Name: high-resolution respirometry to assess bioenergetics in cells and tissues using chamber- and plate-based respirometers
Uploaded: 2021-10-26T13:00:00.000+00:00
Duration: 9 min 53 s
Description: Watch this Scientific Journal Video about High-Resolution Respirometry to Assess Bioenergetics in Cells and Tissues Using Chamber- and Plate-Based Respirometers at JoVE.com

This work was supported by funding from the Academy of Finland (C.B.J), the Magnus Ehrnroot Foundation (C.B.J), and a Doctoral fellowship of the Integrated Life Sciences Graduate School (R.A.).

No conflict of interest to disclose.

Traditionally, mitochondrial bioenergetics&#160;has been studied with Clark-type oxygen electrodes. A lack of resolution and throughput, however, warranted for technological advancement. To date, the O2k (referred to as cHRR) and Seahorse XF96 Flux Analyzer (referred to as mHRR) have been widely adopted in the field of cellular bioenergetics. Here, we present a comprehensible collection of protocols for the analysis of cellular energy metabolism via assessment of mitochondrial respiration using either cHRR or mHRR, discu...

Mitochondria fulfill the key provision of energy and are a compartmentalized organelle contributing to essential cellular bioenergetic and metabolic processes such as anabolism of nucleotides, lipids and amino acids, iron-sulfur cluster biogenesis and are implicated in signaling such as controlled cell death1,2,3. Mitochondrial bioenergetics through oxidative phosphorylation contributes to almost all cellular processes within the cell, and consequently, mitochondrial dysfunctions of primary or secondary origin are associated with a wide spectrum of disease conditions4,5. Mitochondrial dysfunction not only involves alterations in structure or mitochondrial density but also in the quality and regulation of the respiratory system6. This qualitative element encompasses substrate control, coupling characteristics, post-translational modifications, cristae dynamics, and respiratory supercomplexes7,8. Therefore, accurate analysis of mitochondrial bioenergetics for experimental and diagnostic approaches to assess the energy metabolism of the cell is important in health and disease.
Mitochondrial oxidative phosphorylation (OXPHOS) is a sequence of reactions within the respiratory system or electron transfer system (ETS) for the generation of cellular energy through adenosine triphosphate (ATP)9. The multi-enzymatic step to harness energy from electron flow through complexes I and II to complex IV generates an electrochemical proton gradient across the inner mitochondrial membrane, subsequently utilized for phosphorylation of adenosine diphosphate (ADP) to ATP via complex V (F1FO ATP synthase) (Figure 1A).
First, two-electron carriers are generated during the tricarboxylic cycle (TCA), glycolysis, and pyruvate oxidation: nicotinamide adenine dinucleotide (NADH) and dihydroflavine adenine dinucleotide (FADH2). NADH is oxidized at complex I (NADH dehydrogenase), during which two electrons are transferred to coenzyme Q (quinone is reduced to quinol), while protons are pumped into the intermembrane space (IMS). Second, complex II (Succinate dehydrogenase) oxidizes FADH2 and feeds the electrons to coenzyme Q without pumping protons. Third, at complex III (Cytochrome c oxidoreductase), electrons from coenzyme Q are transferred to cytochrome c while protons are pumped into the IMS. Fourth, cytochrome c transfers the electrons to complex IV (Cytochrome c oxidase), the final complex to pump protons, and where oxygen functions as an electron acceptor to assimilate protons, ultimately forming water. It is this oxygen that mitochondria consume which can be measured by an oxygraph. Finally, the protons generated from complex I, complex III, and complex IV are used to rotate complex V, thereby generating ATP9.
Importantly, electron transfer occurs not only in a linear fashion, otherwise denoted as the electron transport chain. Instead, electrons can be transferred to the coenzyme Q pool through multiple respiratory pathways and facilitate convergent electron flow. NADH-substrates and succinate, for example, can enter via complex I and complex II, respectively. Electrons from fatty acid oxidation can be donated via the electron transferring flavoprotein complex. Indeed, a comprehensive analysis of OXPHOS requires a holistic approach with appropriate fuel substrates (Figure 1A).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/63000/63000fig1v2.jpg" /> 
