The authors thank the staff members of the Department of Physiology in the Faculty of Medicine in Hradec Kr&#225;lov&#233; and the Department of Pathophysiology in the Third Faculty of Medicine for the help with chemicals and samples preparation. This work was supported by Charles University grant programs PROGRES Q40/02, Czech Ministry of Health grant NU21-01-00259, Czech science foundation grant 18-10144 and INOMED project CZ.02.1.01/0.0/0.0/18_069/0010046 funded by the Ministry of Education, Youth and Sports of the Czech Republic and by the European Union.

1. One day before the assay
<ol>
	<li>Preparation of reagents and substrates.
	<ol>
		<li>Mitochondrial assay solution (MAS): Prepare stock solutions of all reagents as described in Table 1. Warm the stocks of mannitol and sucrose to 37 &#176;C to dissolve completely. Mix the reagents to prepare 2x MAS, then warm the mixture to 37 &#176;C. Adjust the pH with 5N KOH to 7.4 (~7 mL), then add water to bring the volume up to 1 L. Filter-sterilize&#160;and store the aliquots at -20 &#176;C until the measurement day.</li>
		<li>Bovine serum albumin (5% BSA): Dissolve 5 g of BSA in 90 mL of prewarmed sterile water on a magnetic stirrer and avoid shaking. Adjust the pH to 7.4 with 5 N KOH, and then add water to bring the volume up to 100 mL. Filter-sterilize and store the aliquots at -20 &#176;C until the measurement day.</li>
		<li>Mitochondrial substrates: Prepare 1 M stock solutions of sodium succinate, sodium pyruvate, and sodium glutamate in sterile water. Prepare 100 mM stock solution of sodium malate in sterile water and use prewarmed sterile water to prepare a 10 mM stock solution of&#160;palmitoyl carnitine. Adjust pH of each solution to 7.4 by 5 N KOH and filter-sterilize. Store the substrates at 2-8 &#176;C. At the time of use, warm palmitoyl carnitine to 37 &#176;C to dissolve any precipitates. For later use, store aliquots of all the substrates except pyruvate at -20 &#176;C.</li>
		<li>Mitochondrial inhibitors: Use dimethyl sulfoxide (DMSO) to prepare stock solutions of 25 mM oligomycin, 50 mM carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP), 20 mM rotenone, and 20 mM antimycin A. Store the aliquots at -20 &#176;C.</li>
	</ol>
	</li>
	<li>Seeding and treating the cells: As shown in Figure 2, seed the cells in columns 2-11. Columns 1 and 12 must be left empty to serve as background wells. In this work, HepG2 and A549 cells were used.&#160;
	<ol>
		<li>Seed the cells at a density of 20,000 cells per well. Use 50-80 &#181;L of cell culture medium for seeding.</li>
		<li>Fill the blank wells with an equal volume of cell culture medium and incubate the cells at 37 &#176;C in a humidified incubator with 5% CO2. Allow the cells to attach for 3-4 hours, and then add 100 &#181;L of cell culture medium to all wells.</li>
		<li>With that final medium addition, apply the treatment in columns 7&#8211;11. In this work, the experimental group was treated with 1 mM metformin hydrochloride for 16 hours, and the control group was treated with an equal volume of sterile distilled water as a vehicle control.</li>
	</ol>
	</li>
	<li>Hydrating the sensors: Pipette 200 &#181;L of sterile water per well into the utility plate, then carefully return the sensor cartridge while immersing the sensors in water. Incubate the cartridge in a CO2-free incubator at 37 &#176;C till the next day.</li>
	<li>The assay protocol template: Switch on the analyzer (see Table of Materials) and the controller unit. Start the instrument control and data acquisition software and design the assay protocol as described in Table 2. Under Group Definitions, create four injection strategies where Port A differs according to the injected substrate (Figure 3). Name the strategies after the substrates or their abbreviations.</li>
	<li>To ports B, C, and D, assign the compounds&#160;oligomycin, FCCP, and rotenone/antimycin A, respectively. Create eight groups and name them as shown in Figure 4. Under Plate Map assign the groups to the corresponding wells, then save the protocol as a ready-to-use template. Leave the analyzer switched on to allow the temperature to stabilize overnight. Keep the analyzer in a place with a stable temperature to avoid sudden temperature changes.</li>
</ol>
2. The day of the assay
<ol>
	<li>Replacing water with the calibrant: Discard the water from the utility plate and pipette 200 &#181;L of prewarmed calibrant per well into the utility plate. Return the cartridge to the CO2-free incubator until the time of the assay. To avoid rapid evaporation of the calibrant, maintain a source of humidity inside the incubator and turn off or reduce the fan speed to a minimum.</li>
	<li>Preparing the working solutions: Start by warming 2x MAS, 5% BSA, and sterile water to 37 &#176;C. Meanwhile, allow the inhibitor stocks to reach room temperature. Use warm 2x MAS and sterile distilled water to prepare 5 mL of the working concentration of the substrates and inhibitors as described in Table 3.</li>
	<li>Loading the injection ports: As shown in Figure 3, load 20 &#181;L of the substrates into port A. Load succinate/rotenone mixture into port A of rows A and B. Load pyruvate/malate mixture into port A of rows C and D. Load glutamate/malate mixture into port A of rows E and F. Load palmitoyl carnitine/malate mixture into port A of rows G and H. For the whole plate, load port B with 22 &#181;L of oligomycin preparation, port C with 25 &#181;L of FCCP preparation, and port D with 27 &#181;L of rotenone/antimycin A mixture.</li>
	<li>Starting the calibration step: Under Run Assay tab, click on Start Run to start the assay. Insert the loaded sensor cartridge and start the calibration step. Wait for the calibration to complete before proceeding to the next step.</li>
	<li>Preparation of the assay medium (MAS-BSA-rPFO): To prepare 20 mL of the assay medium, mix 10 mL of 2x MAS, 9.2 mL of sterile water, and 0.8 mL of 5% BSA in a 50 mL tube. Add 2 &#181;L of 10&#160;&#181;M&#160;rPFO to attain a concentration of 1 nM and resuspend the mixture with gentle pipetting. Avoid shaking and do not use a vortex mixer for mixing. Incubate the tube at 37 &#176;C until the time of use.</li>
	<li>Washing the cells: Wash the cells and the empty blank wells two times with prewarmed calcium- and magnesium-free phosphate buffered saline (PBS) using a multichannel pipette. Avoid reusing the same tips to discard the cell culture medium and to add PBS. Perform this step outside the laminar flow to protect the cells from drying out by the airflow.</li>
	<li>Cell permeabilization in assay medium: Using a multichannel pipette, discard the PBS and replace it with 180 &#181;L of the prewarmed assay medium (MAS-BSA-rPFO).</li>
	<li>Starting the measurement: Immediately after permeabilization, replace the utility plate of the calibrated sensor cartridge with the cell plate&#160;and start the measurement.</li>
</ol>

