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Term	Abbreviation	Description
Light-enhanced dark respiration	LEDR	Light-enhanced dark respiration LEDR is a sharp (negative) maximum of dark respiration in plants in response to illumination, measured immediately after switching off the light. LEDR is supported by respiratory substrates produced during photosynthesis and closely reflects light-enhanced photorespiration (Xue et al 1996). Based on this assumption, the total photosynthetic oxygen flux TP is calculated as the sum of the measured net photosynthetic oxygen flux NP plus the absolute value of LEDR.
Limiting pO2	p_lim	In the transition from aerobic to anaerobic metabolism, there is a limiting p_O2, p_lim, below which anaerobic energy flux is switched on and CR ratios become more exothermic than the oxycaloric equivalent. p_lim may be significanlty below the critical p_O2.
Linearity		Linearity is the ability of the method to produce test results that are proportional, either directly or by a well-defined mathematical transformation, to the concentration of the analyte in samples within a given range. This property is inherent in the Beer-Lambert law for absorbance alone, but deviations occur in scattering media. It is also a property of fluorescence, but a fluorophore may not exhibit linearity, particularly over a large range of concentrations.
Living cells	ce	Cell viability in living cells should be >95 % for various experimental investigations, including cell respirometry. Viable cells (vce) are characterized by an intact plasma membrane barrier function. The total cell count (N_ce) is the sum of viable cells (N_vce) and dead cells (N_dce). In contrast, the plasma membrane can be permeabilized selectively by mild detergents (digitonin), to obtain the mt-preparation of permeabilized cells used for cell ergometry. Living cells are frequently labelled as intact cells in the sense of the total cell count, but intact may suggest dual meanings of viable or unaffected by a disease or mitochondrial injury.
Malate-aspartate shuttle		The malate-aspartate shuttle involves the glutamate-aspartate carrier and the 2-oxoglutarate carrier exchanging malate^2- for 2-oxoglutarate^2-. Cytosolic and mitochondrial malate dehydrogenase and transaminase complete the shuttle for the transport of cytosolic NADH into the mitochondrial matrix. It is most important in heart, liver and kidney.
Microplates		Microplate readers allow large numbers of sample reactions to be assayed in well format microtitre plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 µL per well. a wide range of applications involve the use of fluorescence measurements , although they can also be used in conjunction with absorbance measurements.
Mitochondrial marker	mt-marker	Mitochondrial markers are structural or functional properties that are specific for mitochondria. A structural mt-marker is the area of the inner mt-membrane or mt-volume determined stereologically, which has its limitations due to different states of swelling. If mt-area is determined by electron microscopy, the statistical challenge has to be met to convert area into a volume. When fluorescent dyes are used as mt-marker, distinction is necessary between mt-membrane potential dependent and independent dyes. mtDNA or cardiolipin content may be considered as a mt-marker. Mitochondrial marker enzymes may be determined as molecular (amount of protein) or functional properties (enzyme activities). Respiratory capacity in a defined respiratory state of a mt-preparation can be considered as a functional mt-marker, in which case respiration in other respiratory states is expressed as flux control ratios. » MiPNet article
Mitochondrial membrane potential	mtMP, ΔΨ_p⁺, Δ_elF_ep⁺ [V]	The mitochondrial membrane potential difference, mtMP or ΔΨ_p⁺ = Δ_elF_ep⁺, is the electric part of the protonmotive force, Δp = Δ_mF_eH⁺. Δ_elF_ep⁺ = Δ_mF_eH⁺ - Δ_dF_eH⁺ ΔΨ_p⁺ = Δp - Δµ_H+·(z_H⁺·F)^-1 ΔΨ_p⁺ is the potential difference across the mitochondrial inner membrane (mtIM), expressed in the electric unit of volt [V]. Electric force of the mitochondrial membrane potential is the electric energy change per ‘motive’ charge or per charge moved across the transmembrane potential difference, with the number of ‘motive’ charges expressed in the unit coulomb [C].
Mitochondrial respiration		Integrative measure of the dynamics of complex coupled metabolic pathways, including metabolite transport across the mt-membranes, TCA cycle function with electron transfer through dehydrogenases in the mt-matrix, membrane-bound electron transfer mET-pathway, the transmembrane proton circuit, and the phosphorylation system.
N-junction		The N-junction is a junction for convergent electron flow in the electron transfer pathway (ET-pathway) from type N substrates (further details »N-pathway control state) through the mt-NADH pool to Complex I (CI), and further transfer through the Q-junction to Complex III (CIII). Representative type N substrates are pyruvate (P), glutamate (G) and malate (M). The corresponding dehydrogenases (PDH, GDH, MDH) and some additional TCA cycle dehydrogenases (isocitrate dehydrogenase, oxoglutarate dehydrogenase generate NADH, the substrate of Complex I (CI). The concept of the N-junction and F-junction provides a basis for defining categories of SUIT protocols based on Electron-transfer-pathway states.
NADH calibration - DatLab		NADH calibration
NADH electron transfer-pathway state	N	The NADH electron transfer-pathway state (N) is obtained by addition of NADH-linked substrates (CI-linked), feeding electrons into the N-junction catalyzed by various mt-dehydrogenases. N-supported flux is induced in mt-preparations by the addition of NADH-generating substrate combinations of pyruvate (P), glutamate (G), malate (M), oxaloacetate (Oa), oxoglutarate (Og), citrate, hydroxybutyrate. These N-junction substrates are (indirectly) linked to Complex I by the corresponding dehydrogenase-catalyzed reactions reducing NAD⁺ to NADH+H⁺ + H⁺. The most commonly applied N-junction substrate combinations are: PM, GM, PGM. The malate-anaplerotic pathway control state (M alone) is a special case related to malic enzyme (mtME). The glutamate-anaplerotic pathway control state (G alone) supports respiration through glutamate dehydrogenase (mtGDH). Oxidation of tetrahydrofolate is a NAD(P)H linked pathway with formation of formate. In mt-preparations, succinate dehydrogenase (SDH; CII) is largely substrate-limited in N-linked respiration, due to metabolite depletion into the incubation medium. The residual involvement of S-linked respiration in the N-pathway control state can be further suppressed by the CII-inhibitor malonic acid). In the N-pathway control state ET pathway level 4 is active.