Figure 1: Mitochondrial oxidative phosphorylation and specific substrate and inhibitor protocols. (A) Mitochondrion and scheme of the electron transfer system (CI-CIV) and mitochondrial F1F0 ATP synthase (CV). All structures are from PDB. The figures only depict substrates and inhibitors described in this study). (B) Sample trace of oxygen flux in intact HEK293 cells using standard protocol in a mHRR device. (C) Sample trace of oxygen flux in intact HEK293 cells using standard protocol in a cHRR device. (D) Sample trace of oxygen flux in permeabilized human fibroblasts from a healthy donor with respective SUIT protocol. Abbreviations: 1 = Routine respiration of intact cells; 2 = State 2; 3 = State 3(I); 4 = State 3(I) with cytC; 5 = State 3 (I+II); 6 = Leak(OM); 7 = ETS capacity; 8 = S(ROT); 9 = ROX; 10 = TMPD; 11 = Az. ROT = Rotenone, AM = Antimycin, ATP = Adenosine triphosphate, Az = Azide, OM = Oligomycin, FCCP = Carbonyl cyanide p-trifluoro-methoxyphenyl-hydrazone; Asc = Ascorbate, TMPD = N,N,N&#8242;,N&#8242;-tetramethyl-p-phenylenediamine, Succ = Succinate, M = Malate, P = Pyruvate, ADP = Adenosine diphosphate, NAD = Nicotinamide adenine dinucleotide, IMS = Intermembrane space, FAD = Flavin adenine dinucleotide. <a href="https://www.jove.com/files/ftp_upload/63000/63000fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Analysis of mitochondrial OXPHOS capacity using HRR has become an instrumental biochemical method of diagnostic value not only for primary mitochondrial defects10,11 but extending to all other realms of biology such as cancer and ageing12. HRR allows the determination of cellular respiration by the analysis of mitochondrial OXPHOS capacity, which directly reflects individual or combined mitochondrial respiratory complex deficiency, and indirectly is associated with cellular dysfunction and altered energy metabolism9. Methodologically, respiration measurements are performed using cells, tissue, or isolated mitochondria11,13,14, with frozen material only partially suitable15,16. Frozen tissue is shown to have an intact ETS with maintained supercomplex stability15. Thus, as opposed to traditional TCA intermediates, respective substrates are directly fed into the ETS. However, coupling between the ETS and ATP synthesis is lost as the membrane integrity is compromised through freeze damage (ice crystal formation).
Respiration experiments normally take place at a physiological temperature of 37 &#176;C for endotherms in either non-permeabilized or permeabilized cells or tissue. While the former considers the cytosolic metabolic context, the latter provides the energetic contribution of individual OXPHOS complexes and the ATPase through the addition of specific substrates (and inhibitors). The sequence and variation of substrates and inhibitors have led to the development of a diverse array of SUIT protocols17 and assays18 to address various scientific questions of OXPHOS function (reviewed under12). The basic protocol of cellular respiration assesses four different states: i) routine respiration&#160;- the respiration in a respective respiration media without any addition of substrates or inhibitors consuming but endogenous substrates. This state can reveal general OXPHOS or secondary-induced respiration defects caused, for example, by altered metabolite profiles. Next, the addition of the ATPase inhibitor oligomycin reveals the permeability of the inner mitochondrial membrane to protons, defined as ii) leak respiration.&#160;Subsequent titration of a protonophore such as the uncoupler carbonyl cyanide p-trifluoro-methoxyphenyl-hydrazone (FCCP) allows to determine the state at which ETS capacity is maximal in an open-transmembrane proton circuit mode, defined as iii) uncoupled respiration. Importantly, an uncoupled state can also occur by experimental interventions through excessive mechanical damage to the mitochondrial membranes. Conversely, the non-coupled state refers to respiratory uncoupling by an intrinsic mechanism that is physiologically controlled. Finally, complete inhibition of the ETS by addition of the complex III inhibitor antimycin and complex I inhibitor rotenone determines residual oxygen consumption (ROX) from non-mitochondrial oxygen-consuming processes (Figure 1A-C).
Mitochondrial bioenergetics consists of five distinct respiration states19,20. State 1 respiration is without any additional substrates or ADP, except for what is endogenously available. After the addition of ADP, but still, no substrates, state 2 respiration is achieved. When substrates are added, allowing electron transfer and ATP synthesis, state 3 respiration is reached. In this state, OXPHOS capacity can be defined at saturating concentrations of ADP, inorganic phosphate, oxygen, NADH- and succinate-linked substrates. State 4 respiration or LEAK respiration can be defined as a state without ADP or chemically inhibited ATP synthases while having sufficient substrates. Lastly, when all oxygen is depleted (anoxic) in a closed-chamber setting, state 5 respiration is observed.
