Property:Description
From Bioblast
This is a property of type Text.
D
'''Dihydro-orotate dehydrogenase''' is an electron transfer complex of the inner mitochondrial membrane, converting dihydro-orotate (Dho) into orotate, and linking electron transfer through the [[Q-junction]] to pyrimidine synthesis and thus to the control of biogenesis. +
'''Dihydroethidium''' (also called hydroethidine) is a cell permeant fluorescent probe used to analyse superoxide presence. It is a reduced form of ethidium that presents blue fluorescence, and after oxidation by superoxide becomes able to intercalate DNA and emits red fluorescence (excitation wavelength ~518–535 nm, emission ~605–610 nm). It has been used to detect superoxide by HPLC and by fluorescence microscopy. +
Dilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber. +
'''Dimensions''' are defined in the SI {''Quote''}: Physical quantities can be organized in a system of dimensions, where the system used is decided by convention. Each of the seven base quantities used in the SI is regarded as having its own dimension. .. All other quantities, with the exception of [[count]]s, are derived quantities, which may be written in terms of base quantities according to the equations of physics. The dimensions of the derived quantities are written as products of powers of the dimensions of the base quantities using the equations that relate the derived quantities to the base quantities.
There are quantities ''Q'' for which the defining equation is such that all of the dimensional exponents in the equation for the dimension of ''Q'' are zero. This is true in particular for any quantity that is defined as the ratio of two quantities of the same kind. .. There are also some quantities that cannot be described in terms of the seven base quantities of the SI, but have the nature of a [[count]]. Examples are a number of molecules, a number of cellular or biomolecular entities (for example copies of a particular nucleic acid sequence), or degeneracy in quantum mechanics. Counting quantities are also quantities with the associated unit one. {''end of Quote'': p 136, [[Bureau International des Poids et Mesures 2019 The International System of Units (SI)]]} +
'''Dimethyl sulfoxide''' is a polar aprotic solvent that dissolves both polar and nonpolar compounds and is miscible in a wide range of organic solvents as well as water. DMSO may also be used as a cryoprotectant, added to cell media to reduce ice formation and thereby prevent cell death during the freezing process. +
'''Dinitrochlorobenzene (1-chloro-2,4-dinitrobenzene)''' (DNCB) is a glutathione (GSH) inhibitor. +
'''2,4-dinitrophenole''' (C<sub>6</sub>H<sub>4</sub>N<sub>2</sub>O<sub>5</sub>; M = 184.11 g·mol<sup>-1</sup>) is a protonophore acting as an [[uncoupler]] of [[oxidative phosphorylation]]. +
A '''directive''' is a legal act of the European Union, which requires member states to achieve a particular result without dictating the means of achieving that result. +
The '''Directory of Open Access Journals''' is a free online directory that indexes and provides access to open access peer-reviewed journals. +
In a '''discontinuous system''', gradients in [[continuous system]]s across the length, ''l'', of the diffusion path [m], are replaced by differences across compartmental boundaries of zero thickness, and the local concentration is replaced by the free activity, ''α'' [mol·dm<sup>-3</sup>]. The length of the diffusion path may not be constant along all diffusion pathways, spacial direction varies (''e.g.'', in a spherical particle surrounded by a semipermeable membrane), and information on the diffusion paths may even be not known in a discontinuous system. In this case (''e.g.'', in most treatments of the [[protonmotive force]]) the diffusion path is moved from the (ergodynamic) isomorphic [[force]] term to the (kinetic) [[mobility]] term. The synonym of a discontinuous system is '''compartmental''' or discretized system. In the first part of the definition of discontinuous systems, three compartments are considered: (1) the source compartment A, (2) the sink compartment B, and (3) the internal barrier compartment with thickness ''l''. In a two-compartmental description, a system boundary is defined of zero thickness, such that the barrier comparment (''e.g.'', a semipermeable membrane) is either part of the system (internal) or part of the environment (external). Similarly, the intermediary steps in a chemical reaction may be explicitely considered in an ergodnamic multi-comparment system; alternatively, the kinetic analysis of all intermediary steps may be collectively considered in the catalytic reaction ''mobility'', reducing the measurement to a two-compartmental analysis of the substrate and product compartments. +
A '''dispersion device''' diffracts light at different angles according to its wavelength. Traditionally, prisms and [[diffraction gratings]] are used, the latter now being the most commonly used device in a [[spectrofluorometer]] or [[spectrophotometer]]. +
'''Display DatLab help'''
In this section, we present some issues that could happen during your data analysis related to the graphs display and how to fix them quickly.
Case in which an issue might occur:
::* While analysing your data, trying to close the program while the graph is still being loaded. If you cancel the closing window, the graph will not be loaded at the screen.
In the event of a frozen display of the graphs, try the alternatives below:
::* Click on: Graph > Autoscale time axis
::* Click on: Graph > Scaling (F6); then press OK to confirm the scaling and induce the program to reload the graphs (no changes in the graphs are required). +
The Power-O2k number, which is set in the pull-down menu Oroboros O2k \ [[O2k configuration]], is shown in the active graph. To show it in graphs copied to clipboard, the option "Show Oroboros icon in clipboard files" must be enabled in the Graph-menu [[Graph options - DatLab]]. +
If '''Display numerical value''' the current numerical values are displayed in the graph for the active plots on the Y1 axis and Y2 axis (during data acquisition only). +
The sodium salt of '''Dithionite''' Na<sub>2</sub>S<sub>2</sub>O<sub>4</sub> (Dit) is the 'zero oxygen solution powder' used for [[Oxygen calibration - DatLab |calibration of oxygen sensors]] at [[Zero calibration | zero oxygen concentration]], or for stepwise reduction of oxygen [[concentration]]s in [[MiPNet14.06 Instrumental O2 background |instrumental O<sub>2</sub> background tests]]. It is not recommended to use dithionite in experiments with biological samples or several multisensor approaches, for these see [[Setting the oxygen concentration]]. +
The most common cause of '''drift''' is variation in the intensity of the [[light source]]. The effect of this can be minimised by carrying out a [[balance]] at frequent intervals. +
If a sample contains a number of absorbing substances, it is sometimes possible to select discrete pairs of wavelengths at which the change in [[absorbance]] of a particular substance (due to oxidation or reduction, for example) is largely independent of changes in the [[absorbance]] of other substances present. '''Dual wavelength analysis''' can be carried out for [[cytochrome c]] by subtracting the [[absorbance]] at 540 nm from that at 550nm in order to give a measure of the degree of reduction. Similarly, by subtracting the [[absorbance]] at 465 nm from that at 444 nm, an indicator of the [[redox state]] of [[Complex IV | cytochrome ''aa''<sub>3</sub>]] can be obtained. +
[[Electron-transfer-pathway state |ET-pathway level 2]] is supported by '''duroquinol''' DQ feeding electrons into Complex III (CIII) with further electron transfer to CIV and oxygen. Upstream pathways are inhibited by rotenone and malonic acid in the absence of other substrates linked to ET-pathways with entry into the Q-junction. +
'''Dyscoupled respiration''' is [[LEAK respiration]] distinguished from intrinsically (physiologically) uncoupled and from extrinsic experimentally [[Uncoupler|uncoupled]] respiration as an indication of extrinsic uncoupling (pathological, toxicological, pharmacological by agents that are not specifically applied to induce uncoupling, but are tested for their potential dyscoupling effect). Dyscoupling indicates a mitochondrial dysfunction.
In addition to intrinsic uncoupling, dyscoupling occurs under pathological and toxicological conditions. Thus a distinction is made between physiological uncoupling and pathologically defective dyscoupling in mitochondrial respiration. +
E
» [[Energy]], [[Exergy]] ''E''
» [[elementary charge]] ''e'' = 1.602 176 634∙10<sup>-19</sup> C∙x<sup>-1</sup>
» [[Euler's number]] ''e'' ~ 2.718 281 828 459
» [[ET capacity]] ''E'' +
[[File:J(E-L).jpg|50 px|E-L coupling efficiency]] The '''''E-L'' coupling efficiency''', ''j<sub>E-L</sub>'' = (''E-L'')/''E'' = 1-''L/E'', is 0.0 at zero coupling (''L''=''E'') and 1.0 at the limit of a fully coupled system (''L''=0). The background state is the [[LEAK respiration|LEAK]] state which is stimulated to flux in the [[electron transfer pathway]] reference state by [[uncoupler]] titration. LEAK states ''L''<sub>N</sub> or ''L''<sub>T</sub> may be stimulated first by saturating ADP (rate ''P'' in the OXPHOS state) with subsequent uncoupler titration to the ET state with maximum rate ''E''. The ''E-L'' coupling efficiency is based on measurement of a [[coupling-control ratio]] ([[LEAK-control ratio]], ''L/E''), whereas the thermodynamic or [[ergodynamic efficiency]] of coupling between ATP production (phosphorylation of ADP to ATP) and oxygen consumption is based on measurement of the output/input flux ratio (P»/O<sub>2</sub> ratio) and output/input force ratio (Gibbs force of phosphorylation/Gibbs force of oxidation). The [[biochemical coupling efficiency]] expressed as the ''E-L'' coupling efficiency is independent of kinetic control by the ''E-P'' control efficiency, and is equal to the [[P-L control efficiency |''P-L'' control efficiency]] if ''P=E'' as evaluated in a [[coupling-control protocol]].
» [[#Biochemical_coupling_efficiency:_from_0_to_.3C1 | '''MiPNet article''']] +
[[Image:E-L.jpg|50 px|E-L net ET capacity]] The '''''E-L'' net ET capacity''' is the [[ET capacity]] corrected for [[LEAK respiration]]. ''E-L'' is the respiratory capacity potentially available for ion transport and phosphorylation of ADP to ATP. Oxygen consumption in the ET-pathway state, therefore, is partitioned into the ''E-L'' net ET capacity and LEAK respiration ''L<sub>P</sub>'', compensating for proton leaks, slip and cation cycling: ''E'' = ''E-L''+''L<sub>P</sub>'' (see [[P-L net OXPHOS capacity]]). +
[[File:J(E-P).jpg|50 px|E-P control efficiency]] The '''''E-P'' control efficiency''', ''j<sub>E-P</sub>'' = (''E-P'')/''E'' = 1-''P/E'', is an expression of the relative limitation of [[OXPHOS capacity]] by the capacity of the [[phosphorylation system]]. It is the normalized ''E-P'' excess capacity. ''j<sub>E-P</sub>'' = 0.0 when OXPHOS capacity is not limited by the phosphorylation system at zero ''E-P'' excess capacity, ''P''=''E'', when the phosphorylation system does not exert any control over OXPHOS capacity. ''j<sub>E-P</sub>'' increases with increasing control of the phosphorylation system over OXPHOS capacity. ''j<sub>E-P</sub>'' = 1 at the limit of zero phosphorylation capacity. The [[OXPHOS]] state of mt-preparations is stimulated to [[electron transfer pathway]] capacity ''E'' by [[uncoupler]] titration, which yields the [[E-P excess capacity |''E-P'' excess capacity]]. +
[[Image:ExP.jpg|60 px|link=E-P excess capacity|''E-P'' excess capacity]] The '''''E-P'' excess capacity''' is the difference of the [[ET capacity]] and [[OXPHOS capacity]]. At ''E-P'' > 0, the capacity of the [[phosphorylation system]] exerts a limiting effect on OXPHOS capacity. In addition, ''E-P'' depends on coupling efficiency, since ''P'' aproaches ''E'' at increasing uncoupling. +
[[Image:j(E-R).jpg|50 px|E-R control efficiency]] The '''''E-R'' control efficiency''', ''j<sub>E-R</sub>'' = (''E-R'')/''E'' = 1-''R/E'', is an expression of the relative scope of increasing [[ROUTINE respiration]] in living cells by uncoupler titrations to obtain [[ET capacity]]. ''j<sub>E-R</sub>'' = 0.0 for zero ''E-R'' reserve capacity when ''R''=''E''; ''j<sub>E-R</sub>'' = 1.0 for the maximum limit when ''R''=0. The [[ROUTINE]] state of living cells is stimulated to [[electron transfer pathway]] capacity by [[uncoupler]] titration, which yields the [[E-R reserve capacity |''E-R'' reserve capacity]]. Since ET capacity is significantly higher than [[OXPHOS capacity]] in various cell types (as shown by '''[[cell ergometry]]'''), ''j<sub>E-R</sub>'' is not a reserve capacity available for the cell to increase oxidative phosphorylation, but strictly a scope (reserve) for uncoupling respiration. Similarly, the apparent [[E-P excess ET capacity |''E-P'' excess ET capacity]] is not a respiratory reserve in the sense of oxidative phosphorylation. +
[[Image:ExR.jpg|60 px|E-R reserve capacity]] The '''''E-R'' reserve capacity''' is the difference of [[ET capacity]] and [[ROUTINE respiration]]. For further information, see [[Cell ergometry]]. +
[[File:E.jpg]] '''T capacity''' is the respiratory electron-transfer-pathway capacity ''E'' of mitochondria measured as oxygen consumption in the noncoupled state at optimum [[uncoupler]] concentration. This optimum concentration is obtained by stepwise titration of an established protonophore to induce maximum oxygen flux as the determinant of ET capacity. The experimentally induced noncoupled state at optimum uncoupler concentration is thus distinguished from (''1'') a wide range of uncoupled states at any experimental uncoupler concentration, (''2'') physiological uncoupled states controlled by intrinsic uncoupling (e.g. UCP1 in brown fat), and (''3'') pathological dyscoupled states indicative of mitochondrial injuries or toxic effects of pharmacological or environmental substances. ET capacity in mitochondrial preparations requires the addition of defined fuel substrates to establish an ET-pathway competent state.
» [[#Why ET capacity, why not State 3u.3F | '''MiPNet article''']] +
[[Electron transfer pathway]] competent state, ''see'' '''[[Electron-transfer-pathway state]]'''. +
See '''[[Electron-transfer-pathway state]]''' +
[[File:EUROMIT.jpg|left|250px]]
'''EUROMIT''' is a group based in Europe for organizing '''International Meetings on Mitochondrial Pathology'''. +
'''Ectotherms''' are organisms whose body temperatures conform to the thermal environment. In many cases, therefore, ectotherms are [[poicilotherms | poicilothermic]]. +
'''Editorial board participation''' is a topic addressed in [[COPE core practices for research]]. +
'''Bendavia''' ('''Elamipretide''') was developed as a mitochondria-targeted drug against degenerative diseases, including cardiac ischemia-reperfusion injury. Clinical trials showed variable results. It is a cationic tetrapeptide which readily passes cell membranes, associates with [[cardiolipin]] in the mitochondrial inner membrane. Supercomplex-associated CIV activity significantly improved in response to elamipretide treatment in the failing human heart. +
According to David Fell, "Elasticities are properties of individual enzymes and not the metabolic system. The elasticity of an enzyme to a metabolite is related to the slope of the curve of the enzyme's rate plotted against metabolite concentration, taken at the metabolite concentrations found in the pathway in the metabolic state of interest. It can be obtained directly as the slope of the logarithm of the rate plotted against the logarithm of the metabolic concentration. The elasticity will change at each point of the curve (s,v) and must be calculated for the specific concentration of the metabolite (s) that will give a specific rate (r) of the enzyme activity" (See Figure).
[[File:Elasticity_Measurement.jpg]] +
'''Current''' or electric [[flow]] ''I''<sub>el</sub> is the [[advancement]] of [[charge]] per unit of time, expressed in the SI base unit [[ampere]] [C·s<sup>-1</sup> = A]. Electrons or ions are the current-carrying [[motive entity |motive entities]] of electric flow. Electrons e<sup>-</sup> are negatively charged subatomic particles carrying 'negative electricity' with a mass that is about 1/1700 of the smallest particle — the proton — carrying 'positive electricity' (Thompson 1906). Correspondingly the [[velocity]] of electrons is much higher than that of protons or any other (larger) ion. Current is the velocity ''v'' of paticles times the number of motive charges. Therefore, electron current ''I''<sub>e<sup>-</sup></sub> is of a different nature from electric current ''I''<sub>el''χ''</sub> carried by all species ''i'' of ions ''X<sub>i</sub>'' (cations and anions) summarized as ''χ'' = Σ(''z<sub>i</sub>''·''X<sub>i</sub>''). Whereas ''I''<sub>e<sup>-</sup></sub> is the net translocation of electrons moving forwards and backwards, ''I''<sub>el''χ''</sub> is the net translocation of charges carried by different cations and anions. In contrast, ion current ''I''<sub>elX</sub> of a specific ion X is the partial translocation of charges carried by net translocation of ion X only. If cation current ''I''<sub>elX<sup>+</sup></sub> is antagonized entirely by counterion current ''I''<sub>elY<sup>-</sup></sub> as the process of antiport, then the electric current ''I''<sub>el''χ''</sub> is zero. The (net) electric current in a compartmental system is driven by the electric force Δ<sub>el</sub>''F''<sub>p<sup>+</sup></sub> or electric potential difference Δ''Ψ''<sub>p<sup>+</sup></sub>, whereas a compensated ion/counterion antiport current is insensitive to the electric potential difference. +
'''Electric current density''' is [[current]] divided by area, ''j''=''I''·''A''<sup>-1</sup> [C·m<sup>-2</sup>]. Compare: [[density]]. +
[[File:Table Physical constants.png|right|400px|thumb|]] The '''electrochemical constant''' ''f'' has the SI unit for energy per charge per temperature [J·C<sup>-1</sup>·K<sup>-1</sup>].
''f'' = ''k''·''e''<sup>-1</sup>, the [[Boltzmann constant]] ''k'' divided by the [[elementary charge]] ''e''.
