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  • '''Close''' a DatLab file.  +
  • '''Cyclic voltammetry'''  +
  • '''Extinction''' is a synonym for [[absorbance]].  +
  • '''FADH2''' and '''FAD''': see [[Flavin adenine dinucleotide]].  +
  • '''Hydroxylamine''' is an inhibitor of [[catalase]].  +
  • '''International Oxygraph Course''' (IOC), see [[O2k-Workshops]].  +
  • '''NADH calibration'''  +
  • '''Performance estimation'''  +
  • '''Q calibration'''  +
  • '''Select O2k - DatLab'''  +
  • '''T-Shirt Oroboros black/organic cotton''': An Oroboros on the front.  +
  • '''[[Template:Base quantities and count]]'''  +
  • '''pX calibration'''  +
  • ''See'' '''[[N/NS pathway control ratio]]'''  +
  • ''See'' '''[[Pathway control efficiency]]'''  +
  • ''See'' '''[[Pathway control ratio]]'''  +
  • ''See'' '''[[S-pathway control state]] (previous: CII-linked)  +
  • ''See'' '''[[S/NS pathway control ratio]]'''  +
  • ''See'' '''[[population]]'''.  +
  • ''See:'' '''[[Inorganic phosphate]]'''  +
  • '''''J''<sub>max</sub>''' is t'''''J''<sub>max</sub>''' is the maximum pathway flux (e.g. [[oxygen flux]]) obtained at saturating substrate concentration. ''J''<sub>max</sub> is a function of metabolic state. In hyperbolic ADP or oxygen kinetics, ''J''<sub>max</sub> 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 ''c''<sub>50</sub> or [[P50|''p''<sub>50</sub>]].[[P50|''p''<sub>50</sub>]].  +
  • '''''N,N,N',N'''-Tetramethyl-''p''-phenyle'''''N,N,N',N'''-Tetramethyl-''p''-phenylenediamine dihydrochloride, TMPD''', is applied as an artificial substrate for reducing [[cytochrome c|cytochrome ''c'']] in the respirometric assay for [[Complex IV|cytochrome ''c'' oxidase]] (CIV) activity. It is maintained in a reduced state by [[ascorbate]] and undergoes [[autoxidation]] as a function of [[oxygen pressure]], TMPD, ascorbate and cytochrome ''c'' concentration.orbate and cytochrome ''c'' concentration.  +
  • '''''p''<sub>50</sub>''' is th'''''p''<sub>50</sub>''' is the oxygen partial pressure at which (a) respiratory flux is 50% of maximum oxygen flux, [[Jmax|''J''<sub>max</sub>]], at saturating oxygen levels. The oxygen affinity is indirectly proportional to the ''p''<sub>50</sub>. The ''p''<sub>50</sub> depends on metabolic state and rate. (b) ''p''<sub>50</sub> is the oxygen partial pressure at which oxygen binding (on myoglobin, haemoglobin) is 50%, or desaturation is 50%.n partial pressure at which oxygen binding (on myoglobin, haemoglobin) is 50%, or desaturation is 50%.  +
  • '''2,4-dinitrophenole''' (C<sub>6</sub>H<sub>4</sub>N<sub>2</sub>O<sub>5</sub>; M = 184.11 g·mol<sup>-1</sup>) is a protonophore acting as an [[uncoupler]] of [[oxidative phosphorylation]].  +
  • '''2-Deoxyglucose''', also known as 2-deoxy-D-glucose is a glucose derivative that has the 2-hydroxyl group replaced by hydrogen. It competitively inhibits glycolysis by blocking hexokinase and phosphohexoseisomerase.  +
  • '''2-mercaptoacetate''' is an inhibitor of'''2-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]]).[[Osiki 2016 FASEB J]]).  +
  • '''4'''#### '''''O2k-Catalogue: O2k-Modules'''''. O2k-Modules can be obtained with the O2k or added later, and can be simply installed by the user.  +
  • '''4,5,6,7-Tetrachloro-2-trifluoromethylbenzimidazole''' is a protonophore or [[uncoupler]] of oxidative phosphorylation.  +
  • '''8-Hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS)''' is a ratiometric pH fluorophore; pKa = 7.3. Relative molecular mass: ''M''<sub>r</sub> = 524.39  +
  • '''AMP-activated protein kinase''' is a regulatory protein which acts as crucial cellular energy sensor by sensing AMP, [[ADP]] and/or Ca<sup>2+</sup> levels in response to metabolic stresses or drug administration.  +
  • '''ATP synthase''' or F-ATPase (F<sub&g'''ATP synthase''' or F-ATPase (F<sub>1</sub>F<sub>O</sub>-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]].[[oligomycin]].  +
  • '''ATPases''' are enzymes that hydrolyse [[ATP]]'''ATPases''' are enzymes that hydrolyse [[ATP]], releasing [[ADP]] and [[inorganic phosphate]]. The contamination of isolated mitochondria with ATPases from other organelles and endogenous adenylates can lead to the production of ADP, which can stimulate respiration. This situation would lead to an overestimation of [[LEAK respiration]] measured in the absence of ADP, ''L''(n) and subsequent inhibition of respiration by oligomycin, ''L''(Omy). of respiration by oligomycin, ''L''(Omy).  +
  • '''Acceleration''', '''''a''''', is the ch'''Acceleration''', '''''a''''', is the change of [[velocity]] over time [m·s<sup>-2</sup>].</br> '''''a''''' = d'''''v'''''/d''t''</br>The symbol ''g'' is used for acceleration of free fall. The standard acceleration of free fall is defined as ''g''<sub>n</sub> = 9.80665 [m·s<sup>-2</sup>].ned as ''g''<sub>n</sub> = 9.80665 [m·s<sup>-2</sup>].  +
  • '''Acclimation''' is an immediate time scale adaption expressing phenotypic plasticity in response to changes of a single variable under controlled laboratory conditions.  +
  • '''Acclimatization''' is an immediate time scale adaption expressing phenotypic plasticity in response to changes of habitat conditions and life style where several variables may change simultaneously.  +
  • '''Acyl-CoA dehydrogenases''' ACADs are lo'''Acyl-CoA dehydrogenases''' ACADs are localized in the mitochondrial matrix. Several ACADs are distinguished: short-chain (SCAD), medium-chain (MCAD), and long-chain (LCAD). ACAD9 is expressed in human brain. ACADs catalyze the reaction</br>:::: acyl-CoA + FAD → ''trans''-2-enoyl-CoA + FADH<sub>2</sub>→ ''trans''-2-enoyl-CoA + FADH<sub>2</sub>  +
  • '''Acyl-CoA oxidase''' is considered as a '''Acyl-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 (>C<sub>20</sub>). Electrons are directly transferred from FADH<sub>2</sub> to O<sub>2</sub> with the formation of H<sub>2</sub>O<sub>2</sub>.t; to O<sub>2</sub> with the formation of H<sub>2</sub>O<sub>2</sub>.  +
  • '''Acylcarnitines''' are esters derivative'''Acylcarnitines''' are esters derivative of [[carnitine]] and [[fatty acid]]s, involved in the metabolism of fatty acids. Long-chain acylcarnitines such as [[palmitoylcarnitine]] must be transported in this form, conjugated to carnitine, into the mitochondria to deliver fatty acids for fatty acid oxidation and energy production. Medium-chain acylcarnitines such as [[octanoylcarnitine]] are also frequently used for high-resolution respirometry.tly used for high-resolution respirometry.  +
  • '''Adaptation''' is an evolutionary time scale expression of phenotypic plasticity in response to selective pressures prevailing under various habitat conditions.  +
  • '''Add:''' A new graph is added at the bottom of the screen. Select plots for display in the new graph, Ctrl+F6. '''Delete: Delete one of the graphs displayed in DatLab.  +
  • '''Additivity''' ''A''<sub>''α&β'''Additivity''' ''A''<sub>''α&β''</sub> describes the principle 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-linked substrate state |NS or CI<small>&</small>II e-input]]). Further additivity may be observed by convergent electron flow through [[Glycerophosphate_dehydrogenase_Complex|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 [[Mitochondrial preparations|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 separately measured respiratory capacities, N + S, is identical to the capacity measured in the state with combined substrates, NS (CI<small>&</small>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 does not limit OXPHOS capacity ([[Excess E-P capacity factor |excess ''E-P'' capacity factor]] is zero). In most cases, however, additivity is incomplete, NS < N+S.Excess E-P capacity factor |excess ''E-P'' capacity factor]] is zero). In most cases, however, additivity is incomplete, NS < N+S.  +
  • '''Adenine 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.  +
  • '''Adenosine diphosphate''' is a nucleotid'''Adenosine diphosphate''' is a nucleotide. In [[OXPHOS]] core metabolism, ADP is a substrate of [[ANT]] and [[ATP synthase]] in the [[phosphorylation system]]. ADP is the discharged or low-energy counterpart of [[ATP]]. ADP can accept chemical energy by regaining a phosphate group to become ATP, in substrate-level phosphorylation (in anaerobic catabolism), at the expense of solar energy (in photosynthetic cells) or chemiosmotic energy (respiration in heterotrophic cells). ADP is added to [[mitochondrial preparations]] at kinetically saturating concentrations to induce the active state for evaluation of [[OXPHOS capacity]].[[OXPHOS capacity]].  +
  • '''Adenosine 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]]).  +
  • '''Adenylate 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.  +
  • '''Advancement per volume''' or volume-spe'''Advancement per volume''' or volume-specific advancement, d<sub>tr</sub>''Y'', is related to [[advancement]] of a transformation, d<sub>tr</sub>''Y'' = d<sub>tr</sub>''ξ''∙''V''<sup>-1</sup> [MU∙L<sup>-1</sup>]. Compare d<sub>tr</sub>''Y'' with the amount of substance ''j'' per volume, ''c''<sub>''j''</sub> ([[concentration]]), related to [[amount]], ''c''<sub>''j''</sub> = ''n''<sub>''j''</sub>∙''V''<sup>-1</sup> [mol∙''V''<sup>-1</sup>]. Advancement per volume is particularly introduced for chemical reactions, d<sub>r</sub>''Y'', and has the dimension of concentration (amount per volume [mol∙L<sup>-1</sup>]). In an [[open system]] at steady-state, however, the concentration does not change as the reaction advances. Only in [[closed system]]s and [[isolated system]]s, specific advancement equals the change in concentration divided by the stoichiometric number, d<sub>r</sub>''Y'' = d''c''<sub>''j''</sub>/''ν''<sub>''j''</sub> (closed system) d<sub>r</sub>''Y'' = d<sub>r</sub>''c''<sub>''j''</sub>/''ν''<sub>''j''</sub> (general) With a focus on ''internal'' transformations (i; specifically: chemical reactions, r), d''c''<sub>''j''</sub> is replaced by the partial change of concentration, d<sub>r</sub>''c''<sub>''j''</sub> (a transformation variable or process variable). d<sub>r</sub>''c''<sub>''j''</sub> contributes to the total change of concentration, d''c''<sub>''j''</sub> (a system variable or variable of state). In open systems at steady-state, d<sub>r</sub>''c''<sub>''j''</sub> is compensated by ''external processes'', d<sub>e</sub>''c''<sub>''j''</sub> = -d<sub>r</sub>''c''<sub>''j''</sub>, exerting an effect on the total concentration change of substance ''j'', d''c''<sub>''j''</sub> = d<sub>r</sub>''c''<sub>''j''</sub> + d<sub>e</sub>''c''<sub>''j''</sub> = 0 (steady state) d''c''<sub>''j''</sub> = d<sub>r</sub>''c''<sub>''j''</sub> + d<sub>e</sub>''c''<sub>''j''</sub> (general)sses'', d<sub>e</sub>''c''<sub>''j''</sub> = -d<sub>r</sub>''c''<sub>''j''</sub>, exerting an effect on the total concentration change of substance ''j'', d''c''<sub>''j''</sub> = d<sub>r</sub>''c''<sub>''j''</sub> + d<sub>e</sub>''c''<sub>''j''</sub> = 0 (steady state) d''c''<sub>''j''</sub> = d<sub>r</sub>''c''<sub>''j''</sub> + d<sub>e</sub>''c''<sub>''j''</sub> (general)  +
  • '''Air calibration''' of an oxygen sensor '''Air 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, ''c''<sub>O2</sub> [µM], is obtained at any partial pressure by multiplying the partial pressure by the oxygen solubility, ''S''<sub>O2</sub> [µM/kPa]. ''S''<sub>O2</sub> is a function of temperature and composition of the salt solution, and is thus a function of the experimental medium. The [[Oxygen_solubility_factor|solubility factor]] of the medium, ''F''<sub>M</sub>, expresses the oxygen solubility relative to pure water at any experimental temperature. ''F''<sub>M</sub> is 0.89 in serum (37 °C) and 0.92 in [[MiR06]] or [[MiR05]] (30 °C and 37 °C).iR05]] (30 °C and 37 °C).  +
  • '''Allegations of research misconduct''' a'''Allegations of research misconduct''' are handled with care. Publishers and editors shall take reasonable steps to identify and prevent the publication of papers where research misconduct has occurred, including plagiarism, citation manipulation, and data falsification/fabrication, among others. In no case shall a journal or its editors encourage such misconduct, or knowingly allow such misconduct to take place. In the event that a journal's publisher or editors are made aware of any allegation of research misconduct relating to a published article in their journal, the publisher or editor shall follow [https://publicationethics.org/core-practices COPE's guidelines] (or equivalent) in dealing with allegations.r equivalent) in dealing with allegations.  +
  • '''Alternative quinol oxidases''' AOX are '''Alternative quinol oxidases''' AOX are membrane-bound enzymes capable of supporting [[cyanide]]- and [[antimycin A]]-resistant mitochondrial respiration. AOX catalyzes the oxidation of ubiquinol and the reduction of oxygen to water in a four-electron process. As this bypasses several proton-translocating steps, induction of this alternative pathway is associated with a reduction of ATP production per oxygen consumed. AOX is found in most plants (including microalgae), many fungi and protists, but is not expressed in animals. AOX is inhibited by [[salicylhydroxamic acid]] (SHAM). Expression and activity of the enzyme are modified by environmental conditions such as temperature, oxidative stress, nutrient availability, and pathogens such as viruses.ailability, and pathogens such as viruses.  +
  • '''Aluminium trolley''' (700x500x60 mm); carrying capacity 120 kg; incl. packing box; for transport of O2k. '''Discontinued'''  +
  • '''Amp calibration''' indicates the calibration of the amperometric O2k-channel.  +
  • '''Amplex<sup>®</sup> UltraRed'''Amplex<sup>®</sup> UltraRed''' (AmR) is used as an [[extrinsic fluorophores |extrinsic fluorophore]] for measurement of [[hydrogen peroxide]] production ([[ROS]]) by cells or mitochondrial preparations. The reaction of H<sub>2</sub>O<sub>2</sub> and AmR is catalyzed by [[horseradish peroxidase]] to produce the red fluorescent compound [[resorufin]] (excitation wavelength 563 nm, emission 587 nm; the fluorescent product according to the supplier is called UltroxRed in the case of Amplex<sup>®</sup> UltraRed which has a similar structure to resorufin). The change of emitted fluorescence intensity is directly proportional to the concentration of H<sub>2</sub>O<sub>2</sub> added, whereby the H<sub>2</sub>O<sub>2</sub> is consumed.n of H<sub>2</sub>O<sub>2</sub> added, whereby the H<sub>2</sub>O<sub>2</sub> is consumed.  +
  • '''Amytal''' sodium salt (synonym: amobarbital; 5-Ethyl-5-isoamylbarbituric acid) is a barbiturate drug and an inhibitor of [[Complex I]].  +
  • '''Anaerobic''' metabolism takes place wit'''Anaerobic''' 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]].[[limiting oxygen pressure]].  +
  • '''Anaplerosis''' is the process of format'''Anaplerosis''' is the process of formation of intermediates of the [[tricarboxylic acid cycle]]. [[Malic enzyme]] (mtME), [[phosphoenolpyruvate carboxykinase]] (PEPCK), propionyl-CoA carboxylase, [[pyruvate carboxylase]] and [[proline dehydrogenase]] play important roles in anaplerosis.[[proline dehydrogenase]] play important roles in anaplerosis.  +
  • '''Anaplerotic pathway control states''' a'''Anaplerotic 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).anaplerotic substrate control states (aN).  +
  • '''Antimycin A''' is an inhibitor of [[Complex III]]'''Antimycin A''' is an inhibitor of [[Complex III]] (CIII). It binds to the Qi site of CIII and inhibits the transfer of electrons from heme ''b''<sub>H</sub> to oxidized Q (Qi site inhibitor). High concentrations of antimycin A also inhibit acyl-CoA oxidase and D-amino acid oxidase.lso inhibit acyl-CoA oxidase and D-amino acid oxidase.  +
  • '''Aqua destillata''' (a.d.) is the Latin '''Aqua destillata''' (a.d.) is the Latin name for '''distilled [[water]]''', H<sub>2</sub>O. 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.illed water but also with high-purity deionised water.  +
  • '''Artemisinin''' and various derivatives '''Artemisinin''' and various derivatives are potent anti-malaria drugs which have additionally anti-tumorigenic effects, particularly when targeted at mitochondria. The anti-malaria effect is associated with artemisinin's action on heme. Mitochondria are involved in the synthesis of heme, and may play additional roles in the anti-tumorigenic effect of artemisinin.he anti-tumorigenic effect of artemisinin.  +
  • '''Aspirin''' is a widely applied drug that requires dosage adjusted to individual body mass. It is a non-selective COX inhibitor and exerts an effect on long-chain fatty acid transport into mitochondria.  +
  • '''Atractyloside''' is an inhibitor of the'''Atractyloside''' is an inhibitor of the [[Adenine nucleotide translocator|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.otides through the mitochondrial membrane.  +
  • '''Attribute''' in general is a characteristic or property. In databases an attribute describes a column in a table. Rows then represent the according attribute values.  +
  • '''Auranofin''' (AF) is a gold complex which inhibites thioredoxin reductase (TrxR).  +
  • '''Automatic pan''' (only for real-time da'''Automatic 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.iewing earlier sections of the experiment.  +
  • '''Autoscale Y1 (Y2) axes''': Autoscaling the measured values (full data range) on the Y1 (Y2) axis in the selected [[plot]].  +
  • '''Autoscale time axis''' gives an overview of the entire experimental period.  +
  • '''Autoscale''' zooms in or out of the selected period with [[Autoscale time axis]], [[Autoscale Y1 (Y2) axes]] and [[Automatic pan]].  +
  • '''Bandwidth''' 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 pressure''', ''p''<sub>'''Barometric pressure''', ''p''<sub>b</sub>, 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, ''p''<sub>O<sub>2</sub></sub>, 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]].[[pressure]].  +
  • '''Basal respiration''' or '''basal metabo'''Basal 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_1990_Biochim Biophys Acta|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_2011_FASEB J|Larsen et al 2011]] [3]).</br>» [[Basal_respiration#Basal_respiration_in_physiology.2C_cellular_bioenergetics_and_mitochondrial_physiology | '''MiPNet article''']][Basal_respiration#Basal_respiration_in_physiology.2C_cellular_bioenergetics_and_mitochondrial_physiology | '''MiPNet article''']]  +
  • '''Bendavia''' ('''Elamipretide''') was de'''Bendavia''' ('''Elamipretide''') was developed as a mitochondria-targeted drug against degenerative diseases, including cardiac ischemia-reperfusion injury. Clinical trials showed variable results. It is a cationic tetrapeptide which readily passes cell membranes, associates with [[cardiolipin]] in the mitochondrial inner membrane. Supercomplex-associated CIV activity significantly improved in response to elamipretide treatment in the failing human heart.tide treatment in the failing human heart.  +
  • '''Beryllium sulfate''' is used in combination with [[sodium fluoride]] to form beryllium trifluoride (BeF<sup>3−</sup>), to inhibit the [[ATP synthase]] if it is exposed by disruption of the mitochondrial membranes.  +
  • '''Bioactive mitObesity compounds''' are d'''Bioactive mitObesity compounds''' are drugs and nutraceuticals with more or less reproducible beneficial effects in the treatment of diverse preventable degenerative diseases implicated in comorbidities linked to obesity, characterized by common mechanisms of action targeting mitochondria.chanisms of action targeting mitochondria.  +
  • '''Biological reference interval''' or reference interval is the central 95 % interval of the distribution of reference values.  +
  • '''Biopsy preservation solution''', for preservation of tissue samples, preparation of muscle fibres, and permeabilization with [[saponin]].  +
  • '''Blebbistatin''' is a widely used muscle'''Blebbistatin''' is a widely used muscle and non-muscle myosin II-specific inhibitor that block contractile activity. Blebbistatin shows selectivity and high affinity for multiple class II myosins. Blebbistatin is commonly employed in respirometric experiments with permeabilized muscle fibers (pfi). Permeabilized muscle fibers are sensitive to low oxygen supply due to diffusion restrictions that limit mitochondrial respiration at the core of the fiber bundle. Therefore, hyperoxic conditions are required to counteract this limitation. Further studies have shown that the addition of blebbistatin in the respiration medium prevents fiber contraction, reduces the oxygen sensitivity and allows the study of ADP kinetics in pfi at normoxic oxygen levels. However, other studies described that the presence of blebbistatin does not prevent the oxygen dependence in pfi. Moreover, several limitations of blebbistatin i.e. low solubility in water, cytotoxicity and phototoxicity have been described.ity and phototoxicity have been described.  +
  • '''Blood cell preparation''' (bcp) is one of the key steps in diagnostic protocols.  +
  • '''Blood plasma''' is the non-cellular com'''Blood plasma''' is the non-cellular component of the blood. Plasma lacks cellular components of the blood, [[red blood cell]]s, [[white blood cell]]s, and [[platelet]]s. However, there are many proteins in plasma, i.e. fibrinogen, albumin and globulin. Both blood plasma and [[platelet-rich plasma]] maintain clotting activity after whole blood separation.ing activity after whole blood separation.  +
  • '''Blood serum''' is a purified plasma in '''Blood 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.d phase after blood or plasma coagulation.  +
  • '''Bongkrekik 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]].  +
  • '''CE''' marking is a mandatory conformity marking for certain products sold within the European Economic Area (EEA).  +
  • '''CHNO-fuel substrates''' are reduced car'''CHNO-fuel substrates''' are reduced carbon-hydrogen-nitrogen-oxygen substrates which are oxidized in the [[exergonic]] process of [[cell respiration]]. Mitochondrial pathways are stimulated by CHNO-fuel substrates feeding electrons into the [[ETS]] at different levels of integration and in the presence or absence of inhibitors acting on specific enzymes which are gate-keepers and control various pathway segments.pers and control various pathway segments.  +
  • '''COPE core practices for research''' are applicable to all involved in publishing scholarly literature.  +
  • '''Ca<sup>2+</sup>''' is a maj'''Ca<sup>2+</sup>''' is a major signaling molecule in both prokaryotes and eukaryotes. Its cytoplasmic concentration is tightly regulated by transporters in the plasma membrane and in the membranes of various organelles. For this purpose, it is either extruded from the cell through exchangers and pumps or stored in organelles such as the endoplasmic reticulum and the mitochondria. Changes in the concentration of the cation regulate numerous enzymes including many involved in ATP utilizing and in ATP generating pathways and thus ultimately control metabolic activity of mitochondria and of the entire cell. Measuring changes in Ca<sup>2+</sup> levels is thus of considerable interest in the context of [[high-resolution respirometry]].[[high-resolution respirometry]].  +
  • '''Calcium Green'''<sup>TM</sup&g'''Calcium Green'''<sup>TM</sup> (CaG) denotes a family of [[extrinsic fluorophores]] applied for measurement of Ca<sup>2+</sup> concentration with [[mitochondrial preparations]]. This dye fluoresces when bound to Ca<sup>2+</sup>. When measuring mitochondrial calcium uptake it is possible to observe the increase of the CaG signal upon calcium titration, followed by the decrease of CaG signal due to the uptake.n calcium titration, followed by the decrease of CaG signal due to the uptake.  +
  • '''Calorespirometry''' is the method of me'''Calorespirometry''' 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., as a test of the aerobic energy balance.  +
  • '''Carbohydrates''', also known as '''sacc'''Carbohydrates''', also known as '''saccharides''', are molecules composed of carbon, hydrogen and oxygen. These molecules can be divided by size and complexity into monosaccharides, disaccharides, oligosaccharides, and polysaccharides. [[Glucose]] is a monosaccharide considered the primary source of energy in cells and a metabolic intermediate. This carbohydrate undergoes glycolysis, with the generation of [[pyruvate]], that can enter the [[TCA cycle]]. </br></br>Carbohydrates such as glucose and fructose may also be involved in the [[Crabtree effect]].[[Crabtree effect]].  +
  • '''Carbonyl cyanide m-chlorophenyl hydrazo'''Carbonyl cyanide m-chlorophenyl hydrazone''', CCCP (U; C<sub>9</sub>H<sub>5</sub>ClN<sub>4</sub>; ''F''<sub>W</sub> = 204.62) is a protonophore (H<sup>+</sup> 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.ochondrial respiration, particularly to avoid inhibition of respiration at higher CCCP concentrations.  +
  • '''Carboxy SNARF® 1''' is a cell-impermean'''Carboxy 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.</br></br>Relative molecular mass: ''M''<sub>r</sub> = 453.45molecular mass: ''M''<sub>r</sub> = 453.45  +
  • '''Carboxyatractyloside''' CAT is a highly'''Carboxyatractyloside''' 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.ondrial membrane potential, and apoptosis.  +
  • '''Cardiolipin''', CL, is a double phospho'''Cardiolipin''', 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.</br> Contributed by [[Sparagna G]] 2016-04-18[[Sparagna G]] 2016-04-18  +
  • '''Carnitine 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 acetyltransferase''' (CrAT) i'''Carnitine 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.[[pyruvate dehydrogenase]] complex (PDC) activity.  +
  • '''Carnitine acyltransferases''' mediate t'''Carnitine 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 ([[acylcarnitine]]s). 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.id oxidation (FAO) cycle in the mt-matrix.  +
  • '''Carnitine palmitoyltransferase I''' (CP'''Carnitine palmitoyltransferase I''' (CPT-I, also known as carnitine acyltransferase I) is a regulatory enzyme in mitochondrial long-chain acyl-CoA uptake and further oxidation. CPT-I is associated with the mt-outer membrane mtOM and catalyses the formation of [[acylcarnitine]]s from acyl-CoA and L-carnitine. In the next step, acyl-carnitines are transported to the mitochondrial matrix via [[carnitine-acylcarnitine translocase]] in exchange for free [[carnitine]]. In the inner side of the mtIM [[carnitine palmitoyltransferase II]] converts the acyl-carnitines to carnitine and acyl-CoAs. There are three enzyme isoforms: CPT-1A (liver type), CPT-1B (muscle type), CPT-1C (brain type). Isoforms have significantly different kinetic and regulatory properties. Malonyl-CoA is an endogenous inhibitor of CPT-I.l-CoA is an endogenous inhibitor of CPT-I.  +
  • '''Carnitine palmitoyltransferase II''' (C'''Carnitine palmitoyltransferase II''' (CPT-II, also known as carnitine acyltransferase II) is part of the carnitine shuttle which is responsible for the mitochondrial transport of long-chain fatty acids. CPT-II is located on the inner side of the mtIM and converts the [[acylcarnitine]]s (produced in the reaction catalyzed by [[carnitine palmitoyltransferase I]]) to carnitine and acyl-CoAs, which undergo ß-oxidation in the mitochondrial matrix. Free carnitines are transported out of the mitochondrial matrix in exchange for acyl-carnitines via an integral mtIM protein [[carnitine-acylcarnitine translocase]] (CACT). Short- and medium-chain fatty acids do not require the carnitine shuttle for mitochondrial transport.itine shuttle for mitochondrial transport.  +
  • '''Carnitine''' is an important factor for'''Carnitine''' 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.ly the L-isomer is physiologically active.  +
  • '''Carnitine-acylcarnitine translocase''' '''Carnitine-acylcarnitine translocase''' (CACT) is part of the carnitine shuttle which mediates the mitochondrial transport of long-chain fatty acids where the [[fatty acid oxidation]] occurs. </br>CACT is an internal mt-IM protein and transports [[acylcarnitine]]s into the mitochondrial matrix in exchange for free [[carnitine]].[[carnitine]].  +
