MitoPedia: Terms and abbreviations

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MitoPedia

MitoPedia: Terms and abbreviations

MitoPedia - high-resolution terminology - matching measurements at high-resolution.
The MitoPedia terminology is developed continuously in the spirit of Gentle Science.


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

References

  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«


TermAbbreviationDescription
1OctM;2D;3PG;4S;5U;6Rot-FNS(Oct,PGM)1OctM;2D;3PG;4S;5U;6Rot-.png
1PGM;2D;3S;4Rot;5U-NS(PGM)1PGM;2D;3S;4Rot;5U-.png
1PGM;2D;3S;4U;5Rot-NS(PGM)1PGM;2D;3S;4U;5Rot-.png
1PGM;2D;3U;4S;5Rot-NS(PGM)1PGM;2D;3U;4S;5Rot-.png
1PM;2D;3G;4U;5S;6Rot-NS(PGM)1PM;2D;3G;4U;5S;6Rot-.png
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 nucleotid. 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 production of ADP, which can stimulate respiration. This situation would lead to an overestimations of LEAK measured in the absence of ADP, L(n).
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.
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.
ActivityaThe activity (relative activity) is a dimensionless quantity related to the concentration or partial pressure of dissolved substances. 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.

For a dissolved gas G, the activity is the partial pressure, pG [Pa] (strictly: fugacity), divided by the unit partial pressure, p° = 1 Pa. The partial pressure is related to the concentration of the gas by the solubility, SG [Pa/mol] (see Oxygen solubility):

aG = cG·SG/p°

In general, the relative activity is defined by the chemical potential, µX

aX = exp[(µX-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.
Additive effect of convergent electron flowAα&βAdditivity describes the princple of substrate control of mitochondrial respiration with convergent electron flow. The additive effect of convergent electron flow is a consequence of electron flow converging at the Q-junction from respiratory Complexes I and II (NS or CI&II e-input). Further additivity may be observed by convergent electron flow through glycerophosphate dehydrogenase and electron-transferring flavoprotein complex. Convergent electron flow corresponds to the operation of the TCA cycle and mitochondrial substrate supply in vivo. Physiological substrate combinations supporting convergent NS e-input are required for reconstitution of intracellular TCA cycle function. Convergent electron flow simultaneously through Complexes I and II into the Q-junction supports higher OXPHOS-capacity and ET-capacity than separate electron flow through either CI or CII. The convergent NS effect may be completely or partially additive, suggesting that conventional bioenergetic protocols with mt-preparations have underestimated cellular OXPHOS-capacities, due to the gating effect through a single branch. Complete additivity is defined as the condition when the sum of separatly measured respiratory capacities, N + S, is identical to the capacity measured in the state with combined substrates, NS (CI&II). This condition of complete additivity, NS=N+S, would be obtained if electron channeling through supercomplex CI, CIII and CIV does not interact with the pool of redox intermediates in the pathway from CII to CIII and CIV, and if the capacity of the phosphorylation system (≈P) does not limit OXPHOS-capacity (excess E-P capacity factor is zero). In most cases, however, additivity is incomplete, NS < N+S.
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],

Advancement.png
Advancement per volumedtrY [MU∙L-1]Advancement per volume or volume-specific advancement, dtrY, is related to advancement of a transformation, dtrY = dtrξV-1 [MU∙L-1]. Compare dtrY with the amount of substance j per volume, cj (concentration), related to amount, cj = njV-1 [mol∙V-1]. Advancement per volume is particularly introduced for chemical reactions, drY, and has the dimension of concentration (amount per volume [mol∙L-1]). In an open system at steady-state, however, the concentration does not change as the reaction advances. Only in closed systems and isolated systems, specific advancement equals the change in concentration divided by the stoichiometric number,
drY = dcj/νj (closed system) 
drY = drcj/νj (general) 

With a focus on internal transformations (i; specifically: chemical reactions, r), dcj is replaced by the partial change of concentration, drcj (a transformation variable or process variable). drcj contributes to the total change of concentration, dcj (a system variable or variable of state). In open systems at steady-state, drcj is compensated by external processes, decj = -drcj, exerting an effect on the total concentration change of substance j,

dcj = drcj + decj = 0 (steady state)
dcj = drcj + decj (general)
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.
Air calibrationR1Air calibration of an oxygen sensor (polarographic oxygen sensor) is performed routinely on any day before starting a respirometric experiment. The volume fraction of oxygen in dry air is constant. An aqueous solution in equilibrium with air has the same partial pressure as that in water vapour saturated air. The water vapour is a function of temperature only. The partial oxygen pressure in aqueous solution in equilibrium with air is, therefore, a function of total barometric pressure and temperature. Bubbling an aqueous solution with air generates deviations from barometric pressure within small gas bubbles and is, therefore, not recommended. To equilibrate an aqueous solution ata known partial pressure of oxygen [kPa], the aqueous solution is stirred rigorously in a chamber enclosing air at constant temperature. The concentration of oxygen, cO2 [µM], is obtained at any partial pressure by multiplying the partial pressure by the oxygen solubility, SO2 [µM/kPa]. SO2 is a function of temperature and composition of the salt solution, and is thus a function of the experimental medium. The solubility factor of the medium, FM, expresses the oxygen solubility relative to pure water at any experimental temperature. FM is 0.89 in serum (37 °C) and 0.92 in MiR06 or MiR05 (30 °C and 37 °C).
Alternative oxidaseAOXThe alternative oxidase is a membrane-bound enzyme capable of supporting cyanide-and antimycin A-resistant mitochondrial respiration. It catalyzes the oxidation of ubiquinol and the reduction of oxygen to water in a four electron process. As this bypasses several proton-translocating steps, inducton of this alternative pathway is associated with a dramatic reduction of ATP production. Expression and activity of the enzyme is modified by environmental conditions such as temperature, oxidative stress, nutrient availability, as well as by pathogens such as viruses. AOX can be found in most plants (including microalgae), many fungi and protists, but is not expressed in animals.
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 of specified elementary entities, Ni of that substance i, and the universal proportionality constant is the reciprocal value of the Avogadro constant [1],
ni = Ni/NA

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

dni = dini + deni

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 i, 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 i is formed as a product of the reaction within the system. deni is negative if i flows out of the system and appears as a product in the surroundings [2].
Amp calibration - DatLabAmp calibration indicates the calibration of the amperometric O2k-channel.
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 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), phosphoenopyruvate 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: arXiv.org 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.
AscorbateAsIn respiratory assays for cytochrome c oxidase activity (Complex IV, CIV), ascorbate is added as regenerating system for maintaining TMPD in a reduced state. As has to be titrated into the respiration medium prior to the addition of TMPD, otherwise the reaction velocity of autoxidation is permanently elevated.
Asia Society for Mitochondrial Research and MedicineASMRM
ASMRM LOGO.JPG
The Asia Society for Mitochondrial Research and Medicine (ASMRM) was founded in 2003 to share the latest knowledge on mitochondrial research.
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.
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
The Avogadro constant, NA, has the SI unit [mol-1] (IUPAC), but more strictly the units for particles per amount is [x·mol-1] (compare Elementary charge). Therefore, the reciprocal of the Avogadro constant is the proportionality factor between the amount of substance and the number of specified elementary entities of that substance. 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.
Background stateYThe background state, Y, is the non-activated or inhibited respiratory state at background flux, which is low in relation to the higher flux 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 factor. 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.
Barometric pressurepb [Pa]Barometric pressure, pb, is an important variable measured for calibration of oxygen sensors in solutions equilibrated with air. The atm-standard pressure (1 atm = 760 mmHg = 101.325 kPa) has been replaced by the SI standard pressure of 100 kPa. The partial pressure of oxygen, pO2, in air is a function of barometric pressure, which changes with altitude and locally with weather conditions. The partial oxygen pressure declines by 12% to 14% per 1,000 m up to 6,000 m altitude, and by 15% to 17% per 1,000 m between 6,000 and 9,000 m altitude. The O2k-Barometric Pressure Transducer is built into the Oroboros O2k as a basis for accurate air calibrations in high-resolution respirometry. For highest-level accuracy of calculation of oxygen pressure, it is recommended to compare at regular intervals the barometric pressure recording provided by the O2k with a calibrated barometric pressure recording at an identical time point and identical altitude. The concept of gas pressure or barometric pressure can be related to the generalized concept of isomorphic pressure.
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.