''f'' = ''R''·''F''<sup>-1</sup>, the [[gas constant]] ''R'' divided by the [[Faraday constant]] ''F''. +
[[Image:Electrolyte Reference-Electrode.jpg|right|180px|link=http://www.bioblast.at/index.php/Electrolyte%5CReference-Electrode]]'''Electrolyte\Reference-Electrode''' for [[Reference-Electrode\2.4 mm]] +
'''Electron flow''' through the mitochondrial [[Electron transfer pathway]] (ET-pahway) is the scalar component of chemical reactions in oxidative phosphorylation ([[OXPHOS]]). Electron flow is most conveniently measured as oxygen consumption (oxygraphic measurement of [[oxygen flow]]), with four electrons being taken up when oxygen (O<sub>2</sub>) is reduced to water. +
Electrons that escape the [[electron transfer pathway]] without completing the reduction of oxygen to water at cytochrome ''c'' oxidase, causing the production of [[Reactive_oxygen_species |ROS]]. The rate of electron leak depends on the topology of the complex, the redox state of the moiety responsible of electron leakiness and usually on the protonmotive force ([[Protonmotive force|Δ''p'']]). In some cases, the [[Protonmotive force|Δ''p'']] dependance relies more on the ∆pH component than in the ∆''Ψ''. +
In the mitochondrial '''electron transfer pathway''' (ET pathway) electrons are transferred from externally supplied reduced fuel substrates to oxygen. Based on this experimentally oriented definition (see [[ET capacity]]), the ET pathway consists of (1) the [[membrane-bound ET pathway]] with respiratory complexes located in the inner mt-membrane, (2) [[TCA cycle]] and other mt-matrix dehydrogenases generating NADH and succinate, and (3) the carriers involved in metabolite transport across the mt-membranes.
» [[#Electron transfer pathway versus electron transport chain |'''MiPNet article''']] +
[[File:SUIT-catg FNSGpCIV.jpg|right|400px]]
'''Electron-transfer-pathway states''' are obtained in [[mitochondrial preparations]] (isolated mitochondria, permeabilized cells, permeabilized tissues, tissue homogenate) by depletion of endogenous substrates and addition to the mitochondrial respiration medium of fuel substrates (CHNO) activating specific mitochondrial pathways, and possibly inhibitors of specific pathways. Mitochondrial electron-transfer-pathway states have to be defined complementary to mitochondrial [[coupling-control state]]s. [[Coupling-control state]]s require [[Electron-transfer-pathway state|ET-pathway competent states]], including oxygen supply. [[Categories of SUIT protocols]] are defined according to mitochondrial ET-pathway states.
» [[#ET_pathway_states |'''MiPNet article''']] +
'''Electron-transferring flavoprotein Complex''' (CETF) is a respiratory Complex localized at the matrix face of the inner mitochondrial membrane, supplies electrons to Q, and is thus an enzyme Complex of the mitochondrial [[Electron transfer pathway]] (ET-pathway). CETF links the ß-oxidation cycle with the membrane-bound electron transfer system in [[fatty acid oxidation]] (FAO). +
'''Electronic-TIP2k Upgrading\O2k-Main Unit Series A-D - Former Product ''': not required for [[O2k-Core]], the [[O2k-Main Unit]] has to be returned to the OROBOROS workshop. +
'''Electronic-TIP2k Upgrading\O2k-Main Unit Series E - Former Series ''': not required for [[O2k-Core]], free of charge for Series E in conjunction with the purchase of the [[TIP2k-Module]], the [[O2k-Main Unit]] has to be returned to the OROBOROS workshop. +
[[File:Table Physical constants.png|right|400px|thumb|]] The '''elementary charge''' or proton charge ''e'' has the SI unit coulomb [C], but more strictly coulomb per elementary unit [C·x<sup>-1</sup>]. -''e'' is the charge per electron. Elementary charge ''e'' is the charge per [[elementary entity]] H<sup>+</sup> with SI unit [C] but canonical SI unit [C·x<sup>-1</sup>]. When the charge ''Q''<sub>el</sub> [C] of a number ''N''<sub>e</sub> [x] of electrons e is divided by the count ''N''<sub>e</sub>, then the [[particle charge]] ''Q<sub>N<sub>X</sub></sub>'' (''Q<sub><u>N</u>X</sub>'') charge per elementary entity is obtained, -''e'' = ''Q''<sub>el</sub>/''N''<sub>e</sub> [C·x<sup>-1</sup>]. ''e'' is also used as an atomic unit. +
[[File:Count-vs-number.png|right|120px|link=Unit]]
An '''elementary entity''' is an [[entity]] of type ''X'', distinguished as a single ''[[unit]]'' of countable objects (''X'' = molecules, cells, organisms, particles, parties, items) or events (''X'' = beats, collisions, emissions, decays, celestial cycles, instances, occurrences, parties). "An elementary entity may be an atom, a molecule, an ion, an electron, any other particle or specified group of particles" ([[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |Bureau International des Poids et Mesures 2019)]]. An elementary entity, therefore, needs to be distinguished from non-countable entities and the general class of entities ''X''. This distinction is emphasized by the term 'elementary' (synonymous with 'elementary entity') with symbol ''U''<sub>''X''</sub> and [[unit |elementary unit]] [x].
If an object is defined as an assembly of particles (a party of two, a molecule as the assembly of a stoichiometric number of atoms), then the elementary is the assembly but not the assembled particle. A number of defined elementaries ''U''<sub>''X''</sub> is a [[count]], ''N''<sub>''X''</sub> = ''N''·''U''<sub>''X''</sub> [x], where ''N'' is a number, and as such ''N'' is dimensionless, and ''N'' is a ''number'' (stop) and is not 'a number of ..'. Elementaries are added as items to a count. The elementary ''U''<sub>''X''</sub> has the [[dimension]] U of the [[count]] ''N''<sub>''X''</sub>. The elementary ''U''<sub>''X''</sub> has the same unit [x] as the count ''N''<sub>''X''</sub>, or more accurately it gives the count the defining 'counting-unit', which is the 'elementary unit' [x]. From the definition of count as the number (''N'') of elementaries (''U'') of entity type ''X'', it follows that count divided by elementary is a pure number, ''N'' = ''N''<sub>''X''</sub>·''U''<sub>''X''</sub><sup>-1</sup>. The unit x of a count can neither be the entity ''X'' nor a number. The elementary of type ''X'' defines the identity ''X'' of the elementary ''U''<sub>''X''</sub> with the unit 'elementary unit' with symbol [x]. Since a count ''N''<sub>''X''</sub> is the number of elementary entities, the elementary ''U''<sub>''X''</sub> is not a count (''U''<sub>''X''</sub> is not identical with ''N''·''U''<sub>''X''</sub>).
[[File:Count-vs-number.png|right|120px|link=Elementary entity]]The '''elementary unit''' [x] is the unit of a [[count]] ''N''<sub>''X''</sub> [x]. The [[International System of Units]] defines the unit of a count as 1. Then the '''N'''umber 1 is the '''U'''nit of the '''C'''ount of '''E'''ntities — NUCE. This causes a number of formal inconsistencies which are resolved by introducing the elementary unit [x] as the abstracted unit of Euclid’s unit, which is an [[elementary entity]] ''U''<sub>''X''</sub> [x], and as the unit of Euclid’s number, which is a count ''N''<sub>''X''</sub> [x]. +
'''Enable DL-Protocol editing''' is a novel function of DatLab 7.4 offering a new feature in DL-Protocols: flexibility. Fixed sequences of events and marks can be changed (Skip/Added) in a SUIT protocol by the user. Moreover, the text, instructions, concentrations and titration volumes of injections in a specific DL-Protocol can be edited and saved as [[Export_DL-Protocol_User_(*.DLPU)| user-specific DL-Protocol]] [File]\Export\DL-Protocol User (*.DLPU). To enable it, under the 'Protocols' tab in the menu, select the option 'Enable DL-Protocol editing', and then select the plot in which the marks will be set (''e.g.,'' O2 flux per V). Select the 'Overview' window, where you will be able to edit events and marks names, definition/state, final concentration and titration volumes, as well as select a mark as 'multi' for multiple titration steps, skip a mark, or add a new event or mark. After saving, [[Export_DL-Protocol_User_(*.DLPU)|export a DL-Protocol User (DLPU)]] and load it before running the next experiments. If users of DatLab versions older than DatLab 7.4 wish to alter the nature of the chemicals used or the sequence of injections, we ask them to [https://www.oroboros.at/index.php/o2k-technical-support/ contact the O2k-Technical Support].
For more information:
[[Image:PlayVideo.jpg|50px|link=https://www.youtube.com/watch?v=Vd66dHx-MyI]] [https://www.youtube.com/watch?v=Vd66dHx-MyI Export DL-Protocol User (*.DLPU)] +
'''Endergonic''' transformations or processes can proceed in the forward direction only by coupling to an [[exergonic]] process with a driving force more negative than the positive force of the endergonic process. The backward direction of an endergonic process is exergonic. The distinction between endergonic and [[endothermic]] processes is at the heart of [[ergodynamics]], emphasising the concept of [[exergy]] changes, linked to the performance of [[work]], in contrast to [[enthalpy]] changes, linked to [[heat]] or thermal processes, the latter expression being terminologically linked to ''thermodynamics''. +
An [[energy]] transformation is '''endothermic''' if the [[enthalpy]] change of a closed system is positive when the process takes place in the forward direction and heat is absorbed from the environment under isothermal conditions (∆<sub>e</sub>''Q'' > 0) without performance of work (∆<sub>e</sub>''W'' = 0). The same energy transformation is [[exothermic]] if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are [[exergonic]]. +
'''Endothermy''' is the constant regulation of body temperature by metabolic heat production and control of heat exchange with the environment. +
Heat and work are forms of '''energy''' [1 cal = 4.184 J]. Energy [J] is a fundamental term that is used in physics and physical chemistry with various meanings [1]. These meanings become explicit in the following equations relating to systems at constant [[volume]] (d''V'' = 0) or constant gas [[pressure]] (d''p'' = 0). Energy is exchanged between a system and the environment across the system boundaries in the form of [[heat]], d<sub>e</sub>''Q'', total or available [[work]], d<sub>et</sub>''W'' (or d<sub>et</sub>''W''), and [[matter]], d<sub>mat</sub>''U'' (or d<sub>mat</sub>''H'') [2],
d''U'' = (d<sub>e</sub>''Q'' + d<sub>et</sub>''W'') + d<sub>mat</sub>''U'' ; d''V'' = 0 [Eq. 1a]
d''H'' = (d<sub>e</sub>''Q'' + d<sub>e</sub>''W'') + d<sub>mat</sub>''H'' ; d''p'' = 0 [Eq. 1b]
Whereas d''U'' (or d''H'') describe the [[internal-energy]] change (or [[enthalpy]] change) of the ''system'', heat and work are ''external'' energy changes (subscript e; et: external total; e: external excluding pressure-volume work), and d<sub>mat</sub>''U'' (or d<sub>mat</sub>''H'') are the exchange of matter expressed in internal-energy (or enthaply) equivalents. In closed systems, d<sub>mat</sub>''U'' = 0 (d<sub>mat</sub>''H'' = 0). The energy balance equation [Eq. 1] is a form of the First Law of Thermodynamics, which is the law of conservation of internal-energy, stating that energy cannot be generated or destroyed: energy can only be transformed into different forms of work and heat, and transferred in the form of matter.
Notably, the term '''energy''' is general and vague, since energy may be associated with either the first or second law of thermodynamics. Work is a form of energy exchange [Eq. 1], but can be seen as [[exergy]] exchange in conjunction with d<sub>e</sub>''G'' = d<sub>e</sub>''W'' in a closed system [Eq. 3b].
An equally famous energy balance equation considers energy changes of the system only, in the most simple form for isothermal systems (d''T'' = 0):
d''U'' = d''A'' + ''T''∙d''S'' = d''U'' + d''B'' [Eq. 2a]
d''H'' = d''G'' + ''T''∙d''S'' = d''G'' + d''B'' [Eq. 2b]
The internal-energy change, d''U'' (enthalpy change, d''H'') is the sum of ''free'' energy change ([[Helmholtz energy]], d''A''; or Gibbs energy = [[exergy]] change, d''G'') and ''bound'' energy change ([[bound energy]], d''B'' = ''T''∙d''S''). The bound energy is that part of the energy change that is always bound to an exchange of heat.
A third energy balance equation accounts for changes of the system in terms of irreversible internal processes (i) occuring within the system boundaries, and reversible external processes (e) of transfer across the system boundaries (at constant gas pressure),
d''H'' = d<sub>i</sub>''H'' + d<sub>e</sub>''H'' [Eq. 3a]
d''G'' = d<sub>i</sub>''G'' + d<sub>e</sub>''G'' [Eq. 3b]
The energy conservation law of thermodynamics (first law) can be formulated as d<sub>i</sub>''H'' = 0 (at constant gas pressure), whereas the generally negative sign of the [[dissipated energy]], d<sub>i</sub>''G'' ≡ d<sub>i</sub>''D'' ≤ 0, is a formulation of the second law of thermodynamics. Insertion into Eq. 3 yields,
d''H'' = d<sub>e</sub>''H'' [Eq. 4a]
d''G'' = d<sub>i</sub>''D'' + d<sub>e</sub>''W'' + d<sub>mat</sub>''G'' [Eq. 4b]
When talking about energy transformations, the term energy is used in a general sense without specification of these various forms of energy.
The '''energy charge''' of the adenylate system or adenylate energy charge (AEC) has been defined by Atkinson and Walton (1967) as (ATP + ½ ADP)/(AMP + ADP + ATP). Wheather the AEC is a fundamental metabolic control parameter remains a controversial topic. +
Core '''energy metabolism''' is the integrated biochemical process supplying the cell with ATP, utilizing ATP for various forms of work including biogenesis, maintaining ion and redox balance, and in specific organisms or tissues dissipating heat for temperature regulation. +
'''Energy saving in research''' must rank as a priority of social responsibility — ever since the [[Club of Rome]] published 50 years ago the seminal book on ''The limits to growth'' (1972) [1], and more so today in face of the global threat of climate change and the russian war in aggression against Ukraine.
Energy saving in research does not and must not clash with quality in research. Application of high-quality and predefined [[MitoPedia: SUIT |experimental protocols]] combined with evaluation of [[Replica |repeatability]] and [[Repetitions |reproducibility]] represents primary strategies for energy saving in research. Publication of irreproducible results — adding to the [[reproducibility crisis]] — is the most wasteful aspect of research in terms of resources including [[energy]] (more properly: [[exergy]]). [[Paywall journalism]] is wasteful in terms of financial resources. Dramatically increasing numbers of scientific publications is a pathway towards waste of energy [2].
Besides large-scale strategies on e(n)xergy saving in research — quality versus quantity —, everybody's everyday contributions to energy saving count: to cut greenhouse gas emissions, save biological and geological diversity, and improve equality across societies, gender, continents, and countries.
Do scientists take responsibility for energy saving? Or does biomedical research merely find excuses? Scientific institutions in academia and industry must implement energy saving strategies to reduce waste according to the European Union's [https://energy.ec.europa.eu/topics/energy-efficiency/energy-efficiency-targets-directive-and-rules/energy-efficiency-directive_en Energy efficiency directive], and to consume less energy (exergy) by using it more efficiently ([https://energy.ec.europa.eu/topics/energy-efficiency/energy-efficiency-targets-directive-and-rules/energy-efficiency-targets_en Energy efficiency targets]).
Possible — important but much neglected — contributions include:
* Re-use materials as a superior strategy than recycling, and reduce application of disposable items.
* Reduce waste in cleaning procedures, but do not compromise the [[MiPNet19.03 O2k-cleaning and ISS |quality of cleaning procedures]].
* Replace inefficient equipment (e.g. water baths) by efficient electronic [[O2k-Peltier Temperature Control |Peltier temperature control]].
* Select conferences that you attend by evaluating their 'green deal' strategy. Combine in a single trip participation in a conference and possibly offered satellite events.
* Turn off non-essential equipment; reduce energy-wasting stand-by modes; turn off computer screens and other equipment at the mains when not in use. The monitor consumes over half of the energy used by the average computer. Lower your screen brightness.
* Turn off the lights when you do not gain from extra illumination, when you leave the lab during the day or at the end of every day.
* Reduce heating of the rooms to 19 °C, cooling of rooms to 25 °C. Apply energy-efficient heating and cooling strategies.
* Define your personal energy saving targets at homeoffice and in your workplace.
* Contact your energy quality manager, to suggest improvement of infrastructure and guidelines that help you and other members in the team to comply with energy saving targets.
