration and various metabolic activities in live cells. However, a vast majority of these are developed for cultured cells and have not been optimized for intact tissue samples and for application ex vivo. Described here is a detailed step-by-step protocol, using microplate-based fluorescence technology, to directly measure oxygen consumption rate (OCR) as an indicator of mitochondrial respiration, as well as extracellular acidification rate (ECAR) as an indicator of glycolysis, in intact ex vivo retinal tissue. This method has been used to successfully assess metabolic activities in adult mouse retina and demonstrate its application in investigating cellular mechanisms of aging and disease.

The data reported here are representative mitochondrial stress assay showing OCR trace (Figure 1) and glycolytic rate assay showing OCR trace and ECAR trace (Figure 2), which were performed using freshly dissected 1 mm retinal punch disks from 4 months old transgenic Nrl-L-EGFP mice36 (C57B/L6 background). These mice express GFP specifically in rod photoreceptors without altering normal retinal development, histology, and physiol...

Watch this Scientific Journal Video about Determination of Mitochondrial Respiration and Glycolysis in Ex Vivo Retinal Tissue Samples at JoVE.com

Determination of Mitochondrial Respiration and Glycolysis in Ex Vivo Retinal Tissue Samples

Described here is a detailed protocol for performing mitochondrial stress assay and glycolytic rate assay in ex vivo retinal tissue samples using a commercial bioanalyzer.

Determination of Mitochondrial Respiration and Glycolysis in Ex Vivo Retinal Tissue Samples

Mitochondrial respiration is a critical energy-generating pathway in all cells, especially retinal photoreceptors that possess a highly active metabolism. ...

