The work was supported in part by NIH grant R01 AR060456 (FL). We thank Dr. Michael Robinson and Elizabeth Krizman (The Children&#39;s Hospital of Philadelphia) for their generous help with the scintillation counter.

The use of radioactive materials (RAM) requires prior approval by a designated safety committee at each institution. RAMs used in this protocol have been approved by Environmental Health &#38; Radiation Safety (EHRS) at the University of Pennsylvania. The use of animals requires prior approval by the Institutional Animal Care and Use Committee (IACUC) at the home institution. The following study was approved by IACUC at The Children&#39;s Hospital of Philadelphia.
1. Preparation of stock solutions for 14C-labeled substrates
<ol>
	<li>Make 4 mM bovine serum albumin (BSA) stock solution by mixing 11 g of BSA and 33.1 mL of Dulbecco&#39;s phosphate-buffered saline (DPBS) and shaking it gently at room temperature for ~3 h until BSA is fully dissolved. Warm the BSA stock solution in a 70 &#176;C water bath before use.</li>
	<li>Air-dry 50 &#181;Ci 14C-oleate (50 &#181;Ci/&#181;mol in ethanol) in the vial with the lid off for 8 h in a designated RAM working hood. Add 312.5 &#181;L of H2O and then 3.5 mg (11.5 &#181;mol) of sodium oleate. Mix thoroughly.</li>
	<li>Warm the resulting solution to 70 &#176;C in a water bath. Add 0.9375 mL of the prewarmed BSA stock solution to yield 10 mM hot oleate stock solution (containing a 1:11.5 ratio of 14C-oleate to unlabeled oleate). Aliquot the stock solution and store it at -20 &#176;C for long-term use.</li>
	<li>Use 14C-glucose and 14C-glutamine directly after thawing.</li>
</ol>
2. Preparation of medium containing 14C-labeled substrates
NOTE: To ensure reliable concentrations of energy substrates in the media, custom-made media must be used with fresh substrates added shortly before use. Here, a custom-made Minimum Essential Medium (MEM&#945;) without glucose, pyruvate, glutamine, phenol red, or sodium bicarbonate is used. However, an optimal medium should be determined for each cell type.
<ol>
	<li>Reconstitute 8.67 g of the medium powder in 1 L of purified water. Add 2.2 g of sodium bicarbonate to achieve a pH of 7.4 and filter the solution using 0.22 &#181;m vacuum filtration.</li>
	<li>Add fresh ingredients to obtain the complete medium (cMEM&#945;) with final concentrations of 5.5 mM glucose, 2 mM glutamine, 1 mM pyruvate, and 10% fetal bovine serum (FBS). Further supplement cMEM&#945; with 100 mM L-carnitine and 10 &#181;M HEPES to facilitate fatty acid oxidation.</li>
	<li>Immediately before use, add 14C-labeled substrates to freshly prepared cMEM&#945; to make hot media. To make the oleate hot medium, add the 10 mM hot oleate stock solution to cMEM&#945; for a final concentration of 100 &#181;M oleate (1:100 dilution, final radioactivity 0.4 &#181;Ci/mL). 
	NOTE: The 10 mM hot oleate stock containing a 1:11.5 ratio of hot:cold oleate (see step 1.3) is used to achieve a physiological level of 100 &#181;M total oleate in the media while minimizing the amount of radioactive material.</li>
	<li>Make 10 mM unlabeled oleate stock by adding 24.36 mg of sodium oleate to 2 mL of H2O in a water bath at 70 &#176;C for ~20 min until completely dissolved before mixing quickly with 6 mL of the 4 mM BSA stock solution prewarmed to 70 &#176;C. Transfer to a 37 &#176;C water bath for 1 h and filter through a 0.22 &#181;m filter. Aliquot and store at -20 &#176;C for long-term use.</li>
	<li>To make glucose hot medium, add 14C-glucose to a final concentration of 1.333 &#181;M (1:4,125 dilution, final radioactivity 0.4 &#181;Ci/mL). To make glutamine hot medium, add 14C-glutamine to the final concentration of 2 &#181;M (1:1,000 dilution, final radioactivity 0.4 &#181;Ci/mL).</li>
	<li>Supplement the glucose and glutamine hot medium with a 10 mM stock solution of unlabeled oleate from step 2.4 to achieve the final concentration of 100 &#181;M oleate, the same as that in the oleate hot medium.</li>
</ol>
3. Preparation of cells
NOTE: Calvarial preosteoblasts and bone marrow macrophages are used as examples here. Users should prepare their cell type of choice according to appropriate protocols. Optimize the concentration of collagenase II to be used for digestion in pilot experiments as the enzymatic activity may vary among different lots.
<ol>
	<li>Isolation and culture of calvarial preosteoblasts
	<ol>
		<li>Sacrifice postnatal day 3-5 (P3-5) pups by decapitation and transfer them to ice-cold DPBS containing Penicillin-Streptomycin (P/S).</li>
		<li>Expose the calvaria by removing the skin and soft tissue. Collect the middle region by cutting away the surrounding tissues from back to front in DPBS (Figure 1A). Scratch the inner and outer surfaces of the calvaria gently using tweezers to help release the cells upon subsequent digestion.</li>
		<li>Prepare a 2 mg/mL and a 4 mg/mL solution of Collagenase type II in DPBS and filter each solution with a fresh 0.22 &#181;m filter. Digest the cleaned calvaria first with the 2 mg/mL collagenase solution for 15 min and discard the digestion solution. Digest the cleaned samples in 4 mg/mL collagenase solution 3 times for 15 min each time, pooling and saving the digestion solution.</li>
		<li>Filter the digestion solution through 70 &#181;m cell strainers and centrifuge the filtrate at 300 &#215; g for 5 min. Resuspend the cell pellet in cMEM&#945; (see step 2.2) containing 10% FBS and P/S.</li>