'''Enthalpy''', ''H'' [J], can under conditions of constant gas pressure neither be destroyed nor created (first law of thermodynamics: d<sub>i</sub>''H''/d''t'' = 0). The distinction between enthalpy and [[internal-energy]] of a system is due to external pressure-volume [[work]] carried out reversibly at constant gas pressure. The enthalpy change of the system, d''H'', at constant pressure, is the internal-energy change, d''U'', minus reversible pressure-volume work,
d''H'' = d''U'' - d<sub>''V''</sub>''W''
Pressure-volume work, d<sub>''V''</sub>''W'', at constant pressure, is the gas pressure, ''p'' [Pa = J·m<sup>-3</sup>], times change of volume, d''V'' [m<sup>3</sup>],
d<sub>''V''</sub>''W'' = -''p''·d''V'' [J]
The ''available'' work, d<sub>e</sub>''W'', is distinguished from external total work, d<sub>et</sub>''W'', [1]
d<sub>e</sub>''W'' = d<sub>et</sub>''W'' - d<sub>''V''</sub>''W''
The change of enthalpy of a system is due to internal and external changes,
d''H'' = d<sub>i</sub>''H'' + d<sub>e</sub>''H''
Since d<sub>i</sub>''H'' = 0 (first law of thermodynamics), the d''H'' is balanced by exchange of heat, work, and matter,
d''H'' = (d<sub>e</sub>''Q'' + d<sub>e</sub>''W'') + d<sub>mat</sub>''H'' ; d''p'' = 0
The exchange of matter is expressed in enthalpy equivalents with respect to a [[reference state]] (formation, f, or combustion, c). The value of d''H'' in an open system, therefore, depends on the arbitrary choice of the reference state. In contrast, the terms in parentheses are the sum of all (total, t) partial energy transformations,
d<sub>t</sub>''H'' = (d<sub>e</sub>''Q'' + d<sub>e</sub>''W'')
A partial enthalpy change of transformation, d<sub>tr</sub>''H'', is distinguished from the total enthalpy change of all transformations, d<sub>t</sub>''H'', and from the enthalpy change of the system, d''H''. In a closed system, d''H'' = d<sub>t</sub>''H''. The enthalpy change of transformation is the sum of the [[Gibbs energy]] (free energy) change of transformation, d<sub>tr</sub>''G'', and the [[bound energy]] change of transformation at constant temperature and pressure, d<sub>tr</sub>''B'' = ''T''·d''S'',
d<sub>tr</sub>''H'' = d<sub>tr</sub>''G'' + d<sub>tr</sub>''B''
An '''entity''' of type ''X'' is something that can measured as an [[extensive quantity]] or counted as an [[elementary entity]]. The term entity with symbol ''X'', therefore, has a general meaning, including but not limited to elementary entities ''U''<sub>''X''</sub>. The distinction can be emphasized by using the term entity-type ''X'', to avoid confusion of an entity ''X'' with the more restricted definition of elementary entity ''U''<sub>''X''</sub> as a ''single'' countable object or event. +
Physicochemical '''equality''' (symbol =) indicates in an equation not only numerical [[equivalence]] (symbol ≡), but an identity of the full meaning. +
Numerical '''equivalence''' (symbol ≡) indicates that two quantities are numerically equal, even if the full meaning may be different. For instance: 1 ≡ 1·1 and 1 ≡ 1/1. In contrast to ≡, the symbol = indicates physicochemical [[equality]]. +
The '''ergodynamic efficiency''', ''ε'' (compare [[thermodynamic efficiency]]), is a power ratio between the output power and the (negative) input power of an energetically coupled process. Since [[power]] [W] is the product of a [[flow]] and the conjugated thermodynamic [[force]], the ergodynamic efficiency is the product of an output/input flow ratio and the corresponding force ratio. The efficiency is 0.0 in a fully uncoupled system (zero output flow) or at level flow (zero output force). The maximum efficiency of 1.0 can be reached only in a fully (mechanistically) coupled system at the limit of zero flow at ergodynamic equilibrium. The ergodynamic efficiency of coupling between ATP production (DT phosphorylation) and oxygen consumption is the flux ratio of DT phosphorylation flux and oxygen flux (P»/O<sub>2</sub> ratio) multiplied by the corresponding force ratio. Compare with the [[OXPHOS-coupling efficiency]]. +
The mission of '''ergodynamics''' is the revelation of relations of general validity. "''Thermodynamics deals with relationships between properties of systems at equilibrium and with differences in properties between various equilibrium states. It has nothing to do with time. Even so, it is one of the most powerful tools of physical chemistry''" [1]. '''Ergodynamics''' is the theory of exergy changes (from the Greek word 'erg' which means [[work]]). Ergodynamics includes the fundamental aspects of thermodynamics ('[[heat]]') and the thermodynamics of irreversible processes (TIP; nonequilibrium thermodynamics), and thus links thermodynamics to kinetics. In its most general scope, ergodynamics is the science of [[energy]] transformations. Classical thermodynamics includes [[open system]]s, yet as a main focus it describes [[closed system]]s. This is reflected in a nomenclature that is not easily applicable to the more general case of open systems [2]. At present, IUPAC recommendations [3] fall short of providing adequate guidelines for describing energy transformations in open systems. +
[[File:Ethanol.png|left|80px|Ethanol]]
<div>
</div><div>'''Ethanol''' or ethyl alcohol, C<sub>2</sub>H<sub>6</sub>O or EtOH, is widely used in the laboratory, particularly as a solvent and cleaning agent. There are different grades of high purity ethanol. Up to a purity of 95.6 % ethanol can be separated from water by destillation. Higher concentrations than 95% require usage of additives that disrupt the azeotrope composition and allow further distillation. Ethanol is qualified as "absolute" if it contains no more than one percent water. Whenever 'ethanol abs.' is mentioned without further specification in published protocols, it refers to ≥ 99 % ethanol a.r. (analytical reagent grade).
</div><div>
</div><div></div> +
'''Ethics on publishing''' follow [https://publicationethics.org/core-practices COPE's guidelines] (or equivalent). A journal's policy on publishing ethics should be clearly visible on its website, and should refer to: (1) Journal policies on authorship and contributorship; (2) How the journal will handle complaints and appeals; (3) Journal policies on conflicts of interest / competing interests; (4) Journal policies on data sharing and reproducibility; (5) Journal's policy on ethical oversight; (6) Journal's policy on intellectual property; and (7) Journal's options for post-publication discussions and corrections. +
'''Ethylene glycol tetraacetic acid''' (EGTA) is a chelator for heavy metals, with high affinity for Ca<sup>2+</sup> but low affinity for Mg<sup>2+</sup>. Sigma E 4378. +
'''Etomoxir''' (Eto; 2[6(4-chlorophenoxy)hexyl]oxirane-2-carboxylate) is an irreversible inhibitor of [[carnitine palmitoyltransferase I]] (CPT-I) on the outer face of the mitochondrial inner membrane. Eto inhibits [[fatty acid oxidation]] by blocking the formation of acyl carnitines from long-chain fatty acids which require the carnitine shuttle for transport into mitochondria. In contrast to long-chain fatty acids, the transport of short- and medium-chain fatty acids is carnitine-independent. +
[[File:Mito-and-Chlora EBEC.png|270px]]
'''EBEC''' is a group based in Europe that organizes the '''European Bioenergetics Conference'''. +
I am often asked by reviewers to discuss the effects of pentobarbitol euthansia on mithochondrial function.
[[Takaki 1997 JJP]]: This paper has been helpful in this discussion. (edit by [[Staples JF]]) +
An '''event''' in [[DatLab]] is a defined point in time, labelled by a name (1 to 10 characters). An event applies to all plots of the selected O2k-Chamber. The event is shown by a vertical line in the graph and the label of the event is shown on the top (DatLab 6 and lower: on the bottom). The default name is the sequential number of the event. It is recommended to edit event labels with a minimum number of characters, and to explain the abbreviation in the 'Definition' box. The final concentration and titration volume can be entered into the corresponding boxes, if the event relates to the titration of a substance. A short comment can be entered to describe the event in detail.
'''Set events''' - Manual events are entered (real-time, connected to the O2k) by pressing [F4] at the time of the event (e.g. to indicate a manual titration into the chamber). An event belongs either to chamber A, chamber B, or both. Instrumental events are added automatically, e.g. when the stirrer (A or B) or illumination (both chambers) is switched on or off.
After setting a new event the Edit event window pops up. Pressing F4 defines the time point of the event. Full attention can then be paid to the experiment. Edit the event later, as it is possible to insert an event at any chosen moment of the plotted record of the experiment by placing the cursor anywhere in the graph at the selected time point by pressing Ctrl and clicking the left mouse button.
'''Edit event''' - Left click on the name of an existing event to open the Edit event window to edit or Delete event.
In events obtained from a selected [[DL-Protocols |protocol]], the entire sequence of consecutive events is defined with event names, definitions, concentrations and titration volumes.
'''Name''' - Enter an event name of 1 to 10 characters. Short names (e.g. O instead of Open) are recommended.
''' Comment''' - Further information can be entered into the text field.
Select O2k-chamber A, B or both. The Event will be shown on plots for both or one selected chamber.
»[[DL-Protocols#DL-Protocol_principles|Protocol events]]
An '''examination''' is a set of operations having the object of determining the value or characteristics of a property. In some disciplines (e.g. microbiology) an examination is the total activity of a number of tests, observations or measurements. +
The '''Exclusion criteria''' include factors or characteristics that make the recruited population ineligible for the outcome parameter. With the [[Inclusion criteria]], this factor must be a cofounder for the outcome parameter +
'''Exergonic''' transformations or processes can spontaneously proceed in the forward direction, entailing the irreversible loss of the potential to performe [[work]] (''erg'') with the implication of a positive internal [[entropy production]]. [[Ergodynamic equilibrium]] is obtained when an exergonic (partial) process is compensated by a coupled [[endergonic]] (partial) process, such that the Gibbs energy change of the total transformation is zero. Final [[thermodynamic equilibrium]] is reached when all exergonic processes are exhausted and all [[force]]s are zero. The backward direction of an exergonic process is endergonic. The distinction between exergonic and [[exothermic]] processes is at the heart of [[ergodynamics]], emphasising the concept of [[exergy]] changes, linked to the performance of [[work]], in contrast to [[enthalpy]] changes, linked to [[heat]] or thermal processes, the latter expression being terminologically linked to ''thermo''dynamics. +
'''Exergy''' includes external and internal [[work]]. Exergy as the external work is defined in the First Law of thermodynamics as a specific form of [[energy]]. Exergy as the dissipated Gibbs or Helmholtz energy is the irreversibly dissipated (internal) loss of the potential of performing work as defined in the Second Law of Thermodynamics.
Changes of exergy d''G'' plus [[bound energy]] yield the [[enthalpy]] change:
d''H'' = d''G'' + ''T''∙d''S'' = d''G'' + d''B'' +
An [[energy]] transformation is '''exothermic''' if the [[enthalpy]] change of a closed system is negative when the process takes place in the forward direction and heat is lost to the environment under isothermal conditions (∆<sub>e</sub>''Q'' < 0) without performance of work (∆<sub>e</sub>''W'' = 0). The same energy transformation is [[endothermic]] if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are [[exergonic]]. +
A number of replica, ''N'', of '''experiment'''s on one [[sample type]] is designed to obtain statistical information about the involved [[population]](s) and to test hypotheses about a population and about differences between populations, when experiments are carried out on different sample types. An experiment may involve various [[assay]]s, ''e.g.'', a respirometric assay and an assay for protein determination. +
An '''experimental code''' can be entered in the [[Sample - DatLab|Sample]] window, containing up to 10 digits. +
'''Experimental log''' provides an automatically generated experimental protocol with detailed information about the O2k settings and calibrations, the [[Sample - DatLab|Sample]] information and various [[Events - DatLab |Events]]. Time-dependent information can be viewed for a single chamber or both chambers. The filter can be selected for viewing minimum information, intermittent by default, or all information. The experimental log can be viewed and saved as a PDF file by clicking on [Preview]. +
it is a function of DatLab (available from version 7.4 onwards) that enables the export of user specific protocols (DL-Protocol User) to the SUIT protocol folder from which they can be uploaded for subsequent measurements. +
'''Export as CSV''' (*.csv) exports plots and events to a text file for further use in Excel and other programs. +
In the context of MiP''events'', '''extended abstracts''' are accepted for preprint publication in [[MitoFit Preprints]] upon evaluation by the MitoFit Preprints Scientific Advisory Board. Publishing extended abstracts with MitoFit Preprints does not preclude later full journal publication, but will make your work fully citable, by assigning each manuscript a unique DOI number, and facilitate discovery and feedback. +
'''Extensive quantities''' pertain to a total system, e.g. [[oxygen flow]]. An extensive quantity increases proportional with system size. The magnitude of an extensive quantity is completely additive for non-interacting subsystems, such as mass or flow expressed per defined system. The magnitude of these quantities depends on the extent or size of the system ([[Cohen 2008 IUPAC Green Book |Cohen et al 2008]]). +
'''External flows''' across the system boundaries are formally reversible. Their irreversible facet is accounted for internally as transformations in a heterogenous system ([[internal flow]]s, ''I''<sub>i</sub>). +
'''Extinction''' is a synonym for [[absorbance]]. +
The '''extinction coefficient''' (''ε'') of a substance is the [[absorbance]] of a 1 µmolar concentration over a 1 cm pathlength and is wavelength-dependent. +
'''Extrinsic fluorophores''' are molecules labelled with a fluorescent dye (as opposed to intrinsic fluorescence or autofluorescence of molecules which does not require such labelling). They are available for a wide range of parameters including ROS (H<sub>2</sub>O<sub>2</sub>, [[Amplex red]]) (HOO<sup>-</sup>, MitoSOX) , mitochondrial membrane potential ([[Safranin]], JC1, [[TMRM]], [[Rhodamine 123]]), Ca<sup>2+</sup> ([[Fura2]], Indo 1, [[Calcium Green]]), pH (Fluorescein, HPTS, SNAFL-1), Mg<sup>2+</sup> ([[Magnesium Green]]) and redox state (roGFP). +
The term '''extroduction''' is ambiguous and needs introduction. An ''external'' extroduction aims at providing a specific exit that opens the door to the parent article. Once you popped up into the article box, there are various ''internal'' extroductions to push down by following hyperlinks to references, keywords, supplementary material, and to the external extroduction. Once you have pushed one level down, there may be hyperlinks to push down further ([[Hofstadter 1979 Harvester Press |Hofstadter 1979]]). One needs to keep track of the links in a nested network of open tabs, to pop up all the way back for returning to the initial reference level. +
F
[[File:SUIT-catg F.jpg|right|300px|F-junction]]
The '''F-junction''' is a junction for [[convergent electron flow]] in the [[electron transfer pathway]] (ET-pathway) from fatty acids through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]) to [[electron transferring flavoprotein]] (CETF), and further transfer through the [[Q-junction]] to [[Complex III]] (CIII). The concept of the F-junction and [[N-junction]] provides a basis for defining [[categories of SUIT protocols]]. Fatty acid oxidation, in the [[F-pathway control state]], not only depends on electron transfer through the F-junction (which is typically rate-limiting) but simultaneously generates NADH and thus depends on N-junction throughput. Hence FAO can be inhibited completely by inhibition of Complex I (CI). In addition and independent of this source of NADH, the N-junction substrate malate is required as a co-substrate for FAO in mt-preparations, since accumulation of AcetylCoA inhibits FAO in the absence of malate. Malate is oxidized in a reaction catalyzed by malate dehydrogenase to oxaloacetate (yielding NADH), which then stimulates the entry of AcetylCoA into the TCA cycle catalyzed by citrate synthase. +
'''F1000Research''' is an Open Research publishing platform for life scientists, offering immediate publication of articles and other research outputs without editorial bias. All articles benefit from transparent peer review and the inclusion of all source data. It is thus not a preprint server, but posters and slides can be published without author fees. Published posters and slides receive a DOI ([[digital object identifier]]) and become citable after a very basic check by our in-house editors. +
'''FCCP''' (Carbonyl cyanide p-trifluoro-methoxyphenyl hydrazone, C<sub>10</sub>H<sub>5</sub>F<sub>3</sub>N<sub>4</sub>O) is a protonophore or [[uncoupler]]: added at uncoupler concentration U<sub>''c''</sub>; ''c'' is the [[optimum uncoupler concentration]] in titrations to obtain maximum mitochondrial respiration in the [[noncoupled respiration|noncoupled]] state of [[ET capacity]]. +
[[File:SUIT-catg FN.jpg|right|300px|F-junction]]
FN is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]], or CI-linked pathway control) in combination with one or several fatty acids, which are supplied to feed electrons into the [[F-junction]] through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH<sub>2</sub> and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). This physiological substrate combination is required for partial reconstitution of [[TCA cycle]] function and convergent electron-input into the [[Q-junction]], to compensate for metabolite depletion into the incubation medium. FS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria. +
[[File:SUIT-catg FNS.jpg|right|300px|F-junction]]
FNS is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]], or CI-linked pathway control) in combination with [[succinate]] ([[S-pathway control state]]; S- or CII-linked) and one or several fatty acids, which are supplied to feed electrons into the [[F-junction]] through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH<sub>2</sub> and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). This physiological substrate combination is required for partial reconstitution of [[TCA cycle]] function and convergent electron-input into the [[Q-junction]], to compensate for metabolite depletion into the incubation medium. FNS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria. +
[[Image:SUIT-catg_FNSGp.jpg|right|400px|Convergent electron flow]]
'''MitoPathway control state:''' FNSGp
:[[Octanoylcarnitine]] or [[Palmitoylcarnitine]] & [[Pyruvate]] &/or [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]].
'''SUIT protocol:''' [[SUIT-002]]
This substrate combination supports convergent electron flow to the [[Q-junction]]. +
The '''Faraday constant''' ''F'' links the electric charge [C] to amount [mol], and thus relates the [[electrical format]] <u>''e''</u> [C] to the [[molar format]] <u>''n''</u> [mol]. The Farady constant, ''F'' = ''e''·''N''<sub>A</sub> = 96 485.33 C/mol, is the product of [[elementary charge]], ''e'' = 1.602176634∙10<sup>-19</sup> C/x, and the [[Avogadro constant]], ''N''<sub>A</sub> = 6.02214076∙10<sup>23</sup> x/mol. The dimensionless unit [x] is not explicitely considered by IUPAC. +
'''Fatty acids''' are carboxylic acids with a carbon aliphatic chain. The fatty acids can be divided by the length of this chain, being considered as short-chain (1–6 carbons), medium-chain (7–12 carbons) and long-chain and very long-chain fatty acids (>12 carbons).
Long-chain fatty acids must be bound to [[Carnitine|carnitine]] to enter the mitochondrial matrix, in a reaction that can be catalysed by [[Carnitine acyltransferase|carnitine acyltransferase]]. For this reason, long-chain fatty acids, such as [[Palmitate|palmitate]] (16 carbons) is frequently supplied to mt-preparations in the activated form of [[Palmitoylcarnitine|palmitoylcarnitine]].
Fatty acids with shorter chains, as [[Octanoate|octanoate]] (8 carbons) may enter the mitochondrial matrix, however, in HRR they are more frequently supplied also in the activated form, such as [[Octanoylcarnitine|octanoylcarnitine]].