This protocol provides real-time analysis of two major bioenergetic pathways:mitochondrial respiration and glycolysis in freshly dissected ex vivo mouse retinal tissues. Traditional seahorse analysis was focused on cultured monolayered cells, while this protocol allows researchers to study mitochondrial activity in freshly dissected tissues, specifically the retina. This technique is used to study mitochondria's activities and glycolysis flags in retinas of inherited retinal degeneration mouse models.It is a useful tool to retinal research and also has potential to be applied to other type of tissue to develop potential therapies. The most difficult part of this protocol is to obtain quality punch discs from freshly dissected mouse retina, so it's recommended that the individual who will perform this technique has good retinal dissecting skills. The day before the experiment, open the sensor cartridge cassette and add one milliliter of calibration medium to each well of the utility plate.Incubate overnight in a carbon dioxide-free incubator at 37 degrees Celsius to activate the fluorophores. On the day of the experiment, prepare assay medium in dilute compound drugs from stock. Warm up the assay medium in the 37 degrees Celsius water bath.Set up the assay program on the machine as described in the text manuscript. Open the lid of the cassette containing mesh inserts. Pipette eight microliters of the coating mix to each mesh insert, then use a pipette tip to gently spread the droplet around to distribute the coating mix equally throughout the mesh insert.Close the cassette and allow the mesh inserts to incubate at room temperature for at least 25 minutes for absorption. After incubation, wash the mesh inserts by pipetting four milliliters of the assay medium directly onto the inserts. Gently shake the cassette to ensure all mesh inserts are washed with the assay medium.To prepare the retinal punch, enucleate the eyes from an adult euthanized mouse and place them into ice cold PBS in a Petri dish, then place the Petri dish under a dissection microscope. Using microscissors, cut off the optic nerve, then carefully remove the extrarectus muscles attached outside the eyeball. Using a 30 gauge needle, punch a hole at the edge of the cornea.Then use fine dissection microscissors to make a circular cut along the edge of the cornea. Using sharp dissection forceps, remove the cornea, lens, and the vitreous humor from the eye cup. Make several small cuts on the scleral layer at the rim of the eye cup using fine dissection microscissors.Use two sharp dissection forceps to hold onto the scleral tissue at each side and pull on the scleral layer very carefully to remove it from the neural retina. Repeat this around the eye cup until all sclera is removed and an intact retinal cup is obtained. Make radial cuts on the retinal cup to flatten it and generate several distinct sections using dissection microscissors.Next, using a one millimeter diameter biopsy puncher, cut one retinal disc from each section of the flattened retinal cup. Punch at an equal distance from the optic nerve head. Transfer the pre-coated mesh inserts into the dissection Petri dish using forceps.With the help of two super fine eyelash brushes, place the retinal punch disc at the center of the mesh insert with the ganglion cell layer side down touching the mesh and the photoreceptor layer facing up. To load the sensor cartridge, take the hydrated sensor cartridge plate cassette out of the 37 degree Celsius incubator. After removing the hydro booster cover, place the sensor cartridge back on the utility plate.Load the desired volume of injection compound solutions into appropriate ports by holding the pipette tip at a 45 degree angle, inserting the pipette tip halfway into an injection port with the bevel of the tip against the opposite wall of the injection port. Gently load the compound into each port. Load the sensor cartridge into the machine for calibration by clicking start run button to open the machine tray.Place the sensor cartridge into the machine and click I am ready button to start calibration. Load desired volume of the assay medium into each well of the islet capture plate. Using forceps, grab the rim of the mesh insert containing retinal punch discs and take it out from the Petri dish.Lightly tap the bottom of the mesh insert on an absorbing wipe tissue to remove extra liquid and put it into the well of the islet capture plate. Repeat this step until all mesh inserts with retinal punches are placed into the islet capture plate filling the background correction wells and blank wells with empty mesh inserts. Using two Graefe forceps, press the rim of each mesh insert carefully and gently, making sure that these are securely inserted at the bottom of the islet capture plate.Place the loaded islet capture plate into a 37 degree Celsius incubator for five minutes to warm up, then eject the utility plate after the calibration is complete. Replace it with the islet capture plate containing retinal punches and resume the assay run by clicking the load cell plate button. After the run is complete, eject the sensor cartridge and islet capture plate containing retinal punches by clicking eject button, then click the done button so that the data is automatically saved as a ASYR file and screen change automatically to result display.The mitochondrial stress assay showing an OCR trace and glycolytic rate assay showing both OCR and ECAR trace were performed using freshly dissected one millimeter retinal punch discs. In the mitochondrial stress assay, Bam15 was injected to uncouple proton gradient from mitochondrial ATP production, resulting in the increase of OCR to maximal level. Rotenone and antimycin A were injected to inhibit mitochondria respiration at complex one and complex three respectively, resulting in a drop in the OCR to the minimal level.The difference between the maximal level of OCR and the last measurement of the basal OCR level reflects mitochondrial reserve capacity. In the glycolytic rate assay, injection of rotenone and antimycin A shuts down mitochondrial respiration and drives glycolysis higher. Glycolysis is seized by injecting 2-deoxy-d-glucose, which competes with glucose for hexokinase binding, causing the ECAR to drop to the minimal level.The difference between the maximal level of glyco ECAR in the last measure of glyco ECAR basal level reflects the glycolysis reserve capacity. To produce reliable data, it's critical to obtain good quality of retinal punch discs and to limit the total dissecting time within 1.5 hour. Following the experiment, one can quantify the DNA of protein content of a retinal disc in a well and use that to normalize the seahorse data.So this protocol was utilized to study development, aging, and disease in the retina. Tissue preference or reliance for different fuel substrates such as glucose or fatty acids was also analyzed.

