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This page provides a simple browsing interface for finding entities described by a property and a named value. Other available search interfaces include the page property search, and the ask query builder.

List of results

Submitochondrial particles + ('''Submitochondrial particles''' (smtp) co … '''Submitochondrial particles''' (smtp) consist of membrane fragments which retain most of the enzymatic machinery required in electron transfer and [[oxidative phosphorylation]]. Such membrane fragments are continuous closed vesicles formed by resealing of mt-membrane fragments after disruption of the mitochondrial structure. smtp are used to isolate the inner-[[membrane-bound ET pathway]] (mETS) from the upstream modules of the [[Electron transfer pathway]] (ETS) which are located in the mt-matrix and outer mt-membrane (transporters). smtp are obtained by treatment of mitochondria with membrane-dispersing agents such as digitonin at high concentration or by sonic irradiation.igh concentration or by sonic irradiation.)
Subsample + ('''Subsamples''' can be obtained (1) from … '''Subsamples''' can be obtained (1) from a homogenous [[sample]] (e.g. cell suspension, tissue homogenate, isolated mitochondria), (2) as subsamples obtained by splitting a sample into comparable parts (e.g. permeabilized muscle fibres from a biopsy split into different chambers for repeated measurements), or (3) repetitive sampling (e.g. taking multiple biopsies) at a single time point. Subsamples may be used for (i) application of different types of [[assay]] (e.g. for measurement of respiration and enzyme activities), and (ii) a number of [[repetitions]], ''n'', of the same assay on the same sample.n'', of the same assay on the same sample.)
Subscripts in physical chemistry + ('''Subscripts in physical chemistry''' are … '''Subscripts in physical chemistry''' are used to differentiate symbols of different quantities. While these subscripts need to be short to be readable, they have to be distinct and well defined. Several subscripts relate to fundamental terms and concepts, summarized in a list below. and concepts, summarized in a list below.)
Pathway control ratio + ('''Substrate control ratios''' are [[flux control ratio]] … '''Substrate control ratios''' are [[flux control ratio]]s ''FCR'', at a constant mitochondrial [[coupling-control state]]. Whereas there are only three well-defined coupling-control states of mitochondrial respiration, ''L'', ''P'', ''E'' ([[LEAK respiration]], [[OXPHOS]], [[Electron transfer pathway]]), numerous [[Electron-transfer-pathway state]]s are possible. Careful selection of the reference state, ''J''ref, is required, for which some guidelines may be provided without the possibility to formulate general rules. ''FCR'' are best defined by taking ''J''ref as the maximum flux (e.g. [[NS |NS''E'']]), such that flux in various other respiratory states, ''Ji'', is smaller or equal to ''J''ref. However, this is not generally possible with ''FCR''. For instance, the [[N/S pathway control ratio]] (at constant coupling-control state) may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The [[S-pathway control state]] may be selected preferentially as ''J''ref, if mitochondria with variable [[N]]-linked injuries are studied. In contrast, the [[reference state]], ''Z'', is strictly defined for [[flux control efficiency]].[[flux control efficiency]].)
Succinate dehydrogenase + ('''Succinate dehydrogenase''' is a [[TCA cycle]] … '''Succinate dehydrogenase''' is a [[TCA cycle]] enzyme converting [[succinate]] to [[fumarate]] while reducing FAD to FADH2. SDH is the largest component of the mt-inner membrane [[Complex II]] (CII) and thus part of the TCA cycle and [[electron transfer pathway]].[[electron transfer pathway]].)
Succinyl-CoA ligase + ('''Succinyl-CoA ligase''' (SUCLA or SUCLG) … '''Succinyl-CoA ligase''' (SUCLA or SUCLG) is a TCA cycle enzyme converting succinyl-CoA + ADP or (GDP) + Pi to [[succinate]] + ATP (GTP). Two different isoforms exsist: SUCLA (EC: 6.2.1.5) is the ATP-forming isoenzyme, SUCLG (EC: 6.2.1.4) is the GTP-forming isoenzyme. Both reactions are reversible. This reaction is attributed to mitochondrial substrate-level phosphorylation, which is considered as an alternative way of ATP synthesis because it is partially independent from the respiratory chain and from the mitochondrial proton motive force.rom the mitochondrial proton motive force.)
Sulfide quinone reductase + ('''Sulfide quinone reductase''' (SQR) is i … '''Sulfide quinone reductase''' (SQR) is involved in electron transfer from sulfide which is used as a hydrogen donor by the mitochondrial respiratory system. SQR is associated with a [[dioxygenase]] and a [[sulfur transferase]] to release thiosulfate (H2S2O3).(H2S2O3).)
