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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.)
P/O ratio + (P/O ratio stands for phosphate to atomic oxygen ratio, where P indicates phosphorylation of ADP to ATP (or GDP to GTP).)
Equality + (Physicochemical '''equality''' (symbol =) indicates in an equation not only numerical [[equivalence]] (symbol ≡), but an identity of the full meaning.)
Intracellular oxygen + (Physiological, '''intracellular oxygen pressure''' is significantly lower than air saturation under normoxia, hence respiratory measurements carried out at air saturation are effectively hyperoxic for cultured cells and isolated mitochondria.)
RT + (RT indicates '''room temperature''' or 25 °C. ''RT'' is the [[gas constant]] ''R'' [kJ/mol] multiplied by absolute [[temperature]] ''T'' [K]. This is the motive force quantum in the amount format ([[Gnaiger 2020 BEC MitoPathways]]).)
Warburg effect + (Recently, controversies had a renaissance … Recently, controversies had a renaissance on the much neglected Crabtree effect (aerobic glycolysis in a large range of cells exposed to glucose or fructose, with fully functional mitochondria; Crabtree 1929; Gnaiger and Kemp 1990) versus the '''Warburg effect''' (loss of mitochondrial function inducing cancer and stimulating compensatory aerobic glycolysis in the presence of oxygen; Warburg 1956; see list of references for reviews). Today it is widely accepted that ‘''the Warburg effect is not consistent across all cancer types''’ (Potter et al 2016) and reprogramming of mitochondrial energy metabolism represents a functional adjustment of cancer cells (Schöpf et al 2020).tment of cancer cells (Schöpf et al 2020).)
NADH fluorescence + (Reduced nicotinamide adenine dinucleotide ([[NADH]]) is amongst the [[intrinsic fluorophores]] and can be used as an intracellular indicator of hypoxia. The excitation wavelength is 340 nm and emission is at 460 nm.)
2-Hydroxyglutarate + (Reduction of [[oxoglutarate]] … Reduction of [[oxoglutarate]] (2OG or alpha-ketoglutarate) to '''2-hydroxyglutarate''' (2HG) is driven by NADPH. 2HG is also formed in side reactions of [[lactate dehydrogenase]] and [[malate dehydrogenase]]. Millimolar 2HG concentrations are found in some cancer cells compared to , whereas side activities of lactate and malate dehydrogenase form submillimolar s-2-hydroxyglutarate (s-2HG). However, even wild-type IDH1 and IDH2, notably under shifts toward reductive carboxylation glutaminolysis or changes in other enzymes, lead to “intermediate” 0.01–0.1 mM 2HG levels, for example, in breast carcinoma compared with nanomolar concentrations in benign cells. 2HG is considered an important player in reprogramming metabolism of cancer cells. reprogramming metabolism of cancer cells.)
Publicly deposited protocols + (Researchers need to be introduced into adh … Researchers need to be introduced into adhering to '''publicly deposited protocols'''. [[Prespecified protocols |Prespecified]] and [[time-stamped protocols]] that are publicly deposited may help to save Millions of Euros that may otherwise be wasted on research that is lacking coherent standards.search that is lacking coherent standards.)
Oxygen flow + (Respiratory '''oxygen flow''' is the oxyge … Respiratory '''oxygen flow''' is the oxygen consumption per total [[system]], which is an [[extensive quantity]]. [[Flow]] is advancement of a transformation in a system per time [mol·s-1], when 'system' is defined as the experimental system (e.g. an open or closed chamber). Flow is distinguished from the size-specific quantity [[flux]] obtained by normalization of flow per volume of the experimental system [mol·s-1·m-3]. An experimental object, e.g. a living cell, may be considered as the 'experimental system'. Then oxygen flow per cell has the unit [mol·s-1·x-1], where [x] is the [[elementary unit]] for a [[count]]. Oxygen flow or respiration per cell [amol·s-1·x-1] = [pmol·s-1·Mx-1] is normalized for the cell count, distinguished from [[oxygen flux]] (e.g. per mg protein or wet mass). These are different forms of [[normalization of rate]].zation of rate]].)
Reverse electron flow from CII to CI + (Reverse electron flow from CII to CI stimu … Reverse electron flow from CII to CI stimulates production of [[ROS]] when mitochondria are incubated with succinate without rotenone in the LEAK state at a high [[mt-membrane potential]]. Depolarisation of the mt-membrane potential (''e.g.'' after ADP addition to stimulate OXPHOS) leads to inhibition of RET and therefore, decrease of RET-initiated ROS production. RET can be also measured when mitochondria are respiring using [[Glycerophosphate |Gp]] without rotenone in the [[LEAK respiration|LEAK]] state. Addition of IQ-side inhibitors (ubiquinone-binding side of CI) of [[Complex I |CI]] usually block RET. The following SUIT protocols allow you to measure RET-initiated H2O2 flux in [[mitochondrial preparations]]: [[SUIT-009]] and [[SUIT-026]].[[SUIT-026]].)
Rhodamine 123 + (Rhodamine 123 (Rh123) is an [[extrinsic fluorophores|extrinsic fluorophore]] … Rhodamine 123 (Rh123) is an [[extrinsic fluorophores|extrinsic fluorophore]] and can be used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. Rh123 is a lipophilic cation that is accumulated by mitochondria in proportion to Δ''ψ''mt. Using ethanol as the solvent, the excitation maximum is 511 nm and the emission maximum is 534 nm. The recommended excitation and emission wavelengths in PBS are 488 and 515-575 nm, respectively (Sigma-Aldrich). are 488 and 515-575 nm, respectively (Sigma-Aldrich).)