  • '''Carriers for malate: * [[dicarboxylate carrier]] * [[tricarboxylate carrier]] * [[2-oxoglutarate carrier]]  +
  • '''Catalase''' catalyzes the dismutation o'''Catalase''' catalyzes the dismutation of [[hydrogen peroxide]] to water and [[oxygen]]. Perhaps all cells have catalase, but mitochondria of most cells lack catalase. Cardiac mitochondria are exceptional in having mt-catalase activity (rat heart mitochondria: Radi et al 1991; mouse heart mitochondria: Rindler et al 2013). [[Hydroxylamine]] is an inhibitor of catalase, which is also inhibited by [[cyanide]] and [[azide]].</br></br>Mitochondrial respiration medium [[MiR05]] was developed considering the intracellular conditions of mitochondria in living cells. In mitochondrial preparations, enzymes and substrates present in the cytosol (such as catalase) are diluted when the plasma membrane is removed. Therefore, the addition of catalase is recommended when working with mitochondrial preparations, to consume any H<sub>2</sub>O<sub>2</sub> generated during the assay.2</sub>O<sub>2</sub> generated during the assay.  +
  • '''Catalytic activity''' of an enzyme is m'''Catalytic activity''' of an enzyme is measured by an enzyme assay and is expressed in units of katal (kat [mol∙s<sup>-1</sup>]). More commonly (but not conforming to SI units or IUPAC recommendations) enzyme activity is expressed in units U [mol∙min<sup>-1</sup>].tivity is expressed in units U [mol∙min<sup>-1</sup>].  +
  • '''Cell culture media''', like RPMI or DMEM, used for [[HRR]] of living cells.  +
  • '''Cell respiration''' channels metabolic '''Cell 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]].</br></br>In internal or '''cell respiration''' in contrast to [[fermentation]], redox balance is maintained by external electron acceptors, transported into the cell from the environment. The chemical potential between electron donors and electron acceptors drives the [[electron transfer pathway]], generating a chemiosmotic potential that in turn drives ATP synthesis.tential that in turn drives ATP synthesis.  +
  • '''Charge''' ''Q''<sub>el</sub> is the quantity of electricity expressed in the SI unit coulomb [C]. ''Q''<sub>el''X''</sub> [C] indicates the charge carried by the quantity of a specified ion ''X''.  +
  • '''Chinese numerals''' The Arabic numeral '''Chinese numerals'''</br>The Arabic numeral system used today in China was introduced to China by the Europeans in the early 17<sup>th</sup> century. But the Chinese character-based number systems are still in use. The financial numerals are used only when writing an amount on a form for remitting money at a bank. They function as anti-fraud numerals. </br></br>The character 零 (zero) appeared very early in ancient Chinese writing. However, at that time, it did not mean "nothing", but "bits and pieces", "not much". 一百零五(105) means in Chinese: In addition to a hundred, there is a fraction of five. With the introduction of the Arabic numerals, 105 is exactly pronounced “one hundred zero five”, the character 零 corresponds exactly to the symbol 0. Thus, the character 零has the meaning of 0. But the character 〇 was one of the Chinese characters created and promulgated by the only empress (with greater achievements than countless emperors) in the history of China in 690 AD (much later than the invention of 0 in India) for the purpose of demonstrating her power. At that time the character 〇 meant “star”, representing a round planet. It is now used as a synonym for the 零 (zero). planet. It is now used as a synonym for the 零 (zero).  +
  • '''Chloroplasts''' (Greek chloros: green; '''Chloroplasts''' (Greek chloros: green; plastes: the one who forms) are small structures within the cells that conduct [[photosynthesis]]. They are a type of organelle called plastids that are present in eukaryotic plant cells (algae, aquatic and terrestrial plants) and characterized by having two membranes and a high concentration of the pigment Chlorophyll. Like [[mitochondria]], they originated through the endosymbiosis of a cyanobacteria by an early eukaryotic cell and they have their own DNA which replicates during cell division. In addition to photosynthesis, in their internal matrix called stroma they also carry out other metabolic functions within the plant cells such as fatty acid synthesis or amino acid synthesis.ty acid synthesis or amino acid synthesis.  +
  • '''Choline dehydrogenase''' (EC 1.1.99.1) '''Choline 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 [[Electron transfer pathway]]. Analogous to [[succinate dehydrogenase]] (CII), electron transfer from choline dehydrogenase is FAD-linked downstream to Q. Choline is an [[ET-pathway substrate types]] 3.[[ET-pathway substrate types]] 3.  +
  • '''Citreoviridin''' 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.  +
  • '''Coenzyme 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 Q''' or ubiquinone (2,3-dimeth'''Coenzyme Q''' or ubiquinone (2,3-dimethoxy-5-methyl-6-polyprenyl-1,4-benzoquinone) was discovered in 1957 by the group of Crane. It is a lipid composed of a benzoquinone ring with an isoprenoid side chain, two methoxy groups and one methyl group. The length of the isoprenoid chain varies depending on the species; for example, six isoprenoid units (CoQ<sub>6</sub>) is the most commonly found CoQ in ''Saccharomyces cerevisiae'', eight units in ''Escherichia coli'' (CoQ<sub>8</sub>), nine units in ''Caenorhabditis elegans'' and rodents (CoQ<sub>9</sub>), ten units in humans (CoQ<sub>10</sub>), and some species have more than one CoQ form, e.g. human and rodent mitochondria contain different proportions of CoQ<sub>9</sub> and CoQ<sub>10</sub>. These redox compounds exist in three different forms: [[quinone]] (oxidized), [[quinol]] (reduced), and an intermediate [[semiquinone]].</br></br>''More details'' » '''[[Q-junction]]'''[Q-junction]]'''  +
  • '''Comorbidities''' are common in obesogen'''Comorbidities''' are common in obesogenic lifestyle-induced early aging. These are preventable, non-communicable diseases with strong associations to obesity. In many studies, cause and effect in the sequence of onset of comorbidities remain elusive. Chronic degenerative diseases are commonly obesity-induced. The search for the link between obesity and the etiology of diverse preventable diseases lead to the hypothesis, that mitochondrial dysfunction is the common mechanism, summarized in the term 'mitObesity'.nism, summarized in the term 'mitObesity'.  +
  • '''Complex I''', '''NADH:ubiquinone oxidor'''Complex 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]]. There is a widespread ambiguity on the 'lonely H<sup>+</sup> (the lonely [[hydron]])' surrounding Complex I: [[Ambiguity crisis - NAD and H+ |CI ambiguities]].[[Ambiguity crisis - NAD and H+ |CI ambiguities]].  +
  • '''Complex III''' or coenzyme Q : cytochro'''Complex III''' or coenzyme Q : cytochrome c - oxidoreductase, sometimes also called the cytochrome ''bc''<sub>1</sub> complex is a complex of the [[electron transfer pathway]]. It catalyzes the reduction of cytochrome ''c'' by oxidation of [[coenzyme Q]] (CoQ) and the concomitant [[Proton pump|pumping of 4 protons]] from the cathodic (negative) mitochondrial matrix to the anodic (positive) intermembrane space.l matrix to the anodic (positive) intermembrane space.  +
  • '''Complex IV''' or '''cytochrome ''c'' ox'''Complex IV''' or '''cytochrome ''c'' oxidase''' is the terminal oxidase of the mitochondrial [[electron transfer system]], reducing [[oxygen]] to [[water]], with reduced [[cytochrome c |cytochrome ''c'']] as a substrate. Concomitantly to that, CIV [[Proton pump|pumps protons]] against the electrochemical protonmotive force. CIV is frequently abbreviated as COX or CcO. It is the 'ferment' (Atmungsferment) of Otto Warburg, shown to be related to the cytochromes discovered by David Keilin.he cytochromes discovered by David Keilin.  +
  • '''Concentrated ammonia solution''' (25 % '''Concentrated 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.</br></br>'''Source:''' A commercially available solution from a drugstore is sufficient for this cleaning purposere is sufficient for this cleaning purpose  +
  • '''Concentration''' [mol·L<sup>-1<'''Concentration''' [mol·L<sup>-1</sup>] is a volume-specific quantity for diluted [[sample]]s s. In a concentration, the sample is expressed in a variety of [[format]]s: [[count]], amount, [[charge]], [[mass]], [[energy]]. In solution chemistry, amount concentration is [[amount of substance]] ''n''<sub>B</sub> per volume ''V'' of the solution, ''c''<sub>B</sub> = [B] = ''n''<sub>B</sub>·''V''<sup>-1</sup> [mol·dm<sup>-3</sup>] = [mol·L<sup>-1</sup>]. The standard concentration, ''c''°, is defined as 1 mol·L<sup>-1</sup> = 1 M. [[Count]] concentration ''C<sub>X</sub>'' = ''N<sub>X</sub>''·''V''<sup>-1</sup> [x·L<sup>-1</sup>] is the concentration of the number ''N<sub>X</sub>'' of elementary entities ''X'', for which the less appropriate term 'number concentration' is used by [[Cohen 2008 IUPAC Green Book |IUPAC]]. If the sample is expressed as volume ''V''<sub>s</sub> (''e.g.'', ''V''<sub>O<sub>2</sub></sub>), then the 'volume-concentration' of ''V''<sub>s</sub> in ''V'' is termed '[[volume fraction]]', ''Φ''<sub>s</sub> = ''V''<sub>s</sub>·''V''<sup>-1</sup> (''e.g.'', volume fraction of O<sub>2</sub> in dry air, ''Φ''<sub>O<sub>2</sub></sub>) = 0.20946). [[Density]] is the mass concentration in a volume ''V''<sub>S</sub> of pure sample S. </br></br>A ''change'' of concentration, d''c''<sub>X</sub>, in isolated or closed [[system]]s at constant [[volume]] is due to internal transformations ([[advancement per volume]]) only. In closed compressible systems (with a gas phase), the concentration of the gas changes, when pressure-volume work is performed on the system. In open systems, a change of concentration can additionally be due to [[external flow]] across the system boundaries.flow]] across the system boundaries.  +
  • '''Connect to O2k''' connects DatLab with '''Connect 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 [[DatLab data file| DLD file]]. Then data recording starts with experimental time set at zero.starts with experimental time set at zero.  +
  • '''Coupled respiration''' drives oxidative'''Coupled 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]].[[free ROUTINE activity]].  +
  • '''Coupling-control efficiencies''' are [[flux control efficiency |flux control efficiencies]] ''j<sub>Z-Y</sub>'' at a constant [[ET-pathway competent state]].  +
  • '''Coupling-control ratios''' ''CCR'' are '''Coupling-control ratios''' ''CCR'' are [[flux control ratio]]s ''FCR'' at a constant mitochondrial [[pathway-control state]]. In mitochondrial preparations, there are three well-defined coupling states of respiration: [[LEAK respiration]], [[OXPHOS]], and [[Electron transfer pathway |Electron-transfer-pathway state]] (ET state). In these states, the corresponding respirtory rates are symbolized as ''L'', ''P'', and ''E''. In living cells, the OXPHOS state cannot be induced, but in the [[ROUTINE]] state the respiration rate is ''R''. A reference rate ''Z'' is defined by taking ''Z'' as the maximum flux, i.e. flux ''E'' in the ET-state, such that the lower and upper limits of the ''CCR'' are defined as 0.0 and 1.0. Then there are two mitochondrial ''CCR'', [[L/E |''L/E'']] and [[P/E |''P/E'']], and two ''CCR'' for living cells, [[L/E |''L/E'']] and [[ROUTINE-control ratio |''R/E'']].[[ROUTINE-control ratio |''R/E'']].  +
  • '''Coupling-control states''' are defined '''Coupling-control states''' are defined in [[mitochondrial preparations]] (isolated mitochondria, permeabilized cells, permeabilized tissues, homogenates) as [[LEAK respiration]], [[OXPHOS]], and [[ET-pathway |ET]] states, with corresponding respiration rates (''L, P, E'') in any [[electron-transfer-pathway state]] which is competent for electron transfer. These coupling states are induced by titration of ADP and uncouplers, and application of specific inhibitors of the [[phosphorylation pathway]]. In [[living cells]], the coupling-control states are [[LEAK respiration]], [[ROUTINE]], and [[ET pathway |ET]] states of respiration with corresponding rates ''L, R, E'', using membrane-permeable inhibitors of the [[phosphorylation system]] (e.g. [[oligomycin]]) and [[uncoupler]]s (e.g. [[CCCP]]). [[Coupling-control protocol]]s induce these coupling-control states sequentially at a constant [[electron-transfer-pathway state]].[[electron-transfer-pathway state]].  +
  • '''Creatine''' 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]]).  +
  • '''Curcumin''' has been shown to possess s'''Curcumin''' 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 [http://www.ncbi.nlm.nih.gov/pubmed/23984717 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. induced oxidative damage to mitochondria.  +
  • '''Current''' or electric [[flow]]'''Current''' or electric [[flow]] ''I''<sub>el</sub> is the [[advancement]] of [[charge]] per unit of time, expressed in the SI base unit [[ampere]] [C·s<sup>-1</sup> = A]. Electrons or ions are the current-carrying [[motive entity |motive entities]] of electric flow. Electrons e<sup>-</sup> are negatively charged subatomic particles carrying 'negative electricity' with a mass that is about 1/1700 of the smallest particle — the proton — carrying 'positive electricity' (Thompson 1906). Correspondingly the [[velocity]] of electrons is much higher than that of protons or any other (larger) ion. Current is the velocity ''v'' of paticles times the number of motive charges. Therefore, electron current ''I''<sub>e<sup>-</sup></sub> is of a different nature from electric current ''I''<sub>el''χ''</sub> carried by all species ''i'' of ions ''X<sub>i</sub>'' (cations and anions) summarized as ''χ'' = Σ(''z<sub>i</sub>''·''X<sub>i</sub>''). Whereas ''I''<sub>e<sup>-</sup></sub> is the net translocation of electrons moving forwards and backwards, ''I''<sub>el''χ''</sub> is the net translocation of charges carried by different cations and anions. In contrast, ion current ''I''<sub>elX</sub> of a specific ion X is the partial translocation of charges carried by net translocation of ion X only. If cation current ''I''<sub>elX<sup>+</sup></sub> is antagonized entirely by counterion current ''I''<sub>elY<sup>-</sup></sub> as the process of antiport, then the electric current ''I''<sub>el''χ''</sub> is zero. The (net) electric current in a compartmental system is driven by the electric force Δ<sub>el</sub>''F''<sub>p<sup>+</sup></sub> or electric potential difference Δ''Ψ''<sub>p<sup>+</sup></sub>, whereas a compensated ion/counterion antiport current is insensitive to the electric potential difference.tal system is driven by the electric force Δ<sub>el</sub>''F''<sub>p<sup>+</sup></sub> or electric potential difference Δ''Ψ''<sub>p<sup>+</sup></sub>, whereas a compensated ion/counterion antiport current is insensitive to the electric potential difference.  +
  • '''Cuvettes''' are used in [[fluorometry]]'''Cuvettes''' 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.ty fused silica cuvettes may be necessary.  +
  • '''Cyanide''' (usually added as KCN) is a competitive inhibitor of [[Complex_IV| cytochcrome ''c'' oxidase (CIV)]]. Inhibition is reversed by pyruvate and high oxygen levels.  +
  • '''Cyclic voltammetry''' (CV) is a type of'''Cyclic voltammetry''' (CV) is a type of electrochemical measurement which is applied with the [[Q-Module]] as quality control to </br>(''1'') determine the oxidation and reduction peak potentials of [[Coenzyme Q]] in the specific experimental condition, (2) check the quality of the [[Q-Sensor]], and (''3'') test the interference of chemicals used in the HRR assay with the Q-Sensor. In CV, the [[Q-Sensor]] with the [[three-electrode system]] is used to obtain information about the analyte ([[Coenzyme Q|CoQ]]) by measuring the current (''I'') as the electric potential (''V'') between two of the electrodes is varied. In CV the electric potential between the glassy carbon (GC) and the Ag/AgCl reference electrode changes linearly versus time in cyclical phases, while the current is detected between GC and platinum electrode (Pt). The detected current is plotted versus the applied voltage to obtain the typical cyclic voltammogram trace (Figure 1). The presence of substances that are oxidized/reduced will result in current between GC and Pt, which can be seen as characteristic peaks in the voltammogram at a defined potential. The oxidation or the reduction peak potential values are used to set the GC (integrated into the [[Q-Sensor]]) for a separate experiment to measure the [[Q redox state]] of a biological sample. The oxidation and reduction peak potentials can be influenced by 1) the respiration medium, 2) the type of [[Coenzyme Q | CoQ]], 3) the polarization window, 4) the scan speed, 5) the number of cycles, 6) the concentration of the analyte (CoQ), and 7) the initial polarization voltage. <be></br>:::-''See'': [[MiPNet24.12 NextGen-O2k: Q-Module]].</br>:::::[[MiPNet24.16 DatLab8.0: CV-Module]][[MiPNet24.16 DatLab8.0: CV-Module]]  +
  • '''Cyclosporin A''' (CsA) is a cyclic unde'''Cyclosporin 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 [[PTP|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.jection after solid organ transplantation.  +
  • '''Cytochrome ''c''''' is a component of t'''Cytochrome ''c''''' is a component of the Electron transfer-pathway ([[Electron transfer pathway]]) in mitochondria. It is a small heme protein loosely associated with the outer side of the inner mitochondrial membrane. The heme group of cytochrome ''c'' transfers electrons from [[Complex III]] to [[Complex IV]]. The release of cytochrome ''c'' into the cytoplasm is associated with apoptosis. Cytochrome ''c'' is applied in [[HRR]] to test the integrity of the [[mitochondrial outer membrane]] ([[cytochrome c control efficiency]]).[[cytochrome c control efficiency]]).  +
  • '''D number''' is the unique code given fo'''D number''' is the unique code given for each [[SUIT]] protocol. In the same [[MitoPedia: SUIT |SUIT protocol]] family (SUIT-###), there might be different protocols, specifically designed for different [[sample]] type (''e.g.'', different [[mitochondrial preparations]]) or for different applications (''e.g.'', O2, [[AmR]], [[Mitochondrial membrane potential|Fluo]], [[MgG]]). Since the use of different kinds of sample or application may result in slightly different steps, each protocol receives a different D-number.ch protocol receives a different D-number.  +
  • '''DL-Protocols''' (DLP) can be selected i'''DL-Protocols''' (DLP) can be selected in DatLab 7 in the pull-down menu 'Protocol': Set DL-Protocol / O2 limit. A DL-Protocol defines the sequence of [[Events - DatLab |Events]] and [[Marks - DatLab |Marks]] and can be assigned to O2k-Chamber A or B, or both. Linked to DL-Protocols are templates for storing exported data in a database and for data analysis. Instrumental DL-Protocols are used for calibrations and instrumental quality control, without experimental sample in the incubation medium. DL-Protocols for [[substrate-uncoupler-inhibitor titration]] (SUIT) provide a guide through a sequence of [[coupling-control state]]s and [[Electron-transfer-pathway state]]s. A [[MitoPedia:_SUIT|library]] of evaluated and tested standard DL-Protocols is provided by the Oroboros team. The Titration-Injection-microPump [[TIP2k]] can be programmed for automatic control of titration steps in a DL-Protocol. In DatLab 7.4, it is possible to edit a DL-Protocol and save it as a [[Export_DL-Protocol_User_(*.DLPU)| user-specific DL-Protocol]] (*.DLPU). For more information, see: [[Enable DL-Protocol editing]]. A '''Lower O2 limit [µM]''' can be defined for each chamber, to trigger an automatic warning when the experimental O<sub>2</sub> concentration declines below this limit as a WARNING to remind the user that re-oxygenation of the medium may be required.ser that re-oxygenation of the medium may be required.  +
  • '''DTPA''' (Diethylenetriamine-N,N,N',N,N-'''DTPA''' (Diethylenetriamine-N,N,N',N,N-pentaacetic acid, pentetic acid,(Carboxymethyl)imino]bis(ethylenenitrilo)-tetra-acetic acid) is a polyaminopolycarboxylic acid (like EDTA) chelator of metal cations. DTPA wraps around a metal ion by forming up to eight bounds, because each COO- group and and N-center serves a center for chelation. With transition metals the number of bounds is less than eight. The compound is not cell membrane permeable. In general, it chelates multivalent ions stronger than EDTA.lates multivalent ions stronger than EDTA.  +
  • '''DatLab templates''' can be imported for O2k-setups, graph layouts, mark names, TIP2k setups and marks statistics configurations. :::: See also » [[Manage setups and templates - DatLab|Manage setups and templates]]  +
  • '''DatLab-Upgrading\4.1-5.2''': Upgrading DatLab 4.x to 5.2, incl. O2k-Manual, with free follow-up updates of DatLab 5.2. '''Discontinued''': see higher [[DatLab]] version.  +
  • '''Data to text file (*.csv)''' exports pl'''Data to text file (*.csv)''' exports plots and events to a text file for further use in Excel and other programs.</br></br>'''Events to text file (*.csv)''' exports all information in Events to a text file (*.csv). This file may be used as a protocol, including the comments in the Events.col, including the comments in the Events.  +
  • '''DataCite''' is a global community of or'''DataCite''' is a global community of organizations and researchers identifying and citing research outputs and resources. We provide services to create persistent records of research, enable discovery and reuse, and support workflows throughout the research lifecycle.rkflows throughout the research lifecycle.  +
  • '''Dead cells''' dce are characterized by the loss of plasma membrane barrier function. The total cell count (''N''<sub>ce</sub>) is the sum of viable cells (''N''<sub>vce</sub>) and dead cells (''N''<sub>dce</sub>).  +
  • '''Delete''' 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.  +
  • '''Density''', mass density ''ρ'' = ''m''·'''Density''', mass density ''ρ'' = ''m''·''V''<sup>-1</sup> [kg·m<sup>-3</sup>], is mass ''m'' divided by volume ''V''. Surface density ''ρ''<sub>A</sub> = ''m''·''A''<sup>-1</sup> [kg·m<sup>-2</sup>] ([[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |SI]]). For a pure [[sample]] S, the mass density ''ρ''<sub>S</sub> = ''m''<sub>S</sub>·''V''<sub>S</sub><sup>-1</sup> [kg·m<sup>-3</sup>] is the [[mass]] ''m'' of pure sample S per [[volume]] ''V''<sub>S</sub> of the pure sample. With density ''ρ'' thus defined, the 'amount density' of substance B is ''ρ''<sub>B</sub> = ''n''<sub>B</sub>·''V''<sub>B</sub><sup>-1</sup> [mol·m<sup>-3</sup>]. This is not a commonly used expression, but the inverse is defined as the [[molar volume]] of a pure substance ([[Cohen 2008 IUPAC Green Book |IUPAC]]), ''V''<sub>m,B</sub> = ''V''<sub>B</sub>·''n''<sub>B</sub><sup>-1</sup> [m<sup>3</sup>·mol<sup>-1</sup>]. The pure sample is a pure gas, pure liquid or pure solid of a defined elementary entity. The amount [[concentration]], ''c''<sub>B</sub> = ''n''<sub>B</sub>·''V''<sup>-1</sup> [mol·m<sup>-3</sup>] is the amount ''n''<sub>B</sub> of substance B divided by the volume ''V'' of the mixture ([[Cohen 2008 IUPAC Green Book |IUPAC]]), and this is not called an 'amount density'. The term 'amount density' is reserved for an amount of substance per volume ''V''<sub>S</sub> of the pure substance. This explicit distinction between 'density' related to the volume of the ''sample'' and 'concentration' related to the total volume of the ''mixture'' is very helpful to avoid confusion. Further clarification is required in cases, when the mass density ''ρ''<sub>s</sub> of the sample in the mixture differs from the mass density ''ρ''<sub>S</sub> of the pure sample before mixing. Think of a sample S of pure ethanol with a volume of 1 L at 25 °C, which is mixed with a volume of 1 L of pure water at 25 °C: after the temperature of the mixture has equilibrated to 25 °C, the total volume of the mixture is less than 2 L, such that the volume ''V''<sub>S</sub> of 1 L pure ethanol has diminished to a smaller volume ''V''<sub>s</sub> of ethanol in the mixture; the density of ethanol in the mixture is higher than the density of pure ethanol (this is incomplete [[additivity]]). The volume ''V''<sub>s</sub> of sample s in a mixture is by definition smaller than the total volume ''V'' of the mixture. Sample volume ''V''<sub>S</sub> and system volume ''V'' are identical, but this applies only to the case of a ''pure'' sample. ''Concentration'' is related to samples s per total volume ''V'' of the mixture, whereas ''density'' is related to samples S or s per volume ''V''<sub>S</sub> = ''V'' or ''V''<sub>s</sub> < ''V'', respectively ([[BEC 2020.1]]).  +
  • '''Derivative spectroscopy''' can be used '''Derivative 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..early dependent upon the wavelength, etc..  +
  • '''Diapause''' is a preprogrammed form of '''Diapause''' 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]. » [[Diapause#Diapause versus quiescence| '''MiPNet article''']][Diapause#Diapause versus quiescence| '''MiPNet article''']]  +
  • '''Diffraction gratings''' are [[dispersion devices]]'''Diffraction 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.to be incorporated to prevent overlapping.  +
  • '''Digitonin''' is a mild detergent that p'''Digitonin''' 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]]).[[SUIT-010 O2 ce-pce D008]]).  +
  • '''Dihydro-orotate dehydrogenase''' is an '''Dihydro-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.sis and thus to the control of biogenesis.  +
  • '''Dihydroethidium''' (also called hydroet'''Dihydroethidium''' (also called hydroethidine) is a cell permeant fluorescent probe used to analyse superoxide presence. It is a reduced form of ethidium that presents blue fluorescence, and after oxidation by superoxide becomes able to intercalate DNA and emits red fluorescence (excitation wavelength ~518–535 nm, emission ~605–610 nm). It has been used to detect superoxide by HPLC and by fluorescence microscopy.de by HPLC and by fluorescence microscopy.  +
  • '''Dimensions''' are defined in the SI {'''''Dimensions''' are defined in the SI {''Quote''}: Physical quantities can be organized in a system of dimensions, where the system used is decided by convention. Each of the seven base quantities used in the SI is regarded as having its own dimension. .. All other quantities, with the exception of [[count]]s, are derived quantities, which may be written in terms of base quantities according to the equations of physics. The dimensions of the derived quantities are written as products of powers of the dimensions of the base quantities using the equations that relate the derived quantities to the base quantities.</br></br>There are quantities ''Q'' for which the defining equation is such that all of the dimensional exponents in the equation for the dimension of ''Q'' are zero. This is true in particular for any quantity that is defined as the ratio of two quantities of the same kind. .. There are also some quantities that cannot be described in terms of the seven base quantities of the SI, but have the nature of a [[count]]. Examples are a number of molecules, a number of cellular or biomolecular entities (for example copies of a particular nucleic acid sequence), or degeneracy in quantum mechanics. Counting quantities are also quantities with the associated unit one. {''end of Quote'': p 136, [[Bureau International des Poids et Mesures 2019 The International System of Units (SI)]]}[[Bureau International des Poids et Mesures 2019 The International System of Units (SI)]]}  +
  • '''Dimethyl sulfoxide''' is a polar aproti'''Dimethyl 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.nt cell death during the freezing process.  +
  • '''Dinitrochlorobenzene (1-chloro-2,4-dinitrobenzene)''' (DNCB) is a glutathione (GSH) inhibitor.  +
