The Fralin Life Science Research Institute and The Metabolic Phenotyping Core at Virginia Tech supported this work.

NOTE: This protocol begins after one has isolated mitochondria from red skeletal muscle. Mitochondria were isolated as previously described from ~ 75 - 100 mg of red skeletal muscle13. Between 5 - 10 &#181;g/&#181;l of mitochondrial protein will be attained from this amount of tissue by resuspending the final mitochondrial pellet in &#8804;50 &#181;l of isolation buffer for mitochondria (IBM) 2 (See Frisard et al13).
1. Setup
<ol>
	<li>Prepare working stock solutions (Table 1) and mitochondrial assay solution (MAS) mixes (Table 2) for subsequent assays. 
	Note: Most of the preparation for the assays can be done in advance as most stocks solutions and MAS can be stored.</li>
	<li>Hydrate a respirometric assay cartridge in 1 ml calibration solution the night before the experiment in a non-CO2 incubator at 37 &#176;C.</li>
	<li>The day of the experiment, take out frozen stocks (substrates and mitochondrial modulators, MAS mix, MAS w/o BSA, Table 1) and thaw in 37 &#176;C bath or incubator.</li>
	<li>Prepare all substrate solutions (Table 3) and injections (Table 4-5) and adjust pH as desired (pH&#160;7.4). After the pH is adjusted, store on ice.</li>
	<li>Program the multi-well oxygen consumption measurement machine to proper mix, wait, and measure parameters (See Table 6) and label background and group/condition wells by first entering the analysis software, followed by the &#8220;Standard&#8221; mode.
	<ol>
		<li>Enter into the &#8220;Guest&#8221; forum and click on the &#8220;Assay Wizard&#8221;. Once in the &#8220;Assay Wizard&#8221;, click on &#8220;Protocol&#8221; to change mix, wait, and measure parameters. Label the background wells under the &#8220;Back. Correction&#8221; tab and be sure to highlight &#8220;Do background correction&#8221;.</li>
		<li>Label conditions by first clicking on the &#8220;Groups &#38; Labels&#8221; tab, followed by the &#8220;Group Info&#8221; tab. After these parameters are entered, click &#8220;End&#8221;, followed by &#8220;Save Template&#8221;.</li>
	</ol>
	</li>
</ol>
2. The Assay Run
<ol>
	<li>Load the injection solutions into an assay run cartridge and start the calibration by first entering the analysis software, followed by entering the &#8220;Standard&#8221; mode. Enter into the &#8220;Guest&#8221; forum. Open the template saved in Step 1.5 under the &#8220;XF&#8221; drive, under the &#8220;Templates&#8221; tab. Once open, click &#8220;Start&#8221; to begin calibration. 
	Note: The assay run cartridge must be entered into the machine with the notched corner to the bottom left. This takes about 30 min. Take care to inject solutions into the proper ports. Injections in Table 4-5 are listed in order of loading.</li>
	<li>Gently, but thoroughly mix the mitochondria stock by stirring the solution with a 200 &#181;l pipette tip, followed by gently triturating the stock with a 200 &#181;l pipette tip that has had its orifice widened by cutting ~ 3 mm off the end of the tip with scissors.</li>
	<li>Perform a bicinchoninic acid (BCA) assay to determine the protein concentration of the mitochondrial stock.</li>
	<li>Using the stock concentration acquired from step 2.3, resuspend 10&#160;&#181;g of mitochondrial protein/200&#160;&#181;l of the succinate/ rotenone substrate mix (Table 3). Resuspend 14 &#181;g of mitochondrial protein/ 200 &#181;l of the remaining substrate mixes (This must be done for each substrate mix) (Table 3). Place all mitochondrial protein/substrate mixes on ice. 
	Note: The optimal amount of mitochondrial protein per well for each assay was determined as previously described9. It was determined that the pyruvate /malate, palmitoyl carnitine/malate, glutamate/malate and electron flow assays utilizes 3.5 &#181;g of mitochondrial protein, while the succinate/rotenone assay utilizes 2.5 &#181;g of mitochondrial protein per well. Therefore, the researcher needs to resuspend enough mitochondrial protein for 4 replicates in this step since either 2.5 &#181;g or 3.5 &#181;g per 50 &#181;l is loaded per well (See step 2.6).</li>
	<li>Mix the mitochondria/ substrate solutions gently, but thoroughly by stirring the solution with a 200 &#181;l pipette tip, followed by gently triturating the stock with a 200 &#181;l pipette tip that has had ~ 3 mm of its end cut off.</li>
	<li>Place a cell culture plate on ice and in triplicate, load 50 &#181;l/well of each of the mitochondria/substrate mixes. The developers of the microplate based respirometric assay recommend leaving a minimum of two blank (no mitochondria) wells, preferably on either side on the cell culture plate.</li>
	<li>Spin the cell culture plate at 2,000 g for 20 min at 4 &#176;C. While the plate is spinning, warm up the substrate solutions in a 37 &#176;C water bath.</li>
	<li>After the spin is complete, carefully load 450 &#181;l of each substrate solution on top of its respective wells (i.e., load the pyruvate/malate substrate to the wells that have mitochondria initially resuspended in this substrate solution). Be sure to load the plate at RT. Note: Blank wells should be loaded with 500 &#181;l of substrate. Blank wells designated for the electron flow assay should be loaded with the electron flow substrate (Pyruvate/Malate + FCCP), while the coupled assay blank wells can be loaded with any coupling assay substrate. 
	Note: If performing the coupled and electron flow assays on the same plate, the researcher must reassign background wells to the respective assays after the assay run is complete using the &#8220;XF Reader&#8221; platform via the &#8220;Instrument&#8221; tab. Once within the &#8220;Instrument&#8221; setting, click on the &#8220;Administration&#8221; tab, followed by &#8220;Background Correction&#8221;. Hit &#8220;End Instrument Setup Mode&#8221; when complete. This is because the combination of ascorbate/TMPD can consume O2, thus a separate background correction is needed for each assay type.</li>
	<li>After the 450 &#181;l of substrate is added to each well, view the layer of mitochondria in the well to ensure the mitochondria are dispersed evenly in a single monolayer (20X magnification [See Rogers9, Figure 4]). Wells that do not appear to have an evenly distributed monolayer can be removed post hoc.</li>
	<li>After checking for mitochondrial adherence, insert the microplate into the respirometric assay instrument and start the assay run by clicking &#8220;OK&#8221;. 
	Note: The calibration from step 2.1 must be complete before the run will begin. Once the researcher clicks&#160;&#8220;OK&#8221;, the machine will eject the utility plate that was used for calibration.
	<ol>
		<li>Remove the utility plate and place the cell culture plate that contains the mitochondria on the tray. The blue notch on the cell culture plate should be placed in the bottom left corner of the tray. Click on, &#8220;continue&#8221; to start the assay run.</li>
	</ol>
	</li>
	<li>After the run is complete, eject the cell culture plate and cartridge by pressing &#8220;Eject&#8221; on the screen.
	<ol>
		<li>Once the plate is ejected, remove and discard the cell culture plate and cartridge and click &#8220;Continue&#8221; on the screen. The run will be automatically saved as an .xls file in the &#8220;Data&#8221; file.</li>
	</ol>
	</li>
	<li>Open this file and change the display from &#8220;O2&#8221; to &#8220;OCR&#8221; by hitting the downward arrow under the &#8220;Y1:&#8221; marker.
	<ol>
		<li>Next change &#8220;Middle Point&#8221; to &#8220;Point-to-Point Rates&#8221; under the &#8220;Rate Data Displayed As:&#8221; option. Click &#8220;OK&#8221; to apply these changes.</li>
	</ol>
	</li>
	<li>Click the &#8220;Well Group Mode&#8221; tab on bottom left of the screen to group wells of similar conditions together. Finally, click the &#8220;Sample Mean/Standard Error&#8221; tab toward the middle of the screen, to the left. Alternatively, these commands can be setup before the assay begins in the &#8220;Assay Wizard&#8221; setting. 
	Note: Each condition will have a mean &#177; standard deviation displayed for each rate and each condition. There are rate measurements taken per condition&#160;(State 2[Coupling]/State3u [Electron Flow] respiration followed by four injections). Use the mean of the State 2 rate of the second measurement, determine State 4o at the minimum point after oligomycin injection, use the maximum point for State 3 and State 3u after ADP and FCCP injection, respectively, and use the minimum point for Antimycin A induced respiration for the Coupling Assays. Use the maximum point for pyruvate/malate induced State 3u respiration, use the minimum point for rotenone induced respiration, use the maximum point for succinate induced State 3u respiration, and use the minimum point for Antimycin A induced respiration for the Electron Flow assay. All experiments were performed 3 times and the data shown are the results of a representative&#160;tracing.</li>
</ol>