Bioblasts + (Richard Altmann (1894) defined the 'elemen … Richard Altmann (1894) defined the 'elementary organisms' as '''Bioblasts'''. He observed granula in cells stained with osmium and viewed ‘the protoplasm as a colony of bioblasts’. "Microorganisms and granula are at an equivalent level and represent elementary organisms, which are found wherever living forces are acting, thus we want to describe them by the common term bioblasts. In the bioblast, that morphological unit of living matter appears to be found." [[Altmann 1894 Verlag Von Veit & Comp|Altmann 1894]]; p. 141. Altmann is thus considered as the discoverer of [[mitochondria]] (the granula), which constitute together with the microorganisms the ''bioblasts'' (the elementary organisms). Bioblasts are the aliens with permanent residence in our cells ([[Bioblasts#Bioblasts_.E2.80.93_the_aliens_with_permanent_residence_in_our_cells|Gnaiger 2010]]).oblasts#Bioblasts_.E2.80.93_the_aliens_with_permanent_residence_in_our_cells|Gnaiger 2010]]).)
Save - DatLab + (Save a DatLab file.)
Save as - DatLab + (Save as a DatLab file.)
Zenodo + (Science Europe: "Zenodo is an open source … Science Europe: "Zenodo is an open source and free repository for storing data, code, materials, and any research artefact. It was created by CERN and launched within the frame of the OpenAIRE project, commissioned by the European Commission. It aims at fostering free and easy access to scientific results, scientific data, software, and publications to all researchers."are, and publications to all researchers.")
ASAPbio + (Science only progresses as quickly and eff … Science only progresses as quickly and efficiently as it is shared. But even with all of the technological capabilities available today, the process of publishing scientific work is taking longer than ever. '''ASAPbio''' (Accelerating Science and Publication in biology) is a scientist-driven nonprofit working to address this problem by promoting innovation and transparency in life sciences communication.In 2015, ASAPbio founder Ron Vale published an analysis of the increasing time to first-author publication among graduate students at UCSF, and proposed a more widespread use of preprints in the life sciences as a potential solution.the life sciences as a potential solution.)

Substrate control state + (See '''[[Electron-transfer-pathway state]]''')

Physiological pathway-control state + (See [[Electron-transfer-pathway state]].)
Fluorescent marker + (See [[Extrinsic fluorophores]])
Delete points + (Select '''Delete points''' in the [[Marks - DatLab |Mark information]] window to remove all data points in the marked section of the active plot. See also [[Interpolate points]] and [[Restore points]] or [[Recalculate slope]].)
Interpolate points + (Select '''Interpolate points''' in the [[Marks - DatLab |Mark information]] window to interpolate all data points in the marked section of the active graph. See also [[Delete points]] and [[Restore points]] or [[Recalculate slope]].)
Mouse control: Zoom + (Select '''Mouse Control: Zoom''' in the Graph-menu or press [Ctrl+Z].)
Recalculate slope + (Select '''Recalculate slope''' (Recalc. sl … Select '''Recalculate slope''' (Recalc. slope) in the [[Marks - DatLab |Mark information]] window to restore data points in the marked section of the active Flux / Slope plot, if [[Delete points]] or [[Interpolate points]] was used before. The entire plot is recalculated, such that other marked sections which may have been deleted are also restored. Compare [[Restore points]].[[Restore points]].)
Restore points + (Select '''Restore points''' in the [[Marks - DatLab |Mark information]] window to restore data points in the marked section of the active signal plot, if [[Delete points]] or [[Interpolate points]] was used before. Compare [[Recalculate slope]].)
Manage setups and templates - DatLab + (Setups and templates in DatLab can be renamed or deleted under '''Manage setups''' or '''Manage templates'''.)
Graph options - DatLab + (Several display options can be applied to a DatLab graph under '''Graph options'''.)
Comma for separating a term and its abbreviation + (Should we used a '''comma for separating a … Should we used a '''comma for separating a term and its abbreviation''' in the text? The SI Brochure frequently does not use a comma. The comma might be added, if it helps to clarify the distinction between the term and its abbreviation. The example “reduced Q fraction, ''Q''r” – the sequence of Q and ''Q''r may be confusing without comma. There will always be examples, where it is not clear, if a comma is needed.l always be examples, where it is not clear, if a comma is needed.)
Multicomponent analysis + (Similarly to the [[least squares method]] … Similarly to the [[least squares method]], '''multicomponent analysis''' makes use of all of the data points of the spectrum in order to analyse the concentration of the component parts of a measured spectrum. To do this, two or more reference spectra are combined using iterative statistical techniques in order to achieve the best fit with the measured spectrum.e the best fit with the measured spectrum.)
Holode + (Small entetic units are counted into the reference system on a balance opposite to the experimental system with the large sample, which in balance contains as many abstract units as the count of entetic units in the reference system.)
Sodium phosphate buffer + (Sodium phosphate buffer, '''Na-PB''', for [[HRR]] with freeze-dried baker´s yeast.)
Spline + (Some [[spectrofluorometer]] … Some [[spectrofluorometer]] or [[spectrophotometer]] software offers the possibility of '''spline''' interpolation of the spectral data points. This makes use of a polynomial (the number of '''spline''' points is entered by the user) to interpolate the curve between the data points.rpolate the curve between the data points.)
Mitochondrial density + (Specific '''mitochondrial density''' is '' … Specific '''mitochondrial density''' is ''DmtE'' = ''mtE''·''mX''-1 [mtEU·kg-1]. If the amount of mitochondria, ''mtE'', is expressed as mitochondrial mass, then ''DmtE'' is the mass fraction of mitochondria in the sample. If ''mtE'' is expressed as mitochondrial volume, ''V''mt, and the mass of sample, ''mX'', is replaced by volume of sample, ''VX'', then ''DmtE'' is the volume fraction of mitochondria in the sample.eplaced by volume of sample, ''VX'', then ''DmtE'' is the volume fraction of mitochondria in the sample.)