NS-S pathway control efficiency	j_NS-S	The NS-S pathway control efficiency expresses the relative stimulation of succinate supported respiration (S) by NADH-linked substrates (N), with the S-pathway control state as the background state and the NS-pathway control state as the reference state. In typical SUIT protocols with type N and S substrates, flux in the NS-pathway control state NS is inhibited by rotenone to measure flux in the S-pathway control state, S(Rot) or S. Then the NS-S pathway control efficiency in the ET-coupling state is j_{(NS-S)_E} = (NS_E-S_E)/NS_E The NS-S pathway control efficiency expresses the fractional change of flux in a defined coupling-control state when inhibition by rotenone is removed from flux under S-pathway control in the presence of a type N substrate combination. Experimentally rotenone Rot is added to the NS-state. The reversed protocol, adding N-substrates to a S-pathway control background does not provide a valid estimation of S-respiration with succinate in the absence of Rot, since oxaloacetate accumulates as a potent inhibitor of succinate dehydrogenase CII.
Nigericin		Nigericin is a H⁺/K⁺ antiporter, which allows the electroneutral transport of these two ions in opposite directions across the mitochondrial inner membrane following the K⁺ concentration gradient. In the presence of K⁺, nigericin decreases pH in the mitchondrial matrix, thus, almost fully collapses the transmembrane ΔpH, which leads to the compensatory increase of the electric mt-membrane potential. Therefore, it is ideal to use to dissect the two components of the protonmotive force, ΔpH and mt-membrane potential. It is recommended to use the lowest possible concentration of nigericin, which creates a maximal mitochondrial hyperpolarization. In the study of Komlodi 2018 J Bioenerg Biomembr, 20 nM was applied on brain mitochondria isolated from guinea-pigs using 5 mM succinate in the LEAK state which caused maximum hyperpolarisation, but did not fully dissipate the transmembrane ΔpH. Other groups (Selivanov et al 2008; Lambert et al 2004), however, used 100 nM nigericin, which in their hands fully collapsed transmembrane ΔpH using succinate as a respiratory substrate on isolated rat brain and skeletal muscle in the LEAK state.
Noise		In fluorometry and spectrophotometry, noise can be attributed to the statistical nature of the photon emission from a light source and the inherent noise in the instrument’s electronics. The former causes problems in measurements involving samples of analytes with a low extinction coefficient and present only in low concentrations. The latter becomes problematic with high absorbance samples where the light intensity emerging from the sample is very small.
Noncoupled respiration	E	Noncoupled respiration is distinguished from general (pharmacological or mechanical) uncoupled respiration, to give a label to an effort to reach the state of maximum uncoupler-activated respiration without inhibiting respiration. Noncoupled respiration, therefore, yields an estimate of ET capacity. Experimentally uncoupled respiration may fail to yield an estimate of ET capacity, due to inhibition of respiration above optimum uncoupler concentrations or insufficient stimulation by sub-optimal uncoupler concentrations. Optimum uncoupler concentrations for evaluation of (noncoupled) ET capacity require inhibitor titrations (Steinlechner-Maran 1996 Am J Physiol Cell Physiol; Huetter 2004 Biochem J; Gnaiger 2008 POS). Noncoupled respiration is maximum electron flow in an open-transmembrane proton circuit mode of operation (see ET capacity). » MiPNet article
Normalization of rate		Normalization of rate (respiratory rate, rate of hydrogen peroxide production, growth rate) is required to report experimental data. Normalization of rates leads to a diversity of formats. Normalization is guided by physicochemical principles, methodological considerations, and conceptual strategies. The challenges of measuring respiratory rate are matched by those of normalization. Normalization of rates for: (1) the number of objects (cells, organisms); (2) the volume or mass of the experimental sample; and (3) the concentration of mitochondrial markers in the instrumental chamber are sample-specific normalizations, which are distinguished from system-specific normalization for the volume of the instrumental chamber (the measuring system). Metabolic flow, I, per countable object increases as the size of the object is increased. This confounding factor is eliminated by expressing rate as sample-mass specific or sample-volume specific flux, J. Flow is an extensive quantity, whereas flux is a specific quantity. If the aim is to find differences in mitochondrial function independent of mitochondrial density, then normalization to a mitochondrial marker is imperative. Flux control ratios and flux control efficiencies are based on internal normalization for rate in a reference state, are independent of externally measured markers and, therefore, are statistically robust.
Nuclear respiratory factor 1	NRF-1	Nuclear respiratory factor 1 is a transcription factor downstream of PGC-1alpha involved in coordinated expression of nDNA and mtDNA.
O2k	O2k	O2k - Oroboros O2k: the modular system for high-resolution respirometry.
O2k-FluoRespirometer		The Oroboros O2k-FluoRespirometer - the experimental system complete for high-resolution respirometry (HRR), including fluorometry, the TIP2k and the O2k-sV-Module allowing simultaneous monitoring of oxygen consumption together with either ROS production (AmR), mt-membrane potential (TMRM, Safranin and Rhodamine 123), Ca²⁺ (CaG) or ATP production (MgG). The O2k-FluoRespirometer supports all add-on O2k-Modules: O2k-TPP+ ISE-Module, O2k-pH ISE-Module, O2k-NO Amp-Module, enabling measurement of mt-membrane potential with ion sensitive electrodes (ISE for TPP⁺ or TPMP⁺) or pH.
O2k-sV-Module	O2k-sV-Module	The O2k-sV-Module is the O2k small-volume module, comprised of two Duran® glass chambers of 12 mm inner diameter specifically developed to perform high-resolution respirometry with reduced amounts of biological sample, and all the components necessary for a smaller operation volume V of 0.5 mL. The current DatLab version is included in the delivery of this revolutionary module.
