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A '''norm''' is a rule that is enforced by members of a community. +
A glance '''inside the [[Oroboros O2k]]''' +
A user name is +
Close DatLab files and '''quit''' the program. +
Descr +
Nuclear receptors are ligand-dependent transcription factors. +
Open a previously recorded [[DatLab]] file. +
See '''[[Electron-transfer-pathway state]]''' +
See [[Electron-transfer-pathway state]]. +
See [[Extrinsic fluorophores]] +
Select '''Mouse Control: Zoom''' in the Graph-menu or press [Ctrl+Z]. +
The French Group of Bioenergetics... +
The [[Mitochondrial outer membrane| '''mitochondrial outer membrane''']] +
The hydride anion is the species H−. +
The illumination in both chambers is switched on/off. +
[[Extrinsic fluorophores]]; fluorescent markers. +
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[[File:1GM;2D;3S;4U;5Rot-.png|400px|SUIT-011]] +
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[[File:1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp-.png|400px|SUIT-001]] +
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[[File:1S;2D;2c;3P;4Rot;5Ama.png|400px|SUIT9]] +
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[[File:Ce1;1Dig;1S;2D;2c;3P;4Rot;5Ama.png|520px|SUIT-009]] +
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A '''closed system''' is a system with bou … A '''closed system''' is a system with boundaries that allow external exchange of energy (heat and work), but do not allow exchange of matter. A limiting case is light and electrons which cross the system boundary when work is exchanged in the form of light or electric energy. If the surroundings are maintained at constant temperature, and heat exchange is rapid to prevent the generation of thermal gradients, then the closed system is isothermal. A frequently considered case are closed isothermal systems at constant pressure (and constant volume with aqueous solutions). Changes of closed systems can be partitioned according to internal and external sources. Closed systems may be homogenous (well mixed and isothermal), continuous with gradients, or [[Discontinuous system|discontinuous]] with compartments (heterogenous).[[Discontinuous system|discontinuous]] with compartments (heterogenous). +
A '''coenzyme''' or cosubstrate is a [[cofactor]] … A '''coenzyme''' or cosubstrate is a [[cofactor]] that is attached loosely and transiently to an enzyme, in contrast to a [[prosthetic group]] that is attached permanently and tightly. The coenzyme is required by the corresponding enzyme for its activity (IUPAC definition). A coenzyme is 'a low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons' (IUPAC definition).l groups or electrons' (IUPAC definition). +
A '''cofactor''' is 'an organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely ([[coenzyme]]) or tightly ([[prosthetic group]])' (IUPAC definition). +
A '''coupling-control protocol CCP''' indu … A '''coupling-control protocol CCP''' induces different [[coupling control state]]s at a constant [[electron-transfer-pathway state]]. [[Residual oxygen consumption]] (''Rox'') is finally evaluated for ''Rox'' correction of flux. The CCP may be extended, when further respiratory states (e.g. cell viability test; CIV assay) are added to the coupling control module consisting of three coupling control states. The term '''phosphorylation control protocol''', PCP, has been introduced synonymous for CCP.» [[Coupling_control_protocol#From_PCP_to_CCP |'''MiPNet article''']][Coupling_control_protocol#From_PCP_to_CCP |'''MiPNet article''']] +
A '''dataset''' is a collection of data. In the context of databases a dataset represents the collection of entries in a database-table. In this table columns represent [[Attribute|attributes]] and rows display the according values of the entries. +
A '''decimal marker''' is used to separate … A '''decimal marker''' is used to separate the integral part of numbers from the decimal part. The SI recommends: "the symbol for the decimal marker shall be either the point on the line or the comma on the line". In English language versions, the dot (point on the line) should be used uniquely as the decimal marker. To avoid ambiguities, BEC follows the SI recommendation that “Numbers may be divided in groups of three in order to facilitate reading; neither dots nor commas are ever inserted in the spaces between groups” (pages 183-184).he spaces between groups” (pages 183-184). +
A '''detector''' is a device that converts … A '''detector''' is a device that converts the light falling upon it into a current or voltage that is proportional to the light intensity. The most common devices in current use for [[fluorometry]] and [[spectrophotometry]] are [[photodiodes]] and [[photodiode arrays]].[[photodiode arrays]]. +
A '''difference spectrum''' is an [[absorbance spectrum]] … A '''difference spectrum''' is an [[absorbance spectrum]] obtained by subtracting that of one substance from that of another. For example, a '''difference spectrum''' may be plotted of the [[absorbance spectrum]] obtain ed from reduced [[cytochrome c]] and subtracting the [[absorbance spectrum]] from the same concentration of [[cytochrome c]] in its oxidised state. The [[difference spectrum]] may be used to quantify the amount to which the [[cytochrome c]] is reduced. This can be achieved with the aid of a [[reference spectrum]] (or spectra) and the [[least squares method]].[[least squares method]]. +
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. +
A '''dispersion device''' diffracts light … 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]].[[spectrophotometer]]. +
A '''fluorophore''' is a fluorescent subst … 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., also referred to as fluorescent markers. +
A '''free radical''' is any atom or molecu … 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]] (H2O2) and the hydroxyl radical (HO•)./sub>O2) and the hydroxyl radical (HO•). +
A '''harmonized standard''' is a European [[standard]] developed by a recognized European Standards Organisation: CEN, CENELEC, or ETSI. +
A '''healthy reference population''', HRP, … 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/m2].e body mass index, BMI [kg/m2]. +
A '''high signal at zero oxygen''' may be … 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.ensor head and an electrical leak current. +
A '''light-emitting diode''' (LED) is a li … 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].visible, ultraviolet, and infrared range]. +
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, a … 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.t of any of its primary intended purposes. +
A '''metabolic control variable''' ''X'' c … A '''metabolic control variable''' ''X'' causes the transition between a [[background state]] Y (background rate ''YX'') and a [[reference state]] Z (reference rate ''ZX''). ''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).ate but present in the background state (step change from Z to Y). +
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'''. +
A '''number''' ''N'' is a [[count]] … A '''number''' ''N'' is a [[count]] ''N''''X'' [x] divided by the [[elementary entity]] ''U''''X'' [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.pt of number is tightly entangled with units, counts and entities. +
A '''numeral''' is the symbol representing … 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).6 times 10 (or 2 times 30; or 1 times 60). +
A '''plot''' in DatLab represents a specific [[O2k signals and output|channel]] in the graph. To change the [[Layout for DatLab graphs]] go to [Graph]/'''[[Select plots - DatLab |Select plots]]''' to open the '''Graph layout''' window. +
A '''polarization voltage''' of 600 mV to … A '''polarization voltage''' of 600 mV to 800 mV is applied between anode and cathode of the [[polarographic oxygen sensor]], resulting in a current when oxygen is consumed. The current is converted by the electronics to a voltage (raw signal) which must not be confused with the polarization voltage.be confused with the polarization voltage. +
A '''population''' (or '''group''') defines the [[sample type]] of an [[experiment]], before sample preparation. The population (or group) size represents the upper limit of the [[sample size]], ''N''. +
A '''preprint''' is {''Quote''} a way in w … A '''preprint''' is {''Quote''} a way in which a manuscript containing scientific results can be rapidly communicated from one scientist, or a group of scientists, to the entire scientific community {''end of Quote''}. Preprints are disseminated without peer review, e.g. in the preprint server [[MitoFit Preprints]]. In contrast, the journal [[Bioenergetics Communications]] publishes peer-reviewed articles, which preferentially are communicated in advance in MitoFit Preprints.municated in advance in MitoFit Preprints. +
A '''product''' in a chemical reaction has a positive [[stoichiometric number]] since it is produced, whereas a [[substrate]] has a negative stoichiometric number since it is consumed. +
A '''prosthetic group''' is a [[cofactor]] … A '''prosthetic group''' is a [[cofactor]] that is attached permanently and tightly or even covalently to an enzyme and that is regenerated in each enzymatic turnover. Thus a prostethic group is distinguished from a [[coenzyme]] or cosubstrate that is attached loosely and transiently. Like a coenzyme, the prosthetic group is required by an enzyme for its activity. A prosthetic group is 'a tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity' (IUPAC definition).FMN/FMNH2 and FAD/FADH2 are prosthetic groups of [[Complex I]] and [[Complex II]], respectively.[[Complex II]], respectively. +
A '''quantity''' is the attribute of a phe … A '''quantity''' is the attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively. A [[dimension |dimensional]] quantity is a number (variable, parameter, or constant) connected to its dimension, which is different from 1. {''Quote''} The value of a quantity is generally expressed as the product of a number and a unit. The unit is simply a particular example of the quantity concerned which is used as a reference, and the number is the ratio of the value of the quantity to the unit. {''end of Quote'': Bureau International des Poids et Mesures 2019 The International System of Units (SI), p. 127)}.ernational System of Units (SI), p. 127)}. +
A '''reference spectrum''' for a substance is an [[absorbance spectrum]] of the same substance at a known concentration and [[redox state]]. +
A '''requirement''' is a singular documented physical or functional need that a particular design, product or process must be able to perform. +
A '''sample''' is one or more parts taken … A '''sample''' is one or more parts taken from an ensemble that is studied. A sample is either stored for later quantification or prepared and possibly separated into subsamples, which are enclosed in a system for qualitative or quantitative investigation. A pure sample S is a pure gas, pure liquid or pure solid of a defined elementary [[entity]]-type. A pure biological sample is a cell type, tissue, or organism without its solid, liquid or gaseous environment. Then the system used to investigate sample S contains only entities of entity-type S, and the [[volume]] ''V''S [L] and [[mass]] ''m''S [kg] of the pure (sub)sample S are identical to the volume ''V'' and mass ''m'' of the experimental [[system]]. A pure sample S may be mixed with other components to be investigated as a solution, mixture, or suspension, indicated by the symbol s in contrast to the pure sample S. A sample s is obtained in combination with other components, such that the [[volume]] ''V''s [L] and [[mass]] ''m''s [kg] of the sample s are larger than the volume ''V''S and mass ''m''S of the pure sample S. For example, the number of cells ''N''ce [Mx] can be counted in a sample s of a cell suspension, whereas the mass ''m''ce [mg] of cells requires a pure sample S of cells to be measured on a mass-balance. Clarity of statistical representation is improved, if the symbol ''N'' is used for the number of [[primary sample]]s taken from a study group, and the symbol ''n'' is used for the number of subsamples studied as technical repeats.[[primary sample]]s taken from a study group, and the symbol ''n'' is used for the number of subsamples studied as technical repeats. +
A '''scalar''' is a pysicochemical quantit … A '''scalar''' is a pysicochemical quantity that is fully described by its magnitude. A potential difference, differences of concentration or pressure are scalars, whereas a potential gradient is a [[vector]]. Similarly, the [[protonmotive force]] and metabolic oxygen [[flux]] are scalars, whereas the fundamental [[force]]s of physics and [[velocity]] are vectors.[[velocity]] are vectors. +
A '''solution''' is {''Quote''}: A liquid … A '''solution''' is {''Quote''}: A liquid or solid phase containing more than one substance, when for convenience one (or more) substance, which is called the solvent, is treated differently from the other substances, which are called solutes. When, as is often but not necessarily the case, the sum of the mole fractions of solutes is small compared with unity, the solution is called a dilute solution. A superscript attached to the ∞ symbol for a property of a solution denotes the property in the limit of infinite dilution {''end of Quote'': [http://goldbook.iupac.org/S05746.html IUPAC Gold Book]}.[[Solutions#Stock-.2C_storage-_and_working-solutions:_How_do_they_differ.3F |» '''MiPNet article''']]Solutions#Stock-.2C_storage-_and_working-solutions:_How_do_they_differ.3F |» '''MiPNet article''']] +
A '''spectrofluorometer''' makes use of a … A '''spectrofluorometer''' makes use of a [[spectrometer]] to measure and analyse the fluorescent emission spectra from a [[fluorophore]]. It will typically differ from an [[absorbance]] [[spectrophotometer]] in that it will have a larger [[slit width]] (to increase [[sensitivity]]) and use a longer [[integration time]]. The configuration of the illuminating and receiving optics also differ from [[spectrophotometry]] in that the excitation source is directed perpendicularly to the position of the emission [[detector]] so that the intensity of the excitation signal reaching the [[detector]] is minimised.[[detector]] is minimised. +
A '''spectrophotometer''' is an instrument … A '''spectrophotometer''' is an instrument that consists of an entrance slit, a dispersion device (see [[dispersion devices]] and a [[detector]] for the purpose of measuring the intensity of light emerging from a sample across a given wavelength range. A [[light source]] is also necessary in order for the instrument to function, and this may be located within the instrument or from an external source using [[lightguides]] or other [[optics]].[[optics]]. +
A '''standard''' is an established [[norm]] or [[requirement]] in regard to a defined system. It can consist of a formal document that establishes uniform criteria, methods, processes and practices.See also [[Harmonized standard]]. +
A '''stirrer test''' is performed in the [[Oroboros O2k]] … A '''stirrer test''' is performed in the [[Oroboros O2k]] for quick evaluation of the performance of the [[OroboPOS]] and for [[POS calibration - dynamic|dynamic calibration]]. Stirring is stopped in both chambers and restarted after a selected period. The default period is 30 s, for experiments at 37 °C. At lower experimental temperature, this period should be prolonged (60 s at 25 °C). In the [[O2k-Open Support#O2k_Quality_Control |SOP (O2k Quality Control)]] for the [[O2k-Open_Support#1._O2_sensor_test|O2 sensor test]], the stirrer test is performed in the 'open' chamber in conjunction with [[Air calibration]]. In general, the stirrer test can be performed equally with an open or closed chamber. Upon automatic re-start of the stirrer (On), the increase of the oxygen signal should be rapid and monoexponential.the oxygen signal should be rapid and monoexponential. +
A '''three-electrode system''' is the setu … A '''three-electrode system''' is the setup used in the [[Q-Sensor]], which is an integral part of the [[Q-Module]]. This system is used in voltammetry (including [[cyclic voltammetry]]) to study the current as a function of the applied potential using three different electrodes: 1) the working electrode 2) the reference electrode, and 3) the counter electrode. In the [[Q-Sensor]], the working or detecting electrode is a glassy carbon (GC) electrode that is set to a given potential and makes contact with the analyte. The potential of the working electrode is controlled by the constant potential of the a silver/silver chloride (Ag/AgCl) reference electrode, which does not pass any current. The applied potential on the surface of the GC should be sufficient to either oxidize reduced analyte (in this case [[Coenzyme Q]]) or to reduce oxidized analyte. Thus, the counter electrode is a platinum electrode (Pt) that passes a current to counter these redox events by completing the circuit that is rate-limited by electron transfer on the GC. To determine the reduced Q fraction the GC electrode is set at the oxidation peak potential, which can be determined with [[cyclic voltammetry]].[[cyclic voltammetry]]. +
A '''tissue homogenate''' (thom) is obtained through mechanical micro-disruption of fresh tissue and the cell membranes are mechanically permeabilized. +
A '''user''' code or name is entered upon starting [[DatLab]]. This window pops up automatically after opening DatLab. Usernames are connected with personal [[Layout for DatLab graphs |graph layouts]]. +
A '''vector''' is a pysicochemical quantit … A '''vector''' is a pysicochemical quantity with magnitude and spatial direction of a [[gradient]]. Symbols for vectors are written in bold face. For example, [[velocity]], '''''v''''', and the fundamental [[force]]s of physics, '''''F''''', are vectors. An infinitesimal area is a vector, d'''''A''''', perpendicular to the plane. d'''''A''''', perpendicular to the plane. +
A '''working measurement standard''' is a standard that is used routinely to calibrate or check material measures, measuring instruments or reference materials [SOURCE: VIM:1993, 6.7]. +
A [[medical device]] … 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.h other diagnostic goods for in vitro use. +
A [[system]] … A [[system]] is in a '''steady state''' if the state variables of a dynamic system do not change over time due to exchange processes with the environment, which compensate for internal dissipative transformations — such as chemical reactions or diffusion — and thus prevent any changes of the system and externalize dissipative changes to the environment. The dynamic nature of the steady state differentiates it from the thermodynamic equilibrium state. {''Quote''} Steady states can be obtained only in [[open system]]s, in which changes by internal transformations, ''e.g.'', O2 consumption, are instantaneously compensated for by external fluxes across the system boundary, ''e.g.'', O2 supply, thus preventing a change of O2 concentration in the system (Gnaiger 1993). Mitochondrial [[respiratory states]] monitored in [[closed system]]s satisfy the criteria of pseudo-steady states for limited periods of time, when changes in the system ([[concentration]]s of O2, fuel substrates, ADP, Pi, H+) do not exert significant effects on metabolic fluxes (respiration, phosphorylation). Such pseudo-steady states require respiratory media with sufficient buffering capacity and substrates maintained at kinetically-saturating concentrations, and thus depend on the kinetics of the processes under investigation. {''end of Quote'': [[BEC 2020.1]]}. Whereas fluxes may change at a steady state over time, concentrations are maintained constant. The 'respiratory steady state' (Chance and Williams 1955) is characterized by constant fluxes (O2 flux, H2O2 flux) and measured variables of state (cytochrome redox states, Q redox state, NADH redox state, mitochondrial membrane potential). [[High-resolution respirometry]] allows for the measurement of several parameters (''e.g.'' O2 flux, H2O2 flux, mitochondrial membrane potential) at pseudo-steady states, when changes of [[concentration]]s in the [[closed system]] do not exert any control on fluxes. Combination with the [[TIP2k-Module| Titration-Injection microPump (TIP2k)]] allows operation with programmable titration regimes at steady-state ADP concentration (Gnaiger 2001), oxygen concentration (oxystat mode; Gnaiger et al 2000, Harrison et al 2015) or steady-state pH (pH-stat more), yielding an expanded flexibility in experimental design by combining the technical advantages of closed and [[open system]]s approaches.en system]]s approaches. +