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Contributed by Sparagna GC 2016-04-24
Basal respirationBMRBasal respiration or basal metabolic rate (BMR) is the minimal rate of metabolism required to support basic body functions, essential for maintenance only. BMR (in humans) is measured at rest 12 to 14 hours after eating in a physically and mentally relaxed state at thermally neutral room temperature. Maintenance energy requirements include mainly the metabolic costs of protein turnover and ion homeostasis. In many aerobic organisms, and particularly well studied in mammals, BMR is fully aerobic, i.e. direct calorimetry (measurement of heat dissipation) and indirect calorimetry (measurement of oxygen consumption multiplied by the oxycaloric equivalent) agree within errors of measurement (Blaxter KL 1962. The energy metabolism of ruminants. Hutchinson, London: 332 pp [1]). In many cultured mammalian cells, aerobic glycolysis contributes to total ATP turnover (Gnaiger and Kemp 1990 [2]), and under these conditions, 'respiration' is not equivalent to 'metabolic rate'. Basal respiration in humans and skeletal muscle mitochondrial function (oxygen kinetics) are correlated (Larsen et al 2011 [3]). » MiPNet article
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.
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 efficiencyj≈P or j≈EOXPHOS coupling efficiency ET-coupling efficiency The biochemical coupling efficiency may be expressed as the OXPHOS coupling efficiency, j≈P = (P-L)/P = 1-L/P, or ET-coupling efficiency, j≈E = (E-L)/E = 1-L/E, which are equivalent at zero excess E-P capacity (ExP = E-P = 0).
Biochemical threshold effectDue to threshold effects, even a large defect diminishing the velocity of an individual enzyme results in only minor changes of pathway flux.
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.
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, RBC, WBC and platelets. However, there are many proteins in plasma, i.e. fibrinogen, albumin and globulin. Both blood plasma and PRP 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.
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] (compare Gas constant).
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.
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).
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 the of 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).
Calorespirometric ratioCR ratio [kJ/mol]The calorimetric/respirometric or calorespirometric ratio (CR ratio) is the ratio of calorimetrically and respirometrically measured heat and oxygen flux, determinded by calorespirometry. The experimental CR ratio is compared with the theoretically derived oxycaloric equivalent, and agreement in the range of -450 to -480 kJ/mol O2 indicates a balanced aerobic energy budget (Gnaiger and Staudigl 1987). In the transition from aerobic to anaerobic metabolism, there is a limiting pO2, plim, below which CR ratios become more exothermic since anaerobic energy flux is switched on.
CalorespirometryCRCalorespirometry is the method of measuring simultaneously metabolic heat flux (calorimetry) and oxygen flux (respirometry). The calorespirometric ratio (CR ratio; heat/oxygen flux ratio) is thus experimentally determined and can be compared with the theoretical oxycaloric equivalent, as a test of the aerobic energy balance.
CarbohydrateCarbohydrates, also known as saccharides, are molecules composed of carbon, hydrogen and oxygen. These molecules can be divided by size and complexity in 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 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 hydrazoneCCCP, UCarbonyl 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
CERG

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 ICPT 1Carnitine palmitoyltransferase I (CPT 1) 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. 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) transports acyl-carnitines into the mitochondrial matrix in exchange for free L-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).
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 culture mediaCell culture media, like RPMI or DMEM, used for HRR of intact cells.
Cell ergometryBiochemical cell ergometry aims at measurement of JO2max (compare VO2max or VO2peak in exercise ergometry of humans and animals) of cell respiration linked to phosphorylation of ADP to ATP. The corresponding OXPHOS capacity is based on saturating concentrations of ADP, [ADP]*, and inorganic phosphate, [Pi]*, available to the mitochondria. This is metabolically opposite to uncoupling respiration, which yields ET-capacity. The OXPHOS state can be established experimentally by selective permeabilization of cell membranes with maintenance of intact mitochondria, titrations of ADP and Pi to evaluate kinetically saturating conditions, and establishing fuel substrate combinations which reconstitute physiological TCA cycle function. Uncoupler titrations are applied to determine the apparent ET-pathway excess over OXPHOS capacity and to calculate OXPHOS- and ET-coupling efficiency , j≈P and j≈E. These normalized flux ratios are the basis to calculate the ergometric or ergodynamic efficiency, ε = j · f, where f is the normalized force ratio. » MiPNet article
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 the use of external electron acceptors, transported into the cell from the environment. The chemical potential from electron donors to electron acceptors is converted in the Electron transfer-pathway to generate 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 standard Chamber volume of the O2k is 2.0 ml of aqueous medium with or without sample, excluding the volume of the stirrer and the volume of the capillary of the stopper.
ChannelF7» See O2k signals and output
Charge numberzThe charge number of an ion or electrochemical reaction is the charge divided by the elementary charge of the ion or of electrons transferred in the reaction as defined in the reaction equation. z is a positive integer. zB = QB·e-1
Chemical background correction of oxygen fluxChemical background correction of oxygen flux is the correction of oxygen flux for the side reaction of autooxidation, as a function of oxygen concentration.
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.
Choline dehydrogenaseCholine dehydrogenase (EC 1.1.99.1) 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 ET-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 synthaseCSCondensation of oxaloacetate with acetyl-CoA yields citrate as an entry into the TCA cycle, with CS located in the mt-matrix.
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.
ClassificationClassification of in vitro diagnostic medical devices (IVD) describes the category to which an IVD belongs.
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 systemA closed system is a system with boundaries that allow external exchange of energy (heat and work), but do not allow exchange of matter. A limiting case is light and electrons which cross the system boundary when work is exchanged in the form of light or electric energy. If the surroundings are maintained at constant temperature, and heat exchange is rapid to prevent the generation of thermal gradients, then the closed system is isothermal. A frequently considered case are closed isothermal systems at constant pressure (and constant volume with aqueous solutions). Changes of closed systems can be partitioned according to internal and external sources. Closed systems may be homogenous (well mixed and isothermal), continuous with gradients, or discontinuous with compartments (heterogenous).
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, redox system (oxidized ubiquinone, partially reduced semiquinone, fully reduced ubiquinol) of the ET-pathway. More details » Q-junction.
Company of ScientistsCompaSci
Company of Scientists
The Company of Scientists evolves as a concept for implementing scientific innovations on the market.
Complex ICIComplex I, NADH:ubiquinone oxidoreductase (EC 1.6.5.3), 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 ET-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 ET-pathway. It catalyzes the reduction of cytochrome c by oxidation of coenzyme Q (CoQ) and the concomitant pumping of 4 protons from the mitochondrial matrix to the intermembrane space.
Complex IVCIVComplex IV or cytochrome c oxidase is the terminal oxidase of the mitochondrial ET-pathway, reducing oxygen to water, with reduced cytochrome c as a substrate. 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.
Complex IV single stepCIVCIV: Electron flow through Complex IV (cytochrome c oxidase) is measured in intact mitochondria after inhibiton of CIII by antimycin A, and addition of ascorbate (As) and the artificial substrate TMPD (Tm). Ascorbate has to be titrated first. It reduces TMPD, which further reduces cytochrome c, which is the substrate of CIV. Since CIV is a proton pump of the electron transfer-pathway, the single step of CIV-linked respiration can be measured in different coupling states: L, P, and E. Measurement of CIV activity requires uncoupler titrations to eliminate any potential control by the phosphorylation system, and a cytochrome c test to avoid any limitation by cytochrome c release. Total oxygen uptake in the ascorbate&TMPD(&c) stimulated state (Tm) has to be corrected for chemical background oxygen consumption.
Concentrationc [mol·L-1]Concentration or density is a volume-specific quantity, expressing the number of particles as number per volume, or as properties of the particles in a variety of formats (amount, charge, mass, volume or energy per volume of the system). In chemistry, amount concentration is amount per volume, cB = [B] = nB·V-1 [mol·m-3]. The standard concentration, c°, is defined as 1 mol·dm-3 = 1 mol·L-1 = 1 M.

Concentration {quote}: 1. Group of four quantities characterizing the composition of a mixture with respect to the volume of the mixture (mass, amount, volume and number concentration).