Sulfite oxidase + ('''Sulfite oxidase''' (SO) is a dimeric en … '''Sulfite oxidase''' (SO) is a dimeric enzyme, located in the intermembrane space of mitochondria, with each monomer containing a single Mo cofactor and cyt b5-type heme [1]. SO catalyzes the oxidation of sulfite to sulfate as the terminal step in the metabolism of sulfur amino acids and is vital for human health. Inherited mutations in SO result in severe neurological problems, stunted brain growth, and early death [2]. Function: SO catalyzes the terminal reaction in the oxidative degradation of sulfur amino acids with the formation of a sulfate, electrons pass to cytochrom ''c'' and are further utilized in the respiratory system.Sulfite + O2 + H2O --> Sulfate + H2O2 Localization: The level of expression of SO differs in various tissues with main predominant localization in liver, kidney, skeletal muscle, heart, placenta, and brain in humans and liver, kidney, heart, brain, and lung in rats [3]. Deficiency: SO is vital for metabolic pathways of sulfur amino acids (cysteine and methionine). Complete lack of this enzyme, typically caused by gene mutation, leads to lethal disease called sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.ed sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.)
Synchronous time axes + ('''Synchronous time axes''' sets, if ticked, the time axes of all graphs at an identical range and offset, which is particularly useful while panning.)
T-Shirt: Oroboros black/organic cotton + ('''T-Shirt Oroboros black/organic cotton''': An Oroboros on the front.)
TIP2k and O2k-upgrade\B + ('''TIP2k and O2k-Upgrade\B''': Titration-Injection microPump TIP2k, including the electronic upgrade of the O2k-main unit returned to workshop (Series B-D). '''Discontinued''')
TIP2k cooling box + ('''TIP2k-Cooling Box''': Cooling box for TIP2k syringes. '''Discontinued''')
TIP2k-Needle Safety Support + ('''TIP2k-Needle Safety Support''': for safe storage of TIP2k-needles when not required during the experiment. This item is a standard component of the [[TIP2k-Module]].)
TMRM + ('''TMRM''' (tetramethylrhodamine methyl es … '''TMRM''' (tetramethylrhodamine methyl ester) is an [[extrinsic fluorophores|extrinsic fluorophore]] used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. TMRM is a lipophilic cation that is accumulated in the mitochondrial matrix in proportion to Δ''ψ''mt. Upon accumulation of the dye it exhibits a red shift in its absorption and fluorescence emission spectrum. The fluorescence intensity is quenched when the dye is accumulated in the mitochondrial matrix.en the dye is accumulated in the mitochondrial matrix.)
Tetrahydrofolate + ('''Tetrahydrofolate''', THF, is the substrate in mitochondrial folate-mediated 1C metabolism, an [[NADH-linked pathway]] leading to the formation of formate which is exported to the cytosol.)
Tetraphenylphosphonium + ('''Tetraphenylphosphonium''' (TPP+). A lipophilic molecular probe in conjunction with an ion selective electrode (ISE) for [[Mitochondrial membrane potential | measuring the mitochondrial membrane potential]].)
Thenoyltrifluoroacetone + ('''Thenoyltrifluoroacetone''' TTFA is a noncompetitive inhibitor of CII binding on the quinone-binding (SDHC/SDHD).)
Thioredoxin reductase + ('''Thioredoxin reductase''' (TrxR) is a family of enzymes able to reduce thioredoxin in mammals.)
Time resolution + ('''Time resolution''' in respirometric measurements is influenced by three parameters: the [[response time of the POS]], the data sampling interval and the number of points used for flux calculation.)
Traceability + ('''Traceability''' is the property of the … '''Traceability''' is the property of the result of a measurement or the value of a standard whereby it can be related to stated references, usually national or international standards, through an unbroken chain of comparisons all having stated uncertainties [SOURCE: VIM:1993, definition 6.10].nties [SOURCE: VIM:1993, definition 6.10].)
Trueness of measurement + ('''Trueness of measurement''' is the close … '''Trueness of measurement''' is the closeness of agreement between the average value obtained from a large series of results of measurements and a true value (adapted from ISO 3534-1:1993, definition 3.12). The degree of trueness is usually expressed numerically by the statistical measure bias that is inversely related to trueness and is the difference between the expectation of the results of measurement and a true value of the [[measurand]].[[measurand]].)
Trueness + ('''Trueness''' is understood as the lack of [[bias]] and the instrument calibration procedures are the key factor on establishing and correcting it.)