Resolution + (Spectral resolution is a measure of the ab … Spectral resolution is a measure of the ability of an instrument to differentiate between two adjacent wavelengths. Two wavelengths are normally considered to be resolved if the minimum detector output signal (trough) between the two peaks is lower than 80 % of the maximum. The resolution of a [[spectrofluorometer]] or [[spectrophotometer]] is dependent on its [[bandwidth]].[[bandwidth]].)
Stop measurement + (Stop data acquisition. The [[DatLab data file]] will be saved automatically.)
Custom-made stoppers + (Stoppers can be custom-made for applications with user-specific sensors according to customer specifications.)
Tartronic acid + (Tartronic acid (hydroxymalonic acid, C3H4O5; molecular weight 120.06) is an inhibitor of [[malic enzyme]].)
Taurine + (Taurine, or 2-Aminoethan sulfonic acid, is … Taurine, or 2-Aminoethan sulfonic acid, is one of the most abundant low-molecular-weight organic constituents in animals and humans. It has a multitude of functions in different types of tissue, one of which is the stabilization of membranes. Because of this and its antioxidative effect, taurine is a component of the respiration media MiR05 and MiR06 to preserve mitochondrial function. MiR06 to preserve mitochondrial function.)
Chinese Society of Mitochondrial Research and Medicine + (The '''Chinese Society of Mitochondrial Research and Medicine''' (Chinese-Mit) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]].)
Crabtree effect + (The '''Crabtree effect''' describes the ob … The '''Crabtree effect''' describes the observation that respiration is frequently inhibited when high concentrations of glucose or fructose are added to the culture medium - a phenomenon observed in numerous cell types, particularly in proliferating cells, not only tumor cells but also bacteria and yeast. The Pasteur effect (suppression of glycolysis by oxygen) is the converse of the Crabtree effect (suppression of respiration by high concentration of glucose or fructose).igh concentration of glucose or fructose).)
Default label + (The '''Default label''' is the system default value for the axis label. These labels are changed automatically, according to the selected channel and unit. To change this label enter a [[Custom label]].)
Directory of Open Access Journals + (The '''Directory of Open Access Journals''' is a free online directory that indexes and provides access to open access peer-reviewed journals.)
Exclusion criteria + (The '''Exclusion criteria''' include factors or characteristics that make the recruited population ineligible for the outcome parameter. With the [[Inclusion criteria]], this factor must be a cofounder for the outcome parameter)
Faraday constant + (The '''Faraday constant''' ''F'' links the … The '''Faraday constant''' ''F'' links the electric charge [C] to amount [mol], and thus relates the [[electrical format]] ''e'' [C] to the [[molar format]] ''n'' [mol]. The Farady constant, ''F'' = ''e''·''N''A = 96 485.33 C/mol, is the product of [[elementary charge]], ''e'' = 1.602176634∙10-19 C/x, and the [[Avogadro constant]], ''N''A = 6.02214076∙1023 x/mol. The dimensionless unit [x] is not explicitely considered by IUPAC.= 6.02214076∙1023 x/mol. The dimensionless unit [x] is not explicitely considered by IUPAC.)
Inclusion criteria + (The '''Inclusion criteria''' are based on … The '''Inclusion criteria''' are based on key features of the target population that the researchers will use to answer their question. These criteria should identify the study population in a consistent, reliable, uniform, and objective manner. With the [[Exclusion criteria]], this factor must be a cofounder for the outcome parametert be a cofounder for the outcome parameter)
International Standard Serial Number + (The '''International Standard Serial Numbe … The '''International Standard Serial Number''', ISSN, is a code used to identify periodical publications, independent of which media are used (print and/or electronic). - [[Bioenergetics Communications]], BEC: [https://portal.issn.org/resource/ISSN/2791-4690 ISSN 2791-4690]rg/resource/ISSN/2791-4690 ISSN 2791-4690])
International System of Units + (The '''International System of Units''' (S … The '''International System of Units''' (SI) is the modern form of the metric system of [[unit]]s for use in all aspects of life, including international trade, manufacturing, security, health and safety, protection of the environment, and in the basic science that underpins all of these. The system of quantities underlying the SI and the equations relating them are based on the present description of nature and are familiar to all scientists, technologists and engineers. The definition of the SI units is established in terms of a set of seven defining constants. The complete system of units can be derived from the fixed values of these defining constants, expressed in the units of the SI. These seven defining constants are the most fundamental feature of the definition of the entire system of units. These particular constants were chosen after having been identified as being the best choice, taking into account the previous definition of the SI, which was based on seven base units, and progress in science (p. 125).e units, and progress in science (p. 125).)
International Union of Pure and Applied Chemistry, IUPAC + (The '''International Union of Pure and App … The '''International Union of Pure and Applied Chemistry''' (IUPAC) celebrated in 2019 the 100th anniversary, which coincided with the [https://iupac.org/united-nations-proclaims-international-year-periodic-table-chemical-elements/ International Year of the Periodic Table of Chemical Elements (IYPT 2019)]. IUPAC {''Quote''} notes that marking Mendeleev's achievement will show how the periodic table is central to connecting cultural, economic, and political dimensions of global society “through a common language” {''end of Quote''} (Horton 2019). 2019 is proclaimed as the [https://iupac.org/united-nations-proclaims-international-year-periodic-table-chemical-elements/ International Year of the Periodic Table of Chemical Elements (IYPT 2019)]. For a '''common language''' in mitochondrial physiology and bioenergetics, the IUPAC ''Green book'' (Cohen et al 2008) is a most valuable resource, which unfortunately is largely neglected in bioenergetics textbooks. Integration of [[ergodynamics |open systems and non-equilibrium thermodynamic]] approaches remains a challenge for developing a common language (Gnaiger 1993; [[BEC 2020.1]]).C 2020.1]]).)