Several methods exist to assess cellular energy states14 with two devices dominating the current real-time assessment of OXPHOS through analysis of oxygen consumption, measured as the function of the decrease in oxygen over time in a closed-chamber system with different applicability dependent on the experimental model and research question: the Oroboros 2k high-resolution respirometer and the Seahorse XF extracellular flux analyzer. Both devices record the oxygen consumption rates as a decrease in picomoles (pmol) of oxygen (O2) per second as an absolute value within the chamber or microplate well. The specific oxygen consumption per mass is obtained by normalizing the respective oxygen consumption in a specific buffer recipe per number of cells (millions), tissue weight (mg), or protein amount.
The O2k (Oroboros Instruments) is a closed two-chamber system equipped with a polarographic oxygen sensor (abbreviated as chamber-based high-resolution respirometer: cHRR). Each experimental chamber holds 2 mL of liquid which is kept homogenous by magnetic stirrers. The polarographic oxygen sensor utilizes an amperometric approach to measure the oxygen: it contains a gold cathode, a silver/silver chloride anode, and in between a KCI solution creating an electrochemical cell upon which a voltage (0.8 V) is applied. Oxygen from the assay medium diffuses through a 25 &#181;m fluorinated ethylene propylene membrane (O2-permeable) and undergoes reduction at the cathode, producing hydrogen peroxide. At the anode, silver is oxidized by hydrogen peroxide, generating an electric current. This electric current (ampere) is linearly related to the partial oxygen pressure. The partial pressure of oxygen and the oxygen solubility factor of the assay medium are used to compute the oxygen concentration. Since oxygen partial pressure is dependent on experimental temperature and polarographic measurements are temperature-sensitive, fluctuations in temperature need precise (&#177;0.002 &#176;C) regulation by a Peltier heating block. Temperature can be controlled within a range of 4 &#176;C and 47 &#176;C.
The Seahorse XF extracellular flux analyzer (Agilent) is a plate-based system with 24- or 96-well microplate format in which three fluorescence electrodes measure oxygen consumption over time in each well (abbreviated as microplate-based high-resolution respirometer: mHRR). A maximum of four ports in the assay cartridge are available for automated injection during the assay. An assay contains multiple cycles, each with three phases: 1) mixing, 2) waiting, and 3) measurement. During the measurement phase, sensor probes are lowered into the microplate creating a temporarily closed chamber containing 7-10 &#181;L volume to measure emitted light. This light is emitted by polymer-embedded fluorophores on the tip of the sensor probes, which sense O2 based on phosphorescence quenching. The intensity of the fluorescence signal is proportional to O2 and influenced by the temperature of the sensor and assay medium. Therefore, accurate oxygen estimation requires a relative approach with a background well without any sample. Restoring oxygen concentration occurs during the mixing phase when the sensor moves up and down to mix the volume above the temporary chamber. Each cycle computes one oxygen consumption rate. Temperature can be controlled within a range of 16 &#176;C and 42 &#176;C.
HRR is the gold standard to assess cellular bioenergetics in primary and mitochondria-associated diseases and general cellular metabolism. In this study, basic protocols for HRR are provided to assess OXPHOS function in cells and tissues.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/63000/63000fig2v2.jpg" /> 
Figure 2: Workflow for cell and tissue preparations for cHRR, and cell preparation for mHRR respirometry. (A) Outline of provided protocols. (B) Mammalian cells (step 1.2): HEK293 pellet equaling 3 x 106 cells (left panel). Non-fibrous tissue (step 1.3): Preparation of murine cerebellum lysate in 2 mL Teflon potter (middle panel). Saponin-induced skeletal muscle permeabilization (step 1.4) right panel) for cHRR respirometry. (C) Standard microplate seeding layout (step 2.4) and confluency check for the analysis of eukaryotic cells (HEK293) for mHRR respirometry. (D, E) Scheme of injection port loading for mHRR respirometry (step 2.4). <a href="https://www.jove.com/files/ftp_upload/63000/63000fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table><tbody><tr><td>2 mL Potter-Elvehjem Glass/PTFE Tissue Grinder/Homogenizer</td><td>Omni International</td><td>07-358029</td><td></td></tr><tr><td>95% O&lt;sub&gt;2&lt;/sub&gt;, 5% CO&lt;sub&gt;2&lt;/sub&gt; medical gas mixture</td><td></td><td></td><td>Potter for tissue grinding</td></tr><tr><td>ADP</td><td>Sigma</td><td>A 4386</td><td></td></tr><tr><td>Antimycin A</td><td>Sigma</td><td>A 8674</td><td>Chemical</td></tr><tr><td>Ascorbate</td><td>Merck</td><td>PHR1279-1G</td><td>Chemical, dissolve in ethanol</td></tr><tr><td>BSA (fatty accid free)</td><td>Sigma</td><td>A 6003</td><td>Chemical</td></tr><tr><td>CaCO&lt;sub&gt;3&lt;/sub&gt;</td><td>Sigma</td><td>C 