USB-RS232 Serial Adapter + ('''USB-RS232 Serial Adapter''', for connec … '''USB-RS232 Serial Adapter''', for connecting the [[RS232-Cable]] attached to the [[O2k-Main Unit]] (Series A-D) to the USB port of the PC or laptop. This is not required for O2k-Series E, nor when using a PC or laptop with a serial RS232 port. '''Discontinued'''th a serial RS232 port. '''Discontinued''')
Uncertainty of measurement + ('''Uncertainty of measurement''' is a para … '''Uncertainty of measurement''' is a parameter, associated with the result of a [[measurement]], that characterizes the dispersion of the values that could reasonably be attributed to the [[measurand]]. The parameter can be, for example, a standard deviation (or a given multiple of it), or the half-width of an interval having a stated level of confidence. The components of uncertainty are evaluated experimentally from statistical distributions (Type A) or evaluated from assumed probability distributions based on experience or other information (Type B). All components are expressed as standard uncertainties that are combined into one final expression.at are combined into one final expression.)
Uncoupling protein 1 + ('''Uncoupling protein 1''' (UCP1) is also … '''Uncoupling protein 1''' (UCP1) is also called thermogenin and is predominantly found in brown adipose tissue (BAT). UCP1 belongs to the gene family of [[uncoupling proteins]]. It is vital for the maintenance of body temperature, especially for small mammals. As the essential component of non-shivering thermogenesis, it possesses the ability to build and open a pore in the inner mitochondrial membrane through which protons may flow along their electrochemical gradient, generated by respiration, bypassing the ATP-producing re-entry site at the F1F0-ATP synthase. Thereby the energy stored in the electrochemical gradient is dissipated as heat.rochemical gradient is dissipated as heat.)
Uncoupling protein 2 + ('''Uncoupling protein 2''' (UCP2) belongs to the gene family of [[uncoupling proteins]]. Whereas [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]], this may not be the case for UCP2.)
Uncoupling proteins + ('''Uncoupling proteins''' (UCPs) are mitoc … '''Uncoupling proteins''' (UCPs) are mitochondrial anion carrier proteins that can be found in the inner mitochondrial membranes of animals and plants. [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]] by dissipating the electrochemical proton gradient ([[mitochondrial membrane potential]]), generated by the [[electron transfer pathway]] by pumping protons from the mitochondrial matrix to the mitochondrial intermembrane space. to the mitochondrial intermembrane space.)
Units in figures and tables + ('''Units in figures and tables''' are spec … '''Units in figures and tables''' are specified together with the numerical values. The ''value'' of a quantity ''Q'' is the product of a [[number]] ''N'' and a [[unit]] ''u''''Q''. Abstract units ''u''''Q'' (such as dm3=L, kg, J) are linked to measured quantities (such as volume, mass, energy): Eq.(1) ''Q''''u'' = ''N''·''u''''Q''The multiplication in Eq.(1) can be handled like any mathematical equation and re-arranged to the form which indicates the meaning (left) of a number (right): Eq.(2a) ''Q''''u''/''u''''Q'' = ''N'' Eq.(2b) ''N''''X''/x = ''N''When numbers are given on the axes of figures and in tables, the corresponding labels should be indicated according to Eq.(2), where Eq.(2a) applies to measured quantities, whereas Eq.(2b) relates to the countable quantity, i.e. [[count]] with unit [x]. For example, the axis label for volume-specific oxygen flux may be written as ''J''''V'',O2 / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''O2 / [amol/(s·x)].s ''J''''V'',O2 / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''O2 / [amol/(s·x)].)
Velocity + ('''Velocity''', '''''v''''' [m·s … '''Velocity''', '''''v''''' [m·s-1], is the [[speed]] in a defined spatial direction, and as such velocity is a [[vector]]. Velocity is the [[advancement]] in distance per unit time, '''''v''''' ≡ d'''''z''''' ∙ d''t''-1 [m·s-1] d'''''z''''' ∙ d''t''-1 [m·s-1])
Viable cells + ('''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).)
Viton + ('''Viton'''® is a fluoroelastomer with excellent resistance to aggressive fuels and chemicals. Viton is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (Viton O-rings).)
Volume + ('''Volume''' ''V'' is a derived quantity b … '''Volume''' ''V'' is a derived quantity based on the SI base quantity [[length]] [m] and is expressed in terms of [[SI base units]] in the derived unit cubic meter [m3]. The liter [L = dm3] is a conventional unit of volume for concentration and is used for most solution chemical kinetics. The volume ''V'' contained in a system (experimental chamber) is separated from the environment by the system boundaries; this is called the volume of the system, and described in practical language as big/small (derived from [[length]], [[height]]) or voluminous. Systems are defined at constant volume or constant [[pressure]]. For a pure sample S, the volume ''V''S of the pure sample equals the volume ''V'' of the system, ''V''S = ''V''. For [[sample]] s in a mixture, the ratio ''V''s·''V''-1 is the nondimensional [[volume fraction]] ''Φ''s of sample s. Quantities divided by volume are [[concentration]]s of sample s in a mixture, such as [[count]] concentration ''CX'' = ''NX''·''V''-1 [x·L-1], and amount of substance concentration ''C''B = ''n''B·''V''-1 [mol·L-1]. Mass concentration is [[density]] ''ρ''s = ''m''s·''V''-1 [kg·L-1]. In closed compressible systems (with a gas phase), the concentration of the gas increases, when pressure-volume [[work]] is performed on the system.is performed on the system.)