Korean Society of Mitochondrial Research and Medicine + (The '''Korean Society of Mitochondrial Research and Medicine''' (KSMRM) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]].)
MitoFit DOI Data Center + (The '''MitoFit DOI Data Center''' is respo … The '''MitoFit DOI Data Center''' is responsible for the provision of digital identifiers, for the storage and ensuring the persistence of the scientific objects, the provision of access, review process and maintenance of the Metadata, and quality control.ance of the Metadata, and quality control.)
Mitochondrial Physiology Network + (The '''Mitochondrial Physiology Network''' is the on-line Oroboros journal.)
N/NS pathway control ratio + (The '''N/NS [[pathway control ratio]] … The '''N/NS [[pathway control ratio]]''' is obtained when succinate is added to N-linked respiration in a defined coupling state. N and NS are abbreviations for respiration in the [[N-pathway control state]] (with pyruvate, glutamate, malate, or other ETS competent N-linked substrate combinations) and the [[NS-pathway control state]] (N in combination with succinate). NS indicates respiration with a cocktail of substrates supporting the N- and S-pathways.bstrates supporting the N- and S-pathways.)
N/S pathway control ratio + (The '''N/S [[pathway control ratio]] … The '''N/S [[pathway control ratio]]''' is obtained from SUIT protocols when the [[N-pathway control state |N-pathway flux]] and [[S-pathway control state |S-pathway flux]] are measured in the same [[coupling control state]]. The N/S pathway control ratio may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The S-pathway control state may be selected preferentially as reference state, if mitochondria are studied with respect to N-pathway injuries.tudied with respect to N-pathway injuries.)
NS-N pathway control efficiency + (The '''NS-N [[pathway control efficiency]]''', ''j''NS-N = 1-N/NS, expresses the fractional change of flux when succinate is added to the [[N-pathway control state]] in a defined [[coupling-control state]].)
NS-S pathway control efficiency + (The '''NS-S pathway control efficiency''' … The '''NS-S pathway control efficiency''' expresses the relative stimulation of succinate supported respiration (S) by NADH-linked substrates (N), with the [[S-pathway control state]] as the [[background state]] and the [[NS-pathway control state]] as the [[reference state]]. In typical [[SUIT protocol]]s with [[Electron-transfer-pathway state |type N and S substrates]], flux in the [[NS-pathway control state]] NS is inhibited by [[rotenone]] to measure flux in the [[S-pathway control state]], S(Rot) or S. Then the NS-S pathway control efficiency in the ET-coupling state is ''j''(NS-S)''E'' = (NS''E''-S''E'')/NS''E''The NS-S pathway control efficiency expresses the fractional change of flux in a defined [[coupling-control state]] when inhibition by [[rotenone]] is removed from flux under S-pathway control in the presence of a type N substrate combination. Experimentally rotenone Rot is added to the NS-state. The reversed protocol, adding N-substrates to a S-pathway control background does not provide a valid estimation of S-respiration with succinate in the absence of Rot, since [[oxaloacetate]] accumulates as a potent inhibitor of [[succinate dehydrogenase]] CII.[[succinate dehydrogenase]] CII.)
O2k signal line + (The '''O2k signal line''' is underneath th … The '''O2k signal line''' is underneath the [[O2k status line]]. It shows, depending on the [[O2k series]], on the left side the O2k number, the time of the experiment, the oxygen raw signal of each chamber, the [[block temperature]], the [[barometric pressure]], the Peltier power, the recorded amperometric and potentiometric raw signal, the enviromental (room) temperature and the signal from internal sensors recording the humidity and temperature of the electronics. On the right side of the O2k signal line the current [[User code - DatLab|user]], the DatLab version and the [[O2k serial number]] are displayed.[[O2k serial number]] are displayed.)
O2k-Accessory Box + (The '''O2k-Accessory Box''' contains components of the [[POS-Service Kit]] and the [[O2k-Assembly Kit]] and is shipped with the O2k.)
O2k-Assembly Kit + (The '''O2k-Assembly Kit''' is a component … The '''O2k-Assembly Kit''' is a component of the [[Oroboros O2k]], consisting of 2 [[Stirrer-Bar\white PVDF\15x6 mm|PVDF Stirrer-Bars]], 2 [[PEEK]] O2k-Stoppers, [[OroboPOS-Connector]]s for O2k-series A-I and NextGen-O2k series XA (attached to the [[O2k-Main Unit]]) and cables (power supply, USB-connection). Several components of the O2k-Assembly Kit are included in the [[O2k-Accessory Box]] either for shipment or for storage.[[O2k-Accessory Box]] either for shipment or for storage.)