A back-up power supply may be required to secure '''uninterrupted power supply'''. +
A combination of mouse and keyboard commands provides convenient control of graphs in DatLab 8. +
A comprehensive library of SUIT protocols … A comprehensive library of SUIT protocols including DatLab example traces, instructions, brief explanatory texts, links to relevant pages, representative diagrams and templates for data evaluation can be browsed from inside DatLab 7.4. Click on menu [Protocols]\SUIT: Browse DL-Protocols and templates to open a folder with all the [[MitoPedia: SUIT|SUIT protocols]] provided with the DatLab 7.4. [[Run DL-Protocol/Set O2 limit| DL-Protocols]] (DLP) for different [[MitoPedia: Sample preparations|sample preparations]] can be chosen to assess multiple sequences of respiratory [[Coupling control state|coupling control ]] and [[Electron-transfer-pathway state|ET-pathway ]] states. DL-Protocols posses unique D## codes and comprise a fixed sequence of events and marks which cannot be changed by the user. However, the users can edit titration volumes and concentrations in the Overview window of a DL-protocol, save the overview, and export the file as a [[Export DL-Protocol User (*.DLPU)|user-specific DL-Protocol]] [File / Export / A or B: Export DL-Protocol User (*.DLPU)]. In DatLab 7.4, fixed sequence of events and marks can be changed (Skip/Added) in a SUIT protocol by the user. Moreover, editions of 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). For more information, see: [[Enable DL-Protocol editing]].[[Enable DL-Protocol editing]]. +
A major task in establishing a procedure f … A major task in establishing a procedure for measurement of [[mitochondrial membrane potential]] using probe molecules is the evaluation of inhibitory concentrations of the probe molecule on the activity of respiration. The '''TPP+ inhibitory effect''' (this also applies to TPMP+ and other indicator molecules) is frequently ignored. Accurate knowledge of a threshold concentration is required to evaluate the necessary limit of detection of TPP+, and for restriction of experimental TPP+ concentrations below the inhibitory range.ion of experimental TPP+ concentrations below the inhibitory range. +
A number of replica, ''N'', of '''experime … 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.ay and an assay for protein determination. +
A variety of '''light sources''' are avail … 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.t practicable, and at a much reduced cost. +
According to David Fell, "Elasticities are … 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]][[File:Elasticity_Measurement.jpg]] +
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. +
After selection of the Amperometric, Amp c … After selection of the Amperometric, Amp channel in the '''[[O2k configuration]]''', an Amperometric, Amp tab will appear in the '''O2k control''' [F7] window. Set the desired light intensity (0-1600) in the field ´Fluo intensity´ and the desired amplification of the signal (1-1000) in the field ´Gain for Fluo sensor´in the Amperometric, Amp window followed by a left-click '''Send to O2k'''. Switching off the [[Illumination on/off|illumination]] before each fluorometric measurement is routinely required.ometric measurement is routinely required. +
After starting [[DatLab]] either the '''Connection window''' opens automatically by default or open [[O2k control]] by pressing [F7] and select the communication port. +
Also known as attenuation or extinction, ' … Also known as attenuation or extinction, '''absorbance''' (''A'') is a measure of the difference between the [[incident light]] intensity (''I''0) and the intensity of light emerging from a sample (''I''). It is defined as:''A'' = log (''I''0/''I'') is defined as: ''A'' = log (''I''0/''I'') +
An '''Intrinsic flourophore''' is a naturally occurring [[fluorophore]] of which [[NADH]], aromatic amino acids and flavins are examples. +
An '''absorption spectrum''' is similar to an [[absorbance spectrum]] of a sample, but plotted as a function of [[absorption]] against wavelength. +
An '''entity''' of type ''X'' is something … 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''''X''. 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''''X'' as a ''single'' countable object or event.ub>''X'' as a ''single'' countable object or event. +
An '''event''' in [[DatLab]] … 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]][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. +
An '''experimental code''' can be entered in the [[Sample - DatLab|Sample]] window, containing up to 10 digits. +
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. +
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. +
An '''open system''' is a system with boun … 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''ext).[[external flow]]s, ''I''ext). +
An '''outlier''' is a member of a set of v … An '''outlier''' is a member of a set of values which is inconsistent with other members of that set. An outlier can arise by chance from the expected population, originate from a different population, or be the result of an incorrect recording or other blunder. Many schemes use the term outlier to designate a result that generates an action signal. This is not the intended use of the term. While outliers will usually generate action signals, it is possible to have action signals from results that are not outliers [SOURCE: ISO 5725‑1:1994, modified].liers [SOURCE: ISO 5725‑1:1994, modified]. +
An '''outlier-skewness index''' ''OSI'' is … An '''outlier-skewness index''' ''OSI'' is defined for evaluation of the distribution of data sets with outliers including separate clusters or skewness in relation to a normal distribution with equivalence of the average and median. The ''OSI'' is derived from [http://www.statisticshowto.com/pearsons-coefficient-of-skewness/ Pearson’s coefficient of skewness] 2:: Pearson 2 coefficient = 3 · (average-median)/SDThe outlier-skewness index ''OSI'' introduces the absolute value of the arithmetic mean, ''m'' = ABS(average + median)/2, for normalization:: ''OSI'' = (average-median)/(''m'' + SD) : ''OSI'' = (average-median)/[ABS(average+median)/2 + SD]At the limit of a zero value of ''m'', the ''OSI'' equals the Pearson 2 coefficient (without the multiplication factor of 3). At high ''m'' with small standard deviation (SD), the ''OSI'' is effectively the difference between the average and the median normalized for ''m'', (average-median)/''m''.malized for ''m'', (average-median)/''m''. +
An '''uncoupler''' is a protonophore ([[CCCP]] … An '''uncoupler''' is a protonophore ([[CCCP]], [[FCCP]], [[DNP]], [[SF6847]]) which cycles across the inner mt-membrane with transport of protons and dissipation of the electrochemical proton gradient. Mild uncoupling may be induced at low uncoupler concentrations, the noncoupled state of [[ET capacity]] is obtained at optimum uncoupler concentration for maximum flux, whereas at higher concentrations an uncoupler-induced inhibition is observed. uncoupler-induced inhibition is observed. +
An [[energy]] … 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 (∆e''Q'' > 0) without performance of work (∆e''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]].ergonic]]. +
An [[energy]] … 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 (∆e''Q'' < 0) without performance of work (∆e''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]].ergonic]]. +
An experimental '''assay''' is a method to … An experimental '''assay''' is a method to obtain a measurement with a defined instrument on a [[sample]] or [[subsample]]. Multiple assay types may be applied on the same sample or subsample, if the measurement does not destroy it. For instance, the wet weight of a permeabilized muscle fibre preparation can be determined based on a specific laboratory protocol (gravimetric assay), maintaining the functional integrity of the sample, which then can be used in a respirometric assay, followed by a spectrophotometric assay for measurement of protein content. The experimental design determines which types of assays have to be applied for a complete experiment. Destructive assays, such as determination of protein content or dry weight, can be applied on a sample only after performing a respirometric assay, or on a separate subsample. The experimental variability is typically dominated by the assay with the lowest [[resolution]] or signal to noise ratio. The signal to noise ratio may be increased by increasing the number, ''n'', of [[repetitions]] of measurements on subsamples. Evaluation of procedural variation ('experimental noise') due to instrumental resolution and handling requires subsampling from homogenous samples.uires subsampling from homogenous samples. +
An experimental '''sample type''' is the object of an [[experiment]]. A sample type is defined by the specifications of the [[population]] and by a specific sample preparation (see [[MitoPedia: Sample preparations]]). +
As per the 2017 UNESCO Recommendation on S … As per the 2017 UNESCO Recommendation on Science and Scientific Researchers, the term ‘science’ signifies the enterprise whereby humankind, acting individually or in small or large groups, makes an organized attempt, in cooperation and in competition, by means of the objective study of observed phenomena and its validation through sharing of findings and data and through peer review, to discover and master the chain of causalities, relations or interactions; brings together in a coordinated form subsystems of knowledge by means of systematic reflection and conceptualization; and thereby furnishes itself with the opportunity of using, to its own advantage, understanding of the processes and phenomena occurring in nature and society.phenomena occurring in nature and society. +
As stated on the [https://www.bioenergetic … As stated on the [https://www.bioenergetics-communications.org/index.php/bec/BECPolicies#Journal_policies_on_conflicts_of_interest_.2F_competing_interests Bioenergetics Communications' policy], a '''conflict of interest''' may be of non-financial or financial nature. Examples of conflicts of interest include (but are not limited to)::::* Individuals receiving funding, salary or other forms of payment from an organization, or holding stocks or shares from a company, whose financial situation might be influenced by the publication of the findings;:::* Individuals, their funding organization or employer holding (or applying for) related patents;:::* Official affiliations and memberships with interest groups relating to the content of the publication;:::* Political, religious, or ideological competing interests.For authors, any conflict of interest is declared at the time of submission and included in the published manuscript. For editors and reviewers, conflicts should be taken into account before accepting an assignment.to account before accepting an assignment. +
At '''standard temperature and pressure dr … At '''standard temperature and pressure dry''' (STPD: 0 °C = 273.15 K and 1 atm = 101.325 kPa = 760 mmHg), the molar volume of an ideal gas, ''V''m, and ''V''m,O2 is 22.414 and 22.392 L∙mol-1, respectively. Rounded to three decimal places, both values yield the conversion factor of 0.744 from units used in spiroergometry (''V''O2max [mL O2·min-1]) to SI units [µmol O2·s-1]. For comparison at normal temperature and pressure dry (NTPD: 20 °C), ''V''m,O2 is 24.038 L∙mol-1. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol-1 and 22.689 L∙mol-1 for O2.;/sup>. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol-1 and 22.689 L∙mol-1 for O2. +
Authors retain the copyright for the conte … Authors retain the copyright for the contents of their manuscripts published in [[Bioenergetics Communications]]. {''Quote''} All preprints are posted with a Creative Commons CC BY 4.0 license, ensuring that authors retain '''copyright''' and receive credit for their work, while allowing anyone to read and reuse their work. {''end of Quote''}d and reuse their work. {''end of Quote''} +
Autophagy (self-eating) in general is viewed as a degradation process which removes non-essential or damaged cellular constituents. » [[Mitophagy#Mitochondrial_mitophagy | '''MiPNet article''']] +
Barth Syndome (BTHS) is an X-linked geneti … Barth Syndome (BTHS) is an X-linked genetic condition that is caused by a mutation in the tafazzin gene (taz). This mutation causes cardiolipin abnormalities, cardiomyopathy, neutropenia, muscle weakness, growth delay, and exercise intolerance.[https://www.barthsyndrome.org/about-barth-syndrome/overview-of-barth-syndrome Weblink] Contributed by [[Sparagna GC]] 2016-04-24[[Sparagna GC]] 2016-04-24 +
Biological contamination may be caused by microbial growth in the O2k-Chamber or in the experimental medium. +
Bovine serum albumin is a membrane stabili … Bovine serum albumin is a membrane stabilizer, oxygen radical scavenger, and binds Ca2+ and free fatty acids, hence the rather expensive essentially free fatty acid free BSA is required in mitochondrial isolation and respiration media. Sigma A 6003 fraction V.lation and respiration media. Sigma A 6003 fraction V. +
By clicking/enabling '''Full screen''' in … 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].rview and for Copy to clipboard [ALT+G B]. +
Calcium retention capacity (CaRC) is a mea … Calcium retention capacity (CaRC) is a measure of the capability of mitochondria to retain calcium (Ca2+), primarily in the form of calcium phosphates, in the mitochondrial matrix. By storing calcium in the form of osmotically inactive precipitates the mitochondria contribute to the buffering of cytosolic free Ca2+ levels and thereby to the regulation of calcium-dependent cellular processes. Alterations of CaRC are important in stress phenomena associated with energy limitation and have been linked to neurodegenerative diseases [[Starkov 2010 FEBS J |(Starkov 2013 FEBS J).]]Experimentally, CaRC has been indirectly assessed by determination of respiratory rates of isolated mitochondria which were exposed to continuously increasing doses of Ca2+ by use of the [[TIP2k-Module| Titration-Injection microPump TIP2k]]. The upper limit of CaRC was observed as a sudden decrease of respiration presumed to reflect opening of the permeability transition pore [[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]][[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]] +
Calibration of the sensor response time. See also [[POS calibration - static]]. +
Cataplerosis is the exit of TCA cycle intermediates from the mt-matrix space. +
Cell viability in '''living cells''' shoul … 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''ce) is the sum of viable cells (''N''vce) and dead cells (''N''dce). 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.t dual meanings of ''viable'' or unaffected by a disease or mitochondrial injury. +
Common '''DatLab error messages''' and according actions and solutions are listed here. +
Condensation of [[oxaloacetate]] … Condensation of [[oxaloacetate]] with acetyl-CoA yields citrate as an entry into the [[TCA cycle]]. CS is located in the mt-matrix. CS activity is frequently used as a functional marker of the amount of mitochondria (mitochondrial elementary marker, ''mtE'') for normalization of respiratory flux.'') for normalization of respiratory flux. +
Configure or modify the settings for the O … Configure or modify the settings for the O2k sensorsIn '''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.[[Mark statistics - DatLab|Mark statistics]] windows. +
Coordinated respiratory [[SUIT|SUIT protocols]] … Coordinated respiratory [[SUIT|SUIT protocols]] are designed to include '''cross-linked respiratory states''', which are common to these protocols. Different SUIT protocols address a variety of respiratory control steps which cannot be accomodated in a single protocol. Cross-linked respiratory states are included in each individual coordinated protocol, such that these states can be considered as replicate measurements, which also allow for harmonization of data obtained with these different protocols.a obtained with these different protocols. +
Core '''energy metabolism''' is the integr … 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.ssipating heat for temperature regulation. +
Create an identifier for your Power O2k instrument. Since it is displayed in the status panel (bottom right) and in axis labels, it should be a short code, any combination of digits and letters is allowed. +
DatLab 8: The file type generated is *.dld8. DatLab 7: The file type generated is *.DLD. +
DatLab provides several keyboard shortcuts to allow for quick access to many functions and settings without using a mouse. +
DatLab-Upgrading to DatLab 6: including free follow-up updates for DatLab 6 for the next two years +
Default channel labels can now be changed, … 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. and set the new channel label as desired. +
Different '''Q-pools''' are more or less c … Different '''Q-pools''' are more or less clearly distinguished in the cell, related to a variety of models describing degress of Q-pool behavior. (''1'') [[CoQ]]-pools are distinguished according to their compartmentation in the cell: mitochondrial CoQ (mtCoQ) and CoQ in other organelles versus plasma-membrane CoQ. (''2'') The total mitochondrial CoQ-pool mtCoQ is partitioned into an [[ETS]]-reactive Q-pool, Qra, and an inactive mtCoQ-pool, Qia. (''2a'') The Qra-pool is fully reduced in the form of quinol QH2 under anoxia, and fully oxidized in the form of quinone in aerobic [[mitochondrial preparations]] incubated without [[CHNO-fuel substrate]]s. Intermediate redox states of Qra are sensitive to pathway control and coupling control of mitochondrial electron transfer and [[OXPHOS]]. (''2b'') The Qia-pool remains partially reduced and oxidized independent of aerobic-anoxic transitions. The redox state of Qia is insensitive to changes in mitochondrial respiratory states. (''3'') The Qra-pool is partitioned into Q with Q-pool behavior according to the fluid-state model (synonymous: random-collision model) and Q tightly bound to supercomplexes according to the solid-state model. The two models describe the extremes in a continuum of homogenous or heterogenous Q-pool behavior. The CII-Q-CIII segment of the [[S-pathway]] is frequently considered to follow homogenous Q-pool behavior participating in the Qhom-pool, whereas the CI-Q-CIII segment of the [[N-pathway]] indicates [[supercomplex]] organization and metabolic channeling with different degrees of Q-pool heterogeneity contributing to the Qhet-pool.[[supercomplex]] organization and metabolic channeling with different degrees of Q-pool heterogeneity contributing to the Qhet-pool. +
Dilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber. +
Due to threshold effects, even a large defect diminishing the velocity of an individual enzyme results in only minor changes of pathway flux. +