OXPHOS capacity	P	OXPHOS capacity P is the respiratory capacity of mitochondria in the ADP-activated state of oxidative phosphorylation, at saturating concentrations of ADP and inorganic phosphate (which may not be the case in State 3), oxygen, and defined reduced CHNO-fuel substrates.
Octanoate	Oca	Octanoate (octanoic acid). C₈H₁₆O₂ Common name: Caprylic acid.
Open system		An open system is a system with boundaries that allow external exchange of energy and matter; the surroundings are merely considered as a source or sink for quantities transferred across the system boundaries (external flows, I_ext).
Oroboros Instruments Corp		Oroboros Instruments distributes the gold standard O2k-technology for high-resolution respirometry - HRR - world-wide. The Oroboros Company is a scientifically oriented organization, with emphasis on continuous innovation. The extension of the Oroboros O2k to the O2k-FluoRespirometer sets a new standard. Its modular design provides the flexibility for add-on O2k-Modules (see Oroboros O2k-Catalogue). The O2k is established internationally, with »4294 O2k-Publications in the scientific literature covering areas ranging from fundamental bioenergetics to the analysis of mitochondrial and metabolic diseases, advancing the rapidly growing field of preventive mitochondrial medicine. The Oroboros science team actively participates in science and research (see: publications). Moreover, the Oroboros O2k-Laboratory frequently host international researchers (visiting scientists). Oroboros Instruments organizes international O2k-Workshops on a regular basis. The O2k-Network includes and connects 744 reference laboratories worldwide. The NextGen-O2k extends HRR to include a Q-redox sensor and PhotoBiology module.
Oxidative phosphorylation	OXPHOS	Oxidative phosphorylation (OXPHOS) is the oxidation of reduced fuel substrates by electron transfer to oxygen, chemiosmotically coupled to the phosphorylation of ADP to ATP (P») and accompanied by an intrinsically uncoupled component of respiration. The OXPHOS state of respiration provides a measure of OXPHOS capacity (P), which is frequently corrected for residual oxygen consumption (ROX).
Oxycaloric equivalent	Delta_kH_O2	The oxycaloric equivalent is the theoretically derived enthalpy change of the oxidative catabolic reactions per amount of oxygen respired, Delta_kH_O2, ranging from -430 to -480 kJ/mol O₂. The oxycaloric equivalent is used in indirect calorimetry to calculate the theoretically expected metabolic heat flux from the respirometrically measured metabolic oxygen flux. Calorimetric/respirometric ratios (CR ratios; heat/oxygen flux ratios) are experimentally determined by calorespirometry. A CR ratio more exothermic than the oxycaloric equivalent of -480 kJ/mol indicates the simultaneous involvement of aerobic and anaerobic mechanisms of energy metabolism.
Oxygen calibration - DatLab		O2 calibration is the calibration in DatLab of the oxygen sensor. It is a prerequisite for obtaining accurate measurements of respiration. Accurate calibration of the oxygen sensor depends on (1) equilibration of the incubation medium with air oxygen partial pressure at the temperature defined by the experimenter; (2) zero oxygen calibration; (3) high stability of the POS signal tested for sufficiently long periods of time; (4) linearity of signal output with oxygen pressure in the range between oxygen saturation and zero oxygen pressure; and (5) accurate oxygen solubility for aqueous solutions for the conversion of partial oxygen pressure into oxygen concentration. The standard oxygen calibration procedure is described below for high-resolution respirometry with the calibration routine using instrumental calibration DL-Protocols in DatLab.
Oxygen flow	I_O2 [mol·s^-1] or [mol·s^-1·x^-1]	Respiratory oxygen flow is the oxygen consumption per total system, which is an extensive quantity. Flow is advancement of a transformation in a system per time [mol·s^-1], when 'system' is defined as the experimental system (e.g. an open or closed chamber). Flow is distinguished from the size-specific quantity flux obtained by normalization of flow per volume of the experimental system [mol·s^-1·m^-3]. An experimental object, e.g. a living cell, may be considered as the 'experimental system'. Then oxygen flow per cell has the unit [mol·s^-1·x^-1], where [x] is the elementary unit for a count. Oxygen flow or respiration per cell [amol·s^-1·x^-1] = [pmol·s^-1·Mx^-1] is normalized for the cell count, distinguished from oxygen flux (e.g. per mg protein or wet mass). These are different forms of normalization of rate.
Oxygen flux	J_O2	Oxygen flux, J_O₂, is a specific quantity. Oxygen flux is oxygen flow, I_O₂ [mol·s^-1 per system] (an extensive quantity), divided by system size. Flux may be volume-specific (flow per volume [pmol·s^-1·mL^-1]), mass-specific (flow per mass [pmol·s^-1·mg^-1]), or marker-specific (flow per mtEU). Oxygen flux (e.g., per body mass, or per cell volume) is distinguished from oxygen flow (per number of objects, such as cells), I_O₂ [mol·s^-1·x^-1]. These are different forms of normalization of rate.
Oxygen flux - instrumental background	J°_O₂	Instrumental background oxygen flux, J°_O₂, in a respirometer is due to oxygen consumption by the POS, and oxygen diffusion into or out of the aqueous medium in the O2k-chamber. It is a property of the instrumental system, measured in the range of experimental oxygen levels by a standardized instrumental O₂ background test. The oxygen regime from air saturation towards zero oxygen is applied generally in experiments with isolated mitochondria, and living or permeabilized cells. To overcome oxygen diffusion limitation in permeabilized fibers and homogenates, an elevated oxygen regime is applied, requiring instrumental background test in the same range of elevated oxygen.
Oxygen kinetics		Oxygen kinetics describes the dependence of respiration of isolated mitochondria or cells on oxygen partial pressure. Frequently, a strictly hyperbolic kinetics is observed, with two parameters, the oxygen pressure at half-maximum flux, p₅₀, and maximum flux, Jmax. The p₅₀ is in the range of 0.2 to 0.8 kPa for cytochrome c oxidase, isolated mitochondria and small cells, strongly dependent on J_max and coupling state.