		<li>Count and seed the cells at 4 &#215; 104 cells/cm2&#160;in 10 cm plates. Culture the cells in a 37 &#176;C incubator with 5% CO2 for 3 days.</li>
		<li>Dissociate the cells at 37 &#176;C with 0.25% trypsin-EDTA. Count and seed the cells in 24-well cell culture plates with cMEM&#945; containing 10% FBS and P/S at 7.5 &#215; 105/cm2. Seed at least 4 wells per cell type per substrate and at least three extra wells for each cell type for cell counting before the assay.</li>
		<li>Culture the cells at 37 &#176;C overnight before the substrate oxidation assays.</li>
	</ol>
	</li>
	<li>Isolation and culture of BMMs 
	NOTE: Culture of BMMs requires macrophage colony-stimulating factor (M-CSF), which can be purchased commercially as a recombinant protein. Conditioned medium from the cell line CMG14-12 engineered to express M-CSF is an economical alternative used here13.
	<ol>
		<li>Collect femurs and tibias from 8-week-old mice after removing the muscle and connective tissues. Cut and discard both ends of the bones with sharp scissors.</li>
		<li>Flush out the bone marrow from one femur and one tibia into a 10 cm Petri dish with a syringe fitted with a 23 G needle containing 15 mL of cMEM&#945; with 10% FBS, P/S, and 10% CMG14-12 conditioned medium (BMM medium). Culture the cells in the Petri dish in a 37 &#176;C incubator with 5% CO2.</li>
		<li>After 3 days, discard the culture media and rinse with DPBS. Dissociate the attached cells at 37 &#176;C with 0.25% trypsin-EDTA for 5 min. Centrifuge and resuspend the cell pellet in the BMM medium.</li>
		<li>Count and seed the cells in 24-well cell culture plates at 7.5 &#215; 105/cm2 in the same way as described in 3.1.6. Culture at 37 &#176;C overnight in the BMM medium before starting the assays.</li>
	</ol>
	</li>
</ol>
4. Substrate oxidation assay with CO2 trap
NOTE: An appropriate seeding density should be determined for each cell type to achieve 80-90% confluence before the start of the assay. Note that cell density can affect the metabolic state of the cells.
<ol>
	<li>Wash the cells in the extra wells twice with DPBS. Dissociate the cells with 0.25% trypsin-EDTA and mixed 20 &#181;L cells resuspended in DPBS with 20 &#181;L of acridine orange/propidium iodide (AO/PI) ready-to-use commercial dye solution. Determine the number of live cells with an automated cell counter and record the number for final calculations.</li>
	<li>Wash the cells in the assay wells twice with DPBS. Add 500 &#181;L of hot medium to each assay well in the RAM-designated tissue culture hood. Seal the plates with parafilm and incubate the cells in a RAM-designated incubator at 37 &#176;C for 4 h.</li>
	<li>During incubation, cut filter paper into circular pieces slightly bigger than the area inside the cap of 1.5 ml microcentrifuge tubes and insert the paper snugly into the cap (Figure 1B). Add 200 &#181;L of 1 M perchloric acid to each tube and 20 &#181;L of sodium hydroxide to the filter paper fitted inside the cap.</li>
	<li>After incubation of the cells, transfer 400 &#181;L of culture medium from each well to the prepared tubes and close the caps immediately. Leave the tubes in a tube rack at room temperature for 1 h.</li>
	<li>During incubation, set up a scintillation vial for each tube and fill it with 4 mL of scintillation fluid. Transfer each piece of filter paper to a scintillation vial and incubate at room temperature for 30 min.</li>
	<li>Perform wipe tests on the tissue culture hood, the water bath (used for 14C-oleate preparation), refrigerator, incubator, sink, ground, and any other working area for potential RAM contamination. Put the paper wipes into scintillation vials containing scintillation fluid.</li>
	<li>Measure 14C radioactivity in the scintillation vials with a scintillation counter. Record the reading results. Decontaminate the working environment according to radiation safety guidelines if necessary.</li>
</ol>
5. Data analysis
NOTE: Assuming that each substrate is fully oxidized to release CO2, the substrate oxidation rate can be calculated from the trapped CO2 radioactivity.
<ol>
	<li>Calculate the substrate oxidation rate using Eq (1) and the X, Y, and Z values given in Table 1 for different substrates. 
	Substrate oxidation rate (&#181;mol/cell/h) = <img alt="Equation 1" src="/files/ftp_upload/63568/63568eq01.jpg" />&#160; &#160;(1)
	<ol>
		<li>Calculate the total disintegrations per min (DPM) for each reaction well. For X, use the DPM value (scintillation counter reading) from 0.4 mL of the reaction medium used for CO2 trapping out of 0.5 mL of the total reaction medium. Therefore, the total DPM from each reaction well is X &#215; 1.25.</li>
		<li>Divide the total DPM by a factor of 2,220,000 to convert to &#181;Ci.</li>
		<li>Convert the radioactivity in &#181;Ci to the number of 14C-labeled molecules. Divide the &#181;Ci value by the specific activity (Y) of each labeled substrate. Use the following Y values (Table 1): 14C-glucose: 300 mCi/mmol; 14C-glutamine: 200 mCi/mmol; 14C-oleate: 50 mCi/mmol.</li>
		<li>Calculate the total number of oxidized molecules from the oxidized 14C-labeled molecules by multiplying the latter with the hot-to-total dilution factor (Z). Use the following Z values (Table 1): Glucose: 4,125; glutamine: 1,000; oleate: 12.5.</li>
		<li>Divide the resulting product by cell number (cell#) and 4 (for the reaction time of 4 h) to determine the substrate oxidation rate per cell. Use the cell# determined in the parallel wells at the beginning of the assay.</li>
	</ol>
	</li>
</ol>

