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'''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.  +
The kilogram, symbol kg, is the SI unit of mass. It is defined by taking the fixed numerical value of the Planck constant ''h'' to be 6.626 070 15 × 10<sup>−34</sup> when expressed in the unit J s, which is equal to kg m<sup>2</sup> s<sup>−1</sup>, where the meter and the second are defined in terms of ''c'' and Δ''ν''<sub>Cs</sub>.  +
The '''Korean Society of Mitochondrial Research and Medicine''' (KSMRM) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]].  +
'''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 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]].  +
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[[Image:L over E.jpg|50 px|LEAK control ratio]] The '''''L/E'' coupling-control ratio''' is the flux ratio of [[LEAK respiration]] over [[ET capacity]], as determined by measurement of oxygen consumption in ''L'' and ''E'' sequentially. The ''L/E'' coupling-control ratio is an index of [[uncoupling]] or [[dyscoupling]] at constant ET-capacity. ''L/E'' increases with uncoupling from a theoretical minimum of 0.0 for a fully coupled system, to 1.0 for a fully uncoupled system.  +
[[Image:L over P.jpg|50 px|''L/P'' coupling-control ratio]] The '''''L/P'' coupling-control ratio''' or LEAK/OXPHOS coupling-control ratio combines the effects of coupling (''L/E'') and limitation by the phosphorylation system (''P/E''); ''L/P'' = (''L/E'') / (''P/E'') = 1/[[RCR]].  +
[[Image:L over R.jpg|50 px|''L/R'' coupling-control ratio]] The '''''L/R'' coupling-control ratio''' or LEAK/ROUTINE coupling-control ratio combines the effects of coupling (''L/E''), physiological control of energy demand, and limitation by the OXPHOS capacity.  +
[[File:L.jpg]] '''EAK respiration''' or LEAK oxygen flux ''L'' compensating for [[proton leak]], [[proton slip]], cation cycling and [[electron leak]], is a dissipative component of respiration which is not available for performing biochemical work and thus related to heat production. LEAK respiration is measured in the LEAK state, in the presence of reducing substrate(s), but absence of ADP - abbreviated as ''L''(n) (theoretically, absence of inorganic phosphate presents an alternative), or after enzymatic inhibition of the [[phosphorylation system]], which can be reached with the use of [[oligomycin]] - abbreviated as ''L''(Omy). The '''LEAK state''' is the non-phosphorylating resting state of intrinsic [[Uncoupler|uncoupled]] or [[Dyscoupled respiration|dyscoupled respiration]] when oxygen flux is maintained mainly to compensate for the proton leak at a high chemiosmotic potential, when ATP synthase is not active. In this non-phosphorylating resting state, the electrochemical proton gradient is increased to a maximum, exerting feedback control by depressing oxygen flux to a level determined mainly by the proton leak and the H<sup>+</sup>/O<sub>2</sub> ratio. In this state of maximum protonmotive force, LEAK respiration, ''L'', is higher than the LEAK component of [[OXPHOS capacity]], ''P''. The conditions for measurement and expression of respiration vary ([[oxygen flux]] in the LEAK state, ''J''<sub>O<sub>2</sub>''L''</sub>, or [[oxygen flow]], ''I''<sub>O<sub>2</sub>''L''</sub>). If these conditions are defined and remain consistent within a given context, then the simple symbol ''L'' for respiratory rate can be used as a substitute for the more explicit expression for respiratory activity. » [[LEAK respiration#LEAK respiration: concept-linked terminology of respiratory states |'''MiPNet article''']]  +
[[File:L.jpg |link=LEAK respiration]] The '''LEAK state with ATP''' is obtained in mt-preparations without ATPase activity after ADP is maximally phosphorylated to ATP ([[State 4]]; Chance and Williams 1955) or after addition of high ATP in the absence of ADP ([[Gnaiger 2000 Proc Natl Acad Sci U S A |Gnaiger et al 2000]]). Respiration in the LEAK state with ATP, ''L''(T), is distinguished from ''L''(n) and ''L''(Omy).  +
[[File:L.jpg |link=LEAK respiration]] The '''LEAK state with oligomycin''' is a [[LEAK state]] induced by inhibition of ATP synthase by [[oligomycin]]. ADP and ATP may or may not be present. LEAK respiration with oligomycin, ''L''(Omy), is distinguished from ''L''(n) and ''L''(T).  +
[[File:L.jpg |link=LEAK respiration]] In the '''LEAK state without adenylates''' mitochondrial LEAK respiration, ''L''(n) (n for no adenylates), is measured after addition of substrates, which decreases slowly to the [[LEAK state]] after oxidation of endogenous substrates with no [[adenylates]]. ''L''(n) is distinguished from ''L''(T) and ''L''(Omy).  +
'''Laboratory titration sheet''' contains the sequential titrations in a specific Substrate-uncoupler-inhibitor titration (SUIT) protocol. The laboratory titration sheets for different SUIT protocols are incorporated in DatLab (DL7.1): [[Protocols in DatLab]]  +
'''Lactate dehydrogenase''' is a glycolytic marker enzyme in the cytosol, regenerating NAD<sup>+</sup> from NADH and pyruvate, forming lactate.  +
The concept on '''latent mitochondrial dysfunction''' presents the working hypothesis that the dynamic mitochondrial stress response provides a more sensitive and integrative marker for degenerative disease-related defects compared to acute mitochondrial dysfunction. The risk for developing a disease may be quantified in terms of a stress response, rather than a static pathophysiological state. Acute and latent mitochondrial dysfunction are studied at baseline and in response to a particular (e.g. oxidative) stress, using a mitochondrial stress resistance test.  +
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.  +
This method makes use of all of the data points of the spectrum in order to quantify a measured spectrum with a reference spectrum of known concentration using a '''least squares method''' to match the measured spectrum with the reference spectrum. The technique results in improved accuracy compared with the use of only a few characteristic wavelengths.  +
'''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).  +
[[File:E.jpg |link=ET capacity]] '''Level flow''' is a [[steady state]] of a system with an input process coupled to an output process (coupled system), in which the output force is zero. ''Clearly, energy must be expended to maintain level flow, even though output is zero'' (Caplan and Essig 1983; referring to zero output force, while output flow may be maximum).  +
A variety of '''light sources''' are available for [[fluorometry]] and [[spectrophotometry]]. These include deuterium, mercury and xenon arc lamps and quartz halogen bulbs dependent upon the wavelengths required. However, the advent of [[light emitting diode]]s has greatly increased the possibilities for the application of [[fluorometry]] and [[spectrophotometry]] to areas that were previously not practicable, and at a much reduced cost.  +
A '''light-emitting diode''' (LED) is a light source (semiconductor), used in many every-day applications and specifically in [[fluorometry]]. LEDs are available for specific spectral ranges across wavelengths in the [http://en.wikipedia.org/wiki/Light-emitting_diode#Colors_and_materials visible, ultraviolet, and infrared range].  +
'''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''.  +
'''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.  +
The '''limiting oxygen pressure''', ''p''<sub>l</sub>, is defined as the partial oxygen pressure, ''p''<sub>O2</sub>, below which [[anaerobic]] catabolism is activated to contribute to total ATP generation. The limiting oxygen pressure, ''p''<sub>l</sub>, may be substantially lower than the '''[[critical oxygen pressure]]''', ''p''<sub>c</sub>, below which [[aerobic]] catabolism (respiration or oxygen consumption) declines significantly.  +
In the transition from aerobic to [[anaerobic | anaerobic metabolism]], there is a limiting ''p''<sub>O2</sub>, ''p''<sub>lim</sub>, below which anaerobic energy flux is switched on and [[Calorespirometric ratio|CR ratios]] become more exothermic than the [[oxycaloric equivalent]]. ''p''<sub>lim</sub> may be significanlty below the [[critical pO2|critical ''p''<sub>O2</sub>]].  +
'''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.  +
'''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.  +
[[Armstrong 2010 J Comp Physiol B]]: This paper describes a method for purification of rodent liver mitochdondria using relatively low-speed centrifugation through discontinuous Percoll gradients.  +
With '''Living Communications''', [https://www.bioenergetics-communications.org/index.php/bec Bioenergetics Communications] (BEC) takes the next step from pre-print to re-print. The concept of ''Living Communications'' pursues a novel culture of scientific communication, addressing the conflict between long-term elaboration and validation of results versus sharing without delay improved methods and preliminary findings. Following the preprint concept, updates may be posted on the BEC website of the resource publication. Updated versions of Living Communications are submitted for Open Peer Review with full traceability. In contrast to static papers, evolution of ''Living Communications'' is more resourceful and efficient than a ‘new’ publication. ''Living Communications'' provide a pathway along the scientific culture of lively debate towards tested and trusted milestones of research, from pre-print to re-print, from initial steps to next steps.  +
Cell viability in '''living cells''' should be >95 % for various experimental investigations, including cell respirometry. Viable cells (vce) are characterized by an intact plasma membrane barrier function. The total cell count (''N''<sub>ce</sub>) is the sum of viable cells (''N''<sub>vce</sub>) and dead cells (''N''<sub>dce</sub>). In contrast, the plasma membrane can be permeabilized selectively by mild detergents ([[digitonin]]), to obtain the [[Mitochondrial preparations |mt-preparation]] of [[permeabilized cells]] used for [[cell ergometry]]. Living cells are frequently labelled as ''intact cells'' in the sense of the total cell count, but ''intact'' may suggest dual meanings of ''viable'' or unaffected by a disease or mitochondrial injury.  +
A '''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.  +
'''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 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].  +
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[[File:MITOEAGLE-representation.jpg|150px|left]] The objective of the '''MitoEAGLE''' network is to improve our knowledge on mitochondrial function in health and disease related to Evolution, Age, Gender, Lifestyle and Environment.  +
'''Magnesium 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.  +
[[File:Malic_acid.jpg|left|100px|Malic acid]] '''Malic acid''', C<sub>4</sub>H<sub>6</sub>O<sub>5</sub>, occurs under physiological conditions as the anion '''malate<sup>2-</sup>, M''', with p''K''<sub>a1</sub> = 3.40 and p''K''<sub>a2</sub> = 5.20. L-Malate is formed from fumarate in the [[TCA cycle]] in the mitochondrial matrix, where it is the substrate of [[malate dehydrogenase]] oxidized to [[oxaloacetate]]. Malate is also formed in the cytosol. It cannot permeate through the lipid bilayer of membranes and hence requires a carrier ([[dicarboxylate carrier]], [[tricarboxylate carrier]] and 2-oxoglutarate carrier). Malate alone cannot support respiration of [[Mitochondrial preparations|mt-preparations]] from most tissues, since oxaloacetate accumulates in the absence of [[pyruvate]] or [[glutamate]]. Malate is a [[NADH electron transfer-pathway state |type N substrate]] (N) required for the [[Fatty acid oxidation pathway control state| FAO-pathway]]. In the presence of [[Malate-anaplerotic pathway control state|anaplerotic pathways]] (''e.g.'', [[Malic enzyme|mitochondrial malic enzyme, mtME]]) the capacity of the FAO-pathway can be overestimated due to a contribution of NADH-linked respiration, F(N) (see [[SUIT-002]]).  +
Mitochondrial '''malate dehydrogenase''' is localized in the mitochondrial matrix and oxidizes [[malate]], generated from fumarate by fumarase, to [[oxaloacetate]], reducing NAD<sup>+</sup> to NADH+H<sup>+</sup> in the [[TCA cycle]]. Malate is added as a substrate in most [[N-pathway control state]]s.  +
'''Carriers for malate: * [[dicarboxylate carrier]] * [[tricarboxylate carrier]] * [[2-oxoglutarate carrier]]  +
[[File:M.jpg|left|200px|M]] '''M''': [[Malate]] alone does not support respiration of mt-preparations if [[oxaloacetate]] cannot be metabolized further in the absence of a source of acetyl-CoA. Transport of oxaloacetate across the inner mt-membrane is restricted particularly in liver. Mitochondrial citrate and 2-oxoglutarate (α-ketoglutarate) are depleted by antiport with malate. [[Succinate]] is lost from the mitochondria through the dicarboxylate carrier. OXPHOS capacity with malate alone is only 1.3% of that with [[PM |Pyruvate&Malate]] in isolated rat skeletal muscle mitochondria. However, many mammalian and non-mammalian mitochondria have a mt-isoform of NADP<sup>+-</sup> or NAD(P)<big>+</big>-dependent [[malic enzyme]] (mtME), the latter being particularly active in proliferating cells. Then the [[anaplerotic pathway control state]] with malate alone (aN) supports high respiratory activities comparable to the NADH-linked pathway control states (N) with pyruvate&malate or glutamate&malate substrate combinations ([[PM-pathway control state]], [[GM-pathway control state]]).  +
The malate-aspartate shuttle involves the glutamate-aspartate carrier and the 2-oxoglutarate carrier exchanging malate<sup>2-</sup> for 2-oxoglutarate<sup>2-</sup>. Cytosolic and mitochondrial malate dehydrogenase and transaminase complete the shuttle for the transport of cytosolic NADH into the mitochondrial matrix. It is most important in heart, liver and kidney.  +
'''Malic 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. NAD(P)<sup>+</sup> + L-malate<sup>2-</sup> <--> NAD(P)H + pyruvate<sup>-</sup> + CO<sub>2</sub> 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.  +
'''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 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.  +
Setups and templates in DatLab can be renamed or deleted under '''Manage setups''' or '''Manage templates'''.  +
Manuscripts template for [[MitoFit Preprints]] and [[Bioenergetics Communications]].  +
» See [[Marks - DatLab]]  +
The function '''Mark specifications''' is largely replaced by [[SUIT: Browse DL-Protocols and templates |SUIT DL-Protocols]] and [[Instrumental: Browse DL-Protocols and templates |Instrumental DL-Protocols]] in [https://www.oroboros.at/index.php/product/datlab/ DatLab 7.4]. Mark specifications allow the user to rename [[Marks - DatLab| Marks]] in the active plot and save/recall the settings. Rename marks individually by clicking into the horizontal bar, or use corresponding templates for renaming the entire sequence of marks.  +
In '''Mark statistics''' one [[Plot - DatLab |Plot]] is selected as a source for [[Marks - DatLab|Marks]] over sections of time. Values (e.g. medians) are displayed for these time sections of the source plot and of all selected plots.  +
'''Marks''' 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.  +
The component of the electron transfer system located in the mitochondrial matrix ('''matrix-ETS''') is distringuished from the ETS bound to the mt-inner membrane (membrane-ETS). Electron transfer and corresponding OXPHOS capacities are classically studied in mitochondrial preparations as oxygen consumption supported by various fuel substrates undergoing partial oxidation in the mt-matrix, such as pyruvate, malate, succinate, and others.  +
A '''measurement process''' or a '''measurement''' is a set of operations to determine the value of a [[quantity]].  +
A '''measuring equipment''' is a measuring instrument, software, measurement standard, reference material or auxiliary apparatus, or a combination thereof, necessary to realize a measurement process.  +
A '''medical device''' is an instrument, apparatus, implement, machine, contrivance, implant, in vitro reagent, or other similar or related article, including a component part, or accessory which is (1) intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease, in man or other animals, or (2) intended to affect the structure or any function of the body of man or other animals, and which does not achieve any of its primary intended purposes through chemical action within or on the body of man or other animals and which is not dependent upon being metabolized for the achievement of any of its primary intended purposes.  +
'''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''']]  +
The '''membrane-bound [[electron transfer pathway]] (mET pathway)''' consists in mitochondria mainly of [[respiratory complexes]] CI, CII, electron transferring flavoprotein complex (CETF), glycerophosphate dehydrogenase complex (CGpDH), and choline dehydrogenase, with [[convergent electron flow]] at the [[Q-junction]] (Coenzyme Q), and the two downstream respiratory complexes connected by cytochrome ''c'', CIII and CIV, with oxygen as the final electron acceptor. The mET-pathway is the terminal (downstream) module of the mitochondrial [[ET pathway]] and can be isolated from the ET-pathway in [[submitochondrial particles]] (SmtP).  +
'''Mersalyl''' (C<sub>13</sub>H<sub>17</sub>HgNO<sub>6</sub>) is an inhibitor of the [[Pi symporter]].  +
Metabolic control analysis is a science focused on the understanding of metabolic regulation and control. In metabolism, the reductionist approach has allowed us to know which enzymes, metabolites and genes are involved in a metabolic pathway but this is not enough to understand how it is controlled, resulting in poor results from attempts to increase the rates of selected metabolic pathways. The control of the metabolism is the capacity to alter the metabolic state in response to an external signal. With this definition in mind, we will assess the metabolic control in terms of the strength of any of the responses to the external factor without making the assumption about the function or purpose of that response[1]. ====Bibliography:==== ::1. David Fell. Frontiers in metabolism 2. Understanding the control of metabolism. Portland Press. 1997.  +
A '''metabolic control variable''' ''X'' causes the transition between a [[background state]] Y (background rate ''Y<sub>X</sub>'') and a [[reference state]] Z (reference rate ''Z<sub>X</sub>''). ''X'' may be a stimulator or activator of flux, inducing the step change from background to reference steady state (Y to Z). Alternatively, ''X'' may be an inhibitor of flux, absent in the reference state but present in the background state (step change from Z to Y).  +
The '''meter''', symbol m, is the SI unit of the SI base quantity [[length]] ''l''. It is defined by taking the fixed numerical value of the speed of light ''c'' in vacuum to be 299 792 458 when expressed in the unit m·s<sup>−1</sup>, where the second is defined in terms of the caesium frequency Δ''ν''<sub>Cs</sub>.  +
'''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].  +
'''Mitochondrial Physiology - Historical Collection''' '''Aims''' The growing '''''MiP-Collection''''' aims at preserving scientific instruments that are of historical importance in the field of bioenergetics and mitochondrial physiology. The fast turnover of scientific equipment makes obsolete even comparatively recent instrumentation. The Oroboros O2k was the first commercial mitochondrial respirometer using a computer for data acquisition. Today, [[chart 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. You may consider to make items of scientific historical interest in mitochondrial physiology available to the ''MiP-Collection''. These items of the ''MiP-Collection'' may specifically include historically valuable * equipment and accessories, * books and symposium proceedings, * reprint collections, * pictures, slides, documents.  +
