MitoPedia: Terms and abbreviations

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MitoPedia: Terms and abbreviations


IUPAC guidelines are followed for general terms of physical chemistry[1],[2],[3], extended by concepts of mitochondrial physiology[4] and nonequilibrium thermodynamics[5].


  • Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. - »Bioblast link«
  1. Cohen ER, Cvitas T, Frey JG, Holmström B, Kuchitsu K, Marquardt R, Mills I, Pavese F, Quack M, Stohner J, Strauss HL, Takami M, Thor HL (2008) Quantities, Units and Symbols in Physical Chemistry, IUPAC Green Book, 3rd Edition, 2nd Printing, IUPAC & RSC Publishing, Cambridge. - »Bioblast link«
  2. International Union of Biochemistry and Molecular Biology: Recommendations for terminology and databases for biochemical thermodynamics. - »Open Access«
  3. International Union of Biochemistry (1981) Symbolism and terminology in enzyme kinetics. - »Open Access«
  4. Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. Oroboros MiPNet Publications, Innsbruck:80 pp. - »Bioblast link«
  5. Gnaiger E (1993) Nonequilibrium thermodynamics of energy transformations. Pure Appl Chem 65:1983-2002. - »Bioblast link«

2-Deoxyglucose2-DG2-Deoxyglucose, also known as 2-deoxy-D-glucose is a glucose derivative which has the 2-hydroxyl group replaced by hydrogen. It competitively inhibits glycolysis by blocking hexokinase and phosphohexoseisomerase .
2-Hydroxyglutarate2HGReduction of oxoglutarate (2OG or alpha-ketoglutarate) to 2-hydroxyglutarate (2HG) is driven by NADPH. 2HG is also formed in side reactions of lactate dehydrogenase and malate dehydrogenase. Millimolar 2HG concentrations are found in some cancer cells compared to , whereas side activities of lactate and malate dehydrogenase form submillimolar s-2-hydroxyglutarate (s-2HG). However, even wild-type IDH1 and IDH2, notably under shifts toward reductive carboxylation glutaminolysis or changes in other enzymes, lead to “intermediate” 0.01–0.1 mM 2HG levels, for example, in breast carcinoma compared with nanomolar concentrations in benign cells. 2HG is considered an important player in reprogramming metabolism of cancer cells.
2-mercaptoacetate2-mercaptoacetate is an inhibitor of medium-chain acyl-CoA dehydrogenase, MCAD, the rate-limiting enzyme of octanoylcarnitine oxidation. 2-mercaptoacetate has been used as an inhibitor of fatty acid oxidation (F-pathway control state). In permeabilized rat soleus muscle fibers, pre-incubation with 1 mM 2-mercaptoacetate for 45 min resulted in 58% inhibition of MCAD and decreased octanoylcarnitine&malate stimulated respiration by approximately 60% (Osiki 2016 FASEB J).
ADPDAdenosine diphosphate is a nucleotide. In OXPHOS core metabolism, ADP is a substrate of ANT and ATP synthase in the phosphorylation system. ADP is the discharged or low-energy counterpart of ATP. ADP can accept chemical energy by regaining a phosphate group to become ATP, in substrate-level phosphorylation (in anaerobic catabolism), at the expense of solar energy (in photosynthetic cells) or chemiosmotic energy (respiration in heterotrophic cells). ADP is added to mitochondrial preparations at kinetically saturating concentrations to induce the active state for evaluation of OXPHOS capacity.
AMPKAMPKAMP-activated protein kinase is a regulatory protein which acts as crucial cellular energy sensor by sensing AMP, ADP and/or Ca2+ levels in response to metabolic stresses or drug administration.
ASAPbioScience only progresses as quickly and efficiently as it is shared. But even with all of the technological capabilities available today, the process of publishing scientific work is taking longer than ever. ASAPbio (Accelerating Science and Publication in biology) is a scientist-driven nonprofit working to address this problem by promoting innovation and transparency in life sciences communication. In 2015, ASAPbio founder Ron Vale published an analysis of the increasing time to first-author publication among graduate students at UCSF, and proposed a more widespread use of preprints in the life sciences as a potential solution.
ATPTAdenosine triphosphate is a nucleotid and functions as the major carrier of chemical energy in the cells. As it transfers its energy to other molecules, it looses its terminal phosphate group and becomes adenosine diphosphate (ADP).
ATP synthaseCVATP synthase or F-ATPase (the use of Complex V is discouraged) catalyzes the endergonic phosphorylation of ADP to ATP in an over-all exergonic process that is driven by proton translocation along the protonmotive force. The ATP synthase can be inhibited by oligomycin.
ATPasesATPases are enzymes that hydrolyse ATP, releasing ADP and inorganic phosphate. The contamination of isolated mitochondria with ATPases from other organelles and endogenous adenylates can lead to the production of ADP, which can stimulate respiration. This situation would lead to an overestimation of LEAK respiration measured in the absence of ADP, L(n) and subsequent inhibition of respiration by oligomycin, L(Omy).
AbsorbanceAAlso known as attenuation or extinction, absorbance (A) is a measure of the difference between the incident light intensity (I0) and the intensity of light emerging from a sample (I). It is defined as: A = log (I0/I)
Absorbance spectrumWhen light enters a sample, the amount of light that it absorbs is dependent upon the wavelength of the incident light. The absorbance spectrum is the curve derived by plotting the measured absorbance against the wavelength of the light emerging from the sample over a given wavelength range. An absorbance spectrum may be characterised by peaks and troughs (absorbance maxima and minima) that can be used to identify, and sometimes quantify, different absorbing substances present in a sample.
AbsorptionAbsWhen light enters a sample and emerges with an intensity (I), absorption (Abs) is the fraction of the light absorbed by the sample compared with the incident light intensity (I0): Abs = 1-I/I0. Absorption can also be expressed as Abs = 1-T, where T is the transmittance.
Absorption spectrumAn absorption spectrum is similar to an absorbance spectrum of a sample, but plotted as a function of absorption against wavelength.
AbundanceIn chemistry or physics, abundance or natural abundance refers to the amount of a chemical element isotope existing in nature. The abundance of an isotope on the Earth may vary depending on the place, but remains relatively constant in time (on a short-term scale). In a chemical reaction, the reactant is in abundance when the quantity of a substance is enough (or high) and constant during the reaction. Relative abundance represents the percentage of the total amount of all isotopes of the element. The relative abundance of each isotope in a sample can be identified using mass spectrometry.
Accelerationa, g [m·s-2]Acceleration, a, is the change of velocity over time [m·s-2].
a = dv/dt
The symbol g is used for acceleration of free fall. The standard acceleration of free fall is defined as gn = 9.80665 [m·s-2].
AcclimationAcclimation is an immediate time scale adaptation expressing pheotypic plasticity in response to changes of a single variable under controlled laboratory conditions.
AcclimatizationAcclimatization is an immediate time scale adaptation expressing phenotypic plasticity in response to changes of habitat conditions and life style where several variables may change simultaneously.
AccuracyThe accuracy of a method is the degree of agreement between an individual test result generated by the method and the true value.
Acetyl-CoA, C23H38N7O17P3S, is a central piece in metabolism involved in several biological processes, but its main role is to deliver the acetyl group into the TCA cycle for its oxidation. It can be synthesized in different pathways: (i) in glycolysis from pyruvate, by pyruvate dehydrogenase, which also forms NADH; (ii) from fatty acids β-oxidation, which releases one acetyl-CoA each round; (iii) in the catabolism of some amino acids such as leucine, lysine, phenylalanine, tyrosine and tryptophan.
In the mitochondrial matrix, acetyl-CoA is condensed with oxaloacetate to form citrate through the action of citrate synthase in the tricarboxylic acid cycle. Acetyl-CoA cannot cross the mitochondrial inner membrane but citrate can be transported out of the mitochondria. In the cytosol, citrate can be converted to acetyl-CoA and be used in the synthesis of fatty acid, cholesterol, ketone bodies, acetylcholine, and other processes.
Aconitase is a TCA cycle enzyme that catalyzes the reversible isomerization of citrate to isocitrate. Also, an isoform is also present in the cytosol acting as a trans-regulatory factor that controls iron homeostasis at a post-transcriptional level.
ActivityaThe activity (relative activity) is a dimensionless quantity related to the concentration or partial pressure of a dissolved substance. The activity of a dissolved substance B equals the concentration, cB [mol·L-1], at high dilution divided by the unit concentration, c° = 1 mol·L-1:
aB = cB/c°

This simple relationship applies frequently to substances at high dilutions <10 mmol·L-1 (<10 mol·m-3). In general, the concentration of a solute has to be corrected for the activity coefficient (concentration basis), γB,

aB = γB·cB/c°

At high dilution, γB = 1. In general, the relative activity is defined by the chemical potential, µB

aB = exp[(µB-µ°)/RT]
Acyl-CoA oxidaseAcyl-CoA oxidase is considered as a rate-limiting step in peroxysomal β-oxidation, which carries out few β-oxidation cycles, thus shortening very-long-chain fatty acids (>C20). Electrons are directly transferred from FADH2 to O2 with the formation of H2O2.
AdaptationAdaptation is an evolutionary time scale expression of phenotypic plasticity in response to selective pressures prevailing under various habitat conditions.
Add Graph/Delete bottom graphThe active graph is selected by a left click into the graph. The active graph is highlighted and indicated by the Oroboros logo.

Add: A new graph is added at the bottom of the screen. Select plots for display in the new graph, Ctrl+F6

Delete: By clicking Delete bottom graph in the Graph-menu in DatLab, the bottom graph is deleted, which reappears with the same layout by Add.
Adenine nucleotide translocaseANTThe adenine nucleotide translocator, ANT, exchanges ADP for ATP in an electrogenic antiport across the inner mt-membrane. The ANT is inhibited by atractyloside, carboxyatractyloside and bongkrekik acid. The ANT is a component of the phosphorylation system.
Adenine nucleotidesANAdenine nucleotides, which are also sometimes referred to as adenosines or adenylates, are a group of organic molecules including AMP, ADP and ATP. These molecules present the major players of energy storage and transfer.
Adenylate kinaseADKAdenylate kinase, which is also called myokinase, is a phosphotransferase enzyme that is located in the mitochondrial intermembrane space and catalyzes the rephosphorylation of AMP to ADP in the reaction ATP + AMP ↔ ADP + ADP.
Advancementdtrξ [MU]In an isomorphic analysis, any form of flow is the advancement of a process per unit of time, expressed in a specific motive unit [MU∙s-1], e.g., ampere for electric flow or current, Iel = delξ/dt [A≡C∙s-1], watt for thermal or heat flow, Ith = dthξ/dt [W≡J∙s-1], and for chemical flow of reaction, Ir = drξ/dt, the unit is [mol∙s-1] (extent of reaction per time). The corresponding motive forces are the partial exergy (Gibbs energy) changes per advancement [J∙MU-1], expressed in volt for electric force, ΔelF = ∂G/∂elξ [V≡J∙C-1], dimensionless for thermal force, ΔthF = ∂G/∂thξ [J∙J-1], and for chemical force, ΔrF = ∂G/∂rξ, the unit is [J∙mol-1], which deserves a specific acronym [Jol] comparable to volt [V]. For chemical processes of reaction (spontaneous from high-potential substrates to low-potential products) and compartmental diffusion (spontaneous from a high-potential compartment to a low-potential compartment), the advancement is the amount of motive substance that has undergone a compartmental transformation [mol]. The concept was originally introduced by De Donder [1]. Central to the concept of advancement is the stoichiometric number, νi, associated with each motive component i (transformant [2]).

In a chemical reaction r the motive entity is the stoichiometric amount of reactant, drni, with stoichiometric number νi. The advancement of the chemical reaction, drξ [mol], is defined as,

drξ = drni·νi-1

The flow of the chemical reaction, Ir [mol·s-1], is advancement per time,

Ir = drξ·dt-1

This concept of advancement is extended to compartmental diffusion and the advancement of charged particles [3], and to any discontinuous transformation in compartmental systems [2],

Advantage of preprintsThe advantages of preprints, the excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences are discussed by N Bhalla (2016).
AerobicoxThe aerobic state of metabolism is defined by the presence of oxygen (air) and therefore the potential for oxidative reactions (ox) to proceed, particularly in oxidative phosphorylation (OXPHOS). Aerobic metabolism (with involvement of oxygen) is contrasted with anaerobic metabolism (without involvement of oxygen): Whereas anaerobic metabolism may proceed in the absence or presence of oxygen (anoxic or oxic conditions), aerobic metabolism is restricted to oxic conditions. Below the critical oxygen pressure, aerobic ATP production decreases.
Affinity of reactionA [J·mol-1]The concept of affinity and hence chemical force is deeply rooted in the notion of attraction (and repulsion) of alchemy, which was the foundation of chemistry originally, but diverted away from laboratory experiments towards occult secret societies [1].** Newton's extensive experimental alchemical work and his substantial written track record on alchemy (which he did not publish) is seen today as a key inspiration for his development of the concept of the gravitational force [2-4]. This marks a transition of the meaning of affinity, from the descriptive 'adjacent' (proximity) to the causative 'attractive' (force) [5]. Correspondingly, Lavoisier (1790) equates affinity and force [6]: “... the degree of force or affinity with which the acid adheres to the base” [5]. By discussing the influence of electricity and gravity on chemical affinity, Liebig (1844) considers affinity as a force [7]. This leads to Guldberg and Waage's mass action ratio ('Studies concerning affinity', 1864; see [5]), the free energy and chemical affinity of Helmholtz (1882 [8]), and chemical thermodynamics of irreversible processes [9], where flux-force relations are center stage [10].

According to the IUPAC definition, the affinity of reaction, A [J·mol-1], equals the negative molar Gibbs energy of reaction [11], which is the negative Gibbs force of reaction (derivative of Gibbs energy per advancement of reaction [12]):

-A = ΔrF = ∂G/∂rξ
The historical account of affinity is summarized by concluding, that today affinity of reaction should be considered as an isomorphic motive force and be generalized as such. This will help to (1) avoid confusing reversals of sign conventions (repulsion = negative attraction; pull = negative push), (2) unify symbols across classical and nonequilibrium thermodynamics [12,13], and thus (3) facilitate interdisciplinary communication by freeing ourselves from the alchemical, arcane scientific nomenclature.
Allegations of research misconductAllegations of research misconduct are handled with care. Publishers and editors shall take reasonable steps to identify and prevent the publication of papers where research misconduct has occurred, including plagiarism, citation manipulation, and data falsification/fabrication, among others. In no case shall a journal or its editors encourage such misconduct, or knowingly allow such misconduct to take place. In the event that a journal's publisher or editors are made aware of any allegation of research misconduct relating to a published article in their journal, the publisher or editor shall follow COPE's guidelines (or equivalent) in dealing with allegations.
Alternative oxidaseAOXAlternative quinol oxidases AOX are membrane-bound enzymes capable of supporting cyanide- and antimycin A-resistant mitochondrial respiration. AOX catalyzes the oxidation of ubiquinol and the reduction of oxygen to water in a four-electron process. As this bypasses several proton-translocating steps, induction of this alternative pathway is associated with a reduction of ATP production per oxygen consumed. AOX is found in most plants (including microalgae), many fungi and protists, but is not expressed in animals. AOX is inhibited by salicylhydroxamic acid (SHAM). Expression and activity of the enzyme are modified by environmental conditions such as temperature, oxidative stress, nutrient availability, and pathogens such as viruses.
Ammonia solution concentratedNH3Concentrated ammonia solution (25 % - 30 % ammonium hydroxide solution, ammonia) is used for the service of the polarographic oxygen sensor OroboPOS. After opening the commercial solution, the concentration of ammonia may decline during storage and may render the ammonia stock ineffective for sensor service. Source: A commercially available solution from a drugstore is sufficient for this cleaning purpose
Amount of substancen [mol]The amount of substance, n, is a base physical quantity, and the corresponding SI unit is the mole [mol]. Amount of substance (sometimes abbreviated as 'amount' or 'chemical amount') is proportional to the number NX of specified elementary entities X, and the universal proportionality constant is the reciprocal value of the Avogadro constant (SI),
nX = NX·NA-1

nX contained in a system can change due to internal and external transformations,

dnX = dinX + denX

In the absence of nuclear reactions, the amount of any atom is conserved, e.g., for carbon dinC = 0. This is different for chemical substances or ionic species which are produced or consumed during the advancement of a reaction, r,