Oxygen pressure	p_O2 [kPa]	Oxygen pressure or partial pressure of oxygen [kPa], related to oxygen concentration in solution by the oxygen solubility, S_O2 [µM/kPa].
Oxygen signal		The oxygen signal of the Oroboros O2k is transmitted from the electrochemical polarographic oxygen sensor (OroboPOS) for each of the two O2k-chambers to DatLab. The primary signal is a current [µA] which is converted into a voltage [V] (raw signal), and calibrated in SI units for amount of substance concentration [µmol·L^-1 or µM]. For technical reasons, the raw signal is given in [V] (DatLab 7 and previous) or [µA] (DatLab 8). The value of the raw signal is the same, independent of the displayed unit ([V] or [µA]). In the following sections, only [µA] is used for information on the raw signal, but the same values in [V] apply for the raw signal when using DL7 or previous versions.
Oxygen solubility	S_O₂ [µM/kPa]	The oxygen solubility, S_O₂ [µM/kPa] = [(µmol·L^-1)/kPa], expresses the oxygen concentration in solution in equilibrium with the oxygen pressure in a gas phase, as a function of temperature and composition of the solution. The inverse of oxygen solubility is related to the activity of dissolved oxygen. The oxygen solubility in solution, S_O₂(aq), depends on temperature and the concentrations of solutes in solution, whereas the dissolved oxygen concentration at equilibrium with air, c_O₂^(aq), depends on S_O₂(aq), barometric pressure and temperature. S_O₂(aq) in pure water is 10.56 µM/kPa at 37 °C and 12.56 µM/kPa at 25 °C. At standard barometric pressure (100 kPa), c_O₂^(aq) is 207.3 µM at 37 °C (19.6 kPa partial oxygen pressure) or 254.7 µM at 25 °C (20.3 kPa partial oxygen pressure). In MiR05 and serum, the corresponding saturation concentrations are lower due to the oxygen solubility factor: 191 and 184 µM at 37 °C or 234 and 227 µM at 25 °C.
Oxygen solubility factor	F_M	The oxygen solubility factor of the incubation medium, F_M, expresses the effect of the salt concentration on oxygen solubility relative to pure water. In mitochondrial respiration medium MiR05, MiR05-Kit and MiR06, F_M is 0.92 (determined at 30 and 37 °C) and in culture media is 0.89 (at 37 °C). F_M varies depending on the temperature and composition of the medium. To determine the FM based on the oxygen concentration, specific methods and equipment are needed (see references Rasmussen HN, Rasmussen UF 2003 in MiPNet06.03). For other media, F_M may be estimated using Table 4 in MiPNet06.03. For this purpose KCl based media can be described as "seawater" of varying salinity. The original data on sucrose and KCl-media (Reynafarje et al 1985), however, have been critizesed as artefacts and the F_M of 0.92 is suggested in the temperature range of 10 °C to 40 °C as for MiR05.
P-L control efficiency	j_P-L	The P-L control efficiency (P-L flux control efficiency) is defined as j_P-L = (P-L)/P = 1-L/P. OXPHOS capacity corrected for LEAK respiration is the P-L net OXPHOS capacity, P-L. The P-L control efficiency is the ratio of net to total OXPHOS capacity, which is equal to the biochemical E-L coupling efficiency, if P=E. j_P-L = 1.0 for a fully coupled system (when RCR approaches infinity); j_P-L = 0.0 (RCR=1) for a system with zero respiratory phosphorylation capacity (P-L=0) or zero E-L coupling efficiency (E-L=0 when L=P=E). If State 3 is measured at saturating concentrations of ADP and P_i (State 3 = P), then the respiratory acceptor control ratio RCR equals P/L. Under these conditions, the respiratory control ratio and P-L control efficiency are related by a hyperbolic function, j_P-L = 1-RCR^-1. » MiPNet article
P/E control ratio	P/E	The P/E control ratio (OXPHOS/ET pathway; phosphorylation system control ratio) is an expression of the limitation of OXPHOS capacity by the phosphorylation system. The relative limitation of OXPHOS capacity by the capacity of the phosphorylation system is better expressed by the E-P control efficiency, j_E-P = 1-P/E. The P/E control ratio increases with increasing capacity of the phosphorylation system up to a maximum of 1.0 when it matches or is in excess of ET capacity. P/E also increases with uncoupling. P/E increases from the lower boundary set by L/E (zero capacity of the phosphorylation system), to the upper limit of 1.0, when there is no limitation of P by the phosphorylation system or the proton backpressure (capacity of the phosphorylation system fully matches the ET capacity; or if the system is fully uncoupled). It is important to separate the kinetic effect of ADP limitation from limitation by enzymatic capacity at saturating ADP concentration. » MiPNet article
P50	p₅₀	p₅₀ is the oxygen partial pressure at which (a) respiratory flux is 50% of maximum oxygen flux, J_max, at saturating oxygen levels. The oxygen affinity is indirectly proportional to the p₅₀. The p₅₀ depends on metabolic state and rate. (b) p₅₀ is the oxygen partial pressure at which oxygen binding (on myoglobin, haemoglobin) is 50%, or desaturation is 50%.
PB-Module		The PB-Module has been developed for conducting measurements of PhotoBiology, including photosynthesis. It consists of the PB Light Source and electronic components which are an integral part of the NextGen-O2k. Measurements are recorded and evaluated with the DatLab 8 software.
PH calibration buffers		pH calibration buffers are prepared to obtain two or more defined pH values for calibration of pH electrodes and pH indicator dyes.
POS calibration - dynamic		Calibration of the sensor response time. See also POS calibration - static.
POS calibration - static	F5	Two-point calibration of the polarographic oxygen sensor, comprising Air calibration and Zero calibration. See also POS calibration - dynamic.