Wavelength averaging + ('''Wavelength averaging''' is the averagin … '''Wavelength averaging''' is the averaging of several adjacent data points across the recorded spectrum (spectral [[smoothing]]), to improve the [[signal-to-noise ratio]]. For example, if the instrument recorded 5 data points per nm, the average of the 5 points can be taken for each successive nm across the range of the spectrum to give a 5-point smoothing. This method clearly reduces the wavelength [[resolution]].[[resolution]].)
Work + ('''Work''' [J] is a specific form of [[energy]] … '''Work''' [J] is a specific form of [[energy]] in the First Law of thermodynamics, and a specific form of [[exergy]] in the Second Law of thermodynamics, performed by a closed or open system on its surroundings (the environment). This is the definition of ''external'' work, which is zero in [[isolated system]]s. The term exergy includes external and internal work. Mechanical work is force [N] times path length [m]. The internal-energy change of a closed system, d''U'', is due to external exchange (e) of work and heat, and external total work (et, including pressure-volume work) is the internal-energy change minus heat, det''W'' = d''U'' - de''Q''b>et''W'' = d''U'' - de''Q'')
Zero calibration + ('''Zero calibration''' is, together with [[air calibration]] … '''Zero calibration''' is, together with [[air calibration]], one of the two steps of the POS calibration. It is performed in the [[closed chamber]] after all the oxygen has been depleted by the addition of [[dithionite]] or by respiration of [[Isolated mitochondria |imt]] or [[Living cells |cells]]. Any incubation medium can be used for zero calibration with dithionite or sample. Unlike air calibration, it is not necessary to perform a zero calibration on each experimental day. After performing a zero calibration, it is recommended not running other experiments on the same day. Even after standard cleaning of the O2k-chambers, there might be residual amounts of reduced dithionite in the chamber, affecting the oxygen flux in subsequent experiments performed on the same day.ent experiments performed on the same day.)
DatLab 2 + ('''[[DatLab]] 2''' (DL2) is a MS-DOS programe. DL2 is still used for analysis of [[oxygen kinetics]], after exporting files recorded in recent DatLab versions. A user-friendly O2-kinetics module is in preparation (DL8).)
Substrates as electron donors + ('''[[Substrate]] … '''[[Substrate]]s as electron donors''' are reduced fuel compounds ''S''red that are oxidized to an oxidized product ''P''ox during H+-linked electron transfer, ''S''red → ''P''ox + 2{H+ + e-}. Mitochondrial respiration depends on a continuous flow of electron-supplying substrates across the mitochondrial membranes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.anes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.)
Base quantities and count + ('''[[Template:Base quantities and count]]''')
ArXiv preprint server + ('''arXiv''' is a classic preprint server i … '''arXiv''' is a classic preprint server initiated in 1991 by Paul Ginsparg. {''Quote''} arXiv.org is a highly-automated electronic archive and distribution server for research articles. Covered areas include physics, mathematics, computer science, nonlinear sciences, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. arXiv is maintained and operated by Cornell University with guidance from the arXiv Scientific Advisory Board and the arXiv Member Advisory Board, and with the help of numerous subject moderators. {''end of Quote''}. arXiv rejects abstracts that are submitted without accompanying paper. are submitted without accompanying paper.)
BioRxiv preprint server for biology + ('''bioRxiv''' (pronounced "bio-archive") i … '''bioRxiv''' (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It was launched in 2013 by Cold Spring Harbor Laboratory Press in New York, and is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. bioRxiv is intended for rapid sharing of new research. Some review articles contain new data/analyses and may therefore be deemed appropriate. Reviews that solely summarize existing knowledge are not appropriate and neither are term papers, book excerpts, and undergraduate dissertations.excerpts, and undergraduate dissertations.)
PH calibration buffers + ('''pH calibration buffers''' are prepared to obtain two or more defined pH values for calibration of pH electrodes and pH indicator dyes.)
PH combination electrode 150/6 mm + ('''pH combination electrode''', 150 mm shaft, 6 mm diameter, incl. connection cable with BNC plug. '''Discontinued''' * Replaced by [[O2k-pH ISE-Module]].)