Amount dn.png
A change in the amount of Xi, dni, in an open system is due to both the internal formation in chemical transformations, drni, and the external transfer, deni, across the system boundaries. dni is positive if Xi is formed as a product of the reaction within the system. deni is negative if Xi flows out of the system and appears as a product in the surroundings (Cohen 2008 IUPAC Green Book).
Amp calibration - DatLabAmp calibration indicates the calibration of the amperometric O2k-channel.
AmpereAThe ampere, symbol A, is the SI unit of electric current. It is defined by taking the fixed numerical value of the elementary charge e to be 1.602 176 634 × 10−19 when expressed in the unit C, which is equal to A s, where the second is defined in terms of ΔνCs.
Amperometric,AmpF7After selection of the Amperometric, Amp channel in the O2k configuration, an Amperometric, Amp tab will appear in the O2k control [F7] window. Set the desired light intensity (0-1600) in the field ´Fluo intensity´ and the desired amplification of the signal (1-1000) in the field ´Gain for Fluo sensor´in the Amperometric, Amp window followed by a left-click Send to O2k. Switching off the illumination before each fluorometric measurement is routinely required.
Amplex UltraRedAmRAmplex® UltraRed (AmR) is used as an extrinsic fluorophore for measurement of hydrogen peroxide production (ROS) by cells or mitochondrial preparations. The reaction of H2O2 and AmR is catalyzed by horseradish peroxidase to produce the red fluorescent compound resorufin (excitation wavelength 563 nm, emission 587 nm; the fluorescent product according to the supplier is called UltroxRed in the case of Amplex® UltraRed which has a very similar structure to resorufin). The change of emitted fluorescence intensity is directly proportional to the concentration of H2O2 added, whereby the H2O2 is consumed.
AmplitudeThe amplitude of the absorbance spectrum can be described in terms of the absorbance differences between the characteristic peaks (absorbance maxima) and troughs (absorbance minima) (see absorbance spectrum) for substances present in the sample.
AmytalAmyAmytal sodium salt (synonym: amobarbital; 5-Ethyl-5-isoamylbarbituric acid) is a barbiturate drug and an inhibitor of Complex I.
AnaerobicAnaerobic metabolism takes place without the use of molecular oxygen, in contrast to aerobic metabolism. The capacity for energy assimilation and growth under anoxic conditions is the ultimate criterion for facultative anaerobiosis. Anaerobic metabolism may proceed not only under anoxic conditions or states, but also under hyperoxic and normoxic conditions (aerobic glycolysis), and under hypoxic and microxic conditions below the limiting oxygen pressure.
AnaplerosisAnaplerosis is the process of formation of intermediates of the tricarboxylic acid cycle. Malic enzyme (mtME), phosphoenolpyruvate carboxykinase (PEPCK), propionyl-CoA carboxylase, pyruvate carboxylase and proline dehydrogenase play important roles in anaplerosis.
Anaplerotic pathway control stateaAnaplerotic pathway control states are fuelled by single substrates which are transported into the mitochondrial matrix and increase the pool of intermediates of the tricarboxylic acid cycle. Malic enzyme (mtME), phosphoenopyruvate carboxykinase (PEPCK), propionyl-CoA carboxylase, and pyruvate carboxylase play important roles in anaplerosis. The glutamate-anaplerotic pathway control state and malate-anaplerotic pathway control state are the most important anaplerotic substrate control states (aN).
AnoxicanoxIdeally the term anoxic (anox, without oxygen) should be restricted to conditions where molecular oxygen is strictly absent. Practically, effective anoxia is obtained when a further decrease of experimental oxygen levels does not elicit any physiological or biochemical response. The practical definition, therefore, depends on (i) the techiques applied for oxygen removal and minimizing oxygen diffusion into the experimental system, (ii) the sensitivity and limit of detection of analytical methods of measuring oxygen (O2 concentration in the nM range), and (iii) the types of diagnostic tests applied to evaluate effects of trace amounts of oxygen on physiological and biochemical processes. The difficulties involved in defining an absolute limit between anoxic and microxic conditions are best illustrated by a logarithmic scale of oxygen pressure or oxygen concentration. In the anoxic state (State 5), any aerobic type of metabolism cannot take place, whereas anaerobic metabolism may proceed under oxic or anoxic conditions.
Antimycin AAmaAntimycin A is an inhibitor of Complex III (CIII). It binds to the Qi site of CIII and inhibits the transfer of electrons from heme bH to oxidized Q (Qi site inhibitor). High concentrations of antimycin A also inhibit acyl-CoA oxidase and D-amino acid oxidase.
Ap5AAp5AP1,P5-Di(adenosine-5')pentaphosphate (Ap5A) is an inhibitor of adenylate kinase (ADK), the enzyme which rephosphorylates AMP to ADP, consuming ATP (ATP + AMP ↔ 2 ADP).
Aqua destillataa.d.Aqua destillata (a.d.) is the Latin name for distilled water, H2O. When a.d. is used in various solution protocols, it may indicate that water with the highest possible quality or lowest possible level of impurities should be used, as may be reached not only with distilled water but also with high-purity deionised water.
ArXiv preprint serverarXivarXiv is a classic preprint server initiated in 1991 by Paul Ginsparg. {Quote: is a highly-automated electronic archive and distribution server for research articles. Covered areas include physics, mathematics, computer science, nonlinear sciences, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. arXiv is maintained and operated by Cornell University with guidance from the arXiv Scientific Advisory Board and the arXiv Member Advisory Board, and with the help of numerous subject moderators. ~ end of Quote}. arXiv rejects abstracts that are submitted without accompanying paper.
ArtemisininArtemisinin and various derivatives are potent anti-malaria drugs which have additionally anti-tumorigenic effects, particularly when targeted at mitochondria. The anti-malaria effect is associated with artemisinin's action on heme. Mitochondria are involved in the synthesis of heme, and may play additional roles in the anti-tumorigenic effect of artemisinin.
AscorbateAsIn respiratory assays for cytochrome c oxidase activity (Complex IV, CIV), ascorbate is added as regenerating system to maintain TMPD in a reduced state. It has to be titrated into the respiration medium prior to the addition of TMPD, otherwise the autoxidation reaction velocity is permanently elevated.
Asia Society for Mitochondrial Research and MedicineASMRM
The Asia Society for Mitochondrial Research and Medicine (ASMRM) was founded in 2003 to share the latest knowledge on mitochondrial research.
AspirinAspirin is a widely applied drug that requires dosage adjusted to individual body mass. It is a non-selective COX inhibitor and exerts an effect on long-chain fatty acid transport into mitochondria.
AssayAn experimental assay is a method to obtain a measurement with a defined instrument on a sample or subsample. Multiple assay types may be applied on the same sample or subsample, if the measurement does not destroy it. For instance, the wet weight of a permeabilized muscle fibre preparation can be determined based on a specific laboratory protocol (gravimetric assay), maintaining the functional integrity of the sample, which then can be used in a respirometric assay, followed by a spectrophotometric assay for measurement of protein content. The experimental design determines which types of assays have to be applied for a complete experiment. Destructive assays, such as determination of protein content or dry weight, can be applied on a sample only after performing a respirometric assay, or on a separate subsample. The experimental variability is typically dominated by the assay with the lowest resolution or signal to noise ratio. The signal to noise ratio may be increased by increasing the number, n, of repetitions of measurements on subsamples. Evaluation of procedural variation ('experimental noise') due to instrumental resolution and handling requires subsampling from homogenous samples.
AtractylosideAtrAtractyloside is an inhibitor of the adenine nucleotide translocator (ANT). It is an extremely toxic glycoside that inhibits oxidative phosphorylation by blocking the transfer of adenosine nucleotides through the mitochondrial membrane.
Attached cellsMany cell types are grown in culture as attached cells, such as endothelial or neuronal cells in a monolayer.
AttributeAttribute in general is a characteristic or property. In databases an attribute describes a column in a table. Rows then represent the according attribute values.
AuranofinAFAuranofin (AF) is a gold complex which inhibites thioredoxin reductase (TrxR).
Automatic pan - DatLabAutomatic pan (only for real-time data recording) toggles automatic panning on/off by clicking in the O2k status line. If it is on (green), the time range is maintained while the time axis always shows the currently recorded data, i.e. the value of the offset (minimum value) increases as experimental time proceeds. If it is off (yellow), the time axis is static. This allows for manually panning backwards to observe previous sections of the experiment at a given time range. In this mode, the actual experimental time may be off-scale. Toggle between "Pan auto" and "Pan off" by a left-click on the text. It does not influence continuous data recording. It is recommended to maintain automatic panning on during the experiment, except for specifically viewing earlier sections of the experiment.
AutoscaleAutoscale zooms in or out of the selected period with Autoscale time axis, Autoscale Y1 (Y2) axes and Automatic pan.
Autoscale Y1 (Y2) axesAutoscale Y1 (Y2) axes: Autoscaling the measured values (full data range) on the Y1 (Y2) axis in the selected plot.
Autoscale time axisAutoscale time axis gives an overview of the entire experimental period.
AutoxidationThis definition is insufficient and needs elaboration. Autoxidation is a slow process implying oxidation of carbohydrates through oxygen in open air, leading to a primary formation of peroxides and hydroperoxides. UV radiation can speed up this process.
AveragingIn order to improve the signal-to-noise ratio a number of sequential spectra may be averaged over time. The number of spectra to be averaged can be set prior to carrying out the measurements, or afterwards during data analysis.
Avogadro constantNA [x·mol-1]
Table Physical constants.png
{Quote} The Avogadro constant NA is a proportionality constant between the quantity amount of substance (with unit mole) and the quantity for counting entities ... One mole contains exactly 6.022 140 76 × 1023 elementary entities. This number is the fixed numerical value of the Avogadro constant, NA, when expressed in the unit mol−1 and is called the Avogadro number {Bureau International des Poids et Mesures 2019 The International System of Units (SI) end of quote}. Thus the Avogadro constant NA has the SI unit 'per mole' [mol-1], but more strictly the unit for counting entities per amount is 'units per mole' [x·mol-1] (compare elementary charge). Therefore, NA is 'count per amount' with units 'counting units per mole'. The Avogadro constant times elementary charge is the Faraday constant.
AzideAzdSodium azide is an inhbitor of cytochrome c oxidase (COX, CcO).
BAM15BAM152-fluorophenyl){6-[(2-fluorophenyl)amino](1,2,5-oxadiazolo[3,4-e]pyrazin-5-yl)}amine (BAM15) is a protonophore or uncoupler of oxidative phosphorylation detected in a screen for uncoupling agents exerting less toxicity than commonly used uncouplers and first described by Kennwood et al. 2013. In their comparison of BAM15 with FCCP it was shown to increase oxygen flux to a similar extent as the classical uncoupler, to display a much broader range of concentrations inducing maximum respiration, to stimulate no formation of H2O2, to leave cellular membrane potential unaffected, and to ultimately exert less cytotoxicity.
BME cutoff pointsBME cutoffObesity is defined as a disease associated with an excess of body fat with respect to a healthy reference condition. Cutoff points for body mass excess, BME cutoff points, define the critical values for underweight (-0.1 and -0.2), overweight (0.2), and various degrees of obesity (0.4, 0.6, 0.8, and above). BME cutoffs are calibrated by crossover-points of BME with established BMI cutoffs.
Background stateYThe background state Y (background rate YX) is the non-activated or inhibited respiratory state at background rate, which is low in relation to the higher rate ZX in the reference state Z. The transition from the background state to the reference state is a step change. A metabolic control variable X (substrate, activator) is added to the background state to stimulate flux to the level of the reference state. Alternatively, the metabolic control variable X is an inhibitor, which is present in the background state Y, but absent in the reference state Z. The background state is the baseline of a single step in the definition of the flux control efficiency. In a sequence of step changes, the common baseline state is the state of lowest flux in relation to all steps, which can be used as a baseline correction.
BalanceIn transmission spectrophotometry blank cuvettes are used to record the incident light intensity (I0) prior to absorbance measurements. (See white balance for reflectance spectrophotometry, remittance spectrophotometry).
BandwidthBandwidth is measured in nanometers in terms of the full width half maximum of a peak. This is the portion of the peak that is greater than half of the maximum intensity of that peak.
Barth SyndomeBTHSBarth Syndome (BTHS) is an X-linked genetic condition that is caused by a mutation in the tafazzin gene (taz). This mutation causes cardiolipin abnormalities, cardiomyopathy, neutropenia, muscle weakness, growth delay, and exercise intolerance.


Contributed by Sparagna GC 2016-04-24
Base quantities and countTemplate:Base quantities and count
Baseline stateThe baseline state in a sequence of step changes is the state of lowest flux in relation to all steps, which can be used as a baseline correction. Correction for residual oxygen consumption, ROX, is an example where ROX is the baseline state. In a single step, the baseline state is equivalent to the background state.
Beer-Lambert lawB-L lawThis law states that the transmittance (T) of light though a sample is given by: T = e-εbc, where ε is the molar extinction coefficient, b is the pathlength of the light through the cuvette (in mm) and c is the concentration of the pigment in the sample (in mM). Transforming this equation, it can be seen that the absorbance of light (A) is simply given by A = εbc.
BiasThe bias is defined as the difference between the mean of the measurements and the reference value. In general, the measuring instrument calibration procedures should focus on establishing and correcting it.
BioRxiv preprint server for biologybioRxivbioRxiv (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It was launched in 2013 by Cold Spring Harbor Laboratory Press in New York, and is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. bioRxiv is intended for rapid sharing of new research. Some review articles contain new data/analyses and may therefore be deemed appropriate. Reviews that solely summarize existing knowledge are not appropriate and neither are term papers, book excerpts, and undergraduate dissertations.
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BioblastsBBRichard Altmann (1894) defined the 'elementary organisms' as Bioblasts. He observed granula in cells stained with osmium and viewed ‘the protoplasm as a colony of bioblasts’. "Microorganisms and granula are at an equivalent level and represent elementary organisms, which are found wherever living forces are acting, thus we want to describe them by the common term bioblasts. In the bioblast, that morphological unit of living matter appears to be found." Altmann 1894; p. 141. Altmann is thus considered as the discoverer of mitochondria (the granula), which constitute together with the microorganisms the bioblasts (the elementary organisms). Bioblasts are the aliens with permanent residence in our cells (Gnaiger 2010).
Biochemical coupling efficiencyjE-LE-L coupling efficiency The biochemical coupling efficiency is the E-L coupling efficiency, (E-L)/E = 1-L/E. This is equivalent to the P-L control efficiency, (P-L)/P = 1-L/P, only at zero E-P excess capacity, when P = E). The biochemical coupling efficiency is independent of kinetic control by the phosphorylation system.
Biological contaminationBiological contamination may be caused by microbial growth in the O2k-Chamber or in the experimental medium.
Biological reference intervalBiological reference interval or reference interval is the central 95% interval of the distribution of reference values.
Biopsy preservation solutionBIOPSBiopsy preservation solution, for preservation of tissue samples, preparation of muscle fibres, and permeabilization with saponin.
BlankIn fluorometry and transmission spectrophotometry blank cuvettes (with no samples in them) are used to carry out the balance.
BlebbistatinBlebBlebbistatin is a widely used muscle and non-muscle myosin II-specific inhibitor that block contractile activity. Blebbistatin shows selectivity and high affinity for multiple class II myosins. Blebbistatin is commonly employed in respirometric experiments with permeabilized muscle fibers (pfi). Permeabilized muscle fibers are sensitive to low oxygen supply due to diffusion restrictions that limit mitochondrial respiration at the core of the fiber bundle. Therefore, hyperoxic conditions are required to counteract this limitation. Further studies have shown that the addition of blebbistatin in the respiration medium prevents fiber contraction, reduces the oxygen sensitivity and allows the study of ADP kinetics in pfi at normoxic oxygen levels. However, other studies described that the presence of blebbistatin does not prevent the oxygen dependence in pfi. Moreover, several limitations of blebbistatin i.e. low solubility in water, cytotoxicity and phototoxicity have been described.
Block temperatureThe block temperature of the Oroboros O2k is the continuously measured temperature of the copper block, housing the two glass chambers of the O2k. The block temperature is recorded by DatLab as one of the O2k system channels.
Blood cell preparationbcpBlood cell preparation (bcp) is one of the key steps in diagnostic protocols.
Blood plasmaPlasmaBlood plasma is the non-cellular component of the blood. Plasma lacks cellular components of the blood, red blood cells, white blood cells, and platelets. However, there are many proteins in plasma, i.e. fibrinogen, albumin and globulin. Both blood plasma and platelet-rich plasma maintain clotting activity after whole blood separation.
Blood serumSerumBlood serum is a purified plasma in which the coagulant components were removed from the blood plasma. It contains other substances, i.e. antibodies, antigens and hormones. Serum can be obtained by collecting the liquid phase after blood or plasma coagulation.
Body fat excessBFEIn the healthy reference population (HRP), there is zero body fat excess, BFE, and the fraction of excess body fat in the HRP is expressed - by definition - relative to the reference body mass, M°, at any given height. Importantly, body fat excess, BFE, and body mass excess, BME, are linearly related, which is not the case for the body mass index, BMI.
Body massm [kg]; M [kg·x-1]The body mass, M, is the mass (kilogram [kg]) of an individual (object) [x] and is expressed in units [kg/x]. Whereas the body weight changes as a function of gravitational force (you are weightless at zero gravity; your floating weight in water is different from your weight in air), your mass is independent of gravitational force, and it is the same in air and water.
Body mass excessBMEThe body mass excess, BME, is an index of obesity and as such BME is a lifestyle metric. The BME is a measure of the extent to which your actual body mass, M [kg/x], deviates from M° [kg/x], which is the reference body mass [kg] per individual [x] without excess body fat in the healthy reference population, HRP. A balanced BME is BME° = 0.0 with a band width of -0.1 towards underweight and +0.2 towards overweight. The BME is linearly related to the body fat excess.
Body mass indexBMIThe body mass index, BMI, is the ratio of body mass to height squared (BMI=M·H-2), recommended by the WHO as a general indicator of underweight (BMI<18.5 kg·m-2), overweight (BMI>25 kg·m-2) and obesity (BMI>30 kg·m-2). Keys et al (1972; see 2014) emphasized that 'the prime criterion must be the relative independence of the index from height'. It is exactly the dependence of the BMI on height - from children to adults, women to men, Caucasians to Asians -, which requires adjustments of BMI-cutoff points. This deficiency is resolved by the body mass excess relative to the healthy reference population.
Boltzmann constantk [J·x-1·K-1]
Table Physical constants.png
The Boltzmann constant k has the SI unit [J·K-1] (IUPAC), but more strictly the units for energy per particles per temperature is [J·x-1·K-1].

k = f·e-1, the electrochemical constant f times the elementary charge e.

k = R·NA-1, the gas constant R divided by the Avogadro constant NA.
Bongkrekik acidBkaBongkrekik acid is a selective and potent inhibitor of the adenine nucleotide translocator (ANT). Bka binds to the matrix (negative) site of ANT, opposite of carboxyatractyloside.
Bosy-Westphal 2009 Br J Nutr
Bound energyB [J]The bound energy change in a closed system is that part of the total energy change that is always bound to an exchange of heat,
dB = dU - dA [Eq. 1]
B = ∆H - ∆G [Eq. 2]

The free energy change (Helmoltz or Gibbs; dA or dG) is the total energy change (total inner energy or enthalpy, dU or dH) of a system minus the bound energy change.

Therefore, if a process occurs at equilibrium, when dG = 0 (at constant gas pressure), then dH = dB, and at deW = 0 (dH = deQ + deW; see energy) we obtain the definition of the bound energy as the heat change taking place in an equilibrium process (eq),

dB = T∙dS = deQeq [Eq. 3]
Bovine serum albumineBSABovine serum albumine is a membane stabilizer, oxygen radical scavenger, and binds Ca2+ and free fatty acids, hence the rather expensive essentially free fatty acid free BSA is required in mitochondrial isolation and respiration media. Sigma A 6003 fraction V.
Buffer ZBuffer ZMitochondrial respiration medium, Buffer Z, described by Perry 2011 Biochem J For composition and comparison see: Mitochondrial respiration media: comparison
CDGSH iron-sulfur domain proteinsCISD proteinsThe CDGSH iron-sulfur domain (CISDs) family of proteins uniquely ligate labile 2Fe-2S clusters with a 3Cys-1His motif. CISD1 and CISD3 have been demonstrated to localize to the outer mitochondrial membrane and mitochondrial matrix respectively, however their relationship to mitochondrial physiology remains ill-defined [1]. The best characterized member of the CISD family, CISD1, has been demonstrated to be involved in respiratory capacity, iron homeostasis, and ROS regulation
CECECE marking is a mandatory conformity marking for certain products sold within the European Economic Area (EEA).
CHNO-fuel substrateCHNOCHNO-fuel substrates are reduced carbon-hydrogen-nitrogen-oxygen substrates which are oxidized in the exergonic process of cell respiration. Mitochondrial pathways are stimulated by CHNO-fuel substrates feeding electrons into the ETS at different levels of integration and in the presence or absence of inhibitors acting on specific enzymes which are gate-keepers and control various pathway segments.
CI control ratioN/NS; CI/CI&IISee N/NS pathway control ratio
CII control ratioS/NS; CII/CI&IISee S/NS pathway control ratio
CalciumCaCa2+ is a major signaling molecule in both prokaryotes and eukaryotes. Its cytoplasmic concentration is tightly regulated by transporters in the plasma membrane and in the membranes of various organelles. For this purpose, it is either extruded from the cell through exchangers and pumps or stored in organelles such as the endoplasmic reticulum and the mitochondria. Changes in the concentration of the cation regulate numerous enzymes including many involved in ATP utilizing and in ATP generating pathways and thus ultimately control metabolic activity of mitochondria and of the entire cell. Measuring changes in Ca2+ levels is thus of considerable interest in the context of high-resolution respirometry.
Calcium GreenCaGCalcium Green denotes a family of extrinsic fluorophores applied for measurement of Ca2+ concentration.
Calcium retention capacityCRCCalcium retention capacity (CRC) is a measure of the capability of mitochondria to retain calcium, primarily in the form of calcium phosphates, in the mitochondrial matrix. By storing calcium in the form of osmotically inactive precipitates the mitochondria contribute to the buffering of cytosolic free calcium levels and thereby to the regulation of calcium-dependent cellular processes. Alterations of CRC are believed to be important in stress phenomena associated with energy limitation and have also been linked to neurodegenerative diseases (Starkov 2013 FEBS J). Experimentally, CRC has been indirectly assessed by determination of respiratory rates of isolated mitochondria which were exposed to continuously increasing levels of calcium by use of the Titration-Injection microPump TIP2k. The upper limit of CRC was observed as a sudden decrease of respiration presumed to reflect opening of the permeability transition pore (Hansson 2010 J Biol Chem).
CandelacdThe candela, symbol cd, is the SI unit of luminous intensity in a given direction. It is defined by taking the fixed numerical value of the luminous efficacy of monochromatic radiation of frequency 540 × 1012 Hz, Kcd, to be 683 when expressed in the unit lm W−1.
Canonical ensembleA canonical ensemble is the group of compartments enclosed in an isolated system H, with a smaller compartment A1 in thermal equilibrium with a larger compartment A2 which is the heat reservoir at temperature T. When A1 is large in the canonical sense, if its state can be described in terms of macroscopic thermodynamic quantities of V, T, and p merging with the state described as a probability distribution.
CarbohydrateCarbohydrates, also known as saccharides, are molecules composed of carbon, hydrogen and oxygen. These molecules can be divided by size and complexity into monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Glucose is a monosaccharide considered the primary source of energy in cells and a metabolic intermediate. This carbohydrate undergoes glycolysis, with the generation of pyruvate, that can enter the TCA cycle. Carbohydrates such as glucose and fructose may also be involved in the Crabtree effect.
Carbonyl cyanide m-chlorophenyl hydrazoneCCCPCarbonyl cyanide m-chlorophenyl hydrazone, CCCP (U; C9H5ClN4; FW = 204.62) is a protonophore (H+ ionophore) and is used as a potent chemical uncoupler of oxidative phosphorylation. Like all uncouplers, CCCP concentrations must be titrated carefully to evaluated the optimum concentration for maximum stimulation of mitochondrial respiration, particularly to avoid inhibition of respiration at higher CCCP concentrations.
Carboxy SNARF 1SNARFCarboxy SNARF® 1 is a cell-impermeant pH indicator dye. The pKa of ~7.5 makes it useful for measuring pH in the range of pH 7 to pH 8. The emission shifts from yellow-orange at low pH to deep red fluorescence at high pH. Ratiometric fluorometry, therefore, is applied at two emission wavelengths,such as 580 nm and 640 nm. Relative molecular mass: Mr = 453.45
CarboxyatractylosideCatCarboxyatractyloside, Cat, is a highly selective and potent inhibitor of the adenine nucleotide translocator (ANT). Cat stabilizes the nucleoside binding site of ANT on the cytoplasmic (positive) side of the inner membrane and blocks the exchange of matrix ATP and cytoplasmic ADP. It causes stabilization of the c conformation of ANT leading to permeability transition pore (PTP) opening, loss of mitochondrial membrane potential, and apoptosis.
CardiolipinCLCardiolipin, CL, is a double phospholipid (having 4 fatty acyl chains) in the mitochondrial inner membrane (mtIM) which plays an important role in mitochondrial bioenergetics. CL is involved in the mitochondria-dependent pathway of apoptosis, participates in the function and stabilization of mitochondrial respiratory complexes and supercomplexes and also contributes to mitochondrial integrity. Contributed by Sparagna G 2016-04-18
Cardiovascular Exercise Research GroupCERG

The Cardiovascular Exercise Research Group (CERG) was established in January 2008 and their research focuses on identifying the key cellular and molecular mechanisms underlying the beneficial effects of physical exercise on the heart, arteries and skeletal muscle in the context of disease prevention and management through experimental, clinical and epidemiological studies.