Once in the mitochondrial matrix, the [[Fatty acid oxidation|fatty acid oxidation]] (FAO) occurs, generating acetyl-CoA, NADH and FADH2. In the [[Fatty acid oxidation pathway control state|fatty acid oxidation pathway control state]] electrons are fed into the [[F-junction]] involving the [[electron transferring flavoprotein]] (CETF). FAO cannot proceed without a substrate combination of fatty acids & malate, and inhibition of CI blocks FAO. Low concentration of [[malate]], typically 0.1 mM, does not saturate the [[N-pathway]]; but saturates the [[Fatty acid oxidation pathway control state |F-pathway]]. +
'''Fatty acid oxidation''' is a multi-step process by which [[fatty acid]]s are broken down in [[β-oxidation]] to generate acetyl-CoA, NADH and FADH<sub>2</sub> for further electron transfer to CoQ. Whereas NADH is the substrate of CI, FADH<sub>2</sub> is the substrate of [[electron-transferring flavoprotein complex]] (CETF) which is localized on the matrix face of the mtIM, and supplies electrons from FADH<sub>2</sub> to CoQ. Before the ß-oxidation in the mitochondrial matrix, fatty acids (short-chain with 1-6, medium-chain with 7–12, long-chain with >12 carbon atoms) are activated by fatty acyl-CoA synthases (thiokinases) in the cytosol. For the mitochondrial transport of long-chain fatty acids the mtOM-enzyme [[carnitine palmitoyltransferase I]] (CPT-1; considered as a rate-limiting step in FAO) is required which generates an acyl-carnitine intermediate from acyl-CoA and carnitine. In the next step, an integral mtIM protein [[carnitine-acylcarnitine translocase]] (CACT) catalyzes the entrance of acyl-carnitines into the mitochondrial matrix in exchange for free carnitines. In the inner side of the mtIM, another enzyme [[carnitine palmitoyltransferase 2]] (CPT-2) converts the acyl-carnitines to carnitine and acyl-CoAs, which undergo ß-oxidation in the mitochondrial matrix. Short- and medium-chain fatty acids do not require the carnitine shuttle for mitochondrial transport. [[Octanoate]], but not [[palmitate]], (eight- and 16-carbon saturated fatty acids) may pass the mt-membranes, but both are frequently supplied to mt-preparations in the activated form of [[octanoylcarnitine]] or [[palmitoylcarnitine]]. +
[[File:SUIT-catg F.jpg|right|300px|F-junction]]
In the '''fatty acid oxidation pathway control state''' (F- or FAO-pathway), one or several fatty acids are supplied to feed electrons into the [[F-junction]] through fatty acyl CoA dehydrogenase (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting relative to the N-pathway branch), but simultaneously generates FADH<sub>2</sub> and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). In addition and independent of this source of NADH, the type N substrate malate is required at low concentration (0.1 mM) as a co-substrate for FAO in mt-preparations, since accumulation of Acetyl-CoA inhibits FAO in the absence of malate. Malate is oxidized in a reaction catalyzed by malate dehydrogenase to oxaloacetate (yielding NADH), which then stimulates the entry of Acetyl-CoA into the TCA cycle catalyzed by citrate synthase. Peroxysomal ''β''-oxidation carries out few ''β''-oxidation cycles, thus shortening very-long-chain fatty acids (>C<sub>20</sub>) for entry into mitochondrial ''β''-oxidation. Oxygen consumption by peroxisomal [[acyl-CoA oxidase]] is considered as [[residual oxygen consumption]] rather than cell respiration. +
'''Fermentation''' is the process of [[energy metabolism]] used to supply ATP, where redox balance is maintained with internally produced electron acceptors (such as pyruvate or fumarate), without the use of external electron acceptors (such as O<sub>2</sub>). Fermentation thus contrasts with [[cell respiration]] and is an [[anaerobic]] process, but aerobic fermentation may proceed in the presence of oxygen. +
'''File search''' yields a list of all files labelled by the experimental code in a selected directory . Click on the file to preview the experimental log. With '''File Search''' you can search in all folders and subfolders on your computer for DatLab files with a selected experimental code. The experimental code is entered in the DatLab file in the window "Experiment" ([F3]). When you click on a folder and press the button search, the DatLab file names will appear on the right window. Click on a DatLab file and further information (e.g. Sample information, Background information) will appear in the window below. +
[[Bioenergetics Communications]] and [[MitoFit Preprints]] manuscript template. +
[[Image:Filter Set AmR.JPG|180px|right]]'''Filter Set AmR''': Set of filters for the determination of H2O2 production with [[Amplex UltraRed]]. These filters should be used together with [[Fluorescence-Sensor Green]]. The filter set consists of 6 LED filters (round) and 6 photodiode filters (rectangular). +
[[Image:Filter_Set_MgG_CaG.JPG|180px|right]]'''Filter set MgG / CaG''': Set of filters for the determination of concentraions of Mg2+ or Ca2+ with the fluorophores [[Magnesium green]] and [[Calcium green]], respectively. These filters should be used together with [[Fluorescence-Sensor Blue]] or [[Smart Fluo-Sensor Blue]]. The filter set consists of 6 LED filters (round) and 6 photodiode filters (rectangular). +
[[Image:Filter_Set_Saf.JPG|180px|right]]'''Filter set Saf''': Set of filters for the (qualitative) determination of mitochondrial membrane potential with [[Safranin]]. These filters should be used together with [[Fluorescence-Sensor Blue]] or [[Smart Fluo-Sensor Blue]]. The filter set consists of 6 LED filters (round) and 6 photodiode filters (rectangular). +
[[Image:Filter-Cap.JPG|180px|right]]'''Filter-Cap''': O2k-Fluo LED2-Module (O2k-Series D to G) sensors ([[Fluorescence-Sensor Green]] and [[Fluorescence-Sensor Blue]]) and O2k-FluoRespirometer (O2k-Series H to I) sensors ([[Smart Fluo-Sensor Green]] and [[Smart Fluo-Sensor Blue]]) are equipped with a removable Filter-Cap for exchange of optical filters for the optical pathways from the LED to the sample and from the sample to the photodiode. +
'''Filters''' are materials that have wavelength-dependent transmission characteristics. They are can be used to select the wavelength range of the light emerging from a [[light source]], or the range entering the [[detector]], having passed through the sample. In particular they are used in [[fluorometry]] to exclude wavelengths greater than the excitation wavelength from reaching the sample, preventing absorption interfering with the emitted [[fluorescence]]. Standard '''filters''' can also be used for calibrating purposes. +
'''Flavin adenine dinucleotide''', FAD and FADH<sub>2</sub>, is an oxidation-reduction [[prosthetic group]] (redox cofactor; compare [[NADH]]). FMN and FAD are the prosthetic groups of flavoproteins (flavin dehydrogenases). [[Electron-transfer-pathway state |Type F substrates]] (fatty acids) generate FADH<sub>2</sub>, the substrate of [[electron transferring flavoprotein]] (CETF). Thus FADH<sub>2</sub> forms a junction or funnel of electron transfer to CETF, the [[F-junction]] (compare [[N-junction]], [[Q-junction]]), in the [[F-pathway control state]]. In contrast, FADH<sub>2</sub> is not the substrate but the internal product of [[succinate dehydrogenase]] (CII). FAD is the oxidized (quinone) form, which is reduced to FADH<sub>2</sub> (hydroquinone form) by accepting two electrons and two protons. +
'''Flavonoids''' are a group of bioactive polyphenols with potential antioxidant and anti-inflammatory effects, abundant in fruits and vegetables, and in some medicinal herbs. Flavonoids are synthesized in plants from phenylalanine. Dietary intake of flavonoids as nutraceuticals is discussed for targeting T2D and other degenerative diseases. +
In an isomorphic analysis, any form of '''flow''', ''I'' is the [[advancement]] of a process per unit of time, expressed in a specific motive unit [MU∙s<sup>-1</sup>], ''e.g.'', ampere for electric flow or current [A≡C∙s<sup>-1</sup>], watt for heat flow [W≡J∙s<sup>-1</sup>], and for chemical flow the unit is [mol∙s<sup>-1</sup>]. Flow is an [[extensive quantity]]. The corresponding isomorphic [[force]]s are the partial exergy (Gibbs energy) changes per advancement [J∙MU<sup>-1</sup>], expressed in volt for electric force [V≡J∙C<sup>-1</sup>], dimensionless for thermal force, and for chemical force the unit is [J∙mol<sup>-1</sup>], which deserves a specific acronym ([Jol]) comparable to volt. +
'''Fluorescence''' is the name given to light emitted by a substance when it is illuminated (excited) by light at a shorter wavelength. The [[incident light]] causes an electron transition to a higher energy band in the molecules. The electron then spontaneously returns to its original energy state emitting a photon. The intensity of the emitted light is proportional to the concentration of the substance. Fluorescence is one form of [[Luminescence]], especially Photoluminescence. +
[[Image:Fluorescence-Control Unit lettered.jpg|180px|right]] '''Fluorescence-Control Unit''' with O2k-Front Fixation, Current-Control (O2k-Chamber A and B) for regulation of light intensity of the LED in the fluorescence sensors. This item is a standard component of the [[O2k-Fluorescence LED2-Module]]. +
[[Image:Fluorescence-Sensor Blue.JPG|180px|right]]'''Fluorescence-Sensor Blue''': excitation LED 465 nm (dominant wavelength), photodiode, [[Filter-Cap]] equipped with [[Filter Set Saf]] for measurement of mitochondrial membrane potential with [[Safranin]] when delivered. The filter set [[Filter Set MgG / CaG]] for [[Magnesium green]]® / [[Calcium green]]® measurements is included. +
[[Image:Fluorescence-Sensor Green.JPG|180px|right]]'''Fluorescence-Sensor Green''': excitation LED 525 nm (dominant wavelength), photodiode, [[Filter-Cap]] equipped with [[Filter Set AmR]] for [[Amplex® UltraRed|Amplex UltraRed]] measurements when delivered. +
See [[Extrinsic fluorophores]] +
[[Extrinsic fluorophores]]; fluorescent markers. +
'''Fluorometry''' (or [[fluorimetry]]) is the general term given to the method of measuring the fluorescent emission of a substance following excitation by light at a shorter wavelength. +
A '''fluorophore''' is a fluorescent substance that may occur naturally ([[intrinsic fluorophores]]) or that may be added to a sample or preparation whereby the fluorescence intensity is proportional to the concentration of a specific species or parameter within the sample. These are [[extrinsic fluorophores]], also referred to as fluorescent markers. +
'''Flux''', ''J'', is a [[specific quantity]]. Flux is [[flow]], ''I'' [MU·s<sup>-1</sup> per system] (an [[extensive quantity]]), divided by system size. Flux (''e.g.'', [[oxygen flux]]) may be volume-specific (flow per volume [MU·s<sup>-1</sup>·L<sup>-1</sup>]), mass-specific (flow per mass [MU·s<sup>-1</sup>·kg<sup>-1</sup>]), or marker-specific (e.g. flow per mtEU). The [[motive unit]] [MU] of chemical flow or flux is the advancement of reaction [mol] in the chemical format. +
'''Flux / Slope''' is the time derivative of the signal. In [[DatLab]], Flux / Slope is the name of the pull-down menu for (1) normalization of flux (chamber volume-specific flux, sample-specific flux or flow, or flux control ratios), (2) [[flux baseline correction]], (3) [[Instrumental background oxygen flux]], and (4) [[flux smoothing]], selection of the [[scaling factor]], and stoichiometric normalization using a stoichiometric coefficient.
Before changing the normalization of flux from volume-specific flux to sample-specific flux or flow, or flux control ratios, please be sure to use the standard Layout 04a (Flux per volume) or 04b (Flux per volume overlay). When starting with the instrumental standard Layouts 1-3, which display the O2 slope negative, the sample-specific flux or flow, or flux control ratios will not be automatically background corrected. To obtain the background corrected specific flux or flux control ratios, it is needed to tick the background correction in the lower part of the slope configuration window. Background correction is especially critical when performing measurements in a high oxygen regime or using samples with a low respiratory flux or flow. +
The strategy of '''Flux analysis''' using DatLab depends on the research question and the corresponding settings applied in DatLab when recording the data with the O2k. Usng [[MitoPedia: SUIT |SUIT protocols]], a sequence of respiratory steady-states is measured, marks are set, and numerical data are summarized in [[Mark statistics - DatLab|Mark statistics]] (F2). An AI approach is kept in mind when describing guidelines for evaluation of steady-states during data recording and analysis. +
'''Flux baseline correction''' provides the option to display the plot and all values of the [[flux]] (or [[flow]], or [[flux control ratio]]) as the total flux, ''J'', minus a baseline flux, ''J''<sub>0</sub>.
''J<sub>V</sub>''(bc) = ''J<sub>V</sub>'' - ''J<sub>V</sub>''<sub>0</sub>
''J<sub>V</sub>'' = (d''c''/d''t'') · ''ν''<sup>-1</sup> · ''SF'' - ''J°<sub>V</sub>''
For the oxygen channel, ''J<sub>V</sub>'' is O2 flux per volume [pmol/(s·ml)] (or volume-specific O<sub>2</sub> flux), ''c'' is the oxygen concentration [nmol/ml = µmol/l = µM], d''c''/d''t'' is the (positive) slope of oxygen concentration over time [nmol/(s · ml)], ''ν''<sup>-1</sup> = -1 is the stoichiometric coefficient for the reaction of oxygen consumption (oxygen is removed in the chemical reaction, thus the stoichiometric coefficient is negative, expressing oxygen flux as the negative slope), ''SF''=1,000 is the scaling factor (converting units for the amount of oxygen from nmol to pmol), and ''J°<sub>V</sub>'' is the volume-specific background oxygen flux ([[Instrumental background oxygen flux]]). ''Further details'': [[Flux / Slope]]. +
'''Flux control efficiencies''' express the control of respiration by a [[metabolic control variable]], ''X'', as a fractional change of flux from ''Y<sub>X</sub>'' to ''Z<sub>X</sub>'', normalized for ''Z<sub>X</sub>''. ''Z<sub>X</sub>'' is the [[reference state]] with high (stimulated or un-inhibited) flux; ''Y<sub>X</sub>'' is the [[background state]] at low flux, upon which ''X'' acts.
:: ''j<sub>Z-Y</sub>'' = (''Z<sub>X</sub>-Y<sub>X</sub>'')/''Z<sub>X</sub>'' = 1-''Y<sub>X</sub>''/''Z<sub>X</sub>''
Complementary to the concept of [[flux control ratio]]s and analogous to [[elasticity|elasticities]] of [[metabolic control analysis]], the flux control efficiency of ''X'' upon background ''Y<sub>X</sub>'' is expressed as the change of flux from ''Y<sub>X</sub>'' to ''Z<sub>X</sub>'' normalized for the reference state ''Z<sub>X</sub>''.
» [[Flux_control_efficiency#Flux_control_efficiency:_normalization_of_mitochondrial_respiration | '''MiPNet article''']] +
'''Flux control ratios''' ''FCR''s are ratios of oxygen flux in different respiratory control states, normalized for maximum flux in a common reference state, to obtain theoretical lower and upper limits of 0.0 and 1.0 (0 % and 100 %).
For a given protocol or set of respiratory protocols, flux control ratios provide a fingerprint of coupling and substrate control independent of (''1'') mt-content in cells or tissues, (''2'') purification in preparations of isolated mitochondria, and (''3'') assay conditions for determination of tissue mass or mt-markers external to a respiratory protocol (CS, protein, stereology, etc.). ''FCR'' obtained from a single respirometric incubation with sequential titrations (sequential protocol; [[SUIT|SUIT protocol]]) provide an internal normalization, expressing respiratory control independent of mitochondrial content and thus independent of a marker for mitochondrial amount. ''FCR'' obtained from separate (parallel) protocols depend on equal distribution of subsamples obtained from a homogenous mt-preparation or determination of a common [[mitochondrial marker]]. +
'''Force''' is an [[intensive quantity]]. The product of force times [[advancement]] is the [[work]] (exergy) expended in a process or transformation. Force times flow is [[power]] [W].
# The '''fundamental forces''' '''''F''''' of physics are the gravitational, electroweak (combining electromagnetic and weak nuclear) and strong nuclear forces. These gradient-forces are vectors with spatial direction interacting with the motive particle ''X'', d<sub>'''m'''</sub>'''''F'''''<sub>''X''</sub> [N ≡ J∙m<sup>-1</sup> = m∙kg∙s<sup>-2</sup>]. These forces describe the interaction between particles as [[vector]]s with direction of a [[gradient]] in space, causing a change in the motion ([[acceleration]]) of the particles in the spatial direction of the force. The force acts at a distance, and the distance covered is the advancement. If a force is counteracted by another force of equal magnitude but opposite direction, the accelerating effects of the two forces are balanced such that the velocity of the particle does not change and no work is done beyond the interaction between the two counteracting forces. The total net force is partitioned into ''partial'' forces, and the counteracting force may be called ''resistance''. If the resistance is entirely due to frictional effects, then no work is done and the exergy is completely dissipated.
# '''Isomorphic forces''' can be derived from (''1'') the fundamental forces or (''2'') statistical distributions if large numbers of particles are involved. The isomorphic forces are known as 'generalized' forces of nonequilibrium thermodynamics. An isomorphic '''motive force''', Δ<sub>tr</sub>''F''<sub>''X''</sub>, in thermodynamics or ergodynamics is the partial Gibbs (Helmholtz) energy change per advancement of a transformation (tr).
## In [[continuous system]]s accessible to the analysis of gradients, the '''motive vector forces''', d<sub>'''m'''</sub>'''''F'''''<sub>''X''</sub> (units: newton per amount of particles ''X'' [N∙mol<sup>-1</sup>] or per coulombs of particles [N∙C<sup>-1</sup>]), are vectors interacting with the motive particles ''X''.
