The authors acknowledge the Brazilian agency Coordena&#231;&#227;o de Aperfei&#231;oamento de Pesquisa Pessoal de N&#237;vel Superior (CAPES EPIDEMIAS 09 #88887.505377/2020). P.M. (#88887.512821/2020-00) and T.D. (#88887.512883/2020-00) are research fellowship recipients.

We used the strains w1118 (white) and w[*] Pink1[B9]/FM7i, P{w[+mC]=ActGFP}JMR3 (referred to as Pink1B9) (FlyBase ID: FBgn0029891) from the Bloomington Drosophila stock center (ID number: 34749). In this study, male D. melanogaster PINK1B9-null mutants are compared with male D. melanogaster from the w1118&#160;strain, which is used as a control group (genetic background). Other parameters must be analyzed concomitantly with the respirometry experiments to ensure that the flies have the correct genotype (Pink1B9/Y), such as thorax deformities and locomotion problems, which are well described for pink1B9 mutant flies24,25,26.
1. Animals and housing
<ol>
	<li>Keep the flies in glass bottles containing 10 mL of standard diet (yeast 1.73%, soy flour 0.9%, corn flour 7.3%, agar 0.5%, corn syrup 7.6%, and propionic acid 0.48%) at constant temperature and humidity (25 &#176;C and 60%, respectively), with a 12 h:12 h light/dark cycle.</li>
	<li>For each experiment, use two flies aged 1-3 days post-eclosion. 
	&#8203;NOTE: The PINK1B9-null mutant virgin female flies were crossed with w1118 males to obtain the F1 males with genotype Pink1B9/Y.</li>
</ol>
2. Sample preparation
<ol>
	<li>Prepare the MiR05 buffer as described in Table 1.</li>
	<li>Anesthetize the flies on ice and transfer them to microcentrifuge tubes (two flies per tube).</li>
	<li>In each tube, add 200 &#181;L of chilled MiR05 buffer and homogenize the flies. Homogenize manually, applying gentle pressure (approximately 4-6 strokes of the pestle) to prevent the disintegration of mitochondria.</li>
</ol>
3. High-resolution respirometry calibration of polarographic oxygen sensors
NOTE: The OROBOROS chambers have a total volume of approximately 2 mL. Calibration is required to ensure the oxygen flux is close to 0 pmol to start the assay.
<ol>
	<li>Starting the calibration, add 2 mL of MiR05 to the chamber. Cover the chamber with the stopper leaving no air bubbles; then, carefully pull the stopper to form one single air bubble.</li>
	<li>Open the OROBOROS Dat.Lab software. Enter a temperature of 25 &#176;C in the Block temperature field and click on Connect to Oxygraph-2k (Figure 1A).</li>
	<li>Click and select the folder where the calibration is to be saved and click on Save.</li>
	<li>When a new window opens, name the experiment and the samples (if calibrating, simply enter the name calibration) and click on Save.</li>
	<li>Go to the Layout menu and choose the first option: 01 Calibration Exp. Gr.3 - Temp as shown in Figure 1B.</li>
	<li>Wait for the program to redirect to the calibration layout, wait until the red line shows a standard straight line with points around 0 pmol. Then, select two points: one for chamber A and the other for chamber B (Figure 1C) when the red line is exactly at zero. 
	NOTE: The selected points must have oxygen flux (red line) around 0.
	<ol>
		<li>To mark the points of both chambers, select O2 concentration on the right of the screen, select the marked point, and copy both the temperature and barometric pressure values relative to the point. Paste these values in the boxes below and click on Calibrate and Copy to Clipboard in the lower right corner of the screen as shown in Figure 2.</li>
		<li>Carry out this process for both chambers (A and B), then go to the File menu and select Save and Disconnect. 
		&#8203;NOTE: After the calibration process, the program will redirect the user to the home screen so that the software will be ready to start the HRR test. For this test, we will use the SUIT protocol.</li>
	</ol>
	</li>
</ol>
4. SUIT protocol
<ol>
	<li>With the calibration completed, remove the stoppers and open the chambers.</li>
	<li>Wash the stoppers (holding the tip that does not touch the sample) and chambers with 100% ethanol, 70% ethanol, and distilled water, in that order. 
	NOTE: Repeat the process for every sample change.</li>