Electrons that escape the [[electron transfer pathway]] … 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''.e on the ∆pH component than in the ∆''Ψ''. +
Flux of protons driven by the protonmotive … Flux of protons driven by the protonmotive force across the inner mt-membrane, bypassing the [[ATP synthase]] and thus contributing to [[LEAK respiration]]. Proton leak-flux depends non-linearly (non-ohmic) on the protonmotive [[force]]. Compare: [[Proton slip]].[[Proton slip]]. +
For '''shipping an O2k or parts''', standa … For '''shipping an O2k or parts''', standard operating procedures have to be followed to avoid damage of the instrument and unexpected delays. The [[O2k-Main Unit]] must be shipped only in [[Packing\O2k-Box 1]], without [[O2k-chamber]]s and without [[OroboPOS]]. Two [[O2k-Chamber Holder]]s, two [[OroboPOS-Holder]]s and two [[OroboPOS-Connector]]s are attached to the O2k-Main Unit for transport.tached to the O2k-Main Unit for transport. +
Go in DatLab to [[Mark statistics - DatLab|Mark statistics]] … Go in DatLab to [[Mark statistics - DatLab|Mark statistics]] (F2), select which type of marks you want to export ("All marks in plot" or "DL-Protocol marks", with 3 possibilities each), then click on [Copy to clipboard] to copy selected values and paste them to a '''DatLab-Analysis template''' for numerical and graphical data analysis.for numerical and graphical data analysis. +
H+ forms the '''hydronium ion''' H3O+, which in turn is further solvated by water molecules in clusters such as H5O2+ and H9O4+. +
Heat and work are forms of '''energy''' [1 … 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]], de''Q'', total or available [[work]], det''W'' (or det''W''), and [[matter]], dmat''U'' (or dmat''H'') [2], d''U'' = (de''Q'' + det''W'') + dmat''U'' ; d''V'' = 0 [Eq. 1a] d''H'' = (de''Q'' + de''W'') + dmat''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 dmat''U'' (or dmat''H'') are the exchange of matter expressed in internal-energy (or enthaply) equivalents. In closed systems, dmat''U'' = 0 (dmat''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 de''G'' = de''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'' = di''H'' + de''H'' [Eq. 3a] d''G'' = di''G'' + de''G'' [Eq. 3b]The energy conservation law of thermodynamics (first law) can be formulated as di''H'' = 0 (at constant gas pressure), whereas the generally negative sign of the [[dissipated energy]], di''G'' ≡ di''D'' ≤ 0, is a formulation of the second law of thermodynamics. Insertion into Eq. 3 yields, d''H'' = de''H'' [Eq. 4a] d''G'' = di''D'' + de''W'' + dmat''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 second law of thermodynamics. Insertion into Eq. 3 yields, d''H'' = de''H'' [Eq. 4a] d''G'' = di''D'' + de''W'' + dmat''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. +
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]]) +
IUPAC distinguishes three definitions of ' … IUPAC distinguishes three definitions of 'substrate': (1) The chemical entity whose conversion to a [[product]] or products is catalysed by one or several enzymes. (2) A solution or dry mixture containing all ingredients which are necessary for the growth of a microbial culture or for product formation. (3) Component in the nutrient medium, supplying the organisms with carbon (C-substrate), nitrogen (N-substrate), etc.A substrate in a chemical reaction has a negative [[stoichiometric number]] since it is consumed, whereas a product has a positive stoichiometric number since it is produced.toichiometric number since it is produced. +
Ideally the terms '''anoxia''' and anoxic … Ideally the terms '''anoxia''' and anoxic (anox, without oxygen) should be restricted to conditions where molecular oxygen is strictly absent. Practically, effective anoxia is obtained when a further decrease of experimental oxygen levels does not elicit any physiological or biochemical response. The practical definition, therefore, depends on (i) the techiques applied for oxygen removal and minimizing oxygen diffusion into the experimental system, (ii) the sensitivity and limit of detection of analytical methods of measuring oxygen (O2 concentration in the nM range), and (iii) the types of diagnostic tests applied to evaluate effects of trace amounts of oxygen on physiological and biochemical processes. The difficulties involved in defining an absolute limit between anoxic and [[microxic]] conditions are best illustrated by a logarithmic scale of oxygen pressure or oxygen concentration. In the '''''anoxic state''''' ([[State 5]]), any aerobic type of metabolism cannot take place, whereas '''''[[anaerobic]] metabolism''''' may proceed under oxic or anoxic conditions.lism''''' may proceed under oxic or anoxic conditions. +
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). +
If a sample contains a number of absorbing … 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''3]] can be obtained.[[Complex IV | cytochrome ''aa''3]] can be obtained. +
In '''Copy marks''', [[Marks - DatLab |Marks in DatLab]] are copied from a seleted [[Plot - DatLab |Plot]] to the active plot. +
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. +
In '''chlororespiration''' oxygen is consu … In '''chlororespiration''' oxygen is consumed by a putative respiratory electron transfer system (ETS) within the thylakoid membrane of the [[chloroplasts]] and ATP is produced. It is a process that involves the interaction with the photosynthetic ETS in which NAD(P)H dehydrogenase transfers electrons to oxygen with the assistance of the photosynthetic plastoquinone (PQ), which acts as a non-photochemical redox carrier. Initially described in the unicellular alga ''Chlamydomonas reindhartdii'', chlororespiration was highly disputed for years until the discovery of a NAD(P)H-dehydrogenase (NDH) complex (plastidic encoded) and plastid terminal oxidase (PTOX) (nuclear encoded) in higher-plant chloroplasts. PTOX is homologous to the plant mitochondrial alternative oxidase and has the role of preventing the over-reduction of the PQ pool while the NDH complexes provide a gateway for the electrons to form the ETS and consume oxygen. As a result of this process there is a cyclic electron flow around Photosystem I (PSI) that is activated under stress conditions acting as a photoprotection mechanism and could be involved in protecting against oxidative stress.ed in protecting against oxidative stress. +
In '''reflectance spectrophotometry''' the light from the sample is reflected back to the [[detector]] using mirrors. Before [[absorbance]] measurements can be made, a [[white balance]] is carried out. +
In '''remittance spectrophotometry''' [[incident light]] … In '''remittance spectrophotometry''' [[incident light]] enters a [[scattering]] medium and is scattered back to the receiving optics (usually [[lightguides]]) before being directed to the [[detector]]. Before [[absorbance]] measurements can be made, a [[white balance]] is carried out.[[white balance]] is carried out. +
In '''uncoupler titrations''' various [[uncoupler]] … In '''uncoupler titrations''' various [[uncoupler]]s, such as CCCP, FCCP or DNP are applied to uncouple mitochondrial electron transfer from phosphorylation ([[ATP synthase]], [[ANT]] and [[phosphate carrier]]), particularly with the aim to measure [[ET capacity]]. ET capacity is maximum [[oxygen flux]] measured as [[noncoupled respiration]] with [[optimum uncoupler concentration]].[[optimum uncoupler concentration]]. +
In DatLab '''Copy to clipboard''' can be used to copy selected graphs or values and to paste them to your preferred program or file (e.g. Word, Excel). +
In DatLab 8, the start recording window allows to select protocols or settings before starting recording a file. +
In [[fluorometry]] … 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.ty emerging from the sample is very small. +
In [[fluorometry]] and [[transmission spectrophotometry]] '''blank''' [[cuvettes]] (with no samples in them) are used to carry out the [[balance]]. +
In [[reflectance spectrophotometry]] … In [[reflectance spectrophotometry]] and [[remission spectrophotometry]] a white balance is carried out to determine the intensity of the incident light (''I''''0'') for the purpose of quantitative [[absorbance]] measurements. In [[reflectance spectrophotometry]], a mirror can be used whereas in [[remission spectrophotometry]] a standard white tile is more appropriate.[[remission spectrophotometry]] a standard white tile is more appropriate. +
In a '''discontinuous system''', gradients … 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-3]. 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.al analysis of the substrate and product compartments. +
In an isomorphic analysis, any form of ''' … 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-1], ''e.g.'', ampere for electric flow or current [A≡C∙s-1], watt for heat flow [W≡J∙s-1], and for chemical flow the unit is [mol∙s-1]. Flow is an [[extensive quantity]]. The corresponding isomorphic [[force]]s are the partial exergy (Gibbs energy) changes per advancement [J∙MU-1], expressed in volt for electric force [V≡J∙C-1], dimensionless for thermal force, and for chemical force the unit is [J∙mol-1], which deserves a specific acronym ([Jol]) comparable to volt.for chemical force the unit is [J∙mol-1], which deserves a specific acronym ([Jol]) comparable to volt. +
In an isomorphic analysis, any form of [[flow]] … In an isomorphic analysis, any form of [[flow]] is the '''advancement''' of a process per unit of time, expressed in a specific [[motive unit]] [MU∙s-1], ''e.g.'', ampere for electric flow or current, ''I''el = del''ξ''/d''t'' [A≡C∙s-1], watt for thermal or heat flow, ''I''th = dth''ξ''/d''t'' [W≡J∙s-1], and for chemical flow of reaction, ''I''r = dr''ξ''/d''t'', the unit is [mol∙s-1] ('''extent of reaction''' per time). The corresponding motive [[force]]s are the partial exergy (Gibbs energy) changes per advancement [J∙MU-1], expressed in volt for electric force, Δel''F'' = ∂''G''/∂el''ξ'' [V≡J∙C-1], dimensionless for thermal force, Δth''F'' = ∂''G''/∂th''ξ'' [J∙J-1], and for chemical force, Δr''F'' = ∂''G''/∂r''ξ'', the unit is [J∙mol-1], which deserves a specific acronym [Jol] comparable to volt [V]. For chemical processes of reaction (spontaneous from high-potential substrates to low-potential products) and compartmental diffusion (spontaneous from a high-potential compartment to a low-potential compartment), the advancement is the amount of motive substance that has undergone a compartmental transformation [mol]. The concept was originally introduced by De Donder [1]. Central to the concept of advancement is the [[stoichiometric number]], ''ν''''i'', associated with each motive component ''i'' (transformant [2]).In a chemical reaction r the motive entity is the stoichiometric amount of reactant, dr''n''''i'', with stoichiometric number ''ν''''i''. The advancement of the chemical reaction, dr''ξ'' [mol], is defined as, dr''ξ'' = dr''n''''i''·''ν''''i''-1The flow of the chemical reaction, ''I''r [mol·s-1], is advancement per time, ''I''r = dr''ξ''·d''t''-1This concept of advancement is extended to compartmental diffusion and the advancement of charged particles [3], and to any discontinuous transformation in compartmental systems [2],:::: [[File:Advancement.png|100px]] +
In chemistry or physics, '''abundance''' o … In chemistry or physics, '''abundance''' or '''natural abundance''' refers to the amount of a chemical element isotope existing in nature. The abundance of an isotope on the Earth may vary depending on the place, but remains relatively constant in time (on a short-term scale). In a chemical reaction, the reactant is in abundance when the quantity of a substance is enough (or high) and constant during the reaction. '''Relative abundance''' represents the percentage of the total amount of all isotopes of the element. The relative abundance of each isotope in a sample can be identified using mass spectrometry.can be identified using mass spectrometry. +
In mitochondrial respiratory physiology a … In mitochondrial respiratory physiology a large number of '''pathway and coupling control states''' is encountered, for which a unified system of terms and abbreviations is required. In [[mitochondrial preparations]] there is a large number of potentially complex [[pathway control state]]s, in contrast to only three [[coupling control state]]s (''L'', ''P'', ''E''). Therefore, it is practical to use ''L'', ''P'', and ''E'' as subscripts attached to the abbreviation of the pathway control state.abbreviation of the pathway control state. +
In most cases '''journal publication''' {' … 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.journals by preprint policy] is available. +
In order to improve the [[signal-to-noise ratio]] a number of sequential spectra may be averaged over time. The number of spectra to be averaged can be set prior to carrying out the measurements, or afterwards during data analysis. +
In respiratory assays for cytochrome ''c'' … In respiratory assays for cytochrome ''c'' oxidase activity ([[Complex IV|Complex IV, CIV]]), '''ascorbate''' is added as regenerating system to maintain [[TMPD]] in a reduced state. It has to be titrated into the respiration medium prior to the addition of TMPD, otherwise the [[autoxidation]] reaction velocity is permanently elevated.reaction velocity is permanently elevated. +
In the [[healthy reference population]] … In the [[healthy reference population]] (HRP), there is zero '''body fat excess''', BFE, and the fraction of excess body fat in the HRP is expressed - by definition - relative to the reference body mass, ''M''°, at any given [[height of humans |height]]. Importantly, body fat excess, BFE, and [[body mass excess]], BME, are linearly related, which is not the case for the body mass index, BMI.not the case for the body mass index, BMI. +
In the context of '''quantities, symbols, … In the context of '''quantities, symbols, and units''', a code is required to convert terms defining physicochemical quantities into symbols (encoding) and to decode symbols as used in equations, text, and figures. Then symbols and abbreviations gain meaning. Simple symbols — such as ''Q'' or ''N'' — are used with different meanings depending on context (think of ''Q'' for heat and ''Q'' for electric charge; or ''N'' for number of cells and ''N'' for number of O2 molecules). The context provides the code. When the context is extended, the symbols have to be expanded too, including more detail to avoid confusion (''Q''th versus ''Q''el; ''N''ce versus ''N''O2). Then symbols may appear too complicated, loosing the function of sending their message quickly. There is no single best way to design the right symbol or to replace meaningful symbols (''Q''el) by ambiguous abbreviations (''Q'') — all depends on context. We need to use the adequate medium (words, symbols, and abbreviations; equations, text, and figures; videos and slide presentations) and provide the code to achieve communication. The medium is the message, the message is the meaning — from [https://en.wikipedia.org/wiki/The_Medium_Is_the_Massage Marshall McLuhan] to [[Hofstadter 1979 Harvester Press |Hofstadter]].dter 1979 Harvester Press |Hofstadter]]. +
In the context of MiP''events'', '''extend … 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.er, and facilitate discovery and feedback. +
In the mitochondrial '''electron transfer … 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''']][#Electron transfer pathway versus electron transport chain |'''MiPNet article''']] +
In the pull-down menue [Graph], '''Select … In the pull-down menue [Graph], '''Select plots''' opens the Graph layout window 'Plots'. For each graph, the plots shown with the Y1 or Y2 axis can be selected, axis labels and line styles can be defined, the unit for the calibrated signal can be changed, Flux/Slope can be chosen to be displayed as Flux per volume or as normalized specific flux/flow, the background correction can be switched on or off, and the channel can be selectively displayed as the raw signal. Graph layouts can be selected and loaded or a Graph layout may be saved. »''Compare:'' [[Scaling - DatLab]].[Scaling - DatLab]]. +
In the transition from aerobic to [[anaerobic | anaerobic metabolism]] … In the transition from aerobic to [[anaerobic | anaerobic metabolism]], there is a limiting ''p''O2, ''p''lim, below which anaerobic energy flux is switched on and [[Calorespirometric ratio|CR ratios]] become more exothermic than the [[oxycaloric equivalent]]. ''p''lim may be significanlty below the [[critical pO2|critical ''p''O2]].[[critical pO2|critical ''p''O2]]. +
In the transmission mode, the incident light passes through the sample [[cuvettes]] and the emergent light reaches the [[detector]] directly. Before [[absorbance]] measurements can be made, a [[balance]] is carried out. +
In transmission spectrophotometry [[blank]] … In transmission spectrophotometry [[blank]] [[cuvettes]] are used to record the [[incident light]] intensity (''I''''0'') prior to absorbance measurements. (See [[white balance]] for [[reflectance spectrophotometry]], [[remittance spectrophotometry]]).[[remittance spectrophotometry]]). +
Instrumental [[Run DL-Protocol/Set O2 limit| DL-Protocols]] … 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.an DL-Protocol and/or template as desired. +
Integrative measure of the dynamics of com … 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.n circuit, and the phosphorylation system. +
Intensive quantities are partial derivativ … Intensive quantities are partial derivatives of an extensive quantity by the advancement, dtr''ξ''''X'', 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-1] 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 O2 + 6 CO2 + 6 H2O), Δk''G''Glc [kJ·mol-1], and the specific quantity Gibbs energy per mole glucose contained in a system, ''G''Glc [kJ·mol-1] (with respect to an arbitrarily defined reference state, such as the reference state of formation or combustion).Glc [kJ·mol-1] (with respect to an arbitrarily defined reference state, such as the reference state of formation or combustion). +
It is advisable to replace levels of '''statistical significance''' (*, **, ***) by simply stating the actual ''p''-values. +
Leading preprint service providers use ''' … 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..OSF is based in Charlottesville, VA, USA. +
Low muscle strength is a key characteristic of '''sarcopenia''' due to low muscle quantity and quality, with poor physical performance at severe sarcopenia. Older age may be defined as the age group when sarcopenia becomes a common burden. +
Mammalian '''superoxide dismutase''' (SOD) … Mammalian '''superoxide dismutase''' (SOD) exists in three forms, of which the Mn-SOD occurs in mitochondria (mtSOD, SOD2; 93 kD homotetramer) and many bacteria, in contrast to the Cu-Zn forms of SOD (cytosolic SOD1, extracellular SOD3 anchored to the extracellular matrix and cell surface). [[Superoxide]] anion (O2•-) is a major [[reactive oxygen species]] (ROS) which is dismutated by SOD to [[oxygen]] and [[hydrogen peroxide | H2O2]].hydrogen peroxide | H2O2]]. +
Manuscripts template for [[MitoFit Preprints]] and [[Bioenergetics Communications]]. +
Many cell types are grown in culture as '''attached cells''', such as endothelial or neuronal cells in a monolayer. +
Metabolic control analysis is a science fo … 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.ntrol of metabolism. Portland Press. 1997. +
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]]. +
Mitochondria and the patient: communication between patients, medical professionals, scientists, and the public +