Pathway control ratio	FCR	Substrate control ratios are flux control ratios FCR, at a constant mitochondrial coupling-control state. Whereas there are only three well-defined coupling-control states of mitochondrial respiration, L, P, E (LEAK respiration, OXPHOS, Electron transfer pathway), numerous Electron-transfer-pathway states are possible. Careful selection of the reference state, J_ref, is required, for which some guidelines may be provided without the possibility to formulate general rules. FCR are best defined by taking J_ref as the maximum flux (e.g. NS_E), such that flux in various other respiratory states, J_i, is smaller or equal to J_ref. However, this is not generally possible with FCR. For instance, the N/S pathway control ratio (at constant coupling-control state) may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The S-pathway control state may be selected preferentially as J_ref, if mitochondria with variable N-linked injuries are studied. In contrast, the reference state, Z, is strictly defined for flux control efficiency.
Photodecomposition	PD	Photodecomposition or photodegradation is the process of decay of organic material induced by increasing light intensity. Under aerobic conditions, the enhancement of photodecomposition by light intensity can be quantified by oxygen consumption in a controlled light regime.
Physiological pathway-control state		See Electron-transfer-pathway state.
Polyether ether ketone	PEEK	Polyether ether ketone (PEEK) is a semicrystalline organic polymer thermoplastic, which is chemically very resistant, with excellent mechanical properties. PEEK is compatible with ultra-high vacuum applications, and its resistance against oxygen diffusion make it an ideal material for high-resolution respirometry (POS insulation; coating of stirrer bars; stoppers for closing the O2k-Chamber).
Polyvinylidene fluoride	PVDF	Polyvinylidene fluoride (PVDF) is a pure thermoplastic fluoropolymer, which is chemically very resistant, with excellent mechanical properties. It is used generally in applications requiring the highest purity, strength, and resistance to solvents, acids, bases and heat (Wikipedia). PVDF is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (coating of stirrer bars; stoppers for closing the O2k-Chamber).
Power O2k-FluoRespirometer		Power O2k-FluoRespirometer - optional configuration as additional system for increasing output combined with the O2k-FluoRespirometer (O2k-Series H). The Power O2k-FluoRespirometer includes the TIP2k and the O2k-sV-Module, and supports all add-on O2k-Modules of the Oroboros O2k. It can be added to an existing Oroboros O2k of any O2k-Series. This application does not require an additional ISS-Integrated Suction System and O2k-Titration Set. Furthermore, the OroboPOS-Mounting Tool of the OroboPOS Service Tools can be used from the available O2k and is not included.
Power O2k-Respirometer		The Power O2k-Respirometer is an economical option for using additional O2k-Units to increase output in high-resolution respirometry.
Proton leak		Flux of protons driven by the protonmotive force across the inner mt-membrane, bypassing the ATP synthase and thus contributing to LEAK respiration. Proton leak-flux depends non-linearly (non-ohmic) on the protonmotive force. Compare: Proton slip.
Proton pump		Mitochondrial proton pumps are large enzyme complexes (CI, CIII, CIV, CV) spanning the inner mt-membrane, partially encoded by mtDNA. CI, CIII and CIV are proton pumps that drive protons against the electrochemical protonmotive force, driven by electron transfer from reduced substrates to oxygen. In contrast, ATP synthase (also known as CIV) is a proton pump that utilizes the energy of proton flow along the protonmotive force to drive phosphorylation of ADP to ATP.
Proton slip		Proton slip is a property of the proton pumps (Complexes CI, CIII, and CIV) when the proton slips back to the matrix side within the proton pumping process. Slip is different from the proton leak, which depends on Δp and is a property of the inner mt-membrane (including the boundaries between membrane-spanning proteins and the lipid phase). Slip is an uncoupling process that depends mainly on flux and contributes to a reduction in the biochemical coupling efficiency of ATP production and oxygen consumption. Together with proton leak and cation cycling, proton slip is compensated for by LEAK respiration or LEAK oxygen flux, L. Compare: Proton leak.
Q calibration - DatLab		Q calibration
Q-junction		The Q-junction is a junction for convergent electron flow in the Electron transfer pathway (ET-pathway) from type N substrates and mt-matrix dehydrogenases through Complex I (CI), from type F substrates and FA oxidation through electron-transferring flavoprotein Complex (CETF), from succinate (S) through Complex II (CII), from glycerophosphate (Gp) through glycerophosphate dehydrogenase Complex (CGpDH), from choline through choline dehydrogenase, from dihydro-orotate through dihydro-orotate dehydrogenase, and other enzyme Complexes into the Q-cycle (ubiquinol/ubiquinone), and further downstream to Complex III (CIII) and Complex IV (CIV). The concept of the Q-junction, with the N-junction and F-junction upstream, provides the rationale for defining Electron-transfer-pathway states and categories of SUIT protocols.
ROUTINE respiration	R	In the living cell, ROUTINE respiration (R) or ROUTINE activity in the physiological coupling state is controlled by cellular energy demand, energy turnover and the degree of coupling to phosphorylation (intrinsic uncoupling and pathological dyscoupling). The conditions for measurement and expression of respiration vary (oxygen flux in state R, J_O₂R or oxygen flow in state R, I_O₂R). If these conditions are defined and remain consistent within a given context, then the simple symbol R for respiratory state can be used to substitute the more explicit expression for respiratory activity. R and growth of cells is supported by exogenous substrates in culture media. In media without energy substrates, R depends on endogenous substrates. R cannot be measured in permeabilized cells or isolated mitochondria. R is corrected for residual oxygen consumption (ROX), whereas R´ is the uncorrected apparent ROUTINE respiration or total cellular oxygen consumption of cells including ROX.
Respiratory acceptor control ratio	RCR	The respiratory acceptor control ratio (RCR) is defined as State 3/State 4 [1]. If State 3 is measured at saturating [ADP], RCR is the inverse of the OXPHOS control ratio, L/P (when State 3 is equivalent to the OXPHOS state, P). RCR is directly but non-linearly related to the P-L control efficiency, j_P-L = 1-L/P, with boundaries from 0.0 to 1.0. In contrast, RCR ranges from 1.0 to infinity, which needs to be considered when performing statistical analyses. In living cells, the term RCR has been used for the ratio State 3u/State 4o, i.e. for the inverse L/E ratio [2,3]. Then for conceptual and statistical reasons, RCR should be replaced by the E-L coupling efficiency, 1-L/E [4].