	<li>Homogenize the flies in 200 &#181;L of buffer, place all sample content in the chamber using a micropipette, and relocate the stopper in the chamber, taking care to not create air bubbles. 
	NOTE: If air bubbles form, remove the stopper gently and add 100 &#181;L of MIR05 buffer.</li>
	<li>Click on the Layout menu and select the option 05 Flow by Corrected Volume as shown in Figure 1B.</li>
	<li>Wait to be redirected to a new window. Click on Save to select the folder where the experiment is to be saved.</li>
	<li>Wait for another new window to open. Name the experiment in the space Experimental Code. Then, name each sample in its respective chamber A and B in the Sample field, and set the field Unit to unit. 
	NOTE: Other units can also be chosen, for example, Millions of cells or mg.</li>
	<li>Considering that this protocol uses two flies (2 units) and the chamber volume is 2 mL, in the Concentration field, define 1 per mL (Figure 1D). 
	NOTE: Here, the sample amount was normalized by the number of flies; however, this normalization may be performed by the protein content of the sample, mitochondrial DNA quantification, or activity of citrate synthase.</li>
	<li>When the oxygen flux signal (red line) is steady on the positive value, start the HRR protocol with the titration of substrates, inhibitors, and uncouplers (Figure 3). All the subsequent reagents and equipment are shown in Table 1.
	<ol>
		<li>Add digitonin (5 &#956;g/mL) to permeabilize the mitochondrial membrane.</li>
		<li>Add pyruvate (5 mM), malate (2 mM), and proline (10 mM) substrates and wait until the oxygen flux increases and stabilizes. To mark the event for each reagent addition, press the F4 key on the keyboard and enter the name of each reagent.</li>
		<li>Add ADP (5mM) to couple the mitochondrial respiratory chain and wait for the increase and stabilization of the oxygen flux.</li>
		<li>Add succinate (10 mM) and wait for the increase and stabilization of the oxygen flux.</li>
		<li>Add Oligomycin (2.5 &#181;M) to inhibit ATP synthase and look for a decrease in oxygen flux.</li>
		<li>Wait until the red line stabilizes and uncouple mitochondrial electron transfer using Carbonyl-4-(trifluoromethoxy) phenylhydrazone cyanide (FCCP) with titers of 0.25 &#181;M until the maximum oxygen consumption is reached, demonstrated by the rise of the red line. After stabilization of the oxygen flux, start adding the inhibitors of each complex, one at a time.</li>
		<li>Add Rotenone (0.5 &#181;M), a complex I inhibitor. Wait for the decrease and stabilization of the oxygen flux to add the next inhibitor.</li>
		<li>Add Malonate (5 mM), a complex II inhibitor. Wait for the decrease and stabilization of the oxygen flux to add the next inhibitor.</li>
		<li>Finally, add Antimycin (2.5 &#181;M), a complex III inhibitor. Wait for the decrease followed by the increase and stabilization of the oxygen flux. 
		NOTE: The oxygen flux should stabilize at a positive value but below the value for the last inhibition of mitochondrial protein complexes.</li>
	</ol>
	</li>
	<li>At the end of the analysis, remove all the content of the chambers using a micropipette. Store at -20 &#176;C for future analysis, when necessary.</li>
</ol>
5. Data analysis
<ol>
	<li>Utilize an appropriate statistical software package for data analysis.</li>
	<li>Perform t-tests to assess differences between the two groups. For situations involving multiple treatments, use Analysis of Variance (ANOVA) as a statistical test 27.</li>
	<li>Extract the O2 flux values from the graph generated by the software. OXPHOS CI refers to the value of O2 flux after adding ADP. OXPHOS CII is obtained by subtracting OXPHOS CI&#38;CII - OXPHOS CI. OXPHOS CI&#38;CII is the value of O2 flux extracted after the addition of succinate. ETS CI&#38;CII is the O2 flux value after adding FCCP. ETS CI = FCCP - Rotenone and ETS CII = Rotenone - Malonate.</li>
	<li>Calculate ATP synthesis as the difference between the OXPHOS (P) and LEAK (L) (P - L)28.</li>
	<li>Determine the Respiratory Control Ratio (RCR) by calculating the ratio OXPHOS/LEAK, where RCR = P/L.11</li>
</ol>