determination-mitochondrial-respiration-glycolysis-ex-vivo-retinal

Research

JoVE Journal

Neuroscience

Transfection of Mouse Retinal Ganglion Cells by in vivo Electroporation

The targeting and refinement of RGC projections to the midbrain is a popular and powerful model system for studying how precise patterns of neural connectivity form during development. In mice, retinofugal projections are arranged in a topographic manner and form eye-specific layers in the Lateral Geniculate Nucleus (dLGN) of the thalamus and the Superior Colliculus (SC). The development of these precise patterns of retinofugal projections has typically been studied by labeling populations of RGCs with fluorescent dyes and tracers, such as horseradish peroxidase1-4. However, these methods are too coarse to provide insight into developmental changes in individual RGC axonal arbor morphology that are the basis of retinotopic map formation. They also do not allow for the genetic manipulation of RGCs.
Recently, electroporation has become an effective method for providing precise spatial and temporal control for delivery of charged molecules into the retina5-11. Current retinal electroporation protocols do not allow for genetic manipulation and tracing of retinofugal projections of a single or small cluster of RGCs in postnatal mice. It has been argued that postnatal in vivo electroporation is not a viable method for transfecting RGCs since the labeling efficiency is extremely low and hence requires targeting at embryonic ages when RGC progenitors are undergoing differentiation and proliferation6. 
In this video we describe an in vivo electroporation protocol for targeted delivery of genes, shRNA, and fluorescent dextrans to murine RGCs postnatally. This technique provides a cost effective, fast and relatively easy platform for efficient screening of candidate genes involved in several aspects of neural development including axon retraction, branching, lamination, regeneration and synapse formation at various stages of circuit development. In summary we describe here a valuable tool which will provide further insights into the molecular mechanisms underlying sensory map development.

Transfection of Mouse Retinal Ganglion Cells by in vivo Electroporation

We demonstrate an in vivo electroporation protocol for transfecting single or small clusters of retinal ganglion cells (RGCs) and other retinal cell types in postnatal mice over a wide range of ages. The ability to label and genetically manipulate postnatal RGCs in vivo is a powerful tool for developmental studies.

The targeting and refinement of RGC projections to the midbrain is a popular and powerful model system for studying how precise patterns of neural ...

Determination of Mitochondrial Membrane Potential and Reactive Oxygen Species in Live Rat Cortical Neurons

Mitochondrial membrane potential (&Delta;&Psi;m) is critical for maintaining the physiological function of the respiratory chain to generate ATP. A significant loss of &Delta;&Psi;m renders cells depleted of energy with subsequent death. Reactive oxygen species (ROS) are important signaling molecules, but their accumulation in pathological conditions leads to oxidative stress. The two major sources of ROS in cells are environmental toxins and the process of oxidative phosphorylation. Mitochondrial dysfunction and oxidative stress have been implicated in the pathophysiology of many diseases; therefore, the ability to determine &Delta;&Psi;m and ROS can provide important clues about the physiological status of the cell and the function of the mitochondria. 
Several fluorescent probes (Rhodamine 123, TMRM, TMRE, JC-1) can be used to determine &Delta;&psi;m in a variety of cell types, and many fluorescence indicators (Dihydroethidium, Dihydrorhodamine 123, H2DCF-DA) can be used to determine ROS. Nearly all of the available fluorescence probes used to assess &Delta;&Psi;m or ROS are single-wavelength indicators, which increase or decrease their fluorescence intensity proportional to a stimulus that increases or decreases the levels of &Delta;&Psi;m or ROS. Thus, it is imperative to measure the fluorescence intensity of these probes at the baseline level and after the application of a specific stimulus. This allows one to determine the percentage of change in fluorescence intensity between the baseline level and a stimulus. This change in fluorescence intensity reflects the change in relative levels of &Delta;&Psi;m or ROS. In this video, we demonstrate how to apply the fluorescence indicator, TMRM, in rat cortical neurons to determine the percentage change in TMRM fluorescence intensity between the baseline level and after applying FCCP, a mitochondrial uncoupler. The lower levels of TMRM fluorescence resulting from FCCP treatment reflect the depolarization of mitochondrial membrane potential. We also show how to apply the fluorescence probe H2DCF-DA to assess the level of ROS in cortical neurons, first at baseline and then after application of H2O2. This protocol (with minor modifications) can be also used to determine changes in &#x2206;&#x03A8;m and ROS in different cell types and in neurons isolated from other brain regions.

We demonstrate application of the fluorescence indicator, TMRM, in cortical neurons to determine the relative changes in TMRM fluorescence intensity before and after application of a specific stimulus. We also show application of the fluorescence probe H2DCF-DA to assess the relative level of reactive oxygen species in cortical neurons.

Mitochondrial membrane potential (&Delta;&Psi;m) is critical for maintaining the physiological function of the respiratory chain to generate ATP.  A ...