Respiratory chain	RC	The mitochondrial respiratory chain (RC) consists of enzyme complexes arranged to form a metabolic system of convergent pathways for oxidative phosphorylation. In a general sense, the RC includes (1) the electron transfer pathway (ET-pathway), with transporters for the exchange of reduced substrates across the inner mitochondrial membrane, enzymes in the matrix space (particularly dehydrogenases of the tricarboxylic acid cycle), inner membrane-bound electron transfer complexes, and (2) the inner membrane-bound enzymes of the phosphorylation system.
Respiratory complexes	CI, CII, CIII, CIV, CETF, CGpDH, ..	Respiratory Complexes are membrane-bound enzymes consisting of several subunits which are involved in energy transduction of the respiratory system. » MiPNet article
Respiratory state		Respiratory states of mitochondrial preparations and living cells are defined in the current literature in many ways and with a diversity of terms. Mitochondrial respiratory states must be defined in terms of both, the coupling-control state and the electron-transfer-pathway state.
Respirometry		Respirometry is the quantitative measurement of respiration. Respiration is therefore a combustion, a very slow one to be precise (Lavoisier and Laplace 1783). Thus the basic idea of using calorimetry to explore the sources and dynamics of heat changes were present in the origins of bioenergetics (Gnaiger 1983). Respirometry provides an indirect calorimetric approach to the measurement of metabolic heat changes, by measuring oxygen uptake (and carbon dioxide production and nitrogen excretion in the form of ammonia, urea, or uric acid) and converting the oxygen consumed into an enthalpy change, using the oxycaloric equivalent. Liebig (1842) showed that the substrate of oxidative respiration was protein, carbohydrates, and fat. The sum of these chemical changes of materials under the influence of living cells is known as metabolism (Lusk 1928). The amount (volume STP) of carbon dioxide expired to the amount (volume STP) of oxygen inspired simultaneously is the respiratory quotient, which is 1.0 for the combustion of carbohydrate, but less for lipid and protein. Voit (1901) summarized early respirometric studies carried out by the Munich school on patients and healthy controls, concluding that the metabolism in the body was not proportional to the combustibility of the substances outside the body, but that protein, which burns with difficulty outside, metabolizes with the greatest ease, then carbohydrates, while fats, which readily burns outside, is the most difficultly combustible in the organism. Extending these conclusions on the sources of metabolic heat changes, the corresponding dynamics or respiratory control was summarized (Lusk 1928): The absorption of oxygen does not cause metabolism, but rather the amount of the metabolism determines the amount of oxygen to be absorbed. .. metabolism regulates the respiration.
STPD	STPD	At standard temperature and pressure dry (STPD: 0 °C = 273.15 K and 1 atm = 101.325 kPa = 760 mmHg), the molar volume of an ideal gas, V_m, and V_m,O₂ is 22.414 and 22.392 L∙mol^-1, respectively. Rounded to three decimal places, both values yield the conversion factor of 0.744 from units used in spiroergometry (V_O₂max [mL O₂·min^-1]) to SI units [µmol O₂·s^-1]. For comparison at normal temperature and pressure dry (NTPD: 20 °C), V_m,O₂ is 24.038 L∙mol^-1. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol^-1 and 22.689 L∙mol^-1 for O₂.
SUIT	SUIT	SUIT is the abbreviation for Substrate-Uncoupler-Inhibitor Titration. SUIT protocols are used with mt-preparations to study respiratory control in a sequence of coupling and pathway control states induced by multiple titrations within a single experimental assay. These studies use biological samples economically to gain maximum information with a minimum amount of cells or tissue.
SUIT-001	RP1
SUIT-001 O2 ce-pce D003	RP1 ce-pce
SUIT-001 O2 ce-pce D004	RP1 ce-pce blood
SUIT-001 O2 mt D001	RP1 mt
SUIT-001 O2 pfi D002	RP1 pfi
SUIT-002	RP2
SUIT-002 O2 ce-pce D007	RP2 ce-pce
SUIT-002 O2 ce-pce D007a	RP2 ce-pce blood
SUIT-002 O2 mt D005	RP2 mt
SUIT-002 O2 pfi D006	RP2 pfi
SUIT-003	CCP-ce
SUIT-003 AmR ce D058	AmR effect on ce
SUIT-003 AmR ce D059	AmR effect on ce - control
SUIT-003 Ce1;ce1P;ce3U;ce4Glc;ce5M;ce6Rot;ce7S;1Dig;1c;2Ama;3AsTm;4Azd	cePMGlc,S
SUIT-003 Ce1;ce2U-	ce
SUIT-003 Ce1;ce3U-	ce
SUIT-003 O2 ce D009	CCP-ce short