4830</td><td>Chemical</td></tr><tr><td>Cytochrome c</td><td>Sigma</td><td>C 7752</td><td>Chemical</td></tr><tr><td>Digitonin</td><td>Sigma</td><td>D 5628</td><td>Chemical</td></tr><tr><td>Dithiothreitol</td><td>Sigma</td><td>D 0632</td><td>Chemical, dissolve in DMSO</td></tr><tr><td>D-Sucrose</td><td>Roth</td><td>4621.1</td><td>Chemical</td></tr><tr><td>Dulbecco&amp;rsquo;s modified Eagle&amp;rsquo;s medium (High glucose)</td><td>Fisher Scientific</td><td>41965-039</td><td>Chemical</td></tr><tr><td>Dulbecco&amp;rsquo;s modified Eagle&amp;rsquo;s medium&amp;nbsp;(No Glucose)</td><td>Fisher Scientific</td><td>A14430-01</td><td></td></tr><tr><td>EGTA</td><td>Sigma</td><td>E 4378</td><td></td></tr><tr><td>Etomoxir</td><td>Sigma</td><td>E1905</td><td>Chemical</td></tr><tr><td>Falcon 15 ml Conical Centrifuge Tubes</td><td>Fisher Scientific</td><td>AM12500</td><td>Chemical</td></tr><tr><td>Falcon 50 ml Conical Centrifuge Tubes</td><td>Fisher Scientific</td><td>AM12501</td><td></td></tr><tr><td>FCCP</td><td>Sigma</td><td>C 2920</td><td></td></tr><tr><td>Glucose</td><td>Sigma</td><td>G7021</td><td>Chemical, dissolve in ethanol</td></tr><tr><td>Glutamate</td><td>Sigma</td><td>G 1626</td><td>Chemical</td></tr><tr><td>GlutaMax&amp;nbsp;(100x)&amp;nbsp;(200 nM&amp;nbsp;L-alanyl-L-glutamine dipeptide)</td><td>Fisher Scientific</td><td>35050061</td><td>Chemical</td></tr><tr><td>HEK293 cells</td><td>ATTC</td><td>CRL-1573</td><td></td></tr><tr><td>Hemocytometer</td><td>Fisher Scientific</td><td>0267151B</td><td>Instrument for cell counting</td></tr><tr><td>Hepes</td><td>Sigma</td><td>H 7523</td><td>Chemical</td></tr><tr><td>Imidazole</td><td>Fluka</td><td>56750</td><td>Chemical</td></tr><tr><td>KCl</td><td>Merck</td><td>1.04936</td><td>Chemical</td></tr><tr><td>L-carnitine</td><td>Sigma</td><td>C0283</td><td>Chemical</td></tr><tr><td>Malate</td><td>Sigma</td><td>M 1000</td><td>Chemical</td></tr><tr><td>MES hydrate</td><td>Sigma</td><td>M8250</td><td>Chemical</td></tr><tr><td>MgCl&lt;sub&gt;2&lt;/sub&gt;</td><td>Sigma</td><td>M 9272</td><td>Chemical</td></tr><tr><td>Na&lt;sub&gt;2&lt;/sub&gt;ATP</td><td>Sigma</td><td>A 2383</td><td>Chemical</td></tr><tr><td>Na&lt;sub&gt;2&lt;/sub&gt;Phosphocreatine</td><td>Sigma</td><td>P 7936</td><td>Chemical</td></tr><tr><td>Na-pyruvate&amp;nbsp;(100 mM)&amp;nbsp;(100x)</td><td>Fisher Scientific</td><td>11360070</td><td></td></tr><tr><td>NEAA&amp;nbsp;(Non-essential amino acids) 100x</td><td>Fisher Scientific</td><td>11140035</td><td></td></tr><tr><td>Normal FBS&amp;nbsp;(10x)</td><td>Fisher Scientific</td><td>10500064</td><td></td></tr><tr><td>O&lt;sub&gt;2&lt;/sub&gt;k-Core: Oxygraph-2k</td><td>Oroboros Instruments</td><td>10000-02</td><td>High-resolution respirometry instrument</td></tr><tr><td>O&lt;sub&gt;2&lt;/sub&gt;k-Titration Set</td><td>Oroboros Instruments</td><td>20820-03</td><td>Hamilton syringes for chemical injections</td></tr><tr><td>Oligomycin</td><td>Sigma</td><td>O 4876</td><td>Chemical, dissolve in ethanol</td></tr><tr><td>Palmitoylcarnitine</td><td>Sigma</td><td>P 4509</td><td>Chemical</td></tr><tr><td>Penicillin-Streptomycin</td><td>Fisher Scientific</td><td>15140122</td><td></td></tr><tr><td>Pierce BCA Protein Assay Kit</td><td>Fisher Scientific</td><td>23227</td><td></td></tr><tr><td>Pyruvate</td><td>Sigma</td><td>P 2256</td><td>Chemical</td></tr><tr><td>RIPA-Buffer</td><td>Fisher Scientific</td><td>89900</td><td>Chemical</td></tr><tr><td>Rotenone</td><td>Sigma</td><td>R 8875</td><td>Chemical, dissolve in ethanol</td></tr><tr><td>Saponin</td><td>Sigma</td><td>S7900</td><td>Chemical</td></tr><tr><td>&lt;br/&gt; Seahorse XF DMEM assay medium pack, pH 7.4</td><td>&lt;br/&gt; Agilent, Santa Clara, CA</td><td>103680-100</td><td></td></tr><tr><td>Seahorse XFe96 Extracellular Flux Analyzer</td><td>&lt;br/&gt; Agilent, Santa Clara, CA</td><td></td><td>High-throughput respirometry instrument</td></tr><tr><td>Seahorse XFe96 FluxPak</td><td>&lt;br/&gt; Agilent, Santa Clara, CA</td><td></td><td>&lt;br/&gt; Includes assay plates, cartridges, loading guides for transferring compounds to the assay cartridge, and calibrant solution.</td></tr><tr><td>Small scissors</td><td>Fisher Scientific</td><td>08-951-20</td><td></td></tr><tr><td>Sodium azide</td><td>Sigma</td><td>S2002</td><td>Chemical</td></tr><tr><td>Succinate</td><td>Sigma</td><td>S 2378</td><td>Chemical</td></tr><tr><td>Taurine</td><td>Sigma</td><td>T 8691</td><td>Chemical</td></tr><tr><td>TMPD</td><td>Sigma</td><td>T 3134</td><td>Chemical</td></tr><tr><td>Trypan Blue solution</td><td>Merck</td><td>72-57-1</td><td>Chemical</td></tr><tr><td>Trypsin 0.25% EDTA</td><td>Fisher Scientific</td><td>25200056</td><td></td></tr><tr><td>Two thin-edged forceps</td><td>Fisher Scientific</td><td>12-000-122</td><td></td></tr><tr><td>Uridine stock (500x)</td><td>Sigma</td><td>U3750</td><td>Chemical</td></tr></tbody></table>