<ol>
	<li>Brand, M., Nicholls, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessing+mitochondrial+dysfunction+in+cells.">Assessing mitochondrial dysfunction in cells.</a> Biochem J. 435, 297-312 (2011).</li><li>Wang, H., Hiatt, W. R., Barstow, T. J., Brass, E. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relationships+between+muscle+mitochondrial+DNA+content,+mitochondrial+enzyme+activity+and+oxidative+capacity+in+man:+alterations+with+disease.">Relationships between muscle mitochondrial DNA content, mitochondrial enzyme activity and oxidative capacity in man: alterations with disease.</a> European Journal of Applied Physiology and Occupational Physiology. 80, 22-27 (1999).</li><li>Lauri, A., Pompilio, G., Capogrossi, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mitochondrial+genome+in+aging+and+senescence.">The mitochondrial genome in aging and senescence.</a> Ageing Research Reviews. 18C, 1-15 (2014).</li><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, 1145-1159 (2012).</li><li>Dube, J. J., 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=Effects+of+acute+lipid+overload+on+skeletal+muscle+insulin+resistance,+metabolic+flexibility,+and+mitochondrial+performance.">Effects of acute lipid overload on skeletal muscle insulin resistance, metabolic flexibility, and mitochondrial performance.</a> Endocrinology and Metabolism. 307, E1117-E1124 (2014).</li><li>Disease Control and Prevention Services. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=National+diabetes+statistics+report:+estimates+of+diabetes+and+its+burden+in+the+United+States.">National diabetes statistics report: estimates of diabetes and its burden in the United States.</a> , (2014).</li><li>Guarino, R. D., 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=Method+for+determining+oxygen+consumption+rates+of+static+cultures+from+microplate+measurements+of+pericellular+dissolved+oxygen+concentration.">Method for determining oxygen consumption rates of static cultures from microplate measurements of pericellular dissolved oxygen concentration.</a> Biotechnology and Bioengineering. 86, 775-787 (2004).</li><li>Will, Y., Hynes, J., Ogurtsov, V. I., Papkovsky, D. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+mitochondrial+function+using+phosphorescent+oxygen-sensitive+probes.">Analysis of mitochondrial function using phosphorescent oxygen-sensitive probes.</a> Nature Protocols. 1, 2563-2572 (2007).</li><li>Rogers, G. W., 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+microplate+respiratory+measurements+using+minimal+quantities+of+isolated+mitochondria.">High throughput microplate respiratory measurements using minimal quantities of isolated mitochondria.</a> PloS One. 6, e21746 (2011).</li><li>Wu, 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=Multiparameter+metabolic+analysis+reveals+a+close+link+between+attenuated+mitochondrial+bioenergetic+function+and+enhanced+glycolysis+dependency+in+human+tumor+cells.">Multiparameter metabolic analysis reveals a close link between attenuated mitochondrial bioenergetic function and enhanced glycolysis dependency in human tumor cells.</a> American Journal of Physiology-Cell Physiology. 292, C125-C136 (2007).</li><li>Fernandez-Vizarra, E., Lopez-Perez, M. J., Enriquez, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+biogenetically+competent+mitochondria+from+mammalian+tissues+and+cultured+cells.">Isolation of biogenetically competent mitochondria from mammalian tissues and cultured cells.</a> Methods (San Diego, Calif.). 26, 292-297 (2002).</li><li>Frezza, C., Cipolat, S., Scorrano, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organelle+isolation:+functional+mitochondria+from+mouse+liver,+muscle+and+cultured+fibroblasts.">Organelle isolation: functional mitochondria from mouse liver, muscle and cultured fibroblasts.</a> Nature Protocols. 2, 287-295 (2007).</li><li>Frisard, M. I., 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=Low+levels+of+lipopolysaccharide+modulate+mitochondrial+oxygen+consumption+in+skeletal+muscle.">Low levels of lipopolysaccharide modulate mitochondrial oxygen consumption in skeletal muscle.</a> Metabolism. 64, 416-427 (2015).</li><li>Chance, B., Williams, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+respiratory+chain+and+oxidative+phosphorylation.">The respiratory chain and oxidative phosphorylation.</a> Advances in Enzymology and Related Subjects of Biochemistry. 17, 65-134 (1956).</li><li>Gnaiger, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+pathways+and+respiratory+control.">Mitochondrial pathways and respiratory control.</a> , (2007).</li></ol>

George W. Rogers is an employee of Seahorse Bioscience that manufactures the instrument for which these assays were developed. Open Access fees were provided by, Seahorse Bioscience, a part of Agilent Technologies.

The methods presented in this article provide step-by-step instructions for the performance of a collection of microplate based respirometric assays using mitochondria isolated from 75 - 100 mg of mouse skeletal muscle. These assays can be performed with high precision as evidenced by the tight standard deviation between triplicate wells. Importantly, these respirometric assays allow pinpointing of where abnormalities and/or adaptations may be occurring in the ETC, TCA cycle, &#946;-oxidation pathway, substrate transporters, etc. in a commonly used animal model.
It is important to highlight the rationale for using various fuels and inhibitors used in this protocol. The pyruvate/malate and glutamate/malate respirometric assays allow for the assessment of Complex I mediated respiration, as well as the assessment of their respective transporters, and in the case of glutamate, the deaminase15. Alternatively, the combination of succinate/rotenone allows the assessment of mitochondrial respiratory flux through Complex II of the ETC since rotenone inhibits complex I and succinate provides electrons to Complex II via the reduction of flavin adenine dinucleotide (FADH2)15. These assays provide substrate specific information as to coupling efficiency and maximal respiration. The electron flow assay is unique in that the combination of substrates and inhibitors allows for the assessment of multiple complexes during mitochondrial respiratory flux9. The initial substrate mix of pyruvate/malate + FCCP allows for the evaluation of maximal respiration driven by Complex I, while the injection of rotenone followed by succinate allows for the assessment maximal respiration driven by Complex II. The injection of Antimycin A, an inhibitor of Complex III, followed by the injection of ascorbate/TMPD allow the for the evaluation of respiration driven by Complex IV since the Ascorbate/TMPD is an electron donor to Cytochrome C/Complex IV. While no information on coupling efficiency is obtained, the method is ideal for very small sample sizes that preclude running multiple substrates independently. Finally, the use of palmitoyl carnitine/malate allows for the assessment of the coordination between &#946;-oxidation and the ETC since the reducing equivalent produced from the oxidation of palmitic acid (&#946;-oxidation) feed into the ETC through the electron transferring flavoprotein15. It should be noted that the Coupling and Electron Flow assays could also be used in tandem to identify changes in mitochondrial function due to some intervention (drug treatment, genetic manipulation).
The high precision attained for these assays is primarily due to thorough mixing of the mitochondria, whether it is prior to protein determination, or with the substrate solutions. Along these lines, once the mitochondria is resuspendend in the substrate solutions, it is critical to mix this solution thoroughly prior to loading the cell culture plate as described in Step 2.2 with a widened orifice pipette tip. Failure to mix the mitochondria thoroughly will lead to large variation within the assay. In addition, using a narrow orifice pipette tip will create shearing forces while mixing the mitochondria and increases the potential to damage the mitochondrial membranes and release of Cytochrome C. The adherence step (2.7) is also a critical step in this protocol. Failure to spin the loaded cell culture plate long/fast enough will result in incomplete adherence of the mitochondria to the well, thus leading increased variability between wells and measurements.
The described protocol has been optimized to include: loading an optimal amount of mitochondrial protein per well, using the correct concentrations/preparation methods to make stock and substrate solutions, altering the assay run to ensure mitochondrial state plateaus, and appropriate mixing of the mitochondrial stock and mitochondrial/substrate mixes. Prior to these optimization efforts, the authors encountered pitfalls in the assay run. The following discusses troubleshooting methods/modifications that were helpful in optimizing this protocol. With respect to optimal loading, loading too little mitochondria will not elicit a robust response, while loading too much mitochondria will exhaust the oxygen within the microchamber and lead to inaccurate measurements. Rogers et al9 provides&#160;examples of determining optimal loading amounts of mitochondria per well for microplate based respirometric assays. More often, too much mitochondria is loaded per well as evidenced by state 2 rates over 100-200 pmol/min/well and state 3 rates &#62;1500 pmol/min/well. If over loading occurs, perform an experiment with varying concentration of mitochondrial protein (e.g., between 1 - 10 &#956;g) to elicit OCRs within the dynamic range of the oxygen consumption measurement machine. Preparing and using the correct concentrations of substrates and stocks is of utmost importance. Always use the acid form of substrates/injections and adjust the pH with potassium hydroxide or HCl; sodium buffers/solutions are not recommended. In addition, resuspending substrates/stocks in DMSO or 100% ethanol will result in measurement failure or error. Be sure to use 95% ethanol where noted. It is common for palmitoyl carnitine to precipitate out of the 95% ethanol after thawing the frozen stock, thus causing large variability. Be sure to warm up the palmitoyl carnitine stock and vortex well prior to use. In addition, a highly variable pyruvate/malate assay result may be due to the pyruvate stock being &#62;2 weeks old. Be sure to remake frozen aliquots of pyruvate every 2 weeks. The assay run was modified to 2-min measurements to ensure mitochondrial state plateaus. If observation of exhaustion of ADP is desired, the researcher may extend the measurement time under the &#8220;Protocol&#8221; tab under the &#8220;Assay Wizard&#8221; forum. Finally, large variability occurs when the mitochondrial stock and mitochondria plus substrate solutions aren&#8217;t homogenized fully prior to loading. If variability between wells is high after the assay run, be sure to fully mix the substrate solution prior to the next experiment. Never vortex the mitochondria/substrate solutions, rather stir, mash, and gently triturate with a widened orifice pipette tip.
There are some limitations of this technique that are worth noting. First, the number of wells on the cell culture plate used for these assays is relatively low (i.e., 24 wells and at least 2 designated for blank wells). If it is desired to perform all 5 of these assays on one plate, the researcher is only able to examine the responses from one mouse at a time. However, it should be noted that 96 well instruments are available for higher throughput. Secondly, there are inherent strengths and weaknesses in assessing mitochondrial dysfunction in isolated mitochondria compared to in intact cells1. Some weaknesses include having less physiological relevance compared to intact cells and inducing artifacts from the isolation process. Finally, the success of this method is contingent on the quality of the mitochondrial isolation process.
Although some of these assays have been either developed in different systems or have been validated in other animal models, the methods presented herein are the first to synthesize all of the aforementioned assays for the optimal use in a multi-well oxygen consumption measurement machine using mouse skeletal muscle. Importantly, all 5 of these assays can be performed with the amount of mitochondria isolated from ~75 - 100 mg of mouse skeletal muscle, thus providing high throughput with minimal material. Of great significance, the ability of multi-well oxygen consumption technologies to perform assays with minimal quantities of mitochondria, combined with an optimized isolation method, allows the researcher to perform a multitude of other experiments with the remainder of skeletal muscle tissue (e.g., western blots, RT-PCR, enzymatic assays, etc.), which is often a struggle with this animal model.
In conclusion, the methods presented herein provide step-by-step instructions for the performance of a collection of microplate based respirometric assays using minimal quantities of mouse skeletal muscle. Importantly, the presented methods require minimal quantities of tissue and mitochondria. Once mastered, the techniques described herein will allow researchers to determine a potential mechanism of a compound or gene product on mitochondrial oxygen consumption in a commonly used animal model.