SUIT-003 O2 ce D012	CCP-ce(P)
SUIT-003 O2 ce D028	CCP-ce S permeability test
SUIT-003 O2 ce D037	CCP-ce Crabtree_R
SUIT-003 O2 ce D038	CCP-ce Crabtree_E
SUIT-003 O2 ce D039	CCP-ce microalgae
SUIT-003 O2 ce D050	CCP-ce Snv
SUIT-003 O2 ce D060	CCP-ce Snv,Mnanv
SUIT-003 O2 ce D061	CCP-ce Snv,Mnanv - control
SUIT-003 O2 ce D062	CCP-ce Snv - control
SUIT-003 O2 ce-pce D013	CCVP-Glc,M
SUIT-003 O2 ce-pce D018	CCVP-Glc
SUIT-003 O2 ce-pce D020	CCVP
SUIT-003 pH ce D067	CCP-Crabtree with glycolysis inhibition
SUIT-004	RP1-short
SUIT-004 O2 pfi D010	RP1-short pfi
SUIT-005	RP2-short
SUIT-005 O2 pfi D011	RP2-short pfi
SUIT-006	CCP-mtprep
SUIT-006 O2 ce-pce D029	CCP ce-pce PM
SUIT-006 O2 mt D022	CCP mt S(Rot)
SUIT-006 O2 mt D047	CCP mt PM
SUIT-006 Q ce-pce D073	CCP ce-pce S(Rot)
SUIT-006 Q mt D071	CCP mt S(Rot)
SUIT-007	Glutamate anaplerosis
SUIT-007 O2 ce-pce D030	Glutamate anaplerotic pathway
SUIT-008	PM+G+S_OXPHOS+Rot_ET
SUIT-008 O2 ce-pce D025	Q-junction ce-pce
SUIT-008 O2 mt D026	Q-junction mtprep
SUIT-008 O2 pce D25	NS(PGM)
SUIT-008 O2 pfi D014
SUIT-009 O2 ce-pce D016
SUIT-009 O2 mt D015
SUIT-010	Digitonin test
SUIT-010 O2 ce-pce D008	Dig titration-pce
SUIT-011	GM+S_OXPHOS+Rot_ET
SUIT-011 O2 pfi D024	NS physiological maximum capapcity in fibres
SUIT-012	PM+G_OXPHOS
SUIT-012 O2 ce-pce D052	N(PGM)
SUIT-012 O2 mt D027	N CCP mtprep
SUIT-013 AmR ce D023	O_{2 dependence of H₂O₂ production ce}
SUIT-014	GM+P+S_OXPHOS+Rot_ET
SUIT-014 O2 pfi D042	NS(PGM)
SUIT-015	F+G+P+S_OXPHOS+Rot_ET
SUIT-015 O2 pti D043	FNS(Oct,PGM)
SUIT-016	F+G+S+Rot_OXPHOS+Omy
SUIT-016 O2 pfi D044	FNS(Oct,GM)
SUIT-017	F+G+S_OXPHOS+Rot_ET
SUIT-017 O2 mt D046	FNS(Oct,GM)
SUIT-017 O2 pfi D049	FNS(Oct,GM)
SUIT-018 O2 mt D054
SUIT-019	Pal+Oct+P+G_OXPHOS+S+Rot_ET
SUIT-019 O2 pfi D045	FNS(PalOct,PGM)
SUIT-020	PM+G+S+Rot_OXPHOS+Omy
SUIT-020 O2 mt D032	Q-junction additivity and respiratory control for membrane potential
SUIT-021	OXPHOS (GM+S+Rot+Omy)
SUIT-021 O2 mt D035	NS(GM)
SUIT-022	AOX (ce CN+SHAM)
SUIT-022 O2 ce D051	AOX-ce CN+SHAM
SUIT-023	AOX-ce SHAM+CN
SUIT-023 O2 ce D053	AOX-ce SHAM+CN
SUIT-024	ATPase (PM)
SUIT-024 O2 ce-pce D056	N(PM)
SUIT-025	OXPHOS (F+M+P+G+S+Rot)
SUIT-025 O2 mt D057	FNS(Oct,PGM)
SUIT-027	Malate anaplerosis
SUIT-029 O2 mt D066	QC_imt_PM_T+OXPHOS+c+Omy_ET_G+S+Rot
SUIT-031	PM+S+Rot
SUIT-031 O2 ce-pce D079	PM+S+Rot
SUIT-031 O2 mt D075	PM+S+Rot
SUIT-031 Q ce-pce D074	PM+S+Rot
SUIT-031 Q mt D072	PM+S+Rot
SUITbrowser		Use the SUITbrowser to find the substrate-uncoupler-inhibitor-titration (SUIT) protocol most suitable for addressing your research questions. Open the SUITbrowser: http://suitbrowser.oroboros.at/ How to find a DL-Protocol (DLP)
Select O2k - DatLab		Select O2k - DatLab
Selectivity		Selectivity is the ability of a sensor or method to quantify accurately and specifically the analyte or analytes in the presence of other compounds.
Sensitivity		Sensitivity refers to the response obtained for a given amount of analyte and is often denoted by two factors: the limit of detection and the limit of quantification.
Smoothing		Various methods of smoothing can be applied to improve the signal-to-noise ratio. For instance, data points recorded over time [s] or over a range of wavelengths [nm] can be smoothed by averaging n data points per interval. Then the average of the n points per smoothing interval can be taken for each successively recorded data point across the time range or range of the spectrum to give a n-point moving average smoothing. This method decreases the noise of the signal, but clearly reduces the time or wavelength resolution. More advanced methods of smoothing are applied to retain a higher time resolution or wavelength resolution.
Stability		Stability determines the accuracy of intensity and absorbance measurements as a function of time. Instability (see drift introduces systematic errors in the accuracy of fluorescence and absorbance measurements.
Startup O2k-Respirometer		Startup O2k-Respirometer - the experimental system complete for basic high-resolution respirometry (HRR). The O2k-Respirometer includes the O2k-Main Unit with stainless steel housing, O2k-Assembly Kit, two OroboPOS (polarographic oxygen sensors) and OroboPOS-Service Kit, DatLab software, the ISS-Integrated Suction System, the O2k-Titration Set, and for performing high-resolution respirometry with reduced amounts of biological sample the O2k-sV-Module. The O2k is a sole source apparatus with no other instruments meeting its specifications.