high-resolution respirometry to assess bioenergetics in cells and tissues using chamber- and plate-based respirometers

High-resolution respirometry (HRR) allows monitoring oxidative phosphorylation in real-time for analysis of individual cellular energy states and assessment of respiratory complexes using diversified substrate-uncoupler-inhibitor titration (SUIT) protocols. Here, the usage of two high-resolution respirometry devices is demonstrated, and a basic collection of protocols applicable for the analysis of cultured cells, skeletal and heart muscle fibers, and soft tissues such as the brain and liver are presented. Protocols for cultured cells and tissues are provided for a chamber-based respirometer and cultured cells for a microplate-based respirometer, both encompassing standard respiration protocols. For comparative purposes, CRISPR-engineered HEK293 cells deficient in mitochondrial translation causing multiple respiratory system deficiency are used with both devices to demonstrate cellular defects in respiration. Both respirometers allow for comprehensive measurement of cellular respiration with their respective technical merits and suitability dependent on the research question and model under study.

Here, we provide protocols to determine the mitochondrial bioenergetics in eukaryotic cells, non-fibrous tissue (e.g., cerebellum), and fibrous tissue (e.g., skeletal muscle). For eukaryotic cells, HEK293 with CRISPR-engineered knockout of two different proteins associated with mitochondrial translation resulting in multiple (CRISPRKO1) and severe/complete OXPHOS deficiency (CRISPRKO2) were measured with either cHRR (Figure 3A-C) or mHR...

Watch this Scientific Journal Video about High-Resolution Respirometry to Assess Bioenergetics in Cells and Tissues Using Chamber- and Plate-Based Respirometers at JoVE.com

High-Resolution Respirometry to Assess Bioenergetics in Cells and Tissues Using Chamber- and Plate-Based Respirometers

Assessing oxidative phosphorylation using high-resolution respirometers has become an integral part of the functional analysis of mitochondria and cellular energy metabolism. Here, we present protocols for the analysis of cellular energy metabolism using chamber and microplate-based high-resolution respirometers and discuss the key benefits of each device.

High-resolution respirometry (HRR) allows monitoring oxidative phosphorylation in real-time for analysis of individual cellular energy states and ...

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Research

JoVE Journal

Biology

4.5K Views.  University of Helsinki. Assessing oxidative phosphorylation using high-resolution respirometers has become an integral part of the functional analysis of mitochondria and cellular energy metabolism. Here, we present protocols for the analysis of cellular energy metabolism using chamber and microplate-based high-resolution respirometers and discuss the key benefits of each device.

Video: High-Resolution Respirometry to Assess Bioenergetics in Cells and Tissues Using Chamber- and Plate-Based Respirometers

Analyzing Mitochondrial Physiology and Bioenergetics in Fruit Flies

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 

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 ...