Analyzing Mitochondrial Physiology and Bioenergetics in Fruit Flies

<ol>
	<li>Brand, M. D., Orr, A. L., Perevoshchikova, I. V., Quinlan, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+mitochondrial+function+and+cellular+bioenergetics+in+ageing+and+disease.">The role mitochondrial function and cellular bioenergetics in ageing and disease.</a> Br J Dermatol. 169, 1-8 (2013).</li><li>Ramaccini, 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=Mitochondrial+function+and+dysfunction+in+dilated+cardiomyopathy.">Mitochondrial function and dysfunction in dilated cardiomyopathy.</a> Front Cell Dev Biol. 8, 624216 (2021).</li><li>Zhunina, O. 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=The+role+of+mitochondrial+dysfunction+in+vascular+disease,+tumorigenesis,+and+diabetes.">The role of mitochondrial dysfunction in vascular disease, tumorigenesis, and diabetes.</a> Front Mol Biosci. 8, 671908 (2021).</li><li>Prasun, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+dysfunction+in+metabolic+syndrome.">Mitochondrial dysfunction in metabolic syndrome.</a> Biochim Biophys Acta. 1866 (10), 165838 (2020).</li><li>Bhatti, J. S., Bhatti, G. K., Reddy, P. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+dysfunction+and+oxidative+stress+in+metabolic+disorders+-+A+Step+towards+mitochondria+based+therapeutic+strategies.">Mitochondrial dysfunction and oxidative stress in metabolic disorders - A Step towards mitochondria based therapeutic strategies.</a> Biochim Biophys Acta. 1863 (5), 1066-1077 (2017).</li><li>Perier, C., Vila, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+biology+and+Parkinson's+disease.">Mitochondrial biology and Parkinson's disease.</a> Cold Spring Harb Perspect Med. 2 (2), 009332 (2012).</li><li>DeMaagd, G., Philip, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Parkinson's+disease+and+its+management.">Parkinson's disease and its management.</a> Pharmacy and Therapeutics. 40 (8), 504-532 (2015).</li><li>Miyazaki, N., 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=PINK1-dependent+and+Parkin-independent+mitophagy+is+involved+in+reprogramming+of+glycometabolism+in+pancreatic+cancer+cells.">PINK1-dependent and Parkin-independent mitophagy is involved in reprogramming of glycometabolism in pancreatic cancer cells.</a> Biochem Biophys Res Commun. 625, 167-173 (2022).</li><li>Kopin, I. J., Markey, S. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MPTP+toxicity:+implications+for+research+in+Parkinson's+disease.">MPTP toxicity: implications for research in Parkinson's disease.</a> Annual Review of Neuroscience. 11, 81-96 (1988).</li><li>Connolly, N. M. C., 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=Guidelines+on+experimental+methods+to+assess+mitochondrial+dysfunction+in+cellular+models+of+neurodegenerative+diseases.">Guidelines on experimental methods to assess mitochondrial dysfunction in cellular models of neurodegenerative diseases.</a> Cell Death Differ. 25 (3), 542-572 (2018).</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> Biochem J. 435, 297-312 (2011).</li><li>Haynes, C. M., Fiorese, C. J., Lin, Y. -. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluating+and+responding+to+mitochondrial+dysfunction:+The+UPRmt+and+beyond.">Evaluating and responding to mitochondrial dysfunction: The UPRmt and beyond.</a> Trends Cell Mol Biol. 23 (7), 311-318 (2013).</li><li>Long, Q., Huang, L., Huang, K., Yang, Q. <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+bioenergetics+in+isolated+mitochondria+from+mouse+heart+tissues+using+oroboros+2k-oxygraph.">Assessing mitochondrial bioenergetics in isolated mitochondria from mouse heart tissues using oroboros 2k-oxygraph.</a> Methods Mol Biol. 1966, 237-246 (2019).</li><li>Scheiber, 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=High-resolution+respirometry+in+human+endomyocardial+biopsies+shows+reduced+ventricular+oxidative+capacity+related+to+heart+failure.">High-resolution respirometry in human endomyocardial biopsies shows reduced ventricular oxidative capacity related to heart failure.</a> Exp Mol Med. 51 (2), 1-10 (2019).</li><li>Krumschnabel, G., Eigentler, A., Fasching, M., 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=Chapter+nine+-+use+of+safranin+for+the+assessment+of+mitochondrial+membrane+potential+by+high-resolution+respirometry+and+fluorometry.">Chapter nine - use of safranin for the assessment of mitochondrial membrane potential by high-resolution respirometry and fluorometry.</a> Methods Enzymol. 542, 163-181 (2014).</li><li>Demir, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+potential+use+of+Drosophila+as+an+in+vivo+model+organism+for+COVID-19-related+research:+a+review.">The potential use of Drosophila as an in vivo model organism for COVID-19-related research: a review.</a> Turk J Biol. 45 (4), 559-569 (2021).</li><li>Hales, K. G., Korey, C. A., Larracuente, A. M., Roberts, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetics+on+the+fly:+a+primer+on+the+Drosophila+model+system.">Genetics on the fly: a primer on the Drosophila model system.</a> Genetics. 201 (3), 815-842 (2015).</li><li>McBride, S. M. J., Holloway, S. L., Jongens, T. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+Drosophila+as+a+tool+to+identify+pharmacological+therapies+for+fragile+X+syndrome.">Using Drosophila as a tool to identify pharmacological therapies for fragile X syndrome.</a> Drug Discov Today Technol Technologies. 10 (1), e129-e136 (2013).</li><li>Tennessen, J. M., Barry, W. E., Cox, J., Thummel, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+for+studying+metabolism+in+Drosophila.">Methods for studying metabolism in Drosophila.</a> Methods (San Diego, Calif). 68 (1), 105-115 (2014).</li><li>Bar, S., Prasad, M., Datta, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuromuscular+degeneration+and+locomotor+deficit+in+a+Drosophila+model+of+mucopolysaccharidosis+VII+is+attenuated+by+treatment+with+resveratrol).">Neuromuscular degeneration and locomotor deficit in a Drosophila model of mucopolysaccharidosis VII is attenuated by treatment with resveratrol).</a> Dis Model Mech. 11 (11), (2018).</li><li>Imai, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PINK1-Parkin+signaling+in+Parkinson's+disease:+Lessons+from+Drosophila.">PINK1-Parkin signaling in Parkinson's disease: Lessons from Drosophila.