2. Short form for amount (of substance) concentration (substance concentration in clinical chemistry).

{end of quote: IUPAC Gold Book}

A change of concentration of an elementary entity, i, in a system, dci, can be due to internal transformations (advancement per volume,
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.
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Convergent electron flown.a.
Convergent electron flow
Convergent electron flow is built into the metabolic design of the Electron transfer-pathway. The glycolytic pathways are characterized by important divergent branchpoints: phosphoenolpyruvate (PEPCK) branchpoint to pyruvate or oxaloactetate; pyruvate branchpoint to (aerobic) acetyl-CoA or (anaerobic) lactate or alanine. The mitochondrial Electron transfer-pathway, in contrast, is characterized by convergent junctions: (1) the N-junction and F-junction in the mitochondrial matrix at ET-pathway level 4, with dehydrogenases (including the TCA cycle) and ß-oxidation generating NADH and FADH2 as substrates for Complex I and electron-transferring flavoprotein complex, respectively, and (2) the Q-junction with inner mt-membrane respiratory complexes at ET-pathway level 3, reducing the oxidized ubiquinone and partially reduced semiquinone to the fully reduced ubiquinol, feeding electrons into Complex III.
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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}
Coupled respirationCoupled respiration drives oxidative phosphorylation of the diphosphate ADP to the triphosphate ATP, mediated by proton pumps across the inner mitochondrial membrane. Intrinsically uncoupled respiration, in contrast, does not lead to phosphorylation of ADP, despite of protons being pumped across the inner mt-membrane. Coupled respiration, therefore, is the coupled part of respiratory oxygen flux that pumps the fraction of protons across the inner mt-membrane which is utilized by the phosphorylation system to produce ATP from ADP and Pi. In the OXPHOS state, mitochondria are in a partially coupled state, and the corresponding coupled respiration is the free OXPHOS capacity. In the state of ROUTINE respiration, coupled respiration is the free ROUTINE activity.
Coupling control factorCCFCoupling control factors, CCF, are flux control factors, FCF, 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 substrate control state. In mitochondrial preparations, there are three well-defined coupling states of respiration, L, P, E (LEAK, OXPHOS, ET-pathway). In intact cells, state P cannot be induced, but a ROUTINE state of respiration, R, can be measured. The reference state, Jref, is defined by taking Jref as the maximum flux, i.e. flux in the ET state, E, 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 intact 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, OXPHOS, and ET-pathway 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 application of specific inhibitors of the phosphorylation system, titration of ADP and uncouplers. In living cells, the coupling control states are LEAK, ROUTINE, and ET-pathway states of respiration (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 ET-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).
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 in tumor cells, in bacteria, and yeast. The Pasteur effect (suppression of glycolysis by oxygen) is the converse of the Crabtree effect (aerobic glycolysis to lactate or ethanol).
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) are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. © remains with the authors, who have granted MitoFit an Open Access preprint licence 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.
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.
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 (ET-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 control factorFCFcThe cytochrome c control factor expresses the control of respiration by externally added cytochrome c, c, as a fractional change of flux from substrate state CHO to CHOc. In this flux control factor (FCFc), CHOc is the reference state with stimulated flux; CHO is the background state with CHO substrates, upon which c is added,
FCFc = (JCHOc-JCHO)/JCHOc.
» MiPNet article
DatLab 2DL2DatLab 2 is a MS-DOS programme. It may be necessary to use an emulator to be able to run DatLab 2 on modern computers, especially for the DL2 graphic window (available free of charge):
  • Windows 7 + DOSBOX
  • Linux + DOSemu
  • FreeDOS: www.freedos.org (will also reduce the available CPU power if necessary)
  • "CPUkiller" - to reduce available CPU power.
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.
Example:
  • 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
DatLab
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 oxygen flux: performance and data analysisThe quality of the results are strongly affected by the performance and data analysis. Therefore, we provide guidelines for performing and evaluating respirometric assays.
DatLab templatesDatLab templates can be imported for O2k-setups, graph layouts, mark names, TIP2k setups and marks statistics configurations. To do so, go to DatLab menu 'File\Import\DatLab templates' and choose an apporpriate DatLab template file (*.DLT) from the filesystem. The standard template file generated during DatLab installation can be found in the folder DatLab\DLTemplates.
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.
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.
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 is frequently a quantity divided by volume: mass density or mass concentration is mass per volume, M·V-1 [kg·m-3]; radiant energy density is radiant energy per volume, Q·V-1 [J·m-3]; charge density is charge per volume, Q·V-1 [C·m-3]. However, electric current density is current divided by area, j=I·A-1 [C·m-2]. Number density of entities or number concentration is numbers per volume, CB = NB·V-1 [x·m-3]. In contrast, the amount-of-substance concentration, cB = nB·V-1 [mol·m-3] is not called a substance density (IUPAC). Thus the sample mass concentration is CmX = mX·V-1 [kg·m-3], the mitochondrial concentration is CmtE = mtE·V-1 [mtEU·m-3], whereas the specific mitochondrial density is DmtE = mtE·mX-1 [mtEU·kg-1], and the mitochondrial content per object X is mtENX = mtE·NX-1 [mtEU·x-1] (Gnaiger 2019 MitoFit Preprint Arch).
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.
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). Has been used to detect superoxide by HPLC and by fluorescence microscopy.
Dilution effectDilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber.
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; FW = 184.11) 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-O2kIf Display Power-O2k is enabled in the Graph-menu in DatLab, the Power-O2k number, as set in Oroboros O2k / O2k configuration, is shown in the active graph.
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).
DithioniteDitZero oxygen solution powder, Na2S2O4, used for calibration of oxygen sensors at zero oxygen, or for stepwise reduction of oxygen concentration in instrumental O2 background tests.
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.
Dyscoupled respirationDyscoupled respiration is LEAK respiration distinguished from intrinsically (physiologically) uncoupled and from extrinsic experimentally uncoupled respiration as an indication of extrinsic uncoupling (pathological, toxicological, pharmacological by agents that are not specifically applied to induce uncoupling, but are tested for their potential dyscoupling effect). Dyscoupling indicates a mitochondrial dysfunction. In addition to intrinsic uncoupling, dyscoupling occurs under pathological and toxicological conditions. Thus a distinction is made between physiological uncoupling and pathologically defective dyscoupling in mitochondrial respiration.
ET-capacityEE.jpg ET-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 (i) a wide range of uncoupled states at any experimental uncoupler concentration, (ii) physiological uncoupled states controlled by intrinsic uncoupling (e.g. UCP1 in brown fat), and (iii) 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-coupling efficiencyj≈EET-coupling efficiency The ET-coupling efficiency (E-L coupling control factor) is a normalized flux ratio, j≈E = ≈E/E = (E-L)/E = 1-L/E. j≈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 ET-pathway reference state by uncoupler titration. LEAK states LN or LT may be stimulated first by saturating ADP (State P) with subsequent uncoupler titration to State E. The ET-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 (DT phosphorylation) 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). Biochemical coupling efficiency is either expressed as the ET-coupling efficiency, j≈E, or OXPHOS coupling efficiency, j≈P, obtained in a coupling control protocol (phosphorylation control protocol). » MiPNet article
ET-pathway competent stateET-pathway competent state, see Electron transfer-pathway state.
ET-pathway substrate typesn.a.See Electron transfer-pathway state
EUROMIT
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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.
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 current densityj [C·m-2]Electric current density is current divided by area, j=I·A-1 [C·m-2]. Compare: density.
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(02) is reduced to water.
Electron leakElectrons that escape the electron transfer system without completing the reduction of oxygen to water at cytochrome c oxidase, causing the production of ROS. The rate of electron leak depends on the topology of the complex, the redox state of the moiety responsible of electron leakiness and usually on the protonmotive force (Δp). In some cases, the Δp dependance relies more on the ∆pH component than in the ∆Ψ.
Electron transfer-pathwayET-pathwayIn the mitochondrial electron transfer-pathway (ET-pathway) electrons are transfered 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).
Elementary chargee [C·x-1]
Table Physical constants.png
The elementary charge or proton charge, e, has the SI unit coulomb [C] (IUPAC), but more strictly coulomb per particle [C·x-1], which is also used as an atomic unit.
Enable DL-Protocol editingin progress
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 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,