## In [[discontinuous system]]s that consist of compartments separated by a semipermeable membrane, the '''compartmental motive forces''' are stoichiometric potential differences (∆) across a boundary of zero thickness, distinguished as isomorphic motive forces, ∆<sub>tr</sub>''F''<sub>''X''</sub>, with compartmental instead of spatial direction of the energy transformation, tr. The motive forces are expressed in various [[motive unit]]s, MU [J∙MU<sup>-1</sup>], depending on the energy transformation under study and on the unit chosen to express the motive entity ''X'' and advancement of the process. For the protonmotive force the proton is the motive entity, which can be expressed in a variety of formats with different MU (coulomb, mole, or particle).
[[Image:Forcep for membrane application.jpg|right|180px]]'''Forceps for membrane application''': for [[OroboPOS]] and [[ISE]] membrane application; do not use for tissue preparation. +
[[Image:Forcep for tissue preparation angular tip.jpg|180px|right]]'''Forceps\stainless Steel\angular Tip\fine''': for [[tissue preparation]], stainless steel. Two pairs are used particularly for muscle fiber separation. +
[[Image:Forcep for tissue preparation rounded tip.jpg|right|180px]]'''Forceps\stainless Steel\rounded Tip\sharp''': for [[tissue preparation]], stainless steel, antimagnetic. One pair is recommended for placing the tissue sample onto the [[Microbalance 120 g | microbalance]] and for handling in combination with [[Forceps\stainless Steel\straight Tip\sharp]]. +
[[Image:Forcep for tissue preparation straight tip.jpg|right|180px]]'''Forceps\stainless Steel\straight Tip\sharp''': for [[tissue preparation]], stainless steel, antimagnetic. One pair is recommended for insertion of the sample into the [[O2k-chamber]] and for handling in combination with [[Forceps\stainless Steel\rounded Tip\sharp]]. +
[[File:Table Physical constants.png|right|600px|thumb|Converstion between different motive formats and corresponding motive units ([[Gnaiger 2020 BEC MitoPathways]])]].
Different '''formats''' can be chosen to express physicochemical quantities ([[motive entity |motive entities]] or transformants) in corresponding [[motive unit]]s [MU]. Fundamental formats for electrochemical transformations are:
* <u>''N''</u>: particle or molecular format of a count; MU = x
* <u>''n''</u>: chemical or molar format of amount; MU = mol
* <u>''e''</u>: electrical format of charge; MU = C
* <u>''m''</u>: mass format; MU = kg
* <u>''V''</u>: volume format; MU = m<sup>3</sup>
* <u>''G''</u>: exergy format; MU = J
* <u>''H''</u>: enthalpy format; MU = J
* <u>''S''</u>: entropy format; MU = J·K<sup>-1</sup> +
'''Free activity''' ''α<sub>X</sub>'' [MU·m<sup>-3</sup>] is [[pressure]] divided by isomorphic [[force]]. In the chemical [[amount]] format, ''α<sub>X</sub>'' is expressed in units of concentration of ''X'' [mol·L<sup>-1</sup>]. ''α<sub>X</sub>'' is the local concentration in a concentration gradient. If the concentration gradient is collapsed to a boundary of zero thickness in a compartmental system, ''α<sub>X</sub>'' reflects the singularity in the transition between the two phases or compartments. +
A '''free radical''' is any atom or molecule that contains one or more unpaired electrons in an orbital. The degree of chemical reactivity depends on the localization of unpaired electrons. Free radicals are extremely reactive, and they can either donate or accept an electron from other molecules. Free radicals that include oxygen radicals and derivatives of oxygen are [[reactive oxygen species]] (ROS). Likewise, [[reactive nitrogen species]] (RNS) are nitric oxide-derived compounds. ROS/RNS include oxygen/nitrogen free radicals and non-radicals that are easily converted into radicals. Mitochondria are a main endogenous source of free radicals in cells and consequently are exposed to oxidative-nitrosative damage. Electron transfer in the electron transfer-pathway (ET-pathway) is not perfect, leading an electron leakage. This electron leakage permits the formation of ROS such as [[superoxide]] anion (O2•−), [[hydrogen peroxide]] (H<sub>2</sub>O<sub>2</sub>) and the hydroxyl radical (HO•). +
The French Group of Bioenergetics... +
By clicking/enabling '''Full screen''' in the Graph-menu in DatLab the currently selected graph is shown alone on the full screen (On) or together with the other defined graphs (Off). Full screen is particularly useful for a single channel overview and for Copy to clipboard [ALT+G B]. +
'''Fumarase''' or fumarate hydratase (FH) is an enzyme of the [[tricarboxylic acid cycle]] catalyzing the equilibrium reaction between [[fumarate]] and [[malate]]. Fumarase is found not only in mitochondria, but also in the cytoplasm of all eukaryotes. +
'''Fura2''' is a ratiometric fluorescence probe for the measurement of calcium. Its derivative Fura-2-acetoxymethyl ester (Fura2-AM) is membrane permable and can thus be used to measure intracellular free calcium concentration (Grynkiewicz et al., 1985). For this purpose, cells are incubated with Fura2-AM, which crosses the cell membrane by diffusion and is cleaved into free Fura2 and acetoxymethyl groups by cellular esterases. Intracellular free calcium is measured by exciting the dye at 340 nm and 380 nm, which are the excitation optima of calcium-bound and free Fura2, respectively, and emission detection above 500 nm. Through the ratiometric detection unequal distribution of the dye within the cell and other potential disturbances are largely cancelled out, making this a widely used and relatively reliable tool for calcium measurements. +
G
[[File:GM.jpg|left|200px|GM]] '''GM''': [[Glutamate]] & [[Malate]].
'''MitoPathway control state:''' [[NADH electron transfer-pathway state]]
The '''GM-pathway control state''' (glutamate-malate pathway control state) is established when glutamate&malate are added to isolated mitochondria, permeabilized cells and other mitochondrial preparations. Glutamate and transaminase are responsible for the metabolism of [[oxaloacetate]], comparable to the metabolism with acetyl-CoA and citrate synthase. +
[[File:GMS.jpg|left|200px|GMS]]'''GMS''': [[Glutamate]] & [[Malate]] & [[Succinate]].
'''MitoPathway control:''' NS
Transaminase catalyzes the reaction from oxaloacetate to 2-oxoglutarate, which then establishes a cycle without generation of citrate. OXPHOS is higher with GS (CI&II) compared to GM (CI) or SRot (CII). This documents an additive effect of convergent CI&II electron flow to the Q-junction, with consistent results obtained with permeabilized muscle fibres and isolated mitochondria (Gnaiger 2009). +
The '''gain''' is an amplification factor applied to an input signal to increase the output signal. +
[[File:Table Physical constants.png|left|400px|thumb|]] The '''gas constant''', ''R'' = 8.314462618 J·mol<sup>-1</sup>·K<sup>-1</sup>, has the SI unit for energy per amount per temperature. ''R'' is primarily known from the ideal gas equation, ''pV'' = ''nRT'' or ''p'' = ''cRT''. Therefore, ''RT'' is the ratio of pressure ''p'' and concentration ''c''.
''R'' = ''f''·''F'', the [[electrochemical constant]] ''f'' times the [[Faraday constant]] ''F''.
''R'' = ''k''·''N''<sub>A</sub>, the [[Boltzmann constant]] ''k'' times the [[Avogadro constant]] ''N''<sub>A</sub>. +
Users have to enter their user details the first time they use DatLab 8 on a specific computer. As well, entering some basic settings is required when connecting DatLab 8 with an O2k for the first time. +
'''Gibbs energy''' ''G'' [J] is [[exergy]] which cannot be created internally (subscript i), but in contrast to [[internal-energy]] (d<sub>i</sub>''U''/d''t'' = 0) is not conserved but is dissipated (d<sub>i</sub>''G''/d''t'' < 0) in irreversible energy transformations at constant temperature and (barometric) pressure, ''T'',''p''. Exergy is available as [[work]] in reversible energy transformations (100 % [[efficiency]]), and can be partially conserved when the [[exergonic]] transformation is coupled to an [[endergonic]] transformation. +
'''Glucose''', also known as D-glucose or dextrose, is a monosaccharide and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate. +
[[File:Glutamic_acid.jpg|left|100px|Glutamic acid]]'''Glutamic acid''', C<sub>5</sub>H<sub>9</sub>NO<sub>4</sub>, is an amino acid which occurs under physiological conditions mainly as the anion '''glutamate<sup>-</sup>, G''', with ''p''K<sub>a1</sub> = 2.1, ''p''K<sub>a2</sub> = 4.07 and ''p''K<sub>a3</sub> = 9.47. Glutamate&malate is a substrate combination supporting an N-linked pathway control state, when glutamate is transported into the mt-matrix via the [[glutamate-aspartate carrier]] and reacts with [[oxaloacetate]] in the transaminase reaction to form aspartate and [[oxoglutarate]]. Glutamate as the sole substrate is transported by the electroneutral glutamate<sup>-</sup>/OH<sup>-</sup> exchanger, and is oxidized in the mitochondrial matrix by [[glutamate dehydrogenase]] to α-ketoglutarate ([[oxoglutarate|2-oxoglutarate]]), representing the [[glutamate-anaplerotic pathway control state]]. Ammonia (the byproduct of the reaction) passes freely through the mitochondrial membrane. +
'''Glutamate dehydrogenase''', located in the mitochondrial matrix (mtGDH), is an enzyme that converts [[glutamate]] to α-ketoglutarate [http://en.wikipedia.org/wiki/Glutamate_dehydrogenase]. mtGDH is not part of the TCA cycle, but is involved in [[glutaminolysis]] as an [[anaplerosis |anaplerotic reaction]]. +
[[File:G.jpg|left|200px|G]] '''G''': [[Glutamate]] is an [[Anaplerotic pathway control state |anaplerotic]] [[Electron-transfer-pathway state |NADH-linked type 4 substrate]] (N). When supplied as the sole fuel substrate in the '''glutamate-anaplerotic pathway control state''', G is transported by the electroneutral glutamate-/OH- exchanger, and is oxidised via mt-[[glutamate dehydrogenase]] in the mitochondrial matrix. The G-pathway plays an important role in [[glutaminolysis]]. +
The '''glutamate-aspartate carrier''' catalyzes the electrogenic antiport of glutamate<sup>-</sup> +H<sup>+</sup> for aspartate<sup>-</sup>. It is an important component of the malate-aspartate shuttle in many mitochondria. Due to the symport of glutamate<sup>-</sup> + +H<sup>+</sup>, the glutamate-aspartate antiport is not electroneutal and may be impaired by [[uncoupling]]. [[Aminooxyacetate]] is an [[inhibitor]] of the glutamate-aspartate carrier. +
'''Glycerophosphate''' (synonym: α-glycerophosphate; glycerol-3-phosphate; C<sub>3</sub>H<sub>9</sub>O<sub>6</sub>P) is an organophosphate and it is a component of glycerophospholipids. The mitochondrial [[Glycerophosphate dehydrogenase Complex]] oxidizes glycerophosphate to dihydroxyacetone phosphate and feeds electrons directly to ubiquinone. +
'''Glycerophosphate dehydrogenase complex''' (CGpDH) is a Complex of the electron transfer-pathway localized at the outer face of the mt-inner membrane. CGpDH is thus distinguished from cytosolic GpDH. CGpDH oxidizes [[glycerophosphate]] to dihydroxyacetone phosphate and feeds two electrons into the [[Q-junction]], thus linked to an [[Electron-transfer-pathway state|ET pathway level 3 control state]]. +
[[File:SUIT-catg_Gp.jpg|right|300px|Gp-pathway]]
The '''glycerophosphate pathway control state''' (Gp) is an [[Electron-transfer-pathway state |ET-pathway level 3 control state]], supported by the fuel substrate [[glycerophosphate]] and electron transfer through [[glycerophosphate dehydrogenase Complex]] into the [[Q-junction]]. The [[glycerolphosphate shuttle]] represents an important pathway, particularly in liver and blood cells, of making cytoplasmic [[NADH]] available for mitochondrial [[oxidative phosphorylation]]. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophos-phate dehydrogenase. On the outer face of the inner mitochondrial membrane, mitochondrial glycerophosphate dehydrogenase oxidises glycerophosphate back to dihydroxyacetone phosphate, a reaction not generating NADH but reducing a flavin prosthesic group. The reduced flavoprotein donates its reducing equivalents to the electron transfer-pathway at the level of [[CoQ]]. +
[[File:Gp-shuttle.jpg|left|200px|Gp]]
The '''glycerophosphate shuttle''' makes cytoplasmic NADH available for mitochondrial oxidative phosphorylation. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophosphate dehydrogenase. On the outer face of the inner mitochondrial membrane, [[glycerophosphate dehydrogenase complex]] (mitochondrial glycerophosphate dehydrogenase) oxidizes glycerophosphate back to dihydroxyacetone phosphate, a reaction not generating NADH but reducing a flavin prosthesic group. The reduced flavoprotein transfers its reducing equivalents into the [[Q-junction]], thus representing a [[Electron-transfer-pathway state|ET pathway level 3 control state]]. +
A combination of mouse and keyboard commands provides convenient control of graphs in DatLab 8. +
» ''See'' '''[[Layout for DatLab graphs]]'''. +
Several display options can be applied to a DatLab graph under '''Graph options'''. +
H
'''H2DCFDA''' (dichlorodihydrofluorescein diacetate) is a cell permeant fluorescent probe that has been used as an indicator of ROS presence. It is a reduced form of fluorescein that does not present fluorescence. After entry in the cell, it suffers deacetylation by intracellular esterases, and upon oxidation it is converted to dichlorofluorescein (excitation wavelength ~492–495 nm, emission ~517–527 nm). It may be oxidised by hydrogen peroxide, hydroxyl radical, hypochlorite anion, nitric oxide, peroxyl radical, peroxynitrite, singlet oxygen and superoxide. Has been used as a general indicator of ROS by fluorescence microscopy. +
'''8-Hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS)''' is a ratiometric pH fluorophore; pKa = 7.3.
Relative molecular mass: ''M''<sub>r</sub> = 524.39 +
'''Harmonization''' is the process of minimizing redundant or conflicting [[standard]]s which may have evolved independently. To obtain a common basis in reaching a defined objective, critical [[requirement]]s are identified that need to be retained. +
'''Harmonized European norms''' are [[norm]]s valid for all members of the European Union. They are mandatory parts of the individual national collections of norms. +
'''Harmonized [[SUIT protocols]]''' (H-SUIT) are designed to include [[cross-linked respiratory states]]. When performing harmonized SUIT protocols in parallel, measurements of cross-linked respiratory states can be statistically evaluated as replicates across protocols. Additional information is obtained on respiratory coupling and substrate control by including respiratory states that are not common (not cross-linked) across the harmonized protocols. +
A '''harmonized standard''' is a European [[standard]] developed by a recognized European Standards Organisation: CEN, CENELEC, or ETSI. +
'''Healthy ageing''': 'WHO has released the first World report on ageing and health, reviewing current knowledge and gaps and providing a public health framework for action. The report is built around a redefinition of healthy ageing that centres on the notion of functional ability: the combination of the intrinsic capacity of the individual, relevant environmental characteristics, and the interactions between the individual and these characteristics' (Beard 2016 The Lancet). +
A '''healthy reference population''', HRP, establishes the baseline for the relation between body mass and height in healthy people of zero underweight or overweight, providing a reference for evaluation of deviations towards underweight or overweight and obesity. The WHO Child Growth Standards (WHO-CGS) on height and body mass refer to healthy girls and boys from Brazil, Ghana, India, Norway, Oman and the USA. The Committee on Biological Handbooks compiled data on height and body mass of healthy males from infancy to old age (USA), published before emergence of the fast-food and soft-drink epidemic. Four allometric phases are distinguished with distinct allometric exponents. At heights above 1.26 m/x the allometric exponent is 2.9, equal in women and men, and significantly different from the exponent of 2.0 implicated in the body mass index, BMI [kg/m<sup>2</sup>]. +
'''Heat''' is a form of [[energy]] [J]. The relationship between heat and [[work]] provides the foundation of thermodynamics, which describes transformations from an initial to a final state of a system. In energy transformations heat may pass through the boundary of the system, at an external heat flow of d<sub>e</sub>''Q''/d''t''. +
The '''height of humans''', ''h'', is given in SI units in meters [m]. Humans are countable objects, and the symbol and unit of the number of objects is ''N'' [x]. The average height of ''N'' objects is, ''H'' = ''h''/''N'' [m/x], where ''h'' is the heights of all ''N'' objects measured on top of each other. Therefore, the height per human has the unit [m·x<sup>-1</sup>] (compare [[body mass]] [kg·x<sup>-1</sup>]). Without further identifyer, ''H'' is considered as the standing height of a human, measured without shoes, hair ornaments and heavy outer garments. +
'''Heterothermy''' is the variable regulation of body temperature in [[endothermy | endotherms]] which can change their body temperatures as levels of activity and environmental conditions dictate (e.g. hibernators). In '''regional heterothermy''', temperature gradients are present, e.g. between body core and extremeties. +
The '''hexokinase''' catalyzes the phosphorylation of D-glucose at position 6 by ATP to yield D-glucose 6-phosphate as well as the phosphorylation of many other hexoses like D-fructose, D-mannose, D-glucosamine. +
A '''high signal at zero oxygen''' may be observed during [[zero calibration]] (R0). First, check the quality of the [[dithionite]] solution. The following instructions show how to distinguish between a defective sensor head and an electrical leak current. +
[[Image:O2k-Fluorometer.jpg|200px|left|O2k-FluoRespirometer]] '''High-resolution respirometry, HRR''', is the state-of-the-art approach in mitochondria and cell research to measure respiration in various types of [[mitochondrial preparations]] and [[living cells]] combined with MultiSensor modules.