</a> Neurosci Res. 159, 40-46 (2020).</li><li>Julienne, H., Buhl, E., Leslie, D. S., Hodge, J. J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+PINK1+and+parkin+loss-of-function+mutants+display+a+range+of+non-motor+Parkinson's+disease+phenotypes.">Drosophila PINK1 and parkin loss-of-function mutants display a range of non-motor Parkinson's disease phenotypes.</a> Neurobiol Dis. 104, 15-23 (2017).</li><li>Biswas, S., Bagchi, A. <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+the+structural+dynamics+of+the+mutations+in+the+kinase+domain+of+PINK1+protein+associated+with+Parkinson's+disease.">Analysis of the structural dynamics of the mutations in the kinase domain of PINK1 protein associated with Parkinson's disease.</a> Gene. 857, 147183 (2023).</li><li>Koh, H., Chung, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PINK1+and+Parkin+to+control+mitochondria+remodeling.">PINK1 and Parkin to control mitochondria remodeling.</a> Anat Cell Biol. 43 (3), 179-184 (2010).</li><li>Zhu, M., Li, X., Tian, X., Wu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mask+loss-of-function+rescues+mitochondrial+impairment+and+muscle+degeneration+of+Drosophila+pink1+and+parkin+mutants.">Mask loss-of-function rescues mitochondrial impairment and muscle degeneration of Drosophila pink1 and parkin mutants.</a> Hum Mol Genet. 24 (11), 3272-3285 (2015).</li><li>Park, 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=Mitochondrial+dysfunction+in+Drosophila+PINK1+mutants+is+complemented+by+parkin.">Mitochondrial dysfunction in Drosophila PINK1 mutants is complemented by parkin.</a> Nature. 441 (7097), 1157-1161 (2006).</li><li>Dytham, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Choosing and using statistics: a biologist's guide. , (2011).</li><li>Bonora, 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=ATP+synthesis+and+storage.">ATP synthesis and storage.</a> Purinergic Signal. 8 (3), 343-357 (2012).</li><li>Gon&#231;alves, D. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caffeine+improves+mitochondrial+function+in+PINK1B9-null+mutant+Drosophila+melanogaster.">Caffeine improves mitochondrial function in PINK1B9-null mutant Drosophila melanogaster.</a> J Bioenerg Biomembr. 55 (1), 1-13 (2023).</li><li>Gon&#231;alves, D. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+function+and+cellular+energy+maintenance+during+aging+in+a+Drosophila+melanogaster+model+of+Parkinson+disease.">Mitochondrial function and cellular energy maintenance during aging in a Drosophila melanogaster model of Parkinson disease.</a> Mitochondrion. 65, 166-175 (2022).</li><li>Janowska, J. 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=Mitochondrial+respiratory+chain+complex+I+dysfunction+induced+by+N-methyl+carbamate+ex+vivo+can+be+alleviated+with+a+cell-permeable+succinate+prodrug.">Mitochondrial respiratory chain complex I dysfunction induced by N-methyl carbamate ex vivo can be alleviated with a cell-permeable succinate prodrug.</a> Toxicol In Vitro. 65, 104794 (2020).</li><li>Ngo, D. T. 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=Oxidative+modifications+of+mitochondrial+complex+II+are+associated+with+insulin+resistance+of+visceral+fat+in+obesity.">Oxidative modifications of mitochondrial complex II are associated with insulin resistance of visceral fat in obesity.</a> Physiol Endocrinol Metab. 316 (2), E168-E177 (2019).</li><li>Stroud, D. 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=Accessory+subunits+are+integral+for+assembly+and+function+of+human+mitochondrial+complex+I.">Accessory subunits are integral for assembly and function of human mitochondrial complex I.</a> Nature. 538 (7623), 123-126 (2016).</li><li>Senyilmaz, 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=Regulation+of+mitochondrial+morphology+and+function+by+stearoylation+of+TFR1.">Regulation of mitochondrial morphology and function by stearoylation of TFR1.</a> Nature. 525 (7567), 124-128 (2015).</li><li>Poddighe, 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=Mucuna+pruriens+(Velvet+bean)+rescues+motor,+olfactory,+mitochondrial+and+synaptic+impairment+in+PINK1B9+Drosophila+melanogaster+genetic+model+of+Parkinson's+disease.">Mucuna pruriens (Velvet bean) rescues motor, olfactory, mitochondrial and synaptic impairment in PINK1B9 Drosophila melanogaster genetic model of Parkinson's disease.</a> PloS One. 9 (10), e110802 (2014).</li><li>Pesta, D., 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=High-resolution+respirometry:+OXPHOS+protocols+for+human+cells+and+permeabilized+fibers+from+small+biopsies+of+human+muscle.">High-resolution respirometry: OXPHOS protocols for human cells and permeabilized fibers from small biopsies of human muscle.</a> Methods Mol Biol (Clifton, N.J). 810, 25-58 (2012).</li><li>Winer, L. S. P., Wu, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+analysis+of+glycolytic+and+oxidative+substrate+flux+of+cancer+cells+in+a+microplate.">Rapid analysis of glycolytic and oxidative substrate flux of cancer cells in a microplate.</a> PloS One. 9 (10), e109916 (2014).</li><li>Plitzko, B., Loesgen, S. <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+oxygen+consumption+rate+(OCR)+and+extracellular+acidification+rate+(ECAR)+in+culture+cells+for+assessment+of+the+energy+metabolism.">Measurement of oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in culture cells for assessment of the energy metabolism.</a> Bio Protoc. 8 (10), e2850 (2018).</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> Am J Physiol. Cell Physiol. 292 (1), C125-C136 (2007).</li><li>Divakaruni, A. S., Jastroch, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+practical+guide+for+the+analysis,+standardization+and+interpretation+of+oxygen+consumption+measurements.">A practical guide for the analysis, standardization and interpretation of oxygen consumption measurements.</a> Nat Metab. 4 (8), 978-994 (2022).</li><li>Bingol, B., Sheng, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+of+mitophagy:+PINK1,+Parkin,+USP30+and+beyond.">Mechanisms of mitophagy: PINK1, Parkin, USP30 and beyond.</a> Free Radic Biol Med. 100, 210-222 (2016).</li></ol>