'''Mitochondrial Preservation Medium, MiP03''', developed for preservation of [[isolated mitochondria]].  +
[[File:MiPMap Publication.jpg|left|240px|MiPMap]] The project '''Mitochondrial Physiology Map''' (MiPMap) is initiated to provide an overview of mitochondrial properties in cell types, tissues and species. As part of Bioblast, '''MiPMap''' may be considered as an ''information synthase'' for '''Comparative Mitochondrial Physiology'''. Establishing a comprehensive database will require global input and cooperation. ''A comparative database of mitochondrial physiology may provide the key for understanding the functional implications of mitochondrial diversity from mouse to man, and evaluation of altered mitochondrial respiratory control patterns in health and disease'' ([[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]).  +
MiPNet is the abbreviation for the OROBOROS Journal '''Mitochondrial Physiology Network''', including chapters of the [[O2k-Manual]], [[O2k-Procedures]], [[O2k-Workshops]], and other announcements, starting with MiPNet 01 in 1996. See also »[[MiPNet]].  +
[[Image:MiPsocietyLOGO.JPG|left|200px|link=http://wiki.oroboros.at/index.php/Mitochondrial_Physiology_Society|MiP''society'']] The '''Mitochondrial Physiology Society''' (MiP) has been founded to organize MiP''conferences'', MiP''schools'', and MiP''workshops'' worldwide. MiP has been founded at the Third Conference on Mitochondrial Physiology (MiP2003, Schroecken, Austria). The MiP''society'' is an international organization, based in Europe and operating world-wide.  +
'''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. [[MiR05Cr]] = [[MiR05]] + creatine.  +
[[File:MiR05-Kit.jpg|right|180px]] Mitochondrial Respiration Medium - MiR05-Kit, 1 vial; for a final volume of 250 mL  +
Mitochondrial respiration medium, '''MiR05Cr''', developed for oxygraph incubations of mitochondrial preparations - ''[[permeabilized muscle fibers]]''. MiR05Cr = [[MiR05]] + 20 mM [[Creatine|creatine]].  +
'''Mitochondrial respiration medium, [[MiPNet14.13 Medium-MiR06|MiR06]]''', developed for oxygraph incubations of [[mitochondrial preparations]]. MiR06 = MiR05 plus [[catalase]]. MiR06Cr = MiR06 plus [[creatine]].  +
Mitochondrial respiration medium, '''MiR06Cr''', developed for oxygraph incubations of mitochondrial preparations - ''[[permeabilized muscle fibers]]''. MiR06Cr = [[MiR06]] + 20 mM [[Creatine|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.  +
[[Image:Microbalance_120 g.jpg|right|180px]]'''Microbalance''' max 120 g; 0.01 mg display; particularly for [[wet weight]] determination of [[permeabilized fibres]].  +
[[Image:Microbalance-Transport_Case.jpg|180px|right]]'''Microbalance transport case''', not suitable for shipping  +
'''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.  +
[[Image:Hamilton Syringes for Manual Titration.jpg|right|180px]]Hamilton '''Microsyringe\10 mm<sup>3</sup> 51/0.13 mm''' for manual titrations, 10 mm<sup>3</sup> volume; fixed injection needle with rounded tip: 51 mm length, 0.13 mm inner diameter.  +
[[Image:Microsyringe 100 mm3 51 0.41 mm - Kopie.JPG|right|180px]]Hamilton '''Microsyringe\100 mm<sup>3</sup> 51/0.41 mm''' for manual titrations, 100 mm<sup>3</sup> volume; fixed needle with rounded tip: 51 mm length, 0.41 mm inner diameter. It is recommended for injections of suspensions of isolated mitochondria.  +
[[Image:Microsyringe200 mm3TIP2k.JPG|right|180px]]'''Microsyringe\200 mm3\TIP2k''': Microinjection syringe for [[Titration-Injection microPump]], 200 mm<sup>3</sup> (µl), fixed injection needle with rounded tip, with spacers.  +
[[Image:Microsyringe 25 mm3 51 0.15 mm.JPG|right|180px]]Hamilton '''Microsyringe\25 mm<sup>3</sup> 51/0.15 mm''' for manual titrations, 25 mm<sup>3</sup> volume; fixed needle with rounded tip: 51 mm length, 0.15 mm inner diameter.  +
[[Image:Microsyringe 100 mm3 51 0.41 mm - Kopie.JPG|right|180px]] Hamilton '''Microsyringe\50 mm<sup>3</sup> 51/0.15 mm''' for manual titrations, 50 mm<sup>3</sup> volume; fixed needle with rounded tip: 51 mm length, 0.15 mm inner diameter.  +
[[Image:Microsyringe 500 mm3 TIP2k.JPG|right|180px]]'''Microsyringe\500 mm3\TIP2k''': Microinjection syringe for [[Titration-Injection microPump]], 500 mm<sup>3</sup> (µl), fixed injection needle with rounded tip, with spacers.  +
'''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.  +
'''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.  +
[[File:MitoAction.JPG|230px]]The mission of '''MitoAction''' is to improve quality of life for all who are affected by mitochondrial disorders through support, education and advocacy initiatives.  +
[[File:Mito Canada logo tag web2.png|200px|left|MitoCanada]]The '''MitoCanada Foundation'''. The MitoCanada Foundation is Canada’s only not-for-profit organization focused on mitochondrial disease. Since its founding in 2010, MitoCanada has dedicated over $1 million to fund the work of leading Canadian scientists and to support national awareness and support programs. The MitoCanada Foundation is committed to ensuring that those who live with mitochondrial disease are able to enjoy the best possible quality of life until there is a cure.  +
The '''MitoFit DOI Data Center''' is responsible for the provision of digital identifiers, for the storage and ensuring the persistence of the scientific objects, the provision of access, review process and maintenance of the Metadata, and quality control.  +
[[File:MitoFit Preprints.png|left|200px|link=MitoFit Preprints]] '''MitoFit Preprints''' is an Open Access preprint server for mitochondrial physiology and bioenergetics.  +
'''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.  +
'''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]].  +
[[File:MITOKIT-CII.jpg|right|180px]]'''Cell permeable prodrugs''', composed of [[MitoKit-CII/Succinate-nv]] and [[MitoKit-CII/Malonate-nv]], stimulates (Snv) or inhibits (Mnanv) mitochondrial respiration in CI-deficient human blood cells, fibroblasts and heart fibres, acting on Complex II of the electron transfer system.  +
'''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-s2  +
'''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  +
'''Mitochondrial respiration medium, MitoOx1,''' used by the Budapest groups for respirometry und Amplex Red trials.  +
'''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]].  +
'''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]]. ::::• Readily '''oxidized by superoxide''' but not by other ROS- or RNS-generating systems ::::• '''Absorption/emission maxima''': ~510/580 nm ::::• Use for '''live cell imaging''' ::::• Rapidly and selectively '''targeted to the mitochondria''' '''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.  +
'''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).  +
<br/> [[File:MIG.gif|128 px|left]] 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). [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.  +
[[File:MRS LOGO.JPG|250px|left]] The '''Mitochondria Research Society''' (MRS) is a nonprofit international organization of scientists and physicians. The purpose of MRS is to find a cure for mitochondrial diseases by promoting research on basic science of mitochondria, mitochondrial pathogenesis, prevention, diagnosis and treatment through out the world.  +
[[File:21640 - Mitochondria Targeted Therapeutics logo NEW.jpg|200px|left|Mitochondria-Targeted Drug Development]] The '''Mitochondria-Targeted Drug Development Summit''' was first established in 2021, as an online conference. Due to its success and unmatched focus, the 2<sup>nd</sup> edition returns to Boston this March 2022. This is the only industry-led meeting that unites key stakeholders under a mutual and ambitious objective of '''accelerating the discovery and development of novel drugs that target mitochondrial functions''' for chronic, primary mitochondrial diseases, muscular dystrophy, metabolic disorders, and neurodegenerative diseases. Join our speakers from '''GenSight Biologics, Abliva, Reneo Pharma, Mito BioPharma, Mitokinin''' and more with exciting networking opportunities, panel discussions and dedicated roundtables.  +
The '''mitochondrial ATP-sensitive K<sup>+</sup> channel''' (mtK<sub>ATP</sub> or mitoK<sub>ATP</sub>).  +
[[File:Meet.jpg|200px|left]] The '''Mitochondrial European Education Training''' (MEET) MEET is a project started on January 2013. MEET network is composed by a multi-partner project that intends to mobilize the critical mass of expertise, by linking partners from 8 different countries, among which 8 world-leading basic science and clinical centers of excellence, an 1 SME with direct interest in mitochondrial medicine and 3 associated partners that provide for all trainees no-scientific training. MEET is training 11 ESRs and 3 ERs coming from all over the world supervised in their research by 15 mentors and by their collaborators. MEET combine the efforts of leading clinicians with those of more basic oriented groups and will have important implications for the comprehension and treatment of mitochondria-related pathologies.  +
[[File:Mitochondrial Medicine Society.jpg|200px|left]] The '''Mitochondrial Medicine Society''' (MMS) was founded in 2000 and represents an international group of physicians, researchers and clinicians working towards the better diagnosis, management, and treatment of mitochondrial diseases.  +
The '''Mitochondrial Physiology Network''' is the on-line Oroboros journal.  +
[[File:Mito-Reseach-Guild.JPG|200px|left]] '''The Mitochondrial Research Guild''' is a special interest guild of Seattle Children's Hospital. The guild was founded by a group of families in the Seattle area that are working together to raise awareness, promote research, and improve the quality of medical care that is available to children that are dealing with the devastating and potentially life threatening effects of mitochondrial disease.  +
'''Mitochondrial metabolic competence''' is the organelle's capacity to provide adequate amounts of ATP in due time, by adjusting the mt-membrane potential, mt-redox states and the ATP/ADP ratio according to the metabolic requirements of the cell. The term '''mitochondrial competence''' is also known in a genetic context: Mammalian mitochondria possess a natural competence for DNA import. '''''[[MitoCom_O2k-Fluorometer]]''''' is a '''Mitochondrial Competence''' network, the nucleus of which is formed by the K-Regio project ''[[MitoCom_O2k-Fluorometer|MitoCom Tyrol]]''.  +
'''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>].  +
Specific '''mitochondrial density''' is ''D<sub>mtE</sub>'' = ''mtE''·''m<sub>X</sub>''<sup>-1</sup> [mtEU·kg<sup>-1</sup>]. If the amount of mitochondria, ''mtE'', is expressed as mitochondrial mass, then ''D<sub>mtE</sub>'' is the mass fraction of mitochondria in the sample. If ''mtE'' is expressed as mitochondrial volume, ''V''<sub>mt</sub>, and the mass of sample, ''m<sub>X</sub>'', is replaced by volume of sample, ''V<sub>X</sub>'', then ''D<sub>mtE</sub>'' is the volume fraction of mitochondria in the sample.  +
The '''mitochondrial free radical theory of aging''' goes back to Harman (1956) and ranks among the most popular theories of aging. It is based on postulates which are not unequivocally supported by observation (Bratic, Larsson 2013): (i) Mitochondrial ROS production increases with age caused by progressive mitochondrial dysfunction; (ii) antioxidat capacity declines with age; (iii) mutations of somatic mtDNA accumulate during aging; (iv) a vicious cycle occurs of increased ROS production caused by mtDNA mutations and degenerated mt-function, and due to ROS-induced ROS production.  +
The '''mitochondrial inner membrane''' mtIM is the structure harboring the membrane-bound [[electron transfer system]] ETS including the respiratory complexes working as [[hydrogen ion pump]]s, the mt-[[phosphorylation system]] including the hydrogen ion pump [[ATP synthase]], several substrate transporters involved in the [[electron transfer pathway]], and a variety of other ion pumps that carry [[proton]] charge (Ca<sup>2+</sup>, Mg<sup>2+</sup>). The [[protonmotive force]] is the electrochemical potential difference across the mtIM generated by the [[hydrogen ion pumps]] of the .  +
'''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 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.  +
The '''mitochondrial matrix''' (mt-matrix) is enclosed by the mt-inner membrane mtIM. The terms mitochondrial matrix space or mitochondrial lumen are used synonymously. The mt-matrix contains the enzymes of the [[tricarboxylic acid cycle]], [[fatty acid oxidation]] and a variety of enzymes that have cytosolic counterparts (e.g. [[glutamate dehydrogenase]], [[malic enzyme]]). Metabolite concentrations, such as the concentrations of fuel substrates, adenylates (ATP, ADP, AMP) and redox systems (NADH), can be very different in the mt-matrix, the mt-intermembrane space, and the cytosol. The finestructure of the gel-like mt-matrix is subject of current research.  +
The '''mitochondrial membrane potential''' difference, mtMP or Δ''Ψ''<sub>p<sup>+</sup></sub> = Δ<sub>el</sub>''F''<sub><u>''e''</u>p<sup>+</sup></sub>, is the electric part of the protonmotive [[force]], Δp = Δ<sub>m</sub>''F''<sub><u>''e''</u>H<sup>+</sup></sub>. :::: Δ<sub>el</sub>''F''<sub><u>''e''</u>p<sup>+</sup></sub> = Δ<sub>m</sub>''F''<sub><u>''e''</u>H<sup>+</sup></sub> - Δ<sub>d</sub>''F''<sub><u>''e''</u>H<sup>+</sup></sub> :::: Δ''Ψ''<sub>p<sup>+</sup></sub> = Δp - Δ''µ''<sub>H+</sub>·(''z''<sub>H<sup>+</sup></sub>·''F'')<sup>-1</sup> Δ''Ψ''<sub>p<sup>+</sup></sub> is the potential difference across the mitochondrial inner membrane (mtIM), expressed in the electric unit of volt [V]. Electric force of the mitochondrial membrane potential is the electric energy change per ‘motive’ charge or per charge moved across the transmembrane potential difference, with the number of ‘motive’ charges expressed in the unit coulomb [C].  +
The '''mitochondrial outer membrane''' is the incapsulating membrane which is osmotically not active and contains the cytochrome ''b''<sub>5</sub> enzyme similar to that found in the endoplasmatic reticulum, the translocases of the outer membrane, monoaminooxidase, the palmitoyl-CoA synthetase and carnytil-CoA transferase 1.  +
'''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.  +
Integrative measure of the dynamics of complex coupled metabolic pathways, including metabolite transport across the mt-membranes, [[TCA cycle]] function with electron transfer through dehydrogenases in the mt-matrix, membrane-bound electron transfer [[Membrane-bound ET pathway|mET-pathway]], the transmembrane proton circuit, and the phosphorylation system.  +
Mitochondrial respiratory capacity and control are compared in different '''mitochondrial respiration media''', MiRs, to evaluate the quality of MiRs in preserving mitochondrial function and to harmonize results obtained in various studies using different MiRs. In some cases alterations of the formulation are incorporated to optimize conditions for the simultaneous measurement of multiple parameters, e.g. respiration and [[ROS]] production.  +
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.  +
The '''transcription factor A''' is a gene that encodes a mitochondrial transcription factor that is a key activator of mitochondrial transcription as well as a participant in mitochondrial genome replication. TFAM is downstream of [[Peroxisome proliferator-activated receptor gamma coactivator 1-alpha|PGC-1alpha]].  +
Autophagy (self-eating) in general is viewed as a degradation process which removes non-essential or damaged cellular constituents. » [[Mitophagy#Mitochondrial_mitophagy | '''MiPNet article''']]  +
A '''model''' regarding databases is the representation of a real world object in a computer understandable language. A '''model''' can be defined by the structure of its [[dataset]] and the relations to other '''models'''.  +
'''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. 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.  +
The mole [mol] is the SI base unit for the [[amount |amount of substance]] of a system that contains 6.02214076·10<sup>23</sup> specified elementary entities (see [[Avogadro constant]]). The elementary entities must be specified and may be atoms, molecules, ions, electrons, other particles, or specified groups of such particles.  +
'''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.  +
[[File:Motic Microscope.jpg|right|180px]]'''Motic Microscope SMZ-171 TLED''': for preparation of permeabilized fibres; compact and light stereo microscope, Greenough optical system, switching power supply for use worldwide (100-240V); including auxiliary ESD objective 2.0X(38.6mm).  +
[[File:Motive entities.png|right|300px|From [[Gnaiger 2020 BEC MitoPathways]]]]. A '''motive entity''' ''X''<sub>tr</sub> is an entity involved in a transformation including spacial transfer. Motive entities (transformants) are expressed in different [[motive unit]]s [MU] depending on the energy transformation under study and the chosen [[format]]. [[Flow]]s are defined as advancement in terms of stoichiometric motive entities per time. Isomorphic [[force]]s are partial derivatives of Gibbs energy per advancement. Ions carrying a positive charge (cations) or negative charge (anions) may be considered as a paradigm of motive entities, since Faraday did not coin but introduced the term 'ion', which is old Greek for 'going' — advancing to the cathode or anode and thus generating an electric [[current]].  +
The '''motive unit''' [MU] is the variable SI unit in which the [[motive entity]] (transformant) of a transformation is expressed, which depends on the energy transformation under study and on the chosen [[format]]. Fundamental MU for electrochemical transformations are: * MU = x, for the particle or molecular format, <u>''N''</u> * MU = mol, for the chemical or molar format, <u>''n''</u> * MU = C, for the electrical format, <u>''e''</u>; For the [[protonmotive force]] the motive entity is the proton with charge number ''z''=1. The protonmotive force is expressed in the electrical or molar format with MU J/C=V or J/mol=Jol, respectively. The conjugated flows, ''I'', are expressed in corresponding electrical or molar formats, C/s = A or mol/s, respectively. The [[charge number]], ''z'', has to be considered in the conversion of motive units (compare Table below), if a change not only of units but a transition between the entity [[elementary charge]] and an entity with charge number different from unity is involved (''e.g.'', O<sub>2</sub> with ''z''=4 in a redox reaction). The ratio of elementary charges per reacting O<sub>2</sub> molecule (''z''<sub>O<small>2</small></sub>=4) is multiplied by the elementary charge (''e'', coulombs per proton), which yields coulombs per O<sub>2</sub> [C∙x<sup>-1</sup>]. This in turn is multiplied with the [[Avogadro constant]], ''N''<sub>A</sub> (O<sub>2</sub> molecules per mole O<sub>2</sub> [x∙mol<sup>-1</sup>]), thus obtaining for ''zeN''<sub>A</sub> the ratio of elementary charges [C] per amount of O<sub>2</sub> [mol<sup>-1</sup>]. The conversion factor for O<sub>2</sub> is 385.94132 C∙mmol<sup>-1</sup>.  +
The mark mode is active by default, can be selected in the menu or by [Ctrl+M]. If '''Mouse control: Mark''' is enabled, specific sections of the experiment can be marked in each plot. Usually, marks are set on the plot for oxygen concentration for calibration, whereas marks on the plot for oxygen flux are set for exporting the median or average of flux to a table. »More details: [[Marks - DatLab]].  +
Select '''Mouse Control: Zoom''' in the Graph-menu or press [Ctrl+Z].  +
The [[Mitochondrial outer membrane| '''mitochondrial outer membrane''']]  +