Mitochondrial '''Substrate-uncoupler-inhib … Mitochondrial '''Substrate-uncoupler-inhibitor titration''' ('''SUIT''') [[MitoPedia: SUIT |protocols]] are used with [[mitochondrial preparations]] to study respiratory control in a sequence of coupling and substrates states induced by multiple titrations within a single experimental [[assay]].[[assay]]. +
Mitochondrial '''hydrogen ion pumps''' — f … 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+ 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+ pump that utilizes the exergy of proton flow along the protonmotive force to drive phosphorylation of [[ADP]] to [[ATP]].P]]. +
Mitochondrial '''malate dehydrogenase''' i … Mitochondrial '''malate dehydrogenase''' is localized in the mitochondrial matrix and oxidizes [[malate]], generated from fumarate by fumarase, to [[oxaloacetate]], reducing NAD+ to NADH+H+ in the [[TCA cycle]]. Malate is added as a substrate in most [[N-pathway control state]]s.[[N-pathway control state]]s. +
Mitochondrial '''proton pumps''' are large … Mitochondrial '''proton pumps''' are large enzyme complexes (CI, CIII, CIV, CV) spanning the inner mt-membrane, partially encoded by mtDNA. [[Complex I|CI]], [[CIII]] and [[CIV]] are proton pumps that drive [[proton]]s against the electrochemical [[protonmotive force]], driven by electron transfer from reduced substrates to oxygen. In contrast, [[ATP synthase]] (also known as CIV) is a proton pump that utilizes the energy of proton flow along the protonmotive force to drive phosphorylation of [[ADP]] to [[ATP]].[[ATP]]. +
Mitochondrial respiration medium, '''MiR05Cr''', developed for oxygraph incubations of mitochondrial preparations - ''[[permeabilized muscle fibers]]''. MiR05Cr = [[MiR05]] + 20 mM [[Creatine|creatine]]. +
Mitochondrial respiration medium, '''MiR06Cr''', developed for oxygraph incubations of mitochondrial preparations - ''[[permeabilized muscle fibers]]''. MiR06Cr = [[MiR06]] + 20 mM [[Creatine|creatine]]. +
Mitochondrial respiratory capacity and con … 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.[[ROS]] production. +
Molecular '''hydrogen''' H2< … Molecular '''hydrogen''' H2 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.ithout complete evidence on the underlying mechanisms. +
Most biological samples do not consist sim … Most biological samples do not consist simply of pigments but also particles (e.g. cells, fibres, mitochondria) which scatter the [[incident light]]. The effect of '''scattering''' is an apparent increase in [[absorbance]] due to an increase in pathlength and the loss of light scattered in directions other than that of the detector. Two types of scattering are encountered. For incident light of wavelength ''λ'', Rayleigh scattering is due to particles of diameter < ''λ'' (molecules, sub-cellular particles). The intensity of scatter light is proportional to ''λ''4 and is predominantly backward scattering. Mie scattering is caused by particles of diameter of the order of or greater than ''λ'' (tissue cells). The intensity of scatter light is proportional to 1/''λ'' and is predominantly forward scattering.ional to 1/''λ'' and is predominantly forward scattering. +
Most of the chemicals for SUIT protocol ti … Most of the chemicals for SUIT protocol titrations are prepared by weighing the substance on the balance, transferring to a volumetric glass flask and adding solvent until the intended volume is reached. However, for practical reasons some of the chemical compounds are prepared by just adding the solvent instead of adjusting it's volume. For example, this approach is useful if the substance is very toxic. Then an arbitratry amount is taken, its mass determined on the balance without trying to reach a specific value and the necessary amount of solvent is added. Adding the solvent instead of adjusting its volume is also useful if small amounts are needed (e.g. 1 mL) or if the compound has to be prepared directly before using it like Pyruvate. In these cases the volume contributed by the solute was tested.lume contributed by the solute was tested. +
Most of the nonpolar compounds have to be … Most of the nonpolar compounds have to be diluted in organic solvents such as DMSO or acetonitrile in order to use them for the titrations in the SUIT protocols. However, the solvent (carrier) itself could affect the mitochondrial physiology and promote alterations that we need to take into account. For this reason, it is necessary to run in parallel to our treatment experiment a control experiment on which we will add a '''carrier control titration''' to test if it affects our sample or not.' to test if it affects our sample or not. +
Multiple meanings of Q ::::» [[Coenzyme Q]] Q ::::» [[Charge]] ''Q'', ''Q''el ::::» [[Heat]] ''Q'', ''Q''th +
Nigericin is a H+/K … Nigericin is a H+/K+ antiporter, which allows the electroneutral transport of these two ions in opposite directions across the mitochondrial inner membrane following the K+ concentration gradient. In the presence of K+, 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]].AK respiration|LEAK state]]. +
Not enough is known about '''viruses and mitochondrial medicine''', although several studies point towards a link between viral infection and mitochondrial dysfunction using high-resolution respirometry, with potential impact on drug development. +
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]]. +
O2k-Virtual support includes 8 individual … 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.l sessions that best fit individual needs. +
Obesity is defined as a disease associated … Obesity is defined as a disease associated with an excess of body fat with respect to a healthy reference condition. Cutoff points for [[body mass excess]], '''BME cutoff points''', define the critical values for underweight (-0.1 and -0.2), overweight (0.2), and various degrees of obesity (0.4, 0.6, 0.8, and above). BME cutoffs are calibrated by crossover-points of BME with established BMI cutoffs.oints of BME with established BMI cutoffs. +
Open Access preprints (not peer-reviewed) … Open Access preprints (not peer-reviewed) and articles (peer-reviewed) distributed under the terms of the '''Creative Commons Attribution License''' allow unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. © remains with the authors, who have granted the publisher license in perpetuity.anted the publisher license in perpetuity. +
Organizer of * [http://bioblast.at/index. … 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]][[Clinical Mitochondria- and Environmental Medicine 2018 Heidelberg DE|Klinische MitochondrienMedizin und Umweltmedizin 2018]] +
Oxidative decarboxylation of pyruvate is catalyzed by the '''pyruvate dehydrogenase complex''' in the mt-matrix, and yields acetyl-CoA. +
P/O ratio stands for phosphate to atomic oxygen ratio, where P indicates phosphorylation of ADP to ATP (or GDP to GTP). +
Physicochemical '''equality''' (symbol =) indicates in an equation not only numerical [[equivalence]] (symbol ≡), but an identity of the full meaning. +
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. +
RT indicates '''room temperature''' or 25 °C. ''RT'' is the [[gas constant]] ''R'' [kJ/mol] multiplied by absolute [[temperature]] ''T'' [K]. This is the motive force quantum in the amount format ([[Gnaiger 2020 BEC MitoPathways]]). +
Recently, controversies had a renaissance … Recently, controversies had a renaissance on the much neglected Crabtree effect (aerobic glycolysis in a large range of cells exposed to glucose or fructose, with fully functional mitochondria; Crabtree 1929; Gnaiger and Kemp 1990) versus the '''Warburg effect''' (loss of mitochondrial function inducing cancer and stimulating compensatory aerobic glycolysis in the presence of oxygen; Warburg 1956; see list of references for reviews). Today it is widely accepted that ‘''the Warburg effect is not consistent across all cancer types''’ (Potter et al 2016) and reprogramming of mitochondrial energy metabolism represents a functional adjustment of cancer cells (Schöpf et al 2020).tment of cancer cells (Schöpf et al 2020). +
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. +
Reduction of [[oxoglutarate]] … Reduction of [[oxoglutarate]] (2OG or alpha-ketoglutarate) to '''2-hydroxyglutarate''' (2HG) is driven by NADPH. 2HG is also formed in side reactions of [[lactate dehydrogenase]] and [[malate dehydrogenase]]. Millimolar 2HG concentrations are found in some cancer cells compared to , whereas side activities of lactate and malate dehydrogenase form submillimolar s-2-hydroxyglutarate (s-2HG). However, even wild-type IDH1 and IDH2, notably under shifts toward reductive carboxylation glutaminolysis or changes in other enzymes, lead to “intermediate” 0.01–0.1 mM 2HG levels, for example, in breast carcinoma compared with nanomolar concentrations in benign cells. 2HG is considered an important player in reprogramming metabolism of cancer cells. reprogramming metabolism of cancer cells. +
Researchers need to be introduced into adh … Researchers need to be introduced into adhering to '''publicly deposited protocols'''. [[Prespecified protocols |Prespecified]] and [[time-stamped protocols]] that are publicly deposited may help to save Millions of Euros that may otherwise be wasted on research that is lacking coherent standards.search that is lacking coherent standards. +
Respiratory '''oxygen flow''' is the oxyge … Respiratory '''oxygen flow''' is the oxygen consumption per total [[system]], which is an [[extensive quantity]]. [[Flow]] is advancement of a transformation in a system per time [mol·s-1], when 'system' is defined as the experimental system (e.g. an open or closed chamber). Flow is distinguished from the size-specific quantity [[flux]] obtained by normalization of flow per volume of the experimental system [mol·s-1·m-3]. An experimental object, e.g. a living cell, may be considered as the 'experimental system'. Then oxygen flow per cell has the unit [mol·s-1·x-1], where [x] is the [[elementary unit]] for a [[count]]. Oxygen flow or respiration per cell [amol·s-1·x-1] = [pmol·s-1·Mx-1] is normalized for the cell count, distinguished from [[oxygen flux]] (e.g. per mg protein or wet mass). These are different forms of [[normalization of rate]].zation of rate]]. +
Reverse electron flow from CII to CI stimu … Reverse electron flow from CII to CI stimulates production of [[ROS]] when mitochondria are incubated with succinate without rotenone in the LEAK state at a high [[mt-membrane potential]]. Depolarisation of the mt-membrane potential (''e.g.'' after ADP addition to stimulate OXPHOS) leads to inhibition of RET and therefore, decrease of RET-initiated ROS production. RET can be also measured when mitochondria are respiring using [[Glycerophosphate |Gp]] without rotenone in the [[LEAK respiration|LEAK]] state. Addition of IQ-side inhibitors (ubiquinone-binding side of CI) of [[Complex I |CI]] usually block RET. The following SUIT protocols allow you to measure RET-initiated H2O2 flux in [[mitochondrial preparations]]: [[SUIT-009]] and [[SUIT-026]].[[SUIT-026]]. +
Rhodamine 123 (Rh123) is an [[extrinsic fluorophores|extrinsic fluorophore]] … Rhodamine 123 (Rh123) is an [[extrinsic fluorophores|extrinsic fluorophore]] and can be used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. Rh123 is a lipophilic cation that is accumulated by mitochondria in proportion to Δ''ψ''mt. Using ethanol as the solvent, the excitation maximum is 511 nm and the emission maximum is 534 nm. The recommended excitation and emission wavelengths in PBS are 488 and 515-575 nm, respectively (Sigma-Aldrich). are 488 and 515-575 nm, respectively (Sigma-Aldrich). +
Richard Altmann (1894) defined the 'elemen … Richard Altmann (1894) defined the 'elementary organisms' as '''Bioblasts'''. He observed granula in cells stained with osmium and viewed ‘the protoplasm as a colony of bioblasts’. "Microorganisms and granula are at an equivalent level and represent elementary organisms, which are found wherever living forces are acting, thus we want to describe them by the common term bioblasts. In the bioblast, that morphological unit of living matter appears to be found." [[Altmann 1894 Verlag Von Veit & Comp|Altmann 1894]]; p. 141. Altmann is thus considered as the discoverer of [[mitochondria]] (the granula), which constitute together with the microorganisms the ''bioblasts'' (the elementary organisms). Bioblasts are the aliens with permanent residence in our cells ([[Bioblasts#Bioblasts_.E2.80.93_the_aliens_with_permanent_residence_in_our_cells|Gnaiger 2010]]).oblasts#Bioblasts_.E2.80.93_the_aliens_with_permanent_residence_in_our_cells|Gnaiger 2010]]). +
Science Europe: "Zenodo is an open source … Science Europe: "Zenodo is an open source and free repository for storing data, code, materials, and any research artefact. It was created by CERN and launched within the frame of the OpenAIRE project, commissioned by the European Commission. It aims at fostering free and easy access to scientific results, scientific data, software, and publications to all researchers."are, and publications to all researchers." +
Science only progresses as quickly and eff … Science only progresses as quickly and efficiently as it is shared. But even with all of the technological capabilities available today, the process of publishing scientific work is taking longer than ever. '''ASAPbio''' (Accelerating Science and Publication in biology) is a scientist-driven nonprofit working to address this problem by promoting innovation and transparency in life sciences communication.In 2015, ASAPbio founder Ron Vale published an analysis of the increasing time to first-author publication among graduate students at UCSF, and proposed a more widespread use of preprints in the life sciences as a potential solution.the life sciences as a potential solution. +
Select '''Delete points''' in the [[Marks - DatLab |Mark information]] window to remove all data points in the marked section of the active plot. See also [[Interpolate points]] and [[Restore points]] or [[Recalculate slope]]. +
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]]. +
Select '''Recalculate slope''' (Recalc. sl … Select '''Recalculate slope''' (Recalc. slope) in the [[Marks - DatLab |Mark information]] window to restore data points in the marked section of the active Flux / Slope plot, if [[Delete points]] or [[Interpolate points]] was used before. The entire plot is recalculated, such that other marked sections which may have been deleted are also restored. Compare [[Restore points]].[[Restore points]]. +
Select '''Restore points''' in the [[Marks - DatLab |Mark information]] window to restore data points in the marked section of the active signal plot, if [[Delete points]] or [[Interpolate points]] was used before. Compare [[Recalculate slope]]. +
Setups and templates in DatLab can be renamed or deleted under '''Manage setups''' or '''Manage templates'''. +
Several display options can be applied to a DatLab graph under '''Graph options'''. +
Should we used a '''comma for separating a … Should we used a '''comma for separating a term and its abbreviation''' in the text? The SI Brochure frequently does not use a comma. The comma might be added, if it helps to clarify the distinction between the term and its abbreviation. The example “reduced Q fraction, ''Q''r” – the sequence of Q and ''Q''r may be confusing without comma. There will always be examples, where it is not clear, if a comma is needed.l always be examples, where it is not clear, if a comma is needed. +
Similarly to the [[least squares method]] … 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.e the best fit with the measured spectrum. +
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. +
Sodium phosphate buffer, '''Na-PB''', for [[HRR]] with freeze-dried baker´s yeast. +
Some [[spectrofluorometer]] … Some [[spectrofluorometer]] or [[spectrophotometer]] software offers the possibility of '''spline''' interpolation of the spectral data points. This makes use of a polynomial (the number of '''spline''' points is entered by the user) to interpolate the curve between the data points.rpolate the curve between the data points. +
Specific '''mitochondrial density''' is '' … Specific '''mitochondrial density''' is ''DmtE'' = ''mtE''·''mX''-1 [mtEU·kg-1]. If the amount of mitochondria, ''mtE'', is expressed as mitochondrial mass, then ''DmtE'' is the mass fraction of mitochondria in the sample. If ''mtE'' is expressed as mitochondrial volume, ''V''mt, and the mass of sample, ''mX'', is replaced by volume of sample, ''VX'', then ''DmtE'' is the volume fraction of mitochondria in the sample.eplaced by volume of sample, ''VX'', then ''DmtE'' is the volume fraction of mitochondria in the sample. +
Spectral resolution is a measure of the ab … Spectral resolution is a measure of the ability of an instrument to differentiate between two adjacent wavelengths. Two wavelengths are normally considered to be resolved if the minimum detector output signal (trough) between the two peaks is lower than 80 % of the maximum. The resolution of a [[spectrofluorometer]] or [[spectrophotometer]] is dependent on its [[bandwidth]].[[bandwidth]]. +
Stoppers can be custom-made for applications with user-specific sensors according to customer specifications. +
Tartronic acid (hydroxymalonic acid, C3H4O5; molecular weight 120.06) is an inhibitor of [[malic enzyme]]. +
Taurine, or 2-Aminoethan sulfonic acid, is … Taurine, or 2-Aminoethan sulfonic acid, is one of the most abundant low-molecular-weight organic constituents in animals and humans. It has a multitude of functions in different types of tissue, one of which is the stabilization of membranes. Because of this and its antioxidative effect, taurine is a component of the respiration media MiR05 and MiR06 to preserve mitochondrial function. MiR06 to preserve mitochondrial function. +
The '''Chinese Society of Mitochondrial Research and Medicine''' (Chinese-Mit) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]]. +
The '''Crabtree effect''' describes the ob … The '''Crabtree effect''' describes the observation that respiration is frequently inhibited when high concentrations of glucose or fructose are added to the culture medium - a phenomenon observed in numerous cell types, particularly in proliferating cells, not only tumor cells but also bacteria and yeast. The Pasteur effect (suppression of glycolysis by oxygen) is the converse of the Crabtree effect (suppression of respiration by high concentration of glucose or fructose).igh concentration of glucose or fructose). +
The '''Default label''' is the system default value for the axis label. These labels are changed automatically, according to the selected channel and unit. To change this label enter a [[Custom label]]. +
The '''Directory of Open Access Journals''' is a free online directory that indexes and provides access to open access peer-reviewed journals. +
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 +
The '''Faraday constant''' ''F'' links the … The '''Faraday constant''' ''F'' links the electric charge [C] to amount [mol], and thus relates the [[electrical format]] ''e'' [C] to the [[molar format]] ''n'' [mol]. The Farady constant, ''F'' = ''e''·''N''A = 96 485.33 C/mol, is the product of [[elementary charge]], ''e'' = 1.602176634∙10-19 C/x, and the [[Avogadro constant]], ''N''A = 6.02214076∙1023 x/mol. The dimensionless unit [x] is not explicitely considered by IUPAC.= 6.02214076∙1023 x/mol. The dimensionless unit [x] is not explicitely considered by IUPAC. +
The '''Inclusion criteria''' are based on … 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 parametert be a cofounder for the outcome parameter +
The '''International Standard Serial Numbe … 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]rg/resource/ISSN/2791-4690 ISSN 2791-4690] +
The '''International System of Units''' (S … 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).e units, and progress in science (p. 125). +