Since 2003 this research group organizes the biennial seminar "Exercise in Medicine" in Trondheim, Norway.
CarnitineCarCarnitine is an important factor for the transport of long-chain fatty acids bound to carnitine (carnitine acyltransferase) into the mitochondrial matrix for subsequent β-oxidation. There are two enantiomers: D- and L-carnitine. Only the L-isomer is physiologically active.
Carnitine O-octanoyltransferaseCOTCarnitine O-octanoyltransferase is a mitochondrial enzyme that transfers carnitine to octanoyl-CoA to form Coenzyme A and octanoylcarnitine: Octanoyl-CoA + L-carnitine ↔ CoA + L-octanoylcarnitine.
Carnitine acetyltransferaseCrATCarnitine acetyltransferase (CrAT) is located in the mitochondrial matrix and catalyses the formation of acetyl-carnitine from acetyl-CoA and L-carnitine and thus regulates the acetyl-CoA/free CoA ratio which is essential for pyruvate dehydrogenase complex (PDC) activity.
Carnitine acyltransferaseCarnitine acyltransferases mediate the transport of long-chain fatty acids across the inner mt-membrane by binding them to carnitine. First, long-chain fatty acids are activated by an energy-requiring step in which the fatty acid ester of CoA is formed enzymatically at the expense of ATP. The fatty acids then pass through the inner mt-membrane and enter the mitochondria as carnitine esters. The fatty acyl group is then transferred from carnitine to intramitochondrial CoA and the resulting fatty acyl CoA is used as a substrate in the fatty acid oxidation (FAO) cycle in the mt-matrix.
Carnitine palmitoyltransferase 2CPT-2Carnitine palmitoyltransferase 2 (CPT-2, also known as carnitine acyltransferase II) is part of the carnitine shuttle which is responsible for the mitochondrial transport of long-chain fatty acids. CPT-2 is located on the inner side of the mtIM and converts the acyl-carnitines (produced in the reaction catalyzed by carnitine palmitoyltransferase I) to carnitine and acyl-CoAs, which undergo ß-oxidation in the mitochondrial matrix. Free carnitines are transported out of the mitochondrial matrix in exchange for acyl-carnitines via an integral mtIM protein carnitine-acylcarnitine translocase (CACT). Short- and medium-chain fatty acids do not require the carnitine shuttle for mitochondrial transport.
Carnitine palmitoyltransferase ICPT 1Carnitine palmitoyltransferase I (CPT 1, also known as carnitine acyltransferase I) is a regulatory enzyme in mitochondrial long-chain acyl-CoA uptake and further oxidation. CPT 1 is associated with the outer mt-membrane and catalyses the formation of acylcarnitines from acyl-CoA and L-carnitine. In the next step, acyl-carnitines are transported to the mitochondrial matrix via carnitine-acylcarnitine translocase in exchange for free carnitine. In the inner side of the mtIM carnitine palmitoyltransferase 2 converts the acyl-carnitines to carnitine and acyl-CoAs. There are three enzyme isoforms: CPT 1A (liver type), CPT 1B (muscle type), CPT 1C (brain type). Isoforms have significantly different kinetic and regulatory properties. Malonyl-CoA is an endogenous inhibitor of CPT 1.
Carnitine-acylcarnitine translocaseCACTCarnitine-acylcarnitine translocase (CACT) is part of the carnitine shuttle which mediates the mitochondrial transport of long-chain fatty acids where the fatty acid oxidation occurs. CACT is an internal mt-IM protein and transports acyl-carnitines into the mitochondrial matrix in exchange for free carnitine.
Carrier control titrationsMost of the nonpolar compounds have to be diluted in organic solvents such as DMSO or acetonitrile in order to use them for the titrations in the SUIT protocols. However, the solvent (carrier) itself could affect the mitochondrial physiology and promote alterations that we need to take into account. For this reason, it is necessary to run in parallel to our treatment experiment a control experiment on which we will add a carrier control titration to test if it affects our sample or not.
CatalaseCtlCatalase catalyzes the dismutation of hydrogen peroxide to water and oxygen. Perhaps all cells have catalase, but mitochondria of most cells lack catalase. Cardiac mitochondria are exceptional in having mt-catalase activity (rat heart mitochondria: Radi et al 1991; mouse heart mitochondria: Rindler et al 2013). Hydroxylamine is an inhibitor of catalase, which is also inhibited by cyanide and azide.
Catalytic activitykatCatalytic activity of an enzyme is measured by an enzyme assay and is expressed in units of katal (kat [mol∙s-1]). More commonly (but not conforming to SI units or IUPAC recommendations) enzyme activity is expressed in units U [mol∙min-1].
CataplerosisCataplerosis is the exit of TCA cycle intermediates from the mt-matrix space.
Categories of SUIT protocolsSUIT-catg
SUIT-catg MitoPathway types.jpg

Categories of SUIT protocols group SUIT protocols according to all substrate types involved in a protocol (F, N, S, Gp), independent of the sequence of titrations of substrates and inhibitors which define the Electron-transfer-pathway states. The N-type substrates are listed in parentheses, independent of the sequence of titrations. ROX states may or may not be included in a SUIT protocol, which does not change its category. Similarly, the CIV assay may or may not be added at the end of a SUIT protocol, without effect on the category of a SUIT protocol.

  • F - ET-pathway-level 5: FADH2-linked substrates (FAO) with obligatory support by the N-linked pathway.
  • N - ET-pathway-level 4: NADH-linked substrates (CI-linked).
  • S - ET-pathway-level 3: Succinate (CII-linked).
  • Gp - ET-pathway-level 3: Glycerophosphate (CGpDH-linked).
  • Y(X)- In the SUIT general protocols Y makes reference to the ET-pathway state and X to the combination os substrates added for the corresponding pathway.
» MiPNet article
Cell SymposiaCellSymposiaLogo.jpg Organized by the editors of Cell Press's leading journals, Cell Symposia bring together exceptional speakers and scientists to discuss topics at the forefront of scientific research.
Cell count and normalization in HRRNceThe cell count Nce is the number of cells, expressed in the abstract unit [x] (1 Mx = 106 x). The elementary entity cell Uce [x] is the real unit, the 'single individual cell'. A cell count is the multitude or number N of cells, Nce = N·Uce (Gnaiger MitoFit Preprints 2020.4). Normalization of respiratory rate by cell count yields oxygen flow IO2 expressed in units [amol·s-1·x-1] (=10-18 mol·s-1·x-1).
Cell culture mediaCell culture media, like RPMI or DMEM, used for HRR of living cells.
Cell respirationCell respiration channels metabolic fuels into the chemiosmotic coupling (bioenergetic) machinery of oxidative phosphorylation, being regulated by and regulating oxygen consumption (or consumption of an alternative final electron acceptor) and molecular redox states, ion gradients, mitochondrial (or microbial) membrane potential, the phosphorylation state of the ATP system, and heat dissipation in response to intrinsic and extrinsic energy demands. See also respirometry. In internal or cell respiration in contrast to fermentation, redox balance is maintained by external electron acceptors, transported into the cell from the environment. The chemical potential between electron donors and electron acceptors drives the electron transfer pathway, generating a chemiosmotic potential that in turn drives ATP synthesis.
Cellular substratesCe; Cm1) Cellular substrates in vivo, endogenous; Ce. 2) Cellular substrates in vivo, with exogenous substrate supply from culture medium or serum; Cm.
Chamber volumeThe chamber volume of the O2k is 2.0 mL or 0.5 mL of aqueous medium with or without sample, excluding the volume of the stirrer and the volume of the capillary of the stopper. A modular extension of the O2k, the O2k-sV-Module, was specifically developed to perform high-resolution respirometry with reduced amounts of biological sample, and all components necessary for the smaller operation volume of 0.5 mL.
ChannelF7» See O2k signals and output
ChargeQel [C]Charge Qel is the quantity of electricity expressed in the SI unit coulomb [C]. QelX [C] indicates the charge carried by the quantity of a specified ion X.
Charge numberzXThe charge number of an ion X or electrochemical reaction with unit stoichiometric number of X is the particle charge [C·x-1] divided by the elementary charge [C·x-1]. The particle charge QNX is the charge per count of ions X or per ion X transferred in the reaction as defined in the reaction equation.
Chemical potentialµB [J/mol]The chemical potential of a substance B, µB [J/mol], is the partial derivative of Gibbs energy, G [J], per amount of B, nB [mol], at constant temperature, pressure, and composition other than that of B,
µB = (∂G/∂nB)T,p,nj≠B

The chemical potential of a solute in solution is the sum of the standard chemical potential under defined standard conditions and a concentration (activity)-dependent term,

µB = µB° + RT ln(aB)
The standard state for the solute is refered to ideal behaviour at standard concentration, c° = 1 mol/L, exhibiting infinitely diluted solution behaviour [1]. µB° equals the standard molar Gibbs energy of formation, ΔfGB° [kJ·mol-1]. The formation process of B is the transformation of the pure constituent elements to one mole of substance B, with all substances in their standard state (the most stable form of the element at 100 kPa (1 bar) at the specified temperature) [2].
Chinese Society of Mitochondrial Research and MedicineChinese-MitThe Chinese Society of Mitochondrial Research and Medicine (Chinese-Mit) is a member of ASMRM.
Chinese numeralsChinese numerals

The Arabic numeral system used today in China was introduced to China by the Europeans in the early 17th century. But the Chinese character-based number systems are still in use. The financial numerals are used only when writing an amount on a form for remitting money at a bank. They function as anti-fraud numerals.

The character 零 (zero) appeared very early in ancient Chinese writing. However, at that time, it did not mean "nothing", but "bits and pieces", "not much". 一百零五(105) means in Chinese: In addition to a hundred, there is a fraction of five. With the introduction of the Arabic numerals, 105 is exactly pronounced “one hundred zero five”, the character 零 corresponds exactly to the symbol 0. Thus, the character 零has the meaning of 0. But the character 〇 was one of the Chinese characters created and promulgated by the only empress (with greater achievements than countless emperors) in the history of China in 690 AD (much later than the invention of 0 in India) for the purpose of demonstrating her power. At that time the character 〇 meant “star”, representing a round planet. It is now used as a synonym for the 零 (zero).
Chloroplastspt?Chloroplasts (Greek chloros: green; plastes: the one who forms) are small structures within the cells that conduct photosynthesis. They are a type of organelle called plastids that are present in eukaryotic plant cells (algae, aquatic and terrestrial plants) and characterized by having two membranes and a high concentration of the pigment Chlorophyll. Like mitochondria, they originated through the endosymbiosis of a cyanobacteria by an early eukaryotic cell and they have their own DNA which replicates during cell division. In addition to photosynthesis, in their internal matrix called stroma they also carry out other metabolic functions within the plant cells such as fatty acid synthesis or amino acid synthesis.
ChlororespirationChlororespiration is the phenomenon by which oxygen is consumed by a putative respiratory electron transfer chain (ETC) within the thylakoid membrane of the chloroplasts and ATP is produced. It is a process that involves the interaction with the photosynthetic ETC in which the NAD(P)H dehydrogenase enzyme transfers electrons to oxygen molecules with the assistance of the photosynthetic Plastoquinone (PQ), which acts as a non-photochemical redox carrier. Initially described in the unicellular alga Chlamydomonas reindhartdii, chlororespiration was highly disputed for years until the discovery of a NAD(P)H-dehydrogenase (Ndh) complex (plastidic encoded) and plastid terminal oxidase (PTOX) (nuclear encoded) in higher-plant chloroplasts. The PTOX, which is homologous to the plant mitochondrial alternative oxidase, has the role of preventing the over-reduction of the PQ pool while the Ndh complexes provide a gateway for the electrons to form the ETC and consume oxygen. As a result of this process there is a cyclic electron flow around the Photosystem I (PSI) that has been reported to be activated under stress conditions acting as a photoprotection mechanism and could be involved in protecting against any other stress that implies the increase of ROS formation.
Choline dehydrogenaseCholine dehydrogenase (EC is bound to the inner mt-membrane, oxidizes choline in kidney and liver mitochondria, with electron transfer into the Q-junction, and is thus part of the Electron transfer pathway. Analogous to succinate dehydrogenase (CII), electron transfer from choline dehydrogenase is FAD-linked downstream to Q. Choline is an ET-pathway substrate types 3.
citrate, C6H5O7-3, is a tricarboxylic acid trianion, intermediate of the TCA cycle, obtained by deprotonation of the three carboxy groups of citric acid. Citrate is formed from oxaloacetate and acetyl-CoA through the catalytic activity of the citrate synthase. In the TCA cycle, citrate forms isocitrate by the activity of the aconitase. Citrate can be transported out of the mitochondria by the tricarboxylate transport, situated in the inner mitochondrial membrane. The transport occurs as an antiport of malate from the cytosol and it is a key process for fatty acid and oxaloacetate synthesis in the cytosol.
Citrate synthaseCSCondensation of oxaloacetate with acetyl-CoA yields citrate as an entry into the TCA cycle. CS is located in the mt-matrix. CS activity is frequently used as a functional marker of the amount of mitochondria (mitochondrial elementary marker, mtE) for normalization of respiratory flux.
CitreoviridinCitreoviridin is an inhibitor of the ATP synthase which, differently from the FO subunit binding inhibitor oligmycin, binds to the F1 subunit of the ATP synthase.
Close - DatLabCtrl+F4Close a DLD file. A window "Save changes to file?" pops up offering the options to close the file after saving the changes, or close the file without saving any modifications on the presently open file.
Closed chamberCThe O2k-chamber can be used as a closed system or open system. Gas bubbles must be avoided.
Coenzyme ACoACoenzyme A is a coenzyme playing an essential role in the tricarboxylic acid cycle (oxidation of pyruvate to acetyl-CoA) and fatty acid oxidation. CoA is a thiol that reacts with carboxylic acids to form CoA-activated thioesters.
Coenzyme QQ, CoQCoenzyme Q or ubiquinone (2,3-dimethoxy-5-methyl-6-polyprenyl-1,4-benzoquinone) was discovered in 1957 by the group of Crane. It is a lipid composed of a benzoquinone ring with an isoprenoid side chain, two methoxy groups and one methyl group. The length of the isoprenoid chain varies depending on the species; for example, six isoprenoid units (CoQ6) have been described as the most commonly found CoQ in Saccharomyces cerevisiae, eight units in Escherichia coli, (CoQ8), nine units in Caenorhabditis elegans and rodents (CoQ9), ten units in humans (CoQ10), and some species have more than one CoQ form, e.g. human and rodent mitochondria contain different proportions of CoQ9 and CoQ10. These redox compounds exist in three different forms: quinone (oxidized), quinol (reduced), and an intermediate semiquinone. More details » Q-junction.
Coenzyme Q2CoQ2; Q-2
Coenzyme Q2 or ubiquinone-2 or ubiquinone Q2 is a quinone derivate composed of a benzoquinone ring with an isoprenoid side chain consisting of two isoprenoid groups, with two methoxy groups, and with one methyl group. In HRR it is used to detect the redox changes of the Q-junction in conjunction with the Q-Module, since CoQ2 can react both with mitochondrial complexes (e.g. CI, CII and CIII) at their quinone-binding sites and with the detecting electrode.
Cole 2000 BMJ
Comma for separating a term and its abbreviation,Should we used a comma for separating a term and its abbreviation in the text? The SI Brochure frequently does not use a comma. The comma might be added, if it helps to clarify the distinction between the term and its abbreviation. The example “reduced Q fraction, Qr” – the sequence of Q and Qr may be confusing without comma. There will always be examples, where it is not clear, if a comma is needed.
ComorbidityComorbidities are common in obesogenic lifestyle-induced early aging. These are preventable, non-communicable diseases with strong associations to obesity. In many studies, cause and effect in the sequence of onset of comorbidities remain elusive. Chronic degenerative diseases are commonly obesity-induced. The search for the link between obesity and the etiology of diverse preventable diseases lead to the hypothesis, that mitochondrial dysfunction is the common mechanism, summarized in the term 'mitObesity'.
Company of ScientistsCompaSci
Company of Scientists
The Company of Scientists evolves as a concept for implementing scientific innovations on the market.
Comparison of respirometric methodsThe comparison of respirometric methods provides the basis to evaluate different instrumental platforms and different mitochondrial preparations, as a guide to select the best approach and to critically evaluate published results.
Complex ICIComplex I, NADH:ubiquinone oxidoreductase (EC, is an enzyme complex of the Electron transfer pathway, a proton pump across the inner mt-membrane, responsible for electron transfer to ubiquinone from NADH formed in the mt-matrix. CI forms a supercomplex with Complex III.
Complex I&II-linked substrate stateNSSee NS-pathway control state (previous: CI&II-linked)
Complex I-linked substrate stateNSee N-pathway control state (previous: CI-linked)
Complex IICIIComplex II or succinate:quinone oxidoreductase (SQR) is the only membrane-bound enzyme in the TCA cycle and is part of the Electron transfer pathway. The flavoprotein succinate dehydrogenase is the largest polypeptide of CII, located on the matrix face of the mt-inner membrane. Following succinate oxidation, the enzyme transfers electrons directly to the quinone pool.
Complex II-linked substrate stateSRot, SSee S-pathway control state (previous: CII-linked)
Complex IIICIIIComplex III or coenzyme Q : cytochrome c - oxidoreductase, sometimes also called the cytochrome bc1 complex is a complex of the electron transfer pathway. It catalyzes the reduction of cytochrome c by oxidation of coenzyme Q (CoQ) and the concomitant pumping of 4 protons from the cathodic (negative) mitochondrial matrix to the anodic (positive) intermembrane space.
Complex IVCIVComplex IV or cytochrome c oxidase is the terminal oxidase of the mitochondrial electron transfer system, reducing oxygen to water, with reduced cytochrome c as a substrate. Concomitantly to that, CIV pumps protons against the electrochemical protonmotive force. CIV is frequently abbreviated as COX or CcO. It is the 'ferment' (Atmungsferment) of Otto Warburg, shown to be related to the cytochromes discovered by David Keilin.
Concentrationc [mol·L-1]; C [x·L-1]Concentration [mol·L-1] is a volume-specific quantity for diluted samples s. In a concentration, the sample is expressed in a variety of formats: count, amount, charge, mass, energy. In solution chemistry, amount concentration is amount of substance nB per volume V of the solution, cB = [B] = nB·V-1 [mol·dm-3] = [mol·L-1]. The standard concentration, c°, is defined as 1 mol·L-1 = 1 M. Count concentration CX = NX·V-1 [x·L-1] is the concentration of the number NX of elementary entities X, for which the less appropriate term 'number concentration' is used by IUPAC. If the sample is expressed as volume Vs (e.g., VO2), then the 'volume-concentration' of Vs in V is termed 'volume fraction', Φs = Vs·V-1 (e.g., volume fraction of O2 in dry air, ΦO2) = 0.20946). Density is the mass concentration in a volume VS of pure sample S. A change of concentration, dcX, in isolated or closed systems at constant pressure is due to internal transformations (advancement per volume) only. In closed compressible systems (with a gas phase), the concentration of the gas changes, when pressure-volume work is performed on the system. In open systems, a change of concentration can additionally be due to external flow across the system boundaries.
Connect to O2kConnect to O2k connects DatLab with the O2k. Select the USB port (or Serial port) with the corresponding cable connecting your PC to the O2k. Select the subdirectory for saving the DLD file. Then data recording starts with experimental time set at zero.
Connection windowAfter starting DatLab either the Connection window opens automatically by default or open O2k control by pressing [F7] and select the communication port.
Convergent electron flown.a.
Convergent electron flow
Copy marksIn Copy marks, Marks in DatLab are copied from a seleted Plot to the active plot.
Copy to clipboardIn DatLab Copy to clipboard can be used to copy selected graphs or values and to paste them to your preferred program or file (e.g. Word, Excel).
Copyright{Quote} All preprints are posted with a Creative Commons CC BY 4.0 license, ensuring that authors retain copyright and receive credit for their work, while allowing anyone to read and reuse their work. {end of Quote}
CountNX [x]
Count NX is the number N of elementary entities of entity-type X. The single elementary entity UX is a countable object or event. NX is the number of objects of type X, whereas the term 'entity' and symbol X are frequently used and understood in dual-message code indicating both (1) the entity-type X and (2) a count of NX = 1 x for a single elementary entity UX. 'Count' is synonymous with 'number of entities' (number of particles such as molecules, or objects such as cells). Count is one of the most fundamental quantities in all areas of physics to biology, sociology, economy and philosophy, including all perspectives of the statics of countable objects to the dynamics of countable events. The term 'number of entities' can be used in short for 'number of elementary entities', since only elementary entities can be counted, and as long as it is clear from the context, that it is not the number of different entity types that are the object of the count.
Coupling-control efficiencyCoupling-control efficiencies are flux control efficiencies jZ-Y at a constant ET-pathway competent state.
Coupling-control protocolCCPA coupling-control protocol CCP induces different coupling control states at a constant electron-transfer-pathway state. Residual oxygen consumption (Rox) is finally evaluated for Rox correction of flux. The CCP may be extended, when further respiratory states (e.g. cell viability test; CIV assay) are added to the coupling control module consisting of three coupling control states. The term phosphorylation control protocol, PCP, has been introduced synonymous for CCP. » MiPNet article
Coupling-control ratioCCRCoupling-control ratios CCR are flux control ratios FCR at a constant mitochondrial pathway-control state. In mitochondrial preparations, there are three well-defined coupling states of respiration: LEAK respiration, OXPHOS, and Electron-transfer-pathway state (ET state). In these states, the corresponding respirtory rates are symbolized as L, P, and E. In living cells, the OXPHOS state cannot be induced, but in the ROUTINE state the respiration rate is R. A reference rate Z is defined by taking Z as the maximum flux, i.e. flux E in the ET-state, such that the lower and upper limits of the CCR are defined as 0.0 and 1.0. Then there are two mitochondrial CCR, L/E and P/E, and two CCR for living cells, L/E and R/E.
Coupling-control stateCCSCoupling-control states are defined in mitochondrial preparations (isolated mitochondria, permeabilized cells, permeabilized tissues, homogenates) as LEAK respiration, OXPHOS, and ET states, with corresponding respiration rates (L, P, E) in any electron-transfer-pathway state which is competent for electron transfer. These coupling states are induced by titration of ADP and uncouplers, and application of specific inhibitors of the phosphorylation pathway. In living cells, the coupling-control states are LEAK respiration, ROUTINE, and ET states of respiration with corresponding rates L, R, E, using membrane-permeable inhibitors of the phosphorylation system (e.g. oligomycin) and uncouplers (e.g. CCCP). Coupling-control protocols induce these coupling-control states sequentially at a constant electron-transfer-pathway state.
Coupling/pathway control diagramCPCD
SUIT protocols
Coupling/pathway control diagrams illustrate the respiratory states obtained step-by-step in substrate-uncoupler-inhibitor titrations in a SUIT protocol. Each step (to the next state) is defined by an initial state and a metabolic control variable, X. The respiratory states are shown by boxes. X is usually the titrated substance in a SUIT protocol. If X (ADP, uncouplers, or inhibitors of the phosphorylation system, e.g. oligomycin) exerts coupling control, then a transition is induced between two coupling-control states. If X (fuel substrates, e.g. pyruvate and succinate, or Electron transfer pathway inhibitors, e.g. rotenone) exerts pathway control, then a transition is induced between two Electron-transfer-pathway states. The type of metabolic control (X) is shown by arrows linking two respiratory states, with vertical arrows indicating coupling control, and horizontal arrows indicating pathway control. Marks define the section of an experimental trace in a given respiratory state (steady state). Events define the titration of X inducing a transition in the SUIT protocol. The specific sequence of coupling control and pathway control steps defines the SUIT protocol pattern. The coupling/pathway control diagrams define the categories of SUIT protocols (see Figure).
Cover-Slip black.JPG
A Cover-Slip should be placed on top of the O2k-Stopper to minimize contamination and evaporation of liquid extruding from the capillary of the stopper. The Cover-Slips do not exert any direct effect on oxygen backdiffusion into the O2k-chamber. Use the the Cover-Slip\black to avoid light penetration and disturbance of fluorescence signals and generally for optical measurements in the O2k.
Crabtree effectThe Crabtree effect describes the observation that respiration is frequently inhibited when high concentrations of glucose or fructose are added to the culture medium - a phenomenon observed in numerous cell types, particularly in proliferating cells, not only tumor cells but also bacteria and yeast. The Pasteur effect (suppression of glycolysis by oxygen) is the converse of the Crabtree effect (suppression of respiration by high concentration of glucose or fructose).
CreatineCrCreatine is a nitrogenous organic acid that occurs naturally in vertebrates and helps primarily muscle cells to supply energy by increasing the formation of adenosine triphosphate (ATP).
Creatine kinaseCKThe mitochondrial creatine kinase, also known as phosphocreatine kinase (CPK), facilitates energy transport with creatine and phosphocreatine as diffusible intermediates.
Creative Commons Attribution LicenseOpen Access preprints (not peer-reviewed) and articles (peer-reviewed) distributed under the terms of the Creative Commons Attribution License allow unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. © remains with the authors, who have granted the publisher license in perpetuity.
Critical oxygen pressurepcThe critical oxygen pressure, pc, is defined as the partial oxygen pressure, pO2, below which aerobic catabolism (respiration or oxygen consumption) declines significantly. If anaerobic catabolism is activated simultaneously to compensate for lower aerobic ATP generation, then the limiting oxygen pressure, pl, is equal to the pc. In many cases, however, the pl is substantially lower than the pc.
Cross-linked respiratory statesCLRSCoordinated respiratory SUIT protocols are designed to include cross-linked respiratory states, which are common to these protocols. Different SUIT protocols address a variety of respiratory control steps which cannot be accomodated in a single protocol. Cross-linked respiratory states are included in each individual coordinated protocol, such that these states can be considered as replicate measurements, which also allow for harmonization of data obtained with these different protocols.
CurcuminCurcumin has been shown to possess significant anti-inflammatory, anti-oxidant, anti-carcinogenic, anti-mutagenic, anti-coagulant and anti-infective effects. The protective effects of curcumin on rat heart mitochondrial injuries induced by in vitro anoxia–reoxygenation were evaluated by Xu et al 2013. It was found that curcumin added before anoxia or immediately prior to reoxygenation exhibited remarkable protective effects against anoxia–reoxygenation induced oxidative damage to mitochondria.
Custom labelA Custom label can be entered in this box to rename the axis label. Two lines are available for the axis name and unit.
Custom-made stoppersStoppers can be custom-made for applications with user-specific sensors according to customer specifications.
CuvettesCuvettes are used in fluorometry and transmission spectrophotometry to contain the samples. Use of the term 'cells' for cuvettes is discouraged, to avoid confusion with 'living cells'. Traditionally cuvettes have a square cross-section (10 x 10 mm). For many applications they are made of transparent plastic. Glass cells are used where samples may contain plastic solvents, and for some applications requiring measurements below 300 nm, quartz glass or high purity fused silica cuvettes may be necessary.
CyanideKCNCyanide (usually added as KCN) is a competitive inhibitor of cytochcrome c oxidase (CIV). Inhibition is reversed by pyruvate and high oxygen levels.
Cyclic voltammetryCVCyclic voltammetry (CV) is a type of electrochemical measurement which is applied with the Q-Module as quality control to