dH = (deQ + deW) + dmatH ; dp = 0 

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
Ergodynamic efficiencyεThe ergodynamic efficiency, ε (compare thermodynamic efficiency), is a power ratio between the output power and the (negative) input power of an energetically coupled process. Since power [W] is the product of a flow and the conjugated thermodynamic force, the ergodynamic efficiency is the product of an output/input flow ratio and the corresponding force ratio. The efficiency is 0.0 in a fully uncoupled system (zero output flow) or at level flow (zero output force). The maximum efficiency of 1.0 can be reached only in a fully (mechanistically) coupled system at the limit of zero flow at ergodynamic equilibrium. The ergodynamic efficiency of coupling between ATP production (DT phosphorylation) and oxygen consumption is the flux ratio of DT phosphorylation flux and oxygen flux (P»/O2 ratio) multiplied by the corresponding force ratio. Compare with the OXPHOS coupling efficiency.
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.
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
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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.
Excess E-P capacityExPExcess E-P capacity The excess E-P capacity, ExP, is the difference of the ET-capacity and OXPHOS-capacity, ExP = E-P. At ExP > 0, the capacity of the phosphorylation system exerts a limiting effect on OXPHOS capacity. In addition, ExP depends on coupling efficiency, since P aproaches E at increasing uncoupling.
Excess E-P capacity factorjExPExcess E-P capacity factor The apparent excess E-P capacity factor (E-P coupling control factor), jExP = (E-P)/E = 1-P/E, is an expression of the relative limitation of OXPHOS capacity by the capacity of the phosphorylation system. jExP = 0.0 when OXPHOS is not limited by the phosphorylation system at zero Excess capacity, P=E, when the phosphorylation system does not exert any control over OXPHOS capacity. jExP increases with increasing control of the phosphorylation system over OXPHOS capacity. jExP = 1 at the limit of zero phosphorylation capacity. The OXPHOS state of mt-preparations is stimulated to ET-pathway by uncoupler titration, which yields the excess E-P capacity, ExP=E-P.
Excess E-R capacityExRExcess E-R capacity The Excess E-R capacity, ExR, is the difference of ET-capacity and ROUTINE respiration, ExR = E-R. For further information, see Cell ergometry.
Excess E-R capacity factorjExRExcess E-R capacity factor The apparent excess E-R capacity factor (E-R coupling control factor), jExR = (E-R)/E = 1-R/E, is an expression of the relative scope of increasing ROUTINE respiration in intact cells by uncoupling. jExR = 0.0 for zero excess capacity when R=E; jExR = 1.0 for the maximum limit when R=0. The ROUTINE state of intact cells is stimulated to ET-pathway by uncoupler titration, which yields the excess E-R capacity, ExR=E-R. Since ET-capacity is significantly higher than OXPHOS capacity in various cell types (as shown by cell ergometry), ExR or jExR is not a reserve capacity available for the cell to increase oxidative phosphorylation, but strictly a scope (reserve?) for uncoupling respiration. Similarly, the apparent excess E-P capacity, ExP=E-P, is not a respiratory reserve in the sense of oxidative phosphorylation.
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 wish to alter the nature of the chemicals used or the sequence of injections, we ask them to contact support@oroboros.at.
Extended abstractsIn the context of MiPevents and MitoEAGLE events, extended abstracts are accepted for preprint publication in MitoFit Preprint Archives upon evaluation by MitoEAGLE MC members. Publishing extended abstracts with MitoFit Preprint Archives 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).
External flowIe [MU·s-1]External flows across the system boundaries are formally reversible. Their irreversible facet is accounted for internally as transformations in a heterogenous system (internal flows, Ii).
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).
F-junction
F-junction
The F-junction is a junction for convergent electron flow in the electron transfer-pathway (ET-pathway) from fatty acids through fatty acyl CoA dehydrogenase (reduced form FADH2) to electron transferring flavoprotein (CETF), and further transfer through the Q-junction to Complex III (CIII). The concept of the F-junction and N-junction provides a basis for defining categories of SUIT protocols. Fatty acid oxidation, in the F-pathway control state, not only depends on electron transfer through the F-junction (which is typically rate-limiting) but simultaneously generates 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 N-junction substrate malate is required as a co-substrate for FAO in mt-preparations, since accumulation of AcetylCoA 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 AcetylCoA into the TCA cycle catalyzed by citrate synthase.
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.
FNFN
F-junction
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.
FNSFNS
F-junction
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.
FNSGpFNSGp
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 acidFA

Fatty 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 (4–8 carbons), medium-chain (6–12 carbons) and long-chain (14-22 carbons) fatty acids.

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 production. Fatty acids (short chain with 4–8, medium-chain with 6–12, long chain with 14-22 carbon atoms) are activated by fatty acyl-CoA synthases (thiokinases) in the cytosol. The outer mt-membrane enzyme carnitine palmitoyltransferase I (CPT 1) generates an acyl-carnitine intermediate for transport into the mt-matrix. 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. Electron-transferring flavoprotein complex (CETF) is located on the matrix face of the inner mt-membrane, and supplies electrons from fatty acid β-oxidation (FAO) to CoQ. FAO cannot proceed without a substrate combination of fatty acids & malate, and inhibition of CI blocks FAO completely. Fatty acids are split stepwise into two carbon fragments forming acetyl-CoA, which enters the TCA cycle by condensation with oxaloacetate (CS reaction). Therefore, FAO implies simultaneous electron transfer into the Q-junction through CETF and CI.
Fatty acid oxidation pathway control stateF, FAO
F-junction
In the fatty acid oxidation pathway control state (F, FAO), 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), 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 as a co-substrate for FAO in mt-preparations, since accumulation of AcetylCo 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.
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.
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.
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).
Flux / SlopeJFlux / Slope is the pull-down menu in DatLab 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. A Savitzky-Golay smoothing filter is used in DatLab as a basis of calculating the time derivative (Flux / Slope) of the signal (oxygen, fluorescence, ..). For each signal channel, the signal for the measured substance X is typically calibrated as an amount of substance concentration, cX [µM = nmol/mL]. The signal of the potentiometric channel, however, is primarily expressed logarithmically as pX=-log(cX/c°) and then transformed to cX. The slope is calculated as the change of concentration over time, dcX/dt [nmol/(s · mL)]. In a chemical reaction, the change of substance X is stoichiometrically related to the changes of all other substrates and products involved in the reaction. If the stoichiometry of the reaction is normalized for substance X, then its stoichiometric coefficient is unity and νX equals 1 if the substance is a product formed in the reaction, but νX equals -1 if the substance is a substrate consumed in the reaction. Oxygen is formed in photosynthesis and νX=1 when expressing photosynthesis as oxygen flux. Oxyygen is consumed in aerobic respiration and νX=-1 when expressing respiration as oxygen flux.
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.
Flux baseline correctionbcFlux baseline correction provides the option to display the plot and all values of the flux (or flow, or flux control ratio) as the total flux, J, minus a baseline flux, J0.
JV(bc) = JV - JV0
JV = (dc/dt) · ν-1 · SF - V
For the oxygen channel, JV is O2 flux per volume [pmol/(s·ml)] (or volume-specific O2 flux), c is the oxygen conentration [nmol/ml = µmol/l = µM], dc/dt is the (positive) slope of oxygen concentration over time [nmol/(s · ml)], ν-1 = -1 is the stoichiometric coefficient for the reaction of oxygen consumption (oxygen is removed in the chemical reaction, thus the stoichiometric coefficient is negative, expressing oxygen flux as the negative slope), SF=1,000 is the scaling factor (converting units for the amount of oxygen from nmol to pmol), and V is the volume-specific background oxygen flux (Instrumental background oxygen flux). Further details: Flux / Slope.
Flux control factorFCFFlux control factors express the control of respiration by a metabolic control variable, X, as a fractional change of flux from YX to ZX, normalized for ZX. ZX is the reference state with high (stimulated or un-inhibited) flux; YX is the background state at low flux, upon which X acts.
ΔjX = (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 factor 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 (i) mt-content in cells or tissues, (ii) purification in preparations of isolated mitochondria, and (iii) 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).
Format
Table Physical constants.png
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; MU = x
  • n: chemical or molar format; MU = mol
  • e: electrical format; 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 ET-capacity≈EFree ET-capacity The Free ET-capacity, ≈E, is the ET-capacity corrected for LEAK respiration, ≈E = E-L. ≈E 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 free ET-capacity, ≈E, and LEAK respiration, LP, compensating for proton leaks, slip and cation cycling: E = ≈E+LP (see free OXPHOS capacity).
Free OXPHOS-capacity≈PFree OXPHOS-capacity The free OXPHOS-capacity, ≈P, is the OXPHOS-capacity corrected for LEAK respiration, ≈P = P-L. ≈P is the scope for ADP stimulation, the respiratory capacity potentially available for phosphorylation of ADP to ATP. Oxygen consumption in the OXPHOS state, therefore, is partitioned into the free OXPHOS-capacity, ≈P, strictly coupled to phosphorylation, ~P, and nonphosphorylating LEAK respiration, LP, compensating for proton leaks, slip and cation cycling: P = ≈P+LP. It is frequently assumed that LEAK respiration, L, as measured in the LEAK state, overestimates the LEAK component of respiration, LP, as measured in the OXPHOS state, particularly if the protonmotive force is not adjusted to equivalent levels in L and LP. However, if the LEAK component increases with enzyme turnover during P, the low enzyme turnover during L may counteract the effect of the higher Δpmt.
Free ROUTINE activity≈RFree ROUTINE activity The free ROUTINE activity, ≈R, is ROUTINE respiration corrected for LEAK respiration, ≈R = R-L. ≈R is the respiratory activity available for phosphorylation of ADP to ATP. Oxygen consumption in the ROUTINE state of respiration measured in intact cells, therefore, is partitioned into the free ROUTINE activity, ≈R, strictly coupled to phosphorylation, ~P, and nonphosphorylating LEAK respiration, LR, compensating for proton leaks, slip and cation cycling: R = ≈R+LR. It is frequently assumed that LEAK respiration, L, as measured in the LEAK state, overestimates the LEAK component of respiration, LR, as measured in the ROUTINE state, particularly if the protonmotive force is not adjusted to equivalent levels in L and LR. However, if the LEAK component increases with enzyme turnover during R, the low enzyme turnover during L may counteract the effect of the higher Δpmt.
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
GM: Glutamate & Malate.

MitoPathway control state: NADH Electron transfer-pathway state

When glutamate&malate are added to isolated mitochondria or permeabilized cells, glutamate and transaminase are responsible for the metabolism of oxaloacetate, comparable to the metabolism with acetyl-CoA and citrate synthase.
GMSGMS
GMS
GMS: Glutamate & Malate & Succinate.

