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DatLab provides several keyboard shortcuts to allow for quick access to many functions and settings without using a mouse. +
'''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 - DatLab |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. +
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). +
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[[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]. +
[[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. +
'''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> + RThe 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''']] +
'''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'' 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]]. +
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, this is an '''O2k-MultiSensor''' application of the [[Oroboros O2k-technology]]. The [[NextGen-O2k]] supports all O2k-MultiSensor Modules, while the O2k does not provide for the Q- and NADH-Redox-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). +
Open a previously recorded [[DatLab]] file. +
[[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." +
[[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. +
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