PH combination electrode 70/5 mm + ('''pH-Combination Electrode\70/5 mm''', 70 mm shaft, 5 mm diameter, for 30251-24 stopper. ''' Discontinued ''' * Replaced by [[O2k-pH ISE-Module]].)
PX calibration - DatLab + ('''pX calibration''')
Hydroxybutyrate + ('''β-hydroxybutyrate''' or 3-hydroxybutyrate is a ketone body that can be used as a [[NADH electron transfer-pathway state|NADH-linked substrate]]. The β-hydroxybutyrate dehydrogenase produces acetoacetate while reducing NAD+ to [[NADH]]. )
Complex I-linked substrate state + (''See'' '''[[N-pathway control state]]''' (previous: CI-linked) versus '''[[Complex I]]''')
CI control ratio + (''See'' '''[[N/NS pathway control ratio]]''')
Complex I&II-linked substrate state + (''See'' '''[[NS-pathway control state]]''' (previous: CI&II-linked))
Substrate control efficiency + (''See'' '''[[Pathway control efficiency]]''')
Substrate control ratio + (''See'' '''[[Pathway control ratio]]''')
Complex II-linked substrate state + (''See'' '''[[S-pathway control state]] (previous: CII-linked))
CII control ratio + (''See'' '''[[S/NS pathway control ratio]]''')
Group + (''See'' '''[[population]]'''.)
Phosphate + (''See:'' '''[[Inorganic phosphate]]''')
Standard operating procedures + (''The following definition is incomplete.'' '''Standard operating procedures''' are a set of step-by-step instructions to achieve a predictable, standardized, desired result often within the context of a longer overall process.)
Solution protocols + (''The following definition lacks quality control and is not applied as such in the Oroboros QM.'' '''Solution protocols''' contain media, substrates, uncouplers, inhibitors used in [[SUIT|SUIT protocols]], permeabilization agents, etc.)
Project + (''The following definition lacks quality c … ''The following definition lacks quality control and is not applied as such in the Oroboros QM.''A scientific project is a collection of [[experiment| experiments]] designed to proof or disproof a specific hypothesis. The [[experiment| experiments]] will follow the logic of the scientific discovery [1] on which a hypothesis will support a prediction and this will be tested by experimental [[assay| assays]] (''i.e.'', observations under controlled conditions). The result of these experiments will proof or disproof the specific hypothesis and, usually, provide new hypotheses to test. A scientific project must be carefully designed to obtain relevant statistical information through enough [[replica| data collection]].[1] Popper K (2002) The logic of scientific discovery. Routledge Classics. ISBN: 978-0-415-27843-0outledge Classics. ISBN: 978-0-415-27843-0)
Autoxidation + (''This definition is insufficient and need … ''This definition is insufficient and needs elaboration.''Autoxidation is a slow process implying oxidation of carbohydrates through oxygen in open air, leading to a primary formation of peroxides and hydroperoxides. UV radiation can speed up this process.s. UV radiation can speed up this process.)
Cellular substrates + ((1) Cellular substrates ''in vivo'', endogenous; '''Ce'''. (2) Cellular substrates ''in vivo'', with exogenous substrate supply from culture medium or serum; '''Cm'''. * ''This page needs an update.'')
Natoms O + (0.5 nmol O2; in bioenergetics a variety of expressions is used for units of amount of half a nmol molecular oxygen (natoms oxygen; natoms O; ng.atom O; nmol O), with the identical meaning: 0.5 nmol O2.)
BAM15 + (2-fluorophenyl){6-[(2-fluorophenyl)amino]( … 2-fluorophenyl){6-[(2-fluorophenyl)amino](1,2,5-oxadiazolo[3,4-e]pyrazin-5-yl)}amine ('''BAM15''') is a protonophore or uncoupler of [[Oxidative phosphorylation|oxidative phosphorylation]] detected in a screen for uncoupling agents exerting less toxicity than commonly used uncouplers and first described by [[Kenwood 2013 Mol Metab|Kennwood et al. 2013]]. In their comparison of BAM15 with FCCP it was shown to increase oxygen flux to a similar extent as the classical uncoupler, to display a much broader range of concentrations inducing maximum respiration, to stimulate no formation of H2O2, to leave cellular membrane potential unaffected, and to ultimately exert less cytotoxicity.e potential unaffected, and to ultimately exert less cytotoxicity.)
3-Mercaptopropionic acid + (3-Mercaptopropionic acid (MPA) inhibits long chain [[acyl-CoA dehydrogenase]]s (ACADs).)