MitoPathway control: CI&II

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).
Gas constantR [J·mol-1·K-1]
Table Physical constants.png
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.
GlutamateG
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 anaplerotic pathway control stateG
G
G: Glutamate is an anaplerotic NADH-linked type 4 substrate (N). When supplied as the sole fuel substrate in the glutamate 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 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-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 ino the Q-junction, thus linked to an ET pathway level 3 control state.
Glycerophosphate pathway control stateGp
Gp-pathway
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
Gp
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.
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).
HeatQ [J]Heat is a form of energy. 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.
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.
High-resolution respirometryHRR
O2k-FluoRespirometer
High-resolution respirometry, HRR, is the state-of-the-art approach in mitochondria and cell research to measure respiration in 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. The most advanced way to analyze mitochondrial function is by means of high-resolution respirometry with the Oroboros O2k. 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.
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.
Horseradish peroxidaseHRPHorseradish peroxidase readily combines with hydrogen peroxide (H2O2) and the resultant [HRP-H2O2] complex can oxidize a wide variety of hydrogen donors.
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.
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.
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.
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.
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.
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.
Impressum
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.
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 background oxygen fluxJ°O2Instrumental background oxygen flux, J°O2, in a respirometer is due to oxygen consumption by the POS, and oxygen diffusion into or out of the aqueous medium in the O2k-Chamber. It is a property of the instrumental system, measured in the range of experimental oxygen levels by a standardized instrumental background test. The oxygen regime from air saturation towards zero oxygen is applied generally in experiments with isolated mitochondria and intact or permeabilized cells. To overcome oxygen diffusion limitation in permeabilized fibres and homogenates, an elevated oxygen regime is applied, requiring instrumental background test in the same range of elevated oxygen.

Instrumental background correction eliminates errors by systemic flux compensation, automatically performed by DatLab. If no experimental background test has been performed, the system default values are used, which are a°=-2.0 pmol/(s·ml) for the intercept at zero oxygen concentration, and b°=0.025 for the slope of background flux as a function of oxygen concentration.

Automatic correction for the instrumental background oxygen flux is an essential standard in high resolution respirometry. At the same time an instrumental background experiment is the ultimate test for instrumental performance, evaluating chamber performance after completion of all elements of the Oxygen sensor test. The instrumental background oxygen flux measured at air saturation should reflect the theoretically predicted volume-specific oxygen consumption by the oxygen sensor. The actual agreement using experimental respiration medium provides at the same time a test that excludes microbial contamination of the medium or serves to evaluate any autoxidation processes in newly tested experimental media.
Instrumental: Browse DL-Protocols and templatesDL-Protocols for instrumental calibration and maintenance can be browed from inside DatLab 7.3, example traces with instructions and brief explanatory texts and templates for data evaluation can be opened. Click on menu [Protocols]\Instrumental: Browse DL-Protocols and templates to open a folder with all the DatLab protocols (DLP) for cleaning, calibration, and background determination provided with the USB. Select a sub-directory and open an example trace 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.
Intended useIntended use or Intended purpose is the objective intend of a medical device manufacturer regarding the use of a product, process or service as it is documented by the manufacturer.
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
ISMM
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
ISOTT LOGO.jpg
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 Union of Pure and Applied Chemistry, IUPACIUPACThe International Union of Pure and Applied Chemistry (IUPAC) celebrates in 2019 the 100th anniversary, which coincides 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} [1]. 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 [2] 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 [3,4].
International oxygraph courseIOCInternational Oxygraph Course (IOC), see O2k-Workshops.
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.
IonomycinImyIonomycin (Imy) is a ionophore used to raise intracellular [Ca2+].
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. In irreversible thermodynamics, isomorphic forces are referred to as generalized forces.
Japanese Society of Mitochondrial Research and MedicineJ-mit
J-mit.png
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 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.
Journals in Bioblast
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/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 control ratioL/ELEAK control ratio The LEAK control ratio, or L/E coupling control ratio [1,2], is the flux ratio of LEAK respiration over ET-capacity, as determined by measurement of oxygen consumption in sequentially induced states L and E of respiration. The ET-pathway 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 [3].
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 ATO, L(T), is distinguished from L(n) and L(Omy).
LEAK state with oligomycinL(Omy)L.jpg The LEAK state with Omy 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).
LEAK-respirationLL.jpg EAK-respiration or LEAK oxygen flux, L, compensating for proton leak, proton slip, cation cycling and electron leak, is a dissipative component of respiration which is not available for performing biochemical work and thus related to heat production. LEAK-respiration is measured in the LEAK state, in the presence of reducing substrate(s), but absence of ADP - abbreviated as L(n) (theoretically, absence of inorganic phosphate presents an alternative), or after enzymatic inhibition of the phosphorylation system, which can be reached with the use of oligomycin - abbreviated as L(Omy). The LEAK state is the non-phosphorylating resting state of intrinsic uncoupled or dyscoupled respiration when oxygen flux is maintained mainly to compensate for the proton leak at a high chemiosmotic potential, when ATP synthase is not active. In this non-phosphorylating resting state, the electrochemical proton gradient is increased to a maximum, exerting feedback control by depressing oxygen flux to a level determined mainly by the proton leak and the H+/O2 ratio. In this state of maximum protonmotive force, LEAK-respiration, L, is higher than the LEAK component of OXPHOS capacity, P. The conditions for measurement and expression of respiration vary (oxygen flux in the LEAK state, JO2L, or oxygen flow, IO2L). If these conditions are defined and remain consistent within a given context, then the simple symbol L for respiratory rate can be used as a substitute for the more explicit expression for respiratory activity. » MiPNet article
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.
Laner 2013 Mitochondr Physiol Network MiP2013
Latent mitochondrial dysfunctionThe concept on latent mitochondrial dysfunction presents the working hypothesis that the dynamic mitochondrial stress response provides a more sensitive and integrative marker for degenerative disease-related defects compared to acute mitochondrial dysfunction. The risk for developing a disease may be quantified in terms of a stress response, rather than a static pathophysiological state. Acute and latent mitochondrial dysfunction are studied at baseline and in response to a particular (e.g. oxidative) stress, using a mitochondrial stress resistance test.
Layout for DatLab graphsA Layout in DatLab from the Layout menu or the Graph menu is a predefined selection for standardized display of graphs, plots to be displayed at specific scalings. Any defined graph layout can be selected from the Layout menu for defining initial settings for the plots [Ctrl+F6] and scaling [F6]. A layout can be modified and saved under a specific name.
Least squares methodThis method makes use of all of the data points of the spectrum in order to quantify a measured spectrum with a reference spectrum of known concentration using a least squares method to match the measured spectrum with the reference spectrum. The technique results in improved accuracy compared with the use of only a few characteristic wavelengths.
Level flowEE.jpg Level flow is a steady state of a system with an input process coupled to an output process (coupled system), in which the output force is zero. Clearly, energy must be expended to maintain level flow, even though output is zero (Caplan and Essig 1983; referring to zero output force, while output flow may be maximum).
Light sourceA variety of light sources are available for fluorometry and spectrophotometry. These include deuterium, mercury and xenon arc lamps and quartz halogen bulbs dependent upon the wavelengths required. However, the advent of light emitting diodes has greatly increased the possibilities for the application of fluorometry and spectrophotometry to areas that were previously not practicable, and at a much reduced cost.
Light-emitting diodeLEDA light-emitting diode (LED) is a light source (semiconductor), used in many every-day applications and specifically in fluorometry. LEDs are available for specific spectral ranges across wavelengths in the visible, ultraviolet, and infrared range.
LightguidesLightguides consist of optical fibres (either single or in bundles) that can be used to transmit light to a sample from a remote light source and similarly receive light from a sample and transmit it to a remote detector. They have greatly contributed to the range of applications that for which optical methods can be applied. This is particularly true in the fields of medicine and biology.
Limiting oxygen pressureplThe limiting oxygen pressure, pl, is defined as the partial oxygen pressure, pO2, below which anaerobic catabolism is activated to contribute to total ATP generation. The limiting oxygen pressure, pl, may be substantially lower than the critical oxygen pressure, pc, below which aerobic catabolism (respiration or oxygen consumption) declines significantly.
Limiting pO2plimIn the transition from aerobic to anaerobic metabolism, there is a limiting pO2, plim, below which anaerobic energy flux is switched on and CR ratios become more exothermic than the oxycaloric equivalent. plim may be significanlty below the critical pO2.
LinearityLinearity is the ability of the method to produce test results that are proportional, either directly or by a well-defined mathematical transformation, to the concentration of the analyte in samples within a given range. This property is inherent in the Beer-Lambert law for absorbance alone, but deviations occur in scattering media. It is also a property of fluorescence, but a fluorophore may not exhibit linearity, particularly over a large range of concentrations.
Liver mitochondria purificationArmstrong 2010 J Comp Physiol B: This paper describes a method for purification of rodent liver mitochdondria using relatively low-speed centrifugation through discontinuous Percoll gradients.
Living cellsvceCell viability in living cells should be >95% for various experimental investigations, including cell respirometry. Viable cells (vce) are characterized by an intact plasma membrane. The total cell count (Nce) is the sum of viable cells (Nvce) and dead cells (Ndce). In contrast, the cell membrane of cells can be permeabilized selectively by mild detergents (digitonin), to obtain the mt-preparation of permeabilized cells used for cell ergometry. Living cells are frequently labelled as intact cells in the sense of the total cell count, but intact may suggest the alternative meaning of viable.
LuminescenceLuminescence is spontaneous emission of radiation from an electronically or vibrationally excited species not in thermal equilibrium with its environment (IUPC definition). An alternative definition is "Luminescence is emission of light by a substance not resulting from heat." Luminescence comprises many different pehnomena. Luminescence from direct photoexcitation of the emitting species is called photoluminescence. Both fluorescence and phosphorescence are forms of photoluminescence. In biomedical research also forms of chemiluminescence (e.g.the luciferin reaction) are used. In chemiluminescence the emission of radiation results from a chemical reaction. For other forms of luminescence see the IUPAC Gold Book.
MITOEAGLE in MitoGlobalMitoEAGLE
MITOEAGLE-representation.jpg
The objective of the MitoEAGLE network is to improve our knowledge on mitochondrial function in health and disease related to Evolution, Age, Gender, Lifestyle and Environment.
Magnesium GreenMgGMagnesium Green (MgG) belongs to the extrinsic fluorophores applied for measurement of mitochondrial ATP production with mitochondrial preparations. This dye fluoresces when bound to Mg2+. The technique to measure mitochondrial ATP production is based on the fact that Mg2+ present different dissociation constants for ADP and ATP, and the adenine nucleotide translocase (ANT) exchanges ATP for ADP.
MalateM
Malic acid