  • '''Display DatLab help''' In this section'''Display DatLab help'''</br></br>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.</br></br>Case in which an issue might occur:</br></br>::* 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.</br></br>In the event of a frozen display of the graphs, try the alternatives below:</br></br>::* Click on: Graph > Autoscale time axis</br>::* 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). graphs (no changes in the graphs are required).  +
  • '''Dyscoupled respiration''' is [[LEAK respiration]]'''Dyscoupled respiration''' is [[LEAK respiration]] distinguished from intrinsically (physiologically) uncoupled and from extrinsic experimentally [[Uncoupler|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. </br></br>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. dyscoupling in mitochondrial respiration.  +
  • '''Ectotherms''' are organisms whose body temperatures conform to the thermal environment. In many cases, therefore, ectotherms are [[poicilotherms | poicilothermic]].  +
  • '''Editorial board participation''' is a topic addressed in [[COPE core practices for research]].  +
  • '''Electric current density''' is [[current]] divided by area, ''j''=''I''·''A''<sup>-1</sup> [C·m<sup>-2</sup>]. Compare: [[density]].  +
  • '''Electron flow''' through the mitochondr'''Electron 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 (O<sub>2</sub>) is reduced to water.xygen (O<sub>2</sub>) is reduced to water.  +
  • '''Electron-transferring flavoprotein Comp'''Electron-transferring flavoprotein Complex''' (CETF) is a respiratory Complex localized at the matrix face of the inner mitochondrial membrane, supplies electrons to Q, and is thus an enzyme Complex of the mitochondrial [[Electron transfer pathway]] (ET-pathway). CETF links the ß-oxidation cycle with the membrane-bound electron transfer system in [[fatty acid oxidation]] (FAO).[fatty acid oxidation]] (FAO).  +
  • '''Electronic-TIP2k Upgrading\O2k-Main Unit Series A-D - Former Product ''': not required for [[O2k-Core]], the [[O2k-Main Unit]] has to be returned to the OROBOROS workshop.  +
  • '''Electronic-TIP2k Upgrading\O2k-Main Uni'''Electronic-TIP2k Upgrading\O2k-Main Unit Series E - Former Series ''': not required for [[O2k-Core]], free of charge for Series E in conjunction with the purchase of the [[TIP2k-Module]], the [[O2k-Main Unit]] has to be returned to the OROBOROS workshop.s to be returned to the OROBOROS workshop.  +
  • '''Enable DL-Protocol editing''' is a nove'''Enable DL-Protocol editing''' is a novel function of DatLab 7.4 offering a new feature in DL-Protocols: flexibility. Fixed sequences of events and marks can be changed (Skip/Added) in a SUIT protocol by the user. Moreover, the text, instructions, concentrations and titration volumes of injections in a specific DL-Protocol can be edited and saved as [[Export_DL-Protocol_User_(*.DLPU)| user-specific DL-Protocol]] [File]\Export\DL-Protocol User (*.DLPU). To enable it, under the 'Protocols' tab in the menu, select the option 'Enable DL-Protocol editing', and then select the plot in which the marks will be set (''e.g.,'' O2 flux per V). Select the 'Overview' window, where you will be able to edit events and marks names, definition/state, final concentration and titration volumes, as well as select a mark as 'multi' for multiple titration steps, skip a mark, or add a new event or mark. After saving, [[Export_DL-Protocol_User_(*.DLPU)|export a DL-Protocol User (DLPU)]] and load it before running the next experiments. If users of DatLab versions older than DatLab 7.4 wish to alter the nature of the chemicals used or the sequence of injections, we ask them to [https://www.oroboros.at/index.php/o2k-technical-support/ contact the O2k-Technical Support].</br></br>For more information:</br>[[Image:PlayVideo.jpg|50px|link=https://www.youtube.com/watch?v=Vd66dHx-MyI]] [https://www.youtube.com/watch?v=Vd66dHx-MyI Export DL-Protocol User (*.DLPU)]6dHx-MyI Export DL-Protocol User (*.DLPU)]  +
  • '''Endergonic''' transformations or proces'''Endergonic''' 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''.inologically linked to ''thermodynamics''.  +
  • '''Endothermy''' is the constant regulation of body temperature by metabolic heat production and control of heat exchange with the environment.  +
  • '''Energy saving in research''' must rank '''Energy saving in research''' must rank as a priority of social responsibility — ever since the [[Club of Rome]] published 50 years ago the seminal book on ''The limits to growth'' (1972) [1], and more so today in face of the global threat of climate change and the russian war in aggression against Ukraine.</br></br>Energy saving in research does not and must not clash with quality in research. Application of high-quality and predefined [[MitoPedia: SUIT |experimental protocols]] combined with evaluation of [[Replica |repeatability]] and [[Repetitions |reproducibility]] represents primary strategies for energy saving in research. Publication of irreproducible results — adding to the [[reproducibility crisis]] — is the most wasteful aspect of research in terms of resources including [[energy]] (more properly: [[exergy]]). [[Paywall journalism]] is wasteful in terms of financial resources. Dramatically increasing numbers of scientific publications is a pathway towards waste of energy [2]. </br></br>Besides large-scale strategies on e(n)xergy saving in research — quality versus quantity —, everybody's everyday contributions to energy saving count: to cut greenhouse gas emissions, save biological and geological diversity, and improve equality across societies, gender, continents, and countries.</br></br>Do scientists take responsibility for energy saving? Or does biomedical research merely find excuses? Scientific institutions in academia and industry must implement energy saving strategies to reduce waste according to the European Union's [https://energy.ec.europa.eu/topics/energy-efficiency/energy-efficiency-targets-directive-and-rules/energy-efficiency-directive_en Energy efficiency directive], and to consume less energy (exergy) by using it more efficiently ([https://energy.ec.europa.eu/topics/energy-efficiency/energy-efficiency-targets-directive-and-rules/energy-efficiency-targets_en Energy efficiency targets]).</br></br>Possible — important but much neglected — contributions include:</br>* Re-use materials as a superior strategy than recycling, and reduce application of disposable items.</br>* Reduce waste in cleaning procedures, but do not compromise the [[MiPNet19.03 O2k-cleaning and ISS |quality of cleaning procedures]].</br>* Replace inefficient equipment (e.g. water baths) by efficient electronic [[O2k-Peltier Temperature Control |Peltier temperature control]].</br>* Select conferences that you attend by evaluating their 'green deal' strategy. Combine in a single trip participation in a conference and possibly offered satellite events.</br>* Turn off non-essential equipment; reduce energy-wasting stand-by modes; turn off computer screens and other equipment at the mains when not in use. The monitor consumes over half of the energy used by the average computer. Lower your screen brightness.</br>* Turn off the lights when you do not gain from extra illumination, when you leave the lab during the day or at the end of every day.</br>* Reduce heating of the rooms to 19 °C, cooling of rooms to 25 °C. Apply energy-efficient heating and cooling strategies.</br>* Define your personal energy saving targets at homeoffice and in your workplace.</br>* Contact your energy quality manager, to suggest improvement of infrastructure and guidelines that help you and other members in the team to comply with energy saving targets.team to comply with energy saving targets.  +
  • '''Enthalpy''', ''H'' [J], can under condi'''Enthalpy''', ''H'' [J], can under conditions of constant gas pressure neither be destroyed nor created (first law of thermodynamics: d<sub>i</sub>''H''/d''t'' = 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, d''H'', at constant pressure, is the internal-energy change, d''U'', minus reversible pressure-volume work,</br> d''H'' = d''U'' - d<sub>''V''</sub>''W''</br>Pressure-volume work, d<sub>''V''</sub>''W'', at constant pressure, is the gas pressure, ''p'' [Pa = J·m<sup>-3</sup>], times change of volume, d''V'' [m<sup>3</sup>],</br> d<sub>''V''</sub>''W'' = -''p''·d''V'' [J]</br>The ''available'' work, d<sub>e</sub>''W'', is distinguished from external total work, d<sub>et</sub>''W'', [1]</br> d<sub>e</sub>''W'' = d<sub>et</sub>''W'' - d<sub>''V''</sub>''W''</br>The change of enthalpy of a system is due to internal and external changes,</br> d''H'' = d<sub>i</sub>''H'' + d<sub>e</sub>''H''</br>Since d<sub>i</sub>''H'' = 0 (first law of thermodynamics), the d''H'' is balanced by exchange of heat, work, and matter, </br> d''H'' = (d<sub>e</sub>''Q'' + d<sub>e</sub>''W'') + d<sub>mat</sub>''H'' ; d''p'' = 0 </br>The exchange of matter is expressed in enthalpy equivalents with respect to a [[reference state]] (formation, f, or combustion, c). The value of d''H'' 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,</br> d<sub>t</sub>''H'' = (d<sub>e</sub>''Q'' + d<sub>e</sub>''W'')</br>A partial enthalpy change of transformation, d<sub>tr</sub>''H'', is distinguished from the total enthalpy change of all transformations, d<sub>t</sub>''H'', and from the enthalpy change of the system, d''H''. In a closed system, d''H'' = d<sub>t</sub>''H''. The enthalpy change of transformation is the sum of the [[Gibbs energy]] (free energy) change of transformation, d<sub>tr</sub>''G'', and the [[bound energy]] change of transformation at constant temperature and pressure, d<sub>tr</sub>''B'' = ''T''·d''S'',</br> d<sub>tr</sub>''H'' = d<sub>tr</sub>''G'' + d<sub>tr</sub>''B''bound energy]] change of transformation at constant temperature and pressure, d<sub>tr</sub>''B'' = ''T''·d''S'', d<sub>tr</sub>''H'' = d<sub>tr</sub>''G'' + d<sub>tr</sub>''B''  +
  • '''Ethics on publishing''' follow [https:/'''Ethics on publishing''' follow [https://publicationethics.org/core-practices COPE's guidelines] (or equivalent). A journal's policy on publishing ethics should be clearly visible on its website, and should refer to: (1) Journal policies on authorship and contributorship; (2) How the journal will handle complaints and appeals; (3) Journal policies on conflicts of interest / competing interests; (4) Journal policies on data sharing and reproducibility; (5) Journal's policy on ethical oversight; (6) Journal's policy on intellectual property; and (7) Journal's options for post-publication discussions and corrections.t-publication discussions and corrections.  +
  • '''Ethylene glycol tetraacetic acid''' (EGTA) is a chelator for heavy metals, with high affinity for Ca<sup>2+</sup> but low affinity for Mg<sup>2+</sup>. Sigma E 4378.  +
  • '''Etomoxir''' (Eto; 2[6(4-chlorophenoxy)h'''Etomoxir''' (Eto; 2[6(4-chlorophenoxy)hexyl]oxirane-2-carboxylate) is an irreversible inhibitor of [[carnitine palmitoyltransferase I]] (CPT-I) on the outer face of the mitochondrial inner membrane. Eto inhibits [[fatty acid oxidation]] by blocking the formation of acyl carnitines from long-chain fatty acids which require the carnitine shuttle for transport into mitochondria. In contrast to long-chain fatty acids, the transport of short- and medium-chain fatty acids is carnitine-independent.hain fatty acids is carnitine-independent.  +
  • '''Exergonic''' transformations or process'''Exergonic''' 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 [[force]]s 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 ''thermo''dynamics.inologically linked to ''thermo''dynamics.  +
  • '''Exergy''' includes external and interna'''Exergy''' includes external and internal [[work]]. Exergy as the external work is defined in the First Law of thermodynamics as a specific form of [[energy]]. Exergy as the dissipated Gibbs or Helmholtz energy is the irreversibly dissipated (internal) loss of the potential of performing work as defined in the Second Law of Thermodynamics. </br></br>Changes of exergy d''G'' plus [[bound energy]] yield the [[enthalpy]] change:</br></br> d''H'' = d''G'' + ''T''∙d''S'' = d''G'' + d''B'' = d''G'' + ''T''∙d''S'' = d''G'' + d''B''  +
  • '''Experimental log''' provides an automat'''Experimental log''' provides an automatically generated experimental protocol with detailed information about the O2k settings and calibrations, the [[Sample - DatLab|Sample]] information and various [[Events - DatLab |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].ed as a PDF file by clicking on [Preview].  +
  • '''Extensive quantities''' pertain to a to'''Extensive 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 2008 IUPAC Green Book |Cohen et al 2008]]).[[Cohen 2008 IUPAC Green Book |Cohen et al 2008]]).  +
  • '''External flows''' across the system boundaries are formally reversible. Their irreversible facet is accounted for internally as transformations in a heterogenous system ([[internal flow]]s, ''I''<sub>i</sub>).  +
  • '''Extrinsic fluorophores''' are molecules'''Extrinsic 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 (H<sub>2</sub>O<sub>2</sub>, [[Amplex red]]) (HOO<sup>-</sup>, MitoSOX) , mitochondrial membrane potential ([[Safranin]], JC1, [[TMRM]], [[Rhodamine 123]]), Ca<sup>2+</sup> ([[Fura2]], Indo 1, [[Calcium Green]]), pH (Fluorescein, HPTS, SNAFL-1), Mg<sup>2+</sup> ([[Magnesium Green]]) and redox state (roGFP).[[Magnesium Green]]) and redox state (roGFP).  +
  • '''F1000Research''' is an Open Research pu'''F1000Research''' 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. very basic check by our in-house editors.  +
  • '''FCCP''' (Carbonyl cyanide p-trifluoro-m'''FCCP''' (Carbonyl cyanide p-trifluoro-methoxyphenyl hydrazone, C<sub>10</sub>H<sub>5</sub>F<sub>3</sub>N<sub>4</sub>O) is a protonophore or [[uncoupler]]: added at uncoupler concentration U<sub>''c''</sub>; ''c'' is the [[optimum uncoupler concentration]] in titrations to obtain maximum mitochondrial respiration in the [[noncoupled respiration|noncoupled]] state of [[ET capacity]].[[ET capacity]].  +
  • '''Fatty acid oxidation''' is a multi-step'''Fatty acid oxidation''' is a multi-step process by which [[fatty acid]]s are broken down in [[β-oxidation]] to generate acetyl-CoA, NADH and FADH<sub>2</sub> for further electron transfer to CoQ. Whereas NADH is the substrate of CI, FADH<sub>2</sub> is the substrate of [[electron-transferring flavoprotein complex]] (CETF) which is localized on the matrix face of the mtIM, and supplies electrons from FADH<sub>2</sub> to CoQ. Before the ß-oxidation in the mitochondrial matrix, fatty acids (short-chain with 1-6, medium-chain with 7–12, long-chain with >12 carbon atoms) are activated by fatty acyl-CoA synthases (thiokinases) in the cytosol. For the mitochondrial transport of long-chain fatty acids the mtOM-enzyme [[carnitine palmitoyltransferase I]] (CPT-1; considered as a rate-limiting step in FAO) is required which generates an acyl-carnitine intermediate from acyl-CoA and carnitine. In the next step, an integral mtIM protein [[carnitine-acylcarnitine translocase]] (CACT) catalyzes the entrance of acyl-carnitines into the mitochondrial matrix in exchange for free carnitines. In the inner side of the mtIM, another enzyme [[carnitine palmitoyltransferase 2]] (CPT-2) converts the acyl-carnitines to carnitine and acyl-CoAs, which undergo ß-oxidation in the mitochondrial matrix. Short- and medium-chain fatty acids do not require the carnitine shuttle for mitochondrial transport. [[Octanoate]], but not [[palmitate]], (eight- and 16-carbon saturated fatty acids) may pass the mt-membranes, but both are frequently supplied to mt-preparations in the activated form of [[octanoylcarnitine]] or [[palmitoylcarnitine]].mitoylcarnitine]].  +
  • '''Fatty acids''' are carboxylic acids wit'''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 (1–6 carbons), medium-chain (7–12 carbons) and long-chain and very long-chain fatty acids (>12 carbons).</br>Long-chain fatty acids must be bound to [[Carnitine|carnitine]] to enter the mitochondrial matrix, in a reaction that can be catalysed by [[Carnitine acyltransferase|carnitine acyltransferase]]. For this reason, long-chain fatty acids, such as [[Palmitate|palmitate]] (16 carbons) is frequently supplied to mt-preparations in the activated form of [[Palmitoylcarnitine|palmitoylcarnitine]].</br>Fatty acids with shorter chains, as [[Octanoate|octanoate]] (8 carbons) may enter the mitochondrial matrix, however, in HRR they are more frequently supplied also in the activated form, such as [[Octanoylcarnitine|octanoylcarnitine]].</br></br>Once in the mitochondrial matrix, the [[Fatty acid oxidation|fatty acid oxidation]] (FAO) occurs, generating acetyl-CoA, NADH and FADH2. In the [[Fatty acid oxidation pathway control state|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 [[Fatty acid oxidation pathway control state |F-pathway]].tty acid oxidation pathway control state |F-pathway]].  +
  • '''Fermentation''' is the process of [[energy metabolism]]'''Fermentation''' 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 O<sub>2</sub>). Fermentation thus contrasts with [[cell respiration]] and is an [[anaerobic]] process, but aerobic fermentation may proceed in the presence of oxygen.ic fermentation may proceed in the presence of oxygen.  +
  • '''File search''' yields a list of all fil'''File 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.ormation) will appear in the window below.  +
  • '''Filters''' are materials that have wave'''Filters''' 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.can also be used for calibrating purposes.  +
  • '''Flavin adenine dinucleotide''', FAD and'''Flavin adenine dinucleotide''', FAD and FADH<sub>2</sub>, is an oxidation-reduction [[prosthetic group]] (redox cofactor; compare [[NADH]]). FMN and FAD are the prosthetic groups of flavoproteins (flavin dehydrogenases). [[Electron-transfer-pathway state |Type F substrates]] (fatty acids) generate FADH<sub>2</sub>, the substrate of [[electron transferring flavoprotein]] (CETF). Thus FADH<sub>2</sub> 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, FADH<sub>2</sub> is not the substrate but the internal product of [[succinate dehydrogenase]] (CII). FAD is the oxidized (quinone) form, which is reduced to FADH<sub>2</sub> (hydroquinone form) by accepting two electrons and two protons.educed to FADH<sub>2</sub> (hydroquinone form) by accepting two electrons and two protons.  +
  • '''Flavonoids''' are a group of bioactive '''Flavonoids''' are a group of bioactive polyphenols with potential antioxidant and anti-inflammatory effects, abundant in fruits and vegetables, and in some medicinal herbs. Flavonoids are synthesized in plants from phenylalanine. Dietary intake of flavonoids as nutraceuticals is discussed for targeting T2D and other degenerative diseases.eting T2D and other degenerative diseases.  +
  • '''Fluorescence''' is the name given to li'''Fluorescence''' 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.[[Luminescence]], especially Photoluminescence.  +
  • '''Fluorometry''' (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.  +
  • '''Flux / Slope''' is the time derivative '''Flux / Slope''' is the time derivative of the signal. In [[DatLab]], Flux / Slope is the name of the pull-down menu for (1) normalization of flux (chamber volume-specific flux, sample-specific flux or flow, or flux control ratios), (2) [[flux baseline correction]], (3) [[Instrumental background oxygen flux]], and (4) [[flux smoothing]], selection of the [[scaling factor]], and stoichiometric normalization using a stoichiometric coefficient.</br>Before changing the normalization of flux from volume-specific flux to sample-specific flux or flow, or flux control ratios, please be sure to use the standard Layout 04a (Flux per volume) or 04b (Flux per volume overlay). When starting with the instrumental standard Layouts 1-3, which display the O2 slope negative, the sample-specific flux or flow, or flux control ratios will not be automatically background corrected. To obtain the background corrected specific flux or flux control ratios, it is needed to tick the background correction in the lower part of the slope configuration window. Background correction is especially critical when performing measurements in a high oxygen regime or using samples with a low respiratory flux or flow.mples with a low respiratory flux or flow.  +
  • '''Flux baseline correction''' provides th'''Flux 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, ''J''<sub>0</sub>.</br> ''J<sub>V</sub>''(bc) = ''J<sub>V</sub>'' - ''J<sub>V</sub>''<sub>0</sub></br> ''J<sub>V</sub>'' = (d''c''/d''t'') · ''ν''<sup>-1</sup> · ''SF'' - ''J°<sub>V</sub>''</br>For the oxygen channel, ''J<sub>V</sub>'' is O2 flux per volume [pmol/(s·ml)] (or volume-specific O<sub>2</sub> flux), ''c'' is the oxygen concentration [nmol/ml = µmol/l = µM], d''c''/d''t'' is the (positive) slope of oxygen concentration over time [nmol/(s · ml)], ''ν''<sup>-1</sup> = -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 ''J°<sub>V</sub>'' is the volume-specific background oxygen flux ([[Instrumental background oxygen flux]]). ''Further details'': [[Flux / Slope]].lope]].  +
  • '''Flux control efficiencies''' express th'''Flux control efficiencies''' express the control of respiration by a [[metabolic control variable]], ''X'', as a fractional change of flux from ''Y<sub>X</sub>'' to ''Z<sub>X</sub>'', normalized for ''Z<sub>X</sub>''. ''Z<sub>X</sub>'' is the [[reference state]] with high (stimulated or un-inhibited) flux; ''Y<sub>X</sub>'' is the [[background state]] at low flux, upon which ''X'' acts.</br></br>:: ''j<sub>Z-Y</sub>'' = (''Z<sub>X</sub>-Y<sub>X</sub>'')/''Z<sub>X</sub>'' = 1-''Y<sub>X</sub>''/''Z<sub>X</sub>''</br></br>Complementary to the concept of [[flux control ratio]]s and analogous to [[elasticity|elasticities]] of [[metabolic control analysis]], the flux control efficiency of ''X'' upon background ''Y<sub>X</sub>'' is expressed as the change of flux from ''Y<sub>X</sub>'' to ''Z<sub>X</sub>'' normalized for the reference state ''Z<sub>X</sub>''.</br>» [[Flux_control_efficiency#Flux_control_efficiency:_normalization_of_mitochondrial_respiration | '''MiPNet article''']][Flux_control_efficiency#Flux_control_efficiency:_normalization_of_mitochondrial_respiration | '''MiPNet article''']]  +
  • '''Flux control ratios''' ''FCR''s are rat'''Flux control ratios''' ''FCR''s 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 %). </br></br>For a given protocol or set of respiratory protocols, flux control ratios provide a fingerprint of coupling and substrate control independent of (''1'') mt-content in cells or tissues, (''2'') purification in preparations of isolated mitochondria, and (''3'') assay conditions for determination of tissue mass or mt-markers external to a respiratory protocol (CS, protein, stereology, etc.). ''FCR'' obtained from a single respirometric incubation with sequential titrations (sequential protocol; [[SUIT|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]].[[mitochondrial marker]].  +
  • '''Flux''', ''J'', is a [[specific quantity]]'''Flux''', ''J'', is a [[specific quantity]]. Flux is [[flow]], ''I'' [MU·s<sup>-1</sup> per system] (an [[extensive quantity]]), divided by system size. Flux (''e.g.'', [[oxygen flux]]) may be volume-specific (flow per volume [MU·s<sup>-1</sup>·L<sup>-1</sup>]), mass-specific (flow per mass [MU·s<sup>-1</sup>·kg<sup>-1</sup>]), or marker-specific (e.g. flow per mtEU). The [[motive unit]] [MU] of chemical flow or flux is the advancement of reaction [mol] in the chemical format.ive unit]] [MU] of chemical flow or flux is the advancement of reaction [mol] in the chemical format.  +
  • '''Force''' is an [[intensive quantity]]'''Force''' is an [[intensive quantity]]. The product of force times [[advancement]] is the [[work]] (exergy) expended in a process or transformation. Force times flow is [[power]] [W].</br># 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'', d<sub>'''m'''</sub>'''''F'''''<sub>''X''</sub> [N ≡ J∙m<sup>-1</sup> = m∙kg∙s<sup>-2</sup>]. These forces describe the interaction between particles as [[vector]]s 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.</br># '''Isomorphic forces''' can be derived from (''1'') the fundamental forces or (''2'') statistical distributions if large numbers of particles are involved. The isomorphic forces are known as 'generalized' forces of nonequilibrium thermodynamics. An isomorphic '''motive force''', Δ<sub>tr</sub>''F''<sub>''X''</sub>, in thermodynamics or ergodynamics is the partial Gibbs (Helmholtz) energy change per advancement of a transformation (tr). </br>## In [[continuous system]]s accessible to the analysis of gradients, the '''motive vector forces''', d<sub>'''m'''</sub>'''''F'''''<sub>''X''</sub> (units: newton per amount of particles ''X'' [N∙mol<sup>-1</sup>] or per coulombs of particles [N∙C<sup>-1</sup>]), are vectors interacting with the motive particles ''X''.</br>## In [[discontinuous system]]s 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, ∆<sub>tr</sub>''F''<sub>''X''</sub>, with compartmental instead of spatial direction of the energy transformation, tr. The motive forces are expressed in various [[motive unit]]s, MU [J∙MU<sup>-1</sup>], 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).ntity ''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).  +
  • '''Free activity''' ''α<sub>X</su'''Free activity''' ''α<sub>X</sub>'' [MU·m<sup>-3</sup>] is [[pressure]] divided by isomorphic [[force]]. In the chemical [[amount]] format, ''α<sub>X</sub>'' is expressed in units of concentration of ''X'' [mol·L<sup>-1</sup>]. ''α<sub>X</sub>'' is the local concentration in a concentration gradient. If the concentration gradient is collapsed to a boundary of zero thickness in a compartmental system, ''α<sub>X</sub>'' reflects the singularity in the transition between the two phases or compartments., ''α<sub>X</sub>'' reflects the singularity in the transition between the two phases or compartments.  +
  • '''Fumarase''' 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.  +
  • '''Fura2''' is a ratiometric fluorescence '''Fura2''' 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.ly reliable tool for calcium measurements.  +
  • '''Gibbs energy''' ''G'' [J] is [[exergy]]'''Gibbs energy''' ''G'' [J] is [[exergy]] which cannot be created internally (subscript i), but in contrast to [[internal-energy]] (d<sub>i</sub>''U''/d''t'' = 0) is not conserved but is dissipated (d<sub>i</sub>''G''/d''t'' < 0) in irreversible energy transformations at constant temperature and (barometric) pressure, ''T'',''p''. Exergy is available as [[work]] in reversible energy transformations (100 % [[efficiency]]), and can be partially conserved when the [[exergonic]] transformation is coupled to an [[endergonic]] transformation.[[endergonic]] transformation.  +
  • '''Glucose''', 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.  +
  • '''Glutamate dehydrogenase''', located in '''Glutamate dehydrogenase''', located in the mitochondrial matrix (mtGDH), is an enzyme that converts [[glutamate]] to α-ketoglutarate [http://en.wikipedia.org/wiki/Glutamate_dehydrogenase]. mtGDH is not part of the TCA cycle, but is involved in [[glutaminolysis]] as an [[anaplerosis |anaplerotic reaction]].[anaplerosis |anaplerotic reaction]].  +
  • '''Glycerophosphate dehydrogenase complex''''Glycerophosphate dehydrogenase complex''' (CGpDH) is a Complex of the electron transfer-pathway localized at the outer face of the mt-inner membrane. CGpDH is thus distinguished from cytosolic GpDH. CGpDH oxidizes [[glycerophosphate]] to dihydroxyacetone phosphate and feeds two electrons into the [[Q-junction]], thus linked to an [[Electron-transfer-pathway state|ET pathway level 3 control state]].[[Electron-transfer-pathway state|ET pathway level 3 control state]].  +