Mitochondrial function and dysfunction have gained increasing interest, reflecting growing awareness of the fact that mitochondria play a pivotal role in human health and disease. HRR combines instrumental accuracy and reliability with the versatility of applicable protocols, allowing practically unlimited addition and combination of substrates, inhibitors, and uncouplers using the [[Oroboros O2k-technology]]. Substrate-uncoupler-inhibitor titration (SUIT) protocols allow the interrogation of numerous mitochondrial pathway and coupling states in a single respirometric assay. Mitochondrial respiratory pathways may be analyzed in detail to evaluate even minor alterations in respiratory coupling and pathway control patterns.
The O2k-technology provides sole source instruments, with no other available instrument meeting its specifications for high-resolution respirometry. Technologically, HRR is based on the Oroboros O2k-technology, combining optimized chamber design, application of oxygen-tight materials, electrochemical sensors, Peltier-temperature control, and specially developed software features (DatLab) to obtain the unique sensitive and quantitative resolution of oxygen concentration and oxygen flux, with both, a closed-chamber or open-chamber mode of operation ([[TIP2k-Module|TIP2k]]). Standardized calibration of the polarographic oxygen sensor (static sensor calibration), calibration of the sensor response time (dynamic sensor calibration), and evaluation of instrumental background oxygen flux (systemic flux compensation) provide the experimental basis for high accuracy of quantitative results and quality control in HRR. HRR can be extended for MultiSensor analysis by using the [[O2k-Fluo Smart-Module]]. [[Smart Fluo-Sensor]]s are integrated into the O2k to measure simultaneously fluorometric signals using specific fluorophores. Potentiometric modules are available with ion-selective electrodes (pH, TPP<sup>+)</sup>. The [[PB-Module]] extends HRR to PhotoBiology with accurate control of the light intensity and measurement of photosynthesis. The O2k and the NextGen-O2k support all these O2k-Modules. The [[NextGen-O2k]] all-in-one, however, is unique in supporting Q-Redox and NADH-Redox Modules.
Small entetic units are counted into the reference system on a balance opposite to the experimental system with the large sample, which in balance contains as many abstract units as the count of entetic units in the reference system. +
'''Homeothermy''' is the stable regulation of body temperature in [[endothermy | endotherms]] by metabolic heat production and control of heat exchange with the environment, or in [[ectotherms]] by behavioural means to select a stable thermal environment. +
'''Horseradish peroxidase''' readily combines with hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and the resultant [HRP-H<sub>2</sub>O<sub>2</sub>] complex can oxidize a wide variety of hydrogen donors. +
Molecular '''hydrogen''' H<sub>2</sub> is a constituent of the air with a volume fraction of 0.00005. It is a colorless and odorless gas with a molecular mass of 2.016. Its pharmacological potential and effects on mitochondrial metabolism are discussed in various publications without complete evidence on the underlying mechanisms. +
The terms '''hydrogen ion''' H<sup>+</sup> and [[proton]], p or p<sup>+</sup>, are used synonymously in chemistry. A hydrogen ion is a positively charged molecule. In particle physics, however, a proton is a submolecular and subatomic particle with a positive electric charge. The H<sup>+</sup> ion has no electrons and is a bare charge with only about 1/64 000 of the radius of a hydrogen atom. Free H<sup>+</sup> is extremely reactive, with an extremely short lifetime in aqueous solutions. There H<sup>+</sup> forms the hydronium ion H<sub>3</sub>O<sup>+</sup>, which in turn is further solvated by water molecules in clusters such as H<sub>5</sub>O<sub>2</sub><sup>+</sup> and H<sub>9</sub>O<sub>4</sub><sup>+</sup>. The transfer of H<sup>+</sup> in an acid–base reaction is referred to as ''proton transfer''. The acid is the H<sup>+</sup> donor and the base is the H<sup>+</sup> acceptor. +
Mitochondrial '''hydrogen ion pumps''' — frequently referred to as "proton pumps" — are large enzyme complexes (CI, CIII, CIV, ATP synthase) spanning the mt-inner membrane mtIM, partially encoded by mtDNA. [[Complex I|CI]], [[CIII]] and [[CIV]] are H<sup>+</sup> pumps that drive [[hydrogen ion]]s against the electrochemical [[protonmotive force]] ''pmF'' and thus generating the ''pmF'', driven by electron transfer from reduced substrates to oxygen. In contrast, [[ATP synthase]] (also known as CV) is a H<sup>+</sup> pump that utilizes the exergy of proton flow along the protonmotive force to drive phosphorylation of [[ADP]] to [[ATP]]. +
[[File:H2O2.jpg|left|60px|Hydrogen peroxide]]
'''Hydrogen peroxide''', H<sub>2</sub>O<sub>2</sub> or dihydrogen dioxide, is one of several reactive oxygen intermediates generally referred to as [[reactive oxygen species]] (ROS). It is formed in various enzyme-catalyzed reactions (''e.g.'', [[superoxide dismutase]]) with the potential to damage cellular molecules and structures. H<sub>2</sub>O<sub>2</sub> is dismutated by [[catalase]] to water and [[oxygen]]. H<sub>2</sub>O<sub>2</sub> is produced as a signaling molecule in aerobic metabolism and passes membranes more easily compared to other ROS. +
'''Hydrogen sulfide (H<sub>2</sub>S)''' is involved in signaling and may have have further biological importance. +
Volume-specific '''hydrogenion flux''' or H<sup>+</sup> flux is measured in a closed system as the time derivative of H<sup>+</sup> concentration, expressed in units [pmol·s<sup>-1</sup>·mL<sup>-1</sup>]. H<sup>+</sup> flux can be measured in an open system at steady state, when any acidification of the medium is compensated by external supply of an equivalent amount of base. The extracellular acidification rate (ECAR) is the change of pH in the incubation medium over time, which is zero at steady state. Volume-specific H<sup>+</sup> flux is comparable to volume-specific [[oxygen flux]] [pmol·s<sup>-1</sup>·mL<sup>-1</sup>], which is the (negative) time derivative of oxygen concentration measured in a closed system, corrected for instrumental and chemical background.
[[pH]] is the negative logarithm of hydrogen ion activity. Therefore, ECAR is of interest in relation to acidification issues in the incubation buffer or culture medium. The physiologically relevant metabolic H<sup>+</sup> flux, however, must not be confused with ECAR. +
'''Hydron''' is the general name for the cation H<sup>+</sup> used without regard to the nuclear mass of the hydrogen entity (H is the hydro group), either for H in its natural abundance or without distinction between the isotopes. +
H<sup>+</sup> forms the '''hydronium ion''' H<sub>3</sub>O<sup>+</sup>, which in turn is further solvated by water molecules in clusters such as H<sub>5</sub>O<sub>2</sub><sup>+</sup> and H<sub>9</sub>O<sub>4</sub><sup>+</sup>. +
'''β-hydroxybutyrate''' or 3-hydroxybutyrate is a ketone body that can be used as a [[NADH electron transfer-pathway state|NADH-linked substrate]]. The β-hydroxybutyrate dehydrogenase produces acetoacetate while reducing NAD<sup>+</sup> to [[NADH]].
<br> +
'''Hydroxycinnamate''' (alpha-cyano-4-hydroxycinnamic acid) is an inhibitor of the [[pyruvate carrier]] (0.65 mM). Above 10 mM [[pyruvate]], hydroxycinnamate cannot inhibit respiration from pyruvate, since the weak pyruvic acid can pass the inner mt-membrane in non-dissociated form. +
'''Hydroxylamine''' is an inhibitor of [[catalase]]. +
'''Hyperoxia''' is defined as environmental oxygen pressure above the [[normoxic]] reference level. Cellular and intracellular hyperoxia is imposed on isolated cells and isolated mitochondria at air-level oxygen pressures which are higher compared to cellular and intracellular oxygen pressures under tissue conditions in vivo. Hyperoxic conditions may impose oxidative stress and may increase maximum aerobic performance. +
'''Hyperthermia''' in [[endothermy | endotherms]] is a state of stressful up to lethal elevated body core temperature. In humans, the limit of hyperthermia (fever) is considered as >38.3 °C, compared to [[normothermia]] at a body temperature of 36.5 to 37.5 °C. +
'''Hyphenation''' is used to connect two words (compound words) or two parts of a word to clarify the meaning of a sentence. The same two words may be hyphenated or not depending on context. Hyphenation may present a problem when searching for a term such as '[[Steady state]]'. It is helpful to write 'steady-state measurement', to clarify that the measurement is performed at steady state, rather than implying that a state measurement is steady. But this does not imply that hyphenation is applied to the 'measurement performed at steady state'. Thus, the key word is '[[steady state]]'. Compound adjectives should be hyphenated (steady-state measurement), but if the compound adjective follows the term (measurement at steady state), hyphenation does not add any information and should be avoided. Find more examples and guidelines in the [https://www.grammarly.com/blog/hyphen/ grammarly blog on Hyphen] and in [https://apastyle.apa.org/learn/faqs/when-use-hyphen apastyle.apa.org]. +
'''Hypothermia''' in [[endothermy | endotherms]] is a state of stressful up to lethal low body core temperature. In humans, the limit of hypothermia is considered as 35 °C, compared to [[normothermia]] at a body temperature of 36.5 to 37.5 °C. Hypothermia is classified as mild (32–35 °C), moderate (28–32 °C), severe (20–28 °C), and profound (<20 °C). +
'''Hypoxia''' (hypox) is defined in respiratory physiology as the state when insufficient O<sub>2</sub> is available for respiration, compared to ''environmental'' hypoxia defined as environmental oxygen pressures below the [[normoxic]] reference level. Three major categories of hypoxia are (''1'') environmental hypoxia, (''2'') physiological tissue hypoxia in hyperactivated states (e.g. at ''V''<sub>O<sub>2</sub>max</sub>) with intracellular oxygen demand/supply balance at steady state in tissues at environmental normoxia, compared to tissue normoxia in physiologically balanced states, and (''3'') pathological tissue hypoxia including ischemia and stroke, anaemia, chronic heart disease, chronic obstructive pulmonary disease, severe COVID-19, and obstructive sleep apnea. Pathological hypoxia leads to tissue hypoxia and heterogenous intracellular anoxia. Clinical oxygen treatment ('environmental hyperoxia') may not or only partially overcome pathological tissue hypoxia. +
I
[[File:IRDiRC.png|150px]] The International Rare Diseases Research Consortium (IRDiRC) teams up researchers and organizations investing in rare diseases research in order to achieve two main objectives by the year 2020, namely to deliver 200 new therapies for rare diseases and means to diagnose most rare diseases. +
[[Image:ISE Package 1 TPP or Ca.JPG|180px|right]] '''O2k-TPP+ and Ca2+ ISE\1 Chamber''': [[ISE]]-Package for 1 TPP+ and Ca2+ electrode. +
[[Image:Ca2+ membranes.jpg|right|180px]]'''ISE-Ca2+ Membranes''': PVC, 4 mm diameter, box of 5 membranes.
To be used with the [[O2k-TPP+ ISE-Module]]. +
[[Image:ISE-Compressible_Tube.JPG|180px|right]]'''ISE-Compressible Tube''' for [[Ion-Selective Electrode TPP+ and Ca2+]]. +
[[Image:ISE-Filling Syringe.JPG|right|180px]]'''ISE-Filling Syringe''' with needle for [[Ion-Selective Electrode TPP+ and Ca2+]]. +
[[Image:ISE-Inner_Glass_Electrode.JPG|180px|right]]'''ISE-Inner Glass Electrode''' of [[ISE]], with Ag/AgCl- and Pt-wire +
[[Image:ISA-Membrane Mounting Tool.JPG|180px|right]]'''ISE-Membrane Mounting Tool''' for [[Ion-Selective Electrode TPP+ and Ca2+]].
[[O2k-TPP+ ISE-Module]]: mounting tool included. +
[[Image:ISE-Membrane Seal.JPG|180px|right]]'''ISE-Membrane Seal''' for [[Ion-Selective Electrode TPP+ and Ca2+]]. +
[[Image:ISE-TPP+ Membranes.JPG|right|180px]]'''ISE-TPP+ Membranes''', PVC, 4 mm diameter, box of 5 membranes. +
'''ISO 10012:2003 Measurement management systems — Requirements for measurement processes and measuring equipment''': An effective measurement management system ensures that measuring equipment and measurement processes are fit for their intended use and is important in achieving product quality objectives and managing the risk of incorrect measurement results. The objective of a measurement management system is to manage the risk that measuring equipment and measurement processes could produce incorrect results affecting the quality of an organization’s product. The methods used for the measurement management system range from basic equipment verification to the application of statistical techniques in the measurement process control. +
'''ISO 13528:2015 Statistical methods for use in proficiency testing by interlaboratory comparison''': Proficiency testing involves the use of interlaboratory comparisons to determine the performance of participants (which may be laboratories, inspection bodies, or individuals) for specific tests or measurements, and to monitor their continuing performance. There are a number of typical purposes of proficiency testing [[ISO/IEC 17043 General requirements for proficiency testing |ISO/IEC 17043:2010]]. These include the evaluation of laboratory performance, the identification of problems in laboratories, establishing effectiveness and comparability of test or measurement methods, the provision of additional confidence to laboratory customers, validation of uncertainty claims, and the education of participating laboratories. The statistical design and analytical techniques applied must be appropriate for the stated purpose(s). +
'''ISO 15189:2012 Medical laboratories — Particular requirements for quality and competence''': This International Standard is for use by medical laboratories in developing their quality management systems and assessing their own competence, and for use by accreditation bodies in confirming or recognising the competence of medical laboratories. While this International Standard is intended for use throughout the currently recognised disciplines of medical laboratory services, those working in other services and disciplines could also find it useful and appropriate. +
'''ISO 17511:2003 In vitro diagnostic medical devices -- Measurement of quantities in biological samples -- Metrological traceability of values assigned to calibrators and control materials''': For measurements of quantities in laboratory medicine, it is essential that the quantity is adequately defined and that the results reported to the physicians or other health care personel and patients are adequately accurate (true and precise) to allow correct medical interpretation and comparability over time and space. +
'''ISO 9001:2015 Quality management systems - requirements''': The adoption of a quality management system is a strategic decision for an organization that can help to improve its overall performance and provide a sound basis for sustainable development initiatives. Consistently meeting requirements and addressing future needs and expectations poses a challenge for organizations in an increasingly dynamic and complex environment. To achieve this objective, the organization might find it necessary to adopt various forms of improvement in addition to correction and continual improvement, such as breakthrough change, innovation and re-organization. +
'''ISO/IEC 17025:2005 General requirements for the competence of testing and calibration laboratories''': The use of this International Standard will facilitate cooperation between laboratories and other bodies, and assist in the exchange of information and experience, and in the harmonization of standards and procedures. This International Standard specifies the general requirements for the competence to carry out tests and/or calibrations, including sampling. It covers testing and calibration performed using standard methods, non-standard methods, and laboratory-developed methods. +
'''ISO/IEC 17043:2010 Conformity assessment — General requirements for proficiency testing''': The use of interlaboratory comparisons is increasing internationally. This International Standard provides a consistent basis to determine the competence of organizations that provide proficiency testing. +
[[Image:ISS-Filter and Tubing.JPG|right|180px]]'''ISS-Filter and Tubing''', [[ISS-Integrated Suction System]]. +
[[Image:ISS.jpg|180px|right]]'''ISS-Integrated Suction System''': Suction pump with stainless steel housing, [[ISS-Waste Bottle|2 liter waste bottle]], [[ISS-Filter_and_Tubing|filter and tubing]]; for siphoning off excess medium from the O2k-Stopper and for emptying the [[O2k-chamber]]s. The ISS is included as a standard component of the [[O2k-Core|O2k-FluoRespirometer]]. Media containing living cells or microorganisms, various poisons (inhibitors, uncouplers) and mixtures of proteins and substrates are safely disposed off in the 2-litre waste bottle. +
[[Image:ISS-Lid.JPG|right|180px]]'''ISS-Lid''', for [[ISS-Waste Bottle]], component of the [[ISS-Integrated Suction System]]. +
[[Image:ISS-Steel_Housing.JPG|right|180px]]'''ISS-Steel Housing''', a component of the [[ISS-Integrated Suction System]]. +
[[Image:ISS-Waste Bottle.JPG|right|180px]]'''ISS-Waste Bottle''', 2-liter, component of the [[ISS-Integrated Suction System]]. +
'''Iconic symbols''' are used in [[ergodynamics]] to indicate more explicitely — compared to standard SI or IUPAC symbols — the quantity represented and some boundary conditions. This is particularly the case in normalized quantities (ratios of quantities). Iconic (or canonical) symbols help to clarify the meaning, are based on SI and IUPAC symbols as far as possible, and may be translated into more commonly used, practical symbols. Several ambiguities in SI and IUPAC symbols are eliminated by the systematic structure of iconic symbols, but it may be impossible to avoid all ambiguities, particulary when long (canonical) symbols are abbreviated in a particular context. Clarity is improved always by showing the unit of a quantity together with the symbol of the quantity. Iconic symbols cannot be identical with IUPAC symbols when a different definition is used — this would add to the confusion. For example, the IUPAC symbols ''n''<sub>B</sub> [mol] and ''V''<sub>B</sub> [m<sup>3</sup>] denote amount and volume of B. Consequently, it should be expected, that the symbol ''Q''<sub>B</sub> indicates charge of B [C]. However, the IUPAC symbol ''Q''<sub>B</sub> is used for particle charge per ion B [C·x<sup>-1</sup>]. This prohibits a consistent definition of ''Q''<sub>B</sub> as a potential iconic symbol for charge carried by a given quantity of ions B with unit [C], instead of particle charge per ion B with unit [C·x<sup>-1</sup>]. Hence, the conventional ambigous system forces compatible iconic symbols to be more complicated, using ''Q''<sub>elB</sub> [C] and ''Q''<sub>''<u>N</u>''B</sub> [C·x<sup>-1</sup>] to distinguish charge of B from charge per elementary B. ''Q''<sub>''<u>n</u>''B</sub> [C·mol<sup>-1</sup>] is charge per molar amount of B. +
The chambers of the [[OROBOROS O2k|Oroboros O2k]] are illuminated by an internal LED. The '''illumination''' is switched on and off in [[DatLab]] during the experiment by pressing [F10]. This illumination must be distinguished from light introduced into the chambers by LEDs for the purpose of spectrophotometric and fluorometric measurements. For these, the internal illumination must be switched off. +
The illumination in both chambers is switched on/off. +
'''Impact factor''' is a measure of a scientific journal's citations per publication. The Journal Citation Reports, maintained by Clarivate Analytics, provides the calculated impact factors. The IF is frequently used as an indicator of a journal's importance or prestige, which is nowadays increasingly contested. +
The relative improvement score, ''RIS'', provides a measure of improvement of a trait from a value measured at baseline, ''B'', to a value measured after treatment, ''T'', expressing the total improvement, ''T-B'', in relation to the theoretical scope of improvement and the level of the trait observed at baseline. '''RIS'' incorporates the concept of diminishing returns and consideres maintaining a high value of a trait as an improvement relative to the potential loss. +
A [[medical device]] is an '''in vitro diagnostic medical device (IVD)''' if it is a reagent, calibrator, control material, kit, specimen receptacle, software, instrument, apparatus, equipment or system, whether used alone or in combination with other diagnostic goods for in vitro use. +
The term '''incident light''' is used for a beam of light falling upon a surface. +
The '''Inclusion criteria''' are based on key features of the target population that the researchers will use to answer their question. These criteria should identify the study population in a consistent, reliable, uniform, and objective manner. With the [[Exclusion criteria]], this factor must be a cofounder for the outcome parameter +
'''Inorgnic phosphate''' (P<sub>i</sub>) is a salt of phosphoric acid. In solution near physiological pH, the species HPO<sub>4</sub><sup>2-</sup> and H<sub>2</sub>PO<sub>4</sub><sup>-</sup> dominate.