The main physiological role of skeletal muscle mitochondria is to produce ATP from oxidative phosphorylation1. Importantly, skeletal muscle mitochondria play a specific role in exercise capacity2, aging3, degenerative disease4 and Type II diabetes5. As an aging society, and Type II Diabetes being the 7th leading cause of death in the United States6, the need for methods that assess mitochondrial function has become increasingly more prevalent in biomedical research7,8. Specifically, the measurement of oxygen consumption has exceptional utility in the assessment of mitochondrial function since it represents the coordinated function between mitochondrial and nuclear genomes to express functional components of oxidative phosphorylation9.
Several technologies exist that enable the measurement of oxygen consumption in intact cells and isolated mitochondria7-10. In addition, assays have been developed for multiple cell types and tissues, and in a variety of species that allow for the measurement of mitochondrial pathways and respiratory control9,11,12. However, there is currently a void in the literature in regards to the compilation of all of these assays using isolated mitochondria from mouse skeletal muscle for use in microplate based oxygen consumption technologies. Importantly, use of microplate based respirometric assays is growing among mitochondrial biologists and allows for high throughput measurements using minimal quantities of isolated mitochondria9. Therefore, a collection of microplate based respirometric assays were developed that allow pinpointing of where abnormalities and/or adaptations may be occurring in the electron transport chain (ETC). In addition, two additional microplate based respirometric assays were developed that enable the assessment of the coordination between the tricarboxylic acid (TCA) cycle and the ETC, and between &#223;-oxidation and the ETC. Importantly, the presented methods provide a clear and concise way to measure mechanistic changes in mitochondrial function in a commonly used animal model.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Sucrose</td>
			<td>Sigma Aldrich</td>
			<td>S7903</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>D-Mannitol</td>
			<td>Sigma Aldrich</td>
			<td>63559</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>Potassium phosphate monobasic, minimum 99.0%</td>
			<td>Sigma Aldrich</td>
			<td>P5379</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>Magnesium chloride hexahydrate, ACS reagent, 99.0-102.0%</td>
			<td>Sigma Aldrich</td>
			<td>M9272</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>HEPES minimum 99.5% titration</td>
			<td>Sigma Aldrich</td>
			<td>H3375</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>EGTA</td>
			<td>Sigma Aldrich</td>
			<td>E4378</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>Essentially Fatty&#160;</td>
			<td rowspan="2">Sigma Aldrich</td>
			<td rowspan="2">A6003</td>
			<td rowspan="2">Store at 4&#176;C</td>
		</tr>
		<tr>
			<td>Acid Free- BSA</td>
		</tr>
		<tr>
			<td>Pyruvic Acid, 98%</td>
			<td>Sigma Aldrich</td>
			<td>107360</td>
			<td>Store at 4&#176;C</td>
		</tr>
		<tr>
			<td>Succinic Acid</td>
			<td>Sigma Aldrich</td>
			<td>S9512</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>L(-) Malic Acid, BioXtra, &#8805;95%</td>
			<td>Sigma Aldrich</td>
			<td>M6413</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td rowspan="2">L-Glutamic acid</td>
			<td rowspan="2">Sigma Aldrich</td>
			<td rowspan="2">G1251</td>
			<td rowspan="2">Store at room temperature</td>
		</tr>
		<tr>
		</tr>
		<tr>
			<td>N,N,N&#8242;,N&#8242;-Tetramethyl-p-phenylenediamine</td>
			<td rowspan="2">Sigma Aldrich</td>
			<td rowspan="2">T7394</td>
			<td rowspan="2">Store at room temperature</td>
		</tr>
		<tr>
			<td>99%, powder [TMPD]</td>
		</tr>
		<tr>
			<td>Palmitoyl L-carnitine chloride</td>
			<td>Sigma Aldrich</td>
			<td>P1645</td>
			<td>Store at -20&#176;C</td>
		</tr>
		<tr>
			<td>Oligomycin A, &#8805; 95% (HPLC)</td>
			<td>Sigma Aldrich</td>
			<td>75351</td>
			<td>Store at -20&#176;C</td>
		</tr>
		<tr>
			<td>Carbonyl cyanide 4-(trifluoromethoxy)</td>
			<td rowspan="3">Sigma Aldrich</td>
			<td rowspan="3">C2920</td>
			<td rowspan="3">Store at 2-8&#176;C</td>
		</tr>
		<tr>
			<td>phenylhydrazone</td>
		</tr>
		<tr>
			<td>&#8805;98% (TLC), powder [FCCP]</td>
		</tr>
		<tr>
			<td>Antimycin A from streptomyces sp.</td>
			<td>Sigma Aldrich</td>
			<td>A8674</td>
			<td>Store at -20&#176;C</td>
		</tr>
		<tr>
			<td rowspan="2">Adenosine 5&#8242;-diphosphate monopotassium salt dehydrate [ADP]</td>
			<td rowspan="2">Sigma Aldrich</td>
			<td rowspan="2">A5285</td>
			<td rowspan="2">Store at -20&#176;C</td>
		</tr>
		<tr>
		</tr>
		<tr>
			<td>Rotenone</td>
			<td>Sigma Aldrich</td>
			<td>R8875</td>
			<td>Store at room temperature</td>
		</tr>
		<tr>
			<td>Pierce&#8482; BCA Protein Assay Kit&#160;</td>
			<td>Thermo Scientific</td>
			<td>23225</td>
			<td>N/A</td>
		</tr>
	</tbody>
</table>

using isolated mitochondria from minimal quantities of mouse skeletal muscle for high throughput microplate respiratory measurements

Skeletal muscle mitochondria play a specific role in many disease pathologies. As such, the measurement of oxygen consumption as an indicator of mitochondrial function in this tissue has become more prevalent. Although many technologies and assays exist that measure mitochondrial respiratory pathways in a variety of cells, tissue and species, there is currently a void in the literature in regards to the compilation of these assays using isolated mitochondria from mouse skeletal muscle for use in microplate based technologies. Importantly, the use of microplate based respirometric assays is growing among mitochondrial biologists as it allows for high throughput measurements using minimal quantities of isolated mitochondria. Therefore, a collection of microplate based respirometric assays were developed that are able to assess mechanistic changes/adaptations in oxygen consumption in a commonly used animal model. The methods presented herein provide step-by-step instructions to perform these assays with an optimal amount of mitochondrial protein and reagents, and high precision as evidenced by the minimal variance across the dynamic range of each assay.