<ol>
	<li>Gerencser, A. 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=Quantitative+microplate-based+respirometry+with+correction+for+oxygen+diffusion.">Quantitative microplate-based respirometry with correction for oxygen diffusion.</a> Analytical Chemistry. 81 (16), 6868-6878 (2009).</li><li>Murphy, E., 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=Mitochondrial+function,+biology,+and+role+in+disease:+A+scientific+statement+from+the+American+Heart+Association.">Mitochondrial function, biology, and role in disease: A scientific statement from the American Heart Association.</a> Circulation Research. 118 (12), 1960-1991 (2016).</li><li>Owen, O. E., Kalhan, S. C., Hanson, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+key+role+of+anaplerosis+and+cataplerosis+for+citric+acid+cycle+function.">The key role of anaplerosis and cataplerosis for citric acid cycle function.</a> Journal of Biological Chemistry. 277 (34), 30409-30412 (2002).</li><li>Nicholls, D. G., Ferguson, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Bioenergetics 3. , (2002).</li><li>Brand, M. D., Nicholls, D. G. <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> Biochemical Journal. 435 (2), 297-312 (2011).</li><li>Sta&#328;kov&#225;, 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=Adaptation+of+mitochondrial+substrate+flux+in+a+mouse+model+of+nonalcoholic+fatty+liver+disease.">Adaptation of mitochondrial substrate flux in a mouse model of nonalcoholic fatty liver disease.</a> International Journal of Molecular Sciences. 21 (3), 1101 (2020).</li><li>Salabei, J. K., Gibb, A. A., Hill, B. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+measurement+of+respiratory+activity+in+permeabilized+cells+using+extracellular+flux+analysis.">Comprehensive measurement of respiratory activity in permeabilized cells using extracellular flux analysis.</a> Nature Protocols. 9 (2), 421-438 (2014).</li><li>Divakaruni, A. 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=Thiazolidinediones+are+acute,+specific+inhibitors+of+the+mitochondrial+pyruvate+carrier.">Thiazolidinediones are acute, specific inhibitors of the mitochondrial pyruvate carrier.</a> Proceedings of the National Academy of Sciences of the United States of America. 110 (14), 5422-5427 (2011).</li><li>Divakaruni, A. S., Rogers, G. W., Murphy, A. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+mitochondrial+function+in+permeabilized+cells+using+the+seahorse+XF+analyzer+or+a+Clark-type+oxygen+electrode.">Measuring mitochondrial function in permeabilized cells using the seahorse XF analyzer or a Clark-type oxygen electrode.</a> Current Protocols in Toxicology. 60, 1-16 (2014).</li><li>Elkalaf, M., T&#367;ma, P., Weiszenstein, M., Pol&#225;k, J., Trnka, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+probe+Methyltriphenylphosphonium+(TPMP)+inhibits+the+Krebs+cycle+enzyme+2-Oxoglutarate+dehydrogenase.">Mitochondrial probe Methyltriphenylphosphonium (TPMP) inhibits the Krebs cycle enzyme 2-Oxoglutarate dehydrogenase.</a> PLoS One. 11 (8), 0161413 (2016).</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 (7), 21746 (2011).</li></ol>