[[File:30420-24 MultiSensorConnector.JPG|right|180px]] '''MultiSensor-Connector''': for separate reference electrode and [[ISE]]; only for O2k-Series B and Series C with MultiSensor electronic upgrading before 2011.  +
[[File:30430--24 NO-Attachment.JPG|right|180px]] '''MultiSensor-Preamplifier 1/100''': Required only for O2k-Series A-C, for application of NO (or other amperometric) sensors (single chamber mode of application).  +
Similarly to the [[least squares method]], '''multicomponent analysis''' makes use of all of the data points of the spectrum in order to analyse the concentration of the component parts of a measured spectrum. To do this, two or more reference spectra are combined using iterative statistical techniques in order to achieve the best fit with the measured spectrum.  +
'''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.  +
N
'''N-ethylmaleimide''' is an organic compound that is derived from maleic acid and blocks endogenous Pi transport.  +
[[File:SUIT-catg N.jpg|right|300px|N-junction]] The '''N-junction''' is a junction for [[convergent electron flow]] in the [[electron transfer pathway]] (ET-pathway) from type N substrates (''further details'' »[[N-pathway control state]]) through the mt-[[NADH]] pool to [[Complex I]] (CI), and further transfer through the [[Q-junction]] to [[Complex III]] (CIII). Representative type N substrates are pyruvate (P), glutamate (G) and malate (M). The corresponding dehydrogenases ([[Pyruvate dehydrogenase |PDH]], [[Glutamate dehydrogenase |GDH]], [[Malate dehydrogenase |MDH]]) and some additional TCA cycle dehydrogenases ([[isocitrate dehydrogenase]], [[oxoglutarate dehydrogenase]] generate NADH, the substrate of [[Complex I]] (CI). The concept of the N-junction and [[F-junction]] provides a basis for defining [[categories of SUIT protocols]] based on [[Electron-transfer-pathway state]]s.  +
The '''N/NS [[pathway control ratio]]''' is obtained when succinate is added to N-linked respiration in a defined coupling state. N and NS are abbreviations for respiration in the [[N-pathway control state]] (with pyruvate, glutamate, malate, or other ETS competent N-linked substrate combinations) and the [[NS-pathway control state]] (N in combination with succinate). NS indicates respiration with a cocktail of substrates supporting the N- and S-pathways.  +
The '''N/S [[pathway control ratio]]''' is obtained from SUIT protocols when the [[N-pathway control state |N-pathway flux]] and [[S-pathway control state |S-pathway flux]] are measured in the same [[coupling control state]]. The N/S pathway control ratio 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 reference state, if mitochondria are studied with respect to N-pathway injuries.  +
'''NAD<sup>+</sup>''' and '''NADH''': see [[Nicotinamide adenine dinucleotide]].  +
'''NADH calibration'''  +
[[File:SUIT-catg N.jpg|right|300px|N-junction]] The '''NADH electron transfer-pathway state''' (N) is obtained by addition of [[NADH]]-linked substrates (CI-linked), feeding electrons into the [[N-junction]] catalyzed by various mt-dehydrogenases. N-supported flux is induced in mt-preparations by the addition of NADH-generating substrate combinations of [[pyruvate]] (P), [[glutamate]] (G), [[malate]] (M), [[oxaloacetate]] (Oa), [[oxoglutarate]] (Og), [[citrate]], [[hydroxybutyrate]]. These N-junction substrates are (indirectly) linked to [[Complex I]] by the corresponding dehydrogenase-catalyzed reactions reducing NAD<sup>+</sup> to NADH+H<sup>+</sup> + H<sup>+</sup>. The most commonly applied N-junction substrate combinations are: [[PM]], [[GM]], [[PGM]]. The [[malate-anaplerotic pathway control state]] (M alone) is a special case related to [[malic enzyme]] (mtME). The [[glutamate-anaplerotic pathway control state]] (G alone) supports respiration through [[glutamate dehydrogenase]] (mtGDH). Oxidation of [[tetrahydrofolate]] is a NAD(P)H linked pathway with formation of formate. In mt-preparations, succinate dehydrogenase (SDH; [[CII]]) is largely substrate-limited in N-linked respiration, due to metabolite depletion into the incubation medium. The residual involvement of S-linked respiration in the N-pathway control state can be further suppressed by the CII-inhibitor [[malonic acid]]). In the N-pathway control state [[Electron-transfer-pathway state|ET pathway level 4]] is active.  +
Reduced nicotinamide adenine dinucleotide ([[NADH]]) is amongst the [[intrinsic fluorophores]] and can be used as an intracellular indicator of hypoxia. The excitation wavelength is 340 nm and emission is at 460 nm.  +
[[Image:NADH-Module - 12700-01.jpg|right|180px]] The '''NADH-Module''', is a component of the [[NextGen-O2k]] for simultaneous measurement of oxygen consumption and NAD(P)H autofluorescence. NAD(P)H autofluorescence is used to evaluate the redox state of the NAD(P)H-pool. The NADH-Module incorporates an UV light and [[NADH-Sensor]]s which include a photodiode and specific filters.  +
[[Image:NADH sesnor 003.png|right|180px]] The '''NADH-Sensor''' has been developed as a part of the [[NADH-Module]] for simultaneous monitoring of oxygen consumption and [[NADH redox state]]. The NADH-Sensor is composed of a photodiode and equipped with three supergel R370 Italian blue filters (Rosco, US).  +
'''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]].  +
The '''NS-N [[pathway control efficiency]]''', ''j''<sub>NS-N</sub> = 1-N/NS, expresses the fractional change of flux when succinate is added to the [[N-pathway control state]] in a defined [[coupling-control state]].  +
The '''NS-S pathway control efficiency''' expresses the relative stimulation of succinate supported respiration (S) by NADH-linked substrates (N), with the [[S-pathway control state]] as the [[background state]] and the [[NS-pathway control state]] as the [[reference state]]. In typical [[SUIT protocol]]s with [[Electron-transfer-pathway state |type N and S substrates]], flux in the [[NS-pathway control state]] NS is inhibited by [[rotenone]] to measure flux in the [[S-pathway control state]], S(Rot) or S. Then the NS-S pathway control efficiency in the ET-coupling state is ''j''<sub>(NS-S)''<sub>E</sub>''</sub> = (NS''<sub>E</sub>''-S''<sub>E</sub>'')/NS''<sub>E</sub>'' The NS-S pathway control efficiency expresses the fractional change of flux in a defined [[coupling-control state]] when inhibition by [[rotenone]] is removed from flux under S-pathway control in the presence of a type N substrate combination. Experimentally rotenone Rot is added to the NS-state. The reversed protocol, adding N-substrates to a S-pathway control background does not provide a valid estimation of S-respiration with succinate in the absence of Rot, since [[oxaloacetate]] accumulates as a potent inhibitor of [[succinate dehydrogenase]] CII.  +
[[File:SUIT-catg NS.jpg|right|300px|NS-pathway control]] '''NS-pathway control''' is exerted in the NS-linked substrate state (flux in the NS-linked substrate state, NS; or Complex I<small>&</small>II, CI<small>&</small>II-linked substrate state). NS-OXPHOS capacity provides an estimate of physiologically relevant maximum mitochondrial respiratory capacity. NS is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]] in combination with [[succinate]] ([[Succinate pathway]]; S). Whereas NS expresses substrate control in terms of substrate types (N and S), CI<small>&</small>II defines the same concept in terms of convergent electron transfer to the [[Q-junction]] (pathway control). '''NS''' is the abbreviation for the combination of [[NADH]]-linked substrates (N) and [[succinate]] (S). This physiological substrate combination is required for partial reconstitution of [[TCA cycle]] function and convergent electron-input into the [[Q-junction]], to compensate for metabolite depletion into the incubation medium. NS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria.  +
[[Image:SUIT-catg_FNSGp.jpg|right|400px|Convergent electron flow]] '''MitoPathway control state:''' NSGp :[[Pyruvate]] &/or [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]]. '''SUIT protocol:''' [[SUIT-038]] This substrate combination supports convergent electron flow to the [[Q-junction]].  +
'''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.  +
A '''National Standards Body''' is the national member of the [[International Organization for Standardization]] (ISO).  +
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>.  +
[[Image:NetP over E.jpg|60 px|net P/E control ratio]] The '''net P/E control ratio''', (''P-L'')/''E'', expresses the [[OXPHOS capacity]] (corrected for [[LEAK respiration]]) as a fraction of [[ET capacity]]. The net ''P/E'' control ratio remains constant, if [[dyscoupling]] is fully compensated by an increase of OXPHOS capacity and [[net OXPHOS capacity P-L]], ''P-L'', is maintained constant.  +
[[Image:NetR over E.jpg|60 px|net R/E control ratio]] The '''net ''R/E'' control ratio''', (''R-L'')/''E'', expresses phosphorylation-related respiration (corrected for [[LEAK respiration]]) as a fraction of [[ET capacity]]. The net ''R/E'' control ratio remains constant, if [[dyscoupling]] is fully compensated by an increase of ROUTINE respiration and [[R-L net ROUTINE capacity]], ''R-L'', is maintained constant.  +
[[File:Neurocon LOGO.JPG|200px|left]] '''Neurocon''' is an Indian society organizing international conferences on neurodegenerative and neurodevelopmental diseases.  +
'''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, :::: RH<sub>2</sub> + NAD<sup>+</sup> → NADH + H<sup>+</sup> + R 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]].  +
Nigericin is a H<sup>+</sup>/K<sup>+</sup> antiporter, which allows the electroneutral transport of these two ions in opposite directions across the mitochondrial inner membrane following the K<sup>+</sup> concentration gradient. In the presence of K<sup>+</sup>, nigericin decreases pH in the mitchondrial matrix, thus, almost fully collapses the transmembrane ΔpH, which leads to the compensatory increase of the electric [[Mitochondrial membrane potential|mt-membrane potential]]. Therefore, it is ideal to use to dissect the two components of the [[Protonmotive force|protonmotive force]], ΔpH and [[Mitochondrial membrane potential|mt-membrane potential]]. It is recommended to use the lowest possible concentration of nigericin, which creates a maximal mitochondrial hyperpolarization. In the study of [[Komlodi 2018 J Bioenerg Biomembr]], 20 nM was applied on brain mitochondria isolated from guinea-pigs using 5 mM [[Succinate|succinate]] in the [[LEAK respiration|LEAK state]] which caused maximum hyperpolarisation, but did not fully dissipate the transmembrane ΔpH. Other groups (Selivanov et al 2008; Lambert et al 2004), however, used 100 nM nigericin, which in their hands fully collapsed transmembrane ΔpH using succinate as a respiratory substrate on isolated rat brain and skeletal muscle in the [[LEAK respiration|LEAK state]].  +
'''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).  +
In [[fluorometry]] and [[spectrophotometry]], '''noise''' can be attributed to the statistical nature of the photon emission from a [[light source]] and the inherent noise in the instrument’s electronics. The former causes problems in measurements involving samples of analytes with a low [[extinction coefficient]] and present only in low concentrations. The latter becomes problematic with high [[absorbance]] samples where the light intensity emerging from the sample is very small.  +
[[File:E.jpg |link=ET capacity]] '''Noncoupled respiration''' is distinguished from general (pharmacological or mechanical) [[uncoupled respiration]], to give a label to an effort to reach the state of maximum uncoupler-activated respiration without inhibiting respiration. Noncoupled respiration, therefore, yields an estimate of [[ET capacity]]. Experimentally uncoupled respiration may fail to yield an estimate of ET capacity, due to inhibition of respiration above optimum uncoupler concentrations or insufficient stimulation by sub-optimal uncoupler concentrations. Optimum uncoupler concentrations for evaluation of (noncoupled) ET capacity require inhibitor titrations ([[Steinlechner-Maran 1996 Am J Physiol Cell Physiol]]; [[Huetter 2004 Biochem J]]; [[Gnaiger 2008 POS]]). Noncoupled respiration is maximum [[electron flow]] in an open-transmembrane proton circuit mode of operation (see [[ET capacity]]). » [[#Is_respiration_uncoupled_-_noncoupled_-_dyscoupled.3F |'''MiPNet article''']]  +
A '''norm''' is a rule that is enforced by members of a community.  +
'''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.  +
'''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]]. » [[Normothermia#Normothermia:_from_endotherms_to_ectotherms | '''MiPNet article''']]  +
[[File:Oxia terms.png|right|300px|link=https://www.oroboros.at/index.php/product/oxia/|Oxia]] '''Normoxia''' is a reference state, frequently considered as air-level oxygen pressure at sea level (c. 20 kPa in water vapor saturated air) as environmental normoxia. Intracellular tissue normoxia is variable between organisms and tissues, and intracellular oxygen pressure is frequently well below air-level ''p''<sub>O<sub>2</sub></sub> as a result of cellular (mainly mitochondrial) oxygen consumption and oxygen gradients along the respiratory cascade. Oxygen pressure drops from ambient normoxia of 20 kPa to alveolar normoxia of 13 kPa, while extracellular normoxia may be as low as 1 to 5 kPa in solid organs such as heart, brain, kidney and liver. Pericellular ''p''<sub>O<sub>2</sub></sub> of cells growing in monolayer cell cultures may be [[hypoxic]] compared to tissue normoxia when grown in ambient normoxia (95 % air and 5 % CO<sub>2</sub>) and a high layer of culture medium causing oxygen diffusion limitation at high respiratory activity, but pericellular ''p''<sub>O<sub>2</sub></sub> may be effectively [[hyperoxic]] in cells with low respiratory rate with a thin layer of culture medium (<2 mm). Intracellular oxygen levels in well-stirred suspended small cells (5 - 7 mm diameter; endothelial cells, fibroblasts) are close to ambient ''p''<sub>O<sub>2</sub></sub> of the incubation medium, such that matching the experimental intracellular ''p''<sub>O<sub>2</sub></sub> to the level of intracellular tissue normoxia requires lowering the ambient ''p''<sub>O<sub>2</sub></sub> of the medium to avoid hyperoxia.  +
A '''Notified Body''' is an organisation designated by an EU country to assess the conformity of certain products before being placed on the market.  +
Nuclear receptors are ligand-dependent transcription factors.  +
'''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]].  +
A '''number''' ''N'' (or ''n'') is a [[count]] ''N''<sub>''X''</sub> [x] divided by the [[elementary entity]] ''U''<sub>''X''</sub> [x]. ''X'' must represent the same entity in both occurences. The elementary unit [x] cancels in the division by simplification, such that numbers (for example, numbers 8 or 24) are abstracted from the counted entity ''X''. The concept of number is tightly entangled with units, counts and entities.  +
A '''numeral''' is the symbol representing a specific [[number]]. A numeral is the figure of a number, with different notation types used as a figure (VIII and 8 for Roman and Arabic numerals; 八 and 捌 for practical and financial Chinese). A numeral may consist of one or more characters or digits. 60 and 60.00 are different numerals consisting of two and four digits, respectively, which represent the same number sixty. Sixty is the name of the number 60, with the meaning 'number 60'. ''N'' is not a numeral but a symbol representing the entity 'number'. The equation ''N''=60 assignes the numerical value 60 to the entity 'number'. The numeral 60 is a symbol for a pure number that equals 6 times 10 (or 2 times 30; or 1 times 60).  +
O
[[File:34310-02.jpg|right|180px]]'''O-ring sV\[[Viton]]\9.5x1 mm''', for [[Stopper sV\black PEEK\conical Shaft\central Port | PEEK Stopper sV]], 2 are mounted on each PEEK Stopper sV, box of 8 as spares.  +
[[File:O-ringViton12.5x1 mm.jpg|right|180px]]'''O-ring\[[Viton]]\12.5x1 mm''', for PVDF or PEEK O2k-Stoppers (2-mL O2k-Chamber), box of 8 as spares.  +
'''O-ring\[[Viton]]\12x1 mm''', for PVDF or PEEK O2k-Stoppers, box of 4 as spares. 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]].  +
'''O-ring\[[Viton]]\16x2 mm''', mounted on the [[O2k-Chamber Holder sV]].  +
[[File:Viton O-ring 18x2.jpg|right|180px|link=]] '''O-ring\[[Viton]]\18x2 mm''', mounted on the [[O2k-Chamber Holder]].  +
[[File:POS O-ring for sensor head or POS mounting tool.jpg|right|180px]]'''O-ring\Viton\6x1 mm''' for [[POS-Mounting Tool]].  +
[[File:POS O-ring for sensor head or POS mounting tool.jpg|right|180px]]'''O-ring\Viton\8x1 mm''': for [[OroboPOS]] sensor head. Replaces the O-ring\Viton\9x1 mm  +
[[Image:O2-Zero Powder.jpg|right|180px]]'''O2-Zero Powder''', [[dithionite]] (Na<sub>2</sub>S<sub>2</sub>O<sub>4</sub>), for zero-oxygen calibration of the [[OroboPOS]].  +
'''O2k''' - [[Oroboros O2k]]: the modular system for [[high-resolution respirometry]].  +
The '''O2k-chamber volume calibration''' has to be done before getting started with the [[Oroboros O2k]] to guarantee a standard [[chamber volume]] of 2.0 mL.  +
Default channel labels can now be changed, and new labels set by the user. E.g., rename the Amperometric channel, Amp, to 'H2O2' for H2O2 measurements by fluorometry; rename the potentiometric channel, pX, to TPP+ for mitochondrial membrane measurements with the O2k-pH ISE-Module. For changing the label, go to menu [Oroboros O2k]\O2k channel labels and set the new channel label as desired.  +
Configure or modify the settings for the O2k sensors In '''O2k configuration''', channels (amperometric and potentiometric) can be switched on/off by selecting the according tick box. The Power-O2k number (P1, P2, ..) and numbers for O2 sensors, Amp sensors, pX electrodes and pX reference electrodes are entered or edited here. With the [[O2k-FluoRespirometer]] (O2k-Series H and higher), the serial numbers of the [[Smart Fluo-Sensor|Smart Fluo-Sensors]] are shown automatically under [Amperometric, Amp]. The O2k configuration window pops up when DatLab starts and "Connect to O2k" is pressed for the first time. It is also accessible from the menu "Oroboros O2k" and from within the [[O2k control]] and [[Mark statistics - DatLab|Mark statistics]] windows.  +
After selection of an O2k setup in the '''O2k control''' [F7] window, followed by a left-click '''Send to O2k''', only the following control functions are routinely required during experimental operations.  +
The O2k control panel allows for quick access of O2k instrument settings. It covers the right side of the graphical user interface of DatLab 8. If a DatLab protocol is active, the protocol panel ist shown instead, a tab at the right side allows to switch between O2k control panel and protocol panel.  +
'''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).  +
[[File:Seires number H-Seires.png|right|200 px|The serial number of each O2k is shown on a sticker at the rear of the O2k.]] The '''O2k series''' is specified as the capital letter in the O2k serial number of the [[Oroboros O2k]]. A serial number G-#### or H-#### denotes an Oxygraph from the G or H series, while A-#### denotes an O2k from the A series. With [[DatLab]] running real-time connected to the O2k, the serial number of the currently connected O2k is displayed: (1) in the right corner of the [[O2k status line|status line]], besides the DatLab version number (bottom), and (2) in windows [[O2k control]] [F7] and [[O2k configuration]].  +
The '''O2k signal line''' is underneath the [[O2k status line]]. It shows, depending on the [[O2k series]], on the left side the O2k number, the time of the experiment, the oxygen raw signal of each chamber, the [[block temperature]], the [[barometric pressure]], the Peltier power, the recorded amperometric and potentiometric raw signal, the enviromental (room) temperature and the signal from internal sensors recording the humidity and temperature of the electronics. On the right side of the O2k signal line the current [[User code - DatLab|user]], the DatLab version and the [[O2k serial number]] are displayed.  +