The '''International Union of Pure and App … The '''International Union of Pure and Applied Chemistry''' (IUPAC) celebrated in 2019 the 100th 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]]).C 2020.1]]). +
The '''Korean Society of Mitochondrial Research and Medicine''' (KSMRM) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]]. +
The '''MitoFit DOI Data Center''' is respo … 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.ance of the Metadata, and quality control. +
The '''Mitochondrial Physiology Network''' is the on-line Oroboros journal. +
The '''N/NS [[pathway control ratio]] … 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.bstrates supporting the N- and S-pathways. +
The '''N/S [[pathway control ratio]] … 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.tudied with respect to N-pathway injuries. +
The '''NS-N [[pathway control efficiency]]''', ''j''NS-N = 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''' … 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''(NS-S)''E'' = (NS''E''-S''E'')/NS''E''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.[[succinate dehydrogenase]] CII. +
The '''O2k signal line''' is underneath th … 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.[[O2k serial number]] are displayed. +
The '''O2k-Accessory Box''' contains components of the [[POS-Service Kit]] and the [[O2k-Assembly Kit]] and is shipped with the O2k. +
The '''O2k-Assembly Kit''' is a component … 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-Accessory Box]] either for shipment or for storage. +
The '''O2k-Fluo Smart-Module''' is an ampe … 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), Ca2+ (Calcium Green™), and numerous other applications open for O2k-user innovation. ::: » [[MiPNet28.09 O2k-Fluo Smart-Module manual]]et28.09 O2k-Fluo Smart-Module manual]] +
The '''O2k-Main Basic''' is an integral el … 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 (H2S) sensors.*USB-Port for connection with DatLab (PC or laptop not included)for connection with DatLab (PC or laptop not included) +
The '''O2k-Main Unit''' is a component of … 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.[[O2k-Barometric Pressure Transducer]]), which cannot be obtained separately. +
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. +
The '''O2k-ticket system''' is a customer … 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. issue accompanied by a brief explanation. +
The '''O2 sensor te … The '''O2 sensor test''' is an important component of [[MitoPedia: Oroboros QM |Oroboros Quality Management]]. The [[OroboPOS]] test is described in detail in [[MiPNet06.03 POS-calibration-SOP]], is performed after switching on the [[Oroboros O2k]], and is required as a basis of technical service of the instrument.red as a basis of technical service of the instrument. +
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. +
The '''Oroboros USB-flash drive''' is deli … The '''Oroboros USB-flash drive''' is delivered with the [[Oroboros O2k]]. Copy the folder "Oroboros O2k-Course on HRR" from the '''Oroboros USB-flash drive''' to your computer. This folder contains the DatLab installation program as well as tools to find topics, O2k-manuals and O2k-protocols with corresponding DatLab demo files and templates for training with [[DatLab]].[[DatLab]]. +
The '''Q-redox state''' reflects the redox … The '''Q-redox state''' reflects the redox status of the [[Q-junction]] in the mitochondrial or chloroplast [[ETS|electron transfer system (ETS)]]. [[Coenzyme Q]] (CoQ or Q, [[ubiquinone]]) is a mobile redox component located centrally in the mitochondrial [[ETS]], while plastoquinones are essential mobile components in the photosynthetic system with a similar function. The Q-redox state depends on the balance between reducing capacities of convergent electron entries from fuel substrates into the Q-junction and oxidative capacities downstream of Q to the electron acceptor oxygen. Therefore, deficiencies in the mitochondrial [[ETS]], originating from e.g. the malfunction of respiratory Complexes, can be detected by measuring the changes of the Q-redox state with respect to the respiratory activity.A three-electrode system was implemented into the NextGen-O2k to monitor the Q-redox state continuously and simultaneously with respiratory oxygen consumption. Added CoQ2 reflects the mitochondrial Q-redox state when equilibrating both with the detecting electrode and the biological sites (e.g. Complexes I, II and III).ical sites (e.g. Complexes I, II and III). +
The '''S/NS [[pathway control ratio]] … The '''S/NS [[pathway control ratio]]''' is obtained when [[rotenone]] (Rot) is added to the [[NS-pathway control state]] in a defined [[coupling control state]]. The reversed protocol, adding N-type substrates to a [[S-pathway control state]] as the [[background state]] does not provide a valid estimation of S-linked respiration with succinate in the absence of Rot, since [[oxaloacetate]] accumulates as a potent inhibitor of [[succinate dehydrogenase]] (CII).[[succinate dehydrogenase]] (CII). +
The '''SUIT protocol pattern''' describes the type of the sequence of coupling and substrate control steps in a SUIT protocol, which may be liner, orthogonal, or diametral. +
The '''Science Citation Index''' SCI offers bibliographical access to a curated collection of journals across 178 scientific disciplines. The SCI provides gold-standard lists of established journals. +
The '''Substrate-uncoupler-inhibitor titra … The '''Substrate-uncoupler-inhibitor titration (SUIT) protocol library''' contains a sequential list of SUIT protocols (D001, D002, ..) with links to the specific SUIT pages. Classes of [[SUIT|SUIT protocols]] are explained with coupling and substrate control defined for [[mitochondrial preparations]].[[mitochondrial preparations]]. +
The '''Taiwan Society for Mitochondrial Research and Medicine''' (TSMRM) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]]. +
The '''USB port''' describes the connection between O2k and Computer. With the USB cable connected, select '''USB port''' in the [[Connection window]]. Depending on the O2k series, it is possible to connect with a '''USB port''' or [[Serial port]]. +
The '''abscissa''' is the horizontal axis … The '''abscissa''' is the horizontal axis ''x'' of a rectangular two-dimensional graph with the [[ordinate]] ''y'' as the vertical axis. Values ''X'' are placed horizontally from the origin.See [[Abscissal X/Y regression |Abscissal ''X''/''Y'' regression]].[[Abscissal X/Y regression |Abscissal ''X''/''Y'' regression]]. +
The '''accuracy''' of a method is the degree of agreement between an individual test result generated by the method and the true value. +
The '''activity''' (relative activity) is … The '''activity''' (relative activity) is a dimensionless quantity related to the concentration or partial pressure of a dissolved substance. The activity of a dissolved substance B equals the [[concentration]], ''c''B [mol·L-1], at high dilution divided by the unit concentration, ''c''° = 1 mol·L-1: ''a''B = ''c''B/''c''°This simple relationship applies frequently to substances at high dilutions <10 mmol·L-1 (<10 mol·m-3). In general, the concentration of a [[solute]] has to be corrected for the activity coefficient (concentration basis), ''γ''B, ''a''B = ''γ''B·''c''B/''c''°At high dilution, ''γ''B = 1. In general, the relative activity is defined by the [[chemical potential]], ''µ''B ''a''B = exp[(''µ''B-''µ''°)/''RT'']potential]], ''µ''B ''a''B = exp[(''µ''B-''µ''°)/''RT''] +
The '''adenine nucleotide translocator''', … The '''adenine nucleotide translocator''', ANT, exchanges [[ADP]] for [[ATP]] in an electrogenic antiport across the inner mt-membrane. The ANT is inhibited by [[atractyloside]], [[carboxyatractyloside|carboxyatractyloside]] and [[bongkrekik acid]]. The ANT is a component of the [[phosphorylation system]].[[phosphorylation system]]. +
The '''advantages of preprints''', the excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences are discussed by N Bhalla (2016). +
The '''aerobic''' state of metabolism is d … The '''aerobic''' state of metabolism is defined by the presence of oxygen (air) and therefore the potential for oxidative reactions (ox) to proceed, particularly in [[oxidative phosphorylation]] (OXPHOS). Aerobic metabolism (with involvement of oxygen) is contrasted with [[anaerobic]] metabolism (without involvement of oxygen): Whereas anaerobic ''metabolism'' may proceed in the absence or presence of oxygen (anoxic or oxic ''conditions''), aerobic ''metabolism'' is restricted to oxic ''conditions''. Below the [[critical oxygen pressure]], aerobic ATP production decreases.[[critical oxygen pressure]], aerobic ATP production decreases. +
The '''amount of substance''' ''n'' is a b … The '''amount of substance''' ''n'' is a base physical quantity, and the corresponding SI unit is the [[mole]] [mol]. Amount of substance (sometimes abbreviated as 'amount' or 'chemical amount') is proportional to the number ''N''''X'' of specified elementary entities ''X'', and the universal proportionality constant is the reciprocal value of the [[Avogadro constant]] ([[Bureau International des Poids et Mesures_2019_The International System of Units (SI) |SI]]), ''n''''X'' = ''N''''X''·''N''A-1''n''''X'' contained in a system can change due to internal and external transformations, d''n''''X'' = di''n''''X'' + de''n''''X''In the absence of nuclear reactions, the amount of any atom is conserved, ''e.g.'', for carbon di''n''C = 0. This is different for chemical substances or ionic species which are produced or consumed during the [[advancement]] of a reaction r, :::: [[File:Amount dn.png|100px]]A change in the amount of ''X''''i'', d''n''''i'', in an open system is due to both the internal formation in chemical transformations, dr''n''''i'', and the external transfer, de''n''''i'', across the system boundaries. d''n''''i'' is positive if ''X''''i'' is formed as a product of the reaction within the system. de''n''''i'' is negative if ''X''''i'' flows out of the system and appears as a product in the surroundings ([[Cohen 2008 IUPAC Green Book]]).[Cohen 2008 IUPAC Green Book]]). +
The '''amplitude''' of the [[absorbance spectrum]] … The '''amplitude''' of the [[absorbance spectrum]] can be described in terms of the [[absorbance]] differences between the characteristic peaks (absorbance maxima) and troughs (absorbance minima) (see [[absorbance spectrum]]) for substances present in the sample.[[absorbance spectrum]]) for substances present in the sample. +
The '''background state''' Y (background r … The '''background state''' Y (background rate ''YX'') is the non-activated or inhibited respiratory state at background rate, which is low in relation to the higher rate ''ZX'' in the [[reference state]] Z. The transition from the background state to the reference state is a step change. A [[metabolic control variable]] ''X'' (substrate, activator) is added to the background state to stimulate flux to the level of the reference state. Alternatively, the metabolic control variable ''X'' is an inhibitor, which is present in the background state Y, but absent in the reference state Z. The background state is the baseline of a single step in the definition of the [[flux control efficiency]]. In a sequence of step changes, the common [[baseline state]] is the state of lowest flux in relation to all steps, which can be used as a [[baseline correction]].[[baseline correction]]. +
The '''baseline state''' in a sequence of … The '''baseline state''' in a sequence of step changes is the state of lowest flux in relation to all steps, which can be used as a [[baseline correction]]. Correction for [[residual oxygen consumption]], ROX, is an example where ROX is the baseline state. In a single step, the baseline state is equivalent to the [[background state]].[[background state]]. +
The '''bias''' is defined as the difference between the mean of the measurements and the reference value. In general, the measuring instrument calibration procedures should focus on establishing and correcting it. +
The '''block temperature''' of the [[Oroboros O2k]] is the continuously measured temperature of the copper block, housing the two glass chambers of the O2k. The block temperature is recorded by [[DatLab]] as one of the O2k system channels. +
The '''body mass excess''', BME, is an ind … The '''body mass excess''', BME, is an index of obesity and as such BME is a lifestyle metric. The BME is a measure of the extent to which your actual [[body mass]], ''M'' [kg/x], deviates from ''M''° [kg/x], which is the reference body mass [kg] per individual [x] without excess body fat in the [[healthy reference population]], HRP. A balanced BME is BME° = 0.0 with a band width of -0.1 towards underweight and +0.2 towards overweight. The BME is linearly related to the [[body fat excess]].body fat excess]]. +
The '''body mass index''', BMI, is the rat … The '''body mass index''', BMI, is the ratio of body mass to height squared (BMI=''M''·''H''-2), recommended by the WHO as a general indicator of underweight (BMI<18.5 kg·m-2), overweight (BMI>25 kg·m-2) and obesity (BMI>30 kg·m-2). Keys et al (1972; see 2014) emphasized that 'the prime criterion must be the relative independence of the index from height'. It is exactly the dependence of the BMI on height - from children to adults, women to men, Caucasians to Asians -, which requires adjustments of BMI-cutoff points. This deficiency is resolved by the [[body mass excess]] relative to the [[healthy reference population]].althy reference population]]. +
The '''body mass''' ''M'' is the mass ([[kilogram]] … The '''body mass''' ''M'' is the mass ([[kilogram]] [kg]) of an individual (object) [x] and is expressed in units [kg/x]. Whereas the body weight changes as a function of gravitational force (you are weightless at zero gravity; your floating weight in water is different from your weight in air), your mass is independent of gravitational force, and it is the same in air and water.orce, and it is the same in air and water. +
The '''bound energy''' change in a closed … The '''bound energy''' change in a closed system is that part of the ''total'' [[energy]] change that is always bound to an exchange of [[heat]], d''B'' = d''U'' - d''A'' [Eq. 1] ∆''B'' = ∆''H'' - ∆''G'' [Eq. 2]The ''free'' energy change (Helmoltz or Gibbs; d''A'' or d''G'') is the ''total'' energy change (total inner energy or enthalpy, d''U'' or d''H'') of a system minus the ''bound'' energy change.Therefore, if a process occurs at [[equilibrium]], when d''G'' = 0 (at constant gas pressure), then d''H'' = d''B'', and at de''W'' = 0 (d''H'' = de''Q'' + de''W''; see [[energy]]) we obtain the definition of the bound energy as the heat change taking place in an equilibrium process (eq), d''B'' = ''T''∙d''S'' = de''Q''eq [Eq. 3]rocess (eq), d''B'' = ''T''∙d''S'' = de''Q''eq [Eq. 3] +
The '''cell count''' ''N''ce< … The '''cell count''' ''N''ce is the number of cells, expressed in the abstract [[unit]] [x] (1 Mx = 106 x). The ''elementary entity'' cell ''U''ce [x] is the real unit, the 'single individual cell'. A cell count is the multitude or number ''N'' of cells, ''N''ce = ''N''·''U''ce ([[Gnaiger MitoFit Preprints 2020.4]]). Normalization of respiratory rate by cell count yields oxygen [[flow]] ''I''O2 expressed in units [amol·s-1·x-1] (=10-18 mol·s-1·x-1).gt; expressed in units [amol·s-1·x-1] (=10-18 mol·s-1·x-1). +
The '''chamber volume''' of the O2k is 2.0 … The '''chamber volume''' of the O2k is 2.0 mL or 0.5 mL of aqueous medium with or without sample, excluding the volume of the stirrer and the volume of the capillary of the stopper (see: [[Cell count and normalization in HRR]]). A modular extension of the O2k, the [[O2k-sV-Module]], was specifically developed to perform high-resolution respirometry with reduced amounts of biological sample, and all components necessary for the smaller operation volume of 0.5 mL.or the smaller operation volume of 0.5 mL. +
The '''charge number''' of an ion ''X'' or … The '''charge number''' of an ion ''X'' or electrochemical reaction with unit stoichiometric number of ''X'' is the [[particle charge]] [C·x-1] divided by the [[elementary charge]] [C·x-1]. The particle charge ''Q''''N''''X'' is the charge per count of ions ''X'' or per ion ''X'' transferred in the reaction as defined in the reaction equation.ns ''X'' or per ion ''X'' transferred in the reaction as defined in the reaction equation. +
The '''chemical potential''' of a substanc … The '''chemical potential''' of a substance B, ''µ''B [J/mol], is the partial derivative of Gibbs energy, ''G'' [J], per amount of B, ''n''B [mol], at constant temperature, pressure, and composition other than that of B, ''µ''B = (∂''G''/∂''n''B)''T'',''p'',''nj''≠BThe chemical potential of a [[solute]] in solution is the sum of the standard chemical potential under defined standard conditions and a concentration ([[activity]])-dependent term, ''µ''B = ''µ''B° + ''RT'' ln(''a''B)The standard state for the solute is refered to ideal behaviour at standard concentration, ''c''° = 1 mol/L, exhibiting infinitely diluted solution behaviour [1]. ''µ''B° equals the standard molar Gibbs energy of formation, Δf''G''B° [kJ·mol-1]. The formation process of B is the transformation of the pure constituent elements to one mole of substance B, with all substances in their standard state (the most stable form of the element at 100 kPa (1 bar) at the specified temperature) [2].on of the pure constituent elements to one mole of substance B, with all substances in their standard state (the most stable form of the element at 100 kPa (1 bar) at the specified temperature) [2]. +
The '''comparison of respirometric methods''' provides the basis to evaluate different instrumental platforms and different [[mitochondrial preparations]], as a guide to select the best approach and to critically evaluate published results. +
The '''critical oxygen pressure''', ''p''& … The '''critical oxygen pressure''', ''p''c, is defined as the partial oxygen pressure, ''p''O2, below which [[aerobic]] catabolism (respiration or oxygen consumption) declines significantly. If [[anaerobic]] catabolism is activated simultaneously to compensate for lower aerobic ATP generation, then the '''[[limiting oxygen pressure]]''', ''p''l, is equal to the ''p''c. In many cases, however, the ''p''l is substantially lower than the ''p''c.y cases, however, the ''p''l is substantially lower than the ''p''c. +
The '''cytochrome ''c'' control efficiency … The '''cytochrome ''c'' control efficiency''' expresses the control of respiration by externally added [[cytochrome c | cytochrome ''c'']], c, as a fractional change of flux from substrate state CHNO to CHNOc. These fluxes are corrected for ''Rox'' and may be measured in the OXPHOS state or ET state, but not in the LEAK state. In this [[flux control efficiency]], CHNOc is the [[reference state]] with stimulated flux; CHNO is the [[background state]] with CHNO substrates, upon which c is added: ''j''cyt ''c'' = (''J''CHNOc-''J''CHNO)/''J''CHNOc.>CHNOc-''J''CHNO)/''J''CHNOc. +
The '''data recording interval''' is the t … The '''data recording interval''' is the time interval at which data is sampled with an instrument. In [[DatLab]] the data recording interval is set in the [[O2k control]] window. The system default value is 2 s. A lower data recording interval is selected for kinetic experiments, and when the volume-specific oxygen flux is high (>300 pmol O2·s-1·ml-1). Technically, the O2k instrument (hardware) measures the sensor signal every 10ms (which is NOT the „data recording interval“). By the given data recording interval from DatLab (software) a discrete number of sensor signal points are taken to calculate an average value in the O2k (e.g. a data recording interval of 2 s can take 200 sensor signal points; a data recording interval of 0.5 s can take 50 sensor signal points). This average value is sent to DatLab and is recorded as a raw data point. However, there is a defined threshold: the O2k does not apply more than 200 sensor signal points to calculate the average for the raw data point. For example a data recording interval of 3 s could take 300 sensor signal points but only the 200 most recent sensor signal points are used for averaging.signal points but only the 200 most recent sensor signal points are used for averaging. +