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	<li>Hargreaves, M., Spriet, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Skeletal+muscle+energy+metabolism+during+exercise.">Skeletal muscle energy metabolism during exercise.</a> Nature Metabolism. 2 (9), 817-828 (2020).</li><li>Jeukendrup, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+fat+metabolism+in+skeletal+muscle.">Regulation of fat metabolism in skeletal muscle.</a> Annals of the New York Academy of Sciences. 967, 217-235 (2002).</li><li>Randle, P. J., Garland, P. B., Hales, C. N., Newsholme, E. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+glucose+fatty-acid+cycle.+Its+role+in+insulin+sensitivity+and+the+metabolic+disturbances+of+diabetes+mellitus.">The glucose fatty-acid cycle. Its role in insulin sensitivity and the metabolic disturbances of diabetes mellitus.</a> Lancet. 1 (7285), 785-789 (1963).</li><li>Randle, P. J., Newsholme, E. A., Garland, P. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+glucose+uptake+by+muscle.+8.+Effects+of+fatty+acids,+ketone+bodies+and+pyruvate,+and+of+alloxan-diabetes+and+starvation,+on+the+uptake+and+metabolic+fate+of+glucose+in+rat+heart+and+diaphragm+muscles.">Regulation of glucose uptake by muscle. 8. Effects of fatty acids, ketone bodies and pyruvate, and of alloxan-diabetes and starvation, on the uptake and metabolic fate of glucose in rat heart and diaphragm muscles.</a> Biochemical Journal. 93 (3), 652-665 (1964).</li><li>Taegtmeyer, H., Hems, R., Krebs, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Utilization+of+energy-providing+substrates+in+the+isolated+working+rat+heart.">Utilization of energy-providing substrates in the isolated working rat heart.</a> Biochemical Journal. 186 (3), 701-711 (1980).</li><li>Cha, B. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impaired+fatty+acid+metabolism+in+type+2+diabetic+skeletal+muscle+cells+is+reversed+by+PPARgamma+agonists.">Impaired fatty acid metabolism in type 2 diabetic skeletal muscle cells is reversed by PPARgamma agonists.</a> American Journal of Physiology. Endocrinology and Metabolism. 289 (1), 151-159 (2005).</li><li>Lee, W. C., Guntur, A. R., Long, F., Rosen, C. J. <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+osteoblast:+implications+for+osteoporosis.">Energy metabolism of the osteoblast: implications for osteoporosis.</a> Endocrine Reviews. 38 (3), 255-266 (2017).</li><li>Li, B., 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=Both+aerobic+glycolysis+and+mitochondrial+respiration+are+required+for+osteoclast+differentiation.">Both aerobic glycolysis and mitochondrial respiration are required for osteoclast differentiation.</a> FASEB Journal. 34 (8), 11058-11067 (2020).</li><li>Lee, W. C., Ji, X., Nissim, I., Long, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Malic+enzyme+couples+mitochondria+with+aerobic+glycolysis+in+osteoblasts.">Malic enzyme couples mitochondria with aerobic glycolysis in osteoblasts.</a> Cell Reports. 32 (10), 108108 (2020).</li><li>Kim, S. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fatty+acid+oxidation+by+the+osteoblast+is+required+for+normal+bone+acquisition+in+a+sex-+and+diet-dependent+manner.">Fatty acid oxidation by the osteoblast is required for normal bone acquisition in a sex- and diet-dependent manner.</a> JCI Insight. 2 (16), 92704 (2017).</li><li>Yu, Y., 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=Glutamine+metabolism+regulates+proliferation+and+lineage+allocation+in+skeletal+stem+cells.">Glutamine metabolism regulates proliferation and lineage allocation in skeletal stem cells.</a> Cell Metabolism. 29 (4), 966-978 (2019).</li><li>Karner, C. M., Esen, E., Okunade, A. L., Patterson, B. W., Long, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increased+glutamine+catabolism+mediates+bone+anabolism+in+response+to+WNT+signaling.">Increased glutamine catabolism mediates bone anabolism in response to WNT signaling.</a> The Journal of Clinical Investigation. 125 (2), 551-562 (2015).</li><li>Takeshita, S., Kaji, K., Kudo, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+characterization+of+the+new+osteoclast+progenitor+with+macrophage+phenotypes+being+able+to+differentiate+into+mature+osteoclasts.">Identification and characterization of the new osteoclast progenitor with macrophage phenotypes being able to differentiate into mature osteoclasts.</a> Journal of Bone and Mineral Research. 15 (8), 1477-1488 (2000).</li><li>Itoh, Y., 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=Dichloroacetate+effects+on+glucose+and+lactate+oxidation+by+neurons+and+astroglia+in+vitro+and+on+glucose+utilization+by+brain+in+vivo.">Dichloroacetate effects on glucose and lactate oxidation by neurons and astroglia in vitro and on glucose utilization by brain in vivo.</a> Proceedings of the National Academy of Sciences of the United States of America. 100 (8), 4879-4884 (2003).</li><li>Oba, M., Baldwin, R. L. 4. t. h., Bequette, B. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oxidation+of+glucose,+glutamate,+and+glutamine+by+isolated+ovine+enterocytes+in+vitro+is+decreased+by+the+presence+of+other+metabolic+fuels.">Oxidation of glucose, glutamate, and glutamine by isolated ovine enterocytes in vitro is decreased by the presence of other metabolic fuels.</a> Journal of Animal Science. 82 (2), 479-486 (2004).</li><li>Esen, E., Lee, S. Y., Wice, B. M., Long, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PTH+promotes+bone+anabolism+by+stimulating+aerobic+glycolysis+via+IGF+signaling.">PTH promotes bone anabolism by stimulating aerobic glycolysis via IGF signaling.</a> Journal of Bone and Mineral Research. 30 (11), 1959-1968 (2015).</li><li>Huynh, F. K., Green, M. F., Koves, T. R., Hirschey, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+fatty+acid+oxidation+rates+in+animal+tissues+and+cell+lines.">Measurement of fatty acid oxidation rates in animal tissues and cell lines.</a> Methods in Enzymology. 542, 391-405 (2014).</li><li>Hodson, L., Skeaff, C. M., Fielding, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fatty+acid+composition+of+adipose+tissue+and+blood+in+humans+and+its+use+as+a+biomarker+of+dietary+intake.">Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.</a> Progress in Lipid Research. 47 (5), 348-380 (2008).</li><li>Abdelmagid, S. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+profiling+of+plasma+fatty+acid+concentrations+in+young+healthy+Canadian+adults.">Comprehensive profiling of plasma fatty acid concentrations in young healthy Canadian adults.</a> PLoS One. 10 (2), 0116195 (2015).</li></ol>