Functional Neuroimaging Using Ultrasonic Blood-brain Barrier Disruption and Manganese-enhanced MRI

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains technically challenging. One approach, Activation-Induced Manganese-enhanced MRI (AIM MRI), has been used successfully to map neuronal activity in rodents 1-5. In AIM MRI, Mn2+ acts a calcium analog and accumulates in depolarized neurons 6,7. Because Mn2+ shortens the T1 tissue property, regions of elevated neuronal activity will enhance in MRI. Furthermore, Mn2+ clears slowly from the activated regions; therefore, stimulation can be performed outside the magnet prior to imaging, enabling greater experimental flexibility. However, because Mn2+ does not readily cross the blood-brain barrier (BBB), the need to open the BBB has limited the use of AIM MRI, especially in mice.
One tool for opening the BBB is ultrasound. Though potentially damaging, if ultrasound is administered in combination with gas-filled microbubbles (i.e., ultrasound contrast agents), the acoustic pressure required for BBB opening is considerably lower. This combination of ultrasound and microbubbles can be used to reliably open the BBB without causing tissue damage 8-11.
Here, a method is presented for performing AIM MRI by using microbubbles and ultrasound to open the BBB. After an intravenous injection of perflutren microbubbles, an unfocused pulsed ultrasound beam is applied to the shaved mouse head for 3 minutes. For simplicity, we refer to this technique of BBB Opening with Microbubbles and UltraSound as BOMUS 12. Using BOMUS to open the BBB throughout both cerebral hemispheres, manganese is administered to the whole mouse brain. After experimental stimulation of the lightly sedated mice, AIM MRI is used to map the neuronal response.
To demonstrate this approach, herein BOMUS and AIM MRI are used to map unilateral mechanical stimulation of the vibrissae in lightly sedated mice 13. Because BOMUS can open the BBB throughout both hemispheres, the unstimulated side of the brain is used to control for nonspecific background stimulation. The resultant 3D activation map agrees well with published representations of the vibrissae regions of the barrel field cortex 14. The ultrasonic opening of the BBB is fast, noninvasive, and reversible; and thus this approach is suitable for high-throughput and/or longitudinal studies in awake mice.

A technique is described for broadly opening the blood-brain barrier in the mouse using microbubbles and ultrasound. Using this technique, manganese can be administered to the mouse brain. Because manganese is an MRI contrast agent that accumulates in depolarized neurons, this approach enables imaging of neuronal activity.

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains ...

Ex Vivo Preparations of the Intact Vomeronasal Organ and Accessory Olfactory Bulb

The mouse accessory olfactory system (AOS) is a specialized sensory pathway for detecting nonvolatile social odors, pheromones, and kairomones. The first neural circuit in the AOS pathway, called the accessory olfactory bulb (AOB), plays an important role in establishing sex-typical behaviors such as territorial aggression and mating. This small (&#60;1 mm3) circuit possesses the capacity to distinguish unique behavioral states, such as sex, strain, and stress from chemosensory cues in the secretions and excretions of conspecifics. While the compact organization of this system presents unique opportunities for recording from large portions of the circuit simultaneously, investigation of sensory processing in the AOB remains challenging, largely due to its experimentally disadvantageous location in the brain. Here, we demonstrate a multi-stage dissection that removes the intact AOB inside a single hemisphere of the anterior mouse skull, leaving connections to both the peripheral vomeronasal sensory neurons (VSNs) and local neuronal circuitry intact. The procedure exposes the AOB surface to direct visual inspection, facilitating electrophysiological and optical recordings from AOB circuit elements in the absence of anesthetics. Upon inserting a thin cannula into the vomeronasal organ (VNO), which houses the VSNs, one can directly expose the periphery to social odors and pheromones while recording downstream activity in the AOB. This procedure enables controlled inquiries into AOS information processing, which can shed light on mechanisms linking pheromone exposure to changes in behavior.