O2k-Fluo Smart-Module + (The '''O2k-Fluo Smart-Module''' is an ampe … The '''O2k-Fluo Smart-Module''' is an amperometric add-on module to the [[Startup_O2k-Respirometer| O2k-Respirometer]], adding a new dimension to high-resolution respirometry. Optical sensors are inserted through the front window of the O2k-glass chambers, for measurement of hydrogen peroxide production (Amplex® UltraRed), ATP production (Magnesium Green™), mt-membrane potential (Safranin, TMRM), Ca2+ (Calcium Green™), and numerous other applications open for O2k-user innovation. ::: » [[MiPNet28.09 O2k-Fluo Smart-Module manual]]et28.09 O2k-Fluo Smart-Module manual]])
O2k-Main Basic + (The '''O2k-Main Basic''' is an integral el … The '''O2k-Main Basic''' is an integral element of the [[O2k-Main Unit]]. The Oroboros O2k Main Basic has the following components:*Stainless-Steel Housing*Switching power supply*Microprocessor for integrated control, A/D converters and data handling*Copper-Block with windows to 2 O2k-Chambers*2 Amperometric OroboPOS Plugs*TIP2k socket, providing the basis for add-on of the [[TIP2k]]*2 Potentiometric Plugs for ion sensitive electrodes (ISE: TPP+, Ca2+; pH), providing the basis for add-on of the [[O2k-MultiSensor]] Modules*2 Amperometric Plugs, providing the basis for add-on of the [[O2k-Fluo LED2-Module]] or NO (H2S) sensors.*USB-Port for connection with DatLab (PC or laptop not included)for connection with DatLab (PC or laptop not included))
O2k-Main Unit + (The '''O2k-Main Unit''' is a component of … The '''O2k-Main Unit''' is a component of the [[O2k-Core]]. The O2k-Main Unit consists of functionally defined, integral elements, the ([[O2k-Main Basic]], [[O2k-Peltier Temperature Control]], two [[O2k-Electromagnetic Stirrer Twin-Control]] units, two [[O2k-Amperometric OroboPOS Twin-Channel]]s, [[O2k-Barometric Pressure Transducer]]), which cannot be obtained separately.[[O2k-Barometric Pressure Transducer]]), which cannot be obtained separately.)
O2k chamber volume calibration + (The '''O2k-chamber volume calibration''' has to be done before getting started with the [[Oroboros O2k]] to guarantee a standard [[chamber volume]] of 2.0 mL.)
O2k-ticket system + (The '''O2k-ticket system''' is a customer … The '''O2k-ticket system''' is a customer support platform based on Zammad. This system automatically attributes an unique Ticket number (which is visible on the subject of your e-mail) to each received customer inquiry. For an easy follow-up, all the related correspondence is collected under this Ticket number. * Contact us: '''[email protected]'''In order to provide a helpful and reliable support regarding your O2k/equipment, we suggest to include in your inquiries:* your affiliation and your O2k-serial number - ''See'': [[O2k_series]]* DLD file(s) with your reported issue accompanied by a brief explanation. issue accompanied by a brief explanation.)
Oxygen sensor test + (The '''O2 sensor te … The '''O2 sensor test''' is an important component of [[MitoPedia: Oroboros QM |Oroboros Quality Management]]. The [[OroboPOS]] test is described in detail in [[MiPNet06.03 POS-calibration-SOP]], is performed after switching on the [[Oroboros O2k]], and is required as a basis of technical service of the instrument.red as a basis of technical service of the instrument.)
OXPHOS International + (The '''OXPHOS International''' web portal is a repository of information useful to scholars studying mitochondria. The site is operated as a private "special interests" community hub.)
Oroboros USB-flash drive + (The '''Oroboros USB-flash drive''' is deli … The '''Oroboros USB-flash drive''' is delivered with the [[Oroboros O2k]]. Copy the folder "Oroboros O2k-Course on HRR" from the '''Oroboros USB-flash drive''' to your computer. This folder contains the DatLab installation program as well as tools to find topics, O2k-manuals and O2k-protocols with corresponding DatLab demo files and templates for training with [[DatLab]].[[DatLab]].)
Q-redox state + (The '''Q-redox state''' reflects the redox … The '''Q-redox state''' reflects the redox status of the [[Q-junction]] in the mitochondrial or chloroplast [[ETS|electron transfer system (ETS)]]. [[Coenzyme Q]] (CoQ or Q, [[ubiquinone]]) is a mobile redox component located centrally in the mitochondrial [[ETS]], while plastoquinones are essential mobile components in the photosynthetic system with a similar function. The Q-redox state depends on the balance between reducing capacities of convergent electron entries from fuel substrates into the Q-junction and oxidative capacities downstream of Q to the electron acceptor oxygen. Therefore, deficiencies in the mitochondrial [[ETS]], originating from e.g. the malfunction of respiratory Complexes, can be detected by measuring the changes of the Q-redox state with respect to the respiratory activity.A three-electrode system was implemented into the NextGen-O2k to monitor the Q-redox state continuously and simultaneously with respiratory oxygen consumption. Added CoQ2 reflects the mitochondrial Q-redox state when equilibrating both with the detecting electrode and the biological sites (e.g. Complexes I, II and III).ical sites (e.g. Complexes I, II and III).)
S/NS pathway control ratio + (The '''S/NS [[pathway control ratio]] … The '''S/NS [[pathway control ratio]]''' is obtained when [[rotenone]] (Rot) is added to the [[NS-pathway control state]] in a defined [[coupling control state]]. The reversed protocol, adding N-type substrates to a [[S-pathway control state]] as the [[background state]] does not provide a valid estimation of S-linked respiration with succinate in the absence of Rot, since [[oxaloacetate]] accumulates as a potent inhibitor of [[succinate dehydrogenase]] (CII).[[succinate dehydrogenase]] (CII).)
SUIT protocol pattern + (The '''SUIT protocol pattern''' describes the type of the sequence of coupling and substrate control steps in a SUIT protocol, which may be liner, orthogonal, or diametral.)
Science Citation Index + (The '''Science Citation Index''' SCI offers bibliographical access to a curated collection of journals across 178 scientific disciplines. The SCI provides gold-standard lists of established journals.)