Three electronic '''channel types''' are available in the [[O2k-MultiSensor |O2k-MultiSensor system]]. All channels are available twofold (dual-data), for O2k-Chambers A (left) and B (right), based on numerical signals sent at a fixed data sampling time interval (default: 2 s; range 0.2 s to >10 s).  +
'''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]].  +
The '''O2k-Accessory Box''' contains components of the [[POS-Service Kit]] and the [[O2k-Assembly Kit]] and is shipped with the O2k.  +
'''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]].  +
The '''O2k-Assembly Kit''' is a component of the [[Oroboros O2k]], consisting of 2 [[Stirrer-Bar\white PVDF\15x6 mm|PVDF Stirrer-Bars]], 2 [[PEEK]] O2k-Stoppers, [[OroboPOS-Connector]]s for O2k-series A-I and NextGen-O2k series XA (attached to the [[O2k-Main Unit]]) and cables (power supply, USB-connection). Several components of the O2k-Assembly Kit are included in the [[O2k-Accessory Box]] either for shipment or for storage.  +
'''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.  +
[[Image:Microbalance_Set.jpg|180px|right]]''''' Microbalance Mettler-Toledo'''''  +
'''4'''#### '''''O2k-Catalogue: O2k-Modules'''''. O2k-Modules can be obtained with the O2k or added later, and can be simply installed by the user.  +
[[Image:Chamber holder PVDF Stopper.jpg|right|180px]]'''O2k-Chamber Holder''' (blue POM) for PVDF or PEEK stoppers (2-mL [[O2k-chamber]]), with [[O-ring\Viton\18x2 mm]] and [[V-ring\30-35-4.5 mm]]. Two units of this item are standard components mounted on the [[O2k-Main Unit]].  +
[[File:32100-01.jpg|right|180px]]'''O2k-Chamber Holder sV''' (black POM) for PVDF or PEEK stoppers (0.5-mL [[O2k-chamber]]), with [[O-ring\Viton\16x2 mm]] and [[V-ring\30-35-4.5 mm]].  +
[[File:33100-01.jpg|right|180px]]'''O2k-Chamber sV''': 12 mm inner diameter, Duran® glass polished, with standard operation volume ''V'' of 0.5 mL.  +
[[Image:O2k-Dissection-Set.jpg|180px|right]]'''O2k-Dissection Set''': for [[tissue preparation]], set of 4 pairs of stainless steel, antimagnetic forceps and a pair of scissors.  +
'''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]].  +
[[Image:Fluorescence-Control Unit lettered.jpg|180px|right]] The '''O2k-Fluo LED2-Module''' is a component of the O2k-Fluorometer (O2k-Series D to G). It is an amperometric add-on module to the [[O2k-Core]] (O2k-Series D to G), adding a new dimension to high-resolution respirometry. Optical sensors are inserted through the front window of the O2k-glass chambers, for measurement of hydrogen peroxide production (Amplex® UltraRed), ATP production (Magnesium Green™), mt-membrane potential (Safranin, TMRM, Rhodamine 123), Ca<sup>2+</sup> (Calcium Green™), and numerous other applications open for O2k-user innovation.  +
The '''O2k-Fluo Smart-Module''' is an amperometric add-on module to the [[Startup_O2k-Respirometer| O2k-Respirometer]], adding a new dimension to high-resolution respirometry. Optical sensors are inserted through the front window of the O2k-glass chambers, for measurement of hydrogen peroxide production (Amplex® UltraRed), ATP production (Magnesium Green™), mt-membrane potential (Safranin, TMRM), Ca<sup>2+</sup> (Calcium Green™), and numerous other applications open for O2k-user innovation. ::: » [[MiPNet28.09 O2k-Fluo Smart-Module manual]]  +
[[Image:O2k-Fluorometer.jpg|200px|right|O2k-FluoRespirometer]] The Oroboros '''O2k-FluoRespirometer''' - the experimental system complete for [[high-resolution respirometry]] (HRR), including fluorometry, the [[TIP2k-Module |TIP2k]] and the [[O2k-sV-Module]] allowing simultaneous monitoring of oxygen consumption together with either ROS production (AmR), mt-membrane potential (TMRM, Safranin and Rhodamine 123), Ca<sup>2+</sup> (CaG) or ATP production (MgG). The '''O2k-FluoRespirometer''' supports all add-on [[O2k-Catalogue: O2k-Modules |O2k-Modules]]: [[O2k-TPP+ ISE-Module]], [[O2k-pH ISE-Module]], [[O2k-NO Amp-Module]], enabling measurement of mt-membrane potential with ion sensitive electrodes (ISE for TPP<sup>+</sup> or TPMP<sup>+</sup>) or pH.  +
[[Image:O2k-Fluorometer Series G.jpg|200px|right|O2k-Fluorometer Series G]] '''O2k-Fluorometer Series G - Former Series''' (up to 2017-July) - the experimental system complete for [[high-resolution respirometry]] (HRR) combined with [[fluorometry]]. The O2k-Fluorometer includes the [[O2k-Core]], [[O2k-Fluo LED2-Module]] and [[TIP2k-Module |TIP2k]], and supports all other add-on O2k-Modules of the [[Oroboros O2k]]. The O2k is a sole source apparatus with no other instruments meeting its [[MiPNet06.05 Test Experiments on O2k-Specifications | test experiments on O2k-Specifications]].  +
[[Image:Fuses mains.jpg|right|180px]]'''O2k-Fuse Power Plug\M2.5 A\5x20 mm''': This item is a standard component of the [[O2k-Assembly Kit]] ([[O2k-FluoRespirometer]]), mounted on the socket for the [[O2k-Main Power Cable]], at the rear panel of the [[O2k-Main Unit]].  +
The '''O2k-Main Basic''' is an integral element of the [[O2k-Main Unit]]. The Oroboros O2k Main Basic has the following components: *Stainless-Steel Housing *Switching power supply *Microprocessor for integrated control, A/D converters and data handling *Copper-Block with windows to 2 O2k-Chambers *2 Amperometric OroboPOS Plugs *TIP2k socket, providing the basis for add-on of the [[TIP2k]] *2 Potentiometric Plugs for ion sensitive electrodes (ISE: TPP+, Ca2+; pH), providing the basis for add-on of the [[O2k-MultiSensor]] Modules *2 Amperometric Plugs, providing the basis for add-on of the [[O2k-Fluo LED2-Module]] or NO (H<sub>2</sub>S) sensors. *USB-Port for connection with DatLab (PC or laptop not included)  +
'''O2k-Main Power Cable''', for connecting the main unit to the power supply.  +
[[Image:O2k-Main Power Cable 120 V US-CA.JPG|180px|right]]'''O2k-Main Power Cable\120 V\US-CA''', USA and Canada (120 V).  +
[[Image:O2k-Main_Power_Cable_230_V_AU-NZ.JPG|180px|right]]'''O2k-Main Power Cable\AU-NZ''', Australia and New Zealand (230 V).  +
[[Image:O2k-Main Power Cable 230 V Europe.JPG|right|180px]]'''O2k-Main Power Cable\230 V\Europe'''.  +
The '''O2k-Main Unit''' is a component of the [[O2k-Core]]. The O2k-Main Unit consists of functionally defined, integral elements, the ([[O2k-Main Basic]], [[O2k-Peltier Temperature Control]], two [[O2k-Electromagnetic Stirrer Twin-Control]] units, two [[O2k-Amperometric OroboPOS Twin-Channel]]s, [[O2k-Barometric Pressure Transducer]]), which cannot be obtained separately.  +
When one (or more) analytical parameters are monitored simultaneously with oxygen concentration and oxygen flux in the [[Oroboros O2k]], this is an '''O2k-MultiSensor''' application. The [[O2k-FluoRespirometer]] fully supports the O2k-MultiSensor Modules. For some O2k-MultiSensor applications it is necessary to introduce one or more additional sensors into the chamber through a MultiSensor stopper. Optical applications require the standard black stoppers.  +
[[Image:O2k-NO Amp-Module.jpg|right|180px]]'''O2k-NO Amp-Module''': NO-sensor compatability pack an amperometric add-on for O2k-MultiSensor application The NO sensor is not included.  +
[[Image:O2k-Network.png|left|100px|O2k-Network Reference Laboratory]] '''O2k-Network Reference Laboratories''' build a WorldWide network on [[high-resolution respirometry]] and mitochondrial physiology, the Oroboros [[O2k-Network]].  +
[[O2k-Open Support]] aims at providing expert help quickly. Please, help us sharing our support communication openly with the scientific community.  +
'''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.  +
[[Image:O2k-Info.png|right|30px|link=Oroboros O2k]]'''O2k versus multiwell respirometer''': '''O2k''' stands for Oroboros O2k and '''[[high-resolution respirometry]]''', meeting powerful quality criteria securing '''high output''' and pioneering state-of-the-art [[Gnaiger_2012_MitoPathways|comprehensive OXPHOS analysis]] of substrate control and coupling control of mitochondrial function. 'High throughput' stands for disposable multiwell systems - expensive, with limited scope and extremely high running costs. In respirometry, high throughput is not equivalent to high output. ''If you’re using a biased instrument, it doesn’t matter how many measurements you take – you’re aiming at the wrong target'' ([[Silver 2012 Penguin Press]]).  +
[[File:TPP new.jpg|180px|right]]'''O2k-TPP<sup>+</sup> ISE-Module''': Potentiometric ion-selective electrodes for measurement of mitochondrial membrane potential  +
[[Image:O2k-Titration Set.JPG|right|180px]] The '''O2k-Titration Set''' consists of Hamilton microsyringes (6 x 10 mm<sup>3</sup> and 3 spare plungers, 6 x 25 mm<sup>3</sup>, 1 x 50 mm<sup>3</sup>, 1 x 100 mm<sup>3</sup>, 1 x 500 mm<sup>3</sup>; fixed needles with rounded tips), provided in the [[Syringe Storage Box]] with [[Syringe Labels]], a set of two [[Syringe Racks]] with [[Syringe Collars]], and a set of two [[Tube Racks]].  +
[[File:Oroboros-USB-flash-drive.JPG|right|120px]] The '''O2k-USB Flash Drive''' is a component of the [[Oroboros O2k]] containing: [[DatLab]], O2k-Manual, O2k-Protocols, O2k-Publications, and info on O2k-Workshops.  +
O2k-Virtual support includes 8 individual hours. Via a live video link, Oroboros experts guide you step-by-step on topics of your choice, such as O2k instrumental setup and service of the polarographic oxygen sensors (POS) for instrumental quality control, an essential component of HRR. This offers the opportunity to analyze and discuss your experimental [[DatLab]] files obtained with your O2k with the bioenergetics experts of Oroboros. It offers flexibility to participants and gives the option to choose virtual sessions that best fit individual needs.  +
[[Image:O2k-Window Frame.JPG|right|180px]] '''O2k-Window Frame''': blue POM, with thread for fixation on the [[O2k-Main Unit]], to be removed only for rare cleaning purposes and for front fixation of the [[Fluorescence-Control Unit]], using the [[O2k-Window Tool]].  +
[[Image:O2k-Window Tool.jpg|180px|right]] '''O2k-Window Tool''' for removing the blue [[O2k-Window Frame]] from the [[O2k-Main Unit]], for rare cleaning purposes and for front fixation of the [[Fluorescence-Control Unit]].  +
[[File:O2k-Chamber.jpg|right|180px]] '''O2k-Chamber''': Duran® glass polished, with standard operation volumes (''V'') of 2.0 mL or 0.5 mL (small chamber volume in the [[O2k-sV-Module]], 12 mm inner diameter). The optical properties of Duran® allow application of fluorometric sensors ([http://www.duran-group.com/en/about-duran/duran-properties/optical-properties-of-duran.html Duran® optical properties]).  +
[[File:PH new.jpg|right|180px]]'''O2k-pH ISE-Module''': two pH electrodes and reference electrodes and accessories  +
[[File:11200-01.jpg|180px|right]] The '''O2k-sV-Module''' is the O2k small-volume module, comprised of two Duran® glass chambers of 12 mm inner diameter specifically developed to perform high-resolution respirometry with reduced amounts of biological sample, and all the components necessary for a smaller operation volume ''V'' of 0.5 mL. The current DatLab version is included in the delivery of this revolutionary module.  +
The '''O2k-ticket system''' is a customer support platform based on Zammad. This system automatically attributes an unique Ticket number (which is visible on the subject of your e-mail) to each received customer inquiry. For an easy follow-up, all the related correspondence is collected under this Ticket number. * Contact us: '''[email protected]''' In order to provide a helpful and reliable support regarding your O2k/equipment, we suggest to include in your inquiries: * your affiliation and your O2k-serial number - ''See'': [[O2k_series]] * DLD file(s) with your reported issue accompanied by a brief explanation.  +
Leading preprint service providers use '''OSF Preprints''' as an open source infrastructure to support their communities. You should upload your preprint to whichever preprint server best fits your topic and the community that you would like to reach. If there isn’t a community-driven preprint server for your discipline, OSF Preprints is available for any discipline. Currently, you can only share your preprint on one community preprint server. It’s on our roadmap to allow users to submit a preprint to multiple community preprint servers. However, to improve discoverability across communities, all preprints shared on OSF Preprints and community preprint servers are indexed and searchable via osf.io/preprints. Right now, it is not possible to add subjects. However, you can add tags with additional subject areas or keywords to improve discoverability. COS supports communities operating their own branded community preprint services using OSF Preprints as the backend.OSF is based in Charlottesville, VA, USA.  +
The '''OXPHOS International''' web portal is a repository of information useful to scholars studying mitochondria. The site is operated as a private "special interests" community hub.  +
[[File:P.jpg]] '''OXPHOS capacity''' ''P'' is the respiratory capacity of mitochondria in the ADP-activated state of [[oxidative phosphorylation]], at saturating concentrations of [[ADP]] and inorganic phosphate (which may not be the case in [[State 3]]), oxygen, and defined reduced CHNO-fuel substrates.  +
'''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.  +
'''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]] & [[Malate]]. '''MitoPathway control state:''' F '''SUIT protocols:''' [[SUIT-002]], [[SUIT-015]], [[SUIT-016]], [[SUIT-017]] 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]].  +
'''OctPGM''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocols:''' [[SUIT-002]] :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.  +
'''OctPGMS''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]]. '''MitoPathway control state:''' [[FNS]] '''SUIT protocol:''' [[SUIT-001]], [[SUIT-002]], [[SUIT-015]] This substrate combination supports convergent electron flow to the [[Q-junction]].  +
'''OctPGMSGp''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' FNSGp '''SUIT protocol:''' [[SUIT-002]] This substrate combination supports convergent electron flow to the [[Q-junction]].  +
'''OctPM''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocol:''' [[SUIT-002]], [[SUIT-005]] 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.  +
'''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 [[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).  +
[[File:Open Access logo.png |20px |left]] '''Open Access''' (OA) academic articles comprise all different forms of published research that are distributed online, free of charge and with an open license to facilitate the distribution and reuse. The open access repositories serve as the perfect vehicle to transmit free knowledge, including but not limited to peer-reviewed and non-peer-reviewed academic journal articles, conference papers, theses, book chapters and monographs. Driven by the problems of social inequality caused by restricting access to academic research, the Open Access movement changes the funding system of published literature allowing for more readers and thus increased access to scientific knowledge, as well as addressing the economic challenges and unsustainability of academic publishing. In addition to being free to read (''gratis''), open access articles may also be free to use (''libre'') where the copyright is held by the authors and not the publisher. Definition by the [[Directory of Open Access Journals]] (DOAJ): "We define these as journals where the copyright holder of a scholarly work grants usage rights to others using an open license (Creative Commons or equivalent) allowing for immediate free access to the work and permitting any user to read, download, copy, distribute, print, search, or link to the full texts of articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose."  +
Open a previously recorded [[DatLab]] file.  +
[[File:Open Access logo.png |20px |left]] Building on the essential principles of academic freedom, research integrity and scientific excellence, '''open science''' sets a new paradigm that integrates into the scientific enterprise practices for reproducibility, transparency, sharing and collaboration resulting from the increased opening of scientific contents, tools and processes. Open science is defined as an inclusive construct that combines various movements and practices aiming to make multilingual scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation and communication to societal actors beyond the traditional scientific community. It comprises all scientific disciplines and aspects of scholarly practices, including basic and applied sciences, natural and social sciences and the humanities, and it builds on the following key pillars: open scientific knowledge, open science infrastructures, science communication, open engagement of societal actors and open dialogue with other knowledge systems.  +
The term "open O2k-chamber" refers to a situation in which the liquid phase is allowed to equilibrate with a gas phase, but the stopper is partially inserted using the [[Stopper-Spacer]].  +
An '''open system''' is a system with boundaries that allow external exchange of energy and matter; the surroundings are merely considered as a source or sink for quantities transferred across the system boundaries ([[external flow]]s, ''I''<sub>ext</sub>).  +
'''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.  +
The '''ordinate''' is the vertical axis ''y'' of a rectangular two-dimensional graph with the [[abscissa]] ''x'' as the horizontal axis. Values ''Y'' are placed vertically from the origin. See [[Ordinary Y/X regression |Ordinary ''Y''/''X'' regression]].  +
[[Image:OroboPOS.JPG|right|180px]] The '''OroboPOS''' is a polarographic oxygen sensor (POS), with an amperometric mode of operation. The OroboPOS meets the highest quality criteria in terms of linearity, stability and sensitivity of the signal. The Clark type polarographic oxygen sensor (POS) remains the gold standard for measuring dissolved oxygen in biomedical, environmental and industrial applications over a wide dynamic oxygen range. It consists of a gold cathode, a silver/silverchloride anode and a KCl electrolyte reservoir separated from the sample by a 25 µm membrane (FEP). The main body of the OroboPOS is made of PEEK. With application of a polarization voltage (0.8 V), a current is obtained as an amperometric signal, which is converted to a voltage.  +
[[Image:POS connector and cable connection.jpg|right|180px]]'''OroboPOS-Connector''' (blue POM), with male connection to [[OroboPOS]] head (POS) and with cable and male plug fitting into [[O2k-Main Unit]].  +
The OroboPOS-Connector Service entails routine maintenance and any necessary repairs of the OroboPOS-Connector in the Oroboros electronics workshop (WGT).  +
[[Image:Logo OROBOROS INSTRUMENTS.jpg|180px|left|link=About Oroboros]] :::: '''[[OROBOROS INSTRUMENTS |Oroboros Instruments]]''' distributes the gold standard O2k-technology for [[high-resolution respirometry]] - '''HRR''' - [[O2k-Network|world-wide]]. The [[Oroboros_Contact|Oroboros Company]] is a scientifically oriented organization, with emphasis on continuous innovation. The extension of the '''Oroboros O2k''' to the '''[[O2k-FluoRespirometer]]''' sets a new standard. Its modular design provides the flexibility for add-on O2k-Modules (see [[Oroboros O2k-Catalogue]]). The O2k is established internationally, with [[O2k-Publications: Topics |»4294 O2k-Publications]] in the scientific literature covering areas ranging from fundamental bioenergetics to the analysis of mitochondrial and metabolic diseases, advancing the rapidly growing field of preventive mitochondrial medicine. The [[Oroboros Contact|Oroboros science team]] actively participates in science and research ([[AT Innsbruck Oroboros|see: publications]]). Moreover, the Oroboros O2k-Laboratory frequently host international researchers ([[Oroboros Laboratories: visiting scientists |visiting scientists]]). Oroboros Instruments organizes international [[Oroboros_Events#Next_O2k-Workshops |O2k-Workshops]] on a regular basis. The [[O2k-Network]] includes and connects 744 reference laboratories worldwide. The [[NextGen-O2k]] extends HRR to include a Q-redox sensor and PhotoBiology module.  +