The authors declare no conflicts of interest.

The protocol provides an easy-to-use method to determine the oxidation rate of major energy substrates. It is a simpler alternative to other protocols that use flasks containing a central well and capped with rubber stoppers14,15,16. Although the example study here is performed with cell culture, the method can be easily adapted for tissue explants or tissue homogenates containing intact mitochondria, as previously described<sup...

Oxidative phosphorylation (OXPHOS) in eukaryotes is the process by which nutrients are broken down inside mitochondria to release chemical energy in the form of ATP through consumption of oxygen.&#160; Catabolism of various substrates inside mitochondria through the tricarboxylic acid (TCA) cycle generates few ATP molecules directly, but rather stores energy through reduction of the electron carriers nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD+). The reduced carriers are then oxidized by ETC located on the inner membrane of mitochondria to generate a proton concentration gradient across the membrane. The protons eventually flow down their gradient back into the mitochondrial matrix through ATP synthase to produce ATP. OXPHOS is the most efficient means of ATP production from energy substrates and generally preferred in aerobic environments. Previously, aerobic glycolysis-production of lactate from glucose while oxygen is present-was thought to be pathophysiological, often a hallmark of cancer cells. More and more, it is being discovered that some normal cell types use aerobic glycolysis for reasons that have yet to be fully deciphered.
Metabolic flexibility is the capacity for cells or organisms to adapt to changing energy demands and available fuel sources. For example, the energetic demand of skeletal muscle is mainly met by OXPHOS at steady state but by anaerobic glycolysis during high-intensity exercise1. As the exercise duration increases, glucose and fatty acid oxidation contribute more to overall energy production2. However, substrate use is not dependent only on availability, as substrates antagonistically compete during oxidation. Most notably, fatty acid oxidation has been shown to inhibit glucose utilization by skeletal muscle in a phenomenon known as the Randle effect3. A reciprocal effect was demonstrated by subsequent studies4,5. In addition, many diseases are associated with a change in substrate preference and the development of metabolic inflexibility in cells. For instance, fatty acid oxidation is reduced in the skeletal muscle of type II diabetic patients compared to normal control subjects6. The metabolic changes in disease settings are a subject of intense investigation as they may contribute to pathogenesis.
Energy metabolism in skeletal cell types is relatively understudied but has gained attention in recent years7. Previous work has shown that aerobic glycolysis is the dominant energy pathway in calvarial osteoblasts, while glucose oxidation through the TCA cycle plays a role in osteoclast formation8,9. Others have provided evidence for fatty acids as an energy source for osteoblasts10. Glutamine catabolism has also been shown to support osteoblast differentiation from the progenitors11,12. However, a comprehensive understanding of substrate utilization by various skeletal cell types is still lacking. In addition, changes in cellular metabolism during cell differentiation or in response to pathological signals are expected to alter fuel substrate utilization. Described below is an easy-to-use protocol for assaying substrate oxidation in vitro.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.22 &#181;m filters</td>
			<td>Sigma-Aldrich</td>
			<td>SLGVM33RS</td>
			<td>Used to filter BSA solution</td>
		</tr>
		<tr>
			<td>0.25% Trypsin-EDTA</td>
			<td>Gibco</td>
			<td>25200056</td>
			<td>Dissociate cells from cell culture plates</td>
		</tr>
		<tr>
			<td>1.5 mL Eppendorf tubes</td>
			<td>PR1MA</td>
			<td>PR MCT17 RB</td>
			<td>Used for reaction incubation</td>
		</tr>
		<tr>
			<td>10 cm plates</td>
			<td>TPP</td>
			<td>93100</td>
			<td>Used for cell culture</td>
		</tr>
		<tr>
			<td>10 mL syringe</td>
			<td>BD</td>
			<td>302995</td>
			<td>Used to flush marrow from long bones</td>
		</tr>
		<tr>
			<td>10% FBS</td>
			<td>Atlanta biologicals</td>
			<td>S11550</td>
			<td>For Cell culture medium preparation</td>
		</tr>
		<tr>
			<td>14C-Glucose</td>
			<td>PerkinElmer</td>
			<td>NEC042X050UC</td>
			<td>Used to make hot media</td>
		</tr>
		<tr>
			<td>14C-glutamine</td>
			<td>PerkinElmer</td>
			<td>NEC451050UC</td>
			<td>Used to make hot media</td>
		</tr>
		<tr>
			<td>14C-oleate</td>
			<td>PerkinElmer</td>
			<td>NEC317050UC</td>
			<td>Used to make hot media</td>
		</tr>
		<tr>
			<td>23 G needle</td>
			<td>BD</td>
			<td>305120</td>
			<td>Used to flush marrow from long bones</td>
		</tr>
		<tr>
			<td>24-well plates</td>
			<td>TPP</td>
			<td>92024</td>
			<td>Used for cell culture</td>
		</tr>
		<tr>
			<td>70 &#956;m cell strainers</td>
			<td>MIDSCI</td>
			<td>70CELL</td>
			<td>Used to filter supernatant during cavarial digestion</td>