Biochemistry

Calorespirometry: A Powerful, Noninvasive Approach to Investigate Cellular Energy Metabolism

Many cell lines used in basic biological and biomedical research maintain energy homeostasis through a combination of both aerobic and anaerobic respiration. However, the extent to which both pathways contribute to the landscape of cellular energy production is consistently overlooked. Transformed cells cultured in saturating levels of glucose often show a decreased dependency on oxidative phosphorylation for ATP production, which is compensated by an increase in substrate-level phosphorylation. This shift in metabolic poise allows cells to proliferate despite the presence of mitochondrial toxins. In neglecting the altered metabolic poise of transformed cells, results from a pharmaceutical screening may be misinterpreted since the potentially mitotoxic effects may not be detected using model cell lines cultured in the presence of high glucose concentrations. This protocol describes the pairing of two powerful techniques, respirometry and calorimetry, which allows for the quantitative and noninvasive assessment of both aerobic and anaerobic contributions to cellular ATP production. Both aerobic and anaerobic respirations generate heat, which can be monitored via calorimetry. Meanwhile, measuring the rate of oxygen consumption can assess the extent of aerobic respiration. When both heat dissipation and oxygen consumption are measured simultaneously, the calorespirometric ratio can be determined. The experimentally obtained value can then be compared to the theoretical oxycaloric equivalent and the extent of the anaerobic respiration can be judged. Thus, calorespirometry provides a unique method to analyze a wide range of biological questions, including drug development, microbial growth, and fundamental bioenergetics under both normoxic and hypoxic conditions.

This protocol describes calorespirometry, the direct and simultaneous measurement of both heat dissipation and respiration, which provides a noninvasive approach to assess energy metabolism. This technique is used to assess the contribution of both aerobic and anaerobic pathways to energy utilization by monitoring the total cellular energy flow.

Many cell lines used in basic biological and biomedical research maintain energy homeostasis through a combination of both aerobic and anaerobic ...

Bioengineering

Solid Plate-based Dietary Restriction in Caenorhabditis elegans

Reduction of food intake without malnutrition or starvation is known to increase lifespan and delay the onset of various age-related diseases in a wide range of species, including mammals. It also causes a decrease in body weight and fertility, as well as lower levels of plasma glucose, insulin, and IGF-1 in these animals. This treatment is often referred to as dietary restriction (DR) or caloric restriction (CR). The nematode Caenorhabditis elegans has emerged as an important model organism for studying the biology of aging. Both environmental and genetic manipulations have been used to model DR and have shown to extend lifespan in C. elegans. However, many of the reported DR studies in C. elegans were done by propagating animals in liquid media, while most of the genetic studies in the aging field were done on the standard solid agar in petri plates. Here we present a DR protocol using standard solid NGM agar-based plate with killed bacteria.

Solid Plate-based Dietary Restriction in Caenorhabditis elegans

Here we present a protocol for performing solid plate-based dietary restriction in C. elegans with killed bacteria.

Reduction of food intake without malnutrition or starvation is known to increase lifespan and delay the onset of various age-related diseases in a wide ...

PBMC Collection and Cryostorage for Mitochondrial Bioenergetics Analysis

Cryopreservation and Bioenergetic Evaluation of Human Peripheral Blood Mononuclear Cells

The physiological functions of eukaryotic cells rely on energy mainly provided by mitochondria. Mitochondrial dysfunction is linked to metabolic diseases and aging. Oxidative phosphorylation plays a decisive role, as it is crucial for the maintenance of energetic homeostasis. PBMCs have been identified as a minimally invasive sample to measure mitochondrial function and have been shown to reflect disease conditions. However, measurement of mitochondrial bioenergetic function can be limited by several factors in human samples. Limitations are the amount of samples taken, sampling time, which is often spread over several days, and locations. Cryopreservation of the collected samples can ensure consistent collection and measurement of samples. Care should be taken to ensure that the parameters measured are comparable between cryopreserved and freshly prepared cells. Here, we describe methods for isolating and cryopreserving PBMCs from human blood samples to analyze the bioenergetic function of the mitochondria in these cells. PBMC cryopreserved according to the protocol described here show only minor differences in cell number and viability, adenosine triphosphate levels, and measured respiratory chain activity compared with freshly harvested cells. Only 8-24 mL of human blood is needed for the described preparations, making it possible to collect samples during clinical studies multicentrally and determine their bioenergetics on site.

Author Spotlight: Preservation of Bioenergetic Parameters in Peripheral Blood Mononuclear Cells After Cryopreservation 

Isolated peripheral blood mononuclear cells can be used for the analysis of immune functions and disorders, metabolic diseases, or mitochondrial functions. In this work, we describe a standardized method for the preparation of PBMCs from whole blood and the subsequent cryopreservation. Cryopreservation makes this time and place independent.

The physiological functions of eukaryotic cells rely on energy mainly provided by mitochondria. Mitochondrial dysfunction is linked to metabolic diseases ...