[[File:NextGen-O2k All-in-one 2023.jpg|300px|right|NextGen-O2k all-in-one]] '''Oroboros O2k''' - the modular system for [[high-resolution respirometry]] (HRR) for mitochondria and cell research. Oroboros delivers the O2k-technology for high-resolution respirometry in mitochondria and cell research. The O2k allows the measurement of respiration at controlled oxygen levels, combined with redox biology (NADH and CoQ), ROS production, mitochondrial membrane potential, ATP production, Ca<sup>2+</sup>, or pH. HRR expands to HRPB: High-Resolution PhotoBiology. Small amounts of biological samples can be used for bioenergetic and OXPHOS analysis, ranging from isolated mitochondria, permeabilized tissues and permeabilized cells to living cells and tissues slices. The modular O2k-concept is supported by [[DatLab |DatLab]], with high flexibility for extension by add-on [https://www.oroboros.at/index.php/product-category/products/o2k-modules/ O2k-Modules]. All O2k-Modules are supported by the [[NextGen-O2k]]. The [https://www.oroboros.at/index.php/product/q-module/ O2k-Q-Module] and the [https://www.oroboros.at/index.php/product/nadh-module/ O2k-NADH-Module] are exclusively supported by the NextGen-O2k, whereas the O2k-J provides the basis for all other HRR application but cannot be upgraded to the [https://www.oroboros.at/index.php/product/nextgen-o2k-redox/ NextGen-O2k Redox]. The globally tested and trusted high-resolution O2k technology prioritizes both quality and scientific research output in the field of mitochondrial physiology and pathology, extended to PhotoBiology.  +
[[Image:O2k-Core-Concept.jpg|200px|right]] '''Oroboros O2k-Core - Former Series''' '''(O2k-Series D - G)''' - the experimental system complete for basic [[high-resolution respirometry]] (HRR). The O2k-Core includes the [[O2k-Main Unit]] with stainless steel housing, [[O2k-Assembly Kit]], two [[OroboPOS]] (polarographic oxygen sensors) and [[OroboPOS-Service Kit]], [[DatLab]] software, the [[ISS-Integrated Suction System]] and the [[O2k-Titration Set]]. The O2k-Core supports all add-on O2k-Modules of the O2k. On-line display of oxygen flux (rate of respiration) is provided in addition to the conventional 'oxygraphic' plot of oxygen concentration over time. Highest signal stability minimizes the required amounts of biological sample, and provides the basis for resolution in the extreme low-oxygen range. Peltier temperature control provides a thermal stability at ±0.002 °C in the range of 4 °C to 47 °C at typical constant room temperature. Electronically controlled PVDF or PEEK stirrers are integrated in the two-chamber design of the O2k, and a barometric pressure transducer enables automatic oxygen calibrations implemented in the DatLab software. The O2k is a sole source apparatus with no other instruments meeting its [[MiPNet06.05 Test Experiments on O2k-Specifications | specifications]].  +
The '''Oroboros USB-flash drive''' is delivered with the [[Oroboros O2k]]. Copy the folder "Oroboros O2k-Course on HRR" from the '''Oroboros USB-flash drive''' to your computer. This folder contains the DatLab installation program as well as tools to find topics, O2k-manuals and O2k-protocols with corresponding DatLab demo files and templates for training with [[DatLab]].  +
'''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.  +
An '''outlier''' is a member of a set of values which is inconsistent with other members of that set. An outlier can arise by chance from the expected population, originate from a different population, or be the result of an incorrect recording or other blunder. Many schemes use the term outlier to designate a result that generates an action signal. This is not the intended use of the term. While outliers will usually generate action signals, it is possible to have action signals from results that are not outliers [SOURCE: ISO 5725‑1:1994, modified].  +
An '''outlier-skewness index''' ''OSI'' is defined for evaluation of the distribution of data sets with outliers including separate clusters or skewness in relation to a normal distribution with equivalence of the average and median. The ''OSI'' is derived from [http://www.statisticshowto.com/pearsons-coefficient-of-skewness/ Pearson’s coefficient of skewness] 2: : Pearson 2 coefficient = 3 · (average-median)/SD The outlier-skewness index ''OSI'' introduces the absolute value of the arithmetic mean, ''m'' = ABS(average + median)/2, for normalization: : ''OSI'' = (average-median)/(''m'' + SD) : ''OSI'' = (average-median)/[ABS(average+median)/2 + SD] At the limit of a zero value of ''m'', the ''OSI'' equals the Pearson 2 coefficient (without the multiplication factor of 3). At high ''m'' with small standard deviation (SD), the ''OSI'' is effectively the difference between the average and the median normalized for ''m'', (average-median)/''m''.  +
'''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]]).  +
'''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. 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. 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". 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.  +
[[File:Oxaloacetic_acid.jpg|left|100px|Oxaloacetic acid]] '''Oxaloacetic acid''', C<sub>4</sub>H<sub>4</sub>O<sub>5</sub>, occurs under physiological conditions as the anion '''oxaloacetate<sup>2-</sup>, Oa'''. Oxaloacetate is formed from malate by [[Malate dehydrogenase|MDH]]. Oa reacts with acetyl-CoA through [[citrate synthase]] to form citrate, or with [[glutamate]] through transaminase to form [[oxoglutarate]] and aspartate. Oa transport is restricted across the inner [[mitochondrial|mt]]-membrane of various tissues. Oa is a potent inhibitor of [[succinate dehydrogenase]].  +
'''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]]).  +
[[Image:Oxia.png|180px|right]]'''Oxia - HyperOxia to HypOxia''': The Oxia generates gaseous [[oxygen]] and [[hydrogen]] by electrolysis of water using a proton exchange membrane (PEM). O<sub>2</sub> and H<sub>2</sub> gas can be used to control the O<sub>2</sub> regime in the Oroboros O2k ([[Setting_the_oxygen_concentration]]) using the [[Syringe\10 mL\Gas-Injection |10 mL Gas-Injection Syringes]]. Low oxygen concentrations (<50 µM) are used to mimic tissue [[normoxia]] or [[hypoxia]]. Hyperoxic conditions above air saturation (250-600 µM O<sub>2</sub>) are routinely used for high-resolution respirometry of [[permeabilized muscle fibers]] or to induce oxidative stress in cells and [[mitochondrial preparations]].  +
[[File:P.jpg |link=OXPHOS capacity]] '''Oxidative phosphorylation''' (OXPHOS) is the oxidation of reduced fuel substrates by electron transfer to oxygen, chemiosmotically coupled to the phosphorylation of [[ADP]] to [[ATP]] (P») and accompanied by an intrinsically uncoupled component of respiration. The OXPHOS state of respiration provides a measure of [[OXPHOS capacity]] (''P''), which is frequently corrected for [[residual oxygen consumption]] (ROX).  +
'''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.  +
[[File:2-Oxoglutaric_acid.jpg|left|100px|2-Oxoglutaric acid]] '''2-Oxoglutaric acid''' or alpha-ketoglutaric acid, C<sub>5</sub>H<sub>6</sub>O<sub>5</sub>, occurs under physiological conditions as the anion '''2-Oxoglutarate<sup>2-</sup>, Og'''. 2-Oxoglutarate (alpha-ketoglutarate) is formed from isocitrate as a product of [[isocitrate dehydrogenase]] (IDH) in the [[TCA cycle]], and is a substrate of [[oxoglutarate dehydrogenase]] (OgDH). The 2-oxoglutarate carrier exchanges malate<sup>2-</sup> for 2-oxoglutarate<sup>2-</sup> as part of the [[malate-aspartate shuttle]]. In the cytosol, oxoglutarate+aspartate are transaminated to form oxaloacetate+glutamate. Cytosolic malate dehydrogenase converts oxaloacetate+NADH to malate.  +
'''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.  +
The '''oxycaloric equivalent''' is the theoretically derived enthalpy change of the oxidative catabolic reactions per amount of oxygen respired, Delta<sub>k</sub>''H''<sub>O2</sub>, ranging from -430 to -480 kJ/mol O<sub>2</sub>. The oxycaloric equivalent is used in [[indirect calorimetry]] to calculate the theoretically expected metabolic heat flux from the respirometrically measured metabolic oxygen flux. [[Calorespirometric ratio|Calorimetric/respirometric ratios]] (CR ratios; heat/oxygen flux ratios) are experimentally determined by [[calorespirometry]]. A CR ratio more exothermic than the oxycaloric equivalent of -480 kJ/mol indicates the simultaneous involvement of aerobic and anaerobic mechanisms of energy metabolism.  +
[[File:O2.jpg|left|60px|Dioxygen]] '''Molecular oxygen''', O<sub>2</sub> or '''dioxygen''', has two atoms of oxygen, O, which is the chemical element with atomic number 8. The relative molecular mass of O<sub>2</sub>, ''M''<sub>r,O2</sub>, is 32 (or 31.9988). The element O has 8 protons, 8 neutrons and 8 electrons. In the figure, the two electrons in the first electron shell are not shown. Of the six electrons in the outer shell (blue bullets), one electron from each of the two atoms is shared in O<sub>2</sub> forming the covalent bond, and one electron in each atom is unpaired.  +
'''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]].  +
Respiratory '''oxygen flow''' is the oxygen consumption per total [[system]], which is an [[extensive quantity]]. [[Flow]] is advancement of a transformation in a system per time [mol·s<sup>-1</sup>], when 'system' is defined as the experimental system (e.g. an open or closed chamber). Flow is distinguished from the size-specific quantity [[flux]] obtained by normalization of flow per volume of the experimental system [mol·s<sup>-1</sup>·m<sup>-3</sup>]. An experimental object, e.g. a living cell, may be considered as the 'experimental system'. Then oxygen flow per cell has the unit [mol·s<sup>-1</sup>·x<sup>-1</sup>], where [x] is the [[elementary unit]] for a [[count]]. Oxygen flow or respiration per cell [amol·s<sup>-1</sup>·x<sup>-1</sup>] = [pmol·s<sup>-1</sup>·Mx<sup>-1</sup>] is normalized for the cell count, distinguished from [[oxygen flux]] (e.g. per mg protein or wet mass). These are different forms of [[normalization of rate]].  +
'''Oxygen flux''', ''J''<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]].  +
'''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.  +
'''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.  +
'''Oxygen pressure''' or partial [[pressure]] of oxygen [kPa], related to oxygen concentration in solution by the [[oxygen solubility]], ''S''<sub>O2</sub> [µM/kPa].  +
The '''O<sub>2</sub> sensor test''' is an important component of [[MitoPedia: Oroboros QM |Oroboros Quality Management]]. The [[OroboPOS]] test is described in detail in [[MiPNet06.03 POS-calibration-SOP]], is performed after switching on the [[Oroboros O2k]], and is required as a basis of technical service of the instrument.  +
The '''oxygen signal''' of the [[Oroboros O2k]] is transmitted from the electrochemical polarographic oxygen sensor ([[OroboPOS]]) for each of the two O2k-chambers to [[DatLab]]. The primary signal is a current [µA] which is converted into a voltage [V] (raw signal), and calibrated in SI units for amount of substrance concentration [µmol·L<sup>-1</sup> or µM].  +
The '''oxygen solubility''', ''S''<sub>O<sub>2</sub></sub> [µM/kPa] = [(µmol·L<sup>-1</sup>)/kPa], expresses the oxygen concentration in solution in equilibrium with the [[oxygen pressure]] in a gas phase, as a function of temperature and composition of the solution. The inverse of oxygen solubility is related to the [[activity]] of dissolved oxygen. The oxygen solubility in solution, ''S''<sub>O<sub>2</sub></sub>(aq), depends on temperature and the concentrations of solutes in solution, whereas the dissolved oxygen concentration at equilibrium with air, ''c''<sub>O<sub>2</sub></sub><sup>*</sup>(aq), depends on ''S''<sub>O<sub>2</sub></sub>(aq), barometric pressure and temperature. ''S''<sub>O<sub>2</sub></sub>(aq) in pure water is 10.56 µM/kPa at 37 °C and 12.56 µM/kPa at 25 °C. At standard [[barometric pressure]] (100 kPa), ''c''<sub>O<sub>2</sub></sub><sup>*</sup>(aq) is 207.3 µM at 37 °C (19.6 kPa partial oxygen pressure) or 254.7 µM at 25 °C (20.3 kPa partial oxygen pressure). In [[MiR05]] and serum, the corresponding saturation concentrations are lower due to the [[oxygen solubility factor]]: 191 and 184 µM at 37 °C or 234 and 227 µM at 25 °C.  +
The '''oxygen solubility factor''' of the incubation medium, ''F''<sub>M</sub>, expresses the effect of the salt concentration on [[oxygen solubility]] relative to pure water. In mitochondrial respiration medium [[MiR05]], [[MiR05-Kit]] and [[MiR06]], ''F''<sub>M</sub> is 0.92 (determined at 30 and 37 °C) and in culture media is 0.89 (at 37 °C). ''F''<sub>M</sub> varies depending on the temperature and composition of the medium. To determine the FM based on the oxygen concentration, specific methods and equipment are needed (see references Rasmussen HN, Rasmussen UF 2003 in [https://wiki.oroboros.at/index.php/MiPNet06.03_POS-calibration-SOP MiPNet06.03]). For other media, ''F''<sub>M</sub> may be estimated using Table 4 in [https://wiki.oroboros.at/index.php/MiPNet06.03_POS-calibration-SOP MiPNet06.03]. For this purpose KCl based media can be described as "seawater" of varying salinity. The original data on sucrose and KCl-media (Reynafarje et al 1985), however, have been critizesed as artefacts and the ''F''<sub>M</sub> of 0.92 is suggested in the temperature range of 10 °C to 40 °C as for MiR05.  +
P
[[File:J(P-L).jpg|50 px|P-L control efficiency]] The '''''P-L'' control efficiency''' (''P-L'' flux control efficiency) is defined as ''j<sub>P-L</sub>'' = (''P-L'')/''P'' = 1-''L/P''. [[OXPHOS capacity]] corrected for [[LEAK respiration]] is the [[P-L net OXPHOS capacity]], ''P-L''. The ''P-L'' control efficiency is the ratio of net to total OXPHOS capacity, which is equal to the biochemical ''E-L'' coupling efficiency, if ''P''=''E''. ''j<sub>P-L</sub>'' = 1.0 for a fully coupled system (when RCR approaches infinity); ''j<sub>P-L</sub>'' = 0.0 (RCR=1) for a system with zero respiratory phosphorylation capacity (''P-L''=0) or zero [[E-L coupling efficiency |''E-L'' coupling efficiency]] (''E-L''=0 when ''L''=''P''=''E''). If [[State 3]] is measured at saturating concentrations of ADP and P<sub>i</sub> (State 3 = ''P''), then the [[respiratory acceptor control ratio]] RCR equals ''P/L''. Under these conditions, the respiratory control ratio and ''P-L'' control efficiency are related by a hyperbolic function, ''j<sub>P-L</sub>'' = 1-RCR<sup>-1</sup>. » [[#Cell ergometry: OXPHOS-control and ET-coupling efficiency |'''MiPNet article''']]  +
[[Image:P-L.jpg|50 px|P-L net OXPHOS capacity|''P-L'' net OXPHOS capacity]] The '''''P-L'' net OXPHOS capacity''' is the [[OXPHOS capacity]] corrected for [[LEAK respiration]]. ''P-L'' is the scope for ADP stimulation, the respiratory capacity potentially available for phosphorylation of ADP to ATP. Oxygen consumption in the OXPHOS state, therefore, is partitioned into ''P-L'', strictly coupled to phosphorylation ''P»'', and nonphosphorylating LEAK respiration, ''L<sub>P</sub>'', compensating for proton leaks, slip and cation cycling: ''P'' = ''P-L''+''L<sub>P</sub>''. It is frequently assumed that [[LEAK respiration]] ''L'' as measured in the LEAK state, overestimates the LEAK component of respiration, ''L<sub>P</sub>'', as measured in the OXPHOS state, particularly if the protonmotive force is not adjusted to equivalent levels in ''L'' and ''L<sub>P</sub>''. However, if the LEAK component increases with enzyme turnover during ''P'', the low enzyme turnover during ''L'' may counteract the effect of the higher ''pmF''.  +
[[Image:P over E.jpg|50 px|OXPHOS-control ratio]] The '''''P/E'' control ratio''' ([[OXPHOS]]/[[Electron transfer pathway|ET pathway]]; phosphorylation system control ratio) is an expression of the limitation of OXPHOS capacity by the [[phosphorylation system]]. The relative limitation of OXPHOS capacity by the capacity of the phosphorylation system is better expressed by the [[E-P control efficiency |''E-P'' control efficiency]], ''j<sub>E-P</sub>'' = 1-''P/E''. The ''P/E'' control ratio increases with increasing capacity of the phosphorylation system up to a maximum of 1.0 when it matches or is in excess of ET capacity. ''P/E'' also increases with uncoupling. ''P/E'' increases from the lower boundary set by ''[[L/E]]'' (zero capacity of the phosphorylation system), to the upper limit of 1.0, when there is no limitation of ''P'' by the phosphorylation system or the proton backpressure (capacity of the phosphorylation system fully matches the [[ET capacity]]; or if the system is fully [[uncoupled]]). It is important to separate the kinetic effect of ADP limitation from limitation by enzymatic capacity at saturating ADP concentration. » [[#P.2FE_from_mouse_to_man |'''MiPNet article''']]  +
P/O ratio stands for phosphate to atomic oxygen ratio, where P indicates phosphorylation of ADP to ATP (or GDP to GTP).  +
'''''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%.  +
[[Image:PB-Sensor.png|right|180px]] The '''PhotoBiology Light Source (PBLS)''' has been designed as a part of the [[PB-Module]] to provide with an external source of light. This enables experiments for evaluating the production of O<sub>2</sub> in the presence of light. The PBLS consists of one LED and one photodiode mounted on the PBLS head protected by a PMMA plastic cover. Three pairs of PBLS (white, blue, and red) are provided with the PB-Module. The light intensity can be regulated from 0 to 2750 µmol·s<sup>-1</sup>·m<sup>-2</sup> (red PBLS), from 0 to 3000 µmol·s<sup>-1</sup>·m<sup>-2</sup> (blue PBLS), from 0 to 3500 µmol·s<sup>-1</sup>·m<sup>-2</sup> (white PBLS). An integrated photodiode provides real-time measurement of the light intensity allowing for continuous adjustment to the desired value.  +
[[Image:PB-Module.jpg|right|180px]] The '''PB-Module''' has been developed for conducting measurements of [[PhotoBiology]], including [[photosynthesis]]. It consists of the [[PB-Sensor|PB Light Source]] and electronic components which are an integral part of the [[NextGen-O2k]]. Measurements are recorded and evaluated with the DatLab 8 software.  +
[[Image:PBI-Shredder HRR-Set.JPG|180px|right]]'''PBI-Shredder O2k-Set''': Auxiliary O2k-Tool for [[tissue homogenate]] preparation  +
[[Image:PBI-Shredder SG3.jpg|180px|right]] '''PBI-Shredder SG3''' for tissue homogenate preparation, heavy duty high torque SG3 driver with convertible handle, SG3 base with 3 position force setting lever (FSL), battery charger and two lithium ion batteries. The PBI-Shredder SG3 is included in the [[PBI-Shredder O2k-Set]]. Select 230 V or 120 V. Oroboros Instruments: world-wide distributor.  +
'''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.  +
The PC requirements for controlling an O2k and data recording with [[DatLab]] are found [[DatLab installation |here]].  +