		</tr>
		<tr>
			<td>Acridine Orange/Propidium Iodide (AO/PI) dye</td>
			<td>Nexcelom Biosciences</td>
			<td>CS2-0106</td>
			<td>Stains live cells to determine seed density</td>
		</tr>
		<tr>
			<td>Bovine Serum Ablumin</td>
			<td>Proliant Biologicals</td>
			<td>68700</td>
			<td>Used for fatty acid conjugation</td>
		</tr>
		<tr>
			<td>Cellometer Auto 2000</td>
			<td>Nexcelom Biosciences</td>
			<td></td>
			<td>Determine the number of viable cells</td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Thermo Fisher</td>
			<td>Legend Micro 21R</td>
			<td>Used to pellet cells</td>
		</tr>
		<tr>
			<td>Collagenase type II</td>
			<td>Worthington</td>
			<td>LS004176</td>
			<td>Dissociate cells from tissue</td>
		</tr>
		<tr>
			<td>Custom MEM alpha</td>
			<td>GIBCO</td>
			<td>SKU: ME 18459P1</td>
			<td>Used to create custom hot media</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Phosphate-Buffered Saline</td>
			<td>Gibco</td>
			<td>10010023</td>
			<td>Used to dissolve and dilute reagents, and wash culture dishes</td>
		</tr>
		<tr>
			<td>Filter Paper</td>
			<td>Millipore-Sigma</td>
			<td>WHA1001090</td>
			<td>Traps CO2 with sodium hydroxide</td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>g7528</td>
			<td>Used to make custom media</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Gibco</td>
			<td>15630080</td>
			<td>Traps CO2 during cell culture</td>
		</tr>
		<tr>
			<td>L-carnitine</td>
			<td>Sigma-Aldrich</td>
			<td>C0283</td>
			<td>Supplemented for fatty acid oxidation</td>
		</tr>
		<tr>
			<td>L-Glutamine</td>
			<td>Sigma-Aldrich</td>
			<td>g3126</td>
			<td>Used to make custom media</td>
		</tr>
		<tr>
			<td>MEM alpha</td>
			<td>Thermo</td>
			<td>A10490</td>
			<td>Cell culture medium</td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Pecheney Plastic Packaging</td>
			<td>PM998</td>
			<td>Used to seal cell culture dishes</td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Thermo Fisher</td>
			<td>15140122</td>
			<td>Prevents contamination in cell culture</td>
		</tr>
		<tr>
			<td>Perchloric Acid</td>
			<td>Sigma-Aldrich</td>
			<td>244252</td>
			<td>Releases CO2 during metabolic assay</td>
		</tr>
		<tr>
			<td>Pyruvate</td>
			<td>Sigma-Aldrich</td>
			<td>p5280</td>
			<td>Used to make custom media</td>
		</tr>
		<tr>
			<td>Scintillation Counter</td>
			<td>Beckman Coulter</td>
			<td>LS6500</td>
			<td>Determines radioactivity from the filter paper</td>
		</tr>
		<tr>
			<td>Scintillation Fluid</td>
			<td>MP Biomedicals</td>
			<td>882453</td>
			<td>Absorb the energy emitted by RAMs and re-emit it as flashes of light</td>
		</tr>
		<tr>
			<td>Scintillation Vial</td>
			<td>Fisher Scientific</td>
			<td>03-337-1</td>
			<td>Reaction containers for scintillation fluid</td>
		</tr>
		<tr>
			<td>Sodium carbonate</td>
			<td>Sigma-Aldrich</td>
			<td>S5761</td>
			<td>Balance buffer for medium</td>
		</tr>
		<tr>
			<td>Sodium Hydroxide</td>
			<td>Sigma-Aldrich</td>
			<td>58045</td>
			<td>Traps CO2 during metaboilc assay</td>
		</tr>
		<tr>
			<td>Sodium oleate</td>
			<td>SANTA CRUZ</td>
			<td>SC-215879</td>
			<td>BSA conjugated fatty acid preparation</td>
		</tr>
		<tr>
			<td>Vaccum filtration 1000</td>
			<td>TPP</td>
			<td>99950</td>
			<td>Filter cMEM&#945;</td>
		</tr>
	</tbody>
</table>

assessing energy substrate oxidation in vitro with 14co2 trapping

Mitochondria host the machinery for the tricarboxylic acid (TCA) cycle and electron transport&#160;chain (ETC), which generate adenosine triphosphate (ATP) to maintain energy homeostasis. Glucose, fatty acids, and amino acids are the major energy substrates fueling mitochondrial respiration in most somatic cells. Evidence shows that different cell types may have a distinct preference for certain substrates. However, substrate utilization by various cells in the skeleton has not been studied in detail. Moreover, as cellular metabolism is attuned to physiological and pathophysiological changes, direct assessments of substrate dependence in skeletal cells may provide important insights into the pathogenesis of bone diseases.
The following protocol is based on the principle of carbon dioxide release from substrate molecules following oxidative phosphorylation. By using substrates containing radioactively labeled carbon atoms (14C), the method provides a sensitive and easy-to-use assay for the rate of substrate oxidation in cell culture. A case study with primary calvarial preosteoblasts versus bone marrow-derived macrophages (BMMs) demonstrates different utilization of the main substrates between the two cell types.

In this example, the CO2 trapping method is used to compare substrate oxidation by primary calvarial preosteoblasts versus BMMs, which are frequently used for in vitro osteoblast or osteoclast differentiation, respectively. After the primary cells are passaged and cultured in cMEM&#945; overnight, they typically reach 80-90% of confluence and exhibit their characteristic morphology. The calvarial preosteoblasts are notably larger than BMMs (Figure 2). Each cell type is su...