The authors declare no competing interests.

HRR is a powerful technique for studying mitochondrial respiration and energy metabolism in D. melanogaster and other organisms. It provides a detailed and quantitative assessment of mitochondrial function, allowing researchers to gain insights into the bioenergetics of the cells. The protocol presented here describes the evaluation of mitochondrial respiratory chain function and the activity of specific mitochondrial complexes using the SUIT protocol in D. melanogaster. The SUIT protocol involves syste...

Mitochondria are cellular organelles that control important functions, including apoptotic regulation, calcium homeostasis, and participation in biosynthetic pathways. By possessing autonomous genetic material, they are capable of contributing to cellular maintenance and repair processes. Their structure houses the electron transport chain and oxidative phosphorylation, both crucial for cellular energy1,2,3. In particular, energy control is achieved through adenosine triphosphate (ATP) production via oxidative phosphorylation (OXPHOS)2. Disruption of energy metabolism with impairment of mitochondrial functions occurs both in cell survival and death4,5, frequently associated with a wide range of human pathologies, such as cancer, and neurodegenerative diseases such as Parkinson&#39;s Disease (PD)3,6.
PD is a chronic, progressive, and neurological disorder. The primary cause of this disease is the death of brain cells, especially in the substantia nigra, which are responsible for the production of the neurotransmitter dopamine, which controls movement6,7,8. The earliest observation that linked Parkinsonism to mitochondrial dysfunction was made in 1988, in experimental models using toxins that inhibit the respiratory chain Complex I9.
Currently, there are several methods to evaluate mitochondrial dysfunction10,11,12,13; however, compared to conventional approaches, high-resolution respirometry (HRR) presents superior sensitivity and advantages13,14. For example, HRR protocols allow the evaluation of the whole mitochondrial respiratory chain function or the activity of specific mitochondrial complexes14,15. Mitochondrial dysfunctions can be assessed in intact cells, isolated mitochondria, or even ex vivo10,11,13,14.
Mitochondrial dysfunctions are closely associated with many pathological and physiological processes. It is therefore important to study mitochondrial physiology and bioenergetics using genetically and experimentally tractable model systems. In this regard, research on Drosophila melanogaster, the fruit fly, has several advantages. This model shares fundamental cellular characteristics and processes with humans, including the use of DNA as genetic material, common organelles, and conserved molecular pathways involved in development, immunity, and cell signaling. In addition, fruit flies have a rapid life cycle, easy maintenance, low cost, high throughput, and fewer ethical concerns, thus constituting an invaluable tool for dissecting complex cellular processes16,17,18,19,20.
Furthermore, a homolog of the PTEN-induced putative kinase 1 (pink1) gene is expressed in D. melanogaster. It plays a crucial role in the removal of damaged mitochondria through the process of mitophagy8. In humans, mutations in this gene predispose individuals to an autosomal recessive familial form of PD associated with mitochondrial dysfunction8,21,22,23. Consequently, the fruit fly is a powerful animal model for studies on the pathophysiology of PD and screening of drug candidates focusing on mitochondrial dysfunction and bioenergetics. Therefore, the present work explains how to analyze mitochondrial function in a model of PD from D. melanogaster using the HRR technique in the OROBOROS with the Substrate-Uncoupler-Inhibitor-Titration (SUIT) protocol.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>ADP</td>
			<td>Sigma-Aldrich</td>
			<td>A5285</td>
			<td>Adenosine 5&#8242;-diphosphate sodium sal (CAS number 72696-48-1); &#8805;95%; molecular weight = 501.31 g/mol.</td>
		</tr>
		<tr>
			<td>&#193;gar</td>
			<td>Kasv</td>
			<td>K25-1800</td>
			<td>For bacteriologal use</td>
		</tr>
		<tr>
			<td>Antimycin-A</td>
			<td>Sigma-Aldrich</td>
			<td>A8674</td>
			<td>Antimycin A from Streptomyces sp. (CAS number 1397-94-0); molecular weight&#160; 540 g/mol;</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA)</td>
			<td>Sigma-Aldrich</td>
			<td>A7030</td>