Mitochondrial states and rates - terminology beyond MitoEAGLE 2020 + (666 coauthors of the 'MitoEAGLE white paper' [1] collaborated to reach a consensus on terminology related to mitochondrial respiratory states and rates. This page is intended to prepare a questionnaire and follow-up publication.)
Mitochondria Interest Group + ( [[File:MIG.gif|128 px|left]] … [[File:MIG.gif|128 px|left]]The '''Mitochondria Interest Group''' (MIG) is an Inter-Institute Interest Group at the National Institutes of Health (NIH), with members worldwide! MIG is concerned with all aspects of the mitochondrion and diseases in which the mitochondrion is involved. We hold monthly meetings, usually on the second Monday of the month (except when it is a Federal holiday or other special exceptions). [email protected] is an Email list moderated by Ph.D. Steven Zullo as an interactive information platform, with free subscritpion to this mitochondrial network. List members are reminded of their responsibility to critically evaluate the content of the postings. The information, opinions, data, and statements contained herein are not necessarily those of the U. S. Government, the National Institutes of Health (NIH), or MIG and should not be interpreted, acted on or represented as such.be interpreted, acted on or represented as such.)
Custom label + (A '''Custom label''' can be entered in this box to rename the axis label. Two lines are available for the axis name and unit.)
Digital Object Identifier + (A '''Digital Object Identifier''', DOI, is … A '''Digital Object Identifier''', DOI, is a persistent identifier used to uniquely identify online publications in order to ensure they remain traceable, searchable and citable over the long term. Compared to other types of persistent identifiers, the DOI system is widespread and well established in the life sciences arena, and it provides widely accepted visible proof that a publication is citable.sible proof that a publication is citable.)
Layout for DatLab graphs + (A '''Layout''' in [[DatLab]] … A '''Layout''' in [[DatLab]] selected in the Layout menu yields a standardized display of graphs and [[Plot - DatLab |plots]] displayed with specific [[Scaling - DatLab|scalings]]. The graph layout defines initial settings, which can be modified for plots [Ctrl+F6] and scaling [F6]. A modified layout can be saved as user layout without changing the standard layouts.out without changing the standard layouts.)
Lower O2 limit - DatLab + (A '''Lower O2 limit [µM]''' can be defined … A '''Lower O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O2 concentration drops below this limit. It reminds the user that re-oxygenation of the O2k-chamber may be required. For the lower O2 concentration limit, the [[critical oxygen pressure |critical oxygen concentration]] should be considered, which differs between isolated mitochondria, large cells, and permeabilized muscle fibers. A higher limit should be chosen when high oxygen flux is expected, e.g. prior to uncoupler titration. A lower limit is acceptable prior to inhibition of respiration causing low oxygen flux.ptable prior to inhibition of respiration causing low oxygen flux.)
National Standards Body + (A '''National Standards Body''' is the national member of the [[International Organization for Standardization]] (ISO).)
Notified Body + (A '''Notified Body''' is an organisation designated by an EU country to assess the conformity of certain products before being placed on the market.)
Quality audit + (A '''Quality Audit''' is the process of systematic examination of a quality system carried out by an internal or external quality auditor or an audit team.)
Stand alone application + (A '''Stand alone application''' is computer software that can work offline, i.e. does not necessarily require network connection to function or does not even provide the possibility to connect to a network.)
Upper O2 limit - DatLab + (A '''Upper O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O2 concentration rises beyond this limit.)
Web application + (A '''Web application''' is a computer software where the [[user interface]] gets accessed by the user through a web browser.)
Canonical ensemble + (A '''canonical ensemble''' is the group of … A '''canonical ensemble''' is the group of compartments enclosed in an isolated system '''H''', with a smaller compartment A1 in thermal equilibrium with a larger compartment A2 which is the heat reservoir at temperature ''T''. When A1 is large in the canonical sense, if its state can be described in terms of macroscopic thermodynamic quantities of ''V'', ''T'', and ''p'' merging with the state described as a probability distribution.T'', and ''p'' merging with the state described as a probability distribution.)
Closed system + (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).)
Coenzyme + (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).)
Cofactor + (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).)
Coupling-control protocol + (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''']])
Dataset + (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.)
Decimal marker and spaces between groups of numerals + (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).)
Detector + (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]].)
Difference spectrum + (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]].)
Directive + (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.)
Dispersion devices + (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]].)
Fluorophore + (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.)
Free radicals + (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•).)
Harmonized standard + (A '''harmonized standard''' is a European [[standard]] developed by a recognized European Standards Organisation: CEN, CENELEC, or ETSI.)
Healthy reference population + (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].)
High signal at zero oxygen + (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.)
Light-emitting diode + (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].)
