Property:Description
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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. +