Figure 1 represents oxygen consumption rates (OCR) for the pyruvate/malate, succinate/rotenone, palmitoyl carnitine/malate, and glutamate/malate assays (Coupling Assays). These assay tracings are displayed as Oxygen Consumption Rate, or OCR, vs. time, are background correceted, and are displayed as point-to-point rates. Each panel represents oxygen consumption in different mitochondrial states as described by Chance and Williams14. The first panel represents basal oxygen consumption, or State 2. The second panel, after injection of ADP, represents maximal coupled respiration, or State 3. The third panel, after injection of oligomycin A (an inhibitor of Complex V), represents respiration due to proton leak, or State 4o. The fourth panel, after injection of FCCP, represents maximal uncoupled respiration, or State 3u. Finally, the fifth panel, after injection of Antimycin A, represents the inhibition of oxidative respiration. Notably, all mitochondrial states have minimal standard deviation. This is due to thorough mixing of the mitochondrial stock and the mitochondria/substrate mixes, and the attainment of a single monolayer of mitochondria after the adherence spin (Step 2.6). On the other hand, loading unequal mitochondria in each well and not attaining a single monolayer of mitochondria in the well of the microplate leads to increased standard deviation in each state as displayed in Figure 2.
The tracings in Figure 1 display plateaus for each mitochondrial state and for each substrate. The plateau attained after two measurement cycles suggests good mitochondrial quality and that the mitochondria remain adhered to the well throughout the duration of the assay. In addition, the attainment of plateaued maximal rates may be more desirable since this allows the researcher to take the average OCR at these mitochondrial states, thus reducing bias that may occur by arbitrarily selecting a point.
The amount of mitochondria per well was determined by optimization trials. The optimal amount of mitochondria per well should result in State 2 rates between 100-200 pmol/min/well and state 3 rates &#60; 1,500 pmol/min/well, since these values are within the dynamic oxygen sensing range of the multi-well oxygen consumption measurement machine. Loading too much mitochondrial protein per well may result in OCRs beyond the dynamic range of the instrument (Figure 3A). Figure 3 depicts loading 3.5 &#181;g of mitochondrial protein per well (blue tracing) compared to loading 2.5 &#181;g of mitochondrial protein per well (red tracing) for the succinate/rotenone assay. Loading too much mitochondrial protein per well can also lead to the exhaustion of oxygen within the microchamber of the well, thus preventing accurate measurement of OCR for each successive measurement9 (Figure 3B). Point-to-point OCR is the&#160;instantaneous rate of change of the OCR. If flat, the OCR is steady/stable, but if decreasing, then there may be a biologic or technical issue. The steep decline in OCR in State 3 and State 3u respiration (Figure 3A) is caused by the mitochondria exhausting the oxygen supply before the end of the measurement (Figure 3B).
Figure 4 represents OCR vs. time for the electron flow assay. The tracing is corrected and displayed as described for Figure 1. The first panel in this assay represents State 3u respiration on pyruvate/malate via Complex I. The second panel, after injection of rotenone, represents inhibition of Complex I mediated respiration. The third panel, after injection of succinate, represents substrate stimulated State 3u with electrons entering the ETC at Complex II (Complex II mediated respiration). The fourth panel, after injection of Antimycin A, represents inhibition of Complex III and thus total respiration. Finally, the fifth panel, after injection of ascorbate/TMPD, represents Complex IV mediated respiration. Similar to the tracings in Figure 1, all mitochondrial states have minimal standard deviation, and each rate has or nearly has attained a plateau.
<img alt="Figure 1" src="/files/ftp_upload/53216/53216fig1.jpg" /> 
Figure 1.&#160;Coupling Assays. (A) 10 mM Pyruvate/ 5 mM malate, (B) 10 mM succinate/ 2 &#181;M rotenone, (C) 40 &#181;M palmitoyl carnitine/ 1 mM malate, and (D) 10 mM glutamate/ 10 mM malate coupled mitochondrial respiration assay tracings as determined by multi-well measurement of oxygen consumption. Values are expressed as mean &#177; SD. Mitochondrial protein loaded per well was 3.5 &#181;g for all assays except succinate/rotenone, which utilizes 2.5 &#181;g of mitochondrial protein per well. Data represents n=3 paired biological replicates. OCR = Oxygen Consumption Rate; ADP = Adenosine diphosphate; Oligo = Oligomycin A; FCCP = Carbonyl cyanide-4- (trifluoromethoxy) phenylhydrazone; Anti-A = Antimycin A; PYR = Pyruvate; SUCC = Succinate; ROT = Rotenone; PAL-C = palmitoyl carnitine; GLUT = glutamate. &#160;<a href="https://www.jove.com/files/ftp_upload/53216/53216fig1large.png" style="font-size: 14px; line-height: 28px;" target="_blank">Please click here to view a larger version of this figure.</a>&#160;
<img alt="Figure 2" src="/files/ftp_upload/53216/53216fig2.jpg" /> 
Figure 2.&#160;Highly Variable Pyruvate/Malate Assay. Highly variable 10 mM pyruvate/ 5 mM malate assay caused by incompletely mixing mitochondria from the mitochondrial stock in the substrate/MAS mix, thus leading to variable mitochondrial protein loading in each well. Mitochondrial protein loaded per well was 3.5 &#181;g. Data represents n=3 paired biological replicates. OCR=Oxygen Consumption Rate; ADP= Adenosine diphosphate; Oligo= Oligomycin A; FCCP= Carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; Anti-A= Antimycin A; PYR=Pyruvate. <a href="https://www.jove.com/files/ftp_upload/53216/53216fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" src="/files/ftp_upload/53216/53216fig3.jpg" /> 
Figure 3.&#160;Overloading Mitochondrial Protein for the Succinate/Rotenone Assay. (A) Oxygen consumption rates outside the dynamic range of the multi-well oxygen consumption measurement machine caused by loading 3.5 &#181;g of mitochondrial protein per well (blue tracing) compared to loading 2.5 &#181;g of mitochondrial protein per well (red tracing). (B) Oxygen tension approaching zero following ADP and FCCP injections caused by loading excessive mitochondrial protein (3.5 &#181;g) per well (blue tracing) compared to loading an optimal amount (2.5 &#181;g) of mitochondrial protein per well (red tracing). Data represents n = 3 paired biological replicates per mitochondrial protein amount. OCR = Oxygen Consumption Rate; ADP = Adenosine diphosphate; Oligo = Oligomycin A; FCCP = Carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; Anti-A = Antimycin A; SUCC = Succinate; ROT = Rotenone; O2 = Oxygen; mm Hg = millimeters of mercury. <a href="https://www.jove.com/files/ftp_upload/53216/53216fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" src="/files/ftp_upload/53216/53216fig4.jpg" /> 
Figure 4.&#160;Electron Flow Assay. 5 mM pyruvate/ 1 mM malate+ 4 &#181;M FCCP, electron flow mitochondrial respiration assay tracing as determined by multi-well measurement of oxygen consumption. Values are expressed as mean &#177; SD. Mitochondrial protein loaded per well was 3.5 &#181;g. Data represents n=3 paired biological replicates. OCR = Oxygen Consumption Rate; Anti-A = Antimycin A; Asc = Ascorbate; TMPD = N,N,N&#8242;,N&#8242;-tetramethyl-p-phenylenediamine. <a href="https://www.jove.com/files/ftp_upload/53216/53216fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="0">
	<tbody>
		<tr>
			<td>Reagent</td>
			<td>Stock Concentration&#160;</td>
			<td>MW</td>
			<td>Final Volume</td>
			<td>Mass Added</td>
			<td>Comments/Description</td>
		</tr>
		<tr>
			<td></td>
			<td>(M)</td>
			<td>(g/mol)</td>
			<td>(ml)</td>
			<td>(g or ml)</td>
			<td></td>
		</tr>
		<tr>
			<td>EGTA, pH 7.2</td>
			<td>0.1</td>
			<td>380.35</td>
			<td>100 ml of 1M Tris Base</td>
			<td>3.801 g</td>
			<td>Store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>1</td>
			<td>238.3</td>
			<td>250 ml&#160;&#160;of DiH2O</td>
			<td>59. 57 g</td>
			<td>Store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>MgCl2, hexahydrate</td>
			<td>1</td>
			<td>203.31</td>
			<td>250 ml&#160;&#160;of DiH2O</td>
			<td>50.82 g</td>
			<td>Store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Pyruvate pH 7.4</td>