The authors have no conflict of interest to declare.

This protocol is a modification of previously published studies7,8,9,10 and the product user guide. In contrast to the manufacturer&#39;s protocol, 2x MAS is used instead of 3x MAS, since 2&#215; MAS is easier to dissolve and does not form precipitations after freezing. Frozen 2x MAS aliquots can be stored up to six months and show consistent results. Another difference is including ADP in the ...

Microplate-based respirometry has revolutionized mitochondrial research by enabling the study of cellular respiration of a small sample size1. Cellular respiration is generally considered as an indicator of mitochondrial function or &#39;dysfunction&#39;, despite the fact that the mitochondrial range of functions extends beyond energy production2. In aerobic conditions, mitochondria extract the energy stored in different substrates by breaking down and converting these substrates into metabolic intermediates that can fuel the citric acid cycle3 (Figure 1). The continuous flux of substrates is essential for the flow of the citric acid cycle to generate high energy &#39;electron donors&#39;, which deliver electrons to the electron transport chain that generates a proton gradient across the inner mitochondrial membrane, enabling ATP-synthase to phosphorylate ADP to ATP4. Therefore, an experimental design to assay mitochondrial respiration must include the sample nature (intact cells, permeabilized cells, or isolated mitochondria) and mitochondrial substrates.
Cells keep a store of indigenous substrates5, and mitochondria oxidize several types of substrates simultaneously6, which complicates the interpretation of results obtained from experiments performed on intact cells. A common approach to investigate mitochondrial ability to oxidize a selected substrate is to isolate mitochondria or permeabilize the investigated cells5. Although isolated mitochondria are ideal for quantitative studies, the isolation process is laborious. It faces technical difficulties such as the need for large sample size, purity of the yield, and reproducibility of the technique5. Permeabilized cells offer a solution for the disadvantages of mitochondrial isolation; however, routine permeabilizing agents of detergent nature are not specific and may damage mitochondrial membranes5.
Recombinant perfringolysin O (rPFO) was offered as a selective plasma membrane permeabilizing agent7, and it was used successfully in combination with an extracellular flux analyzer in several studies7,8,9,10. We have modified a protocol using rPFO to screen mitochondrial substrate flux using XFe96 extracellular flux analyzer. In this protocol, four different substrate oxidizing pathways in two cellular phenotypes are compared while having sufficient replicates and the proper control for each tested material.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Adinosine 5&#8242; -diphosphate monopotassium salt dihydrate</td>
			<td>Merck</td>
			<td>A5285</td>
			<td>store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Antimycin A</td>
			<td>Merck</td>
			<td>A8674</td>
			<td>store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Merck</td>
			<td>A3803</td>
			<td>store at 2 - 8 &#176;C</td>
		</tr>
		<tr>
			<td>Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone</td>
			<td>Merck</td>
			<td>C2920</td>
			<td>store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide</td>
			<td>Merck</td>
			<td>D8418</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>D-Mannitol</td>
			<td>Merck</td>
			<td>63559</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s phosphate buffered saline</td>
			<td>Gibco</td>
			<td>14190-144</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Ethylene glycol-bis(2-aminoethylether)-N,N,N&#8242;,N&#8242;-tetraacetic acid</td>
			<td>Merck</td>
			<td>03777</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Merck</td>
			<td>H7523</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>L(-)Malic acid disodium salt</td>
			<td>Merck</td>
			<td>M9138</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>L-Glutamic acid sodium salt hydrate</td>
			<td>Merck</td>
			<td>G5889</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Magnissium chloride hexahydrate</td>
			<td>Merck</td>