(1) determine the oxidation and reduction peak potentials of Coenzyme Q in the specific experimental condition, (2) check the quality of the Q-Sensor, and (3) test the interference of chemicals used in the HRR assay with the Q-Sensor. In CV, the Q-Sensor with the three-electrode system is used to obtain information about the analyte (CoQ) by measuring the current (I) as the electric potential (V) between two of the electrodes is varied. In CV the electric potential between the glassy carbon (GC) and the Ag/AgCl reference electrode changes linearly versus time in cyclical phases, while the current is detected between GC and platinum electrode (Pt). The detected current is plotted versus the applied voltage to obtain the typical cyclic voltammogram trace (Figure 1). The presence of substances that are oxidized/reduced will result in current between GC and Pt, which can be seen as characteristic peaks in the voltammogram at a defined potential. The oxidation or the reduction peak potential values are used to set the GC (integrated into the Q-Sensor) for a separate experiment to measure the Q redox state of a biological sample. The oxidation and reduction peak potentials can be influenced by 1) the respiration medium, 2) the type of CoQ, 3) the polarization window, 4) the scan speed, 5) the number of cycles, 6) the concentration of the analyte (CoQ), and 7) the initial polarization voltage. <be>

-See: MiPNet24.12 NextGen-O2k: Q-Module.
Cyclosporin ACsACyclosporin A (CsA) is a cyclic undecapeptide from an extract of soil fungi that binds the cyclophilin D and thus preventing the formation of the mitochondrial permeability transition pore. The interaction of CsA with the cyclophilin D is phosphate mediated but the full mechanism of interaction is not well understood. For example, the deficiency of cyclophilin D in KO models does not prevent mitochondria from permeability transition and from CsA inhibition. Moreover, it is also a is a calcineurin inhibitor and potent immunosuppressive agent used largely as a means of prophylaxis against cellular rejection after solid organ transplantation.
Cytochrome ccCytochrome c is a component of the Electron transfer-pathway (Electron transfer pathway) in mitochondria. It is a small heme protein loosely associated with the outer side of the inner mitochondrial membrane. The heme group of cytochrome c transfers electrons from Complex III to Complex IV. The release of cytochrome c into the cytoplasm is associated with apoptosis. Cytochrome c is applied in HRR to test the integrity of the mitochondrial outer membrane (cytochrome c control efficiency).
Cytochrome c control efficiencyjcThe cytochrome c control efficiency expresses the control of respiration by externally added cytochrome c, c, as a fractional change of flux from substrate state CHNO to CHNOc. In this flux control efficiency, CHNOc is the reference state with stimulated flux; CHNO is the background state with CHNO substrates, upon which c is added:
» MiPNet article
D-numberD###D number is the unique code given for each SUIT protocol. In the same SUIT protocol family (SUIT-###), there might be different protocols, specifically designed for different sample type (e.g., different mitochondrial preparations) or for different applications (e.g., O2, AmR, Fluo, MgG). Since the use of different kinds of sample or application may result in slightly different steps, each protocol receives a different D-number.
DTPADTPADTPA (Diethylenetriamine-N,N,N',N,N-pentaacetic acid, pentetic acid,(Carboxymethyl)imino]bis(ethylenenitrilo)-tetra-acetic acid) is a polyaminopolycarboxylic acid (like EDTA) chelator of metal cations. DTPA wraps around a metal ion by forming up to eight bounds, because each COO- group and and N-center serves a center for chelation. With transition metals the number of bounds is less than eight. The compound is not cell membrane permeable. In general, it chelates multivalent ions stronger than EDTA.
DatLab is the O2k-Software for Data Acquisition & Analysis, specifically developed for high-resolution respirometry with the O2k-FluoRespirometer.

The newest DatLab version is DatLab 7.4, included in the O2k-FluoRespirometer.

The minimum computer requirements are Intel-Core-2 or equivalent CPU, 2GB RAM and Windows XP. However, we recommend Intel i5 or equivalent CPU, 4GB RAM, Windows 10 and SSD. For the proper display of DatLab on your computer, please make sure the “Language settings” are set to English.
DatLab 2DL2DatLab 2 (DL2) is a MS-DOS programe. DL2 is still used for analysis of oxygen kinetics, after exporting files recorded in recent DatLab versions. A user-friendly O2-kinetics module is in preparation (DL8).
DatLab and SUIT protocolsThis is a brief summary of steps to be taken for performing a high-resolution respirometry experiment with SUIT protocols using the OROBOROS Oroboros O2k and DatLab software. (1) Search for a specific SUIT protocol name (go to MitoPedia: SUIT). The list of MitoPedia SUIT protocols can be sorted by categories of SUIT protocols (sorting by SUIT protocol name), which is listed as the 'abbreviation' of the SUIT protocol name. (2) Copy the template for Mark names into your DatLab subdirectory: DatLab\APPDATA\MTEMPLAT. (3) Copy the DatLab-Analysis template for this SUIT protocol. (4) Follow the link to the corresponding publication or MiPNet communication, where the pdf file describing the SUIT protocol is available. (5) A DatLab demo file may be available providing an experimental example. After each sequential titration, a mark is set on the plot for flux or flow. After having set all marks, pull down the 'Mark names' menu, select the corresponding SUIT protocol for mark names, and rename all marks. The Mark names template also provides standard values of the titration volume preceding each mark. (6) Go to 'Mark statistics' [F2], copy to clipboard, and paste into the sample tab in the DatLab-Analysis template.
  • SUIT protocol name: SUIT-011
  • Mark names in DatLab: 1GM;2D;2c;3S;4U;5Rot-
  • DatLab-Analysis template: SUIT_NS(GM)01.xlsx
  • MiPNet communciation: MiPNet12.23 FibreRespiration
  • DatLab demo file: MiPNet12.23 FibreRespiration.DLD
DatLab data fileDLDThe file type generated by DatLab is *.DLD.
DatLab error messagesCommon DatLab error messages and according actions and solutions are listed here.
DatLab installation
We recommend a 'clean install' for DatLab installation: rename your previous DatLab programme subdirectory (e.g. C:\DatLab_OLD). The standard Instrumental and SUIT DL-Protocols package is automatically implemented with the simple DatLab programme installation.
DatLab templatesDatLab templates can be imported for O2k-setups, graph layouts, mark names, TIP2k setups and marks statistics configurations.
See also » Manage setups and templates
DatLab-Analysis templatesGo in DatLab to Mark statistics (F2), select which type of marks you want to export ("All marks in plot" or "DL-Protocol marks", with 3 possibilities each), then click on [Copy to clipboard] to copy selected values and paste them to a DatLab-Analysis template for numerical and graphical data analysis.
DatLab-Upgrading\4.x-5.2DatLab-Upgrading\4.1-5.2: Upgrading DatLab 4.x to 5.2, incl. O2k-Manual, with free follow-up updates of DatLab 5.2. Discontinued: see higher DatLab version.
Data recording intervalF7The data recording interval is the time interval at which data is sampled with an instrument. In DatLab the data recording interval is set in the O2k control window. The system default value is 2 s. A lower data recording interval is selected for kinetic experiments, and when the volume-specific oxygen flux is high (>300 pmol O2·s-1·ml-1).
Technically, the O2k instrument (hardware) measures the sensor signal every 10ms (which is NOT the „data recording interval“). By the given data recording interval from DatLab (software) a discrete number of sensor signal points are taken to calculate an average value in the O2k (e.g. a data recording interval of 2 s can take 200 sensor signal points; a data recording interval of 0.5 s can take 50 sensor signal points). This average value is sent to DatLab and is recorded as a raw data point. However, there is a defined threshold: the O2k does not apply more than 200 sensor signal points to calculate the average for the raw data point. For example a data recording interval of 3 s could take 300 sensor signal points but only the 200 most recent sensor signal points are used for averaging.
DatasetA dataset is a collection of data. In the context of databases a dataset represents the collection of entries in a database-table. In this table columns represent attributes and rows display the according values of the entries.
De Onis 2007 Bull World Health Organization
Decimal marker and spaces between groups of numerals.A decimal marker is used to separate the integral part of numbers from the decimal part. The SI recommends: "the symbol for the decimal marker shall be either the point on the line or the comma on the line". In English language versions, the dot (point on the line) should be used uniquely as the decimal marker. To avoid ambiguities, BEC follows the SI recommendation that “Numbers may be divided in groups of three in order to facilitate reading; neither dots nor commas are ever inserted in the spaces between groups” (pages 183-184).
Default labelThe Default label is the system default value for the axis label. These labels are changed automatically, according to the selected channel and unit. To change this label enter a Custom label.
Delete - DatLabDelete a DLD file. The decision to delete a file containing no useful data can be made most easily when viewing the traces. Only available when disconnected from the O2k.
Delete pointsSelect Delete points in the Mark information window to remove all data points in the marked section of the active plot. See also Interpolate points and Restore points or Recalculate slope.
Densityρ, C, DDensity, mass density ρ = m·V-1 [kg·m-3], is mass m divided by volume V. Surface density ρA = m·A-1 [kg·m-2] (SI). For a pure sample S, the mass density ρS = mS·VS-1 [kg·m-3] is the mass m of pure sample S per volume VS of the pure sample. With density ρ thus defined, the 'amount density' of substance B is ρB = nB·VB-1 [mol·m-3]. This is not a commonly used expression, but the inverse is defined as the molar volume of a pure substance (IUPAC), Vm,B = VB·nB-1 [m3·mol-1]. The pure sample is a pure gas, pure liquid or pure solid of a defined elementary entity. The amount concentration, cB = nB·V-1 [mol·m-3] is the amount nB of substance B divided by the volume V of the mixture (IUPAC), and this is not called an 'amount density'. The term 'amount density' is reserved for an amount of substance per volume VS of the pure substance. This explicit distinction between 'density' related to the volume of the sample and 'concentration' related to the total volume of the mixture is very helpful to avoid confusion. Further clarification is required in cases, when the mass density ρs of the sample in the mixture differs from the mass density ρS of the pure sample before mixing. Think of a sample S of pure ethanol with a volume of 1 L at 25 °C, which is mixed with a volume of 1 L of pure water at 25 °C: after the temperature of the mixture has equilibrated to 25 °C, the total volume of the mixture is less than 2 L, such that the volume VS of 1 L pure ethanol has diminished to a smaller volume Vs of ethanol in the mixture; the density of ethanol in the mixture is higher than the density of pure ethanol (this is incomplete additivity). The volume Vs of sample s in a mixture is by definition smaller than the total volume V of the mixture. Sample volume VS and system volume V are identical, but this applies only to the case of a pure sample. Concentration is related to samples s per total volume V of the mixture, whereas density is related to samples S or s per volume VS = V or Vs < V, respectively (BEC 2020.1).
Derivative spectroscopyDerivative spectroscopy can be used to eliminate interfering artefacts or species. A first order derivative will remove a constant background absorbance across the spectral range. A second order derivative spectrum will remove a species whose absorbance is linearly dependent upon the wavelength, etc..
Deselect channelsF7Channels can be selected/deselected in DatLab in the O2k configuration. Deselect all O2k-MultiSensor channels in O2k-Core applications. Select only the specifically used channels in O2k-MultiSensor applications.
DetectorA detector is a device that converts the light falling upon it into a current or voltage that is proportional to the light intensity. The most common devices in current use for fluorometry and spectrophotometry are photodiodes and photodiode arrays.
DiapauseDiapause is a preprogrammed form of developmental arrest that allows animals to survive harsh environmental conditions and may also allow populations to synchronize periods of growth and reproduction with periods of optimal temperatures and adequate water and food. Diapause is endogenously controlled, and this dormancy typically begins well before conditions become too harsh to support normal growth and development [1,2]. » MiPNet article
Dicarboxylate carrierDICThe dicarboxylate carrier is a transporter which catalyses the electroneutral exchange of malate2- (or succinate2-) for inorganic phosphate, HPO42-.
Difference spectrumA difference spectrum is an absorbance spectrum obtained by subtracting that of one substance from that of another. For example, a difference spectrum may be plotted of the absorbance spectrum obtain ed from reduced cytochrome c and subtracting the absorbance spectrum from the same concentration of cytochrome c in its oxidised state. The difference spectrum may be used to quantify the amount to which the cytochrome c is reduced. This can be achieved with the aid of a reference spectrum (or spectra) and the least squares method.
Different O2 fluxes in left and right chamberWhat are potential causes for different O2 fluxes in the left and right chamber?
Diffraction gratingsDiffraction gratings are dispersion devices that are made from glass etched with fine grooves, spaced at the same order of magnitude as the wavelength of the light to be dispersed, and then coated with aluminium to reflect the light to the photodiode array. Diffraction gratings reflect the light in different orders and filters need to be incorporated to prevent overlapping.
Digital Object IdentifierDOIA Digital Object Identifier, DOI, is a persistent identifier used to uniquely identify online publications in order to ensure they remain traceable, searchable and citable over the long term. Compared to other types of persistent identifiers, the DOI system is widespread and well established in the life sciences arena, and it provides widely accepted visible proof that a publication is citable.
DigitoninDigDigitonin is a mild detergent that permeabilizes plasma membranes selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Digitonin is a natural product and thus the effective concentration has to be determined by titrations for every batch. The optimum effective digitonin concentrations for complete plasma membrane permeabilization of cultured cells can be determined directly in a respirometric protocol (see: SUIT-010 O2 ce-pce D008).
Dihydro-orotate dehydrogenaseDhoDHDihydro-orotate dehydrogenase is an electron transfer complex of the inner mitochondrial membrane, converting dihydro-orotate (Dho) into orotate, and linking electron transfer through the Q-junction to pyrimidine synthesis and thus to the control of biogenesis.
DihydroethidiumDHEDihydroethidium (also called hydroethidine) is a cell permeant fluorescent probe used to analyse superoxide presence. It is a reduced form of ethidium that presents blue fluorescence, and after oxidation by superoxide becomes able to intercalate DNA and emits red fluorescence (excitation wavelength ~518–535 nm, emission ~605–610 nm). It has been used to detect superoxide by HPLC and by fluorescence microscopy.
DimensionDimensions are defined in the SI {quote}: Physical quantities can be organized in a system of dimensions, where the system used is decided by convention. Each of the seven base quantities used in the SI is regarded as having its own dimension. .. All other quantities, with the exception of counts, are derived quantities, which may be written in terms of base quantities according to the equations of physics. The dimensions of the derived quantities are written as products of powers of the dimensions of the base quantities using the equations that relate the derived quantities to the base quantities. There are quantities Q for which the defining equation is such that all of the dimensional exponents in the equation for the dimension of Q are zero. This is true in particular for any quantity that is defined as the ratio of two quantities of the same kind. .. There are also some quantities that cannot be described in terms of the seven base quantities of the SI, but have the nature of a count. Examples are a number of molecules, a number of cellular or biomolecular entities (for example copies of a particular nucleic acid sequence), or degeneracy in quantum mechanics. Counting quantities are also quantities with the associated unit one. {end of quote: p 136, Bureau International des Poids et Mesures 2019 The International System of Units (SI)}
Dimethyl sulfoxideDMSODimethyl sulfoxide is a polar aprotic solvent that dissolves both polar and nonpolar compounds and is miscible in a wide range of organic solvents as well as water. DMSO may also be used as a cryoprotectant, added to cell media to reduce ice formation and thereby prevent cell death during the freezing process.
DinitrochlorobenzeneDNCBDinitrochlorobenzene (1-chloro-2,4-dinitrobenzene) (DNCB) is a glutathione (GSH) inhibitor.
DinitrophenoleDNP2,4-dinitrophenole (C6H4N2O5; M = 184.11 g·mol-1) is a protonophore acting as an uncoupler of oxidative phosphorylation.
DirectiveA directive is a legal act of the European Union, which requires member states to achieve a particular result without dictating the means of achieving that result.
Discontinuous systemIn a discontinuous system, gradients in continuous systems across the length, l, of the diffusion path [m], are replaced by differences across compartmental boundaries of zero thickness, and the local concentration is replaced by the free activity, α [mol·dm-3]. The length of the diffusion path may not be constant along all diffusion pathways, spacial direction varies (e.g., in a spherical particle surrounded by a semipermeable membrane), and information on the diffusion paths may even be not known in a discontinuous system. In this case (e.g., in most treatments of the protonmotive force) the diffusion path is moved from the (ergodynamic) isomorphic force term to the (kinetic) mobility term. The synonym of a discontinuous system is compartmental or discretized system. In the first part of the definition of discontinuous systems, three compartments are considered: (1) the source compartment A, (2) the sink compartment B, and (3) the internal barrier compartment with thickness l. In a two-compartmental description, a system boundary is defined of zero thickness, such that the barrier comparment (e.g., a semipermeable membrane) is either part of the system (internal) or part of the environment (external). Similarly, the intermediary steps in a chemical reaction may be explicitely considered in an ergodnamic multi-comparment system; alternatively, the kinetic analysis of all intermediary steps may be collectively considered in the catalytic reaction mobility, reducing the measurement to a two-compartmental analysis of the substrate and product compartments.
Dispersion devicesA dispersion device diffracts light at different angles according to its wavelength. Traditionally, prisms and diffraction gratings are used, the latter now being the most commonly used device in a spectrofluorometer or spectrophotometer.
Display DatLab helpDisplay DatLab help

In this section, we present some issues that could happen during your data analysis related to the graphs display and how to fix them quickly.

Case in which an issue might occur:

  • While analysing your data, trying to close the program while the graph is still being loaded. If you cancel the closing window, the graph will not be loaded at the screen.