			<td>0.1</td>
			<td>88.06 (Comes as 14.11 M solution)</td>
			<td>40 ml&#160;&#160;of DiH2O</td>
			<td>0.283 ml of pyruvic acid</td>
			<td>Make 1 ml aliquots and store at -20 &#176;C, make fresh every two weeks</td>
		</tr>
		<tr>
			<td>Succinate pH 7.4</td>
			<td>0.5</td>
			<td>118.09</td>
			<td>100 ml&#160;&#160;of DiH2O</td>
			<td>9.4 g of succinic acid</td>
			<td>Make 1 ml aliquots and store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Malate, pH 7.4</td>
			<td>0.5</td>
			<td>134.09</td>
			<td>100 ml&#160;&#160;of 95% Ethanol</td>
			<td>6.7 g of malic acid</td>
			<td>Make 200 &#956;l aliquots and store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>TMPD</td>
			<td>0.01</td>
			<td>164.25</td>
			<td>10&#160;ml&#160;</td>
			<td>0.0164 g</td>
			<td>Make 300 &#956;l&#160;&#160;aliquots and store at -20 &#176;C; Mix with an equimolar amount of ascorbate to keep TMPD reduced</td>
		</tr>
		<tr>
			<td>Palmitoyl L-carnitine chloride</td>
			<td>0.01</td>
			<td>436.07</td>
			<td>1.14 ml&#160;&#160;of 95% Ethanol</td>
			<td>0.005 g</td>
			<td>Make 40 &#956;l&#160;&#160;aliquots and store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Oligomycin A</td>
			<td>0.006</td>
			<td>791.06</td>
			<td>0.987 ml&#160;&#160;of 95% Ethanol</td>
			<td>0.005 g</td>
			<td>Make 20 &#956;l&#160;&#160;aliquots and store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>FCCP</td>
			<td>0.01</td>
			<td>254.17</td>
			<td>3.9 ml&#160;&#160;of 95% Ethanol</td>
			<td>0.01 g</td>
			<td>Make 40 &#956;l&#160;&#160;aliquots and store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Rotenone</td>
			<td>0.001</td>
			<td>394.4</td>
			<td>10 ml&#160;&#160;of 95% Ethanol</td>
			<td>0.0039&#160; g</td>
			<td>Store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Antimycin A</td>
			<td>0.005</td>
			<td>548.63</td>
			<td>9.12 ml&#160;&#160;of 95% Ethanol</td>
			<td>0.025 g</td>
			<td>Store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>K+ ADP</td>
			<td>0.5</td>
			<td>501.32</td>
			<td>3.9 ml&#160;&#160;of DiH2O</td>
			<td>1.0 g&#160;</td>
			<td>Store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Malic Acid, pH 7.4</td>
			<td>0.5</td>
			<td>134.09</td>
			<td>40&#160;ml&#160;</td>
			<td>2.68 g</td>
			<td>Make 200 &#956;l&#160;&#160;aliquots and store at -20 &#176;C</td>
		</tr>
	</tbody>
</table>
Table 1.&#160;Stock Solutions
<table border="0">
	<tbody>
		<tr>
			<td rowspan="2">Reagent</td>
			<td>Stock Concentration&#160;</td>
			<td>Mass Added</td>
			<td rowspan="2">Final Molarity/Percent</td>
		</tr>
		<tr>
			<td>(M)</td>
			<td>(g or ml)</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>--</td>
			<td>11.98 g</td>
			<td>70 mM</td>
		</tr>
		<tr>
			<td>Mannitol</td>
			<td>--</td>
			<td>20.04 g</td>
			<td>220 mM</td>
		</tr>
		<tr>
			<td>Potassium phosphate monobasic</td>
			<td>--</td>
			<td>0.34 g</td>
			<td>5 mM</td>
		</tr>
		<tr>
			<td>MgCl2, hexahydrate</td>
			<td>1</td>
			<td>2.5&#160;ml&#160;</td>
			<td>5 mM</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>1</td>
			<td>1.0&#160;ml&#160;</td>
			<td>2 mM</td>
		</tr>
		<tr>
			<td>EGTA</td>
			<td>0.1</td>
			<td>5.0&#160;ml&#160;</td>
			<td>1 mM</td>
		</tr>
		<tr>
			<td>Essentially Fatty Acid Free- BSA</td>
			<td>--</td>
			<td>&#160;1.0 g</td>
			<td>0.20%</td>
		</tr>
	</tbody>
</table>
Table 2.&#160;MAS Mix. pH 7.4, 500 ml: Aliquot 25 ml and store at -20 &#186;C *Note: Exclude BSA for MAS mix used for assay injections.
<table border="0">
	<tbody>
		<tr>
			<td>Substrate Medium&#160;</td>
			<td>Final Concentration</td>
			<td>Amount of stock (&#181;l)</td>
			<td>Amount of MAS* (ml)</td>
		</tr>
		<tr>
			<td rowspan="2">Pyruvate/Malate</td>
			<td rowspan="2">10 mM/5 mM</td>
			<td>Pyruvate: 1,000</td>
			<td rowspan="2">9</td>
		</tr>
		<tr>
			<td>Malate: 100</td>
		</tr>
		<tr>
			<td rowspan="2">Succicinate/Rotenone</td>
			<td rowspan="2">10 mM/2 &#181;M</td>
			<td>Succinate: 200</td>
			<td rowspan="2">10</td>
		</tr>
		<tr>
			<td>Rotenone 20</td>
		</tr>
		<tr>
			<td rowspan="3">*Pyruvate/Malate + FCCP&#160;</td>
			<td rowspan="3">5 mM/1 mM/4 &#181;M</td>
			<td>Pyruvate: 500</td>
			<td rowspan="3">10</td>
		</tr>
		<tr>
			<td>FCCP: 4</td>
		</tr>
		<tr>
			<td>Malate: 20</td>
		</tr>
		<tr>
			<td>Palmitoyl L-carnitine/Malate</td>
			<td>40 &#181;M/1 mM</td>
			<td>Palmitoylcarnitine: 40 Malate: 20</td>
			<td>10</td>
		</tr>
		<tr>
			<td rowspan="2">Glutamate/Malate</td>
			<td rowspan="2">10 mM/10 mM</td>
			<td>Glutamate: 400</td>
			<td rowspan="2">10</td>
		</tr>
		<tr>
			<td>Malate: 200</td>
		</tr>
	</tbody>
</table>
Table 3.&#160;Substrate Solutions pH 7.4: Make fresh the day of the experiment. *Electron flow assay solution.
<table border="0">
	<tbody>
		<tr>
			<td>Injection Medium&#160;</td>
			<td>Concentration</td>
			<td>Amount of stock&#160; (&#181;l)</td>
			<td>Amount of MAS (ml)</td>
			<td>Amount injected into Cartridge&#160;</td>
			<td>Final Concentration</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td>(After injected in plate)</td>
		</tr>
		<tr>
			<td>ADP&#160;</td>
			<td>50 mM</td>
			<td>300 &#181;l</td>
			<td>3</td>
			<td>50&#160;&#181;l</td>
			<td>5.0 mM</td>
		</tr>
		<tr>
			<td>Oligomycin A&#160;</td>
			<td>20 &#181;M</td>
			<td>10&#160;&#181;l</td>
			<td>3</td>
			<td>55&#160;&#181;l</td>
			<td>2.0 &#181;M</td>
		</tr>
		<tr>
			<td>FCCP&#160;</td>
			<td>40 &#181;M</td>
			<td>12&#160;&#181;l</td>
			<td>3</td>
			<td>60&#160;&#181;l</td>
			<td>4.0 &#181;M</td>
		</tr>
		<tr>
			<td>Antimycin A&#160;</td>
			<td>40 &#181;M</td>
			<td>24&#160;&#181;l</td>
			<td>3</td>
			<td>65&#160;&#181;l</td>
			<td>4.0 &#181;M</td>
		</tr>
	</tbody>
</table>
Table 4.&#160;Injections for Coupled Assays. pH 7.4: Make fresh the day of the experiment. *Coupling assays include (but are not limited to) pyruvate/malate, succinate/rotenone, palmitoyl carnitine/malate, and glutamate/malate.
<table border="0">
	<tbody>
		<tr>
			<td>Injection Medium&#160;</td>
			<td>Concentration</td>
			<td>Amount of stock (g or ul)</td>
			<td>Amount of MAS (ml)</td>
			<td>Amount injected into Cartridge&#160;</td>
			<td>Final Concentration (After injected in plate)</td>
		</tr>
		<tr>
			<td>Rotenone&#160;</td>
			<td>20 &#181;M</td>
			<td>60&#160;&#181;l</td>
			<td>3</td>
			<td>50&#160;&#181;l</td>
			<td>2.0 &#181;M</td>
		</tr>
		<tr>
			<td>Succinate</td>
			<td>50 mM</td>
			<td>300&#160;&#181;l</td>
			<td>3</td>
			<td>55&#160;&#181;l</td>
			<td>5.0 mM</td>
		</tr>
		<tr>
			<td>Antimycin A</td>
			<td>40 &#181;M</td>
			<td>24&#160;&#181;l</td>
			<td>3</td>
			<td>60&#160;&#181;l</td>
			<td>4.0 &#181;M</td>
		</tr>
		<tr>
			<td>TMPD/Ascorabte</td>
			<td>1 mM, 100 mM</td>
			<td>TMPD : 300&#160;&#181;l</td>
			<td>3</td>
			<td>65&#160;&#181;l</td>
			<td>100 &#181;M, 10mM</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td>Ascorbate: 0.059 g</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>
Table 5.&#160;Injections for Electron Flow Assay. pH 7.4: Make fresh the day of the experiment
<table border="0">
	<tbody>
		<tr>
			<td>Command</td>
			<td>Time (min)</td>
			<td># of cycles</td>
		</tr>
		<tr>
			<td>Calibrate</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Wait</td>
			<td>10 min (to allow plate to warm from&#160; adherence step)</td>
			<td></td>
		</tr>
		<tr>
			<td>Mix</td>
			<td>1 min</td>
			<td rowspan="2">2</td>
		</tr>
		<tr>
			<td>Measure</td>
			<td>2 min</td>
		</tr>
		<tr>
			<td>Inject A</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mix</td>
			<td>1 min</td>
			<td rowspan="2">2</td>
		</tr>
		<tr>
			<td>Measure</td>
			<td>2 min</td>
		</tr>
		<tr>
			<td>Inject B</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mix</td>
			<td>1 min</td>
			<td rowspan="2">2</td>
		</tr>
		<tr>
			<td>Measure</td>
			<td>2 min</td>
		</tr>
		<tr>
			<td>Inject C</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mix</td>
			<td>1 min</td>
			<td rowspan="2">2</td>
		</tr>
		<tr>
			<td>Measure</td>
			<td>2 min</td>
		</tr>
		<tr>
			<td>Inject D</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mix</td>
			<td>1 min</td>
			<td rowspan="2">2</td>
		</tr>
		<tr>
			<td>Measure</td>
			<td>2 min</td>
		</tr>
	</tbody>
</table>
Table 6.&#160;Instrument Run Protocol.