[[File:PGM.jpg|left|200px|PGM]] '''PGM''': [[Pyruvate]] & [[Glutamate]] & [[Malate]]. '''MitoPathway control state:''' [[NADH electron transfer-pathway state]] [[Pyruvate]] (P) is oxidatively decarboxylated to acetyl-CoA and CO<sub>2</sub>, yielding [[NADH]] catalyzed by pyruvate dehydrogenase. [[Malate]] (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). Glutamate&malate is a substrate combination supporting an N-linked pathway control state, when glutamate is transported into the mt-matrix via the [[glutamate-aspartate carrier]] and reacts with [[oxaloacetate]] in the [[transaminase]] reaction to form [[aspartate]] and [[oxoglutarate]]. Glutamate as the sole substrate is transported by the electroneutral glutamate<sup>-</sup>/OH<sup>-</sup> exchanger, and is oxidized in the mitochondrial matrix by [[glutamate dehydrogenase]] to α-ketoglutarate ([[oxoglutarate | 2-oxoglutarate]]), representing the [[glutamate-anaplerotic pathway control state]]. 2-oxoglutarate (α-ketoglutarate) is formed from isocitrate (isocitrate dehydrogenase, from oxaloacetate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase.  +
[[File:PGMS.png|left|200px|PGMS]] '''PGMS''': [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]]. '''MitoPathway control state:''' [[NS|NS-pathway control state]] 2-oxoglutarate is produced through the citric acid cycle from citrate by isocitrate dehydrogenase, from oxaloacetate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase. If the 2-oxoglutarate carrier does not outcompete these sources of 2-oxoglutarate, then the TCA cycle operates in full circle with external pyruvate&malate&glutamate&succinate  +
'''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]].  +
PH +
The '''pH value''' or pH is the negative of the base 10 logarithm of the [[activity]] of [[proton]]s (hydrogen ions, H<sup>+</sup>). A [[pH electrode]] reports the pH and is sensitive to the activity of H<sup>+</sup>. In dilute solutions, the hydrogen ion activity is approximately equal to the hydrogen ion [[concentration]]. The symbol pH stems from the term ''potentia hydrogenii''.  +
'''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]].  +
[[Image:PH-Glass Electrode.JPG|180px|right]]'''pH-Glass electrode''' with BNC plug.  +
[[File:M.jpg|left|200px|PM]] '''PM''': [[Pyruvate]] & [[Malate]]. '''MitoPathway control state:''' [[NADH Electron transfer-pathway state]] Upstream of the NAD-junction, [[Pyruvate]] (P) is oxidatively decarboxylated to acetyl-CoA and CO<sub>2</sub>, yielding [[NADH]] catalyzed by pyruvate dehydrogenase. [[Malate]] (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). 2-oxoglutarate (α-ketoglutarate) is formed from isocitrate (isocitrate dehydrogenase).  +
[[File:PMS.jpg|left|200px|PMS]]'''PMS''': [[Pyruvate]] & [[Malate]] & [[Succinate]]. '''MitoPathway control:''' CI&II [[Pyruvate]] (P) is oxidatively decarboxylated to acetyl-CoA and CO<sub>2</sub>, yielding [[NADH]] catalyzed by pyruvate dehydrogenase. [[Malate]] (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). This documents an additive effect of convergent CI&II electron flow to the Q-junction, with consistent results obtained with permeabilized muscle fibres and isolated mitochondria (Gnaiger 2009).  +
Calibration of the sensor response time. See also [[POS calibration - static]].  +
Two-point calibration of the polarographic oxygen sensor, comprising [[Air calibration]] and [[Zero calibration]]. See also [[POS calibration - dynamic]].  +
[[Image:POS Electrolyte powder.jpg|right|180px]]'''[[OroboPOS|POS]]-Electrolyte Powder''', KCl. The powder is dissolved in 10 ml distilled water to yield a 1 M KCl solution.  +
[[Image:Pos_holder.JPG|right|180px]]The '''POS-Holder''', made from blue POM, is screwed into the copper block of the [[O2k-Main Unit]], guiding theguiding the [[OroboPOS|POS]] to the 2-mL [[O2k-chamber]], and keeping the SmartPOS/OroboPOS-Connector in a fixed position for sealing the O2k-chamber with the [[POS-Seal Tip]]. In addition, the POS-Holder fixes the O2k-Chamber in an accurate rotational position by pressing against the angular cut of the glass chamber. Two units of this item are standard components mounted on the [[O2k-Main Unit]].  +
[[File:32300-01.jpg|right|180px]] '''POS-Holder sV''', made from black POM, to be screwed into the copper block of the [[O2k-Main Unit]], guiding the [[OroboPOS|POS]] to the [[O2k-Chamber sV]], and keeping the SmartPOS/OroboPOS-Connector in a fixed position for sealing the O2k-Chamber sV with the [[POS-Seal Tip]]. In addition, the POS-Holder sV fixes the O2k-Chamber sV in an accurate rotational position by pressing against the angular cut of the glass chamber.  +
[[File:POS membrane holder ring.jpg|right|180px|link=]]'''POS-Membrane Ring''', [[PEEK]], holds the membrane against the inner O-ring on the POS housing.  +
[[Image:POS membranes.jpg|right|180px]]'''[[OroboPOS|POS]]-Membranes''', FEP 25 µm; 40/Pck.  +
[[Image:POS mounting tool for membrane application_02.JPG|right|180px]]'''[[OroboPOS|POS]]-Mounting Tool''' for application of [[POS-Membranes]]. It consists of two parts, (i) the membrane guide (larger diameter) and (ii) the membrane ring holder with [[O-ring\Viton\6x1 mm]] for holding the [[POS-Membrane Ring]] during membrane application. Since the O2k-Series G-0075 membrane ring holder have a 2 mm extended ridge for a better grip.  +
[[Image:POS seal tip.jpg|right|180px]]'''POS-Seal Tip''', black butyl rubber gasket with 3 mm pore. 4/Pck, for sealing the [[OroboPOS|POS]] (sensor head) against the [[O2k-chamber |O2k-Chamber]]. Push the wetted POS-Seal Tip over the POS-sensor head, with the pore positioned centrally, not covering any peripheral area of the gold cathode. Do not stretch the gasket across the POS-sensor head.  +
'''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 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].  +
'''pX calibration'''  +
[[Image:Packing O2k-Box1.JPG|right|180px]]'''Packing\O2k-Box 1''': for shipment of the [[O2k-Main Unit]], with polystyrene inlets. Keep the original packing material safely stored, for any future shipping purposes of the O2k-Main Unit.  +
'''Packing\O2k-Box 1+2''' for shipping the [[O2k-Core]]. O2k-WorldWide delivery, insurance and handling are included in the O2k-Core.  +
[[Image:Packing O2k-Box2.JPG|right|180px]]'''Packing\O2k-Box 2''', for shipment of accessories.  +
[[Image:Packing Peli Case.jpg|right|180px]]'''Packing\Peli Case''': Watertight, crushproof, and dust proof case for safe transportation of the O2k: Retractable extension handle, Strong polyurethane wheels with stainless steel bearings, Easy open Double Throw latches, Open cell core with solid wall design - strong, light weight, O-ring seal, Automatic Pressure Equalization Valve, Fold down handles, Stainless steel hardware and padlock protectors, 4 level Pick N Pluck™ with convoluted lid foam, Special foam inlets for O2k. Interior Dimensions: 21.48" x 16.42" x 12.54" (54.5 x 41.7 x 31.8 cm)  +
'''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]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' FNSGp '''SUIT protocol:''' [[SUIT-026]] This substrate combination supports convergent electron flow to the [[Q-junction]].  +
'''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.  +
'''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.  +
'''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.  +
The '''partial oxygen pressure''' ''p''<sub>O<sub>2</sub></sub> [kPa] is the contribution of the O<sub>2</sub> gas pressure to the total gas pressure. According to the gas law, the partial oxygen pressure is ''p''<sub>O<sub>2</sub>(g)</sub> = ''n''<sub>O<sub>2</sub>(g)</sub>·''V''·''RT'', where the [[concentration]] is ''c''<sub>O<sub>2</sub>(g)</sub> = ''n''<sub>O<sub>2</sub>(g)</sub>·''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>]. In aqueous solutions at equilibrium with a gas phase, the partial O<sub>2</sub> pressures are equal in the aqueous phase (aq) and gas phase (g), ''p''<sub>O<sub>2</sub>(aq)</sub> = ''p''<sub>O<sub>2</sub>(g)</sub> at total [[pressure]]s where the partial pressure equals the fugacity. The O<sub>2</sub> concentration in the aqueous phase, however, is much lower than in the gas phase, due to the low [[oxygen solubility]] in water. The activity of dissolved O<sub>2</sub> is expressed by the ''p''<sub>O<sub>2</sub></sub>, where the [[solubility]] can be seen as an activity coefficient.  +
The '''particle charge''' ''Q<sub>N<sub>X</sub></sub>'' (''Q<sub><u>N</u>X</sub>'') or charge per elementary entity is the [[charge]] ''Q''<sub>el''X''</sub> [C] carried by ions of type ''X'' divided by the count ''N<sub>X</sub>'' [x]. The particle charge per proton is the [[elementary charge]] or proton charge ''e''.  +
The '''pascal''' [Pa] is the SI unit for [[pressure]]. [Pa] = [J·m<sup>-3</sup>] = [N·m<sup>-2</sup>] = [m<sup>-1</sup>·kg·s<sup>-2</sup>]. The standard pressure is 100 kPa = 1 bar (10<sup>5</sup> Pa; 1 kPa = 1000 Pa). Prior to 1982 the standard pressure has been defined as 101.325 kPa or 1 standard atmosphere (1 atm = 760 mmHg).  +
In mitochondrial respiratory physiology a large number of '''pathway and coupling control states''' is encountered, for which a unified system of terms and abbreviations is required. In [[mitochondrial preparations]] there is a large number of potentially complex [[pathway control state]]s, in contrast to only three [[coupling control state]]s (''L'', ''P'', ''E''). Therefore, it is practical to use ''L'', ''P'', and ''E'' as subscripts attached to the abbreviation of the pathway control state.  +
'''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]].  +
'''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. 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]].  +
Though often defined from the individual reader's perspective, a paywall can also apply to an institution (such as a library) or the author. '''Paywall journalism''' is the opposite of [[Open Access]]. [[Open Science]] does not accept paywalls with the argument, that the public pays for governmentally funded research, hence research funded by public grants should be published with open access for the public without paywalls. Paywalls are most frequently defined from the perspective of the individual reader, who has to pay for an article or pay a journal subscription as a requisite for obtaining full access to the information that is otherwise hidden behind the paywall ('''reader-paywall journal'''). From the perspective of the authors, however, an '''author-paywall journal''' is defined as any journal which requests publication charges or page charges from the authors for publishing the manuscript Open Access or publishing it at all. Similarly, an '''institutional-paywall journal''' charges an institution – typically university libraries – for granting open access to the members of this institution. As long as paywall journalism prevails in science, at least '''paywall transparence''' should be required, to declare for each publication not only the reader-paywall costs but provide the full information on the author-paywall and institutional-paywall expenses.  +
'''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.  +
'''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). ''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). '''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.  +
[[Image:Pen contact oil.jpg|right|180px]] '''Pen-Contact Oil''', for stable low contact resistance between the [[OroboPOS]] head and the [[OroboPOS-Connector]]. '''Discontinued''' - The Pen-Contact Oil is not part of our product range anymore as it is not absolutely required for ensuring the functioning of the OroboPOS-Connector and the OroboPOS. The Oroboros experts do not use it anymore.  +
'''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.  +
'''Performance estimation'''  +
The (mitochondrial, mt) permeability transition pore (PTP) is an unspecific pore presumed to involve components of both the inner and outer mt membrane which upon opening induces a massive increase of the inner mt membrane permeability for solutes up to 1.5 kDa. It is crucially involved in cell death induction in response to, among other stimuli, radical stress and/or calcium overload and may cause necrosis or apoptosis. It plays an important role in neurodegenerative diseases, cardiac ischemia-reperfusion injury and possibly various other diseases. Previously considered essential molecular constituents such as the voltage-dependent anion channel (VDAC), the adenine nucleotide translocator (ANT) and cyclophilin D (CypD) have all been shown to be important regulators of mtPTP opening, but the molecular entities actually forming the pore are still unknown at present. The opening of the pore can be prevented using [[cyclosporin A]], a compound that binds cyclophilin D avoiding the formation of the pore. In respirometry, mtPTP opening may be observed as a sudden decrease of respiration of isolated mitochondria ([[Hansson 2010 J Biol Chem]]).  +
'''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. '''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. 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.  +
'''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. :» MitoPedia topic: [[Mitochondrial preparations]]  +
'''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.  +
'''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. '''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.  +
'''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]]).  +
'''Phenylsuccinate''' is a competitive inhibitor of succinate transport (20 mM).  +
''See:'' '''[[Inorganic phosphate]]'''  +
The '''phosphate carrier''' (PiC) is a proton/phosphate symporter which transports negatively charged [[inorganic phosphate]] across the inner mt-membrane. The transport can be described either as symport of H<sup>+</sup> with P<sub>i</sub>, or antiport of hydroxide anion against P<sub>i</sub>. The phosphate carrier is a component of the [[phosphorylation system]].  +
'''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''' (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]]).  +
'''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.  +
[[File:Phosphorylation system.jpg|thumb|left|250px|From Gnaiger 2014 MitoPathways]] The '''phosphorylation pathway''' (phosphorylation system) is the functional unit utilizing the protonmotive force to phosphorylate ADP (D) to ATP (T), and may be defined more specifically as the '''P»-system'''. The P»-system consists of [[adenine nucleotide translocase]], [[phosphate carrier]], and [[ATP synthase]]. Mitochondrial [[adenylate kinase]], mt-[[creatine kinase]] and mt-[[hexokinase]] constitute extended components of the P»-system, controlling local AMP and ADP concentrations and forming [[metabolic channel]]s. Since substrate-level phosphorylation is involved in the TCA-cycle, the P»-system includes [[succinyl-CoA ligase]] (GDP to GTP or ADP to ATP).  +
'''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]].  +
'''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.  +
'''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]].  +
'''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]].  +
'''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.  +
'''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.  +
See [[Electron-transfer-pathway state]].  +
'''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.  +
[[File:Pipette Plastic 1 ml-ungraded.JPG|180px|right]]'''Pipette\Plastic\1 mL ungraded''', for filling electrolyte into the reservoir of the [[OroboPOS]].  +
'''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."  +
'''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.  +
'''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]].  +
A '''plot''' in DatLab represents a specific [[O2k signals and output|channel]] in the graph. To change the [[Layout for DatLab graphs]] go to [Graph]/'''[[Select plots - DatLab |Select plots]]''' to open the '''Graph layout''' window.  +
[[Image:Plunger 10 mm3.JPG|right|180px]]'''Plunger\10 mm3''' for [[Microsyringe\10 mm3 51/0.13 mm]], spare.  +
[[Image:Plunger 25 mm3.JPG|right|180px]] '''Plunger\25 mm3''' for [[Microsyringe\25 mm3 51/0.15 mm]], spare. '''Discontinued'''  +
[[Image:Plunger 50 mm3.JPG|right|180px]]'''Plunger\50 mm3''' for [[Microsyringe\50 mm3 51/0.15 mm]], spare. '''Discontinued '''  +
'''Poicilotherms''' are [[ectotherms]] whose body temperatures conform to the temperature of the milieu in a thermally variable environment.  +
A '''polarization voltage''' of 600 mV to 800 mV is applied between anode and cathode of the [[polarographic oxygen sensor]], resulting in a current when oxygen is consumed. The current is converted by the electronics to a voltage (raw signal) which must not be confused with the polarization voltage.  +
'''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]].  +
[[Image:POS polishing cloth for cathode cleaning.jpg|right|180px]]'''Polishing Cloth''' for cathode cleaning. Replace the Polishing Cloth at intervals. A two-year interval may be considered in cases of intensive use.  +
[[Image:POS polishing powder for cathode cleaning.jpg|right|180px]]'''Polishing Powder 0.3 µm''' and '''Polishing Powder 0.05 µm''' for cathode cleaning of OroboPOS and Q-sensors.  +
'''Polyether ether ketone (PEEK)''' is a semicrystalline organic polymer thermoplastic, which is chemically very resistant, with excellent mechanical properties. PEEK is compatible with ultra-high vacuum applications, and its resistance against oxygen diffusion make it an ideal material for high-resolution respirometry ([[POS]] insulation; coating of stirrer bars; stoppers for closing the O2k-Chamber).  +
'''Polyvinylidene fluoride (PVDF)''' 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).  +
A '''population''' (or '''group''') defines the [[sample type]] of an [[experiment]], before sample preparation. The population (or group) size represents the upper limit of the [[sample size]], ''N''.  +
'''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.  +
'''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.  +
'''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.  +
[[File:Power O2k Numbers.JPG|right|180px]]'''Power O2k Numbers''': Single number to label the O2k in a Power O2k-Lab.  +
[[Image:Power_O2k-FluoRespirometer.jpg|200px|right|Power O2k-FluoRespirometer]] '''Power O2k-FluoRespirometer''' - optional configuration as additional system for increasing output combined with the [[O2k-FluoRespirometer]] (O2k-Series H). The Power O2k-FluoRespirometer includes the [[TIP2k-Module |TIP2k]] and the [[O2k-sV-Module]], and supports all add-on O2k-Modules of the [[Oroboros O2k]]. It can be added to an existing [[Oroboros O2k]] of any O2k-Series. This application does not require an additional [[ISS-Integrated Suction System]] and [[O2k-Titration Set]]. Furthermore, the [[OroboPOS-Mounting Tool]] of the OroboPOS Service Tools can be used from the available O2k and is not included.  +
[[Image:Power_O2k_notext.png|200px|right]] The '''Power O2k-Respirometer''' is an economical option for using additional O2k-Units to increase output in [[High-Resolution Respirometry|high-resolution respirometry]].  +
'''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.  +
'''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.  +
'''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).  +
'''Preparation of SUIT chemicals''' describes the preparation of chemicals used in Substrate-Uncoupler-Inhibitor Ttitration (SUIT) protocols.  +
A '''preprint''' is {''Quote''} a way in which a manuscript containing scientific results can be rapidly communicated from one scientist, or a group of scientists, to the entire scientific community {''end of Quote''}. Preprints are disseminated without peer review, e.g. in the preprint server [[MitoFit Preprints]]. In contrast, the journal [[Bioenergetics Communications]] publishes peer-reviewed articles, which preferentially are communicated in advance in MitoFit Preprints.  +
'''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. ''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. 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.  