''See also'': [[Phosphate carrier]] (Pic). +
A glance '''inside the [[Oroboros O2k]]''' +
The standard '''Instrumental and SUIT DL-Protocols''' package is automatically implemented with the simple DatLab programme installation. We recommend a 'clean install': rename your previous DatLab programme subdirectory (''e.g.'' C:\DatLab_OLD).
Updates and newly developed DL protocols can be simply downloaded by clicking on [Protocols]\Install Oroboros protocol package. +
Instrumental [[Run DL-Protocol/Set O2 limit| DL-Protocols]] (DLP) including DatLab example traces, instructions, brief explanatory texts, links to relevant pages and templates for data evaluation can be browsed from inside DatLab 7.4. Click on menu [Protocols]\Instrumental: Browse DL-Protocols and templates to open a folder with all the [[Run DL-Protocol/Set O2 limit| DL-Protocols]] and templates for cleaning, calibration, and background determination provided with the DatLab 7.4. Select a sub-directory and open an DL-Protocol and/or template as desired. +
'''Integration time''' is the time taken to scan a single full range spectrum using [[photodiode arrays]]. It is equivalent to the exposure time for a camera. The shortest integration time defines the fastest response time of a [[spectrophotometer]]. Increasing the integration time increases the [[sensitivity]] of the device. The [[white balance]] or [[balance]] and subsequent measurements must always be carried out at the same integration time. +
Intensive quantities are partial derivatives of an extensive quantity by the advancement, d<sub>tr</sub>''ξ''<sub>''X''</sub>, of an energy transformation tr; ''example:'' [[Force]]. In contrast to [[extensive quantity |extensive quantities]] which pertain to the entire system and are additive, extensive quantities 'take well defined values at each point of the system' ([[Prigogine 1967 Interscience]]) and are non-additive. Intensive and extensive quantities can be easily discriminated by the units, e.g. [J] for the extensive quantity, in contrast to [J·mol<sup>-1</sup>] for the corresponding intensive quantity. In the general definition of thermodynamics, intensive quantities are not distinguished from [[specific quantity |specific quantities]] ([[Cohen 2008 IUPAC Green Book]]). [[Ergodynamics]] emphasizes the contrast between specific quantities which are extensive quantities normalized for a variable expressing system size (mass, volume of the system, amount of substance in a system) and intensive quantities which are normalized for the motive unit of a transformation (mass exchanged, volume change of the system, amount of substance reacting in a system; [[Gnaiger 1993 Pure Appl Chem]]). Intensive and specific quantities are both non-additive, take well defined values at each point of the system, and both corresponding quantities are expressed in identical units, e.g. the intensive quantity Gibbs force of a catabolic reaction (such as oxidation; 0 = -1 Glc - 6 O<sub>2</sub> + 6 CO<sub>2</sub> + 6 H<sub>2</sub>O), Δ<sub>k</sub>''G''<sub>Glc</sub> [kJ·mol<sup>-1</sup>], and the specific quantity Gibbs energy per mole glucose contained in a system, ''G''<sub>Glc</sub> [kJ·mol<sup>-1</sup>] (with respect to an arbitrarily defined reference state, such as the reference state of formation or combustion). +
An '''interlaboratory comparison''' is the organization, performance and evaluation of measurements or tests on the same or similar items by two or more laboratories in accordance with predetermined conditions. +
Within the system boundaries, irreversible '''internal flows''', ''I''<sub>i</sub>,—including chemical reactions and the dissipation of internal gradients of heat and matter—contribute to internal entropy production, d<sub>i</sub>''S''/d''t''. In contrast, [[external flow]]s, ''I''<sub>e</sub>, of heat, work, and matter proceed reversibly across the system boundaries (of zero thickness). Flows are expressed in various [[format]]s per unit of time, with corresponding [[motive unit]]s [MU], such as chemical [mol], electrical [C], mass [kg]. Flow is an [[extensive quantity]], in contrast to [[flux]] as a [[specific quantity]]. +
'''Internal-energy''', ''U'' [J], can neither be destroyed nor created (first law of thermodynamics: d<sub>i</sub>''U''/d''t'' = 0). Note that ''internal'' (subscript i), as opposed to ''external'' (subscript e), must be distinguished from "internal-energy", ''U'', which contrasts with "[[Helmholtz energy]]", ''A'', as [[enthalpy]], ''H'', contrasts with Gibbs energy, ''G''. +
[[File:IMP LOGO.JPG|150px]]The '''International Mito Patients''' is a network of national patient organizations involved in mitochondrial disease. Mitochondrial disease is a rare disease with a limited number of patients per country. The national patient organizations which are a member of IMP each are active and powerful in their own countries. By joining forces IMP can represent a large group of patients and as such be their voice on an international level. +
[[File:ISMM.jpg|150px|left|ISMM]]The '''International Society for Mountain Medicine''' is an interdisciplinary society comprising about xx members worldwide. Its purpose is .. +
[[File:ISOTT LOGO.jpg|200px|left]]
The '''International Society on Oxygen Transport to Tissue''' is an interdisciplinary society comprising about 250 members worldwide. Its purpose is to further the understanding of all aspects of the processes involved in the transport of oxygen from the air to its ultimate consumption in the cells of the various organs of the body. Founded in 1973, the society has been the leading platform for the presentation of many of the technological and conceptual developments within the field both at the meetings themselves and in the proceedings of the society. +
The '''International Standard Serial Number''', ISSN, is a code used to identify periodical publications, independent of which media are used (print and/or electronic). - [[Bioenergetics Communications]], BEC: [https://portal.issn.org/resource/ISSN/2791-4690 ISSN 2791-4690] +
The '''International System of Units''' (SI) is the modern form of the metric system of [[unit]]s for use in all aspects of life, including international trade, manufacturing, security, health and safety, protection of the environment, and in the basic science that underpins all of these. The system of quantities underlying the SI and the equations relating them are based on the present description of nature and are familiar to all scientists, technologists and engineers.
The definition of the SI units is established in terms of a set of seven defining constants. The complete system of units can be derived from the fixed values of these defining constants, expressed in the units of the SI. These seven defining constants are the most fundamental feature of the definition of the entire system of units. These particular constants were chosen after having been identified as being the best choice, taking into account the previous definition of the SI, which was based on seven base units, and progress in science (p. 125). +
The '''International Union of Pure and Applied Chemistry''' (IUPAC) celebrated in 2019 the 100<sup>th</sup> anniversary, which coincided with the [https://iupac.org/united-nations-proclaims-international-year-periodic-table-chemical-elements/ International Year of the Periodic Table of Chemical Elements (IYPT 2019)]. IUPAC {''Quote''} notes that marking Mendeleev's achievement will show how the periodic table is central to connecting cultural, economic, and political dimensions of global society “through a common language” {''end of Quote''} (Horton 2019). 2019 is proclaimed as the [https://iupac.org/united-nations-proclaims-international-year-periodic-table-chemical-elements/ International Year of the Periodic Table of Chemical Elements (IYPT 2019)]. For a '''common language''' in mitochondrial physiology and bioenergetics, the IUPAC ''Green book'' (Cohen et al 2008) is a most valuable resource, which unfortunately is largely neglected in bioenergetics textbooks. Integration of [[ergodynamics |open systems and non-equilibrium thermodynamic]] approaches remains a challenge for developing a common language (Gnaiger 1993; [[BEC 2020.1]]). +
'''International Oxygraph Course''' (IOC), see [[O2k-Workshops]]. +
Organizer of
* [http://bioblast.at/index.php/Klinische_MitochondrienMedizin_und_Umweltmedizin_2015 Klinische MitochondrienMedizin und Umweltmedizin 2015]
* [http://wiki.oroboros.at/index.php/Klinische_MitochondrienMedizin_und_Umweltmedizin_2016_Heidelberg_DE Klinische MitochondrienMedizin und Umweltmedizin 2016]
* [http://wiki.oroboros.at/index.php/Klinische_Mitochondrienmedizin_und_Umweltmedizin_2017_Heidelberg_DE Klinische MitochondrienMedizin und Umweltmedizin 2017]
* [[Clinical Mitochondria- and Environmental Medicine 2018 Heidelberg DE|Klinische MitochondrienMedizin und Umweltmedizin 2018]] +
Select '''Interpolate points''' in the [[Marks - DatLab |Mark information]] window to interpolate all data points in the marked section of the active graph. See also [[Delete points]] and [[Restore points]] or [[Recalculate slope]]. +
Physiological, '''intracellular oxygen pressure''' is significantly lower than air saturation under normoxia, hence respiratory measurements carried out at air saturation are effectively hyperoxic for cultured cells and isolated mitochondria. +
An '''Intrinsic flourophore''' is a naturally occurring [[fluorophore]] of which [[NADH]], aromatic amino acids and flavins are examples. +
[[Image:Ion-Selective_Electrode_TPP+_and_Ca2+.JPG|180px|right]]'''Ion-Selective Electrode TPP+ and Ca2+''': [[ISE]] with 6 mm outer diameter shaft, for [[Stopper\white PVDF\angular Shaft\side+6.2+2.6 mm Port]].
[[O2k-TPP+ ISE-Module]]: 2 ISE. +
[[File:Isocitrate.png|left|100px|isocitrate]]'''isocitrate''', C<sub>6</sub>H<sub>5</sub>O<sub>7</sub><sup>-3</sup>, is a tricarboxylic acid trianion, intermediate of the [[tricarboxylic acid cycle|TCA cycle]], obtained by isomerization of citrate. The process is catalyzed by [[aconitase]], forming the enzyme-bound intermediate ''cis''-aconitate. +
'''Isocitrate dehydrogenase''' forms 2-oxoglutarate from isocitrate in the [[TCA cycle]]. +
'''Isolated mitochondria''', imt, are mitochondria separated from a tissue or cells by breaking the plasma membranes and attachments to the cytoskeleton, followed by centrifugation steps to separate the mitochondria from other components. +
The boundaries of '''isolated system'''s are impermeable for all forms of energy and matter. Changes of isolated systems have exclusively internal origins, ''e.g.'', internal entropy production, d<sub>i</sub>''S''/d''t'', internal formation of chemical species ''i'' which is produced in a reaction ''r'', d<sub>i</sub>''n<sub>i</sub>''/d''t'' = d<sub>r</sub>''n<sub>i</sub>''/d''t''. In isolated systems some internal terms are restricted to zero by various conservation laws which rule out the production or destruction of the respective quantity. +
The term '''isomorphic''' refers to quantities which have [https://www.merriam-webster.com/dictionary/isomorphic ''identical or similar form, shape, or structure'']. In mathematics, an isomorphism defines a [https://www.merriam-webster.com/dictionary/isomorphism ''one-to-one correspondence between two mathematical sets'']. In [[ergodynamics]], isomorphic quantities are defined by equations of identical form. If isomorphic quantities are not expressed in identical units, then these quantities are expressed in different formats which can be converted to identical untis. Example: electric force [V=J/C] and chemical force [Jol=J/mol] are ismorphic [[force]]s; the electrical format [J/C] can be converted to the chemical format [J/mol] by the [[Faraday constant]]. Units not only give meaning to the numerical value of a quantity, but units provide also an abbreviated common language to communicate and compare isomorphic quantities. In irreversible thermodynamics, isomorphic forces are referred to as ''generalized'' forces. +
J
[[File:J-mit.png|100px|left]]The '''Japanese Society of Mitochondrial Research and Medicine''' (J-mit) was founded to share the latest knowledge on mitochondrial research. J-mit is the biggest Asian society of mitochondrial research and medicine and is a member of [[ASMRM]]. +
'''''J''<sub>max</sub>''' is the maximum pathway flux (e.g. [[oxygen flux]]) obtained at saturating substrate concentration. ''J''<sub>max</sub> is a function of metabolic state. In hyperbolic ADP or oxygen kinetics, ''J''<sub>max</sub> is calculated by extrapolation of the hyperbolic function, with good agreement between the calculated and directly measured fluxes, when substrate levels are >20 times the ''c''<sub>50</sub> or [[P50|''p''<sub>50</sub>]]. +
'''Journal indexing''' allows publications to be found on search tools/databases. Each database might have different criteria of inclusion. +
An '''issue''' of a journal or periodical is a number, which typically indicates how many times a [[Journal volume |volume]] of the journal has been published in sequence. +
In most cases '''journal publication''' {''Quote''} will not be affected by posting a preprint. However, there are some publishers that do not consider papers that have already appeared online. We strongly recommend that you check all journals that you might submit to in advance {''end of Quote''}. A [https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy list of academic journals by preprint policy] is available. +
The '''volume''' of a journal or periodical is a number, which in many cases indicates the sequential number of years the journal has been published. Alternatively, the volume number may indicate the current year, independent of the year in which the journal published its first volume. A volume may be subdivided into [[Journal issue |issues]]. +
K
The kelvin, symbol K, is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant ''k'' to be 1.380 649 × 10<sup>−23</sup> when expressed in the unit J x<sup>-1</sup> K<sup>−1</sup>. +
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]]. +
L
[[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]. +
M
[[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). +
<br/>
[[File:MIG.gif|128 px|left]]
The '''Mitochondria Interest Group''' (MIG) is an Inter-Institute Interest Group at the National Institutes of Health (NIH), with members worldwide! MIG is concerned with all aspects of the mitochondrion and diseases in which the mitochondrion is involved. We hold monthly meetings, usually on the second Monday of the month (except when it is a Federal holiday or other special exceptions).
[email protected] is an Email list moderated by Ph.D. Steven Zullo as an interactive information platform, with free subscritpion to this mitochondrial network. List members are reminded of their responsibility to critically evaluate the content of the postings. The information, opinions, data, and statements contained herein are not necessarily those of the U. S. Government, the National Institutes of Health (NIH), or MIG and should not be interpreted, acted on or represented as such. +
[[File:MRS LOGO.JPG|250px|left]]
The '''Mitochondria Research Society''' (MRS) is a nonprofit international organization of scientists and physicians. The purpose of MRS is to find a cure for mitochondrial diseases by promoting research on basic science of mitochondria, mitochondrial pathogenesis, prevention, diagnosis and treatment through out the world. +
[[File:21640 - Mitochondria Targeted Therapeutics logo NEW.jpg|200px|left|Mitochondria-Targeted Drug Development]]
The '''Mitochondria-Targeted Drug Development Summit''' was first established in 2021, as an online conference. Due to its success and unmatched focus, the 2<sup>nd</sup> edition returns to Boston this March 2022.
This is the only industry-led meeting that unites key stakeholders under a mutual and ambitious objective of '''accelerating the discovery and development of novel drugs that target mitochondrial functions''' for chronic, primary mitochondrial diseases, muscular dystrophy, metabolic disorders, and neurodegenerative diseases.
Join our speakers from '''GenSight Biologics, Abliva, Reneo Pharma, Mito BioPharma, Mitokinin''' and more with exciting networking opportunities, panel discussions and dedicated roundtables. +
The '''mitochondrial ATP-sensitive K<sup>+</sup> channel''' (mtK<sub>ATP</sub> or mitoK<sub>ATP</sub>). +
[[File:Meet.jpg|200px|left]] The '''Mitochondrial European Education Training''' (MEET)
MEET is a project started on January 2013. MEET network is composed by a multi-partner project that intends to mobilize the critical mass of expertise, by linking partners from 8 different countries, among which 8 world-leading basic science and clinical centers of excellence, an 1 SME with direct interest in mitochondrial medicine and 3 associated partners that provide for all trainees no-scientific training. MEET is training 11 ESRs and 3 ERs coming from all over the world supervised in their research by 15 mentors and by their collaborators. MEET combine the efforts of leading clinicians with those of more basic oriented groups and will have important implications for the comprehension and treatment of mitochondria-related pathologies. +
[[File:Mitochondrial Medicine Society.jpg|200px|left]]
The '''Mitochondrial Medicine Society''' (MMS) was founded in 2000 and represents an international group of physicians, researchers and clinicians working towards the better diagnosis, management, and treatment of mitochondrial diseases. +
The '''Mitochondrial Physiology Network''' is the on-line Oroboros journal. +
[[File:Mito-Reseach-Guild.JPG|200px|left]]
'''The Mitochondrial Research Guild''' is a special interest guild of Seattle Children's Hospital. The guild was founded by a group of families in the Seattle area that are working together to raise awareness, promote research, and improve the quality of medical care that is available to children that are dealing with the devastating and potentially life threatening effects of mitochondrial disease. +
'''Mitochondrial metabolic competence''' is the organelle's capacity to provide adequate amounts of ATP in due time, by adjusting the mt-membrane potential, mt-redox states and the ATP/ADP ratio according to the metabolic requirements of the cell.