Watch this Scientific Journal Video about Using Isolated Mitochondria from Minimal Quantities of Mouse Skeletal Muscle for High throughput Microplate Respiratory Measurements at JoVE.com

Using Isolated Mitochondria from Minimal Quantities of Mouse Skeletal Muscle for High throughput Microplate Respiratory Measurements

The methods presented provide step-by-step instructions for the performance of a collection of microplate based respirometric assays using isolated mitochondria from minimal quantities of mouse skeletal muscle. These assays are able to measure mechanistic changes/adaptations in mitochondrial oxygen consumption in a commonly used animal model.

Skeletal muscle mitochondria play a specific role in many disease pathologies. As such, the measurement of oxygen consumption as an indicator of ...

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Vidéo: Using Isolated Mitochondria from Minimal Quantities of Mouse Skeletal Muscle for High throughput Microplate Respiratory Measurements

The methods presented provide step-by-step instructions for the performance of a collection of microplate based respirometric assays using isolated mitochondria from minimal quantities of mouse skeletal muscle. These assays are able to measure mechanistic changes/adaptations in mitochondrial oxygen consumption in a commonly used animal...

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isolation of mitochondria from minimal quantities of mouse skeletal muscle for high throughput microplate respiratory measurements

Isolation of Mitochondria from Minimal Quantities of Mouse Skeletal Muscle for High Throughput Microplate Respiratory Measurements

Here, we present a modification of a previously reported method that allows for the isolation of high quality and purified mitochondria from smaller quantities of mouse skeletal muscle. This procedure results in highly coupled mitochondria that respire with high function during microplate based respirometirc...

isolation of intact mitochondria from skeletal muscle by differential centrifugation for high-resolution respirometry measurements

Isolation of Intact Mitochondria from Skeletal Muscle by Differential Centrifugation for High-resolution Respirometry Measurements

Here, a quadriceps muscle specimen is taken from an anaesthetized pig and mitochondria are isolated by differential centrifugation. Then, the respiratory rates of mitochondrial respiratory chain complexes I, II and IV are determined using high-resolution...

preparation and respirometric assessment of mitochondria isolated from skeletal muscle tissue obtained by percutaneous needle biopsy

Preparation and Respirometric Assessment of Mitochondria Isolated from Skeletal Muscle Tissue Obtained by Percutaneous Needle Biopsy

Methods for biopsy of Vastus lateralis, preparation of purified mitochondria, and respirometric profiling are described. The use of small muscle volume makes this technique suitable for clinical research...

isolation and respiratory measurements of mitochondria from arabidopsis thaliana

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

As mitochondria are only a small percentage of the plant cell, they need to be purified for a range of studies. Mitochondria can be isolated from a variety of plant organs by homogenization, followed by differential and density gradient centrifugation to obtain a highly purified mitochondrial...

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

high-throughput contractile measurements of hydrogel-embedded intact mouse muscle fibers using an optics-based system

High-Throughput Contractile Measurements of Hydrogel-Embedded Intact Mouse Muscle Fibers Using an Optics-Based System

Skeletal muscle function can be assessed by quantifying the contractility of isolated muscle fibers, traditionally using laborious, low-throughput approaches. Here, we describe an optics-based, high-throughput method to quantify the contractility of hydrogel-embedded muscle fibers. This approach has applications for drug screening and therapeutic...

measurement of protein import capacity of skeletal muscle mitochondria

Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria

Mitochondria are key metabolic organelles that exhibit a high level of phenotypic plasticity in skeletal muscle. The import of proteins from the cytosol is a critical pathway for organelle biogenesis, essential for the expansion of the reticulum and the maintenance of mitochondrial function.  Therefore, protein import serves as a barometer of cellular health.

myo-mechanical analysis of isolated skeletal muscle

Myo-mechanical Analysis of Isolated Skeletal Muscle

To assess the in vivo effects of therapeutic interventions for muscle disease, methods are needed to quantitate force generation and fatigability in treated muscle. We detail an approach to evaluating myo-mechanical properties in explanted mouse hindlimb muscle. This analysis provides a robust approach to quantitating the effects of genetic modification on muscle function, as well as comparison of therapies in mouse models of muscle...

improved protocol for chromatin immunoprecipitation from mouse skeletal muscle

Improved Protocol for Chromatin Immunoprecipitation from Mouse Skeletal Muscle

A novel protocol for the preparation of chromatin from adult mouse skeletal muscle adapted to the study of gene regulation in muscle fibers by chromatin immunoprecipitation is...

high-resolution fluoro-respirometry of equine skeletal muscle

High-Resolution Fluoro-Respirometry of Equine Skeletal Muscle

Horses have an exceptional aerobic exercise capacity, making equine skeletal muscle an important tissue for both the study of equine exercise physiology as well as mammalian mitochondrial physiology. This article describes techniques for the comprehensive assessment of mitochondrial function in equine skeletal...

mitochondrial isolation from skeletal muscle

Mitochondrial Isolation from Skeletal Muscle

This protocol describes a procedure to study the respiration of mitochondria isolated from skeletal muscles. This method was adapted from Scorrano et al. (2007).  The mitochondrial isolation procedure requires about 2 hours.  The mitochondrial respiration can be completed in about 1...

a high throughput microplate feeder assay for quantification of consumption in drosophila

A High Throughput Microplate Feeder Assay for Quantification of Consumption in Drosophila

The microplate feeder assay offers an economical, high throughput method for quantifying liquid food consumption in Drosophila. A 3D-printed device connects a 96-well microplate in which flies are housed to a 1536-well microplate from which flies consume a feeding solution with a tracer dye. The solution volume decline is measured spectrophotometrically.