The '''dicarboxylate carrier''' is a transporter which catalyses the electroneutral exchange of [[malate]]2- (or [[succinate]]2-) for inorganic [[phosphate]], HPO42-. +
The '''energy charge''' of the adenylate s … 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.l parameter remains a controversial topic. +
The '''ergodynamic efficiency''', ''ε'' (c … 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»/O2 ratio) multiplied by the corresponding force ratio. Compare with the [[OXPHOS-coupling efficiency]].OXPHOS-coupling efficiency]]. +
The '''extinction coefficient''' (''ε'') of a substance is the [[absorbance]] of a 1 µmolar concentration over a 1 cm pathlength and is wavelength-dependent. +
The '''gain''' is an amplification factor applied to an input signal to increase the output signal. +
The '''glutamate-aspartate carrier''' cata … The '''glutamate-aspartate carrier''' catalyzes the electrogenic antiport of glutamate- +H+ for aspartate-. It is an important component of the malate-aspartate shuttle in many mitochondria. Due to the symport of glutamate- + +H+, the glutamate-aspartate antiport is not electroneutal and may be impaired by [[uncoupling]]. [[Aminooxyacetate]] is an [[inhibitor]] of the glutamate-aspartate carrier.[[inhibitor]] of the glutamate-aspartate carrier. +
The '''height of humans''', ''h'', is give … 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-1] (compare [[body mass]] [kg·x-1]). Without further identifyer, ''H'' is considered as the standing height of a human, measured without shoes, hair ornaments and heavy outer garments., measured without shoes, hair ornaments and heavy outer garments. +
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. +
The '''limiting oxygen pressure''', ''p''& … The '''limiting oxygen pressure''', ''p''l, is defined as the partial oxygen pressure, ''p''O2, below which [[anaerobic]] catabolism is activated to contribute to total ATP generation. The limiting oxygen pressure, ''p''l, may be substantially lower than the '''[[critical oxygen pressure]]''', ''p''c, below which [[aerobic]] catabolism (respiration or oxygen consumption) declines significantly.[[aerobic]] catabolism (respiration or oxygen consumption) declines significantly. +
The '''membrane-bound [[electron transfer pathway]] … 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).[[submitochondrial particles]] (SmtP). +
The '''meter''', symbol m, is the SI unit … 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−1, where the second is defined in terms of the caesium frequency Δ''ν''Cs.in terms of the caesium frequency Δ''ν''Cs. +
The '''mitochondrial ATP-sensitive K+ channel''' (mtKATP or mitoKATP). +
The '''mitochondrial free radical theory o … 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.on, and due to ROS-induced ROS production. +
The '''mitochondrial inner membrane''' mtI … 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 (Ca2+, Mg2+). The [[protonmotive force]] is the electrochemical potential difference across the mtIM generated by the [[hydrogen ion pumps]] of the .[[hydrogen ion pumps]] of the . +
The '''mitochondrial matrix''' (mt-matrix) … 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. mt-matrix is subject of current research. +
The '''mitochondrial membrane potential''' … The '''mitochondrial membrane potential''' difference, mtMP or Δ''Ψ''p+ = Δel''F''''e''p+, is the electric part of the protonmotive [[force]], Δp = Δm''F''''e''H+.:::: Δel''F''''e''p+ = Δm''F''''e''H+ - Δd''F''''e''H+:::: Δ''Ψ''p+ = Δp - Δ''µ''H+·(''z''H+·''F'')-1Δ''Ψ''p+ 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].t;p+ 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 '''mitochondrial outer membrane''' is the incapsulating membrane which is osmotically not active and contains the cytochrome ''b''5 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.lmitoyl-CoA synthetase and carnytil-CoA transferase 1. +
The '''motive unit''' [MU] is the variable … 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, ''N''* MU = mol, for the chemical or molar format, ''n''* MU = C, for the electrical format, ''e''; 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.'', O2 with ''z''=4 in a redox reaction). The ratio of elementary charges per reacting O2 molecule (''z''O2=4) is multiplied by the elementary charge (''e'', coulombs per proton), which yields coulombs per O2 [C∙x-1]. This in turn is multiplied with the [[Avogadro constant]], ''N''A (O2 molecules per mole O2 [x∙mol-1]), thus obtaining for ''zeN''A the ratio of elementary charges [C] per amount of O2 [mol-1]. The conversion factor for O2 is 385.94132 C∙mmol-1., thus obtaining for ''zeN''A the ratio of elementary charges [C] per amount of O2 [mol-1]. The conversion factor for O2 is 385.94132 C∙mmol-1. +
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]]. +
The '''oxycaloric equivalent''' is the the … The '''oxycaloric equivalent''' is the theoretically derived enthalpy change of the oxidative catabolic reactions per amount of oxygen respired, Deltak''H''O2, ranging from -430 to -480 kJ/mol O2. The oxycaloric equivalent is used in [[indirect calorimetry]] to calculate the theoretically expected metabolic heat flux from the respirometrically measured metabolic oxygen flux. [[Calorespirometric ratio|Calorimetric/respirometric ratios]] (CR ratios; heat/oxygen flux ratios) are experimentally determined by [[calorespirometry]]. A CR ratio more exothermic than the oxycaloric equivalent of -480 kJ/mol indicates the simultaneous involvement of aerobic and anaerobic mechanisms of energy metabolism.ltaneous involvement of aerobic and anaerobic mechanisms of energy metabolism. +
The '''oxygen signal''' of the [[Oroboros O2k]] … The '''oxygen signal''' of the [[Oroboros O2k]] is transmitted from the electrochemical polarographic oxygen sensor ([[OroboPOS]]) for each of the two O2k-chambers to [[DatLab]]. The primary signal is a current [µA] which is converted into a voltage [V] (raw signal), and calibrated in SI units for amount of substance concentration [µmol·L-1 or µM]. For technical reasons, the raw signal is given in [V] (DatLab 7 and previous) or [µA] (DatLab 8). The value of the raw signal is the same, independent of the displayed unit ([V] or [µA]). In the following sections, only [µA] is used for information on the raw signal, but the same values in [V] apply for the raw signal when using DL7 or previous versions.or the raw signal when using DL7 or previous versions. +
The '''oxygen solubility factor''' of the … The '''oxygen solubility factor''' of the incubation medium, ''F''M, expresses the effect of the salt concentration on [[oxygen solubility]] relative to pure water. In mitochondrial respiration medium [[MiR05]], [[MiR05-Kit]] and [[MiR06]], ''F''M is 0.92 (determined at 30 and 37 °C) and in culture media is 0.89 (at 37 °C). ''F''M varies depending on the temperature and composition of the medium. To determine the FM based on the oxygen concentration, specific methods and equipment are needed (see references Rasmussen HN, Rasmussen UF 2003 in [https://wiki.oroboros.at/index.php/MiPNet06.03_POS-calibration-SOP MiPNet06.03]). For other media, ''F''M may be estimated using Table 4 in [https://wiki.oroboros.at/index.php/MiPNet06.03_POS-calibration-SOP MiPNet06.03]. For this purpose KCl based media can be described as "seawater" of varying salinity. The original data on sucrose and KCl-media (Reynafarje et al 1985), however, have been critizesed as artefacts and the ''F''M of 0.92 is suggested in the temperature range of 10 °C to 40 °C as for MiR05.M of 0.92 is suggested in the temperature range of 10 °C to 40 °C as for MiR05. +
The '''oxygen solubility''', ''S''<sub& … The '''oxygen solubility''', ''S''O2 [µM/kPa] = [(µmol·L-1)/kPa], expresses the oxygen concentration in solution in equilibrium with the [[oxygen pressure]] in a gas phase, as a function of temperature and composition of the solution. The inverse of oxygen solubility is related to the [[activity]] of dissolved oxygen. The oxygen solubility in solution, ''S''O2(aq), depends on temperature and the concentrations of solutes in solution, whereas the dissolved oxygen concentration at equilibrium with air, ''c''O2*(aq), depends on ''S''O2(aq), barometric pressure and temperature. ''S''O2(aq) in pure water is 10.56 µM/kPa at 37 °C and 12.56 µM/kPa at 25 °C. At standard [[barometric pressure]] (100 kPa), ''c''O2*(aq) is 207.3 µM at 37 °C (19.6 kPa partial oxygen pressure) or 254.7 µM at 25 °C (20.3 kPa partial oxygen pressure). In [[MiR05]] and serum, the corresponding saturation concentrations are lower due to the [[oxygen solubility factor]]: 191 and 184 µM at 37 °C or 234 and 227 µM at 25 °C.lubility factor]]: 191 and 184 µM at 37 °C or 234 and 227 µM at 25 °C. +
The '''pH value''' or pH is the negative o … The '''pH value''' or pH is the negative of the base 10 logarithm of the [[activity]] of [[proton]]s (hydrogen ions, H+). A [[pH electrode]] reports the pH and is sensitive to the activity of H+. In dilute solutions, the hydrogen ion activity is approximately equal to the hydrogen ion [[concentration]]. The symbol pH stems from the term ''potentia hydrogenii''.[[concentration]]. The symbol pH stems from the term ''potentia hydrogenii''. +
The '''partial oxygen pressure''' ''p''< … The '''partial oxygen pressure''' ''p''O2 [kPa] is the contribution of the O2 gas pressure to the total gas pressure. According to the gas law, the partial oxygen pressure is ''p''O2(g) = ''n''O2(g)·''V''·''RT'', where the [[concentration]] is ''c''O2(g) = ''n''O2(g)·''V''-1 [mol·m-3], ''R'' is the [[gas constant]], and ''T'' is the absolute temperature, and ''RT'' is expressed in units of chemical force [J·mol-1]. In aqueous solutions at equilibrium with a gas phase, the partial O2 pressures are equal in the aqueous phase (aq) and gas phase (g), ''p''O2(aq) = ''p''O2(g) at total [[pressure]]s where the partial pressure equals the fugacity. The O2 concentration in the aqueous phase, however, is much lower than in the gas phase, due to the low [[oxygen solubility]] in water. The activity of dissolved O2 is expressed by the ''p''O2, where the [[solubility]] can be seen as an activity coefficient.ubility]] can be seen as an activity coefficient. +
The '''particle charge''' ''QN& … The '''particle charge''' ''QNX'' (''QNX'') or charge per elementary entity is the [[charge]] ''Q''el''X'' [C] carried by ions of type ''X'' divided by the count ''NX'' [x]. The particle charge per proton is the [[elementary charge]] or proton charge ''e''.[[elementary charge]] or proton charge ''e''. +
The '''pascal''' [Pa] is the SI unit for [[pressure]] … The '''pascal''' [Pa] is the SI unit for [[pressure]]. [Pa] = [J·m-3] = [N·m-2] = [m-1·kg·s-2].The standard pressure is 100 kPa = 1 bar (105 Pa; 1 kPa = 1000 Pa). Prior to 1982 the standard pressure has been defined as 101.325 kPa or 1 standard atmosphere (1 atm = 760 mmHg).982 the standard pressure has been defined as 101.325 kPa or 1 standard atmosphere (1 atm = 760 mmHg). +
The '''phosphate carrier''' (PiC) is a pro … The '''phosphate carrier''' (PiC) is a proton/phosphate symporter which transports negatively charged [[inorganic phosphate]] across the inner mt-membrane. The transport can be described either as symport of H+ with Pi, or antiport of hydroxide anion against Pi. The phosphate carrier is a component of the [[phosphorylation system]].[[phosphorylation system]]. +
The '''primary sample''' or '''specimen''' … The '''primary sample''' or '''specimen''' is a set of one or more parts initially taken from an object. In some countries, the term “specimen” is used instead of primary sample (or a subsample of it), which is the sample prepared for sending to, or as received by, the laboratory and which is intended for examination.ory and which is intended for examination. +
The '''protonmotive force''' ∆m … The '''protonmotive force''' ∆m''F''H+ is known as Δp in Peter Mitchell’s chemiosmotic theory [1], which establishes the link between electric and chemical components of energy transformation and coupling in [[oxidative phosphorylation]]. The unifying concept of the ''pmF'' ranks among the most fundamental theories in biology. As such, it provides the framework for developing a consistent theory and nomenclature for mitochondrial physiology and bioenergetics. The protonmotive force is not a vector force as defined in physics. This conflict is resolved by the generalized formulation of isomorphic, compartmental [[force]]s, ∆tr''F'', in energy (exergy) transformations [2]. Protonmotive means that there is a potential for the movement of protons, and force is a measure of the potential for motion.The ''pmF'' is generated in [[oxidative phosphorylation]] by oxidation of reduced fuel substrates and reduction of O2 to H2O, driving the coupled proton translocation from the mt-matrix space across the mitochondrial inner membrane (mtIM) through the proton pumps of the [[electron transfer pathway]] (ETS), which are known as respiratory Complexes CI, CIII and CIV. ∆m''F''H+ consists of two partial isomorphic forces: (''1'') The chemical part, ∆d''F''H+, relates to the diffusion (d) of uncharged particles and contains the chemical potential difference§ in H+, ∆''µ''H+, which is proportional to the pH difference, ∆pH. (''2'') The electric part, ∆el''F''p+ (corresponding numerically to ∆''Ψ'')§, is the electric potential difference§, which is not specific for H+ and can, therefore, be measured by the distribution of any permeable cation equilibrating between the negative (matrix) and positive (external) compartment. Motion is relative and not absolute (Principle of Galilean Relativity); likewise there is no absolute potential, but isomorphic forces are stoichiometric potential differences§.The total motive force (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆m''F''H+. Reading this symbol by starting with the proton, it can be seen as ''pmF'', or the subscript m (motive) can be remembered by the name of Mitchell, ∆m''F''H+ = ∆d''F''H+ + ∆el''F''p+With classical symbols, this equation contains the [[Faraday constant]], ''F'', multiplied implicitly by the charge number of the proton (''z''H+ = 1), and has the form [1] ∆p = ∆''µ''H+∙''F''-1 + ∆''Ψ''A partial electric force of 0.2 V in the electrical [[format]], ∆el''F''''e''H+''a'', is 19 kJ∙mol-1 H+''a'' in the molar format, ∆el''F''''n''p+''a''. For 1 unit of ∆pH, the partial chemical force changes by -5.9 kJ∙mol-1 in the molar format, ∆d''F''''n''H+''a'', and by 0.06 V in the electrical format, ∆d''F''''e''H+''a''. Considering a driving force of -470 kJ∙mol-1 O2 for oxidation, the thermodynamic limit of the H+''a''/O2 ratio is reached at a value of 470/19 = 24, compared to the mechanistic stoichiometry of 20 for the [[N-pathway]] with three coupling sites. +
The '''protonmotive pressure''', ∆<sub& … The '''protonmotive pressure''', ∆m''Π''H+ or ''pmP'' [kPa], is an extension of Peter Mitchell’s concept of the [[protonmotive force]] ''pmF'', based on Fick’s law of diffusion and Einstein’s diffusion equation, accounting for osmotic pressure (corresponding to the diffusion term in the ''pmF'') and electric pressure (the electric term or membrane potential in the ''pmF''). The linearity of the generalized flow-pressure relationship explains the non-ohmic flow-force dependence in the proton leak rate as a function of membrane potential.The total motive pressure (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆m''Π''H+, ∆m''Π''H+ = ∆d''Π''H+ + ∆el''Π''p+ub>''Π''H+ = ∆d''Π''H+ + ∆el''Π''p+ +
The '''raw signal''' of the polarographic … The '''raw signal''' of the polarographic oxygen sensor is the [[current]] ''I''el [µA], 1 µA = 10-6 C·s-1, (DatLab 8) or the electric potential difference ([[voltage]]) [V], 1 V = 1 J·C-1, obtained after a current-to-voltage conversion in the O2k (DatLab 7 and previous versions).btained after a current-to-voltage conversion in the O2k (DatLab 7 and previous versions). +
The '''reference state''' Z (reference rat … The '''reference state''' Z (reference rate ''ZX'') is the respiratory state with high flux in relation to the [[background state]] Y with low background flux ''YX''. The transition between the background state and the reference state is a step brought about by a [[metabolic control variable]] ''X''. If ''X'' stimulates flux (ADP, fuel substrate), it is present in the reference state but absent in the background state. If ''X'' is an inhibitor of flux, it is absent in the reference state but present in the background state. The reference state is specific for a single step to define the [[flux control efficiency]]. In contrast, in a sequence of multiple steps, the common reference state is frequently taken as the state with the highest flux in the entire sequence, as used in the definition of the [[flux control ratio]].[[flux control ratio]]. +
The '''respiratory acceptor control ratio' … The '''respiratory acceptor control ratio''' (''RCR'') is defined as [[State 3]]/[[State 4]] [1]. If State 3 is measured at saturating [ADP], ''RCR'' is the inverse of the OXPHOS control ratio, ''[[L/P]]'' (when State 3 is equivalent to the OXPHOS state, ''P''). ''RCR'' is directly but non-linearly related to the [[P-L control efficiency |''P-L'' control efficiency]], ''j''''P-L'' = 1-''L/P'', with boundaries from 0.0 to 1.0. In contrast, ''RCR'' ranges from 1.0 to infinity, which needs to be considered when performing statistical analyses. In living cells, the term ''RCR'' has been used for the ratio [[State 3u]]/[[State 4o]], i.e. for the inverse ''[[L/E]]'' ratio [2,3]. Then for conceptual and statistical reasons, ''RCR'' should be replaced by the [[E-L coupling efficiency |''E-L'' coupling efficiency]], 1-''L/E'' [4].[[E-L coupling efficiency |''E-L'' coupling efficiency]], 1-''L/E'' [4]. +
The '''signal to noise ratio''' is the ratio of the power of the signal to that of the noise. For example, in [[fluorimetry]] it would be the ratio of the square of the [[fluorescence]] intensity to the square of the intensity of the background noise. +
The '''slit width''' determines the amount of light entering the [[spectrofluorometer]] or [[spectrophotometer]]. A larger slit reduces the [[signal-to-noise ratio]] but reduces the wavelength [[resolution]]. +
The '''solubility''' of a gas, ''S''G, is defined as concentration divided by partial pressure, ''S''G = ''c''G·''p''G-1. +
The '''substrate-uncoupler-inhibitor titra … The '''substrate-uncoupler-inhibitor titration ([[SUIT]]) reference protocol''', SUIT RP, provides a common baseline for comparison of mitochondrial respiratory control in a large variety of species, tissues and cell types, mt-preparations and laboratories, for establishing a database on comparative mitochondrial phyisology. The SUIT RP consists of two [[harmonized SUIT protocols]] ([[SUIT-001]] - RP1 and [[SUIT-002]] - RP2). These are coordinated such that they can be statistically evaluated as replicate measurements of [[cross-linked respiratory states]], while additional information is obtained when the two protocols are conducted in parallel. Therefore, these harmonized SUIT protocols are complementary with their focus on specific respiratory coupling and pathway control aspects, extending previous strategies for respirometrc OXPHOS analysis.: [[SUIT-001]] (RP1): 1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10Tm;11Azd: [[SUIT-002]] (RP2): 1D;2OctM;2c;3P;4G;5S;6Gp;7U;8Rot;9Ama;10Tm;11AzdtM;2c;3P;4G;5S;6Gp;7U;8Rot;9Ama;10Tm;11Azd +