Watch this Scientific Journal Video about Assessing Energy Substrate Oxidation In Vitro with 14CO2 Trapping at JoVE.com

Assessing Energy Substrate Oxidation In Vitro with 14CO2 Trapping

This protocol describes an easy-to-use method to examine substrate oxidation by tracking 14CO2&#160;production in vitro.

Assessing Energy Substrate Oxidation In Vitro with 14CO2 Trapping

Mitochondria host the machinery for the tricarboxylic acid (TCA) cycle and electron transport&#160;chain (ETC), which generate adenosine triphosphate ...

assessing-energy-substrate-oxidation-in-vitro-with-14co2-trapping

Research

JoVE Journal

Biology

2.0K Views.  The Children's Hospital of Philadelphia. This protocol describes an easy-to-use method to examine substrate oxidation by tracking 14CO2 production in vitro.

Video: Assessing Energy Substrate Oxidation In Vitro with 14CO2 Trapping

Patch Clamp and Perfusion Techniques for Studying Ion Channels Expressed in Xenopus oocytes

The protocol presented here is designed to study the activation of the large conductance, voltage- and Ca2+-activated K+ (BK) channels. The protocol may also be used to study the structure-function relationship for other ion channels and neurotransmitter receptors1. BK channels are widely expressed in different tissues and have been implicated in many physiological functions, including regulation of smooth muscle contraction, frequency tuning of inner hair cells and regulation of neurotransmitter release2-6. BK channels are activated by membrane depolarization and by intracellular Ca2+ and Mg2+ 6-9. Therefore, the protocol is designed to control both the membrane voltage and the intracellular solution. In this protocol, messenger RNA of BK channels is injected into Xenopus laevis oocytes (stage V-VI) followed by 2-5 days of incubation at 18&deg;C10-13. Membrane patches that contain single or multiple BK channels are excised with the inside-out configuration using patch clamp techniques10-13. The intracellular side of the patch is perfused with desired solutions during recording so that the channel activation under different conditions can be examined. To summarize, the mRNA of BK channels is injected into Xenopus laevis oocytes to express channel proteins on the oocyte membrane; patch clamp techniques are used to record currents flowing through the channels under controlled voltage and intracellular solutions.

Patch Clamp and Perfusion Techniques for Studying Ion Channels Expressed in Xenopus oocytes

Ionic current of BK channels is recorded using patch clamp techniques. BK channels are expressed in Xenopus oocytes by injecting messenger RNA. The intracellular solution during patch clamp recordings is controlled by a perfusion system.

The protocol presented here is designed to study the activation of the large conductance, voltage- and Ca2+-activated K+ (BK) channels. The protocol may ...

Real-time Monitoring of Ligand-receptor Interactions with Fluorescence Resonance Energy Transfer

FRET is a process whereby energy is non-radiatively transferred from an excited donor molecule to a ground-state acceptor molecule through long-range dipole-dipole interactions1. In the present sensing assay, we utilize an interesting property of PDA: blue-shift in the UV-Vis electronic absorption spectrum of PDA (Figure 1) after an analyte interacts with receptors attached to PDA2,3,4,7. This shift in the PDA absorption spectrum provides changes in the spectral overlap (J) between PDA (acceptor) and rhodamine (donor) that leads to changes in the FRET efficiency. Thus, the interactions between analyte (ligand) and receptors are detected through FRET between donor fluorophores and PDA. In particular, we show the sensing of a model protein molecule streptavidin. We also demonstrate the covalent-binding of bovine serum albumin (BSA) to the liposome surface with FRET mechanism. These interactions between the bilayer liposomes and protein molecules can be sensed in real-time. The proposed method is a general method for sensing small chemical and large biochemical molecules. Since fluorescence is intrinsically more sensitive than colorimetry, the detection limit of the assay can be in sub-nanomolar range or lower8. Further, PDA can act as a universal acceptor in FRET, which means that multiple sensors can be developed with PDA (acceptor) functionalized with donors and different receptors attached on the surface of PDA liposomes.

We demonstrate FRET between conjugated polymer polydiacetylene (PDA) and fluorophore attached to the surface of PDA liposomes for the sensing of biomolecules. PDA liposomes also contained receptor molecules on their surfaces for biomolecules to be used as probes. Ligand-receptor interactions lead to changes in the FRET efficiency between the fluorophore and PDA which is the basis of the sensing mechanism.

FRET is a process  whereby energy is non-radiatively transferred from an excited donor molecule to  a ground-state acceptor molecule through long-range ...

Gene Trapping Using Gal4 in Zebrafish

Large clutch size and external development of optically transparent embryos make zebrafish an exceptional vertebrate model system for in vivo insertional mutagenesis using fluorescent reporters to tag expression of mutated genes. Several laboratories have constructed and tested enhancer- and gene-trap vectors in zebrafish, using fluorescent proteins, Gal4- and lexA- based transcriptional activators as reporters 1-7. These vectors had two potential drawbacks: suboptimal stringency (e.g. lack of ability to differentiate between enhancer- and gene-trap events) and low mutagenicity (e.g. integrations into genes rarely produced null alleles). Gene Breaking Transposon (GBTs) were developed to address these drawbacks 8-10. We have modified one of the first GBT vectors, GBT-R15, for use with Gal4-VP16 as the primary gene trap reporter and added UAS:eGFP as the secondary reporter for direct detection of gene trap events. Application of Gal4-VP16 as the primary gene trap reporter provides two main advantages. First, it increases sensitivity for genes expressed at low expression levels. Second, it enables researchers to use gene trap lines as Gal4 drivers to direct expression of other transgenes in very specific tissues. This is especially pertinent for genes with non-essential or redundant functions, where gene trap integration may not result in overt phenotypes. The disadvantage of using Gal4-VP16 as the primary gene trap reporter is that genes coding for proteins with N-terminal signal sequences are not amenable to trapping, as the resulting Gal4-VP16 fusion proteins are unlikely to be able to enter the nucleus and activate transcription. Importantly, the use of Gal4-VP16 does not pre-select for nuclear proteins: we recovered gene trap mutations in genes encoding proteins which function in the nucleus, the cytoplasm and the plasma membrane.