In the event of a frozen display of the graphs, try the alternatives below:

  • Click on: Graph > Autoscale time axis
  • Click on: Graph > Scaling (F6); then press OK to confirm the scaling and induce the program to reload the graphs (no changes in the graphs are required).
Display Power-O2kThe Power-O2k number, which is set in the pull-down menu Oroboros O2k \ O2k configuration, is shown in the active graph. To show it in graphs copied to clipboard, the option "Show Oroboros icon in clipboard files" must be enabled in the Graph-menu Graph options - DatLab.
Display numerical valueIf Display numerical value the current numerical values are displayed in the graph for the active plots on the Y1 axis and Y2 axis (during data acquisition only).
DithioniteDithDithionite Na2S2O4 is the 'zero oxygen solution powder' used for calibration of oxygen sensors at zero oxygen, or for stepwise reduction of oxygen concentrations in instrumental O2 background tests. It is not recommended to use dithionite in experiments with biological samples or several multisensor approaches, for these see Setting the oxygen concentration.
DriftThe most common cause of drift is variation in the intensity of the light source. The effect of this can be minimised by carrying out a balance at frequent intervals.
Dual wavelength analysisIf a sample contains a number of absorbing substances, it is sometimes possible to select discrete pairs of wavelengths at which the change in absorbance of a particular substance (due to oxidation or reduction, for example) is largely independent of changes in the absorbance of other substances present. Dual wavelength analysis can be carried out for cytochrome c by subtracting the absorbance at 540 nm from that at 550nm in order to give a measure of the degree of reduction. Similarly, by subtracting the absorbance at 465 nm from that at 444 nm, an indicator of the redox state of cytochrome aa3 can be obtained.
Ee, E» elementary charge e = 1.602 176 634∙10-19 C∙x-1

» Euler's number e ~ 2.718 281 828 459

» ET capacity E
E-L coupling efficiencyjE-LE-L coupling efficiency The E-L coupling efficiency, jE-L = (E-L)/E = 1-L/E, is 0.0 at zero coupling (L=E) and 1.0 at the limit of a fully coupled system (L=0). The background state is the LEAK state which is stimulated to flux in the electron transfer pathway reference state by uncoupler titration. LEAK states LN or LT may be stimulated first by saturating ADP (rate P in the OXPHOS state) with subsequent uncoupler titration to the ET state with maximum rate E. The E-L coupling efficiency is based on measurement of a coupling-control ratio (LEAK-control ratio, L/E), whereas the thermodynamic or ergodynamic efficiency of coupling between ATP production (phosphorylation of ADP to ATP) and oxygen consumption is based on measurement of the output/input flux ratio (P»/O2 ratio) and output/input force ratio (Gibbs force of phosphorylation/Gibbs force of oxidation). The biochemical coupling efficiency expressed as the E-L coupling efficiency is independent of kinetic control by the E-P control efficiency, and is equal to the P-L control efficiency if P=E as evaluated in a coupling-control protocol. » MiPNet article
E-L net ET capacityE-LE-L net ET capacity The E-L net ET capacity is the ET capacity corrected for LEAK respiration. E-L is the respiratory capacity potentially available for ion transport and phosphorylation of ADP to ATP. Oxygen consumption in the ET-pathway state, therefore, is partitioned into the E-L net ET capacity and LEAK respiration LP, compensating for proton leaks, slip and cation cycling: E = E-L+LP (see P-L net OXPHOS capacity).
E-P control efficiencyjE-PE-P control efficiency The E-P control efficiency, jE-P = (E-P)/E = 1-P/E, is an expression of the relative limitation of OXPHOS capacity by the capacity of the phosphorylation system. It is the normalized E-P excess capacity. jE-P = 0.0 when OXPHOS capacity is not limited by the phosphorylation system at zero E-P excess capacity, P=E, when the phosphorylation system does not exert any control over OXPHOS capacity. jE-P increases with increasing control of the phosphorylation system over OXPHOS capacity. jE-P = 1 at the limit of zero phosphorylation capacity. The OXPHOS state of mt-preparations is stimulated to electron transfer pathway capacity E by uncoupler titration, which yields the E-P excess capacity.
E-P excess capacityE-PE-P excess capacity The E-P excess capacity is the difference of the ET capacity and OXPHOS capacity. At E-P > 0, the capacity of the phosphorylation system exerts a limiting effect on OXPHOS capacity. In addition, E-P depends on coupling efficiency, since P aproaches E at increasing uncoupling.
E-R control efficiencyjE-RE-R control efficiency The E-R control efficiency, jE-R = (E-R)/E = 1-R/E, is an expression of the relative scope of increasing ROUTINE respiration in living cells by uncoupling. jE-R = 0.0 for zero E-R reserve capacity when R=E; jE-R = 1.0 for the maximum limit when R=0. The ROUTINE state of living cells is stimulated to electron transfer pathway capacity by uncoupler titration, which yields the E-R reserve capacity. Since ET capacity is significantly higher than OXPHOS capacity in various cell types (as shown by cell ergometry), jE-R is not a reserve capacity available for the cell to increase oxidative phosphorylation, but strictly a scope (reserve) for uncoupling respiration. Similarly, the apparent E-P excess ET capacity is not a respiratory reserve in the sense of oxidative phosphorylation.
E-R reserve capacityE-RE-R reserve capacity The E-R reserve capacity is the difference of ET capacity and ROUTINE respiration. For further information, see Cell ergometry.
ET capacityEE.jpg T capacity is the respiratory electron-transfer-pathway capacity E of mitochondria measured as oxygen consumption in the noncoupled state at optimum uncoupler concentration. This optimum concentration is obtained by stepwise titration of an established protonophore to induce maximum oxygen flux as the determinant of ET capacity. The experimentally induced noncoupled state at optimum uncoupler concentration is thus distinguished from (1) a wide range of uncoupled states at any experimental uncoupler concentration, (2) physiological uncoupled states controlled by intrinsic uncoupling (e.g. UCP1 in brown fat), and (3) pathological dyscoupled states indicative of mitochondrial injuries or toxic effects of pharmacological or environmental substances. ET capacity in mitochondrial preparations requires the addition of defined fuel substrates to establish an ET-pathway competent state. » MiPNet article
ET-pathway competent stateElectron transfer pathway competent state, see Electron-transfer-pathway state.
ET-pathway substrate typesn.a.See Electron-transfer-pathway state
EUROMIT is a group based in Europe for organizing International Meetings on Mitochondrial Pathology.
EctothermsEctotherms are organisms whose body temperatures conform to the thermal environment. In many cases, therefore, ectotherms are poicilothermic.
ElamipretideBendaviaBendavia (Elamipretide) was developed as a mitochondria-targeted drug against degenerative diseases, including cardiac ischemia-reperfusion injury. Clinical trials showed variable results. It is a cationic tetrapeptide which readily passes cell membranes, associates with cardiolipin in the mitochondrial inner membrane. Supercomplex-associated CIV activity significantly improved in response to elamipretide treatment in the failing human heart.
ElasticityεAccording to David Fell, "Elasticities are properties of individual enzymes and not the metabolic system. The elasticity of an enzyme to a metabolite is related to the slope of the curve of the enzyme's rate plotted against metabolite concentration, taken at the metabolite concentrations found in the pathway in the metabolic state of interest. It can be obtained directly as the slope of the logarithm of the rate plotted against the logarithm of the metabolic concentration. The elasticity will change at each point of the curve (s,v) and must be calculated for the specific concentration of the metabolite (s) that will give a specific rate (r) of the enzyme activity" (See Figure).

Elasticity Measurement.jpg
Electric currentIel [A = C·s-1]; [mol·s-1]; [x·s-1]Current or electric flow Iel is the advancement of charge per unit of time, expressed in the SI base unit ampere [C·s-1 = A]. Electrons or ions are the current-carrying motive entities of electric flow. Electrons e- are negatively charged subatomic particles carrying 'negative electricity' with a mass that is about 1/1700 of the smallest particle — the proton — carrying 'positive electricity' (Thompson 1906). Correspondingly the velocity of electrons is much higher than that of protons or any other (larger) ion. Current is the velocity v of paticles times the number of motive charges. Therefore, electron current Ie- is of a different nature from electric current Ielχ carried by all species i of ions Xi (cations and anions) summarized as χ = Σ(zi·Xi). Whereas Ie- is the net translocation of electrons moving forwards and backwards, Ielχ is the net translocation of charges carried by different cations and anions. In contrast, ion current IelX of a specific ion X is the partial translocation of charges carried by net translocation of ion X only. If cation current IelX+ is antagonized entirely by counterion current IelY- as the process of antiport, then the electric current Ielχ is zero. The (net) electric current in a compartmental system is driven by the electric force ΔelFp+ or electric potential difference ΔΨp+, whereas a compensated ion/counterion antiport current is insensitive to the electric potential difference.
Electric current densityj [C·m-2]Electric current density is current divided by area, j=I·A-1 [C·m-2]. Compare: density.
Electrochemical constantf [J·C-1·K-1]
Table Physical constants.png
The electrochemical constant f has the SI unit for energy per charge per temperature [J·C-1·K-1].

f = k·e-1, the Boltzmann constant k divided by the elementary charge e.

f = R·F-1, the gas constant R divided by the Faraday constant F.
Electrolyte Reference-Electrode.jpg
Electrolyte\Reference-Electrode for Reference-Electrode\2.4 mm
Electron flowIeElectron flow through the mitochondrial Electron transfer pathway (ET-pahway) is the scalar component of chemical reactions in oxidative phosphorylation (OXPHOS). Electron flow is most conveniently measured as oxygen consumption (oxygraphic measurement of oxygen flow), with four electrons being taken up when oxygen (O2) is reduced to water.
Electron transfer pathwayET pathwayIn the mitochondrial electron transfer pathway (ET pathway) electrons are transferred from externally supplied reduced fuel substrates to oxygen. Based on this experimentally oriented definition (see ET capacity), the ET pathway consists of (1) the membrane-bound ET pathway with respiratory complexes located in the inner mt-membrane, (2) TCA cycle and other mt-matrix dehydrogenases generating NADH and succinate, and (3) the carriers involved in metabolite transport across the mt-membranes. » MiPNet article
Electron-transfer-pathway stateET-pathway state
SUIT-catg FNSGpCIV.jpg

Electron-transfer-pathway states are obtained in mitochondrial preparations (isolated mitochondria, permeabilized cells, permeabilized tissues, tissue homogenate) by depletion of endogenous substrates and addition to the mitochondrial respiration medium of fuel substrates (CHNO) activating specific mitochondrial pathways, and possibly inhibitors of specific pathways. Mitochondrial electron-transfer-pathway states have to be defined complementary to mitochondrial coupling-control states. Coupling-control states require ET-pathway competent states, including oxygen supply. Categories of SUIT protocols are defined according to mitochondrial ET-pathway states.

» MiPNet article
Electron-transferring flavoprotein complexCETFElectron-transferring flavoprotein complex (CETF) or electron-transferring flavoprotion is a respiratory complex localized at the matrix face of the inner mitochondrial membrane, supplies electrons from fatty acid oxidation (FAO, ß-oxidation) to CoQ, and is thus an enzyme complex of the mitochondrial Electron transfer pathway (ET-pathway).
Electronic-TIP2k Upgrading\O2k-Main Unit Series A-DElectronic-TIP2k Upgrading\O2k-Main Unit Series A-D - Former Product : not required for O2k-Core, the O2k-Main Unit has to be returned to the OROBOROS workshop.
Electronic-TIP2k Upgrading\O2k-Main Unit Series EElectronic-TIP2k Upgrading\O2k-Main Unit Series E - Former Series : not required for O2k-Core, free of charge for Series E in conjunction with the purchase of the TIP2k-Module, the O2k-Main Unit has to be returned to the OROBOROS workshop.
Elementary chargee [C·x-1]
Table Physical constants.png
The elementary charge or proton charge e has the SI unit coulomb [C], but more strictly coulomb per elementary unit [C·x-1]. -e is the charge per electron. Elementary charge e is the charge per elementary entity H+ with SI unit [C] but canonical SI unit [C·x-1]. When the charge Qel [C] of a number Ne [x] of electrons e is divided by the count Ne, then the particle charge QNX (QNX) charge per elementary entity is obtained, -e = Qel/Ne [C·x-1]. e is also used as an atomic unit.
Elementary entityUX [x]

An elementary entity is an entity of type X, distinguished as a single unit of countable objects (X = molecules, cells, organisms, particles, parties, items) or events (X = beats, collisions, emissions, decays, celestial cycles, instances, occurrences, parties). "An elementary entity may be an atom, a molecule, an ion, an electron, any other particle or specified group of particles" (Bureau International des Poids et Mesures 2019). An elementary entity, therefore, needs to be distinguished from non-countable entities and the general class of entities X. This distinction is emphasized by the term 'elementary' (synonymous with 'elementary entity') with symbol UX and elementary unit [x].

If an object is defined as an assembly of particles (a party of two, a molecule as the assembly of a stoichiometric number of atoms), then the elementary is the assembly but not the assembled particle. A number of defined elementaries UX is a count, NX = N·UX [x], where N is a number, and as such N is dimensionless, and N is a number (stop) and is not 'a number of ..'. Elementaries are added as items to a count. The elementary UX has the dimension U of the count NX. The elementary UX has the same unit [x] as the count NX, or more accurately it gives the count the defining 'counting-unit', which is the 'elementary unit' [x]. From the definition of count as the number (N) of elementaries (U) of entity type X, it follows that count divided by elementary is a pure number, N = NX·UX-1. The unit x of a count can neither be the entity X nor a number. The elementary of type X defines the identity X of the elementary UX with the unit 'elementary unit' with symbol [x]. Since a count NX is the number of elementary entities, the elementary UX is not a count (UX is not identical with N·UX).
Enable DL-Protocol editingIn DatLab 7.4, fixed sequences of events and marks can be changed (Skip/Added) in a SUIT protocol by the user. Moreover, the text, instructions, concentrations and titration volumes of injections in a specific DL-Protocol can be edited and saved as user-specific DL-Protocol [File]\Export\DL-Protocol User (*.DLPU). To enable it, select in the menu 'Protocols' the option 'Enable DL-Protocol editing', then select the plot in which the marks will be set (e.g., O2 flux per V). Select the 'Overview' window, where you will be able to edit events and marks names, definition/state, final concentration and titration volumes, as well as select a mark as 'multi' for multiple titration steps, skip a mark, or add a new event or mark. After saving, export a DL-Protocol User (DLPU) and load it before running the next experiments.

For more information:

PlayVideo.jpg Export DL-Protocol User (*.DLPU)
EndergonicEndergonic transformations or processes can proceed in the forward direction only by coupling to an exergonic process with a driving force more negative than the positive force of the endergonic process. The backward direction of an endergonic process is exergonic. The distinction between endergonic and endothermic processes is at the heart of ergodynamics, emphasising the concept of exergy changes, linked to the performance of work, in contrast to enthalpy changes, linked to heat or thermal processes, the latter expression being terminologically linked to thermodynamics.
EndothermicAn energy transformation is endothermic if the enthalpy change of a closed system is positive when the process takes place in the forward direction and heat is absorbed from the environment under isothermal conditions (∆eQ > 0) without performance of work (∆eW = 0). The same energy transformation is exothermic if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are exergonic.
EndothermyEndothermy is the constant regulation of body temperature by metabolic heat production and control of heat exchange with the environment.
EnergyE; various [J]Heat and work are forms of energy [1 cal = 4.184 J]. Energy [J] is a fundamental term that is used in physics and physical chemistry with various meanings [1]. These meanings become explicit in the following equations relating to systems at constant volume (dV = 0) or constant gas pressure (dp = 0). Energy is exchanged between a system and the environment across the system boundaries in the form of heat, deQ, total or available work, detW (or detW), and matter, dmatU (or dmatH) [2],
dU = (deQ + detW) + dmatU ; dV = 0 [Eq. 1a]
dH = (deQ + deW) + dmatH ; dp = 0 [Eq. 1b]

Whereas dU (or dH) describe the internal-energy change (or enthalpy change) of the system, heat and work are external energy changes (subscript e), and dmatU (or dmatH) are the exchange of matter expressed in internal-energy (or enthaply) equivalents. In closed systems, dmatU = 0 (dmatH = 0). The energy balance equation [Eq. 1] is a form of the First Law of Thermodynamics, which is the law of conservation of internal-energy (or enthalpy), stating that energy cannot be generated or destroyed: energy can only be transformed into different forms of work and heat, and transferred in the form of matter.

Notably, the term energy is general and vague, since energy may be associated with either the first or second law of thermodynamics.

An equally famous energy balance equation considers energy changes of the system only, in the most simple form for isothermal systems (dT = 0):

dU = dA + T∙dS = dU + dB [Eq. 2a]
dH = dG + T∙dS = dG + dB [Eq. 2b]

The internal-energy change, dU (enthalpy change, dH) is the sum of free energy change (Helmholtz energy, dA; or Gibbs energy, dG) and bound energy change (bound energy, dB = T∙dS). The bound energy is that part of the energy change that is always bound to an exchange of heat.

A third energy balance equation accounts for changes of the system in terms of irreversible internal processes (i) occuring within the system boundaries, and reversible external processes (e) of transfer across the system boundaries (at constant gas pressure),

 dH = diH + deH [Eq. 3a]
 dG = diG + deG [Eq. 3b]

The energy conservation law of thermodynamics (first law) can be formulated as diH = 0 (at constant gas pressure), whereas the generally negative sign of the dissipated energy, diG ≡ diD ≤ 0, is a formulation of the second law of thermodynamics. Insertion into Eq. 3 yields,

 dH = deH [Eq. 4a]
 dG = diD + deW + dmatG [Eq. 4b]
When talking about energy transformations, the term energy is used in a general sense without specification of these various forms of energy.
Energy chargeAECThe energy charge of the adenylate system or adenylate energy charge (AEC) has been defined by Atkinson and Walton (1967) as (ATP + ½ ADP)/(AMP + ADP + ATP). Wheather the AEC is a fundamental metabolic control parameter remains a controversial topic.
Energy metabolismCore energy metabolism is the integrated biochemical process supplying the cell with ATP, utilizing ATP for various forms of work including biogenesis, maintaining ion and redox balance, and in specific organisms or tissues dissipating heat for temperature regulation.
EnthalpyH [J]Enthalpy, H [J], can under conditions of constant gas pressure neither be destroyed nor created (first law of thermodynamics: diH/dt = 0). The distinction between enthalpy and internal-energy of a system is due to external pressure-volume work carried out reversibly at constant gas pressure. The enthalpy change of the system, dH, at constant pressure, is the internal-energy change, dU, minus reversible pressure-volume work,
dH = dU - dVW

Pressure-volume work, dVW, at constant pressure, is the gas pressure, p [Pa = J·m-3], times change of volume, dV [m3],

dVW = -p·dV [J]

The available work, deW, is distinguished from external total work, detW, [1]

deW = detW - dVW

The change of enthalpy of a system is due to internal and external changes,

 dH = diH + deH

Since diH = 0 (first law of thermodynamics), the dH is balanced by exchange of heat, work, and matter,


The exchange of matter is expressed in enthalpy equivalents with respect to a reference state (formation, f, or combustion, c). The value of dH in an open system, therefore, depends on the arbitrary choice of the reference state. In contrast, the terms in parentheses are the sum of all (total, t) partial energy transformations,

dtH = (deQ + deW)

A partial enthalpy change of transformation, dtrH, is distinguished from the total enthalpy change of all transformations, dtH, and from the enthalpy change of the system, dH. In a closed system, dH = dtH. The enthalpy change of transformation is the sum of the Gibbs energy (free energy) change of transformation, dtrG, and the bound energy change of transformation at constant temperature and pressure, dtrB = T·dS,

dtrH = dtrG + dtrB
EntityXAn entity of type X is something that can measured as an extensive quantity or counted as an elementary entity. The term entity with symbol X, therefore, has a general meaning, including but not limited to elementary entities UX. The distinction can be emphasized by using the term entity-type X, to avoid confusion of an entity X with the more restricted definition of elementary entity UX as a single countable object or event.
ErgodynamicsIs there a need for defining ergodynamics? "Thermodynamics deals with relationships between properties of systems at equilibrium and with differences in properties between various equilibrium states. It has nothing to do with time. Even so, it is one of the most powerful tools of physical chemistry" [1]. Ergodynamics is the theory of exergy changes (from the Greek word 'erg' which means work). Ergodynamics includes the fundamental aspects of thermodynamics ('heat') and the thermodynamics of irreversible processes (TIP; nonequilibrium thermodynamics), and thus links thermodynamics to kinetics. In its most general scope, ergodynamics is the science of energy transformations. Classical thermodynamics includes open systems, yet as a main focus it describes closed systems, which is reflected in a nomenclature that is not easily applicable to the more general case of open systems [2]. At present, IUPAC recommendations [3] fall short of providing adequate guidelines for describing energy transformations in open systems.
Ethics on publishingEthics on publishing follow COPE's guidelines (or equivalent). A journal's policy on publishing ethics should be clearly visible on its website, and should refer to: (1) Journal policies on authorship and contributorship; (2) How the journal will handle complaints and appeals; (3) Journal policies on conflicts of interest / competing interests; (4) Journal policies on data sharing and reproducibility; (5) Journal's policy on ethical oversight; (6) Journal's policy on intellectual property; and (7) Journal's options for post-publication discussions and corrections.
Ethylene glycol tetraacetic acidEGTAEthylene glycol tetraacetic acid (EGTA) is a chelator for heavy metals, with high affinity for Ca2+ but low affinity for Mg2+. Sigma E 4378.
EtomoxirEtoEtomoxir (Eto; 2[6(4-chlorophenoxy)hexyl]oxirane-2-carboxylate) is an irreversible inhibitor of carnitine palmitoyltransferase-1 (CPT-1) on the outer face of the inner mitochondrial membrane. Eto inhibits the transport of the long-chain fatty acids from the cytosol into the mitochondrial matrix, thereby blocking the formation of acyl carnitines in the cytosol, leading finally to inhibition of the fatty acid oxidation. Of note, in contrast to long-chain fatty acids, the transport of short- and medium chain fatty acids is carnitine-independent. The commercially available white compound is soluble in water.
European Bioenergetics Conference
EBEC is a group based in Europe that organizes the European Bioenergetics Conference.
Euthanyl/PentobarbitolEuthanylI am often asked by reviewers to discuss the effects of pentobarbitol euthansia on mithochondrial function. Takaki 1997 JJP: This paper has been helpful in this discussion. (edit by Staples JF)
Events - DatLabF4An event in DatLab is a defined point in time, labelled by a name (1 to 10 characters). An event applies to all plots of the selected O2k-Chamber. The event is shown by a vertical line in the graph and the label of the event is shown on the top (DatLab 6 and lower: on the bottom). The default name is the sequential number of the event. It is recommended to edit event labels with a minimum number of characters, and to explain the abbreviation in the 'Definition' box. The final concentration and titration volume can be entered into the corresponding boxes, if the event relates to the titration of a substance. A short comment can be entered to describe the event in detail.