SUIT protocol library + (The '''Substrate-uncoupler-inhibitor titra … The '''Substrate-uncoupler-inhibitor titration (SUIT) protocol library''' contains a sequential list of SUIT protocols (D001, D002, ..) with links to the specific SUIT pages. Classes of [[SUIT|SUIT protocols]] are explained with coupling and substrate control defined for [[mitochondrial preparations]].[[mitochondrial preparations]].)
Taiwan Society for Mitochondrial Research and Medicine + (The '''Taiwan Society for Mitochondrial Research and Medicine''' (TSMRM) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]].)
USB port + (The '''USB port''' describes the connection between O2k and Computer. With the USB cable connected, select '''USB port''' in the [[Connection window]]. Depending on the O2k series, it is possible to connect with a '''USB port''' or [[Serial port]].)
Abscissa + (The '''abscissa''' is the horizontal axis … The '''abscissa''' is the horizontal axis ''x'' of a rectangular two-dimensional graph with the [[ordinate]] ''y'' as the vertical axis. Values ''X'' are placed horizontally from the origin.See [[Abscissal X/Y regression |Abscissal ''X''/''Y'' regression]].[[Abscissal X/Y regression |Abscissal ''X''/''Y'' regression]].)
Accuracy + (The '''accuracy''' of a method is the degree of agreement between an individual test result generated by the method and the true value.)
Activity + (The '''activity''' (relative activity) is … The '''activity''' (relative activity) is a dimensionless quantity related to the concentration or partial pressure of a dissolved substance. The activity of a dissolved substance B equals the [[concentration]], ''c''B [mol·L-1], at high dilution divided by the unit concentration, ''c''° = 1 mol·L-1: ''a''B = ''c''B/''c''°This simple relationship applies frequently to substances at high dilutions <10 mmol·L-1 (<10 mol·m-3). In general, the concentration of a [[solute]] has to be corrected for the activity coefficient (concentration basis), ''γ''B, ''a''B = ''γ''B·''c''B/''c''°At high dilution, ''γ''B = 1. In general, the relative activity is defined by the [[chemical potential]], ''µ''B ''a''B = exp[(''µ''B-''µ''°)/''RT'']potential]], ''µ''B ''a''B = exp[(''µ''B-''µ''°)/''RT''])
Adenine nucleotide translocase + (The '''adenine nucleotide translocator''', … The '''adenine nucleotide translocator''', ANT, exchanges [[ADP]] for [[ATP]] in an electrogenic antiport across the inner mt-membrane. The ANT is inhibited by [[atractyloside]], [[carboxyatractyloside|carboxyatractyloside]] and [[bongkrekik acid]]. The ANT is a component of the [[phosphorylation system]].[[phosphorylation system]].)
Advantage of preprints + (The '''advantages of preprints''', the excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences are discussed by N Bhalla (2016).)
Aerobic + (The '''aerobic''' state of metabolism is d … The '''aerobic''' state of metabolism is defined by the presence of oxygen (air) and therefore the potential for oxidative reactions (ox) to proceed, particularly in [[oxidative phosphorylation]] (OXPHOS). Aerobic metabolism (with involvement of oxygen) is contrasted with [[anaerobic]] metabolism (without involvement of oxygen): Whereas anaerobic ''metabolism'' may proceed in the absence or presence of oxygen (anoxic or oxic ''conditions''), aerobic ''metabolism'' is restricted to oxic ''conditions''. Below the [[critical oxygen pressure]], aerobic ATP production decreases.[[critical oxygen pressure]], aerobic ATP production decreases.)
Amount of substance + (The '''amount of substance''' ''n'' is a b … The '''amount of substance''' ''n'' is a base physical quantity, and the corresponding SI unit is the [[mole]] [mol]. Amount of substance (sometimes abbreviated as 'amount' or 'chemical amount') is proportional to the number ''N''''X'' of specified elementary entities ''X'', and the universal proportionality constant is the reciprocal value of the [[Avogadro constant]] ([[Bureau International des Poids et Mesures_2019_The International System of Units (SI) |SI]]), ''n''''X'' = ''N''''X''·''N''A-1''n''''X'' contained in a system can change due to internal and external transformations, d''n''''X'' = di''n''''X'' + de''n''''X''In the absence of nuclear reactions, the amount of any atom is conserved, ''e.g.'', for carbon di''n''C = 0. This is different for chemical substances or ionic species which are produced or consumed during the [[advancement]] of a reaction r, :::: [[File:Amount dn.png|100px]]A change in the amount of ''X''''i'', d''n''''i'', in an open system is due to both the internal formation in chemical transformations, dr''n''''i'', and the external transfer, de''n''''i'', across the system boundaries. d''n''''i'' is positive if ''X''''i'' is formed as a product of the reaction within the system. de''n''''i'' is negative if ''X''''i'' flows out of the system and appears as a product in the surroundings ([[Cohen 2008 IUPAC Green Book]]).[Cohen 2008 IUPAC Green Book]]).)
Amplitude + (The '''amplitude''' of the [[absorbance spectrum]] … The '''amplitude''' of the [[absorbance spectrum]] can be described in terms of the [[absorbance]] differences between the characteristic peaks (absorbance maxima) and troughs (absorbance minima) (see [[absorbance spectrum]]) for substances present in the sample.[[absorbance spectrum]]) for substances present in the sample.)