The term '''mitochondrial competence''' is also known in a genetic context: Mammalian mitochondria possess a natural competence for DNA import.
'''''[[MitoCom_O2k-Fluorometer]]''''' is a '''Mitochondrial Competence''' network, the nucleus of which is formed by the K-Regio project ''[[MitoCom_O2k-Fluorometer|MitoCom Tyrol]]''. +
'''Mitochondrial concentration''' is ''C<sub>mtE</sub>'' = ''mtE''·''V''<sup>-1</sup> [mtEU·m<sup>-3</sup>]. mt-Concentration is an experimental variable, dependent on sample concentration. +
'''Mitochondrial content''' per object ''X'' is ''mtE<sub><u>N</u>X</sub>'' = ''mtE''·''N<sub>X</sub>''<sup>-1</sup> [mtEU·x<sup>-1</sup>]. +
Specific '''mitochondrial density''' is ''D<sub>mtE</sub>'' = ''mtE''·''m<sub>X</sub>''<sup>-1</sup> [mtEU·kg<sup>-1</sup>]. If the amount of mitochondria, ''mtE'', is expressed as mitochondrial mass, then ''D<sub>mtE</sub>'' is the mass fraction of mitochondria in the sample. If ''mtE'' is expressed as mitochondrial volume, ''V''<sub>mt</sub>, and the mass of sample, ''m<sub>X</sub>'', is replaced by volume of sample, ''V<sub>X</sub>'', then ''D<sub>mtE</sub>'' is the volume fraction of mitochondria in the sample. +
The '''mitochondrial free radical theory of aging''' goes back to Harman (1956) and ranks among the most popular theories of aging. It is based on postulates which are not unequivocally supported by observation (Bratic, Larsson 2013):
(i) Mitochondrial ROS production increases with age caused by progressive mitochondrial dysfunction;
(ii) antioxidat capacity declines with age;
(iii) mutations of somatic mtDNA accumulate during aging;
(iv) a vicious cycle occurs of increased ROS production caused by mtDNA mutations and degenerated mt-function, and due to ROS-induced ROS production. +
The '''mitochondrial inner membrane''' mtIM is the structure harboring the membrane-bound [[electron transfer system]] ETS including the respiratory complexes working as [[hydrogen ion pump]]s, the mt-[[phosphorylation system]] including the hydrogen ion pump [[ATP synthase]], several substrate transporters involved in the [[electron transfer pathway]], and a variety of other ion pumps that carry [[proton]] charge (Ca<sup>2+</sup>, Mg<sup>2+</sup>). The [[protonmotive force]] is the electrochemical potential difference across the mtIM generated by the [[hydrogen ion pumps]] of the . +
'''Mitochondrial marker'''s are structural or functional properties that are specific for mitochondria. A structural mt-marker is the area of the inner mt-membrane or mt-volume determined stereologically, which has its limitations due to different states of swelling. If mt-area is determined by electron microscopy, the statistical challenge has to be met to convert area into a volume. When fluorescent dyes are used as mt-marker, distinction is necessary between mt-membrane potential dependent and independent dyes. mtDNA or cardiolipin content may be considered as a mt-marker. [[Mitochondrial marker enzymes]] may be determined as molecular (amount of protein) or functional properties (enzyme activities). Respiratory capacity in a defined respiratory state of a mt-preparation can be considered as a functional mt-marker, in which case respiration in other respiratory states is expressed as [[flux control ratio]]s. » [[Mitochondrial marker#Mitochondrial markers and expression of mitochondrial respiration| '''MiPNet article''']] +
'''Mitochondrial marker enzymes''' are enzymes that are specifically present in mitochondria, in the mt-matrix, the inner mt-membrane, the inter-membrane space, or the outer mt-membrane. +
The '''mitochondrial matrix''' (mt-matrix) is enclosed by the mt-inner membrane mtIM. The terms mitochondrial matrix space or mitochondrial lumen are used synonymously. The mt-matrix contains the enzymes of the [[tricarboxylic acid cycle]], [[fatty acid oxidation]] and a variety of enzymes that have cytosolic counterparts (e.g. [[glutamate dehydrogenase]], [[malic enzyme]]). Metabolite concentrations, such as the concentrations of fuel substrates, adenylates (ATP, ADP, AMP) and redox systems (NADH), can be very different in the mt-matrix, the mt-intermembrane space, and the cytosol. The finestructure of the gel-like mt-matrix is subject of current research. +
The '''mitochondrial membrane potential''' difference, mtMP or Δ''Ψ''<sub>p<sup>+</sup></sub> = Δ<sub>el</sub>''F''<sub><u>''e''</u>p<sup>+</sup></sub>, is the electric part of the protonmotive [[force]], Δp = Δ<sub>m</sub>''F''<sub><u>''e''</u>H<sup>+</sup></sub>.
:::: Δ<sub>el</sub>''F''<sub><u>''e''</u>p<sup>+</sup></sub> = Δ<sub>m</sub>''F''<sub><u>''e''</u>H<sup>+</sup></sub> - Δ<sub>d</sub>''F''<sub><u>''e''</u>H<sup>+</sup></sub>
:::: Δ''Ψ''<sub>p<sup>+</sup></sub> = Δp - Δ''µ''<sub>H+</sub>·(''z''<sub>H<sup>+</sup></sub>·''F'')<sup>-1</sup>
Δ''Ψ''<sub>p<sup>+</sup></sub> is the potential difference across the mitochondrial inner membrane (mtIM), expressed in the electric unit of volt [V]. Electric force of the mitochondrial membrane potential is the electric energy change per ‘motive’ charge or per charge moved across the transmembrane potential difference, with the number of ‘motive’ charges expressed in the unit coulomb [C]. +
The '''mitochondrial outer membrane''' is the incapsulating membrane which is osmotically not active and contains the cytochrome ''b''<sub>5</sub> enzyme similar to that found in the endoplasmatic reticulum, the translocases of the outer membrane, monoaminooxidase, the palmitoyl-CoA synthetase and carnytil-CoA transferase 1. +
'''Mitochondrial preparations''' (mtprep) are isolated mitochondria (imt), tissue homogenate (thom), mechanically or chemically permeabilized tissue (permeabilized fibers, pfi) or permeabilized cells (pce). In mtprep the plasma membranes are either removed (imt) or mechanically (thom) and chemically permeabilized (pfi), while mitochondrial functional integrity and to a large extent mt-structure are maintained in incubation media optimized to support mitochondrial physiological performance. According to this definition, submitochondrial particles (smtp) are not a mtprep, since mitochondrial structure is altered although specific mitochondrial functions are preserved. +
Integrative measure of the dynamics of complex coupled metabolic pathways, including metabolite transport across the mt-membranes, [[TCA cycle]] function with electron transfer through dehydrogenases in the mt-matrix, membrane-bound electron transfer [[Membrane-bound ET pathway|mET-pathway]], the transmembrane proton circuit, and the phosphorylation system. +
Mitochondrial respiratory capacity and control are compared in different '''mitochondrial respiration media''', MiRs, to evaluate the quality of MiRs in preserving mitochondrial function and to harmonize results obtained in various studies using different MiRs. In some cases alterations of the formulation are incorporated to optimize conditions for the simultaneous measurement of multiple parameters, e.g. respiration and [[ROS]] production. +
666 coauthors of the 'MitoEAGLE white paper' [1] collaborated to reach a consensus on terminology related to mitochondrial respiratory states and rates. This page is intended to prepare a questionnaire and follow-up publication. +
The '''transcription factor A''' is a gene that encodes a mitochondrial transcription factor that is a key activator of mitochondrial transcription as well as a participant in mitochondrial genome replication. TFAM is downstream of [[Peroxisome proliferator-activated receptor gamma coactivator 1-alpha|PGC-1alpha]]. +
Autophagy (self-eating) in general is viewed as a degradation process which removes non-essential or damaged cellular constituents.
» [[Mitophagy#Mitochondrial_mitophagy | '''MiPNet article''']] +
A '''model''' regarding databases is the representation of a real world object in a computer understandable language. A '''model''' can be defined by the structure of its [[dataset]] and the relations to other '''models'''. +
'''Molar mass''' ''M'' is the mass of a chemical compound divided by its amount-of-substance measured in moles. It is defined as ''M''<sub>B</sub> = ''m''/''n''<sub>B</sub>, where ''m'' is the total mass of a sample of pure substance and ''n''<sub>B</sub> is the amount of substance B given in moles. The definition applies to pure substance. The molar mass allows for converting between the mass of a substance and its amount for bulk quantities. It is calculated as the sum of standard atomic weights of all atoms that form one entity of the substance.
The appropriate [[SI base units]] is kg·mol<sup>-1</sup>. However, for historical as well as usability reasons, g·mol<sup>-1</sup> is almost always used instead. +
The mole [mol] is the SI base unit for the [[amount |amount of substance]] of a system that contains 6.02214076·10<sup>23</sup> specified elementary entities (see [[Avogadro constant]]). The elementary entities must be specified and may be atoms, molecules, ions, electrons, other particles, or specified groups of such particles. +
'''Monoamine oxidases''' are enzymes bound to the outer membrane of mitochondria and they catalyze the oxidative deamination of monoamines. Oxygen is used to remove an amine group from a molecule, resulting in the corresponding aldehyde and ammonia. Monoamine oxidases contain the covalently bound cofactor [[FAD]] and are, thus, classified as flavoproteins. +
[[File:Motic Microscope.jpg|right|180px]]'''Motic Microscope SMZ-171 TLED''': for preparation of permeabilized fibres; compact and light stereo microscope, Greenough optical system, switching power supply for use worldwide (100-240V); including auxiliary ESD objective 2.0X(38.6mm). +
[[File:Motive entities.png|right|300px|From [[Gnaiger 2020 BEC MitoPathways]]]].
A '''motive entity''' ''X''<sub>tr</sub> is an entity involved in a transformation including spacial transfer. Motive entities (transformants) are expressed in different [[motive unit]]s [MU] depending on the energy transformation under study and the chosen [[format]]. [[Flow]]s are defined as advancement in terms of stoichiometric motive entities per time. Isomorphic [[force]]s are partial derivatives of Gibbs energy per advancement. Ions carrying a positive charge (cations) or negative charge (anions) may be considered as a paradigm of motive entities, since Faraday did not coin but introduced the term 'ion', which is old Greek for 'going' — advancing to the cathode or anode and thus generating an electric [[current]]. +
The '''motive unit''' [MU] is the variable SI unit in which the [[motive entity]] (transformant) of a transformation is expressed, which depends on the energy transformation under study and on the chosen [[format]]. Fundamental MU for electrochemical transformations are:
* MU = x, for the particle or molecular format, <u>''N''</u>
* MU = mol, for the chemical or molar format, <u>''n''</u>
* MU = C, for the electrical format, <u>''e''</u>;
For the [[protonmotive force]] the motive entity is the proton with charge number ''z''=1. The protonmotive force is expressed in the electrical or molar format with MU J/C=V or J/mol=Jol, respectively. The conjugated flows, ''I'', are expressed in corresponding electrical or molar formats, C/s = A or mol/s, respectively.
The [[charge number]], ''z'', has to be considered in the conversion of motive units (compare Table below), if a change not only of units but a transition between the entity [[elementary charge]] and an entity with charge number different from unity is involved (''e.g.'', O<sub>2</sub> with ''z''=4 in a redox reaction). The ratio of elementary charges per reacting O<sub>2</sub> molecule (''z''<sub>O<small>2</small></sub>=4) is multiplied by the elementary charge (''e'', coulombs per proton), which yields coulombs per O<sub>2</sub> [C∙x<sup>-1</sup>]. This in turn is multiplied with the [[Avogadro constant]], ''N''<sub>A</sub> (O<sub>2</sub> molecules per mole O<sub>2</sub> [x∙mol<sup>-1</sup>]), thus obtaining for ''zeN''<sub>A</sub> the ratio of elementary charges [C] per amount of O<sub>2</sub> [mol<sup>-1</sup>]. The conversion factor for O<sub>2</sub> is 385.94132 C∙mmol<sup>-1</sup>. +
The mark mode is active by default, can be selected in the menu or by [Ctrl+M]. If '''Mouse control: Mark''' is enabled, specific sections of the experiment can be marked in each plot.
Usually, marks are set on the plot for oxygen concentration for calibration, whereas marks on the plot for oxygen flux are set for exporting the median or average of flux to a table.
»More details: [[Marks - DatLab]]. +
Select '''Mouse Control: Zoom''' in the Graph-menu or press [Ctrl+Z]. +
[[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. +
-20and-206-20photodiode-20filters-20(rectangular).){kind=link}
-20for-20regulation-20of-20light-20intensity-20of-20the-20LED-20in-20the-20fluorescence-20sensors.-20This-20item-20is-20a-20standard-20component-20of-20the-20-5B-5BO2k-2DFluorescence-20LED2-2DModule-5D-5D.){kind=link}
,-20photodiode,-20-5B-5BFilter-2DCap-5D-5D-20equipped-20with-20-5B-5BFilter-20Set-20AmR-5D-5D-20for-20-5B-5BAmplex%C2%AE-20UltraRed-7CAmplex-20UltraRed-5D-5D-20measurements-20when-20delivered.){kind=link}
-20teams-20up-20researchers-20and-20organizations-20investing-20in-20rare-20diseases-20research-20in-20order-20to-20achieve-20two-20main-20objectives-20by-20the-20year-202020,-20namely-20to-20deliver-20200-20new-20therapies-20for-20rare-20diseases-20and-20means-20to-20diagnose-20most-20rare-20diseases.){kind=link}
-20was-20founded-20to-20share-20the-20latest-20knowledge-20on-20mitochondrial-20research.-20J-2Dmit-20is-20the-20biggest-20Asian-20society-20of-20mitochondrial-20research-20and-20medicine-20and-20is-20a-20member-20of-20-5B-5BASMRM-5D-5D.){kind=link}
-20and-20limitation-20by-20the-20phosphorylation-20system-20(-27-27P-2FE-27-27)-3B-20-27-27L-2FP-27-27-20%3D-20(-27-27L-2FE-27-27)-20-2F-20(-27-27P-2FE-27-27)-20%3D-201-2F-5B-5BRCR-5D-5D.){kind=link}
,-20physiological-20control-20of-20energy-20demand,-20and-20limitation-20by-20the-20OXPHOS-20capacity.){kind=link}
,-20is-20distinguished-20from-20-27-27L-27-27(n)-20and-20-27-27L-27-27(T).){kind=link}
,-20fixed-20injection-20needle-20with-20rounded-20tip,-20with-20spacers.){kind=link}
,-20fixed-20injection-20needle-20with-20rounded-20tip,-20with-20spacers.){kind=link}
-20or-20inhibits-20(Mnanv)-20mitochondrial-20respiration-20in-20CI-2Ddeficient-20human-20blood-20cells,-20fibroblasts-20and-20heart-20fibres,-20acting-20on-20Complex-20II-20of-20the-20electron-20transfer-20system.){kind=link}
-20is-20a-20nonprofit-20international-20organization-20of-20scientists-20and-20-20physicians.-20The-20purpose-20of-20MRS-20is-20to-20find-20a-20cure-20for-20mitochondrial-20diseases-20by-20-20promoting-20research-20on-20basic-20science-20of-20mitochondria,-20mitochondrial-20pathogenesis,-20-20prevention,-20diagnosis-20and-20treatment-20through-20out-20the-20world.){kind=link}
-20was-20founded-20in-202000-20and-20represents-20an-20international-20group-20of-20physicians,-20researchers-20and-20clinicians-20working-20towards-20the-20better-20diagnosis,-20management,-20and-20treatment-20of-20mitochondrial-20diseases.){kind=link}
-3B-20including-20auxiliary-20ESD-20objective-202.0X(38.6mm).){kind=link}
-20sensors-20(single-20chamber-20mode-20of-20application).){kind=link}
.){kind=link}
,-20box-20of-208-20as-20spares.){kind=link}
,-20for-20zero-2Doxygen-20calibration-20of-20the-20-5B-5BOroboPOS-5D-5D.){kind=link}
-20for-20PVDF-20or-20PEEK-20stoppers-20(2-2DmL-20-5B-5BO2k-2Dchamber-5D-5D),-20with-20-5B-5BO-2Dring-5CViton-5C18x2-20mm-5D-5D-20and-20-5B-5BV-2Dring-5C30-2D35-2D4.5-20mm-5D-5D.-20Two-20units-20of-20this-20item-20are-20standard-20components-20mounted-20on-20the-20-5B-5BO2k-2DMain-20Unit-5D-5D.){kind=link}
-20for-20PVDF-20or-20PEEK-20stoppers-20(0.5-2DmL-20-5B-5BO2k-2Dchamber-5D-5D),-20with-20-5B-5BO-2Dring-5CViton-5C16x2-20mm-5D-5D-20and-20-5B-5BV-2Dring-5C30-2D35-2D4.5-20mm-5D-5D.){kind=link}
,-20mounted-20on-20the-20socket-20for-20the-20-5B-5BO2k-2DMain-20Power-20Cable-5D-5D,-20at-20the-20rear-20panel-20of-20the-20-5B-5BO2k-2DMain-20Unit-5D-5D.){kind=link}
.){kind=link}
.){kind=link}
,-20oxygen,-20and-20defined-20reduced-20CHNO-2Dfuel-20substrates.){kind=link}