			<td>Bovine Serum Albumin (CAS number 9048-46-8); pH 7,0 &#8805; 98%</td>
		</tr>
		<tr>
			<td>Datlab software</td>
			<td>Oroboros Instruments, Innsbruck, Austria</td>
			<td>20700</td>
			<td>Software for data acquisition and analysis</td>
		</tr>
		<tr>
			<td>Digitonin</td>
			<td>Sigma-Aldrich</td>
			<td>D 5628</td>
			<td>CAS number 11024-24-1</td>
		</tr>
		<tr>
			<td>Distilled water</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Drosophila melanogaster strain w[*] Pink1[B9]/FM7i, P{w[+mC]=ActGFP}JMR3</td>
			<td></td>
			<td></td>
			<td>Obtained from Bloomington Drosophila stock center</td>
		</tr>
		<tr>
			<td>Drosophila melanogaster strain&#160;w1118</td>
			<td></td>
			<td></td>
			<td>Obtained&#160; from the Federal University of Santa Maria</td>
		</tr>
		<tr>
			<td>EGTA</td>
			<td>Sigma-Aldrich</td>
			<td>E8145</td>
			<td>Ethylene glycol-bis(2-aminoethylether)-N,N,N&#39;,N&#39;-tetraacetic acid (CAS number 13638-13-3); &#8805;97%; molecular weight =468.28 g/mol</td>
		</tr>
		<tr>
			<td>FCCP</td>
			<td>Sigma-Aldrich</td>
			<td>C2920</td>
			<td>Carbonyl cyanide 4- (trifluoromethoxy)phenylhydrazone&#160; (CAS number 370-86-5); &#8805;98% (TLC), powder&#160;</td>
		</tr>
		<tr>
			<td>GraphPad Prism version 8.0.1.</td>
			<td></td>
			<td></td>
			<td>Software for data acquisition and analysis</td>
		</tr>
		<tr>
			<td>Hepes</td>
			<td>Sigma-Aldrich</td>
			<td>H4034</td>
			<td>4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (CAS number 7365-45-9); &#8805;99,5% (titration), cell cultured tested; molecular weight = 238.30 g/mol</td>
		</tr>
		<tr>
			<td>High-resolution respirometer Oxygraph O2K</td>
			<td>Oroboros Instruments, Innsbruck, Austria</td>
			<td>10022-02</td>
			<td>Startup O2K respirometer kit</td>
		</tr>
		<tr>
			<td>KH2PO4</td>
			<td>Sigma-Aldrich</td>
			<td>P5379</td>
			<td>Monopotassium phosphate (CAS number 7778-77-0); Reagente Plus, molecular weigt = 136.09 g/mol</td>
		</tr>
		<tr>
			<td>KOH</td>
			<td>Sigma-Aldrich</td>
			<td>211473</td>
			<td>Potassium hydroxide (CAS number 1310-58-3); ACS reagent, &#8805;85%, pellets</td>
		</tr>
		<tr>
			<td>Malate</td>
			<td>Sigma-Aldrich</td>
			<td>M1296</td>
			<td>Malonic acid (CAS number 141-82-2); 99%, molecular weight = 104.06 g/mol). A solution is pH adjusted to approximately 7.0.</td>
		</tr>
		<tr>
			<td>Malic acid</td>
			<td>Sigma-Aldrich</td>
			<td>M1000</td>
			<td>(S)-(&#8722;)-2-Hydroxysuccinic acid (CAS number 97-67-6); &#8805;95% ; molecular weight = 134.09 g/mol</td>
		</tr>
		<tr>
			<td>MES</td>
			<td>Sigma-Aldrich</td>
			<td>M3671</td>
			<td>2-(N-Morpholino)ethanesulfonic acid (CAS number 4432-31-9); &#8805;99% (titration); molecular weight = 195.24 g/mol</td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma-Aldrich</td>
			<td>M8266</td>
			<td>Magnesium chloride (CAS number 7786-30-3); anhydrous, &#8805;98%, molecular weight = 95.21 g/mol</td>
		</tr>
		<tr>
			<td>Microcentrifuge tubes</td>
			<td>Eppendorf</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>O2K-Titration Set</td>
			<td>Oroboros Instruments, Innsbruck, Austria</td>
			<td>20820-03</td>
			<td>Hamilton syringes with different volumes</td>
		</tr>
		<tr>
			<td>Oligomycin</td>
			<td>Sigma-Aldrich</td>
			<td>O 4876</td>
			<td>Oligomycin from&#160;Streptomyces diastatochromogenes (CAS number&#160; 1404-19-9); &#8805;90% total oligomycins basis (HPLC)</td>
		</tr>
		<tr>
			<td>Pistil to homogenization</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Proline</td>
			<td>Sigma-Aldrich</td>
			<td>P0380</td>
			<td>L-Proline (CAS number 147-85-3); powder; 99%; molecular weight = 115.13 g/mol</td>
		</tr>
		<tr>
			<td>Pyruvate</td>
			<td>Sigma-Aldrich</td>
			<td>P2256</td>
			<td>Sodium pyruvate (CAS number 113-24-6), &#8805;99%; molecular weight = 110.04 g/mol</td>
		</tr>
		<tr>
			<td>Rotenone</td>
			<td>Sigma-Aldrich</td>
			<td>R8875</td>
			<td>Rotetone (CAS number 83-79-4); &#8805;95%, molecular weight 394.42 g/ mol</td>
		</tr>
		<tr>
			<td>Succinate</td>
			<td>Sigma-Aldrich</td>
			<td>S 2378</td>
			<td>Sodium succinate dibasic hexahydrate (CAS number 6106-21-4); &#8805;99%</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Merck</td>
			<td>107,651,000</td>
			<td>Sucrose for microbiology use (CAS number 57-50-1)</td>
		</tr>
		<tr>
			<td>Taurine</td>
			<td>Sigma-Aldrich</td>
			<td>T0625</td>
			<td>CAS number 107-35-7</td>
		</tr>
	</tbody>
</table>