Set events - Manual events are entered (real-time, connected to the O2k) by pressing [F4] at the time of the event (e.g. to indicate a manual titration into the chamber). An event belongs either to chamber A, chamber B, or both. Instrumental events are added automatically, e.g. when the stirrer (A or B) or illumination (both chambers) is switched on or off. After setting a new event the Edit event window pops up. Pressing F4 defines the time point of the event. Full attention can then be paid to the experiment. Edit the event later, as it is possible to insert an event at any chosen moment of the plotted record of the experiment by placing the cursor anywhere in the graph at the selected time point by pressing Ctrl and clicking the left mouse button. Edit event - Left click on the name of an existing event to open the Edit event window to edit or Delete event. In events obtained from a selected protocol, the entire sequence of consecutive events is defined with event names, definitions, concentrations and titration volumes. Name - Enter an event name of 1 to 10 characters. Short names (e.g. O instead of Open) are recommended. Comment - Further information can be entered into the text field. Select O2k-chamber A, B or both. The Event will be shown on plots for both or one selected chamber.

»Protocol events
ExaminationAn examination is a set of operations having the object of determining the value or characteristics of a property. In some disciplines (e.g. microbiology) an examination is the total activity of a number of tests, observations or measurements.
Exclusion criteriaThe Exclusion criteria include factors or characteristics that make the recruited population ineligible for the outcome parameter. With the Inclusion criteria, this factor must be a cofounder for the outcome parameter
ExergonicExergonic transformations or processes can spontaneously proceed in the forward direction, entailing the irreversible loss of the potential to performe work (erg) with the implication of a positive internal entropy production. Ergodynamic equilibrium is obtained when an exergonic (partial) process is compensated by a coupled endergonic (partial) process, such that the Gibbs energy change of the total transformation is zero. Final thermodynamic equilibrium is reached when all exergonic processes are exhausted and all forces are zero. The backward direction of an exergonic process is endergonic. The distinction between exergonic and exothermic processes is at the heart of ergodynamics, emphasising the concept of exergy changes, linked to the performance of work, in contrast to enthalpy changes, linked to heat or thermal processes, the latter expression being terminologically linked to thermodynamics.
ExothermicAn energy transformation is exothermic if the enthalpy change of a closed system is negative when the process takes place in the forward direction and heat is lost to the environment under isothermal conditions (∆eQ < 0) without performance of work (∆eW = 0). The same energy transformation is endothermic if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are exergonic.
ExperimentA number of replica, N, of experiments on one sample type is designed to obtain statistical information about the involved population(s) and to test hypotheses about a population and about differences between populations, when experiments are carried out on different sample types. An experiment may involve various assays, e.g., a respirometric assay and an assay for protein determination.
Experimental codeF3An experimental code can be entered in the Sample window, containing up to 10 digits.
Experimental log - DatLabCtrl+F3Experimental log provides an automatically generated experimental protocol with detailed information about the O2k settings and calibrations, the Sample information and various Events. Time-dependent information can be viewed for a single chamber or both chambers. The filter can be selected for viewing minimum information, intermittent by default, or all information. The experimental log can be viewed and saved as a PDF file by clicking on [Preview].
Export DL-Protocol User (*.DLPU)Export DL-Protocol User (*.DLPU) Protocol possess unique D### codes and comprise a fixed sequence of events and marks which cannot be changed by the user. However, the user may edit concentrations and titration volumes of injections and store the modified protocol as user-specific DL-Protocol [File]\Export\DL-Protocol User (*.DLPU).

If users of older DatLab versions than DatLab 7.4 wish to alter the nature of the chemicals used or the sequence of injections, we ask them to contact the O2k-Technical Support.

DatLab 7.4

DatLab 7.4 offers a new feature in DL-Protocols: flexibility. Fixed sequence of events and marks can be changed (Skip/Added) in a SUIT protocol by the user. Moreover, editions of text, instructions, concentrations and titration volumes of injections in a specific DL-Protocol can be edited and saved as user-specific DL-Protocol [File]\Export\DL-Protocol User (*.DLPU).

For more information, see: Enable DL-Protocol editing
Extended abstractsIn the context of MiPevents and MitoEAGLE events, extended abstracts are accepted for preprint publication in MitoFit Preprints upon evaluation by MitoEAGLE MC members. Publishing extended abstracts with MitoFit Preprints does not preclude later full journal publication, but will make your work fully citable, by assigning each manuscript a unique DOI number, and facilitate discovery and feedback.
Extensive quantityExtensive quantities pertain to a total system, e.g. oxygen flow. An extensive quantity increases proportional with system size. The magnitude of an extensive quantity is completely additive for non-interacting subsystems, such as mass or flow expressed per defined system. The magnitude of these quantities depends on the extent or size of the system (Cohen et al 2008).
ExtinctionExtinction is a synonym for absorbance.
Extinction coefficientεThe extinction coefficient (ε) of a substance is the absorbance of a 1 µmolar concentration over a 1 cm pathlength and is wavelength-dependent.
Extrinsic fluorophoresExtrinsic fluorophores are molecules labelled with a fluorescent dye (as opposed to intrinsic fluorescence or autofluorescence of molecules which does not require such labelling). They are available for a wide range of parameters including ROS (H2O2, Amplex red) (HOO-, MitoSOX) , mitochondrial membrane potential (Safranin, JC1, TMRM, Rhodamine 123), Ca2+ (Fura2, Indo 1, Calcium Green), pH (Fluorescein, HPTS, SNAFL-1), Mg2+ (Magnesium Green) and redox state (roGFP).
ExtroductionThe term extroduction is ambiguous and needs introduction. An external extroduction aims at providing a specific exit that opens the door to the parent article. Once you popped up into the article box, there are various internal extroductions to push down by following hyperlinks to references, keywords, supplementary material, and to the external extroduction. Once you have pushed one level down, there may be hyperlinks to push down further (Hofstadter 1979). One needs to keep track of the links in a nested network of open tabs, to pop up all the way back for returning to the initial reference level.
F1000ResearchF1000Research is an Open Research publishing platform for life scientists, offering immediate publication of articles and other research outputs without editorial bias. All articles benefit from transparent peer review and the inclusion of all source data. It is thus not a preprint server, but posters and slides can be published without author fees. Published posters and slides receive a DOI (digital object identifier) and become citable after a very basic check by our in-house editors.
FADH2FADH2FAD and FADH2: see Flavin adenine dinucleotide.
FCCPFCCPFCCP (Carbonyl cyanide p-trifluoro-methoxyphenyl hydrazone, C10H5F3N4O) is a protonophore or uncoupler: added at uncoupler concentration Uc; c is the optimum uncoupler concentration in titrations to obtain maximum mitochondrial respiration in the noncoupled state of ET capacity.
FN is induced in mt-preparations by addition of NADH-generating substrates (N-pathway control state, or CI-linked pathway control) in combination with one or several fatty acids, which are supplied to feed electrons into the F-junction through fatty acyl CoA dehydrogenase (reduced form FADH2), to electron transferring flavoprotein (CETF), and further through the Q-junction to Complex III (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH2 and NADH and thus depends on N-junction throughput. Hence FAO can be inhibited completely by inhibition of Complex I (CI). This physiological substrate combination is required for partial reconstitution of TCA cycle function and convergent electron-input into the Q-junction, to compensate for metabolite depletion into the incubation medium. FS in combination exerts an additive effect of convergent electron flow in most types of mitochondria.
FNS is induced in mt-preparations by addition of NADH-generating substrates (N-pathway control state, or CI-linked pathway control) in combination with succinate (S-pathway control state; S- or CII-linked) and one or several fatty acids, which are supplied to feed electrons into the F-junction through fatty acyl CoA dehydrogenase (reduced form FADH2), to electron transferring flavoprotein (CETF), and further through the Q-junction to Complex III (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH2 and NADH and thus depends on N-junction throughput. Hence FAO can be inhibited completely by inhibition of Complex I (CI). This physiological substrate combination is required for partial reconstitution of TCA cycle function and convergent electron-input into the Q-junction, to compensate for metabolite depletion into the incubation medium. FNS in combination exerts an additive effect of convergent electron flow in most types of mitochondria.
Convergent electron flow

MitoPathway control state: FNSGp

Octanoylcarnitine or Palmitoylcarnitine & Pyruvate &/or Glutamate & Malate & Succinate & Glycerophosphate.

SUIT protocol: SUIT-002

This substrate combination supports convergent electron flow to the Q-junction.
Faraday constantF [C/mol]The Faraday constant F links the electric charge [C] to amount [mol], and thus relates the electrical format e [C] to the molar format n [mol]. The Farady constant, F = e·NA = 96,485.33 C/mol, is the product of elementary charge, e = 1.602176634∙10-19 C/x, and the Avogadro constant, NA = 6.02214076∙1023 x/mol. The dimensionless unit [x] is not explicitely considered by IUPAC.
Fatty acidFAFatty acids are carboxylic acids with a carbon aliphatic chain. The fatty acids can be divided by the length of this chain, being considered as short-chain (1–6 carbons), medium-chain (7–12 carbons) and long-chain and very long-chain fatty acids (>12 carbons).

Long-chain fatty acids must be bound to carnitine to enter the mitochondrial matrix, in a reaction that can be catalysed by carnitine acyltransferase. For this reason, long-chain fatty acids, such as palmitate (16 carbons) is frequently supplied to mt-preparations in the activated form of palmitoylcarnitine. Fatty acids with shorter chains, as octanoate (8 carbons) may enter the mitochondrial matrix, however, in HRR they are more frequently supplied also in the activated form, such as octanoylcarnitine.

Once in the mitochondrial matrix, the fatty acid oxidation (FAO) occurs, generating acetyl-CoA, NADH and FADH2. In the fatty acid oxidation pathway control state electrons are fed into the F-junction involving the electron transferring flavoprotein (CETF). FAO cannot proceed without a substrate combination of fatty acids & malate, and inhibition of CI blocks FAO. Low concentration of malate, typically 0.1 mM, does not saturate the N-pathway; but saturates the F-pathway.
Fatty acid oxidationFAOFatty acid oxidation (β-oxidation) is a multi-step process by which fatty acids are broken down to generate acetyl-CoA, NADH and FADH2 for further energy transformation in the mitochondrial matrix. Whereas NADH is the substrate of CI, FADH2 is the substrate of Electron-transferring flavoprotein complex (CETF) which is localized on the matrix face of the mtIM, and supplies electrons from FADH2 to CoQ2. Before the mitochondrial transport for ß-oxidation, fatty acids (short-chain with 1-6, medium-chain with 7–12, long-chain with >12 carbon atoms) are activated by fatty acyl-CoA synthases (thiokinases) in the cytosol. For the mitochondrial transport of long-chain fatty acids the mtOM-enzyme carnitine palmitoyltransferase I (CPT-1; rate-limiting step in FAO) is required which generates an acyl-carnitine intermediate from acyl-CoA and carnitine. In the next step, an integral mtIM protein carnitine-acylcarnitine translocase (CACT) catalyzes the entrance of acyl-carnitines into the mitochondrial matrix in exchange for free carnitines. In the inner side of the mtIM, another enzyme carnitine palmitoyltransferase 2 (CPT-2) converts the acyl-carnitines to carnitine and acyl-CoAs, which undergo ß-oxidation in the mitochondrial matrix. Short- and medium-chain fatty acids do not require the carnitine shuttle for mitochondrial transport. Octanoate, but not palmitate, (eight- and 16-carbon saturated fatty acids) may pass the mt-membranes, but both are frequently supplied to mt-preparations in the activated form of octanoylcarnitine or palmitoylcarnitine.
Fatty acid oxidation pathway control stateF, FAO
In the fatty acid oxidation pathway control state (F- or FAO-pathway), one or several fatty acids are supplied to feed electrons into the F-junction through fatty acyl CoA dehydrogenase (reduced form FADH2), to electron transferring flavoprotein (CETF), and further through the Q-junction to Complex III (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting relative to the N-pathway branch), but simultaneously generates FADH2 and NADH and thus depends on N-junction throughput. Hence FAO can be inhibited completely by inhibition of Complex I (CI). In addition and independent of this source of NADH, the type N substrate malate is required at low concentration (0.1 mM) as a co-substrate for FAO in mt-preparations, since accumulation of Acetyl-CoA inhibits FAO in the absence of malate. Malate is oxidized in a reaction catalyzed by malate dehydrogenase to oxaloacetate (yielding NADH), which then stimulates the entry of Acetyl-CoA into the TCA cycle catalyzed by citrate synthase. Peroxysomal β-oxidation carries out few β-oxidation cycles, thus shortening very-long-chain fatty acids (>C20) for entry into mitochondrial β-oxidation. Oxygen consumption by peroxisomal acyl-CoA oxidase is considered as residual oxygen consumption rather than cell respiration.
FermentationFermentation is the process of energy metabolism used to supply ATP, where redox balance is maintained with internally produced electron acceptors (such as pyruvate or fumarate), without the use of external electron acceptors (such as O2). Fermentation thus contrasts with cell respiration and is an anaerobic process, but aerobic fermentation may proceed in the presence of oxygen.
File search - DatLabCtrl+FFile search yields a list of all files labelled by the experimental code in a selected directory . Click on the file to preview the experimental log. With File Search you can search in all folders and subfolders on your computer for DatLab files with a selected experimental code. The experimental code is entered in the DatLab file in the window "Experiment" ([F3]). When you click on a folder and press the button search, the DatLab file names will appear on the right window. Click on a DatLab file and further information (e.g. Sample information, Background information) will appear in the window below.
Filter Set AmR
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Filter Set AmR: Set of filters for the determination of H2O2 production with Amplex UltraRed. These filters should be used together with Fluorescence-Sensor Green. The filter set consists of 6 LED filters (round) and 6 photodiode filters (rectangular).
Filter Set MgG / CaG
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Filter set MgG / CaG: Set of filters for the determination of concentraions of Mg2+ or Ca2+ with the fluorophores Magnesium green and Calcium green, respectively. These filters should be used together with Fluorescence-Sensor Blue or Smart Fluo-Sensor Blue. The filter set consists of 6 LED filters (round) and 6 photodiode filters (rectangular).
Filter Set Saf
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Filter set Saf: Set of filters for the (qualitative) determination of mitochondrial membrane potential with Safranin. These filters should be used together with Fluorescence-Sensor Blue or Smart Fluo-Sensor Blue. The filter set consists of 6 LED filters (round) and 6 photodiode filters (rectangular).
Filter-Cap: O2k-Fluo LED2-Module (O2k-Series D to G) sensors (Fluorescence-Sensor Green and Fluorescence-Sensor Blue) and O2k-FluoRespirometer (O2k-Series H to I) sensors (Smart Fluo-Sensor Green and Smart Fluo-Sensor Blue) are equipped with a removable Filter-Cap for exchange of optical filters for the optical pathways from the LED to the sample and from the sample to the photodiode.
FiltersFilters are materials that have wavelength-dependent transmission characteristics. They are can be used to select the wavelength range of the light emerging from a light source, or the range entering the detector, having passed through the sample. In particular they are used in fluorometry to exclude wavelengths greater than the excitation wavelength from reaching the sample, preventing absorption interfering with the emitted fluorescence. Standard filters can also be used for calibrating purposes.
Flavin adenine dinucleotideFAD, FADH2Flavin adenine dinucleotide, FAD and FADH2, is an oxidation-reduction coenzyme (redox cofactor; compare NADH). FMN and FAD are the prosthetic groups of flavoproteins (flavin dehydrogenases). Type F substrates (fatty acids) generate FADH2, the substrate of electron transferring flavoprotein (CETF). Thus FADH2 forms a junction or funnel of electron transfer to CETF, the F-junction (compare N-junction, Q-junction), in the F-pathway control state. In contrast, FADH2 is not the substrate but the product of succinate dehydrogenase (CII). FAD is the oxidized (quinone) form, which is reduced to FADH2 (hydroquinone form) by accepting two electrons and two protons.
FlavonoidsFlavonoids are a group of bioactive polyphenols with potential antioxidant and anti-inflammatory effects, abundant in fruits and vegetables, and in some medicinal herbs. Flavonoids are synthesized in plants from phenylalanine. Dietary intake of flavonoids as nutraceuticals is discussed for targeting T2D and other degenerative diseases.
FlowI [MU∙s-1]In an isomorphic analysis, any form of flow, I is the advancement of a process per unit of time, expressed in a specific motive unit [MU∙s-1], e.g., ampere for electric flow or current [A≡C∙s-1], watt for heat flow [W≡J∙s-1], and for chemical flow the unit is [mol∙s-1]. Flow is an extensive quantity. The corresponding isomorphic forces are the partial exergy (Gibbs energy) changes per advancement [J∙MU-1], expressed in volt for electric force [V≡J∙C-1], dimensionless for thermal force, and for chemical force the unit is [J∙mol-1], which deserves a specific acronym ([Jol]) comparable to volt.
FluorescenceFluorescence is the name given to light emitted by a substance when it is illuminated (excited) by light at a shorter wavelength. The incident light causes an electron transition to a higher energy band in the molecules. The electron then spontaneously returns to its original energy state emitting a photon. The intensity of the emitted light is proportional to the concentration of the substance. Fluorescence is one form of Luminescence, especially Photoluminescence.
Fluorescence-Control Unit
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Fluorescence-Control Unit with O2k-Front Fixation, Current-Control (O2k-Chamber A and B) for regulation of light intensity of the LED in the fluorescence sensors. This item is a standard component of the O2k-Fluorescence LED2-Module.
Fluorescence-Sensor Blue
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Fluorescence-Sensor Blue: excitation LED 465 nm (dominant wavelength), photodiode, Filter-Cap equipped with Filter Set Saf for measurement of mitochondrial membrane potential with Safranin when delivered. Filter sets for Magnesium green® / Calcium green® measurements are included.
Fluorescence-Sensor Green
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Fluorescence-Sensor Green: excitation LED 525 nm (dominant wavelength), photodiode, Filter-Cap equipped with Filter Set AmR for Amplex UltraRed measurements when delivered.
Fluorescence-Service Box
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Fluorescence-Service Box: for storage and shipment of theO2k-Fluo LED2-Module.
Fluorescent markerSee Extrinsic fluorophores
Fluorometric dyesExtrinsic fluorophores; fluorescent markers.
FluorometryFluorometry (or fluorimetry) is the general term given to the method of measuring the fluorescent emission of a substance following excitation by light at a shorter wavelength.
FluorophoreA fluorophore is a fluorescent substance that may occur naturally (intrinsic fluorophores) or that may be added to a sample or preparation whereby the fluorescence intensity is proportional to the concentration of a specific species or parameter within the sample. These are extrinsic fluorophores, also referred to as fluorescent markers.
FluxJFlux, J, is a specific quantity. Flux is flow, I [MU·s-1 per system] (an extensive quantity), divided by system size. Flux (e.g., oxygen flux) may be volume-specific (flow per volume [MU·s-1·L-1]), mass-specific (flow per mass [MU·s-1·kg-1]), or marker-specific (e.g. flow per mtEU). The motive unit [MU] of chemical flow or flux is the advancement of reaction [mol] in the chemical format.
Flux / SlopeJFlux / Slope is the time derivative of the signal. In DatLab, Flux / Slope is the name of the pull-down menu for (1) normalization of flux (chamber volume-specific flux, sample-specific flux or flow, or flux control ratios), (2) flux baseline correction, (3) Instrumental background oxygen flux, and (4) flux smoothing, selection of the scaling factor, and stoichiometric normalization using a stoichiometric coefficient.
Flux analysis - DatLabThe strategy of Flux analysis using DatLab depends on the research question and the corresponding settings applied in DatLab when recording the data with the O2k. Usng SUIT protocols, a sequence of respiratory steady-states is measured, marks are set, and numerical data are summarized in Mark statistics (F2). An AI approach is kept in mind when describing guidelines for evaluation of steady-states during data recording and analysis.
JV(bc) = JV - JV0
jZ-Y = (ZX-YX)/ZX = 1-YX/ZX

Complementary to the concept of flux control ratios and analogous to elasticities of metabolic control analysis, the flux control efficiency of X upon background YX is expressed as the change of flux from YX to ZX normalized for the reference state ZX.