A High Throughput Microplate Feeder Assay for Quantification of Consumption in Drosophila

preparation of rat skeletal muscle homogenates for nitrate and nitrite measurements

Preparation of Rat Skeletal Muscle Homogenates for Nitrate and Nitrite Measurements

We present protocols for three different methods for the homogenization of four different muscle groups of rat skeletal muscle tissue to measure and compare the levels of nitrate and nitrite. Furthermore, we compare different sample weights to investigate whether tissue sample size affects the results of homogenization.

measurement of mitochondrial respiration in human and mouse skeletal muscle fibers by high-resolution respirometry

Author Spotlight: Unveiling Mitochondrial Function and Cellular Metabolic Adaptation in Metabolic Diseases

Here, we describe a comprehensive method for measuring mitochondrial oxidative phosphorylation in fresh permeabilized skeletal muscle fibers from either human or mouse muscle. This method allows for the real-time quantification of mitochondrial respiration and the assessment of fuel preference and metabolic flexibility while preserving existing mitochondrial networks and membrane...

Measurement of Mitochondrial Respiration in Human and Mouse Skeletal Muscle Fibers by High-Resolution Respirometry

fiber type identification of human skeletal muscle

Author Spotlight: Deciphering the Mysteries of Skeletal Muscle Fiber Types Using the MyDoBID Technique 

This protocol demonstrates single-fiber isolation from freeze-dried human skeletal muscle and fiber-type classification according to Myosin heavy chain (MHC) isoform using the dot blotting technique. Identified MHC I and II fiber samples can then be further analyzed for fiber type-specific differences in protein expression using western...

MyDoBID- A Novel Technique for Identifying Muscle Fiber Types Efficiently

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isolation and differentiation of primary myoblasts from mouse skeletal muscle explants

Isolation and Differentiation of Primary Myoblasts from Mouse Skeletal Muscle Explants

Myoblasts are proliferating precursor cells that differentiate to form polynucleated myotubes and eventually skeletal muscle myofibers. Here, we present a protocol for efficient isolation and culture of primary myoblasts from young adult mouse skeletal muscles. The method enables molecular, genetic, and metabolic studies of muscle cells in...

confocal live cell imaging of rat skeletal muscle mitochondria

Confocal Live Cell Imaging of Rat Skeletal Muscle Mitochondria  

behavioral and locomotor measurements using an open field activity monitoring system for skeletal muscle diseases

Behavioral and Locomotor Measurements Using an Open Field Activity Monitoring System for Skeletal Muscle Diseases

Open field activity levels are used to assess locomotive and behavioral activity levels. This protocol provides a well-designed, standardized protocol to use in preclinical trials for neuromuscular...

Isolation and Quantitative Immunocytochemical Characterization of Primary Myogenic Cells and Fibroblasts from Human Skeletal Muscle

The repair and regeneration of skeletal muscle requires the action of satellite cells, which are the resident muscle stem cells. These can be isolated from human muscle biopsy samples using enzymatic digestion and their myogenic properties studied in culture. Quantitatively, the two main adherent cell types obtained from enzymatic digestion are: (i) the satellite cells (termed myogenic cells or muscle precursor cells), identified initially as CD56+ and later as CD56+/desmin+ cells and (ii) muscle-derived fibroblasts, identified as CD56&#8211; and TE-7+. Fibroblasts proliferate very efficiently in culture and in mixed cell populations these cells may overrun myogenic cells to dominate the culture. The isolation and purification of different cell types from human muscle is thus an important methodological consideration when trying to investigate the innate behavior of either cell type in culture. Here we describe a system of sorting based on the gentle enzymatic digestion of cells using collagenase and dispase followed by magnetic activated cell sorting (MACS) which gives both a high purity (&#62;95% myogenic cells) and good yield (~2.8 x 106 &#177; 8.87 x 105 cells/g tissue after 7 days in vitro) for experiments in culture. This approach is based on incubating the mixed muscle-derived cell population with magnetic microbeads beads conjugated to an antibody against CD56 and then passing cells though a magnetic field. CD56+ cells bound to microbeads are retained by the field whereas CD56&#8211; cells pass unimpeded through the column. Cell suspensions from any stage of the sorting process can be plated and cultured. Following a given intervention, cell morphology, and the expression and localization of proteins including nuclear transcription factors can be quantified using immunofluorescent labeling with specific antibodies and an image processing and analysis package.

The main adherent cell types derived from human muscle are myogenic cells and fibroblasts. Here, cell populations are enriched using magnetic-activated cell sorting based on the CD56 antigen. Subsequent immunolabelling with specific antibodies and use of image analysis techniques allows quantification of cytoplasmic and nuclear characteristics in individual cells.

The repair and regeneration of skeletal muscle requires the action of satellite cells, which are the resident muscle stem cells. These can be isolated ...

Analysis of Zebrafish Larvae Skeletal Muscle Integrity with Evans Blue Dye

The zebrafish model is an emerging system for the study of neuromuscular disorders. In the study of neuromuscular diseases, the integrity of the muscle membrane is a critical disease determinant. To date, numerous neuromuscular conditions display degenerating muscle fibers with abnormal membrane integrity; this is most commonly observed in muscular dystrophies. Evans Blue Dye (EBD) is a vital, cell permeable dye that is rapidly taken into degenerating, damaged, or apoptotic cells; in contrast, it is not taken up by cells with an intact membrane. EBD injection is commonly employed to ascertain muscle integrity in mouse models of neuromuscular diseases. However, such EBD experiments require muscle dissection and/or sectioning prior to analysis. In contrast, EBD uptake in zebrafish is visualized in live, intact preparations. Here, we demonstrate a simple and straightforward methodology for performing EBD injections and analysis in live zebrafish. In addition, we demonstrate a co-injection strategy to increase efficacy of EBD analysis. Overall, this video article provides an outline to perform EBD injection and characterization in zebrafish models of neuromuscular disease.

In this study, we describe a straightforward method to perform Evans Blue Dye (EBD) analysis on zebrafish larvae. This technique is a powerful tool for the characterization of skeletal muscle integrity and delineation of zebrafish models of muscular dystrophy, and is a valuable method for the development of novel therapeutics.

The zebrafish model is an emerging system for the study of neuromuscular disorders.  In the study of neuromuscular diseases, the integrity of the muscle ...

Induction of Acute Skeletal Muscle Regeneration by Cardiotoxin Injection

Skeletal muscle regeneration is a physiological process that occurs in adult skeletal muscles in response to injury or disease. Acute injury-induced skeletal muscle regeneration is a widely used, powerful model system to study the events involved in muscle regeneration as well as the mechanisms and different players. Indeed, a detailed knowledge of this process is essential for a better understanding of the pathological conditions that lead to skeletal muscle degeneration, and it aids in identifying new targeted therapeutic strategies. The present work describes a detailed and reproducible protocol to induce acute skeletal muscle regeneration in mice through a single intramuscular injection of cardiotoxin (CTX). CTX belongs to the family of snake venom toxins and causes myolysis of myofibers, which eventually triggers the regeneration events. The dynamics of skeletal muscle regeneration is evaluated by histological analysis of muscle sections. The protocol also illustrates the experimental procedures for dissecting, freezing, and cutting the Tibialis Anterior muscle, as well as the routine Hematoxylin &#38; Eosin staining that is widely used for subsequent morphological and morphometric analysis.

This manuscript describes a detailed protocol to induce acute skeletal muscle regeneration in adult mice and subsequent manipulations of the muscles, such as dissection, freezing, cutting, routine staining, and myofiber cross-sectional area analysis.

Skeletal muscle regeneration is a physiological process that occurs in adult skeletal muscles in response to injury or disease. Acute injury-induced ...

Preparation and Culture of Myogenic Precursor Cells/Primary Myoblasts from Skeletal Muscle of Adult and Aged Humans

Skeletal muscle homeostasis depends on muscle growth (hypertrophy), atrophy and regeneration. During ageing and in several diseases, muscle wasting occurs. Loss of muscle mass and function is associated with muscle fiber type atrophy, fiber type switching, defective muscle regeneration associated with dysfunction of satellite cells, muscle stem cells, and other pathophysiological processes. These changes are associated with changes in intracellular as well as local and systemic niches. In addition to most commonly used rodent models of muscle ageing, there is a need to study muscle homeostasis and wasting using human models, which due to ethical implications, consist predominantly of in vitro cultures. Despite the wide use of human Myogenic Progenitor Cells (MPCs) and primary myoblasts in myogenesis, there is limited data on using human primary myoblast and myotube cultures to study molecular mechanisms regulating different aspects of age-associated muscle wasting, aiding in the validation of mechanisms of ageing proposed in rodent muscle. The use of human MPCs, primary myoblasts and myotubes isolated from adult and aged people, provides a physiologically relevant model of molecular mechanisms of processes associated with muscle growth, atrophy and regeneration. Here we describe in detail a robust, inexpensive, reproducible and efficient protocol for the isolation and maintenance of human MPCs&#160;and their progeny&#160;&#8212; myoblasts and myotubes from human muscle samples using enzymatic digestion. Furthermore, we have determined the passage number at which primary myoblasts from adult and aged people undergo senescence in an in vitro culture. Finally, we show the ability to transfect these myoblasts and the ability to characterize their proliferative and differentiation capacity and propose their suitability for performing functional studies of molecular mechanisms of myogenesis and muscle wasting in vitro.