  • '''Glycerophosphate''' (synonym: α-glycero'''Glycerophosphate''' (synonym: α-glycerophosphate; glycerol-3-phosphate; C<sub>3</sub>H<sub>9</sub>O<sub>6</sub>P) 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.hate to dihydroxyacetone phosphate and feeds electrons directly to ubiquinone.  +
  • '''H2DCFDA''' (dichlorodihydrofluorescein '''H2DCFDA''' (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.dicator of ROS by fluorescence microscopy.  +
  • '''Harmonization''' is the process of minimizing redundant or conflicting [[standard]]s which may have evolved independently. To obtain a common basis in reaching a defined objective, critical [[requirement]]s are identified that need to be retained.  +
  • '''Harmonized European norms''' are [[norm]]s valid for all members of the European Union. They are mandatory parts of the individual national collections of norms.  +
  • '''Harmonized [[SUIT protocols]]'''Harmonized [[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.s-linked) across the harmonized protocols.  +
  • '''Healthy ageing''': 'WHO has released th'''Healthy 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). characteristics' (Beard 2016 The Lancet).  +
  • '''Heat''' is a form of [[energy]]'''Heat''' is a form of [[energy]] [J]. The relationship between heat and [[work]] provides the foundation of thermodynamics, which describes transformations from an initial to a final state of a system. In energy transformations heat may pass through the boundary of the system, at an external heat flow of d<sub>e</sub>''Q''/d''t''.al heat flow of d<sub>e</sub>''Q''/d''t''.  +
  • '''Heterothermy''' is the variable regulat'''Heterothermy''' is the variable regulation of body temperature in [[endothermy | 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.t, e.g. between body core and extremeties.  +
  • '''Homeothermy''' is the stable regulation of body temperature in [[endothermy | 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 peroxidase''' readily combines with hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and the resultant [HRP-H<sub>2</sub>O<sub>2</sub>] complex can oxidize a wide variety of hydrogen donors.  +
  • '''Hydrogen sulfide (H<sub>2</sub>S)''' is involved in signaling and may have have further biological importance.  +
  • '''Hydron''' is the general name for the cation H<sup>+</sup> used without regard to the nuclear mass of the hydrogen entity (H is the hydro group), either for H in its natural abundance or without distinction between the isotopes.  +
  • '''Hydroxycinnamate''' (alpha-cyano-4-hydr'''Hydroxycinnamate''' (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.inner mt-membrane in non-dissociated form.  +
  • '''Hyperoxia''' is defined as environmenta'''Hyperoxia''' is defined as environmental oxygen pressure above the [[normoxic]] reference level. Cellular and intracellular hyperoxia is imposed on isolated cells and isolated mitochondria at air-level oxygen pressures which are higher compared to cellular and intracellular oxygen pressures under tissue conditions in vivo. Hyperoxic conditions may impose oxidative stress and may increase maximum aerobic performance. may increase maximum aerobic performance.  +
  • '''Hyperthermia''' in [[endothermy | endotherms]]'''Hyperthermia''' in [[endothermy | 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.[normothermia]] at a body temperature of 36.5 to 37.5 °C.  +
  • '''Hyphenation''' is used to connect two w'''Hyphenation''' is used to connect two words (compound words) or two parts of a word to clarify the meaning of a sentence. The same two words may be hyphenated or not depending on context. Hyphenation may present a problem when searching for a term such as '[[Steady state]]'. It is helpful to write 'steady-state measurement', to clarify that the measurement is performed at steady state, rather than implying that a state measurement is steady. But this does not imply that hyphenation is applied to the 'measurement performed at steady state'. Thus, the key word is '[[steady state]]'. Compound adjectives should be hyphenated (steady-state measurement), but if the compound adjective follows the term (measurement at steady state), hyphenation does not add any information and should be avoided. Find more examples and guidelines in the [https://www.grammarly.com/blog/hyphen/ grammarly blog on Hyphen] and in [https://apastyle.apa.org/learn/faqs/when-use-hyphen apastyle.apa.org].rn/faqs/when-use-hyphen apastyle.apa.org].  +
  • '''Hypothermia''' in [[endothermy | endotherms]]'''Hypothermia''' in [[endothermy | 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). severe (20–28 °C), and profound (<20 °C).  +
  • '''Hypoxia''' (hypox) is defined in respir'''Hypoxia''' (hypox) is defined in respiratory physiology as the state when insufficient O<sub>2</sub> is available for respiration, compared to ''environmental'' hypoxia defined as environmental oxygen pressures below the [[normoxic]] reference level. Three major categories of hypoxia are (''1'') environmental hypoxia, (''2'') physiological tissue hypoxia in hyperactivated states (e.g. at ''V''<sub>O<sub>2</sub>max</sub>) with intracellular oxygen demand/supply balance at steady state in tissues at environmental normoxia, compared to tissue normoxia in physiologically balanced states, and (''3'') pathological tissue hypoxia including ischemia and stroke, anaemia, chronic heart disease, chronic obstructive pulmonary disease, severe COVID-19, and obstructive sleep apnea. Pathological hypoxia leads to tissue hypoxia and heterogenous intracellular anoxia. Clinical oxygen treatment ('environmental hyperoxia') may not or only partially overcome pathological tissue hypoxia.al hyperoxia') may not or only partially overcome pathological tissue hypoxia.  +
  • '''ISO 10012:2003 Measurement management s'''ISO 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.niques in the measurement process control.  +
  • '''ISO 13528:2015 Statistical methods for '''ISO 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 General requirements for 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). be appropriate for the stated purpose(s).  +
  • '''ISO 15189:2012 Medical laboratories — P'''ISO 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.could also find it useful and appropriate.  +
  • '''ISO 17511:2003 In vitro diagnostic medi'''ISO 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.ion and comparability over time and space.  +
  • '''ISO 9001:2015 Quality management system'''ISO 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.gh change, innovation and re-organization.  +
  • '''ISO/IEC 17025:2005 General requirements'''ISO/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.methods, and laboratory-developed methods.  +
  • '''ISO/IEC 17043:2010 Conformity assessmen'''ISO/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.izations that provide proficiency testing.  +
  • '''Iconic symbols''' are used in [[ergodynamics]]'''Iconic symbols''' are used in [[ergodynamics]] to indicate more explicitely — compared to standard SI or IUPAC symbols — the quantity represented and some boundary conditions. This is particularly the case in normalized quantities (ratios of quantities). Iconic (or canonical) symbols help to clarify the meaning, are based on SI and IUPAC symbols as far as possible, and may be translated into more commonly used, practical symbols. Several ambiguities in SI and IUPAC symbols are eliminated by the systematic structure of iconic symbols, but it may be impossible to avoid all ambiguities, particulary when long (canonical) symbols are abbreviated in a particular context. Clarity is improved always by showing the unit of a quantity together with the symbol of the quantity. Iconic symbols cannot be identical with IUPAC symbols when a different definition is used — this would add to the confusion. For example, the IUPAC symbols ''n''<sub>B</sub> [mol] and ''V''<sub>B</sub> [m<sup>3</sup>] denote amount and volume of B. Consequently, it should be expected, that the symbol ''Q''<sub>B</sub> indicates charge of B [C]. However, the IUPAC symbol ''Q''<sub>B</sub> is used for particle charge per ion B [C·x<sup>-1</sup>]. This prohibits a consistent definition of ''Q''<sub>B</sub> as a potential iconic symbol for charge carried by a given quantity of ions B with unit [C], instead of particle charge per ion B with unit [C·x<sup>-1</sup>]. Hence, the conventional ambigous system forces compatible iconic symbols to be more complicated, using ''Q''<sub>elB</sub> [C] and ''Q''<sub>''<u>N</u>''B</sub> [C·x<sup>-1</sup>] to distinguish charge of B from charge per elementary B. ''Q''<sub>''<u>n</u>''B</sub> [C·mol<sup>-1</sup>] is charge per molar amount of B.'B</sub> [C·x<sup>-1</sup>] to distinguish charge of B from charge per elementary B. ''Q''<sub>''<u>n</u>''B</sub> [C·mol<sup>-1</sup>] is charge per molar amount of B.  +
  • '''Impact factor''' is a measure of a scie'''Impact factor''' is a measure of a scientific journal's citations per publication. The Journal Citation Reports, maintained by Clarivate Analytics, provides the calculated impact factors. The IF is frequently used as an indicator of a journal's importance or prestige, which is nowadays increasingly contested. which is nowadays increasingly contested.  +
  • '''Inorgnic phosphate''' (P<sub>i</sub>) is a salt of phosphoric acid. In solution near physiological pH, the species HPO<sub>4</sub><sup>2-</sup> and H<sub>2</sub>PO<sub>4</sub><sup>-</sup> dominate. ''See also'': [[Phosphate carrier]] (Pic).  +
  • '''Instrumental background oxygen flux''','''Instrumental background oxygen flux''', ''J''°<sub>O<sub>2</sub></sub>, 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 O<sub>2</sub> background test. The oxygen regime from air saturation towards zero oxygen is applied generally in experiments with isolated mitochondria, and living or permeabilized cells. To overcome oxygen diffusion limitation in permeabilized fibers and homogenates, an elevated oxygen regime is applied, requiring instrumental background test in the same range of elevated oxygen., requiring instrumental background test in the same range of elevated oxygen.  +
  • '''Integration time''' is the time taken t'''Integration 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. carried out at the same integration time.  +
  • '''Internal-energy''', ''U'' [J], can neit'''Internal-energy''', ''U'' [J], can neither be destroyed nor created (first law of thermodynamics: d<sub>i</sub>''U''/d''t'' = 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''.[[enthalpy]], ''H'', contrasts with Gibbs energy, ''G''.  +
  • '''Ionomycin''' (Imy) is a ionophore used to raise intracellular [Ca<sup>2+</sup>].  +
  • '''Isocitrate dehydrogenase''' forms 2-oxoglutarate from isocitrate in the [[TCA cycle]].  +
  • '''Isolated 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.  +
  • '''Journal indexing''' allows publications to be found on search tools/databases. Each database might have different criteria of inclusion.  +
  • '''Keywords—MitoPedia''' is the concept to'''Keywords—MitoPedia''' is the concept to link keywords in articles published in [[Bioenergetics Communications]] (BEC) to [[MitoPedia]] terms. Authors should consider the message in the selected keywords. Provide consistent definitions of your keywords by linking them to MitoPedia. Extend MitoPedia entries critically by your contributions. The BEC editorial team will hyperlink your keywords with MitoPedia, and a reference to your BEC publication will be generated automatically from the MitoPedia term to your publication. With your contributions, BEC elevates keywords to terms with meaning. Your article gains visibility.th meaning. Your article gains visibility.  +
  • '''Kynurenine hydroxylase''' (kynurenine 3'''Kynurenine hydroxylase''' (kynurenine 3-monooxygenase) is located in the outer mitochondrial membrane. Kynurenine hydroxylase catalyzes the chemical reaction: L-kynurenine + NADPH + H<sup>+</sup> + O<sub>2</sub> ↔ 3-hydroxy-L-kynurenine + NADP<sup>+</sup> + H<sub>2</sub>O</br>Kynurenine hydroxylase belongs to the family of oxidoreductases acting on paired donors, with O<sub>2</sub> as oxidant and incorporation or reduction of oxygen. The oxygen incorporated need not be derived from O<sub>2</sub> 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]].FAD]].  +
  • '''Laboratory titration sheet''' contains '''Laboratory 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]][[Protocols in DatLab]]  +
  • '''Lactate dehydrogenase''' is a glycolytic marker enzyme in the cytosol, regenerating NAD<sup>+</sup> from NADH and pyruvate, forming lactate.  +
  • '''Length''' ''l'' is an SI base quantity '''Length''' ''l'' is an SI base quantity with SI base unit [[meter]] m. Quantities derived from length are [[area]] ''A'' [m<sup>2</sup>] and [[volume]] ''V'' [m<sup>3</sup>]. Length is an extensive quantity, increasing additively with the number of objects. The term 'height' ''h'' is used for length in cases of vertical position (see [[height of humans]]). Length of height per object, ''L''<sub>''U''<sub>''X''</sub></sub> [m·x<sup>-1</sup>] is length per unit-entity ''U''<sub>''X''</sub>, in contrast to lentgth of a system, which may contain one or many entities, such as the length of a pipeline assembled from a number ''N''<sub>''X''</sub> of individual pipes. Length is a quantity linked to direct sensory, practical experience, as reflected in terms related to length: long/short (height: tall/small). Terms such as 'long/short distance' are then used by analogy in the context of the more abstract quantity [[time]] (long/short duration).[time]] (long/short duration).  +
  • '''Light-enhanced dark respiration''' ''LE'''Light-enhanced dark respiration''' ''LEDR'' is a sharp (negative) maximum of dark respiration in plants in response to illumination, measured immediately after switching off the light. ''LEDR'' is supported by respiratory substrates produced during photosynthesis and closely reflects light-enhanced [[photorespiration]] (Xue et al 1996). Based on this assumption, the total photosynthetic oxygen flux ''TP'' is calculated as the sum of the measured net photosynthetic oxygen flux ''NP'' plus the absolute value of ''LEDR''.'NP'' plus the absolute value of ''LEDR''.  +
  • '''Lightguides''' consist of optical fibre'''Lightguides''' 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.rue in the fields of medicine and biology.  +
  • '''Linear phenomenological laws''' are at '''Linear phenomenological laws''' are at the core of the thermodynamics of irreversible processes TIP, considered to apply near equilibrium but more generally in transport processes (e.g. Fick's law). In TIP, linearity is discussed as the dependence of generalized flows ''I'' or fluxes ''J'' on generalized forces, ''J'' = -''L''·''F'', where ''L'' is expected to be constant (as a prerequisite for linearity) and must not be a function of the force ''F'' ([[affinity]]) for [[Onsager 1931 Phys Rev |Onsager reciprocity]] to apply. This paradigm is challenged by the [[ergodynamics |ergodynamic concept]] of fundamentally non-linear isomorphic flux-[[force]] relations and is replaced by the generalized isomorphic flux-[[pressure]] relations. Flows ''I'' [MU·s<sup>-1</sup>] and forces ''F'' [J·MU<sup>-1</sup>] are conjugated pairs, the product of which yields power, ''I''·''F'' = ''P'' [J·s<sup>-1</sup> = W]. Flux ''J'' is system-size specific flow, such that volume-specific flux times force yields volume-specific power, ''P''<sub>''V''</sub> = ''J''·''F'' [W·m<sup>-3</sup>]. Then [[Vector |vectoral]] and [[Discontinuous system |vectorial]] transport processes are inherently non-linear flux-force relationships, with '''''L''''' = '''''u'''''·'''''c''''' in continuous transport processes along a gradient ('''''c''''' is the local concentration), or ''L'' = ''u''·''α'' (''α'' is the [[free activity]] in a discontinuous transport process across a semipermeable membrane) — formally not different from (isomorphic to) [[scalar]] chemical reactions.emical reactions.  +
  • '''Linearity''' is the ability of the meth'''Linearity''' is the ability of the method to produce test results that are proportional, either directly or by a well-defined mathematical transformation, to the concentration of the analyte in samples within a given range. This property is inherent in the [[Beer-Lambert law]] for [[absorbance]] alone, but deviations occur in [[scattering]] media. It is also a property of [[fluorescence]], but a [[fluorophore]] may not exhibit linearity, particularly over a large range of concentrations.arly over a large range of concentrations.  +
  • '''Luminescence''' is spontaneous emission'''Luminescence''' 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 </br>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 [http://goldbook.iupac.org/L03641.html the IUPAC Gold Book].upac.org/L03641.html the IUPAC Gold Book].  +
  • '''Magnesium Green''' (MgG) is an [[extrinsic fluorophores|extrinsic fluorophore]]'''Magnesium Green''' (MgG) is an [[extrinsic fluorophores|extrinsic fluorophore]] that fluoresces when bound to Mg<sup>2+</sup> and is used for measuring mitochondrial ATP production by [[mitochondrial preparations]]. Determination of mitochondrial ATP production is based on the different dissociation constants of Mg<sup>2+</sup> for [[ADP]] and [[ATP]], and the exchange of one ATP for one ADP across the mitochondrial inner membrane by the [[adenine nucleotide translocase]] (ANT). Using the dissociation constants for ADP-Mg<sup>2+</sup> and ATP-Mg<sup>2+</sup> and initial concentrations of ADP, ATP and Mg<sup>2+</sup>, the change in ATP concentration in the medium is calculated, which reflects mitochondrial ATP production. change in ATP concentration in the medium is calculated, which reflects mitochondrial ATP production.  +
  • '''Malic enzyme''' (ME; EC 1.1.1.40) catal'''Malic 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<sup>+</sup> or NADP<sup>+</sup> and a requirement for divalent cations (Mg<sup>2+</sup> or Mn<sup>2+</sup>) as cofactors.</br></br>NAD(P)<sup>+</sup> + L-malate<sup>2-</sup> <--> NAD(P)H + pyruvate<sup>-</sup> + CO<sub>2</sub></br></br>Three groups of ME are distinguished (i) NAD<sup>+</sup>- and (ii) NADP<sup>+</sup>-dependent ME specific for NAD<sup>+</sup> or NADP<sup>+</sup>, respectively, and (iii) NAD(P)<sup>+</sup>- dependent ME with dual specificity for NAD<sup>+</sup> or NADP<sup>+</sup> as cofactor. Three isoforms of ME have been identified in mammals: cytosolic NADP<sup>+</sup>-dependent ME (cNADP-ME or ME1), mitochondrial NAD(P)<sup>+</sup>-dependent ME (mtNAD-ME or ME2; with NAD<sup>+</sup> or NADP<sup>+</sup> as cofactor, preference for NAD<sup>+</sup> under physiological conditions), and mitochondrial NADP<sup>+</sup>-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.[[Tartronic acid]] (hydroxymalonic acid) is an inhibitor of ME.  +
  • '''Malonate''' (malonic acid) is a competitive inhibitor of [[succinate dehydrogenase]] ([[Complex II]]). Malonate is a substrate of [[malonyl-CoA synthase]].  +
  • '''Malonyl-CoA synthase''' or ACSF3 protei'''Malonyl-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.(Complex II inhibitor) and methylmalonate.  +
  • '''Marks''' in [[DatLab]]'''Marks''' 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. or more data points which are not marked.  +
  • '''Maximum oxygen consumption''', ''V''<'''Maximum oxygen consumption''', ''V''<sub>O<sub>2</sub>max</sub>, is and index of cardiorespiratory fitness, measured by spiroergometry on human and animal organisms capable of controlled physical exercise performance on a treadmill or cycle ergometer. ''V''<sub>O<sub>2</sub>max</sub> is the maximum respiration of an organism, expressed as the volume of O<sub>2</sub> at [[STPD]] consumed per unit of time per individual object [mL.min<sup>-1</sup>.x<sup>-1</sup>]. If normalized per body mass of the individual object, ''M'' [kg.x<sup>-1</sup>], mass specific maximum oxygen consumption, ''V''<sub>O<sub>2</sub>max/''M''</sub>, is expressed in units [mL.min<sup>-1</sup>.kg<sup>-1</sup>]. specific maximum oxygen consumption, ''V''<sub>O<sub>2</sub>max/''M''</sub>, is expressed in units [mL.min<sup>-1</sup>.kg<sup>-1</sup>].  +
  • '''Melatonin''' (N-acetyl-5-methoxytryptam'''Melatonin''' (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. » [[#Melatonin and protection from mitochondrial damage |'''MiPNet article''']][#Melatonin and protection from mitochondrial damage |'''MiPNet article''']]  +
  • '''Mersalyl''' (C<sub>13</sub>H<sub>17</sub>HgNO<sub>6</sub>) is an inhibitor of the [[Pi symporter]].  +
  • '''Metformin''' (dimethylbiguanide) is mainly known as an important antidiabetic drug which is effective, however, in a wide spectrum of degenerative diseases. It is an inhibitor of [[Complex I]] and [[glycerophosphate dehydrogenase complex]].  +
  • '''Methylmalonic 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.  +
  • '''Metrology''' 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].  +
  • '''Microplate''' readers allow large numbe'''Microplate''' readers allow large numbers of sample reactions to be assayed in well format microtitre plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 µL per well. a wide range of applications involve the use of [[fluorescence]] measurements , although they can also be used in conjunction with [[absorbance]] measurements.[absorbance]] measurements.  +
  • '''Microxia''' (deep hypoxia) is obtained when trace amounts of O<sub>2</sub> exert a stimulatory effect on respiration above the level where metabolism is switched to a purely [[anaerobic]] mode.  +
  • '''MitoFit protocols''' are moderated by t'''MitoFit 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 aims at a comprehensive [[MitoFit data repository]], which will require global input and cooperation.will require global input and cooperation.  +
  • '''MitoFit registered projects''' are anno'''MitoFit registered projects''' are announced with reference to [[MitoFit protocols]] as [[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]].[[MitoFit data repository]].  +
  • '''MitoKit-CII/Malonate-nv''' (diacetoxyme'''MitoKit-CII/Malonate-nv''' (diacetoxymethyl malonate) is a plasma membrane-permeable prodrug (permeable malonate; Mnanv) that diffuses across the plasma membrane. Cleavage of diacetoxymethyl groups is mediated by intracellular esterases, thus releasing [[malonate]] in the intracellular space. Abliva #: 01-161-s2e intracellular space. Abliva #: 01-161-s2  +
  • '''MitoKit-CII/Succinate-nv''' (diacetoxym'''MitoKit-CII/Succinate-nv''' (diacetoxymethyl succinate) is a plasma membrane-permeable prodrug (permeable succinate; Snv) that diffuses across the plasma membrane. Cleavage of diacetoxymethyl groups is mediated by intracellular esterases, thus releasing [[succinate]] in the intracellular space. Abliva #: 01-118-s4 intracellular space. Abliva #: 01-118-s4  +
  • '''MitoSOX<sup>TM</sup>''' is '''MitoSOX<sup>TM</sup>''' is the version of the [[Dihydroethidium|hydroetidine]] designed to target mitochondria in live cells for the detection of [[superoxide]] (O<sub>2</sub><sup>•-</sup>). The oxidation of the compound by O<sub>2</sub><sup>•-</sup> is easily detected in the red spectrum. One of the advantages of MitoSOX<sup>TM</sup> is its selectivity for O<sub>2</sub><sup>•-</sup> but not for other [[Reactive oxygen species|reactive oxygen species]] or [[Reactive nitrogen species|reactive nitrogen species]]. </br>::::• Readily '''oxidized by superoxide''' but not by other ROS- or RNS-generating systems</br>::::• '''Absorption/emission maxima''': ~510/580 nm</br>::::• Use for '''live cell imaging'''</br>::::• Rapidly and selectively '''targeted to the mitochondria'''</br></br></br>'''MitoSOX<sup>TM</sup>''' 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.hosphonium]], confers a membrane potential sensitivity that creates a series of artifacts and problems not often considered.  +
  • '''Mitochondria''' (Greek ''mitos'': threa'''Mitochondria''' (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).oblast); plural: mitochondria (bioblasts).  +
  • '''Mitochondrial respiration medium, MitoOx1,''' used by the Budapest groups for respirometry und Amplex Red trials.  +
  • '''Mitochondrial Physiology - Historical C'''Mitochondrial Physiology - Historical Collection'''</br></br>'''Aims'''</br></br>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 recorder]]s 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. </br></br>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 </br> </br>* equipment and accessories,</br>* books and symposium proceedings, </br>* reprint collections,</br>* pictures, slides, documents.ollections, * pictures, slides, documents.  +
  • '''Mitochondrial Preservation Medium, MiP03''', developed for preservation of [[isolated mitochondria]].  +
  • '''Mitochondrial concentration''' is ''C<sub>mtE</sub>'' = ''mtE''·''V''<sup>-1</sup> [mtEU·m<sup>-3</sup>]. mt-Concentration is an experimental variable, dependent on sample concentration.  +
  • '''Mitochondrial content''' per object ''X'' is ''mtE<sub><u>N</u>X</sub>'' = ''mtE''·''N<sub>X</sub>''<sup>-1</sup> [mtEU·x<sup>-1</sup>].  +
  • '''Mitochondrial 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 marker'''s are structural'''Mitochondrial marker'''s 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 ratio]]s. » [[Mitochondrial marker#Mitochondrial markers and expression of mitochondrial respiration| '''MiPNet article''']][Mitochondrial marker#Mitochondrial markers and expression of mitochondrial respiration| '''MiPNet article''']]  +
  • '''Mitochondrial metabolic competence''' i'''Mitochondrial 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.</br></br>The term '''mitochondrial competence''' is also known in a genetic context: Mammalian mitochondria possess a natural competence for DNA import.</br></br>'''''[[MitoCom_O2k-Fluorometer]]''''' is a '''Mitochondrial Competence''' network, the nucleus of which is formed by the K-Regio project ''[[MitoCom_O2k-Fluorometer|MitoCom Tyrol]]''.[[MitoCom_O2k-Fluorometer|MitoCom Tyrol]]''.  +
  • '''Mitochondrial preparations''' (mtprep) '''Mitochondrial preparations''' (mtprep) are isolated mitochondria (imt), tissue homogenate (thom), mechanically or chemically permeabilized tissue (permeabilized fibers, pfi) or permeabilized cells (pce). In mtprep the plasma membranes are either removed (imt) or mechanically (thom) and chemically permeabilized (pfi), while mitochondrial functional integrity and to a large extent mt-structure are maintained in incubation media optimized to support mitochondrial physiological performance. According to this definition, submitochondrial particles (smtp) are not a mtprep, since mitochondrial structure is altered although specific mitochondrial functions are preserved.fic mitochondrial functions are preserved.  +
  • '''Mitochondrial respiration medium, Buffer Z''', described by [http://bioblast.at/index.php/Perry_2011_Biochem_J Perry 2011 Biochem J] For composition and comparison see: [[Mitochondrial respiration media: comparison]]  +
  • '''Mitochondrial respiration medium, MiR05'''Mitochondrial respiration medium, MiR05''', developed for oxygraph incubations of [[mitochondrial preparations]]. Respiration of [[living cells]] may be assessed in MiR05 by adding pyruvate (P) as an external source. [[MiR06]] = MiR05 + catalase.</br>[[MiR05Cr]] = [[MiR05]] + creatine.[[MiR05]] + creatine.  +
  • '''Mitochondrial 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.  +
  • '''Mitochondrial respiration medium, MitoO'''Mitochondrial respiration medium, MitoOx2''', developed for oxygraph incubations of [[mitochondrial preparations]] to measure the H<sub>2</sub>O<sub>2</sub> production. MitoOx2 yields a higher optical sensitivity and lower "drift" (oxidation of the fluorophore precurcor without H<sub>2</sub>O<sub>2</sub> present) for Amplex UltraRed(R) than e.g. [[MiR05|MiR05]].[[MiR05|MiR05]].  +
  • '''Mitochondrial respiration medium, [[MiPNet14.13 Medium-MiR06|MiR06]]''', developed for oxygraph incubations of [[mitochondrial preparations]]. MiR06 = MiR05 plus [[catalase]]. MiR06Cr = MiR06 plus [[creatine]].  +