'''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.  +
The '''primary sample''' or '''specimen''' is a set of one or more parts initially taken from an object. In some countries, the term “specimen” is used instead of primary sample (or a subsample of it), which is the sample prepared for sending to, or as received by, the laboratory and which is intended for examination.  +
A '''product''' in a chemical reaction has a positive [[stoichiometric number]] since it is produced, whereas a [[substrate]] has a negative stoichiometric number since it is consumed.  +
'''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.  +
A scientific project is a collection of [[experiment| experiments]] designed to proof or disproof a specific hypothesis. The [[experiment| experiments]] will follow the logic of the scientific discovery [1] on which a hypothesis will support a prediction and this will be tested by experimental [[assay| assays]] (''i.e.'', observations under controlled conditions). The result of these experiments will proof or disproof the specific hypothesis and, usually, provide new hypotheses to test. A scientific project must be carefully designed to obtain relevant statistical information through enough [[replica| data collection]].[1] Popper K (2002) The logic of scientific discover. Routledge Classics. ISBN: 978-0-415-27843-0  +
[[File:Proline.png|left|100px|Proline]] '''Proline''' (Pro), C<sub>5</sub>H<sub>9</sub>NO<sub>2</sub>, is an amino acid which occurs under physiological conditions mainly in the nonpolar form, with ''p''K<sub>a1</sub> = 1.99 ''p''K<sub>a2</sub> = 10.96. Proline is an [[anaplerotic]] substrate that supports both the proline pathway control state and the [[glutamate-anaplerotic pathway control state]]. Proline is used as a single substrate or in combination with carbohydrate-derived metabolites in mitochondria particularly of flight muscle of many (but not all) insects. Proline is oxidized to delta-1-pyrroline-5-carboxylate by the [[mtIM]] L-proline:quinone oxidoreductase ([[proline dehydrogenase]], ProDH), with reduction of FAD to FADH<sub>2</sub> and direct entry into the [[Q-junction]]. delta-1-pyrroline-5-carboxylate is converted to [[glutamate]] by 1-pyrroline-5-carboxylate dehydrogenase.  +
'''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.  +
A '''prosthetic group''' is a [[cofactor]] that is attached permanently and tightly or even covalently to an enzyme and that is regenerated in each enzymatic turnover. Thus a prostethic group is distinguished from a [[coenzyme]] or cosubstrate that is attached loosely and transiently. Like a coenzyme, the prosthetic group is required by an enzyme for its activity. A prosthetic group is 'a tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity' (IUPAC definition). FMN/FMNH<sub>2</sub> and FAD/FADH<sub>2</sub> are prosthetic groups of [[Complex I]] and [[Complex II]], respectively.  +
The terms '''proton''' p and [[hydrogen ion]] H<sup>+</sup> are used synonymously in chemistry. In particle physics, a proton is a subatomic particle with a positive electric charge. Protons and neutrons are collectively referred to as ''nucleons''. The proton is a bare charge with only about 1/64 000 of the radius of a hydrogen atom, and so the free proton is extremely reactive chemically. Therefore, the free proton has an extremely short lifetime in aqueous solutions where it forms the [[hydronium ion]], H<sub>3</sub>O<sup>+</sup>, which in turn is further solvated by water molecules in clusters such as H<sub>5</sub>O<sub>2</sub><sup>+</sup> and H<sub>9</sub>O<sub>4</sub><sup>+</sup>.  +
Flux of protons driven by the protonmotive force across the inner mt-membrane, bypassing the [[ATP synthase]] and thus contributing to [[LEAK respiration]]. Proton leak-flux depends non-linearly (non-ohmic) on the protonmotive [[force]]. Compare: [[Proton slip]].  +
Mitochondrial '''proton pumps''' are large enzyme complexes (CI, CIII, CIV, CV) spanning the inner mt-membrane, partially encoded by mtDNA. [[Complex I|CI]], [[CIII]] and [[CIV]] are proton pumps that drive [[proton]]s against the electrochemical [[protonmotive force]], driven by electron transfer from reduced substrates to oxygen. In contrast, [[ATP synthase]] (also known as CIV) is a proton pump that utilizes the energy of proton flow along the protonmotive force to drive phosphorylation of [[ADP]] to [[ATP]].  +
'''Proton slip''' 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]].  +
The '''protonmotive force''' ∆<sub>m</sub>''F''<sub>H<sup>+</sup></sub> is known as Δp in Peter Mitchell’s chemiosmotic theory [1], which establishes the link between electric and chemical components of energy transformation and coupling in [[oxidative phosphorylation]]. The unifying concept of the ''pmF'' ranks among the most fundamental theories in biology. As such, it provides the framework for developing a consistent theory and nomenclature for mitochondrial physiology and bioenergetics. The protonmotive force is not a vector force as defined in physics. This conflict is resolved by the generalized formulation of isomorphic, compartmental [[force]]s, ∆<sub>tr</sub>''F'', in energy (exergy) transformations [2]. Protonmotive means that there is a potential for the movement of protons, and force is a measure of the potential for motion. The ''pmF'' is generated in [[oxidative phosphorylation]] by oxidation of reduced fuel substrates and reduction of O<sub>2</sub> to H<sub>2</sub>O, driving the coupled proton translocation from the mt-matrix space across the mitochondrial inner membrane (mtIM) through the proton pumps of the [[electron transfer pathway]] (ETS), which are known as respiratory Complexes CI, CIII and CIV. ∆<sub>m</sub>''F''<sub>H<sup>+</sup></sub> consists of two partial isomorphic forces: (''1'') The chemical part, ∆<sub>d</sub>''F''<sub>H<sup>+</sup></sub>, relates to the diffusion (d) of uncharged particles and contains the chemical potential difference<sup>§</sup> in H<sup>+</sup>, ∆''µ''<sub>H<sup>+</sup></sub>, which is proportional to the pH difference, ∆pH. (''2'') The electric part, ∆<sub>el</sub>''F''<sub>p<sup>+</sup></sub> (corresponding numerically to ∆''Ψ'')<sup>§</sup>, is the electric potential difference<sup>§</sup>, which is not specific for H<sup>+</sup> and can, therefore, be measured by the distribution of any permeable cation equilibrating between the negative (matrix) and positive (external) compartment. Motion is relative and not absolute (Principle of Galilean Relativity); likewise there is no absolute potential, but isomorphic forces are stoichiometric potential differences<sup>§</sup>. The total motive force (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆<sub>m</sub>''F''<sub>H<sup>+</sup></sub>. Reading this symbol by starting with the proton, it can be seen as ''pmF'', or the subscript m (motive) can be remembered by the name of Mitchell, ∆<sub>m</sub>''F''<sub>H<sup>+</sup></sub> = ∆<sub>d</sub>''F''<sub>H<sup>+</sup></sub> + ∆<sub>el</sub>''F''<sub>p<sup>+</sup></sub> With classical symbols, this equation contains the [[Faraday constant]], ''F'', multiplied implicitly by the charge number of the proton (''z''<sub>H<sup>+</sup></sub> = 1), and has the form [1] ∆p = ∆''µ''<sub>H<sup>+</sup></sub>∙''F''<sup>-1</sup> + ∆''Ψ'' A partial electric force of 0.2 V in the electrical [[format]], ∆<sub>el</sub>''F''<sub><u>''e''</u>H<sup>+</sup>''a''</sub>, is 19 kJ∙mol<sup>-1</sup> H<sup>+</sup><sub>''a''</sub> in the molar format, ∆<sub>el</sub>''F''<sub><u>''n''</u>p<sup>+</sup>''a''</sub>. For 1 unit of ∆pH, the partial chemical force changes by -5.9 kJ∙mol<sup>-1</sup> in the molar format, ∆<sub>d</sub>''F''<sub><u>''n''</u>H<sup>+</sup>''a''</sub>, and by 0.06 V in the electrical format, ∆<sub>d</sub>''F''<sub><u>''e''</u>H<sup>+</sup>''a''</sub>. Considering a driving force of -470 kJ∙mol<sup>-1</sup> O<sub>2</sub> for oxidation, the thermodynamic limit of the H<sup>+</sup><sub>''a''</sub>/O<sub>2</sub> ratio is reached at a value of 470/19 = 24, compared to the mechanistic stoichiometry of 20 for the [[N-pathway]] with three coupling sites.  
The '''protonmotive pressure''', ∆<sub>m</sub>''Π''<sub>H<sup>+</sup></sub> or ''pmP'' [kPa], is an extension of Peter Mitchell’s concept of the [[protonmotive force]] ''pmF'', based on Fick’s law of diffusion and Einstein’s diffusion equation, accounting for osmotic pressure (corresponding to the diffusion term in the ''pmF'') and electric pressure (the electric term or membrane potential in the ''pmF''). The linearity of the generalized flow-pressure relationship explains the non-ohmic flow-force dependence in the proton leak rate as a function of membrane potential. The total motive pressure (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆<sub>m</sub>''Π''<sub>H<sup>+</sup></sub>, ∆<sub>m</sub>''Π''<sub>H<sup>+</sup></sub> = ∆<sub>d</sub>''Π''<sub>H<sup>+</sup></sub> + ∆<sub>el</sub>''Π''<sub>p<sup>+</sup></sub>  +
'''PubMed''' is a free search tool for articles in the life sciences field.  +
'''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.  +
Researchers need to be introduced into adhering to '''publicly deposited protocols'''. [[Prespecified protocols |Prespecified]] and [[time-stamped protocols]] that are publicly deposited may help to save Millions of Euros that may otherwise be wasted on research that is lacking coherent standards.  +
[[File:Pyruvic_acid.jpg|left|80px|Pyruvic acid]] '''Pyruvic acid''', C<sub>3</sub>H<sub>4</sub>O<sub>3</sub>, is an alpha-keto monocarboxylic acid which occurs under physiological conditions mainly as the anion '''pyruvate<sup>-</sup>, P''', with ''p''K<sub>a</sub> = 2.5. Pyruvate is formed in glycolysis from phosphoenolpyruvate. In the cytosol, pyruvate is a substrate of [[lactate dehydrogenase]]. Pyruvate enters the mitochondrial matrix via a specific low ''K''<sub>m</sub>' H<sup>+</sup>/monocarboxylate cotransporter known as the [[pyruvate carrier]]. Similarly, the plasma membrane of many cell types has H<sup>+</sup>/monocarboxylate cotransporter activity and pyruvate can thus be added as a substrate to living cells. In the mt-matrix the oxidative decarboxylation of pyruvate is catalyzed by [[pyruvate dehydrogenase]] and yields [[acetyl-CoA]]. Pyruvate competitively reverses the inhibition of [[Complex IV | cytochrome ''c'' oxidase]] by [[cyanide]]. Pyruvate is an antioxidant reacting with [[hydrogen peroxide]].  +
'''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.  +
The monocarboxylic acid [[pyruvate]]<sup>-</sup> is exchanged electroneutrally for OH<sup>-</sup> by the '''pyruvate carrier'''. H<sup>+</sup>/anion symport is equivalent to OH<sup>-</sup>/anion antiport.  +
'''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.  +
Oxidative decarboxylation of pyruvate is catalyzed by the '''pyruvate dehydrogenase complex''' in the mt-matrix, and yields acetyl-CoA.  +
The ADP-ATP phosphorylation system or P»-system. ''See'' [[Phosphorylation system]].  +
Q
Q +
Multiple meanings of Q ::::» [[Coenzyme Q]] Q ::::» [[Charge]] ''Q'', ''Q''<sub>el</sub> ::::» [[Heat]] ''Q'', ''Q''<sub>th</sub>  +
'''Q calibration'''  +
[[Image:Q-box 002.jpg|right|180px]]The '''Q-Module''', developed for measuring the [[Q redox state]] and [[cyclic voltammetry]], is supported by the [[NextGen-O2k]] and consists of the [[Q-Sensor]], integrated electronic components in the O2k, and the [[DatLab]] software.  +
[[Image:Q stopper.jpg|right|180px]]The '''Q-Sensor''' has been designed as a part of the [[Q-Module]] for measurements with [[cyclic voltammetry]] and voltammetry, allowing for analysis of the [[Q redox state]]. The Q-Stopper with the reference electrode is called Q-Sensor, which is plugged in the NextGen-O2k. A [[three-electrode system]] is used to detect the [[Q redox state]]. Two of the three electrodes (glassy carbon and platinum electrode) are built into the Q-Stopper, while the reference electrode is removable ([[Reference-Electrode\2.4 mm]]).  +
'''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.  +
[[File:SUIT-catg FNSGp.jpg|right|300px|Q-junction]] The '''Q-junction''' is a junction for [[convergent electron flow]] in the [[Electron transfer pathway]] (ET-pathway) from type N substrates and mt-matrix dehydrogenases through [[Complex I]] (CI), from type F substrates and FA oxidation through [[electron-transferring flavoprotein Complex]] (CETF), from succinate (S) through [[Complex II]] (CII), from glycerophosphate (Gp) through [[glycerophosphate dehydrogenase Complex]] (CGpDH), from choline through [[choline dehydrogenase]], from dihydro-orotate through [[dihydro-orotate dehydrogenase]], and other enzyme Complexes into the Q-cycle (ubiquinol/ubiquinone), and further downstream to [[Complex III]] (CIII) and [[Complex IV]] (CIV). The concept of the Q-junction, with the [[N-junction]] and [[F-junction]] upstream, provides the rationale for defining [[Electron-transfer-pathway state]]s and [[categories of SUIT protocols]].  +
Different '''Q-pools''' are more or less clearly distinguished in the cell, related to a variety of models describing degress of Q-pool behavior. (''1'') [[CoQ]]-pools are distinguished according to their compartmentation in the cell: mitochondrial CoQ (mtCoQ) and CoQ in other organelles versus plasma-membrane CoQ. (''2'') The total mitochondrial CoQ-pool mtCoQ is partitioned into an [[ETS]]-reactive Q-pool, Q<sub>ra</sub>, and an inactive mtCoQ-pool, Q<sub>ia</sub>. (''2a'') The Q<sub>ra</sub>-pool is fully reduced in the form of quinol QH<sub>2</sub> under anoxia, and fully oxidized in the form of quinone in aerobic [[mitochondrial preparations]] incubated without [[CHNO-fuel substrate]]s. Intermediate redox states of Q<sub>ra</sub> are sensitive to pathway control and coupling control of mitochondrial electron transfer and [[OXPHOS]]. (''2b'') The Q<sub>ia</sub>-pool remains partially reduced and oxidized independent of aerobic-anoxic transitions. The redox state of Q<sub>ia</sub> is insensitive to changes in mitochondrial respiratory states. (''3'') The Q<sub>ra</sub>-pool is partitioned into Q with Q-pool behavior according to the fluid-state model (synonymous: random-collision model) and Q tightly bound to supercomplexes according to the solid-state model. The two models describe the extremes in a continuum of homogenous or heterogenous Q-pool behavior. The CII-Q-CIII segment of the [[S-pathway]] is frequently considered to follow homogenous Q-pool behavior participating in the Q<sub>hom</sub>-pool, whereas the CI-Q-CIII segment of the [[N-pathway]] indicates [[supercomplex]] organization and metabolic channeling with different degrees of Q-pool heterogeneity contributing to the Q<sub>het</sub>-pool.  +
The '''Q-redox state''' reflects the redox status of the [[Q-junction]] in the mitochondrial or chloroplast [[ETS|electron transfer system (ETS)]]. [[Coenzyme Q]] (CoQ or Q, [[ubiquinone]]) is a mobile redox component located centrally in the mitochondrial [[ETS]], while plastoquinones are essential mobile components in the photosynthetic system with a similar function. The Q-redox state depends on the balance between reducing capacities of convergent electron entries from fuel substrates into the Q-junction and oxidative capacities downstream of Q to the electron acceptor oxygen. Therefore, deficiencies in the mitochondrial [[ETS]], originating from e.g. the malfunction of respiratory Complexes, can be detected by measuring the changes of the Q-redox state with respect to the respiratory activity. A three-electrode system was implemented into the NextGen-O2k to monitor the Q-redox state continuously and simultaneously with respiratory oxygen consumption. Added CoQ2 reflects the mitochondrial Q-redox state when equilibrating both with the detecting electrode and the biological sites (e.g. Complexes I, II and III).  +
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.  +
In the context of '''quantities, symbols, and units''', a code is required to convert terms defining physicochemical quantities into symbols (encoding) and to decode symbols as used in equations, text, and figures. Then symbols and abbreviations gain meaning. Simple symbols — such as ''Q'' or ''N'' — are used with different meanings depending on context (think of ''Q'' for heat and ''Q'' for electric charge; or ''N'' for number of cells and ''N'' for number of O<sub>2</sub> molecules). The context provides the code. When the context is extended, the symbols have to be expanded too, including more detail to avoid confusion (''Q''<sub>th</sub> versus ''Q''<sub>el</sub>; ''N''<sub>ce</sub> versus ''N''<sub>O<sub>2</sub></sub>). Then symbols may appear too complicated, loosing the function of sending their message quickly. There is no single best way to design the right symbol or to replace meaningful symbols (''Q''<sub>el</sub>) by ambiguous abbreviations (''Q'') — all depends on context. We need to use the adequate medium (words, symbols, and abbreviations; equations, text, and figures; videos and slide presentations) and provide the code to achieve communication. The medium is the message, the message is the meaning — from [https://en.wikipedia.org/wiki/The_Medium_Is_the_Massage Marshall McLuhan] to [[Hofstadter 1979 Harvester Press |Hofstadter]].  +
A '''quantity''' is the attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively. A [[dimension |dimensional]] quantity is a number (variable, parameter, or constant) connected to its dimension, which is different from 1. {''Quote''} The value of a quantity is generally expressed as the product of a number and a unit. The unit is simply a particular example of the quantity concerned which is used as a reference, and the number is the ratio of the value of the quantity to the unit. {''end of Quote'': Bureau International des Poids et Mesures 2019 The International System of Units (SI), p. 127)}.  +
'''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.  +
'''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]].  +
'''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.  +
R
[[File:J(R-L).jpg|50 px|R-L ROUTINE-coupling efficiency]] The '''''R-L'' control efficiency''', ''j<sub>R-L</sub>'' = (''R-L'')/''R'' = 1-''L/R'', is the fraction of [[ROUTINE respiration]] coupled to phosphorylation in living cells. ROUTINE respiration is corrected for [[LEAK respiration]] to obtain the [[R-L net ROUTINE capacity |''R-L'' net ROUTINE capacity]]. The flux control efficiency ''j<sub>R-L</sub>'' is the ''R-L'' net ROUTINE capacity normalized for the reference rate ''R''. The background state is the [[LEAK respiration|LEAK]] state, and the flux control variable is stimulation to ROUTINE respiration by physiologically controlled ATP turnover in living cells.  +
[[Image:R-L.jpg|50 px|R-L net ROUTINE capacity]] The '''''R-L'' net ROUTINE capacity''' is [[ROUTINE respiration]] corrected for [[LEAK respiration]]. ''R-L'' is the respiratory capacity available for phosphorylation of ADP to ATP. Oxygen consumption in the ROUTINE state of respiration measured in living cells, therefore, is partitioned into the ''R-L'' net ROUTINE capacity, strictly coupled to phosphorylation ''P»'', and nonphosphorylating LEAK respiration, ''L<sub>R</sub>'', compensating for proton leaks, slip and cation cycling: ''R'' = ''R-L''+''L<sub>R</sub>''. It is frequently assumed that [[LEAK respiration]] ''L'', as measured in the LEAK state, overestimates the LEAK component of respiration, ''L<sub>R</sub>'', as measured in the ROUTINE state, particularly if the protonmotive force is not adjusted to equivalent levels in ''L'' and ''L<sub>R</sub>''. However, if the LEAK component increases with enzyme turnover during ''R'', the low enzyme turnover during ''L'' may counteract the effect of the higher ''pmF''.  +
[[Image:R over E.jpg|50 px|''R/E'' control ratio]] The '''''R/E'' control ratio''' is the ratio of (partially coupled) [[ROUTINE respiration]] ''R'' and (noncoupled) [[ET capacity]] ''E''. The ''R/E'' control ratio is an expression of how close ROUTINE respiration operates to ET capacity.  +
[[File:R.jpg]] In the living cell, '''ROUTINE respiration''' (''R'') or ROUTINE activity in the physiological coupling state is controlled by cellular energy demand, energy turnover and the degree of coupling to phosphorylation (intrinsic [[uncoupling]] and pathological [[dyscoupling]]). The conditions for measurement and expression of respiration vary ([[oxygen flux]] in state ''R'', ''J''<sub>O<sub>2</sub>''R''</sub> or [[oxygen flow]] in state ''R'', ''I''<sub>O<sub>2</sub>''R''</sub>). If these conditions are defined and remain consistent within a given context, then the simple symbol ''R'' for respiratory state can be used to substitute the more explicit expression for respiratory activity. ''R'' and growth of cells is supported by exogenous substrates in culture media. In media without energy substrates, ''R'' depends on endogenous substrates. ''R'' cannot be measured in [[permeabilized cells]] or [[isolated mitochondria]]. ''R'' is corrected for [[residual oxygen consumption]] (ROX), whereas ''R''´ is the uncorrected apparent ROUTINE respiration or total cellular oxygen consumption of cells including ROX.  +