			<td>M2670</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Oligomycin</td>
			<td>Merck</td>
			<td>O4876</td>
			<td>store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Palmitoyl-DL-carnitine chloride</td>
			<td>Merck</td>
			<td>P4509</td>
			<td>store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Potassium hydroxide</td>
			<td>Merck</td>
			<td>484016</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Potassium phosphate monobasic</td>
			<td>Merck</td>
			<td>P5655</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Rotenone</td>
			<td>Merck</td>
			<td>R8875</td>
			<td>store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Seahorse Wave Desktop Software</td>
			<td>Agilent technologies</td>
			<td></td>
			<td>Download from www.agilent.com</td>
		</tr>
		<tr>
			<td>Seahorse XFe96 Analyzer</td>
			<td>Agilent technologies</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Seahorse XFe96 FluxPak</td>
			<td>Agilent technologies</td>
			<td>102416-100</td>
			<td>XFe96 sensor cartridges and XF96 cell culture microplates</td>
		</tr>
		<tr>
			<td>Sodium pyruvate</td>
			<td>Merck</td>
			<td>P2256</td>
			<td>store at 2 - 8 &#176;C</td>
		</tr>
		<tr>
			<td>Sodium succinate dibasic hexahydrate</td>
			<td>Merck</td>
			<td>S2378</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Merck</td>
			<td>S7903</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>Water</td>
			<td>Merck</td>
			<td>W3500</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>XF calibrant</td>
			<td>Agilent technologies</td>
			<td>100840-000</td>
			<td>store at RT</td>
		</tr>
		<tr>
			<td>XF Plasma membrane permeabilizer</td>
			<td>Agilent technologies</td>
			<td>102504-100</td>
			<td>Recombinant perfringolysin O (rPFO) - Aliquot and store at -20 &#176;C</td>
		</tr>
	</tbody>
</table>

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.

Start by normalizing the results to the second measurement of baseline respiration to show values as oxygen consumption rate percentage (OCR%). The results of the assay are shown in Figures 5, Figure 6, Figure 7, and Figure 8. It is important to assign the proper background wells for each group and inactivate the background wells of other groups. Fi...

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Measuring Mitochondrial Substrate Flux in Recombinant Perfringolysin O-Permeabilized Cells

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 ...

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2.3K Views.  Charles University. 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. 

Video: Measuring Mitochondrial Substrate Flux in Recombinant Perfringolysin O-Permeabilized Cells

A Method For Production of Recombinant mCD1d Protein in Insect Cells.

CD1 proteins constitute a third class of antigen-presenting molecules. They are cell surface glycoproteins, expressed as approximately 50-kDa glycosylated heavy chains that are noncovalently associated with beta2-microglobulin. They bind lipids rather than peptides. Although their structure confirms the similarity of CD1 proteins to MHC class I and class II antigen presenting molecules, the mCD1d groove is relatively narrow, deep, and highly hydrophobic and it has two binding pockets instead of the several shallow pockets described for the classical MHC-encoded antigen-presenting molecules. Based upon their amino acid sequences, such a hydrobphobic groove provides an ideal environment for the binding of lipid antigens. The Natural Killer T (NKT) cells use their TCR to recognize glycolipids bound to or presented by CD1d. T cells reactive to lipids presented by CD1 have been involved in the protection against autoimmune and infectious diseases and in tumor rejection. Thus, the ability to identify, purify , and track the response of CD1-reactive NKT cell is of great importance . The generation of tetramers of alpha Galactosyl ceramide (a-Galcer) with CD1d has significant insight into the biology of NKT cells. Tetramers constructed from other CD1 molecules have also been generated and these new reagents have greatly expanded the knowledge of the functions of lipid-reactive T cells, with potential use in monitoring the response to lipid-based vaccines and in the diagnosis of autoimmune diseases and other treatments.