Immunology and Infection

High-resolution Respirometry to Assess Mitochondrial Function in Permeabilized and Intact Cells

A high-resolution oxygraph is a device for measuring cellular oxygen consumption in a closed-chamber system with very high resolution and sensitivity in biological samples (intact and permeabilized cells, tissues or isolated mitochondria). The high-resolution oxygraph device is equipped with two chambers and uses polarographic oxygen sensors to measure oxygen concentration and calculate oxygen consumption within each chamber. Oxygen consumption rates are calculated using software and expressed as picomoles per second per number of cells. Each high-resolution oxygraph chamber contains a stopper with injection ports, which makes it ideal for substrate-uncoupler-inhibitor titrations or detergent titration protocols for determining effective and optimum concentrations for plasma membrane permeabilization. The technique can be applied to measure respiration in a wide range of cell types and also provides information on mitochondrial quality and integrity, and maximal mitochondrial respiratory electron transport system capacity.

High-resolution respirometry is used to determine mitochondrial oxygen consumption. This is a straightforward technique to determine mitochondrial respiratory chain complexes&#39; (I-IV) respiratory rates, maximal mitochondrial electron transport system capacity, and mitochondrial outer membrane integrity.

A high-resolution oxygraph is a device for measuring cellular oxygen consumption in a closed-chamber system with very high resolution and sensitivity in ...

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

Mitochondria are involved in cellular energy metabolism and use oxygen to produce energy in the form of adenosine triphosphate (ATP). Differential centrifugation at low- and high-speed is commonly used to isolate mitochondria from tissues and cultured cells. Crude mitochondrial fractions obtained by differential centrifugation are used for respirometry measurements. The differential centrifugation technique is based on the separation of organelles according to their size and sedimentation velocity. The isolation of mitochondria is performed immediately after tissue harvesting. The tissue is immersed in an ice-cold homogenization medium, minced using scissors and homogenized in a glass homogenizer with a loose-fitting pestle. The differential centrifugation technique is efficient, fast and inexpensive and the mitochondria obtained by differential centrifugation are pure enough for respirometry assays. Some of the limitations and disadvantages of isolated mitochondria, based on differential centrifugation, are that the mitochondria can be damaged during the homogenization and isolation procedure and that large amounts of the tissue biopsy or cultured cells are required for the mitochondrial isolation.

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

Mitochondria are involved in cellular energy metabolism and use oxygen to produce energy in the form of adenosine triphosphate (ATP). Differential ...

High-resolution Respirometry to Measure Mitochondrial Function of Intact Beta Cells in the Presence of Natural Compounds

High-resolution respirometry allows for the measurement of oxygen consumption of isolated mitochondria, cells and tissues. Beta cells play a critical role in the body by controlling blood glucose levels through insulin secretion in response to elevated glucose concentrations. Insulin secretion is controlled by glucose metabolism and mitochondrial respiration. Therefore, measuring intact beta cell respiration is essential to be able to improve beta cell function as a treatment for diabetes. Using intact 832/13 INS-1 derived beta cells we can measure the effect of increasing glucose concentration on cellular respiration. This protocol allows us to measure beta cell respiration in the presence or absence of various compounds, allowing one to determine the effect of given compounds on intact cell respiration. Here we demonstrate the effect of two naturally occurring compounds, monomeric epicatechin and curcumin, on beta cell respiration under the presence of low (2.5 mM) or high glucose (16.7 mM) conditions. This technique can be used to determine the effect of various compounds on intact beta cell respiration in the presence of differing glucose concentrations.

The goal of this protocol is to measure the effect of glucose-mediated changes to mitochondrial respiration in the presence of natural compounds on intact 832/13 beta cells using high-resolution respirometry.

High-resolution respirometry allows for the measurement of oxygen consumption of isolated mitochondria, cells and tissues. Beta cells play a critical role ...

Determining Respiration in Human Sperm Cells by High-Resolution Respirometry

High-Resolution Respirometry to Assess Mitochondrial Function in Human Spermatozoa

Semen quality is often studied by routine semen analysis, which is descriptive and often inconclusive. Male infertility is associated with altered sperm mitochondrial activity, so the measurement of sperm mitochondrial function is an indicator of sperm quality. High-resolution respirometry is a method of measuring the oxygen consumption of cells or tissues in a closed-chamber system. This technique can be implemented to measure respiration in human sperm and provides information about the quality and integrity of the sperm mitochondria. High-resolution respirometry allows the cells to move freely, which is an a priori advantage in the case of sperm. This technique can be applied with intact or permeabilized spermatozoa and allows for the study of intact sperm mitochondrial function and the activity of individual respiratory chain complexes. The high-resolution oxygraph instrument uses sensors to measure the oxygen concentration coupled with sensitive software to calculate the oxygen consumption. The data are used to calculate respiratory indices based on the oxygen consumption ratios. Consequently, the indices are the proportions of two oxygen consumption rates and are internally normalized to the cell number or protein mass. The respiratory indices are an indicator of sperm mitochondrial function and dysfunction.

Author Spotlight: Advancing Male Infertility Research by Unraveling Sperm Metabolism and Mitochondrial Function 

The analysis of sperm mitochondrial function by high-resolution respirometry permits the measurement of the oxygen consumption of freely moving spermatozoa in a closed-chamber system. The technique can be applied to measure respiration in human spermatozoa, which provides information on sperm mitochondrial characteristics and integrity.