Malic acid, C4H6O5, occurs under physiological conditions as the anion malate2-, M, with pKa1 = 3.40 and pKa2 = 5.20. L-Malate is formed from fumarate in the TCA cycle in the mitochondrial matrix, where it is the substrate of malate dehydrogenase oxidized to oxaloacetate. Malate is also formed in the cytosol. It cannot permeate through the lipid bilayer of membranes and hence requires a carrier (dicarboxylate carrier, tricarboxylate carrier and 2-oxoglutarate carrier). Malate alone cannot support respiration of mt-preparations from most tissues, since oxaloacetate accumulates in the absence of pyruvate or glutamate.

Malate is a type N substrate (N) required for the FAO-pathway. In the presence of anaplerotic pathways (e.g., mitochondrial malic enzyme, mtME) FAO-pathway could be overestimated due to a contribution of NADH-linked respiration, F(N) (see SUIT-002).
Malate anaplerotic pathway control stateM
M
M: Malate alone does not support respiration of mt-preparations if oxaloacetate cannot be metabolized further in the absence of a source of acetyl-CoA. Transport of oxaloacetate across the inner mt-membrane is restricted particularly in liver. Mitochondrial citrate and 2-oxoglutarate (α-ketoglutarate) are depleted by antiport with malate. Succinate is lost from the mitochondria through the dicarboxylate carrier. OXPHOS capacity with malate alone is only 1.3% of that with Pyruvate&Malate in isolated rat skeletal muscle mitochondria. Many mammalian and non-mammalian mitochondria have a mt-isoform of NADP+- or NAD(P)+-dependent malic enzyme (mtME), the latter being particularly active in proliferating cells. Then the anaplerotic pathway control state with malate alone (aN) supports high respiratory activities comparable to the NADH-linked pathway control states (N) with pyruvate&malate or glutamate&malate substrate combinations (PM pathway control state, GM pathway control state).
Malate dehydrogenasemtMDHMitochondrial malate dehydrogenase is localized in the mitochondrial matrix and oxidizes malate, generated from fumarate by fumarase, to oxaloacetate, reducing NAD+ to NADH+H+ in the TCA cycle. Malate is added as a substrate in most N-pathway control states.
Malate transportCarriers for malate:
  1. dicarboxylate carrier
  2. tricarboxylate carrier
  3. 2-oxoglutarate carrier
Malate-aspartate shuttleThe malate-aspartate shuttle involves the glutamate-aspartate carrier and the 2-oxoglutarate carrier exchanging malate2- for 2-oxoglutarate2-. Cytosolic and mitochondrial malate dehydrogenase and transaminase complete the shuttle for the transport of cytosolic NADH into the mitochondrial matrix. It is most important in heart, liver and kidney.
Malic enzymemtMEMalic enzyme (ME; EC 1.1.1.40) catalyzes the oxidative decarboxylation of L-malate to pyruvate with the concomitant reduction of the dinucleotide cofactor NAD+ or NADP+ and a requirement for divalent cations (Mg2+ or Mn2+) as cofactors.

NAD(P)+ + L-malate2- <--> NAD(P)H + pyruvate- + CO2

Three groups of ME are distinguished (i) NAD+- and (ii) NADP+-dependent ME specific for NAD+ or NADP+, respectively, and (iii) NAD(P)+- dependent ME with dual specificity for NAD+ or NADP+ as cofactor. Three isoforms of ME have been identified in mammals: cytosolic NADP+-dependent ME (cNADP-ME or ME1), mitochondrial NAD(P)+-dependent ME (mtNAD-ME or ME2; with NAD+ or NADP+ as cofactor, preference for NAD+ under physiological conditions), and mitochondrial NADP+-dependent ME (mtNADP-ME or ME3). mtNAD-ME plays an important role in anaplerosis when glucose is limiting, particularly in heart and skeletal muscle. Tartronic acid (hydroxymalonic acid) is an inhibitor of ME.
MalonateMnaMalonate (malonic acid) is a competitive inhibitor of succinate dehydrogenase (Complex II). Malonate is a substrate of malonyl-CoA synthase.
Malonyl-CoA synthaseMalonyl-CoA synthase or ACSF3 protein is a mitochondrial fatty-acyl-CoA synthase found in mammals. Traditionally, malonyl-CoA is formed from acetyl-CoA by the action of acetyl-CoA carboxylase. However, Witkowski et al (2011) showed that mammals express malonyl-CoA Synthase (ACSF3) with enzymatic activity in the presence of malonate (Complex II inhibitor) and methylmalonate.
Manage setups and templates - DatLabSetups and templates in DatLab can be renamed or deleted under Manage setups or Manage templates.
Mark informationMarks» See Marks - DatLab
Mark specifications - DatLabMark specifications in DatLab allow the user to rename Marks in the active plot and save/recall the settings. Rename marks individually by clicking into the horizontal bar, or use corresponding templates for renaming the entire sequence of marks.
Mark statistics - DatLabF2In Mark statistics one Plot is selected as a source for Marks over sections of time. Values (e.g. medians) are displayed for these time sections of the source plot and of all selected plots.
Marks - DatLabMarks in DatLab define sections of a plot recorded over time. Marks are set by the user in real-time, or post-experimentally for basic level data analysis. Set Marks to obtain the median, average, standard deviation, outlier index and range of the data within the mark, for calibration of the oxygen signal, flux analysis, or to delete marked data points. Marks are shown by a horizontal bar in the active plot. The default Mark names are given automatically in numerical sequence, independent for each plot. Rename marks individually by clicking into the horizontal bar, or use corresponding templates for renaming the entire sequence of marks.Several marks can be set on any plot, but marks cannot overlap within a plot and are separated by one or more data points which are not marked.
Measurement processA measurement process or a measurement is a set of operations to determine the value of a quantity.
Measuring equipmentA measuring equipment is a measuring instrument, software, measurement standard, reference material or auxiliary apparatus, or a combination thereof, necessary to realize a measurement process.
Medical deviceA medical device is an instrument, apparatus, implement, machine, contrivance, implant, in vitro reagent, or other similar or related article, including a component part, or accessory which is:
  • intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease, in man or other animals, or
  • intended to affect the structure or any function of the body of man or other animals, and which does not achieve any of its primary intended purposes through chemical action within or on the body of man or other animals and which is not dependent upon being metabolized for the achievement of any of its primary intended purposes.
MelatoninaMTMelatonin (N-acetyl-5-methoxytryptamine, aMT) is a highly conserved molecule present in unicellular to vertebrate organisms. Melatonin is synthesized from tryptophan in the pinealocytes by the pineal gland and also is produced in other organs, tissues and fluids (extrapineal melatonin). Melatonin has lipophilic and hydrophilic nature which allows it to cross biological membranes. Therefore, melatonin is present in all subcellular compartments predominantly in the nucleus and mitochondria. Melatonin has pleiotropic functions with powerful antioxidant, anti-inflammatory and oncostatic effects with a wide spectrum of action particularly at the level of mitochondria. » MiPNet article
Membrane-bound ET-pathwaymET-pathwayThe membrane-bound electron transfer-pathway (mET-pathway) consists in mitochondria mainly of respiratory complexes CI, CII, electron transferring flavoprotein complex (CETF), glycerophosphate dehydrogenase complex (CGpDH), and choline dehydrogenase, with convergent electron flow at the Q-junction (Coenzyme Q), and the two downstream respiratory complexes connected by cytochrome c, CIII and CIV, with oxygen as the final electron acceptor. The mET-pathway is the terminal (downstream) module of the mitochondrial ET-pathway and can be isoled from the ET-pathway in submitochondrial particles (SmtP).
MersalylMersalyl (C13H17HgNO6) is an inhibitor of the Pi symporter.
Metabolic control variableXA metabolic control variable, X, causes the transition between a background state, YX, and a reference state, ZX. X may be a stimulator or activator of flux, inducing the step change from background to reference steady state (Y to Z). Alternatively, X may be an inhibitor of flux, absent in the reference state but present in the background state (step change from Z to Y).
Methylmalonic acidMmaMethylmalonic acid (Mma) is a common intermediate in many catabolic processes. In methylmalonic acidemia mitochondrial dysfunction can be observed, related to accumulation of Mma and associated with neurological symptoms.
MetrologyMetrology is the science of measurement, including all aspects both theoretical and practical with reference to measurements, whatever their uncertainty, and in whatever fields of science or technology they occur [SOURCE: VIM:1993, 2.2].
MiP-CollectionMiP-CollectionMitochondrial Physiology - Historical Collection