  • '''Molar mass''' ''M'' is the mass of a c'''Molar mass''' ''M'' is the mass of a chemical compound divided by its amount-of-substance measured in moles. It is defined as ''M''<sub>B</sub> = ''m''/''n''<sub>B</sub>, where ''m'' is the total mass of a sample of pure substance and ''n''<sub>B</sub> is the amount of substance B given in moles. The definition applies to pure substance. The molar mass allows for converting between the mass of a substance and its amount for bulk quantities. It is calculated as the sum of standard atomic weights of all atoms that form one entity of the substance.</br></br>The appropriate [[SI base units]] is kg·mol<sup>-1</sup>. However, for historical as well as usability reasons, g·mol<sup>-1</sup> is almost always used instead.historical as well as usability reasons, g·mol<sup>-1</sup> is almost always used instead.  +
  • '''Monoamine oxidases''' are enzymes boun'''Monoamine oxidases''' are enzymes bound to the outer membrane of mitochondria and they catalyze the oxidative deamination of monoamines. Oxygen is used to remove an amine group from a molecule, resulting in the corresponding aldehyde and ammonia. Monoamine oxidases contain the covalently bound cofactor [[FAD]] and are, thus, classified as flavoproteins.nd are, thus, classified as flavoproteins.  +
  • '''Myxothiazol''' Myx is an inhibitor of [[Complex III]]'''Myxothiazol''' Myx is an inhibitor of [[Complex III]] (CIII). CIII also inhibits [[Complex I|CI]]. Myxothiazol binds to the Q<sub>o</sub> site of CIII (close to cytochrome ''b''<sub>L</sub>) and inhibits the transfer of electrons from reduced QH<sub>2</sub> to the Rieske iron sulfur protein.ons from reduced QH<sub>2</sub> to the Rieske iron sulfur protein.  +
  • '''N-ethylmaleimide''' is an organic compound that is derived from maleic acid and blocks endogenous Pi transport.  +
  • '''NAD<sup>+</sup>''' and '''NADH''': see [[Nicotinamide adenine dinucleotide]].  +
  • '''NS e-input''' or the [[NS-pathway control state]]'''NS e-input''' or the [[NS-pathway control state]] is electron input from a combination of substrates for the [[N-pathway control state]] and [[S-pathway control state]] through Complexes [[CI]] and [[CII]] simultaneously into the [[Q-junction]]. NS e-input corresponds to [[TCA cycle]] function ''in vivo'', with [[convergent electron flow]] through the [[Electron transfer pathway]]. In [[Mitochondrial preparations|mt-preparations]], NS e-input requires addition not only of NADH- (N-) linked substrates (pyruvate&malate or glutamate&malate), but of succinate (S) simultaneously, since [[metabolite depletion]] in the absence of succinate prevents a significant stimulation of S-linked respiration. For more details, see: [[Additive effect of convergent electron flow]].[[Additive effect of convergent electron flow]].  +
  • '''Nagarse''' is a broad specifity proteas'''Nagarse''' is a broad specifity protease from bacteria used to promote breakdown of the cellular structure of "hard" tissues such as skeletal muscle or heart mucsle that cannot be homogenized easily without treatment with a protease. Nagarse is frequently used in protocols for isolating mitochondria from muscle tissue.isolating mitochondria from muscle tissue.  +
  • '''Nicotinamide adenine dinucleotide''', N'''Nicotinamide adenine dinucleotide''', NAD<sup>+</sup> and NADH (pyridine nucleotide coenzymes, NAD and NADP), is an oxidation-reduction coenzyme (redox cofactor; compare [[FADH2 |FADH<sub>2</sub>]]). In the [[NADH electron transfer-pathway state]] fuelled by type N-substrates, mt-matrix dehydrogenases generate NADH, the substrate of [[Complex I]] (CI). The reduced N-substrate RH<sub>2</sub> is oxidized and NAD<sup>+</sup> is reduced to NADH,</br>:::: RH<sub>2</sub> + NAD<sup>+</sup> → NADH + H<sup>+</sup> + R</br>The mt-NADH pool integrates the activity of the [[TCA cycle]] and various matrix dehydrogenases upstream of CI, and thus forms a junction or funnel of electron transfer to CI, the [[N-junction]] (compare [[F-junction]], [[Q-junction]]). NAD<sup>+</sup> and NADH are not permeable through the [[Mitochondrial inner membrane|mt-inner membrane]], mtIM. Therefore, an increase of mitochondrial respiration after the addition of NADH may indicate an alteration of the mtIM integrity. Cytosolic NADH is effectively made available for mitochondrial respiration through the [[malate-aspartate shuttle]] or [[Glycerophosphate_dehydrogenase_Complex|glycerophosphate dehydrogenase Complex]].Glycerophosphate_dehydrogenase_Complex|glycerophosphate dehydrogenase Complex]].  +
  • '''Nitric oxide synthase''', NOS, catalyzes the production of nitric oxide (NO•), which is a [[reactive nitrogen species]]. There are four types of NOS: neuronal NOS (nNOS), endothelial NOS (eNOS), inducible NOS (iNOS) and mitochondrial NOS (mtNOS).  +
  • '''Normalization of rate''' (respiratory r'''Normalization of rate''' (respiratory rate, rate of hydrogen peroxide production, growth rate) is required to report experimental data. Normalization of rates leads to a diversity of formats. Normalization is guided by physicochemical principles, methodological considerations, and conceptual strategies. The challenges of measuring respiratory rate are matched by those of normalization. Normalization of rates for: (''1'') the number of objects (cells, organisms); (''2'') the volume or mass of the experimental sample; and (''3'') the concentration of mitochondrial markers in the instrumental chamber are sample-specific normalizations, which are distinguished from system-specific normalization for the volume of the instrumental chamber (the measuring system). Metabolic ''flow'', ''I'', per [[Count |countable]] object increases as the size of the object is increased. This confounding factor is eliminated by expressing rate as sample-mass specific or sample-volume specific ''flux'', ''J''. [[Flow]] is an [[extensive quantity]], whereas [[flux]] is a [[specific quantity]]. If the aim is to find differences in mitochondrial function independent of mitochondrial density, then normalization to a [[mitochondrial marker]] is imperative. [[Flux control ratio]]s and [[flux control efficiency |flux control efficiencies]] are based on internal normalization for rate in a reference state, are independent of externally measured markers and, therefore, are statistically robust. and, therefore, are statistically robust.  +
  • '''Normothermia''' in endotherms is a stat'''Normothermia''' in endotherms is a state when body core temperature is regulated within standard limits. In humans, normothermia is considered as a body temperature of 36.4 to 37.8 °C. Normothermia, however, has a different definition in the context of [[ectotherms]].</br>» [[Normothermia#Normothermia:_from_endotherms_to_ectotherms | '''MiPNet article''']]Normothermia#Normothermia:_from_endotherms_to_ectotherms | '''MiPNet article''']]  +
  • '''Nuclear respiratory factor 1''' is a transcription factor downstream of [[Peroxisome proliferator-activated receptor gamma coactivator 1-alpha|PGC-1alpha]] involved in coordinated expression of [[nDNA]] and [[mtDNA]].  +
  • '''O-ring\[[Viton]]'''O-ring\[[Viton]]\12x1 mm''', for PVDF or PEEK O2k-Stoppers, box of 4 as spares.</br></br>Two spare boxes of this product are standard components of the [[O2k-Assembly Kit]] ([[O2k-FluoRespirometer]]) as well as the [[O2k-TPP+ ISE-Module]] and the [[O2k-NO Amp-Module]].[[O2k-NO Amp-Module]].  +
  • '''O-ring\[[Viton]]\16x2 mm''', mounted on the [[O2k-Chamber Holder sV]].  +
  • '''O2 calibration''' is the calibration in'''O2 calibration''' is the calibration in DatLab of the oxygen sensor. It is a prerequisite for obtaining accurate measurements of respiration. Accurate calibration of the oxygen sensor depends on (''1'') equilibration of the incubation medium with air oxygen partial pressure at the temperature defined by the experimenter; (''2'') zero oxygen calibration; (''3'') high stability of the POS signal tested for sufficiently long periods of time; (''4'') linearity of signal output with oxygen pressure in the range between oxygen saturation and zero oxygen pressure; and (''5'') accurate oxygen solubility for aqueous solutions for the conversion of partial oxygen pressure into oxygen concentration. The standard oxygen calibration procedure is described below for high-resolution respirometry with the calibration routine using instrumental calibration DL-Protocols in [[DatLab]].[[DatLab]].  +
  • '''O2k repair''' of defective hardware may'''O2k repair''' of defective hardware may require replacement of spare parts. Some electronic or mechanical defects may be solved only by repair of the O2k in the electronics workshop of Oroboros Instruments, ''e.g.'', a defective Peltier unit (temperature control).ective Peltier unit (temperature control).  +
  • '''O2k status line''' is found above the [[O2k signal line]]'''O2k status line''' is found above the [[O2k signal line]]. It contains information about the chamber label, O2 calibration, amperometric calibration, potentiometric calibration, the [[block temperature]], the [[illumination]] in chambers, the TIP2k status and the [[Automatic pan]].[[Automatic pan]].  +
  • '''O2k''' - [[Oroboros O2k]]: the modular system for [[high-resolution respirometry]].  +
  • '''O2k-Amperometric OroboPOS Twin-Channel''''O2k-Amperometric OroboPOS Twin-Channel''': Two-channel variable polarization voltage; current/voltage converter for the polarographic oxygen sensor (POS); amplifyer with digital gain settings (1x, 2x, 4x, 8x); A/D converter; output in the range -10 V to 10 V. Integral component of the [[O2k-Main Unit]].[[O2k-Main Unit]].  +
  • '''O2k-Barometric Pressure Transducer''', '''O2k-Barometric Pressure Transducer''', A/D converter and digital output to DatLab for continuous recording of [[barometric pressure]] [kPa or mmHg], integrated into the air calibration of the POS ([[MiPNet06.03 POS-calibration-SOP]]). Integral component of the [[O2k-Main Unit]]. The warranty on the accuracy of the signal obtained from the O2k-Barometric Pressure Transducer expires within three years.ure Transducer expires within three years.  +
  • '''O2k-Electromagnetic Stirrer Twin-Contro'''O2k-Electromagnetic Stirrer Twin-Control''' for smooth rotation of the [[Stirrer-Bar\white PVDF\15x6 mm|stirrer bars]] in the two [[O2k-chamber]]s; with slow-start function to prevent decoupling of the stirrer bar; regulated stirrer speed in the range of 100 to 800 rpm (decoupling may occur at higher stirrer speeds), independent for the two O2k-Chambers; automatic events sent to DatLab when the stirrer is switched on/off or when the rotation seed is changed by the experimenter. Integral component of the [[O2k-Main Unit]].[[O2k-Main Unit]].  +
  • '''O2k-Main Power Cable''', for connecting the main unit to the power supply.  +
  • '''O2k-Peltier Temperature Control''': Bui'''O2k-Peltier Temperature Control''': Built-in electronic thermostat controlling temperature for two [[O2k-chamber]]s in the range of 4 to 47 °C; ±0.002 °C (at room temperature). Continuous recording of the O2k-Copper Block temperature with DatLab. Temperature change from 20 to 30 °C within 15 min; cooling from 30 to 20 °C within 20 min. Integral component of the [[O2k-Main Unit]]. The electronic temperature control of the O2k replaced the conventional water jacket.2k replaced the conventional water jacket.  +
  • '''Obesity''' is a disease resulting from '''Obesity''' is a disease resulting from excessive accumulation of body fat. In common obesity (non-syndromic obesity) excessive body fat is due to an obesogenic lifestyle with lack of physical exercise ('couch') and caloric surplus of food consumption ('potato'), causing several comorbidities which are characterized as preventable non-communicable diseases. Persistent [[body fat excess]] associated with deficits of physical activity induces a weight-lifting effect on increasing muscle mass with decreasing mitochondrial capacity. Body fat excess, therefore, correlates with [[body mass excess]] up to a critical stage of obesogenic lifestyle-induced [[sarcopenia]], when loss of muscle mass results in further deterioration of physical performance particularly at older age.cal performance particularly at older age.  +
  • '''OctGM''': [[Octanoylcarnitine]] & [[Glutamate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocols:''' [[SUIT-015]], [[SUIT-016]], [[SUIT-017]]  +
  • '''OctGMS''': [[Octanoylcarnitine]] &[[Glutamate]] & [[Malate]]& [[Succinate]]. '''MitoPathway control state:''' [[FNS]] '''SUIT protocols:''' [[SUIT-016]], [[SUIT-017]]  +
  • '''OctM''': [[Octanoylcarnitine]]'''OctM''': [[Octanoylcarnitine]] & [[Malate]].</br></br>'''MitoPathway control state:''' F</br></br>'''SUIT protocols:''' [[SUIT-002]], [[SUIT-015]], [[SUIT-016]], [[SUIT-017]]</br></br>Respiratory stimulation of the [[Fatty acid oxidation pathway control state| FAO-pathway]], F, by [[fatty acid]] FA in the presence of [[malate]] M. Malate is a [[NADH Electron transfer-pathway state |type N substrate]] (N), required for the F-pathway. In the presence of [[Malate-anaplerotic pathway control state|anaplerotic pathways]] (''e.g.'', [[Malic enzyme|mitochondrial malic enzyme, mtME]]) the F-pathway capacity is overestimated, if there is an added contribution of NADH-linked respiration, F(N) (see [[SUIT-002]]). The FA concentration has to be optimized to saturate the [[Fatty acid oxidation pathway control state| FAO-pathway]], without inhibiting or uncoupling respiration. Low concentration of [[malate]], typically 0.1 mM, does not saturate the [[N-pathway]]; but saturates the [[Fatty acid oxidation pathway control state |F-pathway]]. High concentration of [[malate]], typically 2 mM, saturates the [[N-pathway]].[[N-pathway]].  +
  • '''OctPGM''': [[Octanoylcarnitine]]'''OctPGM''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]].</br></br>'''MitoPathway control state:''' [[FN]]</br></br>'''SUIT protocols:''' [[SUIT-002]]</br>:This substrate combination supports N-linked flux which is typically higher than FAO capacity (F/FN<1 in the OXPHOS state). In SUIT-RP1, PMOct is induced after PM(E), to evaluate any additive effect of adding Oct. In SUIT-RP2, FAO OXPHOS capacity is measured first, testing for the effect of increasing malate concentration (compare [[malate-anaplerotic pathway control state]], M alone), and pyruvate and glutamate is added to compare FAO as the background state with FN as the reference state.O as the background state with FN as the reference state.  +
  • '''OctPGMS''': [[Octanoylcarnitine]]'''OctPGMS''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]].</br></br>'''MitoPathway control state:''' [[FNS]]</br></br>'''SUIT protocol:''' [[SUIT-001]], [[SUIT-002]], [[SUIT-015]]</br></br>This substrate combination supports convergent electron flow to the [[Q-junction]].[[Q-junction]].  +
  • '''OctPGMSGp''': [[Octanoylcarnitine]]'''OctPGMSGp''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]].</br></br>'''MitoPathway control state:''' FNSGp</br></br>'''SUIT protocol:''' [[SUIT-002]]</br></br>This substrate combination supports convergent electron flow to the [[Q-junction]].[[Q-junction]].  +
  • '''OctPM''': [[Octanoylcarnitine]]'''OctPM''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Malate]].</br></br>'''MitoPathway control state:''' [[FN]]</br></br>'''SUIT protocol:''' [[SUIT-002]], [[SUIT-005]]</br></br>This substrate combination supports N-linked flux which is typically higher than FAO capacity (F/FN<0 in the OXPHOS state). In SUIT-RP1, PMOct is induced after PM(E), to evaluate any additive effect of adding Oct. In SUIT-RP2, FAO OXPHOS capacity is measured first, testing for the effect of increasing malate concentration (compare [[malate-anaplerotic pathway control state]], M alone), and pyruvate is added to compare FAO as the background state with FN as the reference state. the background state with FN as the reference state.  +
  • '''OctPMS''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Malate]] & [[Succinate]]. '''MitoPathway control state:''' [[FNS]] '''SUIT protocol:''' [[SUIT-005]]  +
  • '''Octanoate''' (octanoic acid). C<sub>8</sub>H<sub>16</sub>O<sub>2</sub> Common name: Caprylic acid.  +
  • '''Octanoylcarnitine''' is a medium-chain fatty acid (octanoic acid: eight-carbon saturated fatty acid) covalently linked to [[carnitine]], frequently applied as a substrate for [[fatty acid oxidation]] (FAO) in [[mitochondrial preparations]].  +
  • '''Oligomycin''' (Omy) is an inhibitor of '''Oligomycin''' (Omy) is an inhibitor of [[ATP synthase]] by blocking its proton channel (Fo subunit), which is necessary for oxidative phosphorylation of ADP to ATP (energy production). The inhibition of ATP synthesis also inhibits respiration. In OXPHOS analysis, Omy is used to induce a [[LEAK respiration]] state of respiration (abbreviated as ''L''(Omy) to differentiate from ''L''(n), LEAK state in the absence of ADP).L''(n), LEAK state in the absence of ADP).  +
  • '''Optics''' are the components that are u'''Optics''' are the components that are used to relay and focus light through a [[spectrofluorometer]] or [[spectrophotometer]]. These would normally consist of lenses and/or concave mirrors. The number of such components should be kept to a minimum due to the losses of light (5-10%) that occur at each surface. light (5-10%) that occur at each surface.  +
  • '''Ouabain''' (synonym: G-strophantin octa'''Ouabain''' (synonym: G-strophantin octahydrate) is a poisonous cardiac glycoside. The classical mechanism of action of ouabain involves its binding to and inhibition of the plasma membrane Na+/K+-ATPase (sodium pump) especially at the higher concentrations. Low (nanomolar and subnanomolar) concentrations of ouabain stimulate the Na-K-ATPase.ions of ouabain stimulate the Na-K-ATPase.  +
  • '''Overfitting''' in statistics is the act'''Overfitting''' in statistics is the act of mistaking noise for a signal. Overfitting makes a model look ‘’better’’ on paper but perform ‘’worse’’ in the real world. This may make it easier to get the model published in an academic journal or to sell to a client, crowding out more honest models from the marketplace. But if the model is fitting noise, it has the potential to hurt the science (quoted from [[Silver 2012 Penguin Press]]).nguin Press]]).  +
  • '''Overlay of plots''' is defined in DatLa'''Overlay of plots''' is defined in DatLab as selection of graph layouts showing identical plots from the two O2k-chambers in each graph. Overlay of plots is selected in [[Graph layout - DatLab |Graph layout]]. Superimposed traces of flux/flow from chambers A and B are then shown in Graph 1, and of concentration in chambers A and B in Graph 2.</br></br>There are basically two ways to superimpose traces recorded in different experiments: Export of the graphics via windows metafile or export of the data to e.g. a spreadsheet program.</br></br>If you export via wmf you also can manipulate the graphics but then usually the lines are broken up in different segments. This can be done in various programs like MS Word, Open Office Draw and even in MSPower Point, though this maybe is the worst program to do this. It is better to manipulate them in a proper program like OO Draw, convert it to an unchangeable picture and then import it to a presentation graphics. Anyway, when you import directly to Power point (or other programs), make sure not to import it as a "picture" but as a metafile. Also in some programs you might afterwards have to "break" it up, or accept a "conversion to a MS Draw object" or other similar linguistic inventions of the software gurus. For this option we suggest to do as much as possible directly in DatLab (setting colors, line widths, ..) using the options in "Plots"/"select plots" and "graph"/"options". </br></br>The “hardcore“ option is to export the data and import it into e.g. a spreadsheet program (MS Excel , OOCalc). It takes longer to have a simple overlay but gives you far less problems later and its easier to make changes later. To do this you can export your dataset "Export"/"Data to Textfile" and then go from there."Data to Textfile" and then go from there.  +
  • '''Oxalomalic acid''' is an inhibitor of a'''Oxalomalic acid''' is an inhibitor of aconitase (and of cytoplasmic NADP-dependent isocitrate dehydrogenase). Aconitase mediates the isomerization of citrate to isocitrate as the first step in the [[TCA_cycle| TCA cycle]]. Oxalomalic acid has been used at 1 mM concentration and after 45 min of pre-incubation to inhibit aconitase in permeabilized rat Soleus muscle fibres, inhibiting the enzyme by 24% ([[Osiki 2016 FASEB J]]).[[Osiki 2016 FASEB J]]).  +
  • '''Oxidative stress''' results from an imb'''Oxidative stress''' results from an imbalance between pro-oxidants and antioxidants shifting the equilibrium in favor of the pro-oxidants. This process can be due by an increment in pro-oxidants, by a depletion of antioxidant systems or both. Oxidative stress generates oxidative damage of proteins, lipids and DNA.dative damage of proteins, lipids and DNA.  +
  • '''Oxoglutarate dehydrogenase''' (α-ketogl'''Oxoglutarate dehydrogenase''' (α-ketoglutarate dehydrogenase) is a highly regulated enzyme of the [[tricarboxylic acid cycle]]. It catalyses the conversion of oxoglutarate (alpha-ketoglutarate) to succinyl-CoA, reduces NAD<sup>+</sup> to [[NADH]] and thus links to [[Complex I]] in the Electron transfer-pathway. OgDH is activated by low Ca<sup>2+</sup> (<20 µM) but inactivated by high Ca<sup>2+</sup> (>100 µM). OgDH is an important source of ROS.y high Ca<sup>2+</sup> (>100 µM). OgDH is an important source of ROS.  +
  • '''Oxygen flux''', ''J''<sub>O<su'''Oxygen flux''', ''J''<sub>O<sub>2</sub></sub>, is a [[specific quantity]]. Oxygen [[flux]] is [[oxygen flow]], ''I''<sub>O<sub>2</sub></sub> [mol·s<sup>-1</sup> per system] (an [[extensive quantity]]), divided by system size. Flux may be volume-specific (flow per volume [pmol·s<sup>-1</sup>·mL<sup>-1</sup>]), mass-specific (flow per mass [pmol·s<sup>-1</sup>·mg<sup>-1</sup>]), or marker-specific (flow per mtEU). Oxygen flux (''e.g.'', per body mass, or per cell volume) is distinguished from oxygen flow (per number of objects, such as cells), ''I''<sub>O<sub>2</sub></sub> [mol·s<sup>-1</sup>·x<sup>-1</sup>]. These are different forms of [[normalization of rate]].lization of rate]].  +
  • '''Oxygen kinetics''' describes the depend'''Oxygen kinetics''' describes the dependence of respiration of isolated mitochondria or cells on oxygen partial pressure. Frequently, a strictly hyperbolic kinetics is observed, with two parameters, the oxygen pressure at half-maximum flux, ''p''<sub>50</sub>, and maximum flux, Jmax. The ''p''<sub>50</sub> is in the range of 0.2 to 0.8 kPa for cytochrome ''c'' oxidase, isolated mitochondria and small cells, strongly dependent on ''J''<sub>max</sub> and coupling state.lls, strongly dependent on ''J''<sub>max</sub> and coupling state.  +
  • '''Oxygen pressure''' or partial [[pressure]] of oxygen [kPa], related to oxygen concentration in solution by the [[oxygen solubility]], ''S''<sub>O2</sub> [µM/kPa].  +
  • '''P1,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).  +
  • '''PGMSGp''': [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' NSGp '''SUIT protocol:''' [[SUIT-038]] This substrate combination supports convergent electron flow to the [[Q-junction]].  +
  • '''POS-Service Kit''', in [[O2k-Accessory Box]] including all oxygen sensor service accessories for membrane mounting and service of the [[OroboPOS|POS]].  +
  • '''PREreview''' encourages scientists to p'''PREreview''' encourages scientists to post their scientific outputs as preprints. PREreview makes it easier to start and run a Preprint Journal Club, or integrate preprint review into conventional journal clubs. PREreview seeks to diversify peer review in the academic community by crowdsourcing pre-publication feedback to improve the quality of published scientific output, and to train early-career researchers (ECRs) in how to review others' scientific work. We want to facilitate a cultural shift in which every scientist posts, reads, and engages with preprints as standard practice in scholarly publishing. We see PREreview as a hub to support and nurture the growth of a community that openly exchanges timely, constructive feedback on emerging scientific outputs. We believe that by empowering ECRs through peer review training programs, thereby increasing the diversity of researchers involved in the peer review process, PREreview will help establish a healthier and more sustainable culture around research dissemination and evaluation. This project was born in April 2017 as a collaboration between Samantha Hindle and Daniela Saderi, scientists and [[ASAPbio]] Ambassadors, with help from Josh Nicholson, at the time working for [https://www.authorea.com/aboutus Authorea].ttps://www.authorea.com/aboutus Authorea].  +
  • '''Packing\O2k-Box 1+2''' for shipping the [[O2k-Core]]. O2k-WorldWide delivery, insurance and handling are included in the O2k-Core.  +
  • '''PalM''': [[Palmitoylcarnitine]] & [[Malate]]. '''MitoPathway control state:''' [[ F | Fatty acid oxidation pathway control state]] '''SUIT protocols:''' [[SUIT-019]]  +
  • '''PalOctM''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Malate]]. '''MitoPathway control state:''' [[ F | Fatty acid oxidation pathway control state]] '''SUIT protocols:''' [[SUIT-019]]  +
  • '''PalOctPGM''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocols:''' [[SUIT-019]]  +
  • '''PalOctPGMS''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]]. '''MitoPathway control state:''' [[FNS]] '''SUIT protocols:''' [[SUIT-019]]  +
  • '''PalOctPM''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Pyruvate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocols:''' [[SUIT-019]]  +
  • '''PalPGMSGp''': [[Palmitoylcarnitine]]'''PalPGMSGp''': [[Palmitoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]].</br></br>'''MitoPathway control state:''' FNSGp</br></br>'''SUIT protocol:''' [[SUIT-026]]</br></br>This substrate combination supports convergent electron flow to the [[Q-junction]].[[Q-junction]].  +
  • '''Palmitate''' is a term for the salts an'''Palmitate''' is a term for the salts and esters of palmitic acid (CH<sub>3</sub>(CH<sub>2</sub>)<sub>14</sub>COOH). Palmitic acid is the first fatty acid produced during fatty acid synthesis and the precursor to longer fatty acids. Palmitate negatively feeds back on acetyl-CoA carboxylase (ACC), which is responsible for converting acetyl-CoA to malonyl-CoA, which in turn is used to add to the growing acyl chain, thus preventing further palmitate generation. In order to dissolve the water-insoluble sodium palmitate, [[Bovine serum albumine| BSA]] is needed to form the water-soluble compound called palmitate:BSA.[[Bovine serum albumine| BSA]] is needed to form the water-soluble compound called palmitate:BSA.  +
  • '''Palmitoyl-CoA''' is a coenzyme A deriva'''Palmitoyl-CoA''' is a coenzyme A derivative of palmitate formed by acyl-CoA synthase. In contrast to medium- and short-chain acyl-CoA, palmitoyl-CoA cannot freely diffuse into the mitochondrial matrix. Formation of palmitoylcarnitine by CPTI is necessary prior to transfer into mitochondria for further fatty acid oxidation (β-oxidation). To study [[Fatty acid oxidation]] using Palmitoyl-CoA, [[Carnitine]] and low amount of malate is needed on mitochondrial preparations.e is needed on mitochondrial preparations.  +
  • '''Palmitoylcarnitine''' is an ester deriv'''Palmitoylcarnitine''' is an ester derivative of [[carnitine]] (long-chain acylcarnitine) involved in the metabolism of fatty acids. Within the cell, palmitoylcarnitine is transported into the mitochondria to deliver palmitate for fatty acid oxidation and energy production.atty acid oxidation and energy production.  +
  • '''Pathway control efficiencies''' are [[flux control efficiency |flux control efficiencies]]'''Pathway control efficiencies''' are [[flux control efficiency |flux control efficiencies]], expressing the relative change of flux in response to a transition between two [[electron-transfer-pathway state]]s due to a change of (''1'') substrate availability or (''2'') inhibition of enzyme steps in the pathway, in a defined [[coupling-control state]].[[coupling-control state]].  +