Semen quality is often studied by routine semen analysis, which is descriptive and often inconclusive. Male infertility is associated with altered sperm ...

Medicine

Real-Time Analysis of Bioenergetics in Primary Human Retinal Pigment Epithelial Cells Using High-Resolution Respirometry

Metabolic dysfunction of retinal pigment epithelial cells (RPE) is a key pathogenic driver of retinal diseases such as age-related macular degeneration (AMD) and proliferative vitreoretinopathy (PVR). Since RPE are highly metabolically-active cells, alterations in their metabolic status reflect changes in their health and function. High-resolution respirometry allows for real-time kinetic analysis of the two major bioenergetic pathways, glycolysis and mitochondrial oxidative phosphorylation (OXPHOS), through quantification of the extracellular acidification rate (ECAR) and oxygen consumption rate (OCR), respectively. The following is an optimized protocol for conducting high-resolution respirometry on primary human retinal pigment epithelial cells (H-RPE). This protocol provides a detailed description of the steps involved in producing bioenergetic profiles of RPE to define their basal and maximal OXPHOS and glycolytic capacities. Exposing H-RPE to different drug injections targeting the mitochondrial and glycolytic machinery results in defined bioenergetic profiles, from which key metabolic parameters can be calculated. This protocol highlights the enhanced response of BAM15 as an uncoupling agent compared to carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) to induce the maximal respiration capacity in RPE. This protocol can be utilized to study the bioenergetic status of RPE under different disease conditions and test the efficacy of novel drugs in restoring the basal metabolic status of RPE.

The metabolic status of human retinal pigment epithelial cells (H-RPE) reflects their health and function. Presented here is an optimized protocol for examining the real-time metabolic flux of H-RPE using high-resolution respirometry.

Metabolic dysfunction of retinal pigment epithelial cells (RPE) is a key pathogenic driver of retinal diseases such as age-related macular degeneration ...

Cellular Respiration

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Quantifying Respiration using Microrespirometers
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">To assemble the microrespirometers needed for the lab, first plug in the hot glue gun to preheat it.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">Push the plunger of a tuberculin syringe all the way in and then cut the end off of the syringe.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Next, insert a capillary tube into the empty needle end of the syringe.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Push the capillary tube in until it touches the tip of the plunger.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Use the hot glue gun to create an airtight seal between the capillary tube and the tuberculin syringe. Make sure that the capillary tube is standing straight up while the glue dries.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Once the glue has dried, pull back on the plunger and make sure the capillary tube is not plugged.
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Next, prepare the manometer fluid by adding red food coloring to soapy water. NOTE: The detergent coats the inside of the capillary tube, preventing the manometer fluid from sticking during the experiment.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">Insert the capillary tube into the manometer fluid and then pull the plunger on the syringe until the entire capillary tube has been filled.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">Then, eject the manometer fluid back out of the microrespirometer.
</div></li><li data-sub-note-item="1-10"><div class="lab-step">With a small piece of absorbent cotton, plug the barrel of the microrespirometer, inserting it into the syringe up to the 0 mL mark. Pack the cotton using a spare capillary tube or a glass disposable pipette.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">Add a single drop of 15% KOH to the cotton using a spare capillary tube or a glass disposable pipette.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">Add some nonabsorbent cotton to the KOH saturated cotton to act as a barrier to the seeds. Pack the cotton using a disposable pipette. The cotton should reach halfway between the 0 mL and 1 mL mark.
</div></li><li data-sub-note-item="1-13"><div class="lab-step">Reinsert the plunger carefully until it reaches the cotton and then remove any excess KOH by pressing it out.
</div></li><li data-sub-note-item="1-14"><div class="lab-step">Set four microrespirometers at each lab station.
</div></li><li data-sub-note-item="1-15"><div class="lab-step">Then, place a lab marker and two small dishes containing the seeds and glass beads for each group alongside the microrespirometers.
</div></li><li data-sub-note-item="1-16"><div class="lab-step">Finally, prepare two water baths by filling them with roughly 6 inches of water. The water level in the bath should comfortably fit two respirometers with the entirety of their two capillary tubes exposed.
</div></li><li data-sub-note-item="1-17"><div class="lab-step">Replace the lids and insert a thermometer in each bath to monitor the temperature. One bath should be set at about 25 &#176;C, and the other at approximately 40 &#176;C.
</div></li></ul></li></ol>

Cellular Respiration: Quantification using Microrespirometers - Prep

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Quantifying Respiration using Microrespirometers
ExpandTo assemble the microrespirometers needed for the lab, first plug in the hot glue gun to preheat ...

High-Resolution Respirometry to Assess Bioenergetics in Cells and Tissues Using Chamber- and Plate-Based Respirometers

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