» MiPNet article
Flux control ratioFCRFlux control ratios FCR are ratios of oxygen flux in different respiratory control states, normalized for maximum flux in a common reference state, to obtain theoretical lower and upper limits of 0.0 and 1.0 (0 % and 100 %). For a given protocol or set of respiratory protocols, flux control ratios provide a fingerprint of coupling and substrate control independent of (1) mt-content in cells or tissues, (2) purification in preparations of isolated mitochondria, and (3) assay conditions for determination of tissue mass or mt-markers external to a respiratory protocol (CS, protein, stereology, etc.). FCR obtained from a single respirometric incubation with sequential titrations (sequential protocol; SUIT protocol) provide an internal normalization, expressing respiratory control independent of mitochondrial content and thus independent of a marker for mitochondrial amount. FCR obtained from separate (parallel) protocols depend on equal distribution of subsamples obtained from a homogenous mt-preparation or determination of a common mitochondrial marker.
ForceF; dmFX; ΔtrFX [J·MU-1]Force is an intensive quantity. The product of force times advancement is the work (exergy) expended in a process or transformation.
  1. The fundamental forces, F, of physics are the gravitational, electroweak (combining electromagnetic and weak nuclear) and strong nuclear forces. These gradient-forces are vectors with spatial direction interacting with the motive particle X, dmFX [N ≡ J∙m-1 = m∙kg∙s-2]. These forces describe the interaction between particles as vectors with direction of a gradient in space, causing a change in the motion (acceleration) of the particles in the spatial direction of the force. The force acts at a distance, and the distance covered is the advancement. If a force is counteracted by another force of equal magnitude but opposite direction, the accelerating effects of the two forces are balanced such that the velocity of the particle does not change and no work is done beyond the interaction between the two counteracting forces. The total net force is partitioned into partial forces, and the counteracting force may be called resistance. If the resistance is entirely due to frictional effects, then no work is done and the exergy is completely dissipated.
  2. Isomorphic forces can be derived from (i) the fundamental forces or (ii) statistical distributions if large numbers of particles are involved. The isomorphic forces are known as 'generalized' forces of nonequilibrium thermodynamics. An isomorphic motive force, ΔtrFX, in thermodynamics or ergodynamics is the partial Gibbs (Helmholtz) energy change per advancement of a transformation (tr).
    1. In continuous systems accessible to the analysis of gradients, the motive vector forces, dmFX (units: newton per amount of particles X [N∙mol-1] or per coulombs of particles [V ≡ N∙C-1]), are vectors interacting with the motive particles X.
    2. In discontinuous systems that consist of compartments separated by a semipermeable membrane, the compartmental motive forces are stoichiometric potential differences (∆) across a boundary of zero thickness, distinguished as isomorphic motive forces, ∆trFX, with compartmental instead of spatial direction of the energy transformation, tr. The motive forces are expressed in various motive units, MU [J∙MU-1], depending on the energy transformation under study and on the unit chosen to express the motive entity X and advancement of the process. For the protonmotive force the proton is the motive entity, which can be expressed in a variety of formats with different MU (coulomb, mole, or particle).
Forceps for membrane application
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Forceps for membrane application: for OroboPOS and ISE membrane application; do not use for tissue preparation.
Forceps\stainless Steel\angular Tip\fine
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Forceps\stainless Steel\angular Tip\fine: for tissue preparation, stainless steel. Two pairs are used particularly for muscle fiber separation.
Forceps\stainless Steel\rounded Tip\sharp
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Forceps\stainless Steel\rounded Tip\sharp: for tissue preparation, stainless steel, antimagnetic. One pair is recommended for placing the tissue sample onto the microbalance and for handling in combination with Forceps\stainless Steel\straight Tip\sharp.
Forceps\stainless Steel\straight Tip\sharp
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Forceps\stainless Steel\straight Tip\sharp: for tissue preparation, stainless steel, antimagnetic. One pair is recommended for insertion of the sample into the O2k-chamber and for handling in combination with Forceps\stainless Steel\rounded Tip\sharp.
Converstion between different motive formats and corresponding motive units (Gnaiger 2020 BEC MitoPathways)

Different formats can be chosen to express physicochemical quantities (motive entities or transformants) in corresponding motive units [MU]. Fundamental formats for electrochemical transformations are:

  • N: particle or molecular format of a count; MU = x
  • n: chemical or molar format of amount; MU = mol
  • e: electrical format of charge; MU = C
  • m: mass format; MU = kg
  • V: volume format; MU = m3
  • G: exergy format; MU = J
  • H: enthalpy format; MU = J
  • S: entropy format; MU = J·K-1
Free radicalsA free radical is any atom or molecule that contains one or more unpaired electrons in an orbital. The degree of chemical reactivity depends on the localization of unpaired electrons. Free radicals are extremely reactive, and they can either donate or accept an electron from other molecules. Free radicals that include oxygen radicals and derivatives of oxygen are reactive oxygen species (ROS). Likewise, reactive nitrogen species (RNS) are nitric oxide-derived compounds. ROS/RNS include oxygen/nitrogen free radicals and non-radicals that are easily converted into radicals. Mitochondria are a main endogenous source of free radicals in cells and consequently are exposed to oxidative-nitrosative damage. Electron transfer in the electron transfer-pathway (ET-pathway) is not perfect, leading an electron leakage. This electron leakage permits the formation of ROS such as superoxide anion (O2•−), hydrogen peroxide (H2O2) and the hydroxyl radical (HO•).
French Group of BioenergeticsFGoBThe French Group of Bioenergetics...
Full screenBy clicking/enabling Full screen in the Graph-menu in DatLab the currently selected graph is shown alone on the full screen (On) or together with the other defined graphs (Off). Full screen is particularly useful for a single channel overview and for Copy to clipboard [ALT+G B].
FumaraseFHFumarase or fumarate hydratase (FH) is an enzyme of the tricarboxylic acid cycle catalyzing the equilibrium reaction between fumarate and malate. Fumarase is found not only in mitochondria, but also in the cytoplasm of all eukaryotes.
Fura2Fura2 is a ratiometric fluorescence probe for the measurement of calcium. Its derivative Fura-2-acetoxymethyl ester (Fura2-AM) is membrane permable and can thus be used to measure intracellular free calcium concentration (Grynkiewicz et al., 1985). For this purpose, cells are incubated with Fura2-AM, which crosses the cell membrane by diffusion and is cleaved into free Fura2 and acetoxymethyl groups by cellular esterases. Intracellular free calcium is measured by exciting the dye at 340 nm and 380 nm, which are the excitation optima of calcium-bound and free Fura2, respectively, and emission detection above 500 nm. Through the ratiometric detection unequal distribution of the dye within the cell and other potential disturbances are largely cancelled out, making this a widely used and relatively reliable tool for calcium measurements.
GM-pathway control stateGM
GM: Glutamate & Malate.

MitoPathway control state: NADH electron transfer-pathway state

The GM-pathway control state (glutamate-malate pathway control state) is established when glutamate&malate are added to isolated mitochondria, permeabilized cells and other mitochondrial preparations. Glutamate and transaminase are responsible for the metabolism of oxaloacetate, comparable to the metabolism with acetyl-CoA and citrate synthase.
GMS: Glutamate & Malate & Succinate.

MitoPathway control: NS

Transaminase catalyzes the reaction from oxaloacetate to 2-oxoglutarate, which then establishes a cycle without generation of citrate. OXPHOS is higher with GS (CI&II) compared to GM (CI) or SRot (CII). This documents an additive effect of convergent CI&II electron flow to the Q-junction, with consistent results obtained with permeabilized muscle fibres and isolated mitochondria (Gnaiger 2009).
GainThe gain is an amplification factor applied to an input signal to increase the output signal.
Gas constantR [J·mol-1·K-1]
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The gas constant R has the SI unit for energy per amount per temperature [J·mol-1·K-1]. R is primarily known from the ideal gas equation, pV = nRT or p = cRT. Therefore, RT is the ratio of pressure p and concentration c.

R = f·F, the electrochemical constant f times the Faraday constant F.