Measurement process + (A '''measurement process''' or a '''measurement''' is a set of operations to determine the value of a [[quantity]].)
Measuring equipment + (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.)
Medical device + (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.)
Metabolic control variable + (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).)
Model + (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'''.)
Norm + (A '''norm''' is a rule that is enforced by members of a community.)
Number + (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.)
Numeral + (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).)
Plot - DatLab + (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.)
Polarization voltage + (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.)
Population + (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''.)
Preprint + (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.)
Product + (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.)
Prosthetic group + (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.)
Quantity + (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)}.)
Reference spectrum + (A '''reference spectrum''' for a substance is an [[absorbance spectrum]] of the same substance at a known concentration and [[redox state]].)
Requirement + (A '''requirement''' is a singular documented physical or functional need that a particular design, product or process must be able to perform.)
Sample + (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.)
Scalar + (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.)
Solutions + (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''']])
Spectrofluorometer + (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.)
Spectrophotometer + (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]].)
Standard + (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]].)
Stirrer test + (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.)
Three-electrode system + (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]].)
Tissue homogenate + (A '''tissue homogenate''' (thom) is obtained through mechanical micro-disruption of fresh tissue and the cell membranes are mechanically permeabilized.)
User code - DatLab + (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]].)
Vector + (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.)
Working measurement standard + (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].)
In vitro diagnostic medical device + (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.)
Steady state + (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.)
Uninterrupted power supply + (A back-up power supply may be required to secure '''uninterrupted power supply'''.)
Graph control - DatLab + (A combination of mouse and keyboard commands provides convenient control of graphs in DatLab 8.)
SUIT: Browse DL-Protocols and templates + (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]].)

Inside the O2k + (A glance '''inside the [[Oroboros O2k]]''')

TPP+ inhibitory effect + (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.)
Experiment + (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.)
User - DatLab + (A user name is)
Light source + (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.)
Elasticity + (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]])
O2k control - DatLab 7 + (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.)
Amperometric,Amp + (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.)
Connection window + (After starting [[DatLab]] either the '''Connection window''' opens automatically by default or open [[O2k control]] by pressing [F7] and select the communication port.)
Absorbance + (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''))
Intrinsic fluorophores + (An '''Intrinsic flourophore''' is a naturally occurring [[fluorophore]] of which [[NADH]], aromatic amino acids and flavins are examples.)
Absorption spectrum + (An '''absorption spectrum''' is similar to an [[absorbance spectrum]] of a sample, but plotted as a function of [[absorption]] against wavelength.)
Entity + (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.)
Events - DatLab + (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]])
Examination + (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.)
Experimental code + (An '''experimental code''' can be entered in the [[Sample - DatLab|Sample]] window, containing up to 10 digits.)
Interlaboratory comparison + (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.)
Journal issue + (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.)
Open system + (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).)
Outlier + (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].)
Outlier-skewness index + (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''.)
Uncoupler + (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.)
Endothermic + (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]].)
Exothermic + (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]].)
Assay + (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.)
Sample type + (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]]).)
Science - the concept + (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.)
Conflict of interest + (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.)
STPD + (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.)
Copyright + (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''})
Mitophagy + (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 + (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 + (Biological contamination may be caused by microbial growth in the O2k-Chamber or in the experimental medium.)
Bovine serum albumin + (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.)
Full screen + (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 + (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).]])
POS calibration - dynamic + (Calibration of the sensor response time. See also [[POS calibration - static]].)
Cataplerosis + (Cataplerosis is the exit of TCA cycle intermediates from the mt-matrix space.)
Living cells + (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.)
Exit - DatLab 7 + (Close DatLab files and '''quit''' the program.)
Close and delete file - DatLab + (Close and delete a file.)
DatLab error messages + (Common '''DatLab error messages''' and according actions and solutions are listed here.)
Citrate synthase + (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.)
O2k configuration + (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.)
Cross-linked respiratory states + (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.)
Energy metabolism + (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.)
DatLab data file + (DatLab 8: The file type generated is *.dld8. DatLab 7: The file type generated is *.DLD.)
Keyboard shortcuts - DatLab + (DatLab provides several keyboard shortcuts to allow for quick access to many functions and settings without using a mouse.)
DatLab-Upgrading to DatLab 6 + (DatLab-Upgrading to DatLab 6: including free follow-up updates for DatLab 6 for the next two years)
O2k channel labels - DatLab 7 + (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.)
Q-pools + (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 effect + (Dilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber.)
Biochemical threshold effect + (Due to threshold effects, even a large defect diminishing the velocity of an individual enzyme results in only minor changes of pathway flux.)
Electron leak + (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''.)
Proton leak + (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]].)
Shipping an O2k + (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.)