Background state + (The '''background state''' Y (background r … The '''background state''' Y (background rate ''YX'') is the non-activated or inhibited respiratory state at background rate, which is low in relation to the higher rate ''ZX'' in the [[reference state]] Z. The transition from the background state to the reference state is a step change. A [[metabolic control variable]] ''X'' (substrate, activator) is added to the background state to stimulate flux to the level of the reference state. Alternatively, the metabolic control variable ''X'' is an inhibitor, which is present in the background state Y, but absent in the reference state Z. The background state is the baseline of a single step in the definition of the [[flux control efficiency]]. In a sequence of step changes, the common [[baseline state]] is the state of lowest flux in relation to all steps, which can be used as a [[baseline correction]].[[baseline correction]].)
Baseline state + (The '''baseline state''' in a sequence of … The '''baseline state''' in a sequence of step changes is the state of lowest flux in relation to all steps, which can be used as a [[baseline correction]]. Correction for [[residual oxygen consumption]], ROX, is an example where ROX is the baseline state. In a single step, the baseline state is equivalent to the [[background state]].[[background state]].)
Bias + (The '''bias''' is defined as the difference between the mean of the measurements and the reference value. In general, the measuring instrument calibration procedures should focus on establishing and correcting it.)
Block temperature + (The '''block temperature''' of the [[Oroboros O2k]] is the continuously measured temperature of the copper block, housing the two glass chambers of the O2k. The block temperature is recorded by [[DatLab]] as one of the O2k system channels.)
Body mass excess + (The '''body mass excess''', BME, is an ind … The '''body mass excess''', BME, is an index of obesity and as such BME is a lifestyle metric. The BME is a measure of the extent to which your actual [[body mass]], ''M'' [kg/x], deviates from ''M''° [kg/x], which is the reference body mass [kg] per individual [x] without excess body fat in the [[healthy reference population]], HRP. A balanced BME is BME° = 0.0 with a band width of -0.1 towards underweight and +0.2 towards overweight. The BME is linearly related to the [[body fat excess]].body fat excess]].)
Body mass index + (The '''body mass index''', BMI, is the rat … The '''body mass index''', BMI, is the ratio of body mass to height squared (BMI=''M''·''H''-2), recommended by the WHO as a general indicator of underweight (BMI<18.5 kg·m-2), overweight (BMI>25 kg·m-2) and obesity (BMI>30 kg·m-2). Keys et al (1972; see 2014) emphasized that 'the prime criterion must be the relative independence of the index from height'. It is exactly the dependence of the BMI on height - from children to adults, women to men, Caucasians to Asians -, which requires adjustments of BMI-cutoff points. This deficiency is resolved by the [[body mass excess]] relative to the [[healthy reference population]].althy reference population]].)
Body mass + (The '''body mass''' ''M'' is the mass ([[kilogram]] … The '''body mass''' ''M'' is the mass ([[kilogram]] [kg]) of an individual (object) [x] and is expressed in units [kg/x]. Whereas the body weight changes as a function of gravitational force (you are weightless at zero gravity; your floating weight in water is different from your weight in air), your mass is independent of gravitational force, and it is the same in air and water.orce, and it is the same in air and water.)
Bound energy + (The '''bound energy''' change in a closed … The '''bound energy''' change in a closed system is that part of the ''total'' [[energy]] change that is always bound to an exchange of [[heat]], d''B'' = d''U'' - d''A'' [Eq. 1] ∆''B'' = ∆''H'' - ∆''G'' [Eq. 2]The ''free'' energy change (Helmoltz or Gibbs; d''A'' or d''G'') is the ''total'' energy change (total inner energy or enthalpy, d''U'' or d''H'') of a system minus the ''bound'' energy change.Therefore, if a process occurs at [[equilibrium]], when d''G'' = 0 (at constant gas pressure), then d''H'' = d''B'', and at de''W'' = 0 (d''H'' = de''Q'' + de''W''; see [[energy]]) we obtain the definition of the bound energy as the heat change taking place in an equilibrium process (eq), d''B'' = ''T''∙d''S'' = de''Q''eq [Eq. 3]rocess (eq), d''B'' = ''T''∙d''S'' = de''Q''eq [Eq. 3])
Cell count and normalization in HRR + (The '''cell count''' ''N''ce< … The '''cell count''' ''N''ce is the number of cells, expressed in the abstract [[unit]] [x] (1 Mx = 106 x). The ''elementary entity'' cell ''U''ce [x] is the real unit, the 'single individual cell'. A cell count is the multitude or number ''N'' of cells, ''N''ce = ''N''·''U''ce ([[Gnaiger MitoFit Preprints 2020.4]]). Normalization of respiratory rate by cell count yields oxygen [[flow]] ''I''O2 expressed in units [amol·s-1·x-1] (=10-18 mol·s-1·x-1).gt; expressed in units [amol·s-1·x-1] (=10-18 mol·s-1·x-1).)
Chamber volume + (The '''chamber volume''' of the O2k is 2.0 … The '''chamber volume''' of the O2k is 2.0 mL or 0.5 mL of aqueous medium with or without sample, excluding the volume of the stirrer and the volume of the capillary of the stopper (see: [[Cell count and normalization in HRR]]). A modular extension of the O2k, the [[O2k-sV-Module]], was specifically developed to perform high-resolution respirometry with reduced amounts of biological sample, and all components necessary for the smaller operation volume of 0.5 mL.or the smaller operation volume of 0.5 mL.)
Charge number + (The '''charge number''' of an ion ''X'' or … The '''charge number''' of an ion ''X'' or electrochemical reaction with unit stoichiometric number of ''X'' is the [[particle charge]] [C·x-1] divided by the [[elementary charge]] [C·x-1]. The particle charge ''Q''''N''''X'' is the charge per count of ions ''X'' or per ion ''X'' transferred in the reaction as defined in the reaction equation.ns ''X'' or per ion ''X'' transferred in the reaction as defined in the reaction equation.)