Ex Vivo Preparations of the Intact Vomeronasal Organ and Accessory Olfactory Bulb

The mouse accessory olfactory bulb (AOB) has been difficult to study in the context of sensory coding. Here, we demonstrate a dissection that produces an ex vivo preparation in which AOB neurons remain functionally connected to their peripheral inputs, facilitating research into information processing of mouse pheromones and kairomones.

The mouse accessory olfactory system (AOS) is a specialized sensory pathway for detecting nonvolatile social odors, pheromones, and kairomones. The first ...

Simultaneous ex vivo Functional Testing of Two Retinas by in vivo Electroretinogram System

An In vivo electroretinogram (ERG) signal is composed of several overlapping components originating from different retinal cell types, as well as noise from extra-retinal sources. Ex vivo ERG provides an efficient method to dissect the function of retinal cells directly from an intact isolated retina of animals or donor eyes. In addition, ex vivo ERG can be used to test the efficacy and safety of potential therapeutic agents on retina tissue from animals or humans. We show here how commercially available in vivo ERG systems can be used to conduct ex vivo ERG recordings from isolated mouse retinas. We combine the light stimulation, electronic and heating units of a standard in vivo system with custom-designed specimen holder, gravity-controlled perfusion system and electromagnetic noise shielding to record low-noise ex vivo ERG signals simultaneously from two retinas with the acquisition software included in commercial in vivo systems. Further, we demonstrate how to use this method in combination with pharmacological treatments that remove specific ERG components in order to dissect the function of certain retinal cell types.

Simultaneous ex vivo Functional Testing of Two Retinas by in vivo Electroretinogram System

Ex vivo ERG can be used to record electrical activity of retinal cells directly from isolated intact retinas of animals or humans. We demonstrate here how common in vivo ERG systems can be adapted for ex vivo ERG recordings in order to dissect the electrical activity of retinal cells.

An In vivo electroretinogram (ERG) signal is composed of several overlapping components originating from different retinal cell types, as well as noise ...

Ex Vivo Optogenetic Dissection of Fear Circuits in Brain Slices

Optogenetic approaches are now widely used to study the function of neural populations and circuits by combining targeted expression of light-activated proteins and subsequent manipulation of neural activity by light. Channelrhodopsins (ChRs) are light-gated cation-channels and when fused to a fluorescent protein their expression allows for visualization and concurrent activation of specific cell types and their axonal projections in defined areas of the brain. Via stereotactic injection of viral vectors, ChR fusion proteins can be constitutively or conditionally expressed in specific cells of a defined brain region, and their axonal projections can subsequently be studied anatomically and functionally via ex vivo optogenetic activation in brain slices. This is of particular importance when aiming to understand synaptic properties of connections that could not be addressed with conventional electrical stimulation approaches, or in identifying novel afferent and efferent connectivity that was previously poorly understood. Here, a few examples illustrate how this technique can be applied to investigate these questions to elucidating fear-related circuits in the amygdala. The amygdala is a key region for acquisition and expression of fear, and storage of fear and emotional memories. Many lines of evidence suggest that the medial prefrontal cortex (mPFC) participates in different aspects of fear acquisition and extinction, but its precise connectivity with the amygdala is just starting to be understood. First, it is shown how ex vivo optogenetic activation can be used to study aspects of synaptic communication between mPFC afferents and target cells in the basolateral amygdala (BLA). Furthermore, it is illustrated how this ex vivo optogenetic approach can be applied to assess novel connectivity patterns using a group of GABAergic neurons in the amygdala, the paracapsular intercalated cell cluster (mpITC), as an example.

Ex Vivo Optogenetic Dissection of Fear Circuits in Brain Slices

Optogenetic approaches are widely used to manipulate neural activity and assess the consequences for brain function. Here, a technique is outlined that&#160;upon in vivo expression of the optical activator Channelrhodopsin, allows for ex vivo analysis of synaptic properties of specific long range and local neural connections in fear-related circuits.

Optogenetic approaches are now widely used to study the function of neural populations and circuits by combining targeted expression of light-activated ...