DatLab-Analysis templates + (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.)
Hydronium ion + (H+ forms the '''hydronium ion''' H3O+, which in turn is further solvated by water molecules in clusters such as H5O2+ and H9O4+.)
Energy + (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.)
Euthanyl/Pentobarbitol + (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]]))
Substrate + (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.)
Anoxia + (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.)
Display numerical value + (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).)
Dual wavelength analysis + (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.)
Copy marks + (In '''Copy marks''', [[Marks - DatLab |Marks in DatLab]] are copied from a seleted [[Plot - DatLab |Plot]] to the active plot.)
Mark statistics - DatLab + (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.)
Chlororespiration + (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.)
Reflectance spectrophotometry + (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.)
Remittance spectrophotometry + (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.)
Uncoupler titrations + (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]].)
Copy to clipboard + (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).)
Start recording - DatLab + (In DatLab 8, the start recording window allows to select protocols or settings before starting recording a file.)
Noise + (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.)
Blank + (In [[fluorometry]] and [[transmission spectrophotometry]] '''blank''' [[cuvettes]] (with no samples in them) are used to carry out the [[balance]].)
White 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.)
Discontinuous system + (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.)
Flow + (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.)
Advancement + (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]])
Abundance + (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.)
Pathway and coupling control states + (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.)
Journal publication + (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.)
Averaging + (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.)
Ascorbate + (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.)
Body fat excess + (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.)
Quantities, symbols, and units + (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]].)
Extended abstracts + (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.)
Electron transfer pathway + (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''']])
Select plots - DatLab + (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]].)
Limiting pO2 + (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]].)
Transmission spectrophotometry + (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.)
Sample - DatLab 7 + (In the window '''Sample''', information is … In the window '''Sample''', information is entered and displayed for the sample (Sample type, Cohort, Sample code, Sample number, Subsample number and sample concentration). Entries can be edited any time during the experiment in real-time or during post-experiment analysis. All related results are recalculated instantaneously with the new parameters. Initially, the Edit experiment window displays information from the last file recorded and saved while connected to the O2k.rded and saved while connected to the O2k.)
Balance + (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: Browse DL-Protocols and templates + (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.)
Mitochondrial respiration + (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 quantity + (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).)
Statistical significance + (It is advisable to replace levels of '''statistical significance''' (*, **, ***) by simply stating the actual ''p''-values.)
OSF Preprint server + (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.)
Sarcopenia + (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.)
Superoxide dismutase + (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]].)
Manuscript template for MitoFit Preprints + (Manuscripts template for [[MitoFit Preprints]] and [[Bioenergetics Communications]].)
Attached cells + (Many cell types are grown in culture as '''attached cells''', such as endothelial or neuronal cells in a monolayer.)
Metabolic control analysis + (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-Publication + (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]].)
Communication - mitochondria and the patient + (Mitochondria and the patient: communication between patients, medical professionals, scientists, and the public)
Substrate-uncoupler-inhibitor titration + (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]].)
Hydrogen ion pump + (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]].)
Malate dehydrogenase + (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.)
Proton pump + (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]].)
MiR06Cr + (Mitochondrial respiration medium, '''MiR06Cr''', developed for oxygraph incubations of mitochondrial preparations - ''[[permeabilized muscle fibers]]''. MiR06Cr = [[MiR06]] + 20 mM [[Creatine|creatine]].)
MiR05Cr + (Mitochondrial respiration medium, '''MiR05Cr''', developed for oxygraph incubations of mitochondrial preparations - ''[[permeabilized muscle fibers]]''. MiR05Cr = [[MiR05]] + 20 mM [[Creatine|creatine]].)
Mitochondrial respiration media: comparison + (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.)
Hydrogen + (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.)
Scattering + (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.)
Volume of the solute + (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.)
Carrier control titrations + (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.)
Q + (Multiple meanings of Q ::::» [[Coenzyme Q]] Q ::::» [[Charge]] ''Q'', ''Q''el ::::» [[Heat]] ''Q'', ''Q''th)
Nigericin + (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]].)
Viruses and mitochondrial medicine + (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.)
Nuclear receptors + (Nuclear receptors are ligand-dependent transcription factors.)
Equivalence + (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 + (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.)
BME cutoff points + (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.)
Creative Commons Attribution License + (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.)
Open - DatLab + (Open a previously recorded [[DatLab]] file.)
Internationale Gesellschaft fuer Regenerative Mitochondrien-Medizin + (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]])
Pyruvate dehydrogenase complex + (Oxidative decarboxylation of pyruvate is catalyzed by the '''pyruvate dehydrogenase complex''' in the mt-matrix, and yields acetyl-CoA.)