[[Image:RS232-Cable.JPG|180px|right]]'''RS232 0-modem-Cable''' for connecting the [[O2k-Main Unit]] to the PC or laptop with [[DatLab]] installed. When using DatLab 5, this cable is replaced by [[USB-Cable 2.0\Type A-B]] for O2k-Series E upwards. ''' Discontinued'''  +
RT +
RT indicates '''room temperature''' or 25 °C. ''RT'' is the [[gas constant]] ''R'' [kJ/mol] multiplied by absolute [[temperature]] ''T'' [K]. This is the motive force quantum in the amount format ([[Gnaiger 2020 BEC MitoPathways]]).  +
'''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.  +
[[File:MNE.jpg|left|110px|MNE]] MNE has transitioned into RNE (Rare New England). Rare New England is an organization providing access to support groups, gatherings, events and resources for those affected by Rare Disease and living in the New England area.  +
The '''raw signal''' of the polarographic oxygen sensor is the '''voltage''' obtained after a current-to-voltage conversion in the O2k. ''O2k-Support page:'' '''[[Oxygen signal]]'''  +
'''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 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]].  +
Select '''Recalculate slope''' (Recalc. slope) in the [[Marks - DatLab |Mark information]] window to restore data points in the marked section of the active Flux / Slope plot, if [[Delete points]] or [[Interpolate points]] was used before. The entire plot is recalculated, such that other marked sections which may have been deleted are also restored. Compare [[Restore points]].  +
'''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.  +
'''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".  +
A '''reference spectrum''' for a substance is an [[absorbance spectrum]] of the same substance at a known concentration and [[redox state]].  +
The '''reference state''' Z (reference rate ''Z<sub>X</sub>'') is the respiratory state with high flux in relation to the [[background state]] Y with low background flux ''Y<sub>X</sub>''. The transition between the background state and the reference state is a step brought about by a [[metabolic control variable]] ''X''. If ''X'' stimulates flux (ADP, fuel substrate), it is present in the reference state but absent in the background state. If ''X'' is an inhibitor of flux, it is absent in the reference state but present in the background state. The reference state is specific for a single step to define the [[flux control efficiency]]. In contrast, in a sequence of multiple steps, the common reference state is frequently taken as the state with the highest flux in the entire sequence, as used in the definition of the [[flux control ratio]].  +
[[Image:Reference Electrode 2.4 mm.jpg|right|180px]]'''Reference-Electrode\2.4 mm''': 2.4 mm diameter glass shaft, for [[ISE]].  +
'''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: <small> # Arese Lucini F, Morone F, Tomassone MS, Makse HA (2021) Diversity increases the stability of ecosystems. https://doi.org/10.1371/journal.pone.0228692 # Begley CG, Ioannidis JPA (2015) Reproducibility in science: improving the standard for basic and preclinical research. https://doi.org/10.1161/CIRCRESAHA.114.303819. # 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 # 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 # 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 # 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 # …. </small> 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:2021-0005  
In '''reflectance spectrophotometry''' the light from the sample is reflected back to the [[detector]] using mirrors. Before [[absorbance]] measurements can be made, a [[white balance]] is carried out.  +
'''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.  +
In '''remittance spectrophotometry''' [[incident light]] enters a [[scattering]] medium and is scattered back to the receiving optics (usually [[lightguides]]) before being directed to the [[detector]]. Before [[absorbance]] measurements can be made, a [[white balance]] is carried out.  +
'''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.  +
[[Image:Replacement-Barrel.jpg|right|180px]]'''Replacement-Barrel''' for [[Reference-Electrode\2.4 mm]], 2.4 mm diameter glass.  +
'''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.  +
The reproducibility crisis is alarming.<sup>1</sup> An experiment or study is ''reproducible'' or ''replicable'' when subsequent experiments confirm the results. This is [[research |re-search]]. However, we can define different types of reproducibility depending on the conditions that we use to replicate the previous work or in the information available. Our aim is to focus mostly on two different kinds<sup>2</sup>: '''1. Direct:''' is when we obtaining the same results using the same experimental conditions, materials, and methods as described in the original experiment. This would be the ideal reproducibility of an experiment. However, it requires a very accurate description of how the original experiment was performed. Some journals are trying to resolve the '''reproducibility crisis''' improving the rigor and the excellence on the reported methods and results (e.g. [https://www.cell.com/star-authors-guide STAR Methods in Cell Press]). '''2. Systematical:''' refers to obtaining the same results, but under different conditions; for example, using another cell line or mouse strain or humman study, or inhibiting a gene pharmacologically instead of genetically. This opens the door to subsequent studies to find the conditions under which an initial finding holds.  +
A '''requirement''' is a singular documented physical or functional need that a particular design, product or process must be able to perform.  +
'''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]].  +
[[File:Ren.png|100px|link=https://wiki.oroboros.at/index.php/File:Ren.png]] Oxygen consumption due to '''residual endogenous substrates'''. ''Ren'' is the respiration in the REN state. It is due to oxidative reactions in [[mt-preparation]]s incubated without addition of fuel substrates in the absence or presence of ADP (in the presence of ADP to stimulate the consumption of endogenous fuel substrates: [[State 2]]). ''Ren'' values may be used as technical replicates when obtained from the same mt-preparation in different protocols. ''Ren'' may be higher than ''Rox''. Correspondingly, Q and NAD are not fully oxidized in the REN state compared to the ROX state. In previous editions (including [[Gnaiger 2020 BEC MitoPathways]]), the REN state was not distinguished from the [[ROX]] state. However, in novel applications (Q-Module and NADH-Module), a distinction of these states is necessary. Care must be taken when assuming ''Ren'' as a substitute of ''Rox'' correction of mitochondrial respiration.  +
[[File:ROX.jpg|100px|link=https://wiki.oroboros.at/images/3/30/ROX.jpg]] '''Residual oxygen consumption''' ''Rox'' — respiration in the ROX state — is due to oxidative side reactions remaining after inhibition of the [[electron transfer pathway]] (ET pathway) in [[mitochondrial preparation]]s or living cells. Different conditions designated as ROX states (different combinations of inhibitors of CI, CII, CIII and CIV) may result in consistent or significantly different levels of oxygen consumption. Hence the best quantitative estimate of ''Rox'' has to be carefully evaluated. Mitochondrial respiration is frequently corrected for ''Rox'' as the [[baseline state]]. Then, total [[ROUTINE]], [[LEAK respiration]], [[OXPHOS]] or [[Electron transfer pathway |ET]] (''R'', ''L'', ''P'' and ''E'') respiration are distinguished from the corresponding ''Rox''-corrected, mitochondrial (ET-pathway linked) fluxes: ''R''(mt), ''L''(mt), ''P''(mt) and ''E''(mt). Alternatively, ''R'', ''L'', ''P'' and ''E'' are defined as ''Rox''-corrected rates, in contrast to total rates ''R''´, ''L''´, ''P''´ and ''E''´. When expressing ''Rox'' as a fraction of ET capacity ([[flux control ratio]]), total flux ''E''´ (not corrected for ''Rox''), should be taken as the reference. ''Rox'' may be related to, but is of course different from [[ROS]] production. In previous editions, (including [[Gnaiger 2020 BEC MitoPathways]]), the [[REN]] state was not distinguished from the ROX state. However, in novel applications (Q-Module and NADH-Module), a distinction of these states is necessary. Care must be taken when assuming ''Ren'' as a substitute of ''Rox'' correction of mitochondrial respiration.  +
Spectral resolution is a measure of the ability of an instrument to differentiate between two adjacent wavelengths. Two wavelengths are normally considered to be resolved if the minimum detector output signal (trough) between the two peaks is lower than 80 % of the maximum. The resolution of a [[spectrofluorometer]] or [[spectrophotometer]] is dependent on its [[bandwidth]].  +
'''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.  +
The '''respiratory acceptor control ratio''' (''RCR'') is defined as [[State 3]]/[[State 4]] [1]. If State 3 is measured at saturating [ADP], ''RCR'' is the inverse of the OXPHOS control ratio, ''[[L/P]]'' (when State 3 is equivalent to the OXPHOS state, ''P''). ''RCR'' is directly but non-linearly related to the [[P-L control efficiency |''P-L'' control efficiency]], ''j''<sub>''P-L''</sub> = 1-''L/P'', with boundaries from 0.0 to 1.0. In contrast, ''RCR'' ranges from 1.0 to infinity, which needs to be considered when performing statistical analyses. In living cells, the term ''RCR'' has been used for the ratio [[State 3u]]/[[State 4o]], i.e. for the inverse ''[[L/E]]'' ratio [2,3]. Then for conceptual and statistical reasons, ''RCR'' should be replaced by the [[E-L coupling efficiency |''E-L'' coupling efficiency]], 1-''L/E'' [4].  +
The mitochondrial '''respiratory chain''' (RC) consists of enzyme complexes arranged to form a metabolic system of convergent pathways for [[oxidative phosphorylation]]. In a general sense, the RC includes (1) the [[electron transfer pathway]] (ET-pathway), with transporters for the exchange of reduced substrates across the inner mitochondrial membrane, enzymes in the matrix space (particularly dehydrogenases of the tricarboxylic acid cycle), inner membrane-bound electron transfer complexes, and (2) the inner membrane-bound enzymes of the [[phosphorylation system]].  +
'''Respiratory Complexes''' 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]] and [[living cells]] are defined in the current literature in many ways and with a diversity of terms. Mitochondrial respiratory states must be defined in terms of both, the [[coupling-control state]] and the [[electron-transfer-pathway state]].  +
'''Respirometry''' 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.''  +
'''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]]).  +
Select '''Restore points''' in the [[Marks - DatLab |Mark information]] window to restore data points in the marked section of the active signal plot, if [[Delete points]] or [[Interpolate points]] was used before. Compare [[Recalculate slope]].  +
'''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.  +
Reverse electron flow from CII to CI stimulates production of [[ROS]] when mitochondria are incubated with succinate without rotenone in the LEAK state at a high [[mt-membrane potential]]. Depolarisation of the mt-membrane potential (''e.g.'' after ADP addition to stimulate OXPHOS) leads to inhibition of RET and therefore, decrease of RET-initiated ROS production. RET can be also measured when mitochondria are respiring using [[Glycerophosphate |Gp]] without rotenone in the [[LEAK respiration|LEAK]] state. Addition of I<sub>Q</sub>-side inhibitors (ubiquinone-binding side of CI) of [[Complex I |CI]] usually block RET. The following SUIT protocols allow you to measure RET-initiated H<sub>2</sub>O<sub>2</sub> flux in [[mitochondrial preparations]]: [[SUIT-009]] and [[SUIT-026]].  +
Rhodamine 123 (Rh123) is an [[extrinsic fluorophores|extrinsic fluorophore]] and can be used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. Rh123 is a lipophilic cation that is accumulated by mitochondria in proportion to Δ''ψ''<sub>mt</sub>. Using ethanol as the solvent, the excitation maximum is 511 nm and the emission maximum is 534 nm. The recommended excitation and emission wavelengths in PBS are 488 and 515-575 nm, respectively (Sigma-Aldrich).  +
'''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]].  +
'''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.  +
'''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].  +
S
The '''S/NS [[pathway control ratio]]''' is obtained when [[rotenone]] (Rot) is added to the [[NS-pathway control state]] in a defined [[coupling control state]]. The reversed protocol, adding N-type substrates to a [[S-pathway control state]] as the [[background state]] does not provide a valid estimation of S-linked respiration with succinate in the absence of Rot, since [[oxaloacetate]] accumulates as a potent inhibitor of [[succinate dehydrogenase]] (CII).  +
'''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.  +
'''SGp''': [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' SGp; obtained with OctPGMSGp(Rot) '''SUIT protocol:''' [[SUIT-001]] and ((SUIT-002  +
[[Template:Keywords: SI base units]] <br/> [[File:SI-units.png|left|80px|link=https://www.bipm.org/utils/common/pdf/si-brochure/SI-Brochure-9-EN.pdf]] <br/> [[File:Expand.png|right|45px |Click to expand or collaps]] <div class="toccolours mw-collapsible mw-collapsed"> ::: <span style="font-size:105%; color:##424242"> '''Bioblast links: SI base units''' - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>></span> <div class="mw-collapsible-content"> :::: '''Entity, count, and number, and SI base quantities''' / '''SI base units''' [[File:SI-units.png|right|200px|link=https://www.bipm.org/utils/common/pdf/si-brochure/SI-Brochure-9-EN.pdf]] :::: {| class="wikitable" |- ! Quantity name !! Symbol !! Unit name !! Symbol !! Comment |- | [[entity |elementary]] || ''U''<sub>''X''</sub> || [[elementary unit]] || [x] || ''U''<sub>''X''</sub>, ''U''<sub>B</sub>; [x] not in SI |- | [[count]] || ''N''<sub>''X''</sub> || [[elementary unit]] || [x] || ''N''<sub>''X''</sub>, ''N''<sub>B</sub>; [x] not in SI |- | [[number]] || ''N'' || - || dimensionless || = ''N''<sub>''X''</sub>·''U''<sub>''X''</sub><sup>-1</sup> |- | [[amount of substance]] || ''n''<sub>B</sub> || [[mole]] || [mol] || ''n''<sub>''X''</sub>, ''n''<sub>B</sub> |- | [[electric current]] || ''I'' || [[ampere]] || [A] || A = C·s<sup>-1</sup> |- | [[time]] || ''t'' || [[second]] || [s] || |- | [[length]] || ''l'' || [[meter]] || [m] || SI: metre |- | [[body mass |mass]] || ''m'' || [[kilogram]] || [kg] || |- | [[thermodynamic temperature]] || ''T'' || [[kelvin]] || [K] || |- | [[luminous intensity]] || ''I''<sub>V</sub> || [[candela]] || [cd] || |} :::: '''Fundamental relationships''' ::::::» [[Avogadro constant]] ''N''<sub>A</sub> ::::::» [[Boltzmann constant]] ''k'' ::::::» [[elementary charge]] ''e'' ::::::» [[Faraday constant]] ''F'' ::::::» [[gas constant]] ''R'' ::::::» [[electrochemical constant]] ''f'' :::: '''SI and related concepts''' ::::::» [[International System of Units]] ::::::» [[elementary unit]] x ::::::» [[SI prefixes]] ::::::» [[International Union of Pure and Applied Chemistry, IUPAC]] ::::::» [[entity]] ::::::» [[quantity]] ::::::» [[dimension]] ::::::» [[format]] ::::::» [[motive unit]] ::::::» [[iconic symbols]] </div> </div> <br/> [[Category:Keywords]]  
There are 20 '''SI prefixes''' defined to represent multiples and submiltiples of SI units.  +
At '''standard temperature and pressure dry''' (STPD: 0 °C = 273.15 K and 1 atm = 101.325 kPa = 760 mmHg), the molar volume of an ideal gas, ''V''<sub>m</sub>, and ''V''<sub>m,O<sub>2</sub></sub> is 22.414 and 22.392 L∙mol<sup>-1</sup>, respectively. Rounded to three decimal places, both values yield the conversion factor of 0.744 from units used in spiroergometry (''V''<sub>O<sub>2</sub>max</sub> [mL O<sub>2</sub>·min<sup>-1</sup>]) to SI units [µmol O<sub>2</sub>·s<sup>-1</sup>]. For comparison at normal temperature and pressure dry (NTPD: 20 °C), ''V''<sub>m,O<sub>2</sub></sub> is 24.038 L∙mol<sup>-1</sup>. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol<sup>-1</sup> and 22.689 L∙mol<sup>-1</sup> for O<sub>2</sub>.  +
'''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.  +
The '''Substrate-uncoupler-inhibitor titration (SUIT) protocol library''' contains a sequential list of SUIT protocols (D001, D002, ..) with links to the specific SUIT pages. Classes of [[SUIT|SUIT protocols]] are explained with coupling and substrate control defined for [[mitochondrial preparations]].  +
[[File:SUIT-nomenclature.jpg|300px|right|SUIT protocols]] The '''SUIT protocol name''' starts with (i) the [[Categories of SUIT protocols |SUIT category]] which shows the [[Electron-transfer-pathway state]]s (ET pathway types; e.g. N, S, NS, FNS, FNSGp), independent of the actual sequence of titrations. (ii) A further distinction is provided in the SUIT name by listing in parentheses the substrates applied in the [[N-pathway control state]]s, again independent of the sequence of titrations, e.g. NS(GM), NS(PM), FNSGp(PGM). (iii) A sequentially selected number is added, e.g. SUIT_FNS(PM)01 (see [[Coupling/pathway control diagram]]). The '''systematic name''' of a SUIT protocol starts with the [[Categories of SUIT protocols |SUIT category]], followed by an underline dash and the sequence of titration steps (mark names, #''X'', separated by a comma). The [[Marks in DatLab |Marks]] define the section of a [[respiratory state]] in the SUIT protocol. The [[Mark names in DatLab |Mark name]] contains the sequential number and the [[metabolic control variable]], ''X''. The metabolic control variable is the name of the preceding SUIT [[event]]. The [[MitoPedia: SUIT |MitoPedia list of SUIT protocols]] can be sorted by the short name or the systematic name (hence by SUIT protocol category. The '''[[SUIT protocol pattern]]''' is best illustrated by a [[coupling/pathway control diagram]].  +
The '''SUIT protocol pattern''' describes the type of the sequence of coupling and substrate control steps in a SUIT protocol, which may be liner, orthogonal, or diametral.  +
The '''substrate-uncoupler-inhibitor titration ([[SUIT]]) reference protocol''', SUIT RP, provides a common baseline for comparison of mitochondrial respiratory control in a large variety of species, tissues and cell types, mt-preparations and laboratories, for establishing a database on comparative mitochondrial phyisology. The SUIT RP consists of two [[harmonized SUIT protocols]] ([[SUIT-001]] - RP1 and [[SUIT-002]] - RP2). These are coordinated such that they can be statistically evaluated as replicate measurements of [[cross-linked respiratory states]], while additional information is obtained when the two protocols are conducted in parallel. Therefore, these harmonized SUIT protocols are complementary with their focus on specific respiratory coupling and pathway control aspects, extending previous strategies for respirometrc OXPHOS analysis. : [[SUIT-001]] (RP1): 1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10Tm;11Azd : [[SUIT-002]] (RP2): 1D;2OctM;2c;3P;4G;5S;6Gp;7U;8Rot;9Ama;10Tm;11Azd  +
[[File:1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp-.png|400px|SUIT-001]]  +
[[File:ce1;1Dig;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd.png|600px|SUIT-RP1]]  +
[[File:ce1;1Dig;1PM;2D;2c;3U;4G;5S;(6Oct);7Rot;8Gp;9Ama;10AsTm;11Azd.png|400px|SUIT-RP1 for PBMC and PLT]]  +
[[File:Mt;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd .png|400px|SUIT-RP1]]  +
[[File:Pfi;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd.png|400px|SUIT-RP1]]  +
[[File:1D;2M.1;3Oct;4M2;5P;6G;7S;8Gp;9U;10Rot-.png|400px]]  +
[[File:ce1;1Dig;1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px|SUIT-RP2]]  +
[[File:ce1;1Dig;1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px|SUIT-RP2 for PBMC and PLT]]  +
[[File:1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px]]  +
[[File:Pfi;1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px|SUIT-RP2]]  +
[[File:Ce1;ce2(Omy);ce3U-.png|250px]] [[File:Ce5S;1Dig;1c-.png|250px]]  +
[[File:ce1;ce2P;ce3Omy;ce4U;ce5Rot;ce6S;ce7Ama.png|500px]]  +
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