A Method to prepare Insect cells and infect them with baculovirus for the the purpose of production of recombinant mCD1d proteinand generating mCD1d tetramers.

CD1 proteins constitute a third class of antigen-presenting molecules. They are cell surface glycoproteins, expressed as approximately 50-kDa glycosylated ...

Probing for Mitochondrial Complex Activity in Human Embryonic Stem Cells

Mitochondria are cytoplasmic organelles that have a primary role in cellular metabolism and homeostasis, regulation of the cell signaling network, and programmed cell death. Mitochondria produce ATP, regulate the cytoplasmic redox state and Ca2+ balance, catabolize fatty acids, synthesize heme, nucleotides, steroid hormones, amino acids, and help assemble iron-sulfur clusters in proteins. Mitochondria also have an essential role in heat production. Mutations of the mitochondrial genome cause several types of human disorder. The accumulation of mtDNA mutations correlates with aging and is suspected to have an important role in the development of cancer. Due to their vitally important role in all cell types, the function of mitochondria must also be critical for stem cells. Key advances have been made in our understanding of stem cell viability, proliferation, and differentiation capacity. But the functional activity of stem cells, in particular their energy status, was not yet been studied in detail. Almost nothing is known about the mitochondrial properties of human embryonic stem cells (hESCs) and their differentiated precursor progeny. One way to understand and evaluate the role of mitochondria in hESC function and developmental potential is to directly measure the activity of mitochondrial respiratory complexes. Here, we describe high resolution clear native gel electrophoresis and subsequent in gel activity visualization as a method for analyzing the five respiratory chain complexes of hESCs.

In this video, we will show you how the mitochondrial respiratory chain complexes of human embryonic stem cells can be analyzed using in gel activity assays.

Mitochondria are cytoplasmic organelles that have a primary role in cellular metabolism and homeostasis, regulation of the cell signaling network, and ...

Simultaneous Measurement of Mitochondrial Calcium and Mitochondrial Membrane Potential in Live Cells by Fluorescent Microscopy

Apart from their essential role in generating ATP, mitochondria also act as local calcium (Ca2+) buffers to tightly regulate intracellular Ca2+ concentration. To do this, mitochondria utilize the electrochemical potential across their inner membrane (&#916;&#936;m) to sequester Ca2+. The influx of Ca2+ into the mitochondria stimulates three rate-limiting dehydrogenases of the citric acid cycle, increasing electron transfer through the oxidative phosphorylation (OXPHOS) complexes. This stimulation maintains &#916;&#936;m, which is temporarily dissipated as the positive calcium ions cross the mitochondrial inner membrane into the mitochondrial matrix.
We describe here a method for simultaneously measuring mitochondria Ca2+ uptake and &#916;&#936;m in live cells using confocal microscopy. By permeabilizing the cells, mitochondrial Ca2+ can be measured using the fluorescent Ca2+ indicator Fluo-4, AM, with measurement of &#916;&#936;m using the fluorescent dye tetramethylrhodamine, methyl ester, perchlorate (TMRM). The benefit of this system is that there is very little spectral overlap between the fluorescent dyes, allowing accurate measurement of mitochondrial Ca2+ and &#916;&#936;m simultaneously. Using the sequential addition of Ca2+ aliquots, mitochondrial Ca2+ uptake can be monitored, and the concentration at which Ca2+ induces mitochondrial membrane permeability transition and the loss of &#916;&#936;m determined.

Mitochondria can utilize the electrochemical potential across their inner membrane (&#916;&#936;m) to sequester calcium (Ca2+), allowing them to shape cytosolic Ca2+ signaling within the cell. We describe a method for simultaneously measuring mitochondria Ca2+ uptake and &#916;&#936;m in live cells using fluorescent dyes and confocal microscopy.

Apart from their essential role in generating ATP, mitochondria also act as local calcium (Ca2+) buffers to tightly regulate intracellular Ca2+ ...