  • '''Peer reviews''' provide a critical asse'''Peer reviews''' provide a critical assessment of a manuscript prior to publication. Bioenergetics Communications publishes [https://www.bioenergetics-communications.org/index.php/bec/BECPolicies#Permanency_of_content.2C_peer-review_process.2C_and_Journal.27s_options_for_post-publication_discussions_and_corrections Open Peer Reviews] for transparency of the review process.s] for transparency of the review process.  +
  • '''PeerJ Preprints''' is the 'pre-print' a'''PeerJ Preprints''' is the 'pre-print' area of the Open Access journal ''PeerJ''. Similar to preprint servers that already exist (for example arXiv.org), authors can submit draft, incomplete, or final versions of articles they are working on. By using this service, authors establish precedent; they can solicit feedback; and they can work on revisions of their manuscript. Once they are ready, they can submit their preprint article into ''PeerJ'' (although it is not a requirement to do so).</br></br>''PeerJ Preprints'' was launched in April 2013. It only accepts submissions in the same subject areas as ''PeerJ'' (biological, medical and environmental sciences) and ''PeerJ Computer Science''. In order to submit to ''PeerJ Preprints'', at least the submitting author must have a user account with ''PeerJ''. There is no pre-publication peer-review of submissions; however we do perform basic checks to ensure conformity with our policies. Submissions are made using the same platform as with the peer-reviewed journals, although some of the requirements are less stringent. Articles are not typeset, but we do provide automated conversion into PDF. The default is for a ''PeerJ Preprints'' publication to be fully open to all viewers (what we call a 'public' pre-print).</br></br>'''PeerJ''' is an Open Access, peer-reviewed, scholarly journal. It considers and publishes research articles in the biological, medical and environmental sciences. It aims for rapid decision making and will publish articles as soon as they are ready. ''PeerJ'' is based in both San Diego, US, and London, UK.sed in both San Diego, US, and London, UK.  +
  • '''Perfluorooctanoic acid''' (PFOA) is a metabolically inert perfluorinated fatty acid which activates [[UCP1]] in brown-fat mitochondria. UCP1-dependent respiration can be stimulated with 600 μM PFOA after inhibition of the phosphorylation system.  +
  • '''Peripheral blood mononuclear cells''' ('''Peripheral blood mononuclear cells''' (PBMC) are a fraction of the leucocyte population in the blood composed by cells with round nucleus. PBMC consist of lymphocytes (T, B and NK cells) and monocytes. During extraction, neutrophils and platelets (PLT) can be found in the PBMC fraction, where PLT are considered as a contamination.ere PLT are considered as a contamination.  +
  • '''Permeabilized cells''' (pce) are mitoch'''Permeabilized cells''' (pce) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane (e.g., with [[digitonin]]), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.</br></br>'''Permeabilized cells''' (pce) are, therefore, not any longer viable or [[living cells]] (ce), since the intactness of cells implies the intactness of the plasma membrane. Any typical quantiative cell viability test (trypan blue etc) evaluating the intactness of the plasma membrane, yields a 100% negative result on fully permeabilized cells.</br></br>For permeabilizing the cell plasma membranes chemically with [[digitonin]], without damaging the [[mitochondrial|mt]]-membranes, the optimum concentration of digitonin must be previously determinated. The protocol [[SUIT-010]] is designed for the evaluation of optimum digitonin concentration for permeabilizing cells, a requirement to account for differences between cell types, the concentration of cells, and variability between batches of the natural product digitonin. batches of the natural product digitonin.  +
  • '''Permeabilized muscle fibers''' (pfi) ar'''Permeabilized muscle fibers''' (pfi) are used as a mitochondrial preparation in respirometry to access mitochondrial function comparable to [[isolated mitochondria]] (imt). pfi are obtained by selectively permeabilizing the plasma membrane mechanically and chemically ([[saponin]]), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.</br></br>:» MitoPedia topic: [[Mitochondrial preparations]][Mitochondrial preparations]]  +
  • '''Permeabilized tissue''' ([[Permeabilized tissue|pti]]'''Permeabilized tissue''' ([[Permeabilized tissue|pti]], see also [[permeabilized muscle fibers]], pfi) or cells ([[Permeabilized cells|pce]]) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane mechanically or [[permeabilization of plasma membrane|chemically]], for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.</br></br>'''Permeabilized cells''' (pce) are, therefore, not any longer viable or [[living cells]] (ce), since the intactness of cells implies the intactness of the plasma membrane. Any typical quantiative cell viability test (trypan blue etc) evaluating the intactness of the plasma membrane, yields a 100% negative result on fully permeabilized cells.ative result on fully permeabilized cells.  +
  • '''Permeabilized tissue''' (pti, see also '''Permeabilized tissue''' (pti, see also [[permeabilized muscle fibers]], pfi) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane mechanically or chemically (e.g., with [[saponin]]), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.[[mitochondrial|mt]]-membranes.  +
  • '''Peroxisome proliferator-activated recep'''Peroxisome proliferator-activated receptor-γ (PPAR-γ) coactivator-1α''' (PGC-1α) is a protein which functions as an inducible transcriptional coactivator, a coregulator of transcription factors, particularly [[NRF-1]] and [[TFAM]]. PGC-1α was first described in 1998 ([[Puigserver 1998 Cell]]). PGC-1α drives the formation of slow-twich muscle fibres ([[Lin 2002 Nature]]) and is increased upon endurance training ([[Norrbom 2004 J Appl Physiol]]). PGC-1α expression is inhibited by the proinflammatory cytokine tumor necrosis factor α (TNF-α) and high levels of leptin. Upregulation of PGC-1α expression is induced by increased [[eNOS]] activity -> [[MiPNet15.05_NO-manual|NO]] -> [[guanylate cyclase]] -> [[cGMP]] ([[Nisoli 2007 Circ Res]]). AMP-activated protein kinase (AMPK) increases PGC-1α expression through SIRT1 ([[Canto 2009 Nature]]).9 Nature]]).  +
  • '''Phenylsuccinate''' is a competitive inhibitor of succinate transport (20 mM).  +
  • '''Phosphocreatine''' is a high energy compound in the skeletal muscle of vertebrates and is present in 4 to 5 times the concentration of ATP.  +
  • '''Phosphoenolpyruvate carboxykinase''' (P'''Phosphoenolpyruvate carboxykinase''' (PEPCK) catalyzes the anabolic reaction of [[oxaloacetate]] (Oxa) to [[phosphoenolpyruvate]] at the expense of GTP. PEPCK is a cytoplasmatic enzyme involved in gluconeogenesis in mouse and rat liver, but 'is found in the mitochondria in the rabbit and chicken, and in both cytoplasm and mitochondria in the guinea pig' ([[Lehninger 1970 Worth Publishers |Lehninger 1970]]). In many anoxia-resistant animals, PEPCK plays an important catabolic role under severe hypoxia and anoxia at the PEPCK branchpoint ([[Hochachka 2002 Oxford Univ Press |Hochachka, Somero 2002)]], feeding malate into the reversed TCA cycle: malate is dismutated to pyruvate catalyzed by [[malic enzyme]] in the oxidative direction, and to fumarate in the reductive direction, leading to formation of succinate and ATP under anoxia ([[Gnaiger 1977 Invertebrate anoxibiosis |Gnaiger 1977]]).[[Gnaiger 1977 Invertebrate anoxibiosis |Gnaiger 1977]]).  +
  • '''Phosphorescence''' is a similar phenome'''Phosphorescence''' is a similar phenomenon to [[fluorescence]]. However, instead of the electron returning to its original energy state following excitation, it decays to an intermediate state (with a different spin value) where it can remain for some time (minutes or even hours) before decaying to its original state. Phosphorescence is one form of [[Luminescence]], especially Photoluminescence.[[Luminescence]], especially Photoluminescence.  +
  • '''PhotoBiology''' is the science of the e'''PhotoBiology''' is the science of the effect of light on biological processes. This includes [[photosynthesis]], photochemistry, photophysics, photomorphogenesis, vision, bioluminescence, circadian rhythms and photodynamic therapy. Phototoxicity results from non-ionizing radiation (i.e. ultraviolet, visible and infrared radiation). Non-ionizing radiation is any type of electromagnetic radiation that does not carry enough energy per quantum (photon energy below 10 eV) to completely remove an electron from an atom or molecule. When photons interact with molecules, the molecules can absorb the photon energy and become excited, reacting with surrounding molecules and stimulating "photochemical" and "photophysical" changes. Respiration may be affected by light during photosynthesis or in dark respiration, with the transient response of [[light-enhanced dark respiration]].[[light-enhanced dark respiration]].  +
  • '''Photodecomposition''' or photodegradati'''Photodecomposition''' or photodegradation is the process of decay of organic material induced by increasing light intensity. Under aerobic conditions, the enhancement of photodecomposition by light intensity can be quantified by oxygen consumption in a controlled light regime. consumption in a controlled light regime.  +
  • '''Photodiode arrays''' are two dimensiona'''Photodiode arrays''' are two dimensional assemblies of [[photodiodes]]. They are frequently used in conjunction with charge coupled devices (CCDs) for digital imaging. They can be used in combination with [[dispersion devices]] to detect wavelength dependent light intensities in a [[spectrofluorometer]] or [[spectrophotometer]].[[spectrophotometer]].  +
  • '''Photodiodes''' are photodetectors that '''Photodiodes''' are photodetectors that convert [[incident light]] into a current or voltage dependent on their configuration. They have replaced photomultiplier tubes for most applications. For fluorometric measurements that do not require spectral data, a single photodiode with suitable [[filters]] can be used. Due to their larger detection area, they are more sensitive than [[photodiode arrays]].[[photodiode arrays]].  +
  • '''Photorespiration''' is the process by w'''Photorespiration''' is the process by which the enzyme RuBisCo oxygenates ribulose biphosphate (RuBP) instead of carboxylating it as part of the Calvin-Benson cycle, creating phosphoglycolate, a product that cannot be used within this cycle, thus dissipating the energy in [[photosynthesis]]. It is estimated that approximately 25 % of RuBisCo reactions are photorespiration, meaning a potential 25 % reduction in photosynthetic output due to the carbon fixed by photorespiration being released as carbon dioxide and nitrogen as ammonia, while the other product, 3-phosphoglycerate (G3P), requires a higher metabolic cost. This process involves a complex network of enzymes and metabolite exchanges between the chloroplasts, peroxisomes and mitochondria. It is also known as the oxidative photosynthetic carbon cycle or C<sub>2</sub> photosynthesis. Environmental conditions tend to affect it, such as temperature and partial pressure of oxygen and carbon dioxide. C<sub>4</sub> plants, CAM plants and algae have biochemical and biophysical mechanisms to overcome the photosynthetic losses due to photorespiration making them more photosynthetically efficient than C<sub>3</sub> plants. [https://www.biotechniques.com/molecular-biology/new-photorespiratory-pathways-the-key-to-humanitys-survival/ Recent plant biotechnology advances] focuse on increasing plant photosynthetic carbon fixation by reducing photorespiration loses.asing plant photosynthetic carbon fixation by reducing photorespiration loses.  +
  • '''Photosynthesis''' is the process that c'''Photosynthesis''' is the process that converts light energy into chemical energy which is subsequently transformed to the physiological energy demand. Photosynthesis has a light-dependent and light-independent (dark) phase. In plants, algae, and cynobacteria, light energy is absorbed during the light phase by the pigment chlorophyll and used to split water and generate adenosine triphosphate (ATP) and reducing power - nicotinamide adenine dinucleotide phosphate (NADPH), with the net production of O<sub>2</sub> as a waste product. During the dark phase ATP and NADPH are used to synthesize carbohydrates from CO<sub>2</sub> through the metabolic pathway called Calvin-Benson cycle. Oxygenic photosynthesis is responsible for producing and maintaining the oxygen concentration of the Earth’s atmosphere. In bacteria such as cyanobacteria, photosynthesis involves the plasma membrane and the cytoplasm. In eukaryotic cells (plants and algae), photosynthesis takes place in the chloroplasts.plants and algae), photosynthesis takes place in the chloroplasts.  +
  • '''Piericidin''' C<sub>25</sub>'''Piericidin''' C<sub>25</sub>H<sub>37</sub>NO<sub>4</sub> is an antibiotic (isolated from ''Streptomyces mobaraensis'') showing similarity with ubiquinone structure which has a potent and competitive inhibitory effect of [[Complex I |CI]] (it competes with endogenous and partially with exogenous Q for binding sites). CI inhibitors have been divided (''1'') depending of the site of action (functional classification): quinone antagonists (e.g. piericidin A, first site), semiquinone antagonists (piericidin A, second site; piericidin B; [[Rotenone| rotenone]] and quinol antagonists (myxothiazol; stigmatellin), and (''2'') depending on their effect on ROS production: inducing ROS production (e.g. rotenone, piericidin A, Rolliniastatin-1 and -2) and preventing ROS production (e.g. stigmatellin, capsaicin, mucidin and coenzyme Q2). In plants, pieridicin A inhibits photosystem II.in, mucidin and coenzyme Q2). In plants, pieridicin A inhibits photosystem II.  +
  • '''Plan S''' is an initiative for [[Open Access]]'''Plan S''' is an initiative for [[Open Access]] publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. According to [https://www.scienceeurope.org/our-priorities/open-access Science Europe], "Plan S requires that recipients of research funding from cOAlition S organisations make the resulting publications available immediately (without embargoes) and under open licences, either in quality Open Access platforms or journals or through immediate deposit in open repositories that fulfil the necessary conditions."ies that fulfil the necessary conditions."  +
  • '''Platelet-rich plasma''' (PRP) is obtain'''Platelet-rich plasma''' (PRP) is obtained as the upper layer at low-speed centrifugation (around 150-200 ''g''), when white and red blood cells sediment and thus get separated from plasma containing the [[platelet]]s. For further details see [[blood cell preparation]].[[blood cell preparation]].  +
  • '''Platelets''' or '''thrombocytes''' (PLT) are cell fragments derived from megakaryocytes with hemostatic function in the blood stream. PLT are anucleated but contain functioning mitochondria that play a critical role in PLT activation.  +
  • '''Poicilotherms''' are [[ectotherms]] whose body temperatures conform to the temperature of the milieu in a thermally variable environment.  +
  • '''Poise'''=A state of balance. '''Redox p'''Poise'''=A state of balance. '''Redox poise''' in electron transport occurs when each electron-carrying intermediate is present in both its oxidized state and its reduced state, in order for that component both to accept and to donate electrons or hydrogen atoms. Redox poise is likely to be essential in the Q-cycle, where the plastosemiquinone participates in one-electron transfer with cytochrome ''b'', despite its tendency to transfer its single electron to oxygen, generating superoxide. When applied to noncyclic electron transport, ''redox poise'' indicates a position of optimal redox state where the activity of components are such that their effective redox potentials favor physiologically useful electron transfer. physiologically useful electron transfer.  +
  • '''Polarographic oxygen sensors''' (POS) a'''Polarographic oxygen sensors''' (POS) are operated with a polarization voltage between the cathode and anode, connected by an electrolyte. Cathode, anode and electrolyte are separated from the analyte by an oxygen-permeable membrane. Oxygen is reduced at the cathode such that the local oxygen concentration is maintained at zero, and diffuses along the concentration gradient from the stirred medium to the cathode, resulting in a linear calibration between oxygen partial pressure and electric current [Amp] (amperometric mode of operation). The [[OroboPOS]] is the POS applied in the [[Oroboros O2k]].[[Oroboros O2k]].  +
  • '''Polyether ether ketone (PEEK)''' is a s'''Polyether ether ketone (PEEK)''' is a semicrystalline organic polymer thermoplastic, which is chemically very resistant, with excellent mechanical properties. PEEK is compatible with ultra-high vacuum applications, and its resistance against oxygen diffusion make it an ideal material for high-resolution respirometry ([[POS]] insulation; coating of stirrer bars; stoppers for closing the O2k-Chamber).rs; stoppers for closing the O2k-Chamber).  +
  • '''Polyvinylidene fluoride (PVDF)''' is a '''Polyvinylidene fluoride (PVDF)''' is a pure thermoplastic fluoropolymer, which is chemically very resistant, with excellent mechanical properties. ''It is used generally in applications requiring the highest purity, strength, and resistance to solvents, acids, bases and heat'' ([http://en.wikipedia.org/wiki/Polyvinylidene_fluoride Wikipedia]). PVDF is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (coating of stirrer bars; stoppers for closing the O2k-Chamber).rs; stoppers for closing the O2k-Chamber).  +
  • '''Post-examination procedures''', in the '''Post-examination procedures''', in the postanalytical phase, are processes following the examination including systematic review, formatting and interpretation, authorization for release, reporting and transmission of the results, and storage of samples of the examinations.nd storage of samples of the examinations.  +
  • '''Potentiometry''' is the general term gi'''Potentiometry''' is the general term given to the method of measuring the electric potential difference between two electrodes connected by an electrolytic solution. The potential of the reference electrode is constant. The other electrode is called the indicator electrode. If this is an ion-selective electrode which is in equilibrium with the solution, the measured electric potential difference is proportional to the (negative) logarithm of the activity of a specific ion in the solution. Examples are the pH glass electrode for measurement of pH, and the TPP<sup>+</sup> electrode for measurement of pTPP and calculation of mt-membrane potential.ment of pTPP and calculation of mt-membrane potential.  +
  • '''Power''' ''P'' [W = J·s<sup>-1<'''Power''' ''P'' [W = J·s<sup>-1</sup>] is [[exergy]] per time, or [[force]] times [[flow]], which cannot be created internally yet is not conserved but is dissipated (''P'' < 0) in irreversible energy transformations at constant temperature and (barometric) pressure, ''T'',''p''. Metabolic power and heat flux of irreversible processes are distinguished as the time rate of Gibbs energy and enthalpy changes, respectively. rate of Gibbs energy and enthalpy changes, respectively.  +
  • '''Pre-examination procedures''', in the p'''Pre-examination procedures''', in the preanalytical phase, are steps starting, in chronological order, from the clinician’s request and including the examination requisition, preparation of the patient, collection of the primary sample, and transportation to and within the laboratory, and ending when the analytical examination procedure begins.e analytical examination procedure begins.  +
  • '''PrePubMed''' indexes preprints from [[ArXiv preprint server |arXiv q-bio]]'''PrePubMed''' indexes preprints from [[ArXiv preprint server |arXiv q-bio]], [[PeerJ Preprints 'pre-print' area of PeerJ |PeerJ Preprints]], [[BioRxiv preprint server for biology |bioRxiv]], [[F1000Research]], [[Preprints multidisciplinary preprint platform |preprints.org]], The Winnower, Nature Precedings, and Wellcome Open Research. Articles are not stored on PrePubMed, but you will be linked to the article at the respective site.ked to the article at the respective site.  +
  • '''Precision of measurement''' is the clos'''Precision of measurement''' is the closeness of agreement between independent results of measurements obtained under stipulated conditions [SOURCE: ISO 3534-1:1993, 3.14]. Precision of measurement cannot be given a numerical value in terms of the [[measurand]], only descriptions such as 'sufficient' or 'insufficient' for a stated purpose. The degree of precision is usually expressed numerically by the statistical measures of imprecision of measurements, such as standard deviation and coefficient of variation, that are inversely related to precision. "Precision" of a given measurement procedure is subdivided according to the specified precision conditions. "[[Repeatability]]" relates to essentially unchanged conditions and is often termed "withinserial" or "within-run precision". "[[Reproducibility]]" relates to changes in conditions, e.g. time, different laboratories, operators, and measuring systems (including different calibrations and reagent batches).fferent calibrations and reagent batches).  +
  • '''Preparation of SUIT chemicals''' describes the preparation of chemicals used in Substrate-Uncoupler-Inhibitor Ttitration (SUIT) protocols.  +
  • '''Preprints''' is a platform dedicated to'''Preprints''' is a platform dedicated to making early versions of research outputs permanently available and citable. We post original research articles and comprehensive reviews, and papers can be updated by authors at any time. Content on ''Preprints'' is not peer-reviewed and can receive feedback from readers. ''Preprints'' focuses on original research articles and comprehensive reviews. Editorials, discussion papers, and commentary are usually not suitable. Preprints is fully owned and funded by MDPI, an open access journal publisher. It is run on a non-profit basis. You do not need to submit to an MDPI journal in order to post a preprint here, any work is welcome. If you do submit to an MDPI journal, you will be invited to submit to Preprints.org during the submission process. </br></br>''Preprints'' has the following features: ''Multidisciplinary'': We cover all research disciplines. ''Open access'': 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. '' Citation via Crossref DOI'': Each preprint has a unique digital object identifier issued by Crossref. This makes them instantly citable and provides a permanent link to the article, even if the URL on our platform changes. New versions of preprints receive a different DOI. ''Comment on any article'': Authors can receive public or private feedback from readers directly from the preprint abstract page. ''Simple submission process'': Submitting a preprint only requires basic information, our team of editors will do the rest and post your preprint as soon as possible. </br></br>MDPI.com is a platform for peer-reviewed, scientific open-access journals operated by MDPI, based in Basel, Switzerland (since 1996). MDPI is a member of the Committee on Publication Ethics ([https://publicationethics.org/ COPE]). To verify the originality of content submitted to our journals, we use [http://www.ithenticate.com/ iThenticate] to check submissions against previous publications. MDPI works with [https://publons.com/about/home/ Publons] to provide reviewers with credit for their work.vide reviewers with credit for their work.  +
  • '''Pressure''' is a fundamental quantity e'''Pressure''' is a fundamental quantity expressing energy per volume. The SI unit of pressure is generally pascal [Pa] = [J·m<sup>-3</sup>]. The term 'stress' (mechanical stress) is used as a synonym for pressure ([[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |SI]]). Pressure is known in physics as mechanical pressure, which is force per area, ''p'' = ''F''·''A''<sup>-1</sup> [Pa] = [N·m<sup>-2</sup>]. In physical chemistry, gas pressure is defined as ''p'' = ''n''·''V''<sup>-1</sup>·''RT'', where the [[concentration]] is ''c'' = ''n''·''V''<sup>-1</sup> [mol·m<sup>-3</sup>], ''R'' is the [[gas constant]], and ''T'' is the absolute temperature, and ''RT'' is expressed in units of chemical force [J·mol<sup>-1</sup>]. van't Hoff's osmotic pressure assumes the same form applied to dissolved substances diffusing across a semipermeable membrane, but concentrations should be replaced by [[activity |activities]]. The activity of dissolved gases is expressed by the [[partial pressure]], where the [[solubility]] can be seen as an activity coefficient. Pressure appears explicitely or implicitely in all chapters of physics and physical chemistry. In contrast to the universal counterparts energy and force, however, the general connections between various isomorphic expressions of pressure remain poorly understood: Pressure is the concentration of the [[force]] at the point of [[action]]. More generally, pressure is the force times concentration at the interphase of interaction.]]. More generally, pressure is the force times concentration at the interphase of interaction.  +
  • '''Problem:''' Layout "01 Calibration Exp.'''Problem:''' Layout "01 Calibration Exp. Gr3-Temp" is selected, a third plot is displayed on the screen but it remains empty (no plot is shown). Newer versions of [[DatLab]] include pre-installed layouts which do not recognize some channel designations from older O2k series.hannel designations from older O2k series.  +
  • '''Proficiency testing''' PT is an evaluat'''Proficiency testing''' PT is an evaluation of participant performance against pre-established criteria by means of interlaboratory comparisons. Some PT providers in the medical area use the term “External Quality Assessment (EQA)” for their proficiency testing schemes, or for their broader programmes, or both. Internal PT strategies may be implemented into laboratory science as practical steps towards PT to achieve reproducibility.eps towards PT to achieve reproducibility.  +
  • '''Proline dehydrogenase''' (ProDH), L-pro'''Proline dehydrogenase''' (ProDH), L-proline:quinone oxidoreductase, is located on the inner side of the [[mtIM]], oxidizing [[proline]] to delta-1-pyrroline-5-carboxylate, with reduction of FAD to FADH<sub>2</sub> and direct entry into the [[Q-junction]], exerting an additive effect of convergent pathways. ProDH is widely distributed in a variety of organisms, is a source of ROS, and may play a role in carcinogenesis. source of ROS, and may play a role in carcinogenesis.  +
  • '''Proton slip''' is a property of the pro'''Proton slip''' is a property of the proton pumps (Complexes CI, CIII, and CIV) when the [[proton]] slips back to the matrix side within the proton pumping process. Slip is different from the [[proton leak]], which depends on Δ''p'' and is a property of the inner mt-membrane (including the boundaries between membrane-spanning proteins and the lipid phase). Slip is an uncoupling process that depends mainly on flux and contributes to a reduction in the [[biochemical coupling efficiency]] of ATP production and oxygen consumption. Together with proton leak and cation cycling, proton slip is compensated for by [[LEAK respiration]] or LEAK oxygen flux, ''L''. Compare: [[Proton leak]].[Proton leak]].  +
  • '''PubMed''' is a free search tool for articles in the life sciences field.  +