The '''transcription factor A''' is a gene … 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]].[[Peroxisome proliferator-activated receptor gamma coactivator 1-alpha|PGC-1alpha]]. +
The '''tricarboxylate carrier''' in the inner mt-membrane exchanges malate2- for citrate3- or isocitrate3-, with co-transport of H+. +
The '''tricarboxylic acid (TCA) cycle''' i … The '''tricarboxylic acid (TCA) cycle''' is a system of enzymes in the mitochondrial matrix arranged in a cyclic metabolic structure, including dehydrogenases that converge in the NADH pool and [[succinate dehydrogenase]] (on the inner side of the inner mt-membrane) for entry into the membrane-bound ET pathway [[Membrane-bound ET pathway|mET pathway]]. [[Citrate synthase]] is a marker enzyme of the TCA cycle, at the gateway into the cycle from [[pyruvate]] via [[acetyl-CoA]]. It is thus the major module of the [[Electron transfer pathway]], upstream of the inner [[Membrane-bound ET pathway|Membrane-bound ET pathway]] (mET-pathway) and downstream of the [[Mitochondrial outer membrane|outer mt-membrane]]. Sections of TCA cycle are required for [[fatty acid oxidation]] (FAO, β-oxidation). [[Anaplerosis|Anaplerotic reactions]] fuel the TCA cycle with other intermediary metabolites. In the cell, the TCA cycle serves also biosynthetic functions by metabolite export from the matrix into the cytosol.e export from the matrix into the cytosol. +
The '''uncoupling-control ratio''' UCR is … The '''uncoupling-control ratio''' UCR is the ratio of ET-pathway/ROUTINE-respiration (''E/R'') in living cells, evaluated by careful [[uncoupler]] titrations ([[Steinlechner-Maran 1996 Am J Physiol Cell Physiol|Steinlechner et al 1996]]). Compare [[ROUTINE-control ratio]] (''R/E'') [[Gnaiger 2008 POS|(Gnaiger 2008)]].[[Gnaiger 2008 POS|(Gnaiger 2008)]]. +
The '''volume''' of a journal or periodica … 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]].[[Journal issue |issues]]. +
The '''wet mass''' of a tissue or biological sample, obtained after blotting the sample to remove an arbitrary amount of water adhering externally to the sample. +
The (mitochondrial, mt) permeability trans … The (mitochondrial, mt) permeability transition pore (PTP) is an unspecific pore presumed to involve components of both the inner and outer mt membrane which upon opening induces a massive increase of the inner mt membrane permeability for solutes up to 1.5 kDa. It is crucially involved in cell death induction in response to, among other stimuli, radical stress and/or calcium overload and may cause necrosis or apoptosis. It plays an important role in neurodegenerative diseases, cardiac ischemia-reperfusion injury and possibly various other diseases. Previously considered essential molecular constituents such as the voltage-dependent anion channel (VDAC), the adenine nucleotide translocator (ANT) and cyclophilin D (CypD) have all been shown to be important regulators of mtPTP opening, but the molecular entities actually forming the pore are still unknown at present. The opening of the pore can be prevented using [[cyclosporin A]], a compound that binds cyclophilin D avoiding the formation of the pore. In respirometry, mtPTP opening may be observed as a sudden decrease of respiration of isolated mitochondria ([[Hansson 2010 J Biol Chem]]).[[Hansson 2010 J Biol Chem]]). +
The 2-chamber design of the O2k helps to '''search for defective O2k components''', by switching components linked to O2k chambers A and B between sides A and B. +
The ADP-ATP phosphorylation system or P»-system. ''See'' [[Phosphorylation system]]. +
The CDGSH iron-sulfur domain (CISDs) famil … The CDGSH iron-sulfur domain (CISDs) family of proteins uniquely ligate labile 2Fe-2S clusters with a 3Cys-1His motif. CISD1 and CISD3 have been demonstrated to localize to the outer mitochondrial membrane and mitochondrial matrix respectively, however their relationship to mitochondrial physiology remains ill-defined [1]. The best characterized member of the CISD family, CISD1, has been demonstrated to be involved in respiratory capacity, iron homeostasis, and ROS regulationcity, iron homeostasis, and ROS regulation +
The O2k control panel allows for quick acc … 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.ween O2k control panel and protocol panel. +
The O2k-chamber can be used as a [[closed system]] or [[open system]]. Gas bubbles must be avoided. +
The OroboPOS-Connector Service entails routine maintenance and any necessary repairs of the OroboPOS-Connector in the Oroboros electronics workshop (WGT). +
The PC requirements for controlling an O2k and data recording with [[DatLab]] are found [[DatLab installation |here]]. +
The Power-O2k number, which is set in the … 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]].[[Graph options - DatLab]]. +
The Titration-Injection microPump (TIP2k) provides automated injection of liquids into both O2k chambers. It is controlled via DatLab, allowing for programmable titration regimes and feedback control. +
The [[dicarboxylate carrier]] catalyses the electroneutral exchange of succinate2- for HPO4-2-. +
The ampere, symbol A, is the SI unit of el … The ampere, symbol A, is the SI unit of electric current. It is defined by taking the fixed numerical value of the elementary charge ''e'' to be 1.602 176 634 × 10−19 when expressed in the unit C, which is equal to A s, where the second is defined in terms of Δ''ν''Cs.the second is defined in terms of Δ''ν''Cs. +
The boundaries of '''isolated system'''s a … 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, di''S''/d''t'', internal formation of chemical species ''i'' which is produced in a reaction ''r'', di''ni''/d''t'' = dr''ni''/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. by various conservation laws which rule out the production or destruction of the respective quantity. +
The calorimetric/respirometric or '''calor … The calorimetric/respirometric or '''calorespirometric ratio''' (CR ratio) is the ratio of calorimetrically and respirometrically measured heat and oxygen flux, determinded by [[calorespirometry]]. The experimental CR ratio is compared with the theoretically derived [[oxycaloric equivalent]], and agreement in the range of -450 to -480 kJ/mol O2 indicates a balanced [[aerobic]] energy budget ([[Gnaiger_1987_PhysiolZool|Gnaiger and Staudigl 1987]]). In the transition from aerobic to [[anaerobic | anaerobic metabolism]], there is a [[Limiting pO2|limiting ''p''O2]], ''p''lim, below which CR ratios become more exothermic since anaerobic energy flux is switched on.h CR ratios become more exothermic since anaerobic energy flux is switched on. +
The candela, symbol cd, is the SI unit of … The candela, symbol cd, is the SI unit of luminous intensity in a given direction. It is defined by taking the fixed numerical value of the luminous efficacy of monochromatic radiation of frequency 540 × 1012 Hz, ''K''cd, to be 683 when expressed in the unit lm W−1.;/sub>, to be 683 when expressed in the unit lm W−1. +
The chambers of the [[OROBOROS O2k|Oroboros O2k]] … 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.nternal illumination must be switched off. +
The component of the electron transfer sys … 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.s pyruvate, malate, succinate, and others. +
The concept of '''affinity''' and hence ch … The concept of '''affinity''' and hence chemical force is deeply rooted in the notion of '''attraction''' (and repulsion) of alchemy, which was the foundation of chemistry originally, but diverted away from laboratory experiments towards occult secret societies [1].** Newton's extensive experimental alchemical work and his substantial written track record on alchemy (which he did not publish) is seen today as a key inspiration for his development of the concept of the gravitational force [2-4]. This marks a transition of the meaning of affinity, from the descriptive 'adjacent' (proximity) to the causative 'attractive' (force) [5]. Correspondingly, Lavoisier (1790) equates affinity and force [6]: “''... the degree of force or affinity with which the acid adheres to the base''” [5]. By discussing the influence of electricity and gravity on chemical affinity, Liebig (1844) considers affinity as a force [7]. This leads to Guldberg and Waage's [[mass action ratio]] ('Studies concerning affinity', 1864; see [5]), the free energy and chemical affinity of Helmholtz (1882 [8]), and chemical thermodynamics of irreversible processes [9], where flux-force relations are center stage [10]. According to the IUPAC definition, the '''affinity of reaction''', ''A'' [J·mol-1], equals the negative molar Gibbs energy of reaction [11], which is the negative Gibbs [[force]] of reaction (derivative of [[Gibbs energy]] per [[advancement]] of reaction [12]): -''A'' = Δr''F'' = ∂''G''/∂r''ξ''The historical account of affinity is summarized by concluding, that today affinity of reaction should be considered as an isomorphic motive '''force''' and be generalized as such. This will help to (''1'') avoid confusing reversals of sign conventions (repulsion = negative attraction; pull = negative push), (''2'') unify symbols across classical and nonequilibrium thermodynamics [12,13], and thus (''3'') facilitate interdisciplinary communication by freeing ourselves from the alchemical, arcane scientific nomenclature.ry communication by freeing ourselves from the alchemical, arcane scientific nomenclature. +
The concept on '''latent mitochondrial dys … 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.ng a mitochondrial stress resistance test. +
The function '''Mark specifications''' is … 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.for renaming the entire sequence of marks. +
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 × 10−23 when expressed in the unit J x-1 K−1. +
The kilogram, symbol kg, is the SI unit of … 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 × 10−34 when expressed in the unit J s, which is equal to kg m2 s−1, where the meter and the second are defined in terms of ''c'' and Δ''ν''Cs.he meter and the second are defined in terms of ''c'' and Δ''ν''Cs. +
The malate-aspartate shuttle involves the … The malate-aspartate shuttle involves the glutamate-aspartate carrier and the 2-oxoglutarate carrier exchanging malate2- for 2-oxoglutarate2-. 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.chondrial matrix. It is most important in heart, liver and kidney. +
The mark mode is active by default, can be … 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]].[Marks - DatLab]]. +
The minimum and the maximum wavelengths ov … The minimum and the maximum wavelengths over which an [[absorbance spectrum]] is measured are described in terms of the [[wavelength range]]. It is determined mainly by the specifications of the [[spectrophotometer]] and the type of [[light source]] used, and the characteristic [[absorbance spectrum]] of the sample being investigated.[[absorbance spectrum]] of the sample being investigated. +
The mission of '''ergodynamics''' is the r … 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.ng energy transformations in open systems. +
The mitochondrial '''creatine kinase''', also known as phosphocreatine kinase (CPK), facilitates energy transport with [[creatine]] and [[phosphocreatine]] as diffusible intermediates. +
The mitochondrial '''respiratory chain''' … The mitochondrial '''respiratory chain''' (RC) consists of enzyme complexes arranged to form a metabolic system of convergent pathways for [[oxidative phosphorylation]]. In a general sense, the RC includes (1) the [[electron transfer pathway]] (ET-pathway), with transporters for the exchange of reduced substrates across the inner mitochondrial membrane, enzymes in the matrix space (particularly dehydrogenases of the tricarboxylic acid cycle), inner membrane-bound electron transfer complexes, and (2) the inner membrane-bound enzymes of the [[phosphorylation system]].[[phosphorylation system]]. +
The mole [mol] is the SI base unit for the … The mole [mol] is the SI base unit for the [[amount |amount of substance]] of a system that contains 6.02214076·1023 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.ther particles, or specified groups of such particles. +
The monocarboxylic acid [[pyruvate]]- is exchanged electroneutrally for OH- by the '''pyruvate carrier'''. H+/anion symport is equivalent to OH-/anion antiport. +
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. +
The quality of the results are strongly affected by the performance and data analysis. Therefore, we provide guidelines for performing and evaluating respirometric assays. +
The relative improvement score, ''RIS'', p … 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.mprovement relative to the potential loss. +
The reproducibility crisis is alarming.< … The reproducibility crisis is alarming.1 An experiment or study is ''reproducible'' or ''replicable'' when subsequent experiments confirm the results. This is [[research |re-search]]. However, we can define different types of reproducibility depending on the conditions that we use to replicate the previous work or in the information available. Our aim is to focus mostly on two different kinds2: '''1. Direct:''' is when we obtaining the same results using the same experimental conditions, materials, and methods as described in the original experiment. This would be the ideal reproducibility of an experiment. However, it requires a very accurate description of how the original experiment was performed. Some journals are trying to resolve the '''reproducibility crisis''' improving the rigor and the excellence on the reported methods and results (e.g. [https://www.cell.com/star-authors-guide STAR Methods in Cell Press]). '''2. Systematical:''' refers to obtaining the same results, but under different conditions; for example, using another cell line or mouse strain or humman study, or inhibiting a gene pharmacologically instead of genetically. This opens the door to subsequent studies to find the conditions under which an initial finding holds.udies to find the conditions under which an initial finding holds. +
The second, symbol s, is the SI unit of ti … The second, symbol s, is the SI unit of time. It is defined by taking the fixed numerical value of the caesium frequency ∆''ν''Cs, the unperturbed ground-state hyperfine transition frequency of the caesium 133 atom, to be 9 192 631 770 when expressed in the unit Hz, which is equal to s−1.ssed in the unit Hz, which is equal to s−1. +
The sign of the '''stoichiometric number'' … The sign of the '''stoichiometric number''' ''ν''X is determined by the nonspatial direction of the transformation (positive for products, negative for substrates), and the magnitude of ''ν''X is determined by the stoichiometric form. For instance, ''ν''A=-1 in the reaction 0 = -1 A + 2 B (-1 glucose converted to +2 lactate), but ''ν''A=-1/6 in the reaction 0 = -1/6 A - 1 B + 1 C (-1/6 glucose and -1 O2 converted to +1 H2CO3).1 B + 1 C (-1/6 glucose and -1 O2 converted to +1 H2CO3). +
The sodium salt of '''Dithionite''' Na< … The sodium salt of '''Dithionite''' Na2S2O4 (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 O2 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]].[[Setting the oxygen concentration]]. +
The standard '''Instrumental and SUIT DL-P … 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.tocols]\Install Oroboros protocol package. +
The strategy of '''Flux analysis''' using … 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.states during data recording and analysis. +
The symbol '''%''' indicates 'per cent' (per hundred). {''Quote''} The internationally recognized symbol % (per cent) may be used with the SI. When it is used, a space separates the number and the symbol %. {''end of Quote''}. +
The symbol '''≡''' indicates (numerical) [[equivalence]], in contrast to = as the symbol for (physicochemical) [[equality]]. +
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]]. +
The term '''extroduction''' is ambiguous a … 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. returning to the initial reference level. +
The term '''incident light''' is used for a beam of light falling upon a surface. +
The term '''isomorphic''' refers to quanti … 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.are referred to as ''generalized'' forces. +
The term '''system''' has a variety of mea … The term '''system''' has a variety of meanings and dictionary definitions in different contexts, ''e.g.'', the [[International System of Units]] (SI), MKSA system, data management system, biological or mechanical system, redox system, [[Electron transfer system]], loosely or completely coupled system, instrumental system. In thermodynamics and [[ergodynamics]], the '''system''' is considered as an experimental system (experimental chamber), separated from the environment as an isolated, adiabatic, closed, or open system. {''Quote'' } The internal domain of any system is separated from the external domain (the surroundings) by a boundary. In theory, energy transformations outside the system can be ignored when describing the system. The surroundings are merely considered as a source or sink for quantities transferred across the system boundary. According to the transfer properties of the boundary, three types of thermodynamic systems are distinguished. (''1'') The boundaries of '''''isolated systems''''' are impermeable for all forms of [[energy]] and matter. Isolated systems do not interact with the surroundings. Strictly, therefore, internal changes of isolated systems cannot be observed from outside since any observation requires interaction. (''2'') The boundaries of '''''closed systems''''' are permeable for [[heat]] and [[work]], but impermeable for [[matter]]. A limiting case is electrons which cross the system boundary when work is exchanged in the form of electric energy [''added'': and light]. The volume of a closed system may be variable. (''3'') The boundaries of '''''open systems''''' allow for the transfer of heat, work and matter. Changes of isolated systems have exclusively internal origins, whereas changes of closed and open systems can be partitioned according to internal and external sources. Production and destruction of a quantity within the system are ''internal'' changes, whereas changes of heat, work and matter due to transfer across the system boundaries are labelled ''extenal''. (External) transfer is thus contrasted with (internal) production or destruction. {''end of Quote'': [[Gnaiger 1993 Pure Appl Chem]]}A system may be treated as a black box. In the analysis of [[Continuous system|continuous]] or [[Discontinuous system |discontinuous system]]s, however, information is implied on the internal structure of the system.d on the internal structure of the system. +
The terms '''hydrogen ion''' H+ … The terms '''hydrogen ion''' H+ and [[proton]], p or p+, 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+ ion has no electrons and is a bare charge with only about 1/64 000 of the radius of a hydrogen atom. Free H+ is extremely reactive, with an extremely short lifetime in aqueous solutions. There H+ forms the hydronium ion H3O+, which in turn is further solvated by water molecules in clusters such as H5O2+ and H9O4+. The transfer of H+ in an acid–base reaction is referred to as ''proton transfer''. The acid is the H+ donor and the base is the H+ acceptor.lt;sup>+. The transfer of H+ in an acid–base reaction is referred to as ''proton transfer''. The acid is the H+ donor and the base is the H+ acceptor. +