Assessing Autophagic Flux by Measuring LC3, p62, and LAMP1 Co-localization Using Multispectral Imaging Flow Cytometry

Autophagy is a catabolic pathway in which normal or dysfunctional cellular components that accumulate during growth and differentiation are degraded via the lysosome and are recycled. During autophagy, cytoplasmic LC3 protein is lipidated and recruited to the autophagosomal membranes. The autophagosome then fuses with the lysosome to form the autolysosome, where the breakdown of the autophagosome vesicle and its contents occurs. The ubiquitin-associated protein p62, which binds to LC3, is also used to monitor autophagic flux. Cells undergoing autophagy should demonstrate the co-localization of p62, LC3, and lysosomal markers. Immunofluorescence microscopy has been used to visually identify LC3 puncta, p62, and/or lysosomes on a per-cell basis. However, an objective and statistically rigorous assessment can be difficult to obtain. To overcome these problems, multispectral imaging flow cytometry was used along with an analytical feature that compares the bright detail images from three autophagy markers (LC3, p62 and lysosomal LAMP1) and quantifies their co-localization, in combination with LC3 spot counting to measure autophagy in an objective, quantitative, and statistically robust manner.

Here, multispectral imaging flow cytometry with an analytical feature that compares bright detail images of 3 autophagy markers and quantifies their co-localization, along with LC3 spot counting, was used to measure autophagy in an objective, quantitative, and statistically robust manner.

Autophagy is a catabolic pathway in which normal or dysfunctional cellular components that accumulate during growth and differentiation are degraded via ...

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

We present a software solution for semi-automated tracking of relative protein concentration along the length of dynamic cellular protrusions.

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex ...

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 ...

Measuring Diurnal Rhythms in Autophagic and Proteasomal Flux

Cells employ several methods for recycling unwanted proteins and other material, including lysosomal and non-lysosomal pathways. The main lysosome-dependent pathway is called autophagy, while the primary non-lysosomal method for protein catabolism is the ubiquitin-proteasome system. Recent studies in model organisms suggest that the activity of both autophagy and the ubiquitin-proteasome system is not constant across the day but instead varies according to a daily (circadian) rhythm. The ability to measure biological rhythms in protein turnover is important for understanding how cellular quality control is achieved and for understanding the dynamics of specific proteins of interest. Here we present a standardized protocol for quantifying autophagic and proteasomal flux in vivo that captures the circadian component of protein turnover. Our protocol includes details for mouse handling, tissue processing, fractionation, and autophagic flux quantification using mouse liver as the starting material.

We describe our protocol for measuring biological rhythms in protein catabolism via autophagy and the proteasome in mouse liver.

Cells employ several methods for recycling unwanted proteins and other material, including lysosomal and non-lysosomal pathways. The main ...

Development of a Mobile Mitochondrial Physiology Laboratory for Measuring Mitochondrial Energetics in the Field

Mitochondrial energetics is a central theme in animal biochemistry and physiology, with researchers using mitochondrial respiration as a metric to investigate metabolic capability. To obtain the measures of mitochondrial respiration, fresh biological samples must be used, and the entire laboratory procedure must be completed within approximately 2 h. Furthermore, multiple pieces of specialized equipment are required to perform these laboratory assays. This creates a challenge for measuring mitochondrial respiration in the tissues of wild animals living far from physiology laboratories as live tissue cannot be preserved for very long after collection in the field. Moreover, transporting live animals over long distances induces stress, which can alter mitochondrial energetics.
This manuscript introduces the Auburn University (AU) MitoMobile, a mobile mitochondrial physiology laboratory that can be taken into the field and used on-site to measure mitochondrial metabolism in tissues collected from wild animals. The basic features of the mobile laboratory and the step-by-step methods for measuring isolated mitochondrial respiration rates are presented. Additionally, the data presented validate the success of outfitting the mobile mitochondrial physiology laboratory and making mitochondrial respiration measurements. The novelty of the mobile laboratory lies in the ability to drive to the field and perform mitochondrial measurements on the tissues of animals captured on site.

We designed and constructed a mobile laboratory to measure respiration rates in isolated mitochondria of wild animals captured at field locations. Here, we describe the design and outfitting of a mobile mitochondrial laboratory and the associated laboratory protocols.

Mitochondrial energetics is a central theme in animal biochemistry and physiology, with researchers using mitochondrial respiration as a metric to ...