Preparing Fresh Retinal Slices from Adult Zebrafish for Ex Vivo Imaging Experiments

The retina is a complex tissue that initiates and integrates the first steps of vision. Dysfunction of retinal cells is a hallmark of many blinding diseases, and future therapies hinge on fundamental understandings about how different retinal cells function normally. Gaining such information with biochemical methods has proven difficult because contributions of particular cell types are diminished in the retinal cell milieu. Live retinal imaging can provide a view of numerous biological processes on a subcellular level, thanks to a growing number of genetically encoded fluorescent biosensors. However, this technique has thus far been limited to tadpoles and zebrafish larvae, the outermost retinal layers of isolated retinas, or lower resolution imaging of retinas in live animals. Here we present a method for generating live ex vivo retinal slices from adult zebrafish for live imaging via confocal microscopy. This preparation yields transverse slices with all retinal layers and most cell types visible for performing confocal imaging experiments using perfusion. Transgenic zebrafish expressing fluorescent proteins or biosensors in specific retinal cell types or organelles are used to extract single-cell information from an intact retina. Additionally, retinal slices can be loaded with fluorescent indicator dyes, adding to the method&#39;s versatility. This protocol was developed for imaging Ca2+ within zebrafish cone photoreceptors, but with proper markers it could be adapted to measure Ca2+ or metabolites in M&#252;ller cells, bipolar and horizontal cells, microglia, amacrine cells, or retinal ganglion cells. The retinal pigment epithelium is removed from slices so this method is not suitable for studying that cell type. With practice, it is possible to generate serial slices from one animal for multiple experiments. This adaptable technique provides a powerful tool for answering many questions about retinal cell biology, Ca2+, and energy homeostasis.

Preparing Fresh Retinal Slices from Adult Zebrafish for Ex Vivo Imaging Experiments

Imaging retinal tissue can provide single-cell information that cannot be gathered from traditional biochemical methods. This protocol describes preparation of retinal slices from zebrafish for confocal imaging. Fluorescent genetically encoded sensors or indicator dyes allow visualization of numerous biological processes in distinct retinal cell types.

The retina is a complex tissue that initiates and integrates the first steps of vision. Dysfunction of retinal cells is a hallmark of many blinding ...

Quantitative Autoradiographic Method for Determination of Regional Rates of Cerebral Protein Synthesis In Vivo

Protein synthesis is required for development and maintenance of neuronal function and is involved in adaptive changes in the nervous system. Moreover, it is thought that dysregulation of protein synthesis in the nervous system may be a core phenotype in some developmental disorders. Accurate measurement of rates of cerebral protein synthesis in animal models is important for understanding these disorders. The method that we have developed was designed to be applied to the study of awake, behaving animals. It is a quantitative autoradiographic method, so it can yield rates in all regions of the brain simultaneously. The method is based on the use of a tracer amino acid, L-[1-14C]-leucine, and a kinetic model of the behavior of L-leucine in the brain. We chose L-[1-14C]-leucine as the tracer because it does not lead to extraneous labeled metabolic products. It is either incorporated into protein or rapidly metabolized to yield 14CO2 which is diluted in a large pool of unlabeled CO2 in the brain. The method and the model also allow for the contribution of unlabeled leucine derived from tissue proteolysis to the tissue precursor pool for protein synthesis. The method has the spatial resolution to determine protein synthesis rates in cell and neuropil layers, as well as hypothalamic and cranial nerve nuclei. To obtain reliable and reproducible quantitative data, it is important to adhere to procedural details. Here we present the detailed procedures of the quantitative autoradiographic L-[1-14C]-leucine method for the determination of regional rates of protein synthesis in vivo.

Protein synthesis is&#160;a critical biological process for cells. In brain, it is required for adaptive changes. Measurement of rates of protein synthesis in the intact brain requires careful methodological considerations. Here we present the L-[1-14C]-leucine quantitative autoradiographic method for determination of regional rates of cerebral protein synthesis in vivo.

Protein synthesis is required for development and maintenance of neuronal function and is involved in adaptive changes in the nervous system. Moreover, it ...