This protocol describes the method of gene trap insertional mutagenesis using Gal4-VP16 as the primary reporter and GFP/RFP as secondary reporters in zebrafish. Approximately one in ten high-expressing F0 fish yield gene trap progeny co-expressing GFP and RFP. The screening procedure can be readily scaled to adapt to the size of the laboratory performing the insertional mutagenesis screen.

Large clutch size and external development of optically transparent embryos make zebrafish an exceptional vertebrate model system for in vivo insertional ...

Determination of Fatty Acid Oxidation and Lipogenesis in Mouse Primary Hepatocytes

Lipid metabolism in liver is complex. In addition to importing and exporting lipid via lipoproteins, hepatocytes can oxidize lipid via fatty acid oxidation, or alternatively, synthesize new lipid via de novo lipogenesis. The net sum of these pathways is dictated by a number of factors, which in certain disease states leads to fatty liver disease. Excess hepatic lipid accumulation is associated with whole body insulin resistance and coronary heart disease. Tools to study lipid metabolism in hepatocytes are useful to understand the role of hepatic lipid metabolism in certain metabolic disorders.
In the liver, hepatocytes regulate the breakdown and synthesis of fatty acids via &#946;-fatty oxidation and de novo lipogenesis, respectively. Quantifying metabolism in these pathways provides insight into hepatic lipid handling. Unlike in vitro quantification, using primary hepatocytes, making measurements in vivo is technically challenging and resource intensive. Hence, quantifying &#946;-fatty acid oxidation and de novo lipogenesis in cultured mouse hepatocytes provides a straight forward method to assess hepatocyte lipid handling. 
Here we describe a method for the isolation of primary mouse hepatocytes, and we demonstrate quantification of &#946;-fatty acid oxidation and de novo lipogenesis, using radiolabeled substrates.

De novo lipogenesis and &#946;-fatty acid oxidation constitute key metabolic pathways in hepatocyte, pathways that are perturbed in several metabolic disorders, including fatty liver disease. Here we demonstrate isolation of mouse primary hepatocytes and describe quantification of &#946;-fatty acid oxidation and lipogenesis.

Lipid metabolism in liver is complex. In addition to importing and exporting lipid via lipoproteins, hepatocytes can oxidize lipid via fatty acid ...

Measurement of Energy Metabolism in Explanted Retinal Tissue Using Extracellular Flux Analysis

High acuity vision is a heavily energy-consuming process, and the retina has developed several unique adaptations to precisely meet such demands while maintaining transparency of the visual axis. Perturbations to this delicate balance cause blinding illnesses, such as diabetic retinopathy. Therefore, the understanding of energy metabolism changes in the retina during disease is imperative to the development of rational therapies for various causes of vison loss. The recent advent of commercially-available extracellular flux analyzers has made the study of retinal energy metabolism more accessible. This protocol describes the use of such an analyzer to measure contributions to retinal energy supply through its two principle arms - oxidative phosphorylation and glycolysis - by quantifying changes in oxygen consumption rates (OCR) and extracellular acidification rates (ECAR) as proxies for these pathways. This technique is readily performed in explanted retinal tissue, facilitating assessment of responses to multiple pharmacologic agents in a single experiment. Metabolic signatures in retinas from animals lacking rod photoreceptor signaling are compared to wild-type controls using this method. A major limitation in this technique is the lack of ability to discriminate between light-adapted and dark-adapted energy utilization, an important physiologic consideration in retinal tissue.

This technique describes real time recording of oxygen consumption and extracellular acidification rates in explanted mouse retinal tissues using an extracellular flux analyzer.

High acuity vision is a heavily energy-consuming process, and the retina has developed several unique adaptations to precisely meet such demands while ...

Assessing Mineral Availability in Fish Feeds using Complementary Methods Demonstrated with the Example of Zinc in Atlantic Salmon

Assessing the availability of dietary micro-minerals is a major challenge in mineral nutrition of fish species. The present article aims to describe a systematic approach combining different methodologies to assess the availability of zinc (Zn) in Atlantic salmon (Salmo salar). Considering that several Zn chemical species can be present in an Atlantic salmon feed, it was hypothesised that Zn availability is influenced by the Zn chemical species present in the feed. Thus, in this study, the first protocol is about how to extract the different Zn chemical species from the feed and to analyze them by a size exclusion chromatography-inductively coupled plasma mass spectroscopy (SEC-ICP-MS) method. Subsequently, an in vitro method was developed to evaluate the solubility of dietary Zn in Atlantic salmon feeds. The third protocol describes the method to study the impact of changing Zn chemical species composition on the uptake of Zn in a fish intestinal epithelial model using a rainbow trout gut cell line (RTgutGC). Together, the findings from the in vitro methods were compared with an in vivo study examining the apparent availability of inorganic and organic sources of Zn supplemented to Atlantic salmon feeds. The results showed that several Zn chemical species can be found in feeds and the efficiency of an organic Zn source depends very much on the amino acid ligand used to chelate Zn. The findings of the in vitro methods had less correlation with that outcome of the in vivo study. Nevertheless, in vitro protocols described in this article provided crucial information regarding Zn availability and its assessment in fish feeds.