The terms '''proton''' p and [[hydrogen ion]] … The terms '''proton''' p and [[hydrogen ion]] H+ are used synonymously in chemistry. In particle physics, a proton is a subatomic particle with a positive electric charge. Protons and neutrons are collectively referred to as ''nucleons''. The proton is a bare charge with only about 1/64 000 of the radius of a hydrogen atom, and so the free proton is extremely reactive chemically. Therefore, the free proton has an extremely short lifetime in aqueous solutions where it forms the [[hydronium ion]], H3O+, which in turn is further solvated by water molecules in clusters such as H5O2+ and H9O4+.;sub>5O2+ and H9O4+. +
There are 20 '''SI prefixes''' defined to represent multiples and submiltiples of SI units. +
There are many '''sides''' of the term 'si … There are many '''sides''' of the term 'side' in our language system. Inside and outside are the sides that are separated by the system boundaries of an experimental [[system]]. + and - are the two sides of numbers separated by 0. Pages in books have opposite sides or front sides versus backsides. Many fundamental terms have opposite sides of the meaning, thus spanning the entire message in the space between their apparently contrasting sides, and transforming the paradox as a perspective into the unified whole, the full, the complete. On the other side, such fundamental terms are fully understood only after ''realization'' of the opposite sides of their meaning — treasures discovered in the etymological origins of the word. It makes sense to open all our senses to comprehend the bright side and the dark side of things. Whereas the student sais "I see a black sheep", Zen decides "You see, that one side of the sheep is black". This is the message to consider both sides before choosing sides, besides overcoming a one-sided point of view. Don't rock side-to-side, but get immersed deeply inside things to see the upsides and downsides of every thing or anything, and more so of nothing. Inside is the insight, for insiders and outsiders of the feedback loop of an [[Ouroboros]].Ouroboros]]. +
This is a brief summary of steps to be tak … This is a brief summary of steps to be taken for performing a high-resolution respirometry experiment with '''[[SUIT protocols]]''' using the OROBOROS [[Oroboros O2k]] and '''[[DatLab]]''' software. (1) Search for a specific [[SUIT protocol name]] (go to [[MitoPedia:_SUIT#SUIT_protocols |MitoPedia: SUIT]]). The list of MitoPedia SUIT protocols can be sorted by [[categories of SUIT protocols]] (sorting by SUIT protocol name), which is listed as the 'abbreviation' of the SUIT protocol name. (2) Copy the template for [[Mark names]] into your DatLab subdirectory: DatLab\APPDATA\MTEMPLAT. (3) Copy the [[DatLab-Analysis templates |DatLab-Analysis template]] for this SUIT protocol. (4) Follow the link to the corresponding publication or MiPNet communication, where the pdf file describing the SUIT protocol is available. (5) A DatLab demo file may be available providing an experimental example. After each sequential titration, a mark is set on the plot for flux or flow. After having set all marks, pull down the 'Mark names' menu, select the corresponding SUIT protocol for mark names, and rename all marks. The Mark names template also provides standard values of the titration volume preceding each mark. (6) Go to 'Mark statistics' [F2], copy to clipboard, and paste into the sample tab in the DatLab-Analysis template.: Example::* SUIT protocol name: [[SUIT-011]]:* Mark names in DatLab: 1GM;2D;2c;3S;4U;5Rot-:* DatLab-Analysis template: SUIT_NS(GM)01.xlsx:* MiPNet communciation: [[MiPNet12.23 FibreRespiration]]:* DatLab demo file: MiPNet12.23 FibreRespiration.DLDemo file: MiPNet12.23 FibreRespiration.DLD +
This law states that the [[transmittance]] … This law states that the [[transmittance]] (''T'') of light though a sample is given by:''T'' = e-''εbc'', where ''ε'' is the molar [[extinction coefficient]], ''b'' is the pathlength of the light through the cuvette (in mm) and ''c'' is the concentration of the pigment in the sample (in mM). Transforming this equation, it can be seen that the [[absorbance]] of light (''A'') is simply given by ''A'' = ''εbc''.absorbance]] of light (''A'') is simply given by ''A'' = ''εbc''. +
This method makes use of all of the data p … 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. of only a few characteristic wavelengths. +
Though often defined from the individual r … Though often defined from the individual reader's perspective, a paywall can also apply to an institution (such as a library) or the author. '''Paywall journalism''' is the opposite of [[Open Access]]. [[Open Science]] does not accept paywalls with the argument, that the public pays for governmentally funded research, hence research funded by public grants should be published with open access for the public without paywalls. Paywalls are most frequently defined from the perspective of the individual reader, who has to pay for an article or pay a journal subscription as a requisite for obtaining full access to the information that is otherwise hidden behind the paywall ('''reader-paywall journal'''). From the perspective of the authors, however, an '''author-paywall journal''' is defined as any journal which requests publication charges or page charges from the authors for publishing the manuscript Open Access or publishing it at all. Similarly, an '''institutional-paywall journal''' charges an institution – typically university libraries – for granting open access to the members of this institution. As long as paywall journalism prevails in science, at least '''paywall transparence''' should be required, to declare for each publication not only the reader-paywall costs but provide the full information on the author-paywall and institutional-paywall expenses.aywall and institutional-paywall expenses. +
Three electronic '''channel types''' are a … 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).rval (default: 2 s; range 0.2 s to >10 s). +
Toggles between stirrer on/off in the left O2k-chamber, returning to the pre set stirrer speed. +
Toggles between stirrer on/off in the right O2k-chamber, returning to the pre set stirrer speed. +
Triethyltin bromide (TET) is a lipophilic [1] inhibitor of the mitochondrial [[ATP synthase]] [2] which is used to induce [[LEAK state]] in [[living cells]] of ''Saccharomyces cerevisiae''. +
Two-point calibration of the polarographic oxygen sensor, comprising [[Air calibration]] and [[Zero calibration]]. See also [[POS calibration - dynamic]]. +
Unspecific binding of the probe molecule T … Unspecific binding of the probe molecule TPP+ in the matrix phase of mitochondria is taken into account as a correction for measurement of the [[mitochondrial membrane potential]]. External unspecific binding is the binding outside of the inner mt-membrane or on the outer side of the inner mt-membrane, in contrast to internal unspecific binding.-membrane, in contrast to internal unspecific binding. +
Use the '''SUITbrowser''' to find the subs … Use the '''SUITbrowser''' to find the substrate-uncoupler-inhibitor-titration ([[SUIT]]) protocol most suitable for addressing your research questions. <big><big>Open the SUITbrowser: http://suitbrowser.oroboros.at/</big></big>[[Image:PlayVideo.jpg|50px|link=https://www.youtube.com/watch?v=8T33sp9KkJk]] [https://www.youtube.com/watch?v=8T33sp9KkJk How to find a DL-Protocol (DLP)]w.youtube.com/watch?v=8T33sp9KkJk How to find a DL-Protocol (DLP)] +
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. +
Valinomycin catalyzes electrogenic K+ transport down the electrochemical transmembrane gradient (150 ng.mg-1 protein). +
Various methods of '''smoothing''' can be … Various methods of '''smoothing''' can be applied to improve the [[signal-to-noise ratio]]. For instance, data points recorded over time [s] or over a range of wavelengths [nm] can be smoothed by averaging ''n'' data points per interval. Then the average of the ''n'' points per smoothing interval can be taken for each successively recorded data point across the time range or range of the spectrum to give a ''n''-point moving average smoothing. This method decreases the [[noise]] of the signal, but clearly reduces the time or wavelength [[resolution]]. More advanced methods of smoothing are applied to retain a higher [[time resolution]] or wavelength resolution.[[time resolution]] or wavelength resolution. +
Volume-specific '''hydrogenion flux''' or … Volume-specific '''hydrogenion flux''' or H+ flux is measured in a closed system as the time derivative of H+ concentration, expressed in units [pmol·s-1·mL-1]. H+ 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+ flux is comparable to volume-specific [[oxygen flux]] [pmol·s-1·mL-1], 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+ flux, however, must not be confused with ECAR.e incubation buffer or culture medium. The physiologically relevant metabolic H+ flux, however, must not be confused with ECAR. +
What are potential causes for '''different O2 fluxes in the left and right chamber'''? +
When light enter a sample, '''transmittance''' (''T'') is the fraction of the intensity (''I'') of the light emerging from the sample compared with the incident light intensity (''I''''0''): ''T'' = ''I''/''I''''0''. +
When light enters a sample and emerges wit … When light enters a sample and emerges with an intensity (''I''), '''absorption''' (''Abs'') is the fraction of the light absorbed by the sample compared with the [[incident light]] intensity (''I''''0''): ''Abs'' = 1-''I''/''I''''0''. Absorption can also be expressed as ''Abs'' = 1-''T'', where ''T'' is the [[transmittance]].[[transmittance]]. +
When light enters a sample, the amount of … When light enters a sample, the amount of light that it absorbs is dependent upon the wavelength of the incident light. The '''absorbance spectrum''' is the curve derived by plotting the measured [[absorbance]] against the wavelength of the light emerging from the sample over a given [[wavelength range]]. An [[absorbance spectrum]] may be characterised by peaks and troughs (absorbance maxima and minima) that can be used to identify, and sometimes quantify, different absorbing substances present in a sample. absorbing substances present in a sample. +
When one (or more) analytical parameters a … 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.tions require the standard black stoppers. +
When the '''TIP2k syringe is blocked''', it must not be used with the TIP2k, and specific cleaning instructions should be followed. +
With '''Living Communications''', [https:/ … 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.e-print, from initial steps to next steps. +
Within the system boundaries, irreversible … Within the system boundaries, irreversible '''internal flows''', ''I''i,—including chemical reactions and the dissipation of internal gradients of heat and matter—contribute to internal entropy production, di''S''/d''t''. In contrast, [[external flow]]s, ''I''e, 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]].ecific quantity]]. +
[[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. +
[[Bioenergetics Communications]] and [[MitoFit Preprints]] manuscript template. +
[[Electron transfer pathway]] competent state, ''see'' '''[[Electron-transfer-pathway state]]'''. +
[[Electron-transfer-pathway state |ET-path … [[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.T-pathways with entry into the Q-junction. +
[[File:11200-01.jpg|180px|right]] The ''' … [[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 delivery of this revolutionary module. +
[[File:1D;2M.1;2H2O;2c;3M.2;3M.5;3M1;3M2;4P;5G;6S10;6S50;7Gp;8U;9Rot;10Ama.png|400px]] +
[[File:1D;2M.1;3Oct;3c;4M.2;4M.5;4M1;4M2;5P;6G;7S10;7S50;8Gp;9U;10Rot;11Ama.png|400px]] +
[[File:1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px]] +
[[File:1D;2M.1;3Pal;3c;4M.2;4M.5;4M1;4M2;5P;6G;7S10;7S50;8Gp;9U;10Rot;11Ama.png|400px]] +
[[File:2-Oxoglutaric_acid.jpg|left|100px|2 … [[File:2-Oxoglutaric_acid.jpg|left|100px|2-Oxoglutaric acid]]'''2-Oxoglutaric acid''' or alpha-ketoglutaric acid, C5H6O5, occurs under physiological conditions as the anion '''2-Oxoglutarate2-, Og'''. 2-Oxoglutarate (alpha-ketoglutarate) is formed from isocitrate as a product of [[isocitrate dehydrogenase]] (IDH) in the [[TCA cycle]], and is a substrate of [[oxoglutarate dehydrogenase]] (OgDH). The 2-oxoglutarate carrier exchanges malate2- for 2-oxoglutarate2- as part of the [[malate-aspartate shuttle]]. In the cytosol, oxoglutarate+aspartate are transaminated to form oxaloacetate+glutamate. Cytosolic malate dehydrogenase converts oxaloacetate+NADH to malate.transaminated to form oxaloacetate+glutamate. Cytosolic malate dehydrogenase converts oxaloacetate+NADH to malate. +
[[File:21640 - Mitochondria Targeted Thera … [[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 2nd 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.tunities, panel discussions and dedicated roundtables. +
[[File:24330-02.jpg|right|180px]]'''Screwdriver allen wrench''', a standard component of the [[O2k-FluoRespirometer]] and [[O2k-sV-Module]]. +
[[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). +
[[File:31330-01 3.jpg|right|280px]] '''TIP2k-Needle Safety Support with cable guide''': for safe storage of TIP2k-needles and MultiSensor Modules cables when not required during the experiment. +
[[File:32001-01.jpg|right|180px]]'''Storage box sV''' empty, for storage of [[O2k-sV-Module]] components. +
[[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:32300-01.jpg|right|180px]] '''POS-H … [[File:32300-01.jpg|right|180px]]'''POS-Holder sV''', made from black POM, to be screwed into the copper block of the [[O2k-Main Unit]], guiding the [[OroboPOS|POS]] to the [[O2k-Chamber sV]], and keeping the SmartPOS/OroboPOS-Connector in a fixed position for sealing the O2k-Chamber sV with the [[POS-Seal Tip]]. In addition, the POS-Holder sV fixes the O2k-Chamber sV in an accurate rotational position by pressing against the angular cut of the glass chamber.inst the angular cut of the glass chamber. +
[[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. +
[[File:33210-01.jpg|right|180px]]'''Stirre … [[File:33210-01.jpg|right|180px]]'''Stirrer-Bar sV\white [[PVDF]]\11.5x6.2 mm''', operated in the 0.5-mL [[O2k-Chamber sV]] at constant stirring speed (standard is 750 rpm, or 12.5 Hz), to provide optimum mixing of the sample in the aqueous medium and ensure a stable signal of the polarographic oxygen sensor ([[OroboPOS]]) placed in a position of maximum current of the medium.position of maximum current of the medium. +
[[File:34000-01.jpg|right|180px]]'''Stoppe … [[File:34000-01.jpg|right|180px]]'''Stopper sV\black PEEK\conical Shaft\central Port''': with conical shaft (with PTFE, graphite, carbon fiber) and one central capillary (1.0 mm diameter; 48.9 mm length), [[Volume-Calibration Ring sV]] (A or B) for volume adjustment 0.5 mL; 2 mounted O-rings ([[O-ring sV\Viton\9.5x1 mm]]).[[O-ring sV\Viton\9.5x1 mm]]). +
[[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:ASMRM LOGO.JPG|200px|left]]The '''Asia Society for Mitochondrial Research and Medicine''' (ASMRM) was founded in 2003 to share the latest knowledge on mitochondrial research. +
[[File:Acetyl coenzyme A 700.png|left|200p … [[File:Acetyl coenzyme A 700.png|left|200px|acetyl-CoA]]'''Acetyl-CoA''', C23H38N7O17P3S, is a central piece in metabolism involved in several biological processes, but its main role is to deliver the acetyl group into the [[TCA cycle]] for its oxidation. It can be synthesized in different pathways: (i) in glycolysis from [[pyruvate]], by pyruvate dehydrogenase, which also forms NADH; (ii) from fatty acids β-oxidation, which releases one acetyl-CoA each round; (iii) in the catabolism of some amino acids such as leucine, lysine, phenylalanine, tyrosine and tryptophan. In the mitochondrial matrix, acetyl-CoA is condensed with [[oxaloacetate]] to form [[citrate]] through the action of [[citrate synthase]] in the [[tricarboxylic acid cycle]]. Acetyl-CoA cannot cross the mitochondrial inner membrane but citrate can be transported out of the mitochondria. In the cytosol, citrate can be converted to acetyl-CoA and be used in the synthesis of fatty acid, cholesterol, ketone bodies, acetylcholine, and other processes. and be used in the synthesis of fatty acid, cholesterol, ketone bodies, acetylcholine, and other processes. +
[[File:Aconitase.jpg|right|500px|aconitase … [[File:Aconitase.jpg|right|500px|aconitase]]'''Aconitase''' is a [[TCA cycle]] enzyme that catalyzes the reversible isomerization of [[citrate]] to [[isocitrate]]. Also, an isoform is also present in the cytosol acting as a trans-regulatory factor that controls iron homeostasis at a post-transcriptional level. tasis at a post-transcriptional level. +
[[File:CERG.gif|200px|left|CERG]] The '''C … [[File:CERG.gif|200px|left|CERG]]The '''Cardiovascular Exercise Research Group''' (CERG) was established in January 2008 and their research focuses on identifying the key cellular and molecular mechanisms underlying the beneficial effects of physical exercise on the heart, arteries and skeletal muscle in the context of disease prevention and management through experimental, clinical and epidemiological studies. Since 2003 this research group organizes the biennial seminar [http://www.ntnu.edu/cerg/seminar-2013 "Exercise in Medicine"] in Trondheim, Norway.ercise in Medicine"] in Trondheim, Norway. +
[[File:CII-ambiguities Graphical abstract. … [[File:CII-ambiguities Graphical abstract.png|300px|left|link=Gnaiger 2023 MitoFit CII]]The current narrative that the reduced coenzymes NADH and FADH2 feed electrons from the tricarboxylic acid (TCA) cycle into the mitochondrial electron transfer system can create ambiguities around respiratory Complex CII. Succinate dehydrogenase or CII reduces FAD to FADH2 in the canonical forward TCA cycle. However, some graphical representations of the membrane-bound electron transfer system (ETS) depict CII as the site of oxidation of FADH2. This leads to the false believe that FADH2 generated by electron transferring flavoprotein (CETF) in fatty acid oxidation and mitochondrial glycerophosphate dehydrogenase (CGpDH) feeds electrons into the ETS through CII. In reality, NADH and succinate produced in the TCA cycle are the substrates of Complexes CI and CII, respectively, and the reduced flavin groups FMNH2 and FADH2 are downstream products of CI and CII, respectively, carrying electrons from CI and CII into the Q-junction. Similarly, CETF and CGpDH feed electrons into the Q-junction but not through CII. The ambiguities surrounding Complex II in the literature call for quality control, to secure scientific standards in current communications on bioenergetics and support adequate clinical applications.nd support adequate clinical applications. +
[[File:CII.png |right|200px|link=Gnaiger 2 … [[File:CII.png |right|200px|link=Gnaiger 2023 MitoFit CII]]'''Complex II''' or '''succinate:quinone oxidoreductase (SQR)''' is the only membrane-bound enzyme in the [[TCA cycle]] and is part of the [[electron transfer pathway]]. The reversible oxidoreduction of succinate and fumarate is catalyzed in a soluble domain and coupled to the reversible oxidoreduction of quinol and quinone in the mitochondrial inner membrane. CII consists in most species of four subunits. The flavoprotein [[succinate dehydrogenase]] is the largest polypeptide of CII, located on the matrix face of the mt-inner membrane. Succinate:quinone oxidoreductases (SQRs, SDHABCD) favour oxidation of succinate and reduction of quinone in the canonical forward direction of the TCA cycle and electron transfer into the [[Q-junction]]. In contrast, quinol:fumarate reductases (QFRs, fumarate reductases, FRDABCD) tend to operate in the reverse direction reducing fumarate and oxidizing quinol.on reducing fumarate and oxidizing quinol. +