Steady state		A system is in a steady state if the state variables of a dynamic system do not change over time due to exchange processes with the environment, which compensate for internal dissipative transformations — such as chemical reactions or diffusion — and thus prevent any changes of the system and externalize dissipative changes to the environment. The dynamic nature of the steady state differentiates it from the thermodynamic equilibrium state. {Quote} Steady states can be obtained only in open systems, in which changes by internal transformations, e.g., O₂ consumption, are instantaneously compensated for by external fluxes across the system boundary, e.g., O₂ supply, thus preventing a change of O₂ concentration in the system (Gnaiger 1993). Mitochondrial respiratory states monitored in closed systems satisfy the criteria of pseudo-steady states for limited periods of time, when changes in the system (concentrations of O₂, fuel substrates, ADP, P_i, H⁺) do not exert significant effects on metabolic fluxes (respiration, phosphorylation). Such pseudo-steady states require respiratory media with sufficient buffering capacity and substrates maintained at kinetically-saturating concentrations, and thus depend on the kinetics of the processes under investigation. {end of Quote: BEC 2020.1}. Whereas fluxes may change at a steady state over time, concentrations are maintained constant. The 'respiratory steady state' (Chance and Williams 1955) is characterized by constant fluxes (O₂ flux, H₂O₂ flux) and measured variables of state (cytochrome redox states, Q redox state, NADH redox state, mitochondrial membrane potential). High-resolution respirometry allows for the measurement of several parameters (e.g. O₂ flux, H₂O₂ flux, mitochondrial membrane potential) at pseudo-steady states, when changes of concentrations in the closed system do not exert any control on fluxes. Combination with the Titration-Injection microPump (TIP2k) allows operation with programmable titration regimes at steady-state ADP concentration (Gnaiger 2001), oxygen concentration (oxystat mode; Gnaiger et al 2000, Harrison et al 2015) or steady-state pH (pH-stat more), yielding an expanded flexibility in experimental design by combining the technical advantages of closed and open systems approaches.
Substrate control state		See Electron-transfer-pathway state
Substrate-uncoupler-inhibitor titration	SUIT	Mitochondrial Substrate-uncoupler-inhibitor titration (SUIT) protocols are used with mitochondrial preparations to study respiratory control in a sequence of coupling and substrates states induced by multiple titrations within a single experimental assay.
TIP2k-Module		TIP2k-Module - Titration-Injection microPump (TIP2k) for two-channel operation with the O2k-FluoRespirometer with automatic control by DatLab of programmable titration regimes and feedback control (oxystat, pH-stat).
TPP+ inhibitory effect		A major task in establishing a procedure for measurement of mitochondrial membrane potential using probe molecules is the evaluation of inhibitory concentrations of the probe molecule on the activity of respiration. The TPP⁺ inhibitory effect (this also applies to TPMP⁺ and other indicator molecules) is frequently ignored. Accurate knowledge of a threshold concentration is required to evaluate the necessary limit of detection of TPP⁺, and for restriction of experimental TPP⁺ concentrations below the inhibitory range.
Taurine		Taurine, or 2-Aminoethan sulfonic acid, is one of the most abundant low-molecular-weight organic constituents in animals and humans. It has a multitude of functions in different types of tissue, one of which is the stabilization of membranes. Because of this and its antioxidative effect, taurine is a component of the respiration media MiR05 and MiR06 to preserve mitochondrial function.
Tetraphenylphosphonium	TPP⁺	Tetraphenylphosphonium (TPP⁺). A lipophilic molecular probe in conjunction with an ion selective electrode (ISE) for measuring the mitochondrial membrane potential.
Time resolution		Time resolution in respirometric measurements is influenced by three parameters: the response time of the POS, the data sampling interval and the number of points used for flux calculation.
Uncoupler titrations		In uncoupler titrations various uncouplers, such as CCCP, FCCP or DNP are applied to uncouple mitochondrial electron transfer from phosphorylation (ATP synthase, ANT and phosphate carrier), particularly with the aim to measure ET capacity. ET capacity is maximum oxygen flux measured as noncoupled respiration with optimum uncoupler concentration.
Uncoupling-control ratio	UCR	The uncoupling-control ratio UCR is the ratio of ET-pathway/ROUTINE-respiration (E/R) in living cells, evaluated by careful uncoupler titrations (Steinlechner et al 1996). Compare ROUTINE-control ratio (R/E) (Gnaiger 2008).
Unspecific binding of TPP+		Unspecific binding of the probe molecule TPP⁺ in the matrix phase of mitochondria is taken into account as a correction for measurement of the mitochondrial membrane potential. External unspecific binding is the binding outside of the inner mt-membrane or on the outer side of the inner mt-membrane, in contrast to internal unspecific binding.
VO2max	V_O₂max; V_O₂max/M	Maximum oxygen consumption, V_O₂max, is and index of cardiorespiratory fitness, measured by spiroergometry on human and animal organisms capable of controlled physical exercise performance on a treadmill or cycle ergometer. V_O₂max is the maximum respiration of an organism, expressed as the volume of O₂ at STPD consumed per unit of time per individual object [mL.min^-1.x^-1]. If normalized per body mass of the individual object, M [kg.x^-1], mass specific maximum oxygen consumption, V_O₂max/M, is expressed in units [mL.min^-1.kg^-1].
Warburg effect		Recently, controversies had a renaissance on the much neglected Crabtree effect (aerobic glycolysis in a large range of cells exposed to glucose or fructose, with fully functional mitochondria; Crabtree 1929; Gnaiger and Kemp 1990) versus the Warburg effect (loss of mitochondrial function inducing cancer and stimulating compensatory aerobic glycolysis in the presence of oxygen; Warburg 1956; see list of references for reviews). Today it is widely accepted that ‘the Warburg effect is not consistent across all cancer types’ (Potter et al 2016) and reprogramming of mitochondrial energy metabolism represents a functional adjustment of cancer cells (Schöpf et al 2020).
Zero calibration	R0	Zero calibration is, together with air calibration, one of the two steps of the POS calibration. It is performed in the closed chamber after all the oxygen has been depleted by the addition of dithionite or by respiration of imt or cells. Any incubation medium can be used for zero calibration with dithionite or sample. Unlike air calibration, it is not necessary to perform a zero calibration on each experimental day. After performing a zero calibration, it is recommended not running other experiments on the same day. Even after standard cleaning of the O2k-chambers, there might be residual amounts of reduced dithionite in the chamber, affecting the oxygen flux in subsequent experiments performed on the same day.

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