  • '''Publication efficiency''' is the fracti'''Publication efficiency''' is the fraction ''F''<sub>r,a/p</sub> of reproducible publications ''N''<sub>r</sub> which are among the number ''N''<sub>a</sub> of publications that receive attention and meaningful interpretation, per total count ''N''<sub>p</sub> of all published communications. Publication efficiency ''F''<sub>r,a/p</sub> = ''F''<sub>r/p</sub>·''F''<sub>a/p</sub> is low due to (''1'') the reproducibility crisis expressed as low reproducibility efficiency ''F''<sub>r/p</sub> = ''N''<sub>r</sub>/''N''<sub>p</sub>, and (''2'') the inflation crisis expressed as low attention efficiency ''F''<sub>a/p</sub> = ''N''<sub>a</sub>/''N''<sub>p</sub>. Estimates of these partial efficiencies vary from field to field. With ''F''<sub>r/p</sub>=0.15 and ''F''<sub>a/p</sub>=0.05, the current publication efficiency is as low as 0.0075, or only 0.75 % of all presently published communictions are reproducible and receive attention and meaningful interpretation. Reduction of the number of irreproducible zero-value publications is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.ons is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.  +
  • '''Pyruvate carboxylase''' synthesizes [[oxaloacetate]]'''Pyruvate carboxylase''' synthesizes [[oxaloacetate]] from [[pyruvate]] and CO<sub>2</sub> as an [[anaplerosis |anaplerotic reaction]] in the mitochondrial matrix of the liver and kidney of higher animals, representing an alternative to the [[malic enzyme]] pathway to oxaloacetate or the [[phosphoenolpyruvate carboxykinase]] reaction (compare glyoxylate cycle in plants and microorganisms). Carboxylation of pyruvate to oxaloacetate requires Mg-ATP. Acetyl CoA is a strong positive modulator. PC can form pyruvate from oxaloacetate to remove an excess of oxaloacetate which inhibits succinate dehydrogenase.f oxaloacetate which inhibits succinate dehydrogenase.  +
  • '''Pyruvate dehydrogenase''' is the first '''Pyruvate dehydrogenase''' is the first component enzyme of the [[pyruvate dehydrogenase complex]], which catalyzes oxidative decarboxylation of [[pyruvate]] in the mt-matrix, and yields [[acetyl-CoA]]. PDH is known as the mitochondrial gatekeeper in the core energy pathway of electron flow into the tricarboxylic acid cycle.on flow into the tricarboxylic acid cycle.  +
  • '''Q-cycle''' refers to the sequential oxi'''Q-cycle''' refers to the sequential oxidation and reduction of the electron carrier Coenzyme Q (CoQ or [[ubiquinone]]) in mitochondria or plastoquinones in the photosynthetic system. Originally, the concept of the Q-cycle was proposed by [[Mitchell P|Peter D Mitchell]]. Following several modifications, the Q-cycle is established, describing how [[CIII]] translocates hydrogen ions against the protonmotive force. The reduced CoQ ([[quinol |ubiquinol]] QH<sub>2</sub>) binds to the Q<sub>o</sub> site of CIII, while the oxidized CoQ ([[ubiquinone]] Q) to the Q<sub>i</sub> site of CIII. First, QH<sub>2</sub> reduces the iron-sulfur protein and feeds cytochrome ''c''<sub>1</sub> with one electron. The other electron is transferred to the ''b''<sub>L</sub> heme and reduces the ''b''<sub>H</sub> heme, which transfers the electron to ubiquinone at the Q<sub>i</sub>-site which is reduced to a [[semiquinone]]. A second QH<sub>2</sub> is required to fully reduce semiquinone to ubiquinol. At the end of the Q-cycle, four protons leave the mt-matrix and enter the intermembrane space, and the reduced cytochrome ''c'' transfers electrons to CIV. The ubiquinol generated at the Q<sub>i</sub>-site can be reused by binding to the Q<sub>o</sub>-site of CIII.chrome ''c'' transfers electrons to CIV. The ubiquinol generated at the Q<sub>i</sub>-site can be reused by binding to the Q<sub>o</sub>-site of CIII.  +
  • '''Quenching''' is the name given to any p'''Quenching''' is the name given to any process that reduces [[fluorescence]] intensity. Molecular oxygen is a [[fluorescence]] and [[phosphorescence]] quencher for some substances – a phenomenon that has been made use of in constructing optical probes for measuring oxygen.cting optical probes for measuring oxygen.  +
  • '''Quinol''' is a class of ''reduced'' org'''Quinol''' is a class of ''reduced'' organic compounds derived from quinone (oxidized form) by two-electron and two-proton reduction. In the mitochondrial electron transfer system, ubiquinol or reduced [[coenzyme Q]] can be found, while in the photosynthetic systems plastoquinols (particularly PQ<sub>9</sub>) are common. These redox compounds exist in three different redox states: [[quinone]] (oxidized), quinol (reduced), and an intermediate [[semiquinone]].[[semiquinone]].  +
  • '''Quinone''' is a class of ''oxidized'' o'''Quinone''' is a class of ''oxidized'' organic compounds with a fully conjugated cyclic dione structure derived from aromatic compounds. [[Ubiquinone]] or coenzmye Q is the naturally occurring quinone in the mitochondrial [[ETS]], while in the photosynthetic system plastoquinones are common. The quinone is reduced either to an unstable semiquinone by one hydrogen atom or to a quinol by two electrons and two protons.a quinol by two electrons and two protons.  +
  • '''Rapamycin''' is an inhibitor of the mam'''Rapamycin''' is an inhibitor of the mammalian/mechanistic target of rapamycin, complex 1 (mTORC1). Rapamycin induces autophagy and dyscouples mitochondrial respiration. Rapamycin delays senescence in human cells, and extends lifespan in mice without detrimental effects on mitochondrial fitness in skeletal muscle. mitochondrial fitness in skeletal muscle.  +
  • '''Reactive nitrogen species''', RNS, are nitric oxide-derived oxidants. The main source of RNS is [[nitric oxide]] (NO•). NO• plays an important role in cell signaling and in oxidative-nitrosative stress.  +
  • '''Reactive oxygen species''', ROS, are mo'''Reactive oxygen species''', ROS, are molecules derived from molecular [[oxygen]], including free oxygen radicals, which are more reactive than O<sub>2</sub>. Physiologically and pathologically important ROS include [[superoxide]], the [[hydroxyl radical]] and [[hydroxide ion]], [[hydrogen peroxide]] and other [[peroxides]]. These are important in cell signalling, oxidative defence mechanisms and [[oxidative stress]].[[oxidative stress]].  +
  • '''Reference material''' (RM) is material '''Reference material''' (RM) is material or substance one or more of whose property values are sufficiently homogeneous and well established to be used for the calibration of an apparatus, the assessment of a measurement procedure, or for assigning values to materials (adapted from VIM: 1993, 6.13). The adjective 'homogeneous' refers to the physical homogeneity between macroscopic parts of the material, not to any microheterogeneity between molecules of the analyte.'''Primary reference material''' is reference material having the highest metrological qualities and whose value is determined by means of a primary reference measurement procedure. The concept "primary calibrator" is subordinate to "calibrator" (see 3.7) and to "primary reference material". 3.7) and to "primary reference material".  +
  • '''References in BEC https-format''' show '''References in BEC https-format''' show (''1'') the list of authors, (''2'') the year of publication in parentheses, (''3'') the title of the publication, and (''4'') the https://doi.org/ link. Removing all the unnecessary detail of journal name and pages, the focus is on authors, year, and title of the reference, which is a concept in line with [[DORA]]. The https-link then does the full job. In exceptional cases when there is no such link, the following formats would apply: a https://pubmed.ncbi.nlm.nih.gov/ link, a link directly to an Open Access pdf, or the old conventional format for the reference. Scientific journals apply ''yesterday's concepts'' in the various formats of references with bewildering abbreviations of journals, volumes, issues, page numbers. We can do ''today's job'' much better using the BEC https-format: </br><small></br># Arese Lucini F, Morone F, Tomassone MS, Makse HA (2021) Diversity increases the stability of ecosystems. https://doi.org/10.1371/journal.pone.0228692</br># Begley CG, Ioannidis JPA (2015) Reproducibility in science: improving the standard for basic and preclinical research. https://doi.org/10.1161/CIRCRESAHA.114.303819. </br># Buranyi S (2017) Is the staggeringly profitable business of scientific publishing bad for science? https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science </br># Cardoso LHD, Doerrier C, Gnaiger E (2021) Magnesium Green for fluorometric measurement of ATP production does not interfere with mitochondrial respiration. https://doi.org/10.26124/bec:2021-0001 </br># Day S, Rennie S, Luo D, Tucker JD (2020) Open to the public: paywalls and the public rationale for open access medical research publishing. https://doi.org/10.1186/s40900-020-0182-y</br># Gnaiger E (2001) Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. https://doi.org/10.1016/S0034-5687(01)00307-3 </br># ….</br></small></br>Compare with a conventional reference format in: Gnaiger E (2021) Beyond counting papers – a mission and vision for scientific publication. https://doi.org/10.26124/bec:2021-0005ic publication. https://doi.org/10.26124/bec:2021-0005  +
  • '''Reliability''' relates the magnitude of'''Reliability''' relates the magnitude of the measurement error in observed measurements (i.e., precision or intermediate precision) to the inherent variability in the ‘error-free’, ‘true’, or underlying level of the quantity between subjects. The value of the reliability takes a value between 0 and 1. When the variability value is zero, indicates that all the variability in the measurements is due to measurement error. And, on the contrary, when the value is 1 indicates that there is a zero error in the measurement error. It is also known as the intraclass correlation, as it equals the correlation between any two measurements made on the same subject.two measurements made on the same subject.  +
  • '''Repetitions''' of an [[experiment]]'''Repetitions''' of an [[experiment]] or [[assay]] are designed to obtain statistical information on the methodological [[precision]] of the measurements. A number of repetitions, ''n'', of measurements are performed on the same sample, applying an identical experimental protocol to subsamples, without providing any information on variability between samples.nformation on variability between samples.  +
  • '''Replica''' are designed in scientific [[study |studies]]'''Replica''' are designed in scientific [[study |studies]] to evaluate the effect of uncontrolled variability on a result obtained from an [[experiment]] on a single [[sample]], to describe the variability and distribution of experimental results, and to obtain statistical information such as the median or average for a defined [[sample size]]. It may be useful to make a terminological distinction between ''replica'' of experiments, ''N'', designed to obtain statistical information on the [[population]], and ''[[repetitions]]'' of [[experiment]]s or [[assay]]s, ''n'', designed to obtain statistical information on the methodological [[precision]] of the measurements. The terms [[study]], [[experiment]] and [[assay]] have to be defined carefully in this context.e to be defined carefully in this context.  +
  • '''Research''' is a term composed of '''se'''Research''' is a term composed of '''search''' and '''re'''. What does this tell us? The best comparison of the English with a German word is ''Untersuchung'', composed of ''suchung'' (search) and ''unter'' (below). The term ''search'' (suchen) is straightforward to understand and comparable in both languages. The prefix ''re'' and ''unter'' are more difficult to reconcile, yet in both languages these perfixes reveal complementary if not nearly identical messages. ''re'' means {''Quote''} back to the original place; again, anew, once more {''end of Quote''} [1], whereas ''unter'' means ''below'' or ''underneath''. Re-search, therefore, is not simply the search or investigation of some topic or problem, it means essentially doing the search again and again (re -> re-producibility) and penetrating ''below'' a simple search by reaching out for an underlying level of the search. The ''re'' in re-search and re-producibility has to be extended ultimately from a single re-search group to inter-laboratory re-investigation. This tells us, therefore, that while ''search'' is valuable, ''re-search'' provides the necessary validation. This re-evaluation of confirmative re-search should be re-cognized as the most important strategy to address the [[reproducibility crisis]].[[reproducibility crisis]].  +
  • '''Resorufin''' is a fluorescence probe us'''Resorufin''' is a fluorescence probe used in various biological assays. Among others, it is the product obtained in the [[Horseradish_peroxidase| Horseradish peroxidase]]-catalyzed assay using [[Amplex_red| Amplex Red]] for the measurement of [[Hydrogen_peroxide| H<sub>2</sub>O<sub>2</sub>]] production.[[Hydrogen_peroxide| H<sub>2</sub>O<sub>2</sub>]] production.  +
  • '''Respiratory Complexes''' are membrane-bound enzymes consisting of several subunits which are involved in energy transduction of the respiratory system. [[Respiratory Complexes#Respiratory Complexes - more than five |» '''MiPNet article''']]  +
  • '''Respiratory states''' of [[mitochondrial preparations]]'''Respiratory states''' of [[mitochondrial preparations]] and [[living cells]] are defined in the current literature in many ways and with a diversity of terms. Mitochondrial respiratory states must be defined in terms of both, the [[coupling-control state]] and the [[electron-transfer-pathway state]].[[electron-transfer-pathway state]].  +
  • '''Respirometry''' is the quantitative mea'''Respirometry''' is the quantitative measurement of respiration. ''Respiration is therefore a combustion, a very slow one to be precise'' (Lavoisier and Laplace 1783). Thus the ''basic idea of using calorimetry to explore the ''sources'' and ''dynamics'' of heat changes were present in the origins of bioenergetics'' ([[Gnaiger_1983_J Exp Zool|Gnaiger 1983]]). Respirometry provides an ''indirect'' calorimetric approach to the measurement of metabolic heat changes, by measuring oxygen uptake (and carbon dioxide production and nitrogen excretion in the form of ammonia, urea, or uric acid) and converting the oxygen consumed into an [[enthalpy]] change, using the [[oxycaloric equivalent]]. Liebig (1842) showed that the substrate of oxidative respiration was protein, carbohydrates, and fat. ''The sum of these chemical changes of materials under the influence of living cells is known as [[metabolism]]'' (Lusk 1928). The amount (volume STP) of carbon dioxide expired to the amount (volume STP) of oxygen inspired simultaneously is the respiratory quotient, which is 1.0 for the combustion of carbohydrate, but less for lipid and protein. Voit (1901) summarized early respirometric studies carried out by the ''Munich school'' on patients and healthy controls, concluding that ''the metabolism in the body was not proportional to the combustibility of the substances outside the body, but that protein, which burns with difficulty outside, metabolizes with the greatest ease, then carbohydrates, while fats, which readily burns outside, is the most difficultly combustible in the organism.'' Extending these conclusions on the ''sources'' of metabolic heat changes, the corresponding ''dynamics'' or respiratory control was summarized (Lusk 1928): ''The absorption of oxygen does not cause metabolism, but rather the amount of the metabolism determines the amount of oxygen to be absorbed. .. metabolism regulates the respiration.''.. metabolism regulates the respiration.''  +
  • '''Resting respiration''' or '''resting me'''Resting respiration''' or '''resting metabolic rate''' (RMR) is measured under standard conditions of an 8–12-h fast and a 12-h abstinence from exercise. In an exemplary study ([[Haugen 2003 Am J Clin Nutr]]), "subjects rested quietly in the supine position in an isolated room with the temperature controlled to 21–24° C. RMR was measured for 15–20 min. Criteria for a valid RMR was a minimum of 15 min of steady state, determined as a <10% fluctuation in oxygen consumption and <5% fluctuation in respiratory quotient". The main difference between RMR and BMR ([[basal metabolic rate]]) is the position of the subject during measurement. Resting metabolic rate is the largest component of the daily energy budget in most human societies and increases with physical training state ([[Speakman 2003 Proc Nutr Soc]]).man 2003 Proc Nutr Soc]]).  +
  • '''Resveratrol''' is a natural bioactive phenol prouced by several plants with antioxidant and anti-inflammatory effects. Dietary intake as nutraceutical is discussed for targeting mitochondria with a wide spectrum of action in degenerative diseases.  +
  • '''Risk management''' is the identification, assessment, and prioritization of risks.  +
  • '''Rotenone''' is an inhibitor of [[Complex I]] (CI) and thus inhibits NADH oxidation. It inhibits the transfer of electrons from iron-sulfur clusters in CI to ubiquinone via binding to the ubiquinone binding site of CI. See also [[Succinate pathway]].  +
  • '''Ruthenium red''' (synonym: ammoniated r'''Ruthenium red''' (synonym: ammoniated ruthenium oxychloride) inhibits the mitochondrial Ca<sup>2+</sup> uniporter. However, in addition it has been shown to interact with and inhibit a large number of other proteins, including ion channels particularly of the Transient Receptor Potential Vanilloid (TRPV) family [1], Ca<sup>2+</sup>-ATPases, and, importantly, the voltage-dependent anion channel (VDAC) [2]. and, importantly, the voltage-dependent anion channel (VDAC) [2].  +
  • '''SF6847''' (C<sub>18</sub>H&'''SF6847''' (C<sub>18</sub>H<sub>22</sub>N<sub>2O</sub>), also known as tyrphostin A9 or malonoben, is a protonophore and a very potent [[uncoupler]] of [[oxidative phosphorylation]], being used in the nM range. Like all uncouplers, SF6847 concentrations must be titrated carefully to evaluate the [[Uncoupler#Optimum_uncoupler_concentration|optimum concentration]] for maximum stimulation of mitochondrial respiration, particularly to avoid inhibition of respiration at higher concentrations.ion, particularly to avoid inhibition of respiration at higher concentrations.  +
  • '''SGp''': [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' SGp; obtained with OctPGMSGp(Rot) '''SUIT protocol:''' [[SUIT-001]] and ((SUIT-002  +
  • '''SUIT''' is the abbreviation for '''S''''''SUIT''' is the abbreviation for '''S'''ubstrate-'''U'''ncoupler-'''I'''nhibitor '''T'''itration. SUIT protocols are used with mt-preparations to study respiratory control in a sequence of coupling and pathway control states induced by multiple titrations within a single experimental assay. These studies use biological samples economically to gain maximum information with a minimum amount of cells or tissue. with a minimum amount of cells or tissue.  +
  • '''Safranin''' is one of the most establis'''Safranin''' is one of the most established dyes for measuring [[mitochondrial membrane potential]] by [[fluorometry]]. It is an [[extrinsic fluorophores |extrinsic fluorophore]] with an excitation wavelength of 495 nm and emission wavelength of 587 nm. Safranin is a potent inhibitor of [[NADH electron transfer-pathway state |N-linked respiration]] and of the [[phosphorylation system]].</br></br>''Synonyms:'' Safranin O, Safranin Y, Safranin T, Gossypimine, Cotton Red, Basic Red2nin T, Gossypimine, Cotton Red, Basic Red2  +
  • '''Salicylhydroxamic acid''' (SHAM; synony'''Salicylhydroxamic acid''' (SHAM; synonym: 2-Hydroxybenzohydroxamic acid N,2-Dihydroxybenzamide) is an inhibitor of the [[alternative oxidase]] (AOX). When AOX is blocked by SHAM, electrons are forced through the CIII-cytochrome ''c'' oxidase pathway, allowing observation of the operation of the CIII-CIV pathway without AOX activity.the CIII-CIV pathway without AOX activity.  +
  • '''Sample mass [[concentration]]''' is ''C''<sub>''m''<sub>s</sub></sub> = ''m''<sub>s</sub>·''V''<sup>-1</sup> [kg·m<sup>-3</sup>].  +
  • '''Sample size''' is an ambiguous term. (1'''Sample size''' is an ambiguous term. (1) Size can be measured as an extensive quantity in terms of [[mass]] ''m''<sub>S</sub> [kg], [[volume]] ''V''<sub>S</sub> [m<sup>3</sup>], or [[energy]] ''E''<sub>S</sub> [J] of a pure [[sample]] S. If the sample consists of countable [[entity |entities]] ''X'', the [[count]] ''N''<sub>''X''</sub> [x] in sample S is an elementary quantity, in contrast to the extensive quantities used as indicators of sample size. (2) In statistics, however, the term 'sample size' does not refer to the individual sample, but indicates on the contrary the number of samples investigated or sampled from a study group. ''N'' is the number of [[sample]]s collected and assayed to obtain representative statistical information on the [[population]]. The population size defines the upper limit of the statistical sample size.[[population]]. The population size defines the upper limit of the statistical sample size.  +
  • '''Saponin''' is a mild detergent that [[Permeabilization of plasma membrane|permeabilizes plasma membranes]]'''Saponin''' is a mild detergent that [[Permeabilization of plasma membrane|permeabilizes plasma membranes]] completely and selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Applied for [[Permeabilized tissue or cells|permeabilization of muscle fibres]].[[Permeabilized tissue or cells|permeabilization of muscle fibres]].  +
  • '''Save and Disconnect''': Stops data acquisition and disconnects from the O2k (only for DatLab 7)  +
  • '''Save as''' a DatLab file. When disconnected from the O2k, save the file under a different file name, optionally in a different directory.  +
  • '''Save''' a DatLab file. When disconnecte'''Save''' a DatLab file. When disconnected from the O2k, save any changes made under the identical file name overwriting the previous file. Such changes do not affect the raw data of the experiment, but relate to calibrations, experimental protocol, marks, events, and layout.</br></br>'''Temporary backup files''' are generated by DatLab in the current user's temp directory, indicated by adding tmp.$$$ to the file name. These files are retained only if the PC has failed during data analysis. During data acquisition, the data are written continuously onto the file, hence backup files are not necessary under these conditions. are not necessary under these conditions.  +
  • '''Scaling factor''' determines the multiplication factor that is applied to the time derivative of the signal.  +
  • '''Scaling''' a graph in [[DatLab]]'''Scaling''' a graph in [[DatLab]] provides flexibility to vary the display of the plots and create Graph layouts. It allows viewing a data plot in differently scaled graphs, zooming the signal and time scales, and scrolling along the axes of the graph provide maximum information on the current experiment. This does not influence the format of stored data. Different ranges for the axes change the appearance of data dramatically. It is highly recommended to use reference layouts. </br></br>»''Compare:'' [[Select plots - DatLab]].[Select plots - DatLab]].  +
  • '''Selectivity''' is the ability of a sensor or method to quantify accurately and specifically the analyte or analytes in the presence of other compounds.  +
  • '''Semiquinone''' is an unstable free radical derived either from the removal of one hydrogen atom with its electron from [[quinol]] (reduced form), or by the addition of a single hydrogen atom to a [[quinone]] (oxidized form).  +
  • '''Sensitivity''' refers to the response obtained for a given amount of analyte and is often denoted by two factors: the limit of detection and the limit of quantification.  +
  • '''Serial port''' describes the connection'''Serial port''' describes the connection between O2k and Computer. </br>With the [[USB-Cable 2.0\Type A-B]] connected, select '''Serial port''' in the [[Connection window]]. Depending on the [[O2k series]], it is possible to connect with a '''Serial port''' or [[USB port]].[[USB port]].  +
  • '''Shredder-Accessory Box''': for storage and shipping of Shredder accessories.  +
  • '''Sirtuins''' are NAD<sup>+</sup'''Sirtuins''' are NAD<sup>+</sup>-dependent deacetylases which play a prominent role as metabolic regulators. Their dependence on intracellular levels of NAD<sup>+</sup> (NAD<sup>+</sup> activates sirtuin activity, whereas NADH inhibits it) makes them suitable as sensors that can detect cellular energy status.</br>[[Sirtuins#Sirtuin_family |» '''MiPNet article''']][[Sirtuins#Sirtuin_family |» '''MiPNet article''']]  +
  • '''Sodium azide''' is an inhibitor of [[Complex IV]]/cytochrome ''c'' oxidase (CIV, COX, CcO).  +
  • '''Sodium fluoride (NaF)''' is used in combination with [[beryllium sulfate]] to form beryllium trifluoride (BeF<sup>3−</sup>), to inhibit the [[ATP synthase]] if it is exposed by disruption of the mitochondrial membranes.  +
  • '''Sodium vanadate (Na<sub>3</sub>VO<sub>4</sub>)''' is used as an ATPase inhibitor.  +
  • '''Solution protocols''' contain media, substrates, uncouplers, inhibitors used in [[SUIT|SUIT protocols]], permeabilization agents, etc.  +
  • '''Specific quantities''' are obtained whe'''Specific quantities''' are obtained when the [[extensive quantity]] is divided by system size, in contrast to [[intensive quantity|intensive quantities]]. ''The adjective'' specific ''before the name of an extensive quantity is often used to mean divided by mass'' ([[Cohen 2008 IUPAC Green Book |Cohen et al 2008]]). A mass-specific quantity (''e.g.'', mass-specific flux is flow divided by mass of the system) is independent of the extent of non-interacting homogenous subsystems. If mass-specific oxygen flux is constant and independent of system size (expressed as mass), then there is no interaction between the subsystems. The well-established scaling law in respiratory physiology reveals a strong interaction of oxygen consumption and body mass by the fact that mass-specific basal metabolic rate (oxygen flux) does not increase proportionally and linearly with body mass. Maximum mass-specific oxygen flux, ''V''<sub>O2max</sub>, is less mass-dependent across a large range of body mass of different mammalian species (Weibel and Hoppeler 2005).ifferent mammalian species (Weibel and Hoppeler 2005).  +
  • '''Spectrophotometry''' is the use of a [[spectrophotometer]]'''Spectrophotometry''' is the use of a [[spectrophotometer]] to measure the transmittance, reflectance or remittance of a material as a function of wavelength. See [[transmission spectrophotometry]], [[reflectance spectrophotometry]] and [[remission spectrophotometry]].[[remission spectrophotometry]].  +
  • '''Spectroscopy''' is a broader term than [[spectrophotometry]] in that it is concerned with the investigation and measurement of spectra produced when matter interacts with or emits any form electromagnetic radiation.  +
  • '''Speed''', ''v'' [m·s<sup>-1</s'''Speed''', ''v'' [m·s<sup>-1</sup>], is the [[distance]], ''s'' [m], covered by a particle per unit time, irrespective of geometrical direction in space. Therefore, speed is not a [[vector]], in contrast to [[velocity]].</br> ''v'' = d''s''/d''t'' [m·s<sup>-1</sup>][velocity]]. ''v'' = d''s''/d''t'' [m·s<sup>-1</sup>]  +
  • '''Spermidine''' is a polycationic bioacti'''Spermidine''' is a polycationic bioactive polyamine mainly found in wheat germ, soybean and various vegetables, involved in the regulation of mitophagy, cell growth and cell death. Like other caloric restriction mimetics, spermidine is effective in cardioprotection, neuroprotection and anticancer immunosuppression by preserving mitochondrial function and control of autophagy.ondrial function and control of autophagy.  +
  • '''Stability''' determines the accuracy of intensity and [[absorbance]] measurements as a function of time. Instability (see [[drift]] introduces systematic errors in the [[accuracy]] of [[fluorescence]] and [[absorbance]] measurements.  +
  • '''Standard operating procedures''' are a set of step-by-step instructions to achieve a predictable, standardized, desired result often within the context of a longer overall process.  +