Chemical potential + (The '''chemical potential''' of a substanc … The '''chemical potential''' of a substance B, ''µ''B [J/mol], is the partial derivative of Gibbs energy, ''G'' [J], per amount of B, ''n''B [mol], at constant temperature, pressure, and composition other than that of B, ''µ''B = (∂''G''/∂''n''B)''T'',''p'',''nj''≠BThe chemical potential of a [[solute]] in solution is the sum of the standard chemical potential under defined standard conditions and a concentration ([[activity]])-dependent term, ''µ''B = ''µ''B° + ''RT'' ln(''a''B)The standard state for the solute is refered to ideal behaviour at standard concentration, ''c''° = 1 mol/L, exhibiting infinitely diluted solution behaviour [1]. ''µ''B° equals the standard molar Gibbs energy of formation, Δf''G''B° [kJ·mol-1]. The formation process of B is the transformation of the pure constituent elements to one mole of substance B, with all substances in their standard state (the most stable form of the element at 100 kPa (1 bar) at the specified temperature) [2].on of the pure constituent elements to one mole of substance B, with all substances in their standard state (the most stable form of the element at 100 kPa (1 bar) at the specified temperature) [2].)
Comparison of respirometric methods + (The '''comparison of respirometric methods''' provides the basis to evaluate different instrumental platforms and different [[mitochondrial preparations]], as a guide to select the best approach and to critically evaluate published results.)
Critical oxygen pressure + (The '''critical oxygen pressure''', ''p''& … The '''critical oxygen pressure''', ''p''c, is defined as the partial oxygen pressure, ''p''O2, below which [[aerobic]] catabolism (respiration or oxygen consumption) declines significantly. If [[anaerobic]] catabolism is activated simultaneously to compensate for lower aerobic ATP generation, then the '''[[limiting oxygen pressure]]''', ''p''l, is equal to the ''p''c. In many cases, however, the ''p''l is substantially lower than the ''p''c.y cases, however, the ''p''l is substantially lower than the ''p''c.)
Cytochrome c control efficiency + (The '''cytochrome ''c'' control efficiency … The '''cytochrome ''c'' control efficiency''' expresses the control of respiration by externally added [[cytochrome c | cytochrome ''c'']], c, as a fractional change of flux from substrate state CHNO to CHNOc. These fluxes are corrected for ''Rox'' and may be measured in the OXPHOS state or ET state, but not in the LEAK state. In this [[flux control efficiency]], CHNOc is the [[reference state]] with stimulated flux; CHNO is the [[background state]] with CHNO substrates, upon which c is added: ''j''cyt ''c'' = (''J''CHNOc-''J''CHNO)/''J''CHNOc.>CHNOc-''J''CHNO)/''J''CHNOc.)
Data recording interval + (The '''data recording interval''' is the t … The '''data recording interval''' is the time interval at which data is sampled with an instrument. In [[DatLab]] the data recording interval is set in the [[O2k control]] window. The system default value is 2 s. A lower data recording interval is selected for kinetic experiments, and when the volume-specific oxygen flux is high (>300 pmol O2·s-1·ml-1). Technically, the O2k instrument (hardware) measures the sensor signal every 10ms (which is NOT the „data recording interval“). By the given data recording interval from DatLab (software) a discrete number of sensor signal points are taken to calculate an average value in the O2k (e.g. a data recording interval of 2 s can take 200 sensor signal points; a data recording interval of 0.5 s can take 50 sensor signal points). This average value is sent to DatLab and is recorded as a raw data point. However, there is a defined threshold: the O2k does not apply more than 200 sensor signal points to calculate the average for the raw data point. For example a data recording interval of 3 s could take 300 sensor signal points but only the 200 most recent sensor signal points are used for averaging.signal points but only the 200 most recent sensor signal points are used for averaging.)
Dicarboxylate carrier + (The '''dicarboxylate carrier''' is a transporter which catalyses the electroneutral exchange of [[malate]]2- (or [[succinate]]2-) for inorganic [[phosphate]], HPO42-.)
Energy charge + (The '''energy charge''' of the adenylate s … The '''energy charge''' of the adenylate system or adenylate energy charge (AEC) has been defined by Atkinson and Walton (1967) as (ATP + ½ ADP)/(AMP + ADP + ATP). Wheather the AEC is a fundamental metabolic control parameter remains a controversial topic.l parameter remains a controversial topic.)
Ergodynamic efficiency + (The '''ergodynamic efficiency''', ''ε'' (c … The '''ergodynamic efficiency''', ''ε'' (compare [[thermodynamic efficiency]]), is a power ratio between the output power and the (negative) input power of an energetically coupled process. Since [[power]] [W] is the product of a [[flow]] and the conjugated thermodynamic [[force]], the ergodynamic efficiency is the product of an output/input flow ratio and the corresponding force ratio. The efficiency is 0.0 in a fully uncoupled system (zero output flow) or at level flow (zero output force). The maximum efficiency of 1.0 can be reached only in a fully (mechanistically) coupled system at the limit of zero flow at ergodynamic equilibrium. The ergodynamic efficiency of coupling between ATP production (DT phosphorylation) and oxygen consumption is the flux ratio of DT phosphorylation flux and oxygen flux (P»/O2 ratio) multiplied by the corresponding force ratio. Compare with the [[OXPHOS-coupling efficiency]].OXPHOS-coupling efficiency]].)
Extinction coefficient + (The '''extinction coefficient''' (''ε'') of a substance is the [[absorbance]] of a 1 µmolar concentration over a 1 cm pathlength and is wavelength-dependent.)
Gain + (The '''gain''