Quantification of Immunostained Caspase-9 in Retinal Tissue

The family of caspases is known to mediate many cellular pathways beyond cell death, including cell differentiation, axonal pathfinding, and proliferation. Since the identification of the family of cell death proteases, there has been a search for tools to identify and expand the function of specific family members in development, health, and disease states. However, many of the currently commercially available caspase tools that are widely used are not specific for the targeted caspase. In this report, we delineate the approach we have used to identify, validate, and target caspase-9 in the nervous system using a novel inhibitor and genetic approaches with immunohistochemical read-outs. Specifically, we used the retinal neuronal tissue as a model to identify and validate the presence and function of caspases. This approach enables the interrogation of cell-type specific apoptotic and non-apoptotic caspase-9 functions and can be applied to other complex tissues and caspases of interest. Understanding the functions of caspases can help to expand current knowledge in cell biology, and can also be advantageous to identify potential therapeutic targets due to their involvement in disease.

Presented here is a detailed immunohistochemistry protocol to identify, validate, and target functionally relevant caspases in complex tissues.

The family of caspases is known to mediate many cellular pathways beyond cell death, including cell differentiation, axonal pathfinding, and ...

OCT-Based Multimodal Imaging of Human Donor Eyes for AMD Research

Ex Vivo OCT-Based Multimodal Imaging of Human Donor Eyes for Research into Age-Related Macular Degeneration

A progression sequence for age-related macular degeneration (AMD) learned from optical coherence tomography (OCT)-based multimodal (MMI) clinical imaging could add prognostic value to laboratory findings. In this work, ex vivo OCT and MMI were applied to human donor eyes prior to retinal tissue sectioning. The eyes were recovered from non-diabetic white donors aged &#8805;80 years old, with a death-to-preservation time (DtoP) of &#8804;6 h. The globes were recovered on-site, scored with an 18 mm trephine to facilitate cornea removal, and immersed in buffered 4% paraformaldehyde. Color fundus images were acquired after anterior segment removal with a dissecting scope and an SLR camera using trans-, epi-, and flash illumination at three magnifications. The globes were placed in a buffer within a custom-designed chamber with a 60 diopter lens. They were imaged with spectral domain OCT (30&#176; macula cube, 30 &#181;m spacing, averaging = 25), near-infrared reflectance, 488 nm autofluorescence, and 787 nm autofluorescence. The AMD eyes showed a change in the retinal pigment epithelium (RPE), with drusen or subretinal drusenoid deposits (SDDs), with or without neovascularization, and without evidence of other causes. Between June 2016 and September 2017, 94 right eyes and 90 left eyes were recovered (DtoP: 3.9 &plusmn; 1.0 h). Of the 184 eyes, 40.2% had AMD, including early intermediate (22.8%), atrophic (7.6%), and neovascular (9.8%) AMD, and 39.7% had unremarkable maculas. Drusen, SDDs, hyper-reflective foci, atrophy, and fibrovascular scars were identified using OCT. Artifacts included tissue opacification, detachments (bacillary, retinal, RPE, choroidal), foveal cystic change, an undulating RPE, and mechanical damage. To guide the cryo-sectioning, OCT volumes were used to find the fovea and optic nerve head landmarks and specific pathologies. The ex vivo volumes were registered with the in vivo volumes by selecting the reference function for eye tracking. The ex vivo visibility of the pathology seen in vivo depends on the preservation quality. Within 16 months, 75 rapid DtoP donor eyes at all stages of AMD were recovered and staged using clinical MMI methods.

Author Spotlight: Ex Vivo OCT-Based Multimodal Imaging of Human Donor Eyes for Research into Age-Related Macular Degeneration  

Laboratory assays can leverage prognostic value from the longitudinal optical coherence tomography (OCT)-based multimodal imaging of age-related macular degeneration (AMD). Human donor eyes with and without AMD are imaged using OCT, color, near-infrared reflectance scanning laser ophthalmoscopy, and autofluorescence at two excitation wavelengths prior to tissue sectioning.

A progression sequence for age-related macular degeneration (AMD) learned from optical coherence tomography (OCT)-based multimodal (MMI) clinical imaging ...