  • '''State 1''' is the first respiratory sta'''State 1''' is the first respiratory state in an oxygraphic protocol described by [[Chance_1955_JBC-III|Chance and Williams (1955)]], when isolated mitochondria are added to mitochondrial respiration medium containing oxygen and inorganic phosphate, but no ADP and no reduced respiratory substrates. In State 1, [[LEAK respiration]] may be supported to some extent by undefined endogenous substrates, which are oxidized and slowly exhausted. After oxidation of endogenous substrates, only residual oxygen consumption remains ([[ROX]]).[[ROX]]).  +
  • '''State 5''' is the [[respiratory state]]'''State 5''' is the [[respiratory state]] obtained in a protocol with isolated mitochondria after a sequence of [[State 1]] to [[State 4]], when the concentration of O<sub>2</sub> is depleted in the closed oxygraph chamber and zero oxygen (the anaerobic state) is reached ([[Chance 1955 JBC-III|Chance and Williams, 1955]]; Table I).</br></br>State 5 is defined in the original publication in two ways: ''State 5 may be obtained by antimycin A treatment or by anaerobiosis'' (Chance and Williams, 1955; page 414). [[Antimycin A]] treatment yields a State 5 equivalent to a state for measurement of [[residual oxygen consumption]], ROX (which may also be induced by [[rotenone]]+[[myxothiazol]]; [[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]). Setting State 5 equivalent to ROX or anoxia (Chance and Williams 1955) can be rationalized only in the context of measurement of cytochrome redox states, whereas in the context of respiration State 5 is usually referred to as [[anoxic]].[[anoxic]].  +
  • '''Stirrer power''' is switched on and off during operation of the [[Oroboros O2k]] in [[DatLab]] by pressing [F11] (left chamber) and [F12] (right chamber), respectively. This is functional only with a stirrer bar added to each O2k chamber.  +
  • '''Stopper-Shaft conical\white [[PVDF]]'''Stopper-Shaft conical\white [[PVDF]]\central Port''': PVDF shaft with one central capillary and conical base, receptacle on the top for collecting excess medium during closing the O2k-Chamber and during titration; component of [[Stopper\white PVDF\conical Shaft\central Port]].</br></br>'''Discontinued'''[[Stopper\white PVDF\conical Shaft\central Port]]. '''Discontinued'''  +
  • '''Stray light''' is defined as the detect'''Stray light''' is defined as the detected light of any wavelength that lies outside the [[bandwidth]] of the selected wavelength. In the presence of '''stray light''' of intensity ''I''<sub>''s''</sub>, the equation for [[transmittance]] (''T'') becomes ''T'' = (''I'' + ''I''<sub>''s''</sub>)/(''I''<sub>''0''</sub> + ''I''<sub>''s''</sub>) where ''I''<sub>''0''</sub> is the incident light intensity and ''I'' is the transmitted light intensity. Clearly, the lower the value of ''I'', the more dominant becomes the '''stray light''' term and so can cause errors in the quantification of low [[fluorescence]] signals or at high levels of [[absorbance]].[[absorbance]].  +
  • '''Strobilurin''': {''Quote''} Strobilurin'''Strobilurin''': {''Quote''} Strobilurins are a group of chemical compounds used in agriculture as fungicides. They are part of the larger group of QoI inhibitors, which act to inhibit {''end of Quote'': [http://en.wikipedia.org/wiki/Strobilurin]} respiratory [[Complex III]].[[Complex III]].  +
  • '''Submitochondrial particles''' (smtp) co'''Submitochondrial particles''' (smtp) consist of membrane fragments which retain most of the enzymatic machinery required in electron transfer and [[oxidative phosphorylation]]. Such membrane fragments are continuous closed vesicles formed by resealing of mt-membrane fragments after disruption of the mitochondrial structure. smtp are used to isolate the inner-[[membrane-bound ET pathway]] (mETS) from the upstream modules of the [[Electron transfer pathway]] (ETS) which are located in the mt-matrix and outer mt-membrane (transporters). smtp are obtained by treatment of mitochondria with membrane-dispersing agents such as digitonin at high concentration or by sonic irradiation.igh concentration or by sonic irradiation.  +
  • '''Subsamples''' can be obtained (1) from '''Subsamples''' can be obtained (1) from a homogenous [[sample]] (e.g. cell suspension, tissue homogenate, isolated mitochondria), (2) as subsamples obtained by splitting a sample into comparable parts (e.g. permeabilized muscle fibres from a biopsy split into different chambers for repeated measurements), or (3) repetitive sampling (e.g. taking multiple biopsies) at a single time point. Subsamples may be used for (i) application of different types of [[assay]] (e.g. for measurement of respiration and enzyme activities), and (ii) a number of [[repetitions]], ''n'', of the same assay on the same sample.n'', of the same assay on the same sample.  +
  • '''Subscripts in physical chemistry''' are'''Subscripts in physical chemistry''' are used to differentiate symbols of different quantities. While these subscripts need to be short to be readable, they have to be distinct and well defined. Several subscripts relate to fundamental terms and concepts, summarized in a list below. and concepts, summarized in a list below.  +
  • '''Substrate control ratios''' are [[flux control ratio]]'''Substrate control ratios''' are [[flux control ratio]]s ''FCR'', at a constant mitochondrial [[coupling-control state]]. Whereas there are only three well-defined coupling-control states of mitochondrial respiration, ''L'', ''P'', ''E'' ([[LEAK respiration]], [[OXPHOS]], [[Electron transfer pathway]]), numerous [[Electron-transfer-pathway state]]s are possible. </br></br>Careful selection of the reference state, ''J''<sub>ref</sub>, is required, for which some guidelines may be provided without the possibility to formulate general rules. ''FCR'' are best defined by taking ''J''<sub>ref</sub> as the maximum flux (e.g. [[NS |NS<sub>''E''</sub>]]), such that flux in various other respiratory states, ''J<sub>i</sub>'', is smaller or equal to ''J''<sub>ref</sub>. However, this is not generally possible with ''FCR''. For instance, the [[N/S pathway control ratio]] (at constant coupling-control state) may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The [[S-pathway control state]] may be selected preferentially as ''J''<sub>ref</sub>, if mitochondria with variable [[N]]-linked injuries are studied. In contrast, the [[reference state]], ''Z'', is strictly defined for [[flux control efficiency]].[[flux control efficiency]].  +
  • '''Succinate dehydrogenase''' is a [[TCA cycle]]'''Succinate dehydrogenase''' is a [[TCA cycle]] enzyme converting [[succinate]] to [[fumarate]] while reducing FAD to FADH<sub>2</sub>. SDH is the largest component of the mt-inner membrane [[Complex II]] (CII) and thus part of the TCA cycle and [[electron transfer pathway]].[[electron transfer pathway]].  +
  • '''Succinyl-CoA ligase''' (SUCLA or SUCLG)'''Succinyl-CoA ligase''' (SUCLA or SUCLG) is a TCA cycle enzyme converting succinyl-CoA + ADP or (GDP) + Pi to [[succinate]] + ATP (GTP). Two different isoforms exsist: SUCLA (EC: 6.2.1.5) is the ATP-forming isoenzyme, SUCLG (EC: 6.2.1.4) is the GTP-forming isoenzyme. Both reactions are reversible. This reaction is attributed to mitochondrial substrate-level phosphorylation, which is considered as an alternative way of ATP synthesis because it is partially independent from the respiratory chain and from the mitochondrial proton motive force.rom the mitochondrial proton motive force.  +
  • '''Sulfide quinone reductase''' (SQR) is i'''Sulfide quinone reductase''' (SQR) is involved in electron transfer from sulfide which is used as a hydrogen donor by the mitochondrial respiratory system. SQR is associated with a [[dioxygenase]] and a [[sulfur transferase]] to release thiosulfate (H<sub>2</sub>S<sub>2</sub>O<sub>3</sub>).(H<sub>2</sub>S<sub>2</sub>O<sub>3</sub>).  +
  • '''Sulfite oxidase''' (SO) is a dimeric en'''Sulfite oxidase''' (SO) is a dimeric enzyme, located in the intermembrane space of mitochondria, with each monomer containing a single Mo cofactor and cyt b5-type heme [1]. SO catalyzes the oxidation of sulfite to sulfate as the terminal step in the metabolism of sulfur amino acids and is vital for human health. Inherited mutations in SO result in severe neurological problems, stunted brain growth, and early death [2]. </br></br>Function: SO catalyzes the terminal reaction in the oxidative degradation of sulfur amino acids with the formation of a sulfate, electrons pass to cytochrom ''c'' and are further utilized in the respiratory system.</br></br>Sulfite + O<sub>2</sub> + H<sub>2</sub>O --> Sulfate + H<sub>2</sub>O<sub>2</sub> </br></br>Localization: The level of expression of SO differs in various tissues with main predominant localization in liver, kidney, skeletal muscle, heart, placenta, and brain in humans and liver, kidney, heart, brain, and lung in rats [3]. </br></br>Deficiency: SO is vital for metabolic pathways of sulfur amino acids (cysteine and methionine). Complete lack of this enzyme, typically caused by gene mutation, leads to lethal disease called sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.ed sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.  +
  • '''Synchronous time axes''' sets, if ticked, the time axes of all graphs at an identical range and offset, which is particularly useful while panning.  +
  • '''TIP2k and O2k-Upgrade\B''': Titration-Injection microPump TIP2k, including the electronic upgrade of the O2k-main unit returned to workshop (Series B-D). '''Discontinued'''  +
  • '''TIP2k-Cooling Box''': Cooling box for TIP2k syringes. '''Discontinued'''  +
  • '''TIP2k-Needle Safety Support''': for safe storage of TIP2k-needles when not required during the experiment. This item is a standard component of the [[TIP2k-Module]].  +
  • '''TMRM''' (tetramethylrhodamine methyl es'''TMRM''' (tetramethylrhodamine methyl ester) is an [[extrinsic fluorophores|extrinsic fluorophore]] used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. TMRM is a lipophilic cation that is accumulated in the mitochondrial matrix in proportion to Δ''ψ''<sub>mt</sub>. Upon accumulation of the dye it exhibits a red shift in its absorption and fluorescence emission spectrum. The fluorescence intensity is quenched when the dye is accumulated in the mitochondrial matrix.en the dye is accumulated in the mitochondrial matrix.  +
  • '''Tetrahydrofolate''', THF, is the substrate in mitochondrial folate-mediated 1C metabolism, an [[NADH-linked pathway]] leading to the formation of formate which is exported to the cytosol.  +
  • '''Tetraphenylphosphonium''' (TPP<sup>+</sup>). A lipophilic molecular probe in conjunction with an ion selective electrode (ISE) for [[Mitochondrial membrane potential | measuring the mitochondrial membrane potential]].  +
  • '''Thenoyltrifluoroacetone''' TTFA is a noncompetitive inhibitor of CII binding on the quinone-binding (SDHC/SDHD).  +
  • '''Thioredoxin reductase''' (TrxR) is a family of enzymes able to reduce thioredoxin in mammals.  +
  • '''Time resolution''' in respirometric measurements is influenced by three parameters: the [[response time of the POS]], the data sampling interval and the number of points used for flux calculation.  +
  • '''Traceability''' is the property of the '''Traceability''' is the property of the result of a measurement or the value of a standard whereby it can be related to stated references, usually national or international standards, through an unbroken chain of comparisons all having stated uncertainties [SOURCE: VIM:1993, definition 6.10].nties [SOURCE: VIM:1993, definition 6.10].  +
  • '''Trueness of measurement''' is the close'''Trueness of measurement''' is the closeness of agreement between the average value obtained from a large series of results of measurements and a true value (adapted from ISO 3534-1:1993, definition 3.12). The degree of trueness is usually expressed numerically by the statistical measure bias that is inversely related to trueness and is the difference between the expectation of the results of measurement and a true value of the [[measurand]].[[measurand]].  +
  • '''Trueness''' is understood as the lack of [[bias]] and the instrument calibration procedures are the key factor on establishing and correcting it.  +
  • '''USB-RS232 Serial Adapter''', for connec'''USB-RS232 Serial Adapter''', for connecting the [[RS232-Cable]] attached to the [[O2k-Main Unit]] (Series A-D) to the USB port of the PC or laptop. This is not required for O2k-Series E, nor when using a PC or laptop with a serial RS232 port. '''Discontinued'''th a serial RS232 port. '''Discontinued'''  +
  • '''Uncertainty of measurement''' is a para'''Uncertainty of measurement''' is a parameter, associated with the result of a [[measurement]], that characterizes the dispersion of the values that could reasonably be attributed to the [[measurand]]. The parameter can be, for example, a standard deviation (or a given multiple of it), or the half-width of an interval having a stated level of confidence. The components of uncertainty are evaluated experimentally from statistical distributions (Type A) or evaluated from assumed probability distributions based on experience or other information (Type B). All components are expressed as standard uncertainties that are combined into one final expression.at are combined into one final expression.  +
  • '''Uncoupling protein 1''' (UCP1) is also '''Uncoupling protein 1''' (UCP1) is also called thermogenin and is predominantly found in brown adipose tissue (BAT). UCP1 belongs to the gene family of [[uncoupling proteins]]. It is vital for the maintenance of body temperature, especially for small mammals. As the essential component of non-shivering thermogenesis, it possesses the ability to build and open a pore in the inner mitochondrial membrane through which protons may flow along their electrochemical gradient, generated by respiration, bypassing the ATP-producing re-entry site at the F1F0-ATP synthase. Thereby the energy stored in the electrochemical gradient is dissipated as heat.rochemical gradient is dissipated as heat.  +
  • '''Uncoupling protein 2''' (UCP2) belongs to the gene family of [[uncoupling proteins]]. Whereas [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]], this may not be the case for UCP2.  +
  • '''Uncoupling proteins''' (UCPs) are mitoc'''Uncoupling proteins''' (UCPs) are mitochondrial anion carrier proteins that can be found in the inner mitochondrial membranes of animals and plants. [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]] by dissipating the electrochemical proton gradient ([[mitochondrial membrane potential]]), generated by the [[electron transfer pathway]] by pumping protons from the mitochondrial matrix to the mitochondrial intermembrane space. to the mitochondrial intermembrane space.  +
  • '''Units in figures and tables''' are spec'''Units in figures and tables''' are specified together with the numerical values. The ''value'' of a quantity ''Q'' is the product of a [[number]] ''N'' and a [[unit]] ''u''<sub>''Q''</sub>. Abstract units ''u''<sub>''Q''</sub> (such as dm<sup>3</sup>=L, kg, J) are linked to measured quantities (such as volume, mass, energy): </br> Eq.(1) ''Q''<sub>''u''</sub> = ''N''·''u''<sub>''Q''</sub></br></br>The multiplication in Eq.(1) can be handled like any mathematical equation and re-arranged to the form which indicates the meaning (left) of a number (right): </br> Eq.(2a) ''Q''<sub>''u''</sub>/''u''<sub>''Q''</sub> = ''N''</br> Eq.(2b) ''N''<sub>''X''</sub>/x = ''N''</br></br>When numbers are given on the axes of figures and in tables, the corresponding labels should be indicated according to Eq.(2), where Eq.(2a) applies to measured quantities, whereas Eq.(2b) relates to the countable quantity, i.e. [[count]] with unit [x]. For example, the axis label for volume-specific oxygen flux may be written as ''J''<sub>''V'',O<sub>2</sub></sub> / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''<sub>O<sub>2</sub></sub> / [amol/(s·x)].s ''J''<sub>''V'',O<sub>2</sub></sub> / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''<sub>O<sub>2</sub></sub> / [amol/(s·x)].  +
  • '''Velocity''', '''''v''''' [m·s<sup>'''Velocity''', '''''v''''' [m·s<sup>-1</sup>], is the [[speed]] in a defined spatial direction, and as such velocity is a [[vector]]. Velocity is the [[advancement]] in distance per unit time,</br> '''''v''''' ≡ d'''''z''''' ∙ d''t''<sup>-1</sup> [m·s<sup>-1</sup>] d'''''z''''' ∙ d''t''<sup>-1</sup> [m·s<sup>-1</sup>]  +
  • '''Viable cells''' vce are characterized by an intact plasma membrane barrier function. The total cell count (''N''<sub>ce</sub>) is the sum of viable cells (''N''<sub>vce</sub>) and dead cells (''N''<sub>dce</sub>).  +
  • '''Viton'''® is a fluoroelastomer with excellent resistance to aggressive fuels and chemicals. Viton is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (Viton O-rings).  +
  • '''Volume''' ''V'' is a derived quantity b'''Volume''' ''V'' is a derived quantity based on the SI base quantity [[length]] [m] and is expressed in terms of [[SI base units]] in the derived unit cubic meter [m<sup>3</sup>]. The liter [L = dm<sup>3</sup>] is a conventional unit of volume for concentration and is used for most solution chemical kinetics. The volume ''V'' contained in a system (experimental chamber) is separated from the environment by the system boundaries; this is called the volume of the system, and described in practical language as big/small (derived from [[length]], [[height]]) or voluminous. Systems are defined at constant volume or constant [[pressure]]. For a pure sample S, the volume ''V''<sub>S</sub> of the pure sample equals the volume ''V'' of the system, ''V''<sub>S</sub> = ''V''. For [[sample]] s in a mixture, the ratio ''V''<sub>s</sub>·''V''<sup>-1</sup> is the nondimensional [[volume fraction]] ''Φ''<sub>s</sub> of sample s. Quantities divided by volume are [[concentration]]s of sample s in a mixture, such as [[count]] concentration ''C<sub>X</sub>'' = ''N<sub>X</sub>''·''V''<sup>-1</sup> [x·L<sup>-1</sup>], and amount of substance concentration ''C''<sub>B</sub> = ''n''<sub>B</sub>·''V''<sup>-1</sup> [mol·L<sup>-1</sup>]. Mass concentration is [[density]] ''ρ''<sub>s</sub> = ''m''<sub>s</sub>·''V''<sup>-1</sup> [kg·L<sup>-1</sup>]. In closed compressible systems (with a gas phase), the concentration of the gas increases, when pressure-volume [[work]] is performed on the system.is performed on the system.  +
  • '''Wavelength averaging''' is the averagin'''Wavelength averaging''' is the averaging of several adjacent data points across the recorded spectrum (spectral [[smoothing]]), to improve the [[signal-to-noise ratio]]. For example, if the instrument recorded 5 data points per nm, the average of the 5 points can be taken for each successive nm across the range of the spectrum to give a 5-point smoothing. This method clearly reduces the wavelength [[resolution]].[[resolution]].  +
  • '''Work''' [J] is a specific form of [[energy]]'''Work''' [J] is a specific form of [[energy]] in the First Law of thermodynamics, and a specific form of [[exergy]] in the Second Law of thermodynamics, performed by a closed or open system on its surroundings (the environment). This is the definition of ''external'' work, which is zero in [[isolated system]]s. The term exergy includes external and internal work. Mechanical work is force [N] times path length [m]. The internal-energy change of a closed system, d''U'', is due to external exchange (e) of work and heat, and external total work (et, including pressure-volume work) is the internal-energy change minus heat,</br> d<sub>et</sub>''W'' = d''U'' - d<sub>e</sub>''Q''b>et</sub>''W'' = d''U'' - d<sub>e</sub>''Q''  +
  • '''Zero calibration''' is, together with [[air calibration]]'''Zero calibration''' is, together with [[air calibration]], one of the two steps of the POS calibration. It is performed in the [[closed chamber]] after all the oxygen has been depleted by the addition of [[dithionite]] or by respiration of [[Isolated mitochondria |imt]] or [[Living cells |cells]]. Any incubation medium can be used for zero calibration with dithionite or sample. Unlike air calibration, it is not necessary to perform a zero calibration on each experimental day. After performing a zero calibration, it is recommended not running other experiments on the same day. Even after standard cleaning of the O2k-chambers, there might be residual amounts of reduced dithionite in the chamber, affecting the oxygen flux in subsequent experiments performed on the same day.ent experiments performed on the same day.  +
  • '''[[DatLab]] 2''' (DL2) is a MS-DOS programe. DL2 is still used for analysis of [[oxygen kinetics]], after exporting files recorded in recent DatLab versions. A user-friendly O2-kinetics module is in preparation (DL8).  +
  • '''[[Substrate]]'''[[Substrate]]s as electron donors''' are reduced fuel compounds ''S''<sub>red</sub> that are oxidized to an oxidized product ''P''<sub>ox</sub> during H<sup>+</sup>-linked electron transfer, ''S''<sub>red</sub> → ''P''<sub>ox</sub> + 2{H<sup>+</sup> + e<sup>-</sup>}. Mitochondrial respiration depends on a continuous flow of electron-supplying substrates across the mitochondrial membranes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.anes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.  +
  • '''arXiv''' is a classic preprint server i'''arXiv''' 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. are submitted without accompanying paper.  +
  • '''bioRxiv''' (pronounced "bio-archive") i'''bioRxiv''' (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.excerpts, and undergraduate dissertations.  +
  • '''pH calibration buffers''' are prepared to obtain two or more defined pH values for calibration of pH electrodes and pH indicator dyes.  +
  • '''pH combination electrode''', 150 mm shaft, 6 mm diameter, incl. connection cable with BNC plug. '''Discontinued''' * Replaced by [[O2k-pH ISE-Module]].  +
  • '''pH-Combination Electrode\70/5 mm''', 70 mm shaft, 5 mm diameter, for 30251-24 stopper. ''' Discontinued ''' * Replaced by [[O2k-pH ISE-Module]].  +
  • '''β-hydroxybutyrate''' or 3-hydroxybutyrate is a ketone body that can be used as a [[NADH electron transfer-pathway state|NADH-linked substrate]]. The β-hydroxybutyrate dehydrogenase produces acetoacetate while reducing NAD<sup>+</sup> to [[NADH]]. <br>  +
  • ''See'' '''[[N-pathway control state]]''' (previous: CI-linked) versus '''[[Complex I]]'''  +
  • ''See'' '''[[NS-pathway control state]]''' (previous: CI<small>&</small>II-linked)  +
  • ''This definition is insufficient and need''This definition is insufficient and needs elaboration.''</br></br>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.s. UV radiation can speed up this process.  +
  • (1) Cellular substrates ''in vivo'', endogenous; '''Ce'''. (2) Cellular substrates ''in vivo'', with exogenous substrate supply from culture medium or serum; '''Cm'''. * ''This page needs an update.''  +
  • 0.5 nmol O<sub>2</sub>; in bioenergetics a variety of expressions is used for units of amount of half a nmol molecular oxygen (natoms oxygen; natoms O; ng.atom O; nmol O), with the identical meaning: 0.5 nmol O<sub>2</sub>.  +
  • 2-fluorophenyl){6-[(2-fluorophenyl)amino](2-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|oxidative phosphorylation]] detected in a screen for uncoupling agents exerting less toxicity than commonly used uncouplers and first described by [[Kenwood 2013 Mol Metab|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 H<sub>2</sub>O<sub>2</sub>, to leave cellular membrane potential unaffected, and to ultimately exert less cytotoxicity.e potential unaffected, and to ultimately exert less cytotoxicity.  +
  • 3-Mercaptopropionic acid (MPA) inhibits long chain [[acyl-CoA dehydrogenase]]s (ACADs).  +
  • 666 coauthors of the 'MitoEAGLE white paper' [1] collaborated to reach a consensus on terminology related to mitochondrial respiratory states and rates. This page is intended to prepare a questionnaire and follow-up publication.  +
  • <br/> [[File:MIG.gif|128 px|left]]<br/> </br>[[File:MIG.gif|128 px|left]]</br>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). </br></br>[email protected] 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.be interpreted, acted on or represented as such.  +
  • A '''Custom label''' can be entered in this box to rename the axis label. Two lines are available for the axis name and unit.  +
  • A '''Digital Object Identifier''', DOI, isA '''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.sible proof that a publication is citable.  +
  • A '''Layout''' in [[DatLab]]A '''Layout''' in [[DatLab]] selected in the Layout menu yields a standardized display of graphs and [[Plot - DatLab |plots]] displayed with specific [[Scaling - DatLab|scalings]]. The graph layout defines initial settings, which can be modified for plots [Ctrl+F6] and scaling [F6]. A modified layout can be saved as user layout without changing the standard layouts.out without changing the standard layouts.  +
  • A '''Lower O2 limit [µM]''' can be definedA '''Lower O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O<sub>2</sub> concentration drops below this limit. It reminds the user that re-oxygenation of the O2k-chamber may be required. For the lower O<sub>2</sub> concentration limit, the [[critical oxygen pressure |critical oxygen concentration]] should be considered, which differs between isolated mitochondria, large cells, and permeabilized muscle fibers. A higher limit should be chosen when high oxygen flux is expected, e.g. prior to uncoupler titration. A lower limit is acceptable prior to inhibition of respiration causing low oxygen flux.ptable prior to inhibition of respiration causing low oxygen flux.  +
  • A '''National Standards Body''' is the national member of the [[International Organization for Standardization]] (ISO).  +
  • A '''Notified Body''' is an organisation designated by an EU country to assess the conformity of certain products before being placed on the market.  +
  • A '''Quality Audit''' is the process of systematic examination of a quality system carried out by an internal or external quality auditor or an audit team.  +
  • A '''Stand alone application''' is computer software that can work offline, i.e. does not necessarily require network connection to function or does not even provide the possibility to connect to a network.  +
  • A '''Upper O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O<sub>2</sub> concentration rises beyond this limit.  +
  • A '''Web application''' is a computer software where the [[user interface]] gets accessed by the user through a web browser.  +
  • A '''canonical ensemble''' is the group ofA '''canonical ensemble''' is the group of compartments enclosed in an isolated system '''H''', with a smaller compartment A<sub>1</sub> in thermal equilibrium with a larger compartment A<sub>2</sub> which is the heat reservoir at temperature ''T''. When A<sub>1</sub> is large in the canonical sense, if its state can be described in terms of macroscopic thermodynamic quantities of ''V'', ''T'', and ''p'' merging with the state described as a probability distribution.T'', and ''p'' merging with the state described as a probability distribution.  +
  • A '''closed system''' is a system with bouA '''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 system|discontinuous]] with compartments (heterogenous).[[Discontinuous system|discontinuous]] with compartments (heterogenous).  +
  • A '''coenzyme''' or cosubstrate is a [[cofactor]]A '''coenzyme''' or cosubstrate is a [[cofactor]] that is attached loosely and transiently to an enzyme, in contrast to a [[prosthetic group]] that is attached permanently and tightly. The coenzyme is required by the corresponding enzyme for its activity (IUPAC definition). A coenzyme is 'a low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons' (IUPAC definition).l groups or electrons' (IUPAC definition).  +