R = k·NA, the Boltzmann constant k times the Avogadro constant NA.
Gentle Science
GlucoseGlcGlucose, also known as D-glucose or dextrose, is a monosaccharide and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate.
Glutamic acid
Glutamic acid, C5H9NO4, is an amino acid which occurs under physiological conditions mainly as the anion glutamate-, G, with pKa1 = 2.1, pKa2 = 4.07 and pKa3 = 9.47. Glutamate&malate is a substrate combination supporting an N-linked pathway control state, when glutamate is transported into the mt-matrix via the glutamate-aspartate carrier and reacts with oxaloacetate in the transaminase reaction to form aspartate and oxoglutarate. Glutamate as the sole substrate is transported by the electroneutral glutamate-/OH- exchanger, and is oxidized in the mitochondrial matrix by glutamate dehydrogenase to α-ketoglutarate (2-oxoglutarate), representing the glutamate-anaplerotic pathway control state. Ammonia (the byproduct of the reaction) passes freely through the mitochondrial membrane.
Glutamate dehydrogenasemtGDHGlutamate dehydrogenase, located in the mitochondrial matrix (mtGDH), is an enzyme that converts glutamate to α-ketoglutarate [1]. mtGDH is not part of the TCA cycle, but is involved in glutaminolysis as an anaplerotic reaction.
Glutamate-anaplerotic pathway control stateG
G: Glutamate is an anaplerotic NADH-linked type 4 substrate (N). When supplied as the sole fuel substrate in the glutamate-anaplerotic pathway control state, G is transported by the electroneutral glutamate-/OH- exchanger, and is oxidised via mt-glutamate dehydrogenase in the mitochondrial matrix. The G-pathway plays an important role in glutaminolysis.
Glutamate-aspartate carrierThe glutamate-aspartate carrier catalyzes the electrogenic antiport of glutamate- +H+ for aspartate-. It is an important component of the malate-aspartate shuttle in many mitochondria. Due to the symport of glutamate- + +H+, the glutamate-aspartate antiport is not electroneutal and may be impaired by uncoupling. Aminooxyacetate is an inhibitor of the glutamate-aspartate carrier.
GlycerophosphateGpGlycerophosphate (synonym: α-glycerophosphate; glycerol-3-phosphate; C3H9O6P) is an organophosphate and it is a component of glycerophospholipids. The mitochondrial Glycerophosphate dehydrogenase complex oxidizes glycerophosphate to dihydroxyacetone phosphate and feeds electrons directly to ubiquinone.
Glycerophosphate dehydrogenase complexCGpDHGlycerophosphate dehydrogenase complex (CGpDH) is a complex of the Electron transfer-pathway localized at the outer face of the inner mt-membrane. CGpDH is thus distinguished from cytosolic GpDH. CGpDH oxidizes glycerophosphate to dihydroxyacetone phosphate and feeds two electrons into the Q-junction, thus linked to an ET pathway level 3 control state.
Glycerophosphate pathway control stateGp
The glycerophosphate pathway control state (Gp) is an ET-pathway level 3 control state, supported by the fuel substrate glycerophosphate and electron transfer through glycerophosphate dehydrogenase complex into the Q-junction. The glycerolphosphate shuttle represents an important pathway, particularly in liver and blood cells, of making cytoplasmic NADH available for mitochondrial oxidative phosphorylation. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophos-phate dehydrogenase. On the outer face of the inner mitochondrial membrane, mitochondrial glycerophosphate dehydrogenase oxidises glycerophosphate back to dihydroxyacetone phosphate, a reaction not generating NADH but reducing a flavin prosthesic group. The reduced flavoprotein donates its reducing equivalents to the electron transfer-pathway at the level of CoQ.
Glycerophosphate shuttleGp shuttle
The glycerophosphate shuttle makes cytoplasmic NADH available for mitochondrial oxidative phosphorylation. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophosphate dehydrogenase. On the outer face of the inner mitochondrial membrane, glycerophosphate dehydrogenase complex (mitochondrial glycerophosphate dehydrogenase) oxidizes glycerophosphate back to dihydroxyacetone phosphate, a reaction not generating NADH but reducing a flavin prosthesic group. The reduced flavoprotein transfers its reducing equivalents into the Q-junction, thus representing a ET pathway level 3 control state.
Gnaiger 2019 MiP2019
Graph layout - DatLab» See Layout for DatLab graphs.
Graph options - DatLabSeveral display options can be applied to a DatLab graph under Graph options.
GroupSee population.
H2DCFDADCF, H2-DCFH2DCFDA (dichlorodihydrofluorescein diacetate) is a cell permeant fluorescent probe that has been used as an indicator of ROS presence. It is a reduced form of fluorescein that does not present fluorescence. After entry in the cell, it suffers deacetylation by intracellular esterases, and upon oxidation it is converted to dichlorofluorescein (excitation wavelength ~492–495 nm, emission ~517–527 nm). It may be oxidised by hydrogen peroxide, hydroxyl radical, hypochlorite anion, nitric oxide, peroxyl radical, peroxynitrite, singlet oxygen and superoxide. Has been used as a general indicator of ROS by fluorescence microscopy.
HPTSHPTS8-Hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) is a ratiometric pH fluorophore; pKa = 7.3. Relative molecular mass: Mr = 524.39
HarmonizationHarmonization is the process of minimizing redundant or conflicting standards which may have evolved independently. To obtain a common basis in reaching a defined objective, critical requirements are identified that need to be retained.
Harmonized European normEN-normHarmonized European norms are norms valid for all members of the European Union. They are mandatory parts of the individual national collections of norms.
Harmonized SUIT protocolsH-SUITHarmonized SUIT protocols (H-SUIT) are designed to include cross-linked respiratory states. When performing harmonized SUIT protocols in parallel, measurements of cross-linked respiratory states can be statistically evaluated as replicates across protocols. Additional information is obtained on respiratory coupling and substrate control by including respiratory states that are not common (not cross-linked) across the harmonized protocols.
Harmonized standardA harmonised standard is a European standard developed by a recognised European Standards Organisation: CEN, CENELEC, or ETSI.
Healthy ageingHealthy ageing: 'WHO has released the first World report on ageing and health, reviewing current knowledge and gaps and providing a public health framework for action. The report is built around a redefinition of healthy ageing that centres on the notion of functional ability: the combination of the intrinsic capacity of the individual, relevant environmental characteristics, and the interactions between the individual and these characteristics' (Beard 2016 The Lancet).
Healthy reference populationHRPA healthy reference population, HRP, establishes the baseline for the relation between body mass and height in healthy people of zero underweight or overweight, providing a reference for evaluation of deviations towards underweight or overweight and obesity. The WHO Child Growth Standards (WHO-CGS) on height and body mass refer to healthy girls and boys from Brazil, Ghana, India, Norway, Oman and the USA. The Committee on Biological Handbooks compiled data on height and body mass of healthy males from infancy to old age (USA), published before emergence of the fast-food and soft-drink epidemic. Four allometric phases are distinguished with distinct allometric exponents. At heights above 1.26 m/x the allometric exponent is 2.9, equal in women and men, and significantly different from the exponent of 2.0 implicated in the body mass index, BMI [kg/m2].
HeatQ, Qth [J]Heat is a form of energy [J]. The relationship between heat and work provides the foundation of thermodynamics, which describes transformations from an initial to a final state of a system. In energy transformations heat may pass through the boundary of the system, at an external heat flow of deQ/dt.
Height of humansh [m]; H [m·x-1]The height of humans, h, is given in SI units in meters [m]. Humans are countable objects, and the symbol and unit of the number of objects is N [x]. The average height of N objects is, H = h/N [m/x], where h is the heights of all N objects measured on top of each other. Therefore, the height per human has the unit [m·x-1] (compare body mass [kg·x-1]). Without further identifyer, H is considered as the standing height of a human, measured without shoes, hair ornaments and heavy outer garments.
HeterothermyHeterothermy is the variable regulation of body temperature in endotherms which can change their body temperatures as levels of activity and environmental conditions dictate (e.g. hibernators). In regional heterothermy, temperature gradients are present, e.g. between body core and extremeties.
HexokinaseHKThe hexokinase catalyzes the phosphorylation of D-glucose at position 6 by ATP to yield D-glucose 6-phosphate as well as the phosphorylation of many other hexoses like D-fructose, D-mannose, D-glucosamine.
Heymsfield 2014 Am J Clin Nutr
High signal at zero oxygenR0A high signal at zero oxygen may be observed during zero calibration. The following instructions show how to further localize and possibly solve this technical problem.
High-resolution respirometryHRR
High-resolution respirometry, HRR, is the state-of-the-art approach in mitochondria and cell research to measure respiration in various types of mitochondrial preparations and living cells combined with MultiSensor modules. Mitochondrial function and dysfunction have gained an increasing interest over the past years, reflecting growing awareness of the fact that mitochondria play a pivotal role in human health and disease. Combining instrumental accuracy and reliability with versatility of applicable protocols - allowing practically unlimited addition and combination of substrates, inhibitors and uncouplers - mitochondrial respiratory pathways may be analyzed in detail to evaluate even minor alterations in respiratory pathway control and/or capacity. The most advanced way to analyze mitochondrial function is by means of high-resolution respirometry with the Oroboros O2k. The O2k is a sole source apparatus, with no other available instrument meeting its specifications for high-resolution respirometry. Substrate-uncoupler-inhibitor titration (SUIT) protocols allow the diagnosis of numerous mitochondrial pathway and coupling defects in a single respirometric assay. Technologically, HRR is based on the Oroboros O2k, combining optimized chamber design, application of oxygen-tight materials, electrochemical sensors, Peltier-temperature control, and specially developed software features (DatLab) to obtain the unique sensitive and quantitative resolution of oxygen concentration and oxygen flux, with both, a closed-chamber or open-chamber mode of operation (TIP2k). Standardized calibration of the polarographic oxygen sensor (static sensor calibration), calibration of the sensor response time (dynamic sensor calibration), and evaluation of instrumental background oxygen flux (systemic flux compensation) provide the experimental basis for high accuracy of quantitative results and quality control in HRR. HRR can be extended for MultiSensor analysis by using the O2k-FluoRespirometer. Smart Fluo-Sensors are integrated into the O2k to measure simultaneously fluorometric signals using specific fluorophores. Potentiometric modules are available with ion selective electrodes (pH, TPP+). The NextGen-O2k is the all-in-one device including the Q-redox sensor and a PhotoBiology (PB) module.
HolodeSmall entetic units are counted into the reference system on a balance opposite to the experimental system with the large sample, which in balance contains as many abstract units as the count of entetic units in the reference system.
HomeothermyHomeothermy is the stable regulation of body temperature in endotherms by metabolic heat production and control of heat exchange with the environment, or in ectotherms by behavioural means to select a stable thermal environment.
Hood 2019 Nutr Diabetes
Horseradish peroxidaseHRPHorseradish peroxidase readily combines with hydrogen peroxide (H2O2) and the resultant [HRP-H2O2] complex can oxidize a wide variety of hydrogen donors.
Hydrogen ionH+The terms hydrogen ion H+ and proton p are used synonymously in chemistry. A hydrogen ion is a positively charged molecule. In particle physics, however, a proton is a submolecular and subatomic particle with a positive electric charge. The H+ ion has no electrons and is a bare charge with only about 1/64 000 of the radius of a hydrogen atom. Free H+ is extremely reactive, with an extremely short lifetime in aqueous solutions. There H+ forms the hydronium ion H3O+, which in turn is further solvated by water molecules in clusters such as H5O2+ and H9O4+. The transfer of H+ in an acid–base reaction is referred to as proton transfer. The acid is the H+ donor and the base is the H+ acceptor.
Hydrogen ion pumpMitochondrial hydrogen ion pumps — frequently referred to as "proton pumps" — are large enzyme complexes (CI, CIII, CIV, ATP synthase) spanning the mt-inner membrane mtIM, partially encoded by mtDNA. CI, CIII and CIV are H+ pumps that drive hydrogen ions against the electrochemical protonmotive force pmF and thus generating the pmF, driven by electron transfer from reduced substrates to oxygen. In contrast, ATP synthase (also known as CV) is a H+ pump that utilizes the exergy of proton flow along the protonmotive force to drive phosphorylation of ADP to ATP.
Hydrogen peroxideH2O2
Hydrogen peroxide
Hydrogen peroxide, H2O2 or dihydrogen dioxide, is one of several reactive oxygen intermediates generally referred to as reactive oxygen species (ROS). It is formed in various enzyme-catalyzed reactions (e.g., superoxide dismutase) with the potential to damage cellular molecules and structures. H2O2 is dismutated by catalase to water and oxygen. H2O2 is produced as a signaling molecule in aerobic metabolism and passes membranes more easily compared to other ROS.
Hydrogen sulfideH2SHydrogen sulfide (H2S) is involved in signaling and may have have further biological importance.
Hydrogenion fluxJH+Volume-specific hydrogenion flux or H+ flux is measured in a closed system as the time derivative of H+ concentration, expressed in units [pmol·s-1·mL-1]. H+ flux can be measured in an open system at steady state, when any acidification of the medium is compensated by external supply of an equivalent amount of base. The extracellular acidification rate (ECAR) is the change of pH in the incubation medium over time, which is zero at steady state. Volume-specific H+ flux is comparable to volume-specific oxygen flux [pmol·s-1·mL-1], which is the (negative) time derivative of oxygen concentration measured in a closed system, corrected for instrumental and chemical background. pH is the negative logarithm of hydrogen ion activity. Therefore, ECAR is of interest in relation to acidification issues in the incubation buffer or culture medium. The physiologically relevant metabolic H+ flux, however, must not be confused with ECAR.
HydroxycinnamateHciHydroxycinnamate (alpha-cyano-4-hydroxycinnamic acid) is an inhibitor of the pyruvate carrier (0.65 mM). Above 10 mM pyruvate, hydroxycinnamate cannot inhibit respiration from pyruvate, since the weak pyruvic acid can pass the inner mt-membrane in non-dissociated form.
HydroxylamineHydroxylamine is an inhibitor of catalase.
HyperthermiaHyperthermia in endotherms is a state of stressful up to lethal elevated body core temperature. In humans, the limit of hyperthermia (fever) is considered as >38.3 °C, compared to normothermia at a body temperature of 36.5 to 37.5 °C.
HyphenationHyphenation is used to connect two words (compound words) or two parts of a word to clarify the meaning of a sentence. The same two words may be hyphenated or not depending on context. Hyphenation may present a problem when searching for a term such as 'Steady state'. It is helpful to write 'steady-state measurement', to clarify that the measurement is performed at steady state, rather than implying that a state measurement is steady. But this does not imply that hyphenation is applied to the 'measurement performed at steady state'. Thus, the key word is 'steady state'. Compound adjectives should be hyphenated (steady-state measurement), but if the compound adjective follows the term (measurement at steady state), hyphenation does not add any information and should be avoided. Find more examples and guidelines in the grammarly blog on Hyphen and in
HypothermiaHypothermia in endotherms is a state of stressful up to lethal low body core temperature. In humans, the limit of hypothermia is considered as 35 °C, compared to normothermia at a body temperature of 36.5 to 37.5 °C. Hypothermia is classified as mild (32–35 °C), moderate (28–32 °C), severe (20–28 °C), and profound (<20 °C).
HypoxichypoxHypoxia (hypox) is defined as the state when insufficient O2 is available for respiration.
IRDiRCIRDiRCIRDiRC.png The International Rare Diseases Research Consortium (IRDiRC) teams up researchers and organizations investing in rare diseases research in order to achieve two main objectives by the year 2020, namely to deliver 200 new therapies for rare diseases and means to diagnose most rare diseases.
ISE Package 1 TPP or Ca
ISE Package 1 TPP or Ca.JPG
O2k-TPP+ and Ca2+ ISE\1 Chamber: ISE-Package for 1 TPP+ and Ca2+ electrode.
ISE-Ca2+ Membranes
Ca2+ membranes.jpg
ISE-Ca2+ Membranes: PVC, 4 mm diameter, box of 5 membranes. To be used with the O2k-TPP+ ISE-Module.
ISE-Compressible Tube
ISE-Compressible Tube.JPG
ISE-Compressible Tube for Ion-Selective Electrode TPP+ and Ca2+.
ISE-Filling Syringe
ISE-Filling Syringe.JPG
ISE-Filling Syringe with needle for Ion-Selective Electrode TPP+ and Ca2+.
ISE-Inner Glass Electrode
ISE-Inner Glass Electrode.JPG
ISE-Inner Glass Electrode of ISE, with Ag/AgCl- and Pt-wire
ISE-Membrane Mounting Tool
ISA-Membrane Mounting Tool.JPG
ISE-Membrane Mounting Tool for Ion-Selective Electrode TPP+ and Ca2+. O2k-TPP+ ISE-Module: mounting tool included.
ISE-Membrane Seal
ISE-Membrane Seal.JPG
'ISE-Membrane Seal for Ion-Selective Electrode TPP+ and Ca2+.
ISE-Service BoxISE-Service Box: for storage and shipment of the O2k-TPP+ ISE-Module or O2k-pH ISE-Module.
ISE-TPP+ Membranes
ISE-TPP+ Membranes.JPG
ISE-TPP+ Membranes, PVC, 4 mm diameter, box of 5 membranes.
ISO 10012:2003 Measurement management systemsISO 10012:2003ISO 10012:2003 Measurement management systems — Requirements for measurement processes and measuring equipment: An effective measurement management system ensures that measuring equipment and measurement processes are fit for their intended use and is important in achieving product quality objectives and managing the risk of incorrect measurement results. The objective of a measurement management system is to manage the risk that measuring equipment and measurement processes could produce incorrect results affecting the quality of an organization’s product. The methods used for the measurement management system range from basic equipment verification to the application of statistical techniques in the measurement process control.
ISO 13528:2015 Statistical methods for use in proficiency testing by interlaboratory comparisonISO 13528:2015ISO 13528:2015 Statistical methods for use in proficiency testing by interlaboratory comparison: Proficiency testing involves the use of interlaboratory comparisons to determine the performance of participants (which may be laboratories, inspection bodies, or individuals) for specific tests or measurements, and to monitor their continuing performance. There are a number of typical purposes of proficiency testing ISO/IEC 17043:2010. These include the evaluation of laboratory performance, the identification of problems in laboratories, establishing effectiveness and comparability of test or measurement methods, the provision of additional confidence to laboratory customers, validation of uncertainty claims, and the education of participating laboratories. The statistical design and analytical techniques applied must be appropriate for the stated purpose(s).
ISO 15189:2012 Medical laboratories — Particular requirements for quality and competenceISO 15189:2012ISO 15189:2012 Medical laboratories — Particular requirements for quality and competence: This International Standard is for use by medical laboratories in developing their quality management systems and assessing their own competence, and for use by accreditation bodies in confirming or recognising the competence of medical laboratories. While this International Standard is intended for use throughout the currently recognised disciplines of medical laboratory services, those working in other services and disciplines could also find it useful and appropriate.
ISO 17511:2003 In vitro diagnostic medical devicesISO 17511:2003ISO 17511:2003 In vitro diagnostic medical devices -- Measurement of quantities in biological samples -- Metrological traceability of values assigned to calibrators and control materials: For measurements of quantities in laboratory medicine, it is essential that the quantity is adequately defined and that the results reported to the physicians or other health care personel and patients are adequately accurate (true and precise) to allow correct medical interpretation and comparability over time and space.
ISO 9001:2015 Quality management systems - requirementsISO 9001:2015ISO 9001:2015 Quality management systems - requirements: The adoption of a quality management system is a strategic decision for an organization that can help to improve its overall performance and provide a sound basis for sustainable development initiatives. Consistently meeting requirements and addressing future needs and expectations poses a challenge for organizations in an increasingly dynamic and complex environment. To achieve this objective, the organization might find it necessary to adopt various forms of improvement in addition to correction and continual improvement, such as breakthrough change, innovation and re-organization.
ISO/IEC 17025:2005 Competence of testing and calibration laboratoriesISO/IEC 17025:2005ISO/IEC 17025:2005 General requirements for the competence of testing and calibration laboratories: The use of this International Standard will facilitate cooperation between laboratories and other bodies, and assist in the exchange of information and experience, and in the harmonization of standards and procedures. This International Standard specifies the general requirements for the competence to carry out tests and/or calibrations, including sampling. It covers testing and calibration performed using standard methods, non-standard methods, and laboratory-developed methods.
ISO/IEC 17043:2010 General requirements for proficiency testingISO/IEC 17043:2010ISO/IEC 17043:2010 Conformity assessment — General requirements for proficiency testing: The use of interlaboratory comparisons is increasing internationally. This International Standard provides a consistent basis to determine the competence of organizations that provide proficiency testing.
ISS-Filter and Tubing
ISS-Filter and Tubing.JPG
ISS-Filter and Tubing, ISS-Integrated Suction System.
ISS-Integrated Suction System
ISS-Integrated Suction System: Suction pump with stainless steel housing, 2 liter waste bottle, filter and tubing; for siphoning off excess medium from the O2k-Stopper and for emptying the O2k-chambers. The ISS is included as a standard component of the O2k-FluoRespirometer. Media containing living cells or microorganisms, various poisons (inhibitors, uncouplers) and mixtures of proteins and substrates are safely disposed off in the 2-litre waste bottle.
ISS-Lid, for ISS-Waste Bottle, component of the ISS-Integrated Suction System.
ISS-Steel Housing
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ISS-Steel Housing, a component of the ISS-Integrated Suction System.
ISS-Waste Bottle
ISS-Waste Bottle.JPG
ISS-Waste Bottle, 2-liter, component of the ISS-Integrated Suction System.
Iconic symbolsIconic symbols are used in ergodynamics to indicate more explicitely — compared to standard SI or IUPAC symbols — the quantity represented. This is particularly the case in normalized quantities (ratios of quantities). Iconic (or canonical) symbols help to clarify the meaning, are based on SI and IUPAC symbols as far as possible, and may be translated into more commonly used, practical symbols. Several ambiguities in SI and IUPAC symbols are eliminated by the systematic structure of iconic symbols, but it may be impossible to avoid all ambiguities, particulary when long (canonical) symbols are abbreviated in a particular context. Clarity is improved always by showing the unit of a quantity together with the symbol of the quantity. Iconic symbols cannot be identical with IUPAC symbols when a different definition is used — this would add to the confusion. For example, the IUPAC symbols nB [mol] and VB [m3] denote amount and volume of B. Consequently, it should be expected, that the symbol QB indicates charge of B [C]. However, the IUPAC symbol QB is used for particle charge per ion B [C·x-1]. This prohibits a consistent definition of QB as a potential iconic symbol for charge carried by a given quantity of ions B with unit [C], instead of particle charge per ion B with unit [C·x-1]. Hence, the conventional ambigous system forces compatible iconic symbols to be more complicated, using QelB [C] and QNB [C·x-1] to distinguish charge of B from charge per elementary B. QnB [C·mol-1] is charge per molar amount of B.
IlluminationF10The chambers of the Oroboros O2k are illuminated by an internal LED. The illumination is switched on and off in DatLab during the experiment by pressing [F10]. This illumination must be distinguished from light introduced into the chambers by LEDs for the purpose of spectrophotometric and fluorometric measurements. For these, the internal illumination must be switched off.
Illumination on/offF10The illumination in both chambers is switched on/off.
Improvement scoreRISThe relative improvement score, RIS, provides a measure of improvement of a trait from a value measured at baseline, B, to a value measured after treatment, T, expressing the total improvement, T-B, in relation to the theoretical scope of improvement and the level of the trait observed at baseline. RIS incorporates the concept of diminishing returns and consideres maintaining a high value of a trait as an improvement relative to the potential loss.
In vitro diagnostic medical deviceIVDA medical device is an in vitro diagnostic medical device (IVD) if it is a reagent, calibrator, control material, kit, specimen receptacle, software, instrument, apparatus, equipment or system, whether used alone or in combination with other diagnostic goods for in vitro use.
Incident lightThe term incident light is used for a beam of light falling upon a surface.
Inclusion criteriaThe Inclusion criteria are based on key features of the target population that the researchers will use to answer their question. These criteria should identify the study population in a consistent, reliable, uniform, and objective manner. With the Exclusion criteria, this factor must be a cofounder for the outcome parameter
Indian Academy of Pediatrics Growth Charts Committee 2015 Indian Pediatr
Inorganic phosphatePiInorgnic phosphate (Pi) is a salt of phosphoric acid. In solution near physiological pH, the species HPO42- and H2PO4- dominate. See also: Phosphate carrier (Pic).
Inside the O2kA glance inside the Oroboros O2k
Install Oroboros protocol packageThe standard Instrumental and SUIT DL-Protocols package is automatically implemented with the simple DatLab programme installation. We recommend a 'clean install': rename your previous DatLab programme subdirectory (e.g. C:\DatLab_OLD). Updates and newly developed DL protocols can be simply downloaded by clicking on [Protocols]\Install Oroboros protocol package.
Instrumental: Browse DL-Protocols and templatesInstrumental DL-Protocols (DLP) including DatLab example traces, instructions, brief explanatory texts, links to relevant pages and templates for data evaluation can be browsed from inside DatLab 7.4. Click on menu [Protocols]\Instrumental: Browse DL-Protocols and templates to open a folder with all the DL-Protocols and templates for cleaning, calibration, and background determination provided with the DatLab 7.4. Select a sub-directory and open an DL-Protocol and/or template as desired.
Integration timeIntegration time is the time taken to scan a single full range spectrum using photodiode arrays. It is equivalent to the exposure time for a camera. The shortest integration time defines the fastest response time of a spectrophotometer. Increasing the integration time increases the sensitivity of the device. The white balance or balance and subsequent measurements must always be carried out at the same integration time.
Intensive quantityIntensive quantities are partial derivatives of an extensive quantity by the advancement, dtrξ, of an energy transformation. See: Force.
Interlaboratory comparisonAn interlaboratory comparison is the organization, performance and evaluation of measurements or tests on the same or similar items by two or more laboratories in accordance with predetermined conditions.
Internal flowIi [MU·s-1]Within the system boundaries, irreversible internal flows, Ii,—including chemical reactions and the dissipation of internal gradients of heat and matter—contribute to internal entropy production, diS/dt. In contrast, external flows, Ie, of heat, work, and matter proceed reversibly across the system boundaries (of zero thickness). Flows are expressed in various formats per unit of time, with corresponding motive units [MU], such as chemical [mol], electrical [C], mass [kg]. Flow is an extensive quantity, in contrast to flux as a specific quantity.
Internal-energyU [J]Internal-energy, U [J], can neither be destroyed nor created (first law of thermodynamics: diU/dt = 0). Note that internal (subscript i), as opposed to external (subscript e), must be distinguished from "internal-energy", U, which contrasts with "Helmholtz energy", A, as enthalpy, H, contrasts with Gibbs energy, G.
International Mito Patients (IMP)IMPIMP LOGO.JPGThe International Mito Patients is a network of national patient organizations involved in mitochondrial disease. Mitochondrial disease is a rare disease with a limited number of patients per country. The national patient organizations which are a member of IMP each are active and powerful in their own countries. By joining forces IMP can represent a large group of patients and as such be their voice on an international level.
International Society for Mountain MedicineISMM
The International Society for Mountain Medicine is an interdisciplinary society comprising about xx members worldwide. Its purpose is ..
International Society on Oxygen Transport to TissueISOTT
The International Society on Oxygen Transport to Tissue is an interdisciplinary society comprising about 250 members worldwide. Its purpose is to further the understanding of all aspects of the processes involved in the transport of oxygen from the air to its ultimate consumption in the cells of the various organs of the body. Founded in 1973, the society has been the leading platform for the presentation of many of the technological and conceptual developments within the field both at the meetings themselves and in the proceedings of the society.
International Standard Serial NumberISSNThe International Standard Serial Number, ISSN, is a code used to identify periodical publications, independent of which media are used (print and/or electronic).
International System of UnitsSIThe International System of Units (SI) is the modern form of the metric system of units for use in all aspects of life, including international trade, manufacturing, security, health and safety, protection of the environment, and in the basic science that underpins all of these. The system of quantities underlying the SI and the equations relating them are based on the present description of nature and are familiar to all scientists, technologists and engineers. The definition of the SI units is established in terms of a set of seven defining constants. The complete system of units can be derived from the fixed values of these defining constants, expressed in the units of the SI. These seven defining constants are the most fundamental feature of the definition of the entire system of units. These particular constants were chosen after having been identified as being the best choice, taking into account the previous definition of the SI, which was based on seven base units, and progress in science (p. 125).
International Union of Pure and Applied Chemistry, IUPACIUPACThe International Union of Pure and Applied Chemistry (IUPAC) celebrated in 2019 the 100th anniversary, which coincided with the International Year of the Periodic Table of Chemical Elements (IYPT 2019). IUPAC {quote} notes that marking Mendeleev's achievement will show how the periodic table is central to connecting cultural, economic, and political dimensions of global society “through a common language” {end of quote} (Horton 2019). 2019 is proclaimed as the International Year of the Periodic Table of Chemical Elements (IYPT 2019). For a common language in mitochondrial physiology and bioenergetics, the IUPAC Green book (Cohen et al 2008) is a most valuable resource, which unfortunately is largely neglected in bioenergetics textbooks. Integration of open systems and non-equilibrium thermodynamic approaches remains a challenge for developing a common language (Gnaiger 1993; BEC 2020.1).
Internationale Gesellschaft fuer Regenerative Mitochondrien-MedizinIGRMM e.V.Organizer of
Interpolate pointsSelect Interpolate points in the Mark information window to interpolate all data points in the marked section of the active graph. See also Delete points and Restore points or Recalculate slope.
Intrinsic fluorophoresAn Intrinsic flourophore is a naturally occurring fluorophore of which NADH, aromatic amino acids and flavins are examples.
Ion-Selective Electrode TPP+ and Ca2+
Ion-Selective Electrode TPP+ and Ca2+.JPG
Ion-Selective Electrode TPP+ and Ca2+: ISE with 6 mm outer diameter shaft, for Stopper\white PVDF\angular Shaft\side+6.2+2.6 mm Port. O2k-TPP+ ISE-Module: 2 ISE.
IonomycinImyIonomycin (Imy) is a ionophore used to raise intracellular [Ca2+].
isocitrate, C6H5O7-3, is a tricarboxylic acid trianion, intermediate of the TCA cycle, obtained by isomerization of citrate. The process is catalyzed by aconitase, forming the enzyme-bound intermediate cis-aconitate.
Isocitrate dehydrogenaseIDHIsocitrate dehydrogenase forms 2-oxoglutarate from isocitrate in the TCA cycle.
Isolated mitochondriaimtIsolated mitochondria, imt, are mitochondria separated from a tissue or cells by breaking the plasma membranes and attachments to the cytoskeleton, followed by centrifugation steps to separate the mitochondria from other components.
Isolated systemThe boundaries of isolated systems are impermeable for all forms of energy and matter. Changes of isolated systems have exclusively internal origins, e.g., internal entropy production, diS/dt, internal formation of chemical species i which is produced in a reaction r, dini/dt = drni/dt. In isolated systems some internal terms are restricted to zero by various conservation laws which rule out the production or destruction of the respective quantity.
IsomorphicThe term isomorphic refers to quantities which have identical or similar form, shape, or structure. In mathematics, an isomorphism defines a one-to-one correspondence between two mathematical sets. In ergodynamics, isomorphic quantities are defined by equations of identical form. If isomorphic quantities are not expressed in identical units, then these quantities are expressed in different formats which can be converted to identical untis. Example: electric force [V=J/C] and chemical force [Jol=J/mol] are ismorphic forces; the electrical format [J/C] can be converted to the chemical format [J/mol] by the Faraday constant. Units not only give meaning to the numerical value of a quantity, but units provide also an abbreviated common language to communicate and compare isomorphic quantities. In irreversible thermodynamics, isomorphic forces are referred to as generalized forces.
Japanese Society of Mitochondrial Research and MedicineJ-mit
The Japanese Society of Mitochondrial Research and Medicine (J-mit) was founded to share the latest knowledge on mitochondrial research. J-mit is the biggest Asian society of mitochondrial research and medicine and is a member of ASMRM.
JmaxJmaxJmax is the maximum pathway flux (e.g. oxygen flux) obtained at saturating substrate concentration. Jmax is a function of metabolic state. In hyperbolic ADP or oxygen kinetics, Jmax is calculated by extrapolation of the hyperbolic function, with good agreement between the calculated and directly measured fluxes, when substrate levels are >20 times the c50 or p50.
Journal indexingJournal indexing allows publications to be found on search tools/databases. Each database might have different criteria of inclusion.
Journal issueAn issue of a journal or periodical is a number, which typically indicates how many times a volume of the journal has been published in sequence.
Journal publicationIn most cases journal publication {Quote} will not be affected by posting a preprint. However, there are some publishers that do not consider papers that have already appeared online. We strongly recommend that you check all journals that you might submit to in advance {end of Quote}. A list of academic journals by preprint policy is available.
Journal volumeThe volume of a journal or periodical is a number, which in many cases indicates the sequential number of years the journal has been published. Alternatively, the volume number may indicate the current year, independent of the year in which the journal published its first volume. A volume may be subdivided into issues.
Journals in Bioblast
KelvinKThe kelvin, symbol K, is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380 649 × 10−23 when expressed in the unit J x-1 K−1.
Keywords-MitoPedia in BECKeywords—MitoPedia is the concept to link keywords in articles published in Bioenergetics Communications (BEC) to MitoPedia terms. Authors should consider the message in the selected keywords. Provide consistent definitions of your keywords by linking them to MitoPedia. Extend MitoPedia entries critically by your contributions. The BEC editorial team will hyperlink your keywords with MitoPedia, and a reference to your BEC publication will be generated automatically from the MitoPedia term to your publication. With your contributions, BEC elevates keywords to terms with meaning. Your article gains visibility.
KilogramkgThe kilogram, symbol kg, is the SI unit of mass. It is defined by taking the fixed numerical value of the Planck constant h to be 6.626 070 15 × 10−34 when expressed in the unit J s, which is equal to kg m2 s−1, where the meter and the second are defined in terms of c and ΔνCs.
Korean Society of Mitochondrial Research and MedicineKSMRMThe Korean Society of Mitochondrial Research and Medicine (KSMRM) is a member of ASMRM.
Kynurenine hydroxylaseKynurenine hydroxylase (kynurenine 3-monooxygenase) is located in the outer mitochondrial membrane. Kynurenine hydroxylase catalyzes the chemical reaction: L-kynurenine + NADPH + H+ + O2 ↔ 3-hydroxy-L-kynurenine + NADP+ + H2O Kynurenine hydroxylase belongs to the family of oxidoreductases acting on paired donors, with O2 as oxidant and incorporation or reduction of oxygen. The oxygen incorporated need not be derived from O2 with NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor. This enzyme participates in tryptophan metabolism. It employs one cofactor, FAD.
L/E coupling-control ratioL/ELEAK control ratio The L/E coupling-control ratio is the flux ratio of LEAK respiration over ET capacity, as determined by measurement of oxygen consumption in L and E sequentially. The L/E coupling-control ratio is an index of uncoupling or dyscoupling at constant ET-capacity. L/E increases with uncoupling from a theoretical minimum of 0.0 for a fully coupled system, to 1.0 for a fully uncoupled system.
L/P coupling-control ratioL/PL/P coupling-control ratio The L/P coupling-control ratio or LEAK/OXPHOS coupling-control ratio combines the effects of coupling (L/E) and limitation by the phosphorylation system (P/E); L/P = (L/E) / (P/E) = 1/RCR.
L/R coupling-control ratioL/RL/R coupling-control ratio The L/R coupling-control ratio or LEAK/ROUTINE coupling-control ratio combines the effects of coupling (L/E), physiological control of energy demand, and limitation by the OXPHOS capacity.
LEAK state with ATPL(T)L.jpg The LEAK state with ATP is obtained in mt-preparations without ATPase activity after ADP is maximally phosphorylated to ATP (State 4; Chance and Williams 1955) or after addition of high ATP in the absence of ADP (Gnaiger et al 2000). Respiration in the LEAK state with ATP, L(T), is distinguished from L(n) and L(Omy).
LEAK state with oligomycinL(Omy)L.jpg The LEAK state with oligomycin is a LEAK state induced by inhibition of ATP synthase by oligomycin. ADP and ATP may or may not be present. LEAK respiration with oligomycin, L(Omy), is distinguished from L(n) and L(T).
LEAK state without adenylatesL(n)L.jpg In the LEAK state without adenylates mitochondrial LEAK respiration, L(n) (n for no adenylates), is measured after addition of substrates, which decreases slowly to the LEAK state after oxidation of endogenous substrates with no adenylates. L(n) is distinguished from L(T) and L(Omy).
Laboratory titration sheetLaboratory titration sheet contains the sequential titrations in a specific Substrate-uncoupler-inhibitor titration (SUIT) protocol. The laboratory titration sheets for different SUIT protocols are incorporated in DatLab (DL7.1): Protocols in DatLab
Lactate dehydrogenaseLDHLactate dehydrogenase is a glycolytic marker enzyme in the cytosol, regenerating NAD+ from NADH and pyruvate, forming lactate.
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