analyzing mitochondrial function in a drosophila melanogaster pink1b9-null mutant using high-resolution respirometry

Neurodegenerative diseases, including Parkinson&#39;s Disease (PD), and cellular disturbances such as cancer are some of the disorders that disrupt energy metabolism with impairment of mitochondrial functions. Mitochondria are organelles that control both energy metabolism and cellular processes involved in cell survival and death. For this reason, approaches to evaluate mitochondrial function can offer important insights into cellular conditions in pathological and physiological processes. In this regard, high-resolution respirometry (HRR) protocols allow evaluation of the whole mitochondrial respiratory chain function or the activity of specific mitochondrial complexes. Furthermore, studying mitochondrial physiology and bioenergetics requires genetically and experimentally tractable models such as Drosophila melanogaster.
This model presents several advantages, such as its similarity to human physiology, its rapid life cycle, easy maintenance, cost-effectiveness, high throughput capabilities, and a minimized number of ethical concerns. These attributes collectively establish it as an invaluable tool for dissecting complex cellular processes. The present work explains how to analyze mitochondrial function using the Drosophila melanogaster PINK1B9-null mutant. The pink1 gene is responsible for encoding PTEN-induced putative kinase 1, through a process recognized as mitophagy, which is crucial for the removal of dysfunctional mitochondria from the mitochondrial network. Mutations in this gene have been associated with an autosomal recessive early-onset familial form of PD. This model can be used to study mitochondrial dysfunction involved in the pathophysiology of PD.

Author Spotlight: Exploring Mitochondrial Function and Chemical Toxicity Using Drosophila melanogaster 

Analyzing Mitochondrial Function in a Drosophila melanogaster PINK1B9-Null Mutant Using High-resolution Respirometry

Our research uses Drosophila melanogaster as an experimental model to understand mitochondrial function in disease and chemical toxicity. Some questions we want to answer are, how does PINK-1 mutation affect mitochondrial function and how is this linked to Parkinson's Disease? How can we revert, or avert, the mitochondrial dysfunction associated with this mutation?High-resolution respirometry requires specialized training for precise operation and data analysis. In addition, the system we used doesn't allow working with several samples simultaneously and is not educated for high-throughput analysis. Since it's only possible to run two samples at the same time, the experimental design must be well delineated.Our findings indicate progressive impairment of the mitochondrial function we face in PINK1-Null mutants, which is characterized by decrease in OXPHOS CI link, and ETS CI&CII link, and a metabolic metabolic shift in ATP production from oxidative to glycolytic in pathways. These findings are closely related to Parkinson's Disease pathophysiology. One of the key points of high-resolution respirometry is its ability to provide direct and accurate measurements of oxygen consumption, allowing for detailed analysis of mitochondrial function and cellular metabolism.Also, it's versatile. It can be used for wide range of sample types, including isolated mitochondria. Considering that mitochondrial dysfunction is a common feature of neurodegenerative diseases, such as Parkinson's disease, in the future, we will focus on investigating how mitochondrial function and energy elevation could be important targets for therapies directed to neurodegenerative diseases.

Here, we that O2 flux in OXPHOS CI (P = 0.0341) and OXPHOS CI&#38;II (P = 0.0392) states is reduced in PINK1B9&#160;null flies when compared to control flies (Figure 4). This result was also observed in previous findings from our group29,30.
CI and CII are key components of the electron transport system (ETS), in which CI is responsible for the transfer of el...