This article explains in detail a systematic approach to assess micro-mineral availability in Atlantic salmon. The methodology includes tools and models with increasing biological complexity: (1) chemical speciation analysis, (2) in vitro solubility, (3) uptake studies in cell lines, and (4) in vivo fish studies.&#160;

Assessing the availability of dietary micro-minerals is a major challenge in mineral nutrition of fish species. The present article aims to describe a ...

Quantification of Cell-Substrate Adhesion Area and Cell Shape Distributions in MCF7 Cell Monolayers

The methods presented here quantify some parameters of confluent adherent cell monolayers from multiple appropriately stained confocal images: adhesion to the substrate as a function of the number and size of focal adhesions, and cell shape, characterized by the cell shape index and other shape descriptors. Focal adhesions were visualized by paxillin staining and cell-cell borders were marked by junction plakoglobin and actin. The methods for cell culture and staining were standard; images represent single focal planes; image analysis was performed using publicly available image processing software. The presented protocols are used to quantify the number and size of focal adhesions and the differences in cell shape distribution in the monolayers, but they can be repurposed for the quantification of the size and shape of any other distinct cellular structure that can be stained (e.g., mitochondria or nuclei). Assessing these parameters is important in the characterization of the dynamic forces in adherent cell layer, including cell adhesion and actomyosin contractility that affects cell shape.

The article describes quantification of 1) the size and number of focal adhesions and 2) cell shape index and its distribution from confocal images of the confluent monolayers of MCF7 cells.

The methods presented here quantify some parameters of confluent adherent cell monolayers from multiple appropriately stained confocal images: adhesion to ...

Assessing Protein Interactions in Live-Cells with FRET-Sensitized Emission

F&#246;rster Resonance Energy Transfer (FRET) is the radiationless transfer of energy from an excited donor to an acceptor molecule and depends upon the distance and orientation of the molecules as well as the extent of overlap between the donor emission and acceptor absorption spectra. FRET permits to study the interaction of proteins in the living cell over time and in different subcellular compartments. Different intensity-based algorithms to measure FRET using microscopy have been described in the literature. Here, a protocol and an algorithm are provided to quantify FRET efficiency based on measuring both the sensitized emission of the acceptor and quenching of the donor molecule. The quantification of ratiometric FRET in the living cell not only requires the determination of the crosstalk (spectral spill-over, or bleed-through) of the fluorescent proteins but also the detection efficiency of the microscopic setup. The protocol provided here details how to assess these critical parameters.

F&#246;rster Resonance Energy Transfer (FRET) between two fluorophore molecules can be used for studying protein interactions in the living cell. Here, a protocol is provided as to how to measure FRET in live cells by detecting sensitized emission of the acceptor and quenching of the donor molecule using confocal laser scanning microscopy.

F&#246;rster Resonance Energy Transfer (FRET) is the radiationless transfer of energy from an excited donor to an acceptor molecule and depends upon the ...

Measuring Mitochondrial Substrate Flux in Recombinant Perfringolysin O-Permeabilized Cells

Mitochondrial substrate flux is a distinguishing characteristic of each cell type, and changes in its components such as transporters, channels, or enzymes are involved in the pathogenesis of several diseases. Mitochondrial substrate flux can be studied using intact cells, permeabilized cells, or isolated mitochondria. Investigating intact cells encounters several problems due to simultaneous oxidation of different substrates. Besides, several cell types contain internal stores of different substrates that complicate results interpretation. Methods such as mitochondrial isolation or using permeabilizing agents are not easily reproducible. Isolating pure mitochondria with intact membranes in sufficient amounts from small samples is problematic. Using non-selective permeabilizers causes various degrees of unavoidable mitochondrial membrane damage. Recombinant perfringolysin O (rPFO) was offered as a more appropriate permeabilizer, thanks to its ability to selectively permeabilize plasma membrane without affecting mitochondrial integrity. When used in combination with microplate respirometry, it allows testing the flux of several mitochondrial substrates with enough replicates within one experiment while using a minimal number of cells. In this work, the protocol describes a method to compare mitochondrial substrate flux of two different cellular phenotypes or genotypes and can be customized to test various mitochondrial substrates or inhibitors.

In this work, we describe a modified protocol to test mitochondrial respiratory substrate flux using recombinant perfringolysin O in combination with microplate-based respirometry. With this protocol, we show how metformin affects mitochondrial respiration of two different tumor cell lines.

Mitochondrial substrate flux is a distinguishing characteristic of each cell type, and changes in its components such as transporters, channels, or ...

Determining Basal Energy Expenditure and the Capacity of Thermogenic Adipocytes to Expend Energy in Obese Mice

Energy expenditure measurements are necessary to understand how changes in metabolism can lead to obesity. Basal energy expenditure can be determined in mice by measuring whole-body oxygen consumption, CO2 production, and physical activity using metabolic cages. Thermogenic brown/beige adipocytes (BA) contribute significantly to rodent energy expenditure, particularly at low ambient temperatures. Here, measurements of basal energy expenditure and total BA capacity to expend energy in obese mice are described in two detailed protocols: the first explaining how to set up the assay to measure basal energy expenditure using analysis of covariance (ANCOVA), a necessary analysis given that energy expenditure co-varies with body mass. The second protocol describes how to measure BA energy expenditure capacity in vivo in mice. This procedure involves anesthesia, needed to limit expenditure caused by physical activity, followed by the injection of beta3-adrenergic agonist, CL-316,243, which activates energy expenditure in BA. These two protocols and their limitations are described in sufficient detail to allow a successful first experiment.

This manuscript describes a protocol to measure the basal metabolic rate and the oxidative capacity of thermogenic adipocytes in obese mice.

Energy expenditure measurements are necessary to understand how changes in metabolism can lead to obesity. Basal energy expenditure can be determined in ...