Imaging of Mitochondrial Peroxide in Living Yeast Cells Using mtHyper7

Imaging of mtHyPer7, a Ratiometric Biosensor for Mitochondrial Peroxide, in Living Yeast Cells

Mitochondrial dysfunction, or functional alteration, is found in many diseases and conditions, including neurodegenerative and musculoskeletal disorders, cancer, and normal aging. Here, an approach is described to assess mitochondrial function in living yeast cells at cellular and subcellular resolutions using a genetically encoded, minimally invasive, ratiometric biosensor. The biosensor, mitochondria-targeted HyPer7 (mtHyPer7), detects hydrogen peroxide (H2O2) in mitochondria. It consists of a mitochondrial signal sequence fused to a circularly permuted fluorescent protein and the H2O2-responsive domain of a bacterial OxyR protein. The biosensor is generated and integrated into the yeast genome using a CRISPR-Cas9 marker-free system, for&#160;more consistent expression compared to plasmid-borne constructs.
mtHyPer7 is quantitatively targeted to mitochondria, has no detectable effect on yeast growth rate or mitochondrial morphology, and provides a quantitative readout for mitochondrial H2O2 under normal growth conditions and upon exposure to oxidative stress. This protocol explains how to optimize imaging conditions using a spinning-disk confocal microscope system and perform quantitative analysis using freely available software. These tools make it possible to collect rich spatiotemporal information on mitochondria both within cells and among cells in a population. Moreover, the workflow described here can be used to validate other biosensors.

Author Spotlight: Advancing Mitochondrial Research - mtHyper7 Biosensor for Subcellular Analysis 

Hydrogen peroxide (H2O2) is both a source of oxidative damage and a signaling molecule. This protocol describes how to measure mitochondrial H2O2 using mitochondria-targeted HyPer7 (mtHyPer7), a genetically encoded ratiometric biosensor, in living yeast. It details how to optimize imaging conditions and perform quantitative cellular and subcellular analysis using freely available software.

Mitochondrial dysfunction, or functional alteration, is found in many diseases and conditions, including neurodegenerative and musculoskeletal disorders, ...

Quantitative Analysis of Mitophagy in Murine Pancreatic &#946;-Cells

Complementary Approaches to Interrogate Mitophagy Flux in Pancreatic &#946;-Cells

Mitophagy is a quality control mechanism necessary to maintain optimal mitochondrial function. Dysfunctional &#946;-cell mitophagy results in insufficient insulin release. Advanced quantitative assessments of mitophagy often require the use of genetic reporters. The mt-Keima mouse model, which expresses a mitochondria-targeted pH-sensitive dual-excitation ratiometric probe for quantifying mitophagy via flow cytometry, has been optimized in &#946;-cells. The ratio of acidic-to-neutral mt-Keima wavelength emissions can be used to robustly quantify mitophagy. However, using genetic mitophagy reporters can be challenging when working with complex genetic mouse models or difficult-to-transfect cells, such as primary human islets. This protocol describes a novel complementary dye-based method to quantify &#946;-cell mitophagy in primary islets using MtPhagy. MtPhagy is a pH-sensitive, cell-permeable dye that accumulates in the mitochondria and increases its fluorescence intensity when mitochondria are in low pH environments, such as lysosomes during mitophagy. By combining the MtPhagy dye with Fluozin-3-AM, a Zn2+ indicator that selects for &#946;-cells, and Tetramethylrhodamine, ethyl ester (TMRE) to assess mitochondrial membrane potential, mitophagy flux can be quantified specifically in &#946;-cells via flow cytometry. These two approaches are highly complementary, allowing for flexibility and precision in assessing mitochondrial quality control in numerous &#946;-cell models.

Author Spotlight: Assessment of Mitophagy Flux in Pancreatic &#946;-Cells Using Effective and Robust Complementary Approaches 

This protocol outlines two methods for the quantitative analysis of mitophagy in pancreatic &#946;-cells: first, a combination of cell-permeable mitochondria-specific dyes, and second, a genetically encoded mitophagy reporter. These two techniques are complementary and can be deployed based on specific needs, allowing for flexibility and precision in quantitatively addressing mitochondrial quality control.

Mitophagy is a quality control mechanism necessary to maintain optimal mitochondrial function. Dysfunctional &#946;-cell mitophagy results in insufficient ...