Watch this Scientific Journal Video about Exploring Mitochondrial Function and Chemical Toxicity Using Drosophila melanogaster at JoVE.com

Here we present a high-resolution respirometry protocol to analyze bioenergetics in PINK1B9-null mutant fruit flies. The method uses the Substrate-Uncoupler-Inhibitor-Titration (SUIT) protocol.

Neurodegenerative diseases, including Parkinson&#39;s Disease (PD), and cellular disturbances such as cancer are some of the disorders that disrupt energy ...

analyzing-mitochondrial-function-drosophila-melanogaster-pink1b9-null

Research

JoVE Journal

Biochemistry

Calibrating Polarographic Oxygen Sensors for High-Resolution Respirometry Analysis in Drosophila melanogaster

Calibrating Polarographic Oxygen Sensors for High-Resolution Respirometry Analysis in Drosophila melanogaster  

To begin, add two milliliters of MIRO five buffer to the Oroboros chamber. Cover the chamber with a stopper without introducing air bubbles. Then carefully pull the stopper to form a single air bubble.Open the Oroboros DatLab software in the block temperature field. Enter a temperature of 25 degrees Celsius and click on Connect to Oxygraph-2k. Click and select the folder where the calibration is to be saved.And click on save. When a new window opens, name the experiment and the samples. Then click on save.Next, go to the layout menu and choose the first option one, calibration experiment. Graph three, temp. When the red line shows a standard straight line with points around zero picomole, select two points, one for chamber A and the other for chamber B.Select oxygen concentration on the right of the screen.Select the marked point and copy the temperature and barometric pressure values relative to the point. Paste these values in the boxes below, and click on calibrate and copy to clipboard. Then go to the file menu and select save and disconnect.

Substrate-Uncoupler-Inhibitor-Titration for Mitochondrial Respiration Analysis in Drosophila melanogaster

Substrate-Uncoupler-Inhibitor-Titration for Mitochondrial Respiration Analysis in Drosophila melanogaster  

After calibrating polarographic oxygen sensors, remove the stoppers and open the chambers. Wash the stoppers and chambers with 100%ethanol, 70%ethanol, and distilled water. Transfer the flies into a microcentrifuge tube.Add 200 microliters of chilled MiR05 buffer into the tube and homogenize the flies by applying gentle pressure with four to six strokes of the pestle. Using a micropipette, transfer the homogenized fly suspension into the chamber. Cover the chamber with a stopper without introducing air bubbles.Next, click on the layout menu and select Option 5, Flow by Corrected Volume. Another new window will open. Here, in the space, experimental code, name the experiment.In the sample field, name each sample in its respective chamber A and B.Then set the unit field to Unit and in the concentration field, define the chamber volume as one per milliliter. To start the high-resolution respirometry, ensure that the oxygen flux signal is steady on the positive value. Add digitonin to permeabilize the mitochondrial membrane.Then add pyruvate, malate, and proline substrates until the oxygen flux increases and stabilizes. Press the F4 key on the keyboard and enter the name of the reagent to mark the event. Add ADP to couple the mitochondrial respiratory chain, and wait for the increase and stabilization of the oxygen flux.Then add succinate and measure the oxygen flux. TO inhibit ATP synthase, add oligomycin and examine for a decrease in oxygen flux. After the red line stabilizes, uncouple the mitochondrial electron transfer using 0.25-micromolar FCCP until maximum oxygen consumption is reached, demonstrated by the rise of the red line.Next, add rotenone complex I inhibitor and wait for the decrease and stabilization of the oxygen flux. Then add malonate complex II inhibitor and measure the oxygen flux. Finally, add antimycin complex III inhibitor and wait for the decrease, followed by the increase and stabilization of the oxygen flux.Click on the GraphPad Prism software to extract the oxygen flux values from the graphs. OXPHOS CI refers to the value of oxygen flux after adding ADP. Then use the given formula to calculate OXHPOS CII.Using the following equation, calculate the ETS CI and CII oxygen values for the uncouples and inhibitors. Then calculate the ATP synthesis as the difference between the OXPHOS and LEAK. Finally, calculate the OXPHOS by LEAK ratio to determine the respiratory control ratio.The oxygen flux in both OXHPOS CI and OXPHOS CI and CII states was significantly reduced in PINK1 B9 null flies. compared to control flies. Additionally, the oxygen flux in ETS CI, ETS CII, and ETS CI and CII state were lower in PINK1 B9 null flies, indicating an impaired electron transfer system compared to the control flies.The disruption in the flux of electrons affects the OXPHOS process, leading to reduced ATP synthesis in the PINK1 B9 null flies. The reduction in the respiratory control ratio of null flies suggests mitochondrial uncoupling, indicating that the mitochondria were less efficient at utilizing oxygen and producing ATP.

614 Views.  Federal University of Santa Maria.  Here we present a high-resolution respirometry protocol to analyze bioenergetics in PINK1B9-null mutant fruit flies. The method uses the Substrate-Uncoupler-Inhibitor-Titration (SUIT) protocol.

Analyzing Mitochondrial Physiology and Bioenergetics in Fruit Flies

Summary