Aims

The growing MiP-Collection aims at preserving scientific instruments that are of historical importance in the field of bioenergetics and mitochondrial physiology. The fast turnover of scientific equipment makes obsolete even comparatively recent instrumentation. The Oroboros O2k was the first commercial mitochondrial respirometer using a computer for data acquisition. Today, chart recorders are nearly forgotten. Due to limitations of storage space, unused scientific equipment is disposed of, despite its potential historical value. The disposal of some unique apparatus constitutes an irreversible loss to science and society, and to the continued appreciation of the foundations of our scientific discipline.

You may consider to make items of scientific historical interest in mitochondrial physiology available to the MiP-Collection. These items of the MiP-Collection may specifically include historically valuable

  • equipment and accessories,
  • books and symposium proceedings,
  • reprint collections,
  • pictures, slides, documents.
MiP03MiP03Mitochondrial Preservation Medium, MiP03, developed for preservation of isolated mitochondria.
MiPMapMiPMap
MiPMap

The project Mitochondrial Physiology Map (MiPMap) is initiated to provide an overview of mitochondrial properties in cell types, tissues and species. As part of Bioblast, MiPMap may be considered as an information synthase for Comparative Mitochondrial Physiology. Establishing a comprehensive database will require global input and cooperation.

A comparative database of mitochondrial physiology may provide the key for understanding the functional implications of mitochondrial diversity from mouse to man, and evaluation of altered mitochondrial respiratory control patterns in health and disease (Gnaiger 2009).
MiPNet-PublicationMiPNetMiPNet is the abbreviation for the OROBOROS Journal Mitochondrial Physiology Network, including chapters of the O2k-Manual, O2k-Procedures, O2k-Workshops, and other announcements, starting with MiPNet 01 in 1996. See also »MiPNet.
MiPSocietyMiP
MiPsociety
The Mitochondrial Physiology Society (MiP) has been founded to organize MiPconferences, MiPschools, and MiPworkshops worldwide. MiP has been founded at the Third Conference on Mitochondrial Physiology (MiP2003, Schroecken, Austria). The MiPsociety is an international organization, based in Europe and operating world-wide.
MiR05MiR05Mitochondrial respiration medium, MiR05, developed for oxygraph incubations of mitochondrial preparations. MiR06 = MiR05 + catalase. MiR05Cr = MiR05 + creatine.
MiR05CrMiR05CrMitochondrial respiration medium, MiR05Cr, developed for oxygraph incubations of mitochondrial preparations - permeabilized muscle fibers. MiR05Cr = MiR05 + 20 mM creatine.
MiR06MiR06Mitochondrial respiration medium, MiR06, developed for oxygraph incubations of mitochondrial preparations. MiR06 = MiR05 plus catalase. MiR06Cr = MiR06 plus creatine.
MiR06CrMiR06CrMitochondrial respiration medium, MiR06Cr, developed for oxygraph incubations of mitochondrial preparations - permeabilized muscle fibers. MiR06Cr = MiR06 + 20 mM creatine.
MiRK03MiRK03Mitochondrial respiration medium, MiRK03, modified after a medium described by Komary 2010 Biochim Biophys Acta, intended for use as medium for H2O2 production measurement with Amplex Red.
MicroplatesMicroplate readers allow large numbers of sample reactions to be assayed in well format microtitre plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 µL per well. a wide range of applications involve the use of fluorescence measurements , although they can also be used in conjunction with absorbance measurements.
MitoActionMitoActionMitoAction.JPGThe mission of MitoAction is to improve quality of life for all who are affected by mitochondrial disorders through support, education and advocacy initiatives.
MitoCanada FoundationmitoCanada
MitoCanada
The MitoCanada Foundation.

The MitoCanada Foundation is Canada’s only not-for-profit organization focused on mitochondrial disease. Since its founding in 2010, MitoCanada has dedicated over $1 million to fund the work of leading Canadian scientists and to support national awareness and support programs.

The MitoCanada Foundation is committed to ensuring that those who live with mitochondrial disease are able to enjoy the best possible quality of life until there is a cure.

TeamMito is MitoCanada’s grassroots awareness and fundraising program that turns people’s sports passions into special events and athletic feats to bring attention to mitochondrial disorders. https://www.facebook.com/TeamMitoCanada/
MitoFit DOI Data CenterMitoFit DOI DCThe MitoFit DOI Data Center is responsible for the provision of digital identifiers, for the storage and ensuring the persistence of the scientific objects, the provision of access, review process and maintenance of the Metadata, and quality control.
MitoFit Preprint ArchivesMitoFit Preprint ArchMitoFit Preprint Archives is an Open Access preprint server for mitochondrial physiology and bioenergetics.
MitoFit protocolsMitoFit protocols are moderated by the MitoFit moderators (MitoFit team), either as protocols with direct reference to publications available to the scientific communicty, or protocols additionally described and made available in Bioblast with full information on authors (including contact details), author contributions, and editor (moderator) in charge. This is part of the MitoFit Quality Control System for establishing a comprehensive MitoFit data repository, which will require global input and cooperation.
MitoFit registered projectMitoFit-RPMitoFit registered projects are announced in the MitoFit Quality Control System with reference to MitoFit protocols, which are considered to be publicly deposited protocols. Project registration is a two-phase process. Guidelines will be defined. (1) Pre-registration of a project requires submission to a MitoFit moderator (editor), including protocol details with reference to MitoPedia protocols, or with submission of protocols for publication (Open Access) in MitoPedia. The MitoFit (Bioblast) editors will edit the submitted protocols (layout) and insert into Bioblast submitted pre-registrations and protocols. (2) MitoFit moderators (editors) will set up a MitoFit accreditation panel, in which the registrant will be included (perhaps not in the long run, to avoid conflict of interests) and/or for which the registrant can suggest delegates (compare peer review). Accredited MitoFit protocols are labelled as MitoFit accredited, and the pre-registered MitoFit project becomes labelled and listed as MitoFit registered project (MitoFit accredited). This is possible before (advance registration), during progress, and after completion of a study (post-registration). A MitoFit registered project receives a code for feeding data into the MitoFit data repository.
MitoGlobalPlayer invitation
MitoKit-CII MitoPediaMitoKit-CIICell permeable prodrugs, composed of NV161/MitoKit-CII and NV118/MitoKit-CII, of the Complex II substrate succinate increase ATP-linked mitochondrial respiration in CI-deficient human blood cells, fibroblasts and heart fibres.
MitoOx1MitoOx1Mitochondrial respiration medium, MitoOx1, used by the Budapest groups for respirometry und Amplex Red trials.
MitoOx2MitoOx2Mitochondrial respiration medium, MitoOx2, developed for oxygraph incubations of mitochondrial preparations to measure the H2O2 production. MitoOx2 yields a higher optical sensitivity and lower "drift" (oxidation of the fluorophore precurcor without H2O2 present) for Amplex UltraRed(R) than e.g. MiR05.
MitoPedia
MitoPedia
MitoPedia: Concepts and methods
MitoPedia: DatLab
MitoPedia: Enzymes
MitoPedia: Ergodynamics
MitoPedia: Fluorometry
MitoPedia: Inhibitors
MitoPedia: Media for respirometry
MitoPedia: MiP and biochemistry
MitoPedia: MiP concepts
MitoPedia: O2k
MitoPedia: O2k hardware
MitoPedia: Oroboros QM
MitoPedia: Permeabilization agents
MitoPedia: Preprints
MitoPedia: Preprints and history
MitoPedia: Respiratory control ratios
MitoPedia: Respiratory states
MitoPedia: Respirometry
MitoPedia: SUIT
MitoPedia: SUIT A
MitoPedia: SUIT B
MitoPedia: SUIT C
MitoPedia: Sample preparations
MitoPedia: Spectrophotometry
MitoPedia: Substrates and metabolites
MitoPedia: Terms and abbreviations
MitoPedia: Uncouplers
MitoSOXMitoSOXTM is the version of the hydroetidine design to target mitochondria in live cells for the detection of superoxide (O2•-). The oxidation of the compund by O2•- is easily detected in the red spectrum. One of the advantages of MitoSOXTM is its selectivity for O2•- but not for other Reactive oxygen species or Reactive nitrogen species.
• Readily oxidized by superoxide but not by other ROS- or RNS-generating systems
Absorption/emission maxima: ~510/580 nm
• Use for live cell imaging
• Rapidly and selectively targeted to the mitochondria