This protocol describes a robust, reproducible and simple method of isolation and culture of myoblast progenitor cells from the skeletal muscle of adult and aged people. The muscles used here include foot and leg muscles. This approach enables the isolation of an enriched population of primary myoblasts for functional studies.

Skeletal muscle homeostasis depends on muscle growth (hypertrophy), atrophy and regeneration. During ageing and in several diseases, muscle wasting ...

Isolation of Type I and Type II Pericytes from Mouse Skeletal Muscles

Pericytes are perivascular multipotent cells that show heterogeneity in different organs or even within the same tissue. In skeletal muscles, there are at least two pericyte subpopulations (called type I and type II), which express different molecular markers and have distinct differentiation capabilities. Using NG2-DsRed and Nestin-GFP double-transgenic mice, type I (NG2-DsRed+Nestin-GFP-) and type II (NG2-DsRed+Nestin-GFP+) pericytes have been successfully isolated. However, the availability of these double-transgenic mice prevents the widespread use of this purification method. This work describes an alternative protocol that allows for the easy and simultaneous isolation of type I and type II pericytes from skeletal muscles. This protocol utilizes the fluorescence-activated cell sorting (FACS) technique and targets PDGFR&#946;, rather than NG2, together with the Nestin-GFP signal. Following isolation, type I and type II pericytes show distinct morphologies. In addition, type I and type II pericytes isolated with this new method, like those isolated from the double-transgenic mice, are adipogenic and myogenic, respectively. These results suggest that this protocol can be used to isolate pericyte subpopulations from skeletal muscles and possibly from other tissues.

This work describes a FACS-based protocol that allows for easy and simultaneous isolation of type I and type II pericytes from skeletal muscles.

Pericytes are perivascular multipotent cells that show heterogeneity in different organs or even within the same tissue. In skeletal muscles, there are at ...

Application of Chronic Stimulation to Study Contractile Activity-induced Rat Skeletal Muscle Phenotypic Adaptations

Skeletal muscle is a highly adaptable tissue, as its biochemical and physiological properties are greatly altered in response to chronic exercise. To investigate the underlying mechanisms that bring about various muscle adaptations, a number of exercise protocols such as treadmill, wheel running, and swimming exercise have been used in the animal studies. However, these exercise models require a long period of time to achieve muscle adaptations, which may be also regulated by humoral or neurological factors, thus limiting their applications in studying the muscle-specific contraction-induced adaptations. Indirect low frequency stimulation (10 Hz) to induce chronic contractile activity (CCA) has been used as an alternative model for exercise training, as it can successfully lead to muscle mitochondrial adaptations within 7 days, independent of systemic factors. This paper details the surgical techniques required to apply the treatment of CCA to the skeletal muscle of rats, for widespread application in future studies.

This protocol describes the use of the chronic contractile activity model of exercise to observe stimulation-induced skeletal muscle adaptations in the rat hindlimb.

Skeletal muscle is a highly adaptable tissue, as its biochemical and physiological properties are greatly altered in response to chronic exercise. To ...

Identification of Skeletal Muscle Satellite Cells by Immunofluorescence with Pax7 and Laminin Antibodies

Immunofluorescence is an effective method that helps to identify different cell types on tissue sections. In order to study the desired cell population, antibodies for specific cell markers are applied on tissue sections. In adult skeletal muscle, satellite cells (SCs) are stem cells that contribute to muscle repair and regeneration. Therefore, it is important to visualize and trace the satellite cell population under different physiological conditions. In resting skeletal muscle, SCs reside between the basal lamina and myofiber plasma membrane. A commonly used marker for identifying SCs on the myofibers or in cell culture is the paired box protein Pax7. In this article, an optimized Pax7 immunofluorescence protocol on skeletal muscle sections is presented that minimizes non-specific staining and background. Another antibody that recognizes a protein (laminin) of the basal lamina was also added to help identify SCs. Similar protocols can also be used to perform double or triple labeling with Pax7 and antibodies for additional proteins of interest.

The precise identification of satellite cells is essential for studying their functions under various physiological and pathological conditions. This article presents a protocol to identify satellite cells on adult skeletal muscle sections by immunofluorescence-based staining.

Immunofluorescence is an effective method that helps to identify different cell types on tissue sections. In order to study the desired cell population, ...

X-ray Diffraction of Intact Murine Skeletal Muscle as a Tool for Studying the Structural Basis of Muscle Disease

Transgenic mouse models have been important tools for studying the relationship of genotype to phenotype for human diseases including those of skeletal muscle. Mouse skeletal muscle has been shown to produce high quality X-ray diffraction patterns on third generation synchrotron beamlines providing an opportunity to link changes at the level of the genotype to functional phenotypes in health and disease by determining the structural consequences of genetic changes. We present detailed protocols for preparation of specimens, collecting the X-ray patterns and extracting relevant structural parameters from the X-ray patterns that may help guide experimenters wishing to perform such experiments for themselves.

We present detailed protocols for performing small-angle X-ray diffraction experiments using intact mouse skeletal muscles. With the wide availability of transgenic mouse models for human diseases, this experimental platform can form a useful test bed for elucidating the structural basis of genetic muscle diseases

Transgenic mouse models have been important tools for studying the relationship of genotype to phenotype for human diseases including those of skeletal ...

Isolation, Culture, Characterization, and Differentiation of Human Muscle Progenitor Cells from the Skeletal Muscle Biopsy Procedure

The use of primary human tissue and cells is ideal for the investigation of biological and physiological processes such as the skeletal muscle regenerative process. There are recognized challenges to working with human primary adult stem cells, particularly human muscle progenitor cells (hMPCs) derived from skeletal muscle biopsies, including low cell yield from collected tissue and a large degree of donor heterogeneity of growth and death parameters among cultures. While incorporating heterogeneity into experimental design requires a larger sample size to detect significant effects, it also allows us to identify mechanisms that underlie variability in hMPC&#160;expansion capacity, and thus allows us to better understand heterogeneity in skeletal muscle regeneration. Novel mechanisms that distinguish the expansion capacity of cultures have the potential to lead to the development of therapies to improve skeletal muscle regeneration.

We present techniques for isolating, culturing, characterizing, and differentiating human primary muscle progenitor cells (hMPCs) obtained from skeletal muscle biopsy tissue. hMPCs obtained and characterized through these methods can be used to subsequently address research questions related to human myogenesis and skeletal muscle regeneration.

The use of primary human tissue and cells is ideal for the investigation of biological and physiological processes such as the skeletal muscle ...

Performing Human Skeletal Muscle Xenografts in Immunodeficient Mice

Treatment effects observed in animal studies often fail to be recapitulated in clinical trials. While this problem is multifaceted, one reason for this failure is the use of inadequate laboratory models. It is challenging to model complex human diseases in traditional laboratory organisms, but this issue can be circumvented through the study of human xenografts. The surgical method we describe here allows for the creation of human skeletal muscle xenografts, which can be used to model muscle disease and to carry out preclinical therapeutic testing. Under an Institutional Review Board (IRB)-approved protocol, skeletal muscle specimens are acquired from patients and then transplanted into NOD-Rag1null IL2r&gamma;null (NRG) host mice. These mice are ideal hosts for transplantation studies due to their inability to make mature lymphocytes and are thus unable to develop cell-mediated and humoral adaptive immune responses. Host mice are anaesthetized with isoflurane, and the mouse tibialis anterior and extensor digitorum longus muscles are removed. A piece of human muscle is then placed in the empty tibial compartment and sutured to the proximal and distal tendons of the peroneus longus muscle. The xenografted muscle is spontaneously vascularized and innervated by the mouse host, resulting in robustly regenerated human muscle that can serve as a model for preclinical studies.

Complex human diseases can be challenging to model in traditional laboratory model systems. Here, we describe a surgical approach to model human muscle disease through the transplantation of human skeletal muscle biopsies into immunodeficient mice.

Treatment effects observed in animal studies often fail to be recapitulated in clinical trials. While this problem is multifaceted, one reason for this ...