MitoSOXTM has been widely used in life cell imaging but it is not free of problems and should be used cautiously. For example, it has been highlighted that the use of potentiometric dyes which accumulates into the mitochondria due to its moiety with Tetraphenylphosphonium, confers a membrane potential sensitivity that creates a series of artifacts and problems not often considered.
MitochondriamtMitochondria (Greek mitos: thread; chondros: granule) are small structures within cells, which function in cell respiration as powerhouses or batteries. Mitochondria belong to the bioblasts of Richard Altmann. Abbreviation: mt, as generally used in mtDNA. Singular: mitochondrion (bioblast); plural: mitochondria (bioblasts).
Mitochondria Interest GroupMIG
MIG.gif

The Mitochondria Interest Group (MIG) is an Inter-Institute Interest Group at the National Institutes of Health (NIH), with members worldwide! MIG is concerned with all aspects of the mitochondrion and diseases in which the mitochondrion is involved. We hold monthly meetings, usually on the second Monday of the month (except when it is a Federal holiday or other special exceptions).

MITOCHONDRIA-L@LIST.NIH.GOV is an Email list moderated by Ph.D. Steven Zullo as an interactive information platform, with free subscritpion to this mitochondrial network. List members are reminded of their responsibility to critically evaluate the content of the postings. The information, opinions, data, and statements contained herein are not necessarily those of the U. S. Government, the National Institutes of Health (NIH), or MIG and should not be interpreted, acted on or represented as such.
Mitochondria Research SocietyMRS
MRS LOGO.JPG
The Mitochondria Research Society (MRS) is a nonprofit international organization of scientists and physicians. The purpose of MRS is to find a cure for mitochondrial diseases by promoting research on basic science of mitochondria, mitochondrial pathogenesis, prevention, diagnosis and treatment through out the world.
Mitochondria and bioblasts: Made history
Mitochondrial ATP-sensitive K+ channelmtKATPThe mitochondrial ATP-sensitive K+ channel (mtKATP or mitoKATP).
Mitochondrial European Education TrainingMEET
Meet.jpg
The Mitochondrial European Education Training (MEET) MEET is a project started on January 2013. MEET network is composed by a multi-partner project that intends to mobilize the critical mass of expertise, by linking partners from 8 different countries, among which 8 world-leading basic science and clinical centers of excellence, an 1 SME with direct interest in mitochondrial medicine and 3 associated partners that provide for all trainees no-scientific training. MEET is training 11 ESRs and 3 ERs coming from all over the world supervised in their research by 15 mentors and by their collaborators. MEET combine the efforts of leading clinicians with those of more basic oriented groups and will have important implications for the comprehension and treatment of mitochondria-related pathologies.
Mitochondrial Medicine SocietyMMS
Mitochondrial Medicine Society.jpg
The Mitochondrial Medicine Society (MMS) was founded in 2000 and represents an international group of physicians, researchers and clinicians working towards the better diagnosis, management, and treatment of mitochondrial diseases.
Mitochondrial Physiology NetworkMitochondr physiol network, MiPNetThe Mitochondrial Physiology Network is the on-line OROBOROS journal.
Mitochondrial Research Guild
Mito-Reseach-Guild.JPG
The Mitochondrial Research Guild is a special interest guild of Seattle Children's Hospital. The guild was founded by a group of families in the Seattle area that are working together to raise awareness, promote research, and improve the quality of medical care that is available to children that are dealing with the devastating and potentially life threatening effects of mitochondrial disease.
Mitochondrial competencemt-competence; MitoComMitochondrial metabolic competence is the organelle's capacity to provide adequate amounts of ATP in due time, by adjusting the mt-membrane potential, mt-redox states and the ATP/ADP ratio according to the metabolic requirements of the cell.

The term mitochondrial competence is also known in a genetic context: Mammalian mitochondria possess a natural competence for DNA import.

MitoCom_O2k-Fluorometer is a Mitochondrial Competence network, the nucleus of which is formed by the K-Regio project MitoCom Tyrol.
Mitochondrial concentrationCmtEMitochondrial concentration is CmtE = mtE·V-1 [mtEU·m-3]. mt-Concentration is an experimental variable, dependent on sample concentration.
Mitochondrial contentmtENXMitochondrial content per object X is mtENX = mtE·NX-1 [mtEU·x-1].
Mitochondrial densityDmtESpecific mitochondrial density is DmtE = mtE·mX-1 [mtEU·kg-1]. If the amount of mitochondria, mtE, is expressed as mitochondrial mass, then DmtE is the mass fraction of mitochondria in the sample. If mtE is expressed as mitochondrial volume, Vmt, and the mass of sample, mX, is replaced by volume of sample, VX, then DmtE is the volume fraction of mitochondria in the sample.
Mitochondrial free radical theory of agingMFRTAThe mitochondrial free radical theory of aging goes back to Harman (1956) and ranks among the most popular theories of aging. It is based on postulates which are not unequivocally supported by observation (Bratic, Larsson 2013):

(i) Mitochondrial ROS production increases with age caused by progressive mitochondrial dysfunction; (ii) antioxidat capacity declines with age; (iii) mutations of somatic mtDNA accumulate during aging;

(iv) a vicious cycle occurs of increased ROS production caused by mtDNA mutations and degenerated mt-function, and due to ROS-induced ROS production.
Mitochondrial inner membranemtIMThe mitochondrial inner membrane is the structure harboring the membrane-bound electron transfer-pathway including the respiratory complexes working as proton pumps, several substrate transporters involved in the ET-pathway, and the mt-phosphorylation system. The mt-membrane potential and proton gradient (collectively the proton motive force) are generated across the mtIM.
Mitochondrial markermt-markerMitochondrial markers are structural or functional properties that are specific for mitochondria. A structural mt-marker is the area of the inner mt-membrane or mt-volume determined stereologically, which has its limitations due to different states of swelling. If mt-area is determined by electron microscopy, the statistical challenge has to be met to convert area into a volume. When fluorescent dyes are used as mt-marker, distinction is necessary between mt-membrane potential dependent and independent dyes. mtDNA or cardiolipin content may be considered as a mt-marker. Mitochondrial marker enzymes may be determined as molecular (amount of protein) or functional properties (enzyme activities). Respiratory capacity in a defined respiratory state of a mt-preparation can be considered as a functional mt-marker, in which case respiration in other respiratory states is expressed as flux control ratios. » MiPNet article
Mitochondrial marker enzymesMitochondrial marker enzymes are enzymes that are specifically present in mitochondria, in the mt-matrix, the inner mt-membrane, the inter-membrane space, or the outer mt-membrane.
Mitochondrial matrixmt-matrixThe mitochondrial matrix (mt-matrix) is enclosed by the inner mt-membrane. The terms mitochondrial matrix space or mitochondrial lumen are used synonymously. The mt-matrix contains the enzymes of the tricarboxylic acid cycle, fatty acid oxidation and a variety of enzymes that have cytosolic counterparts (e.g. glutamate dehydrogenase, malic enzyme). Metabolite concentrations, such as the concentrations of energy substrates, adenylates (ATP, ADP, AMP) and redox systems (NADH), can be very different in the mt-matrix, the mt-intermembrane space, and the cytosol. The finestructure of the gel-like mt-matrix is subject of current research.
Mitochondrial membrane potentialmtMP, Δψ [V]The mitochondrial membrane potential, mtMP, is the electric part of the protonmotive force, ΔpH+.

Δψ = ΔpH+ - ΔµH+ / F

mtMP or Δψ is the potential difference across the inner mitochondrial (mt) membrane, expressed in the electric unit of volt [V]. Electric force of the mitochondrial membrane potential is the electric energy change per ‘motive’ electron or per electron moved across the transmembrane potential difference, with the number of ‘motive’ electrons expressed in the unit coulomb [C].

The chemical part of the protonmotive force, µH+ / F stems from the difference of pH across the mt-membrane. It contains a factor that bridges the gap between the electric force [J/C] and the chemical force [J/mol]. This factor is the Faraday constant, F, for conversion between electric force expressed in joules per coulomb or Volt [V=J/C] and chemical force with the unit joules per mole or Jol [Jol=J/mol],

F = 96.4853 kJol/V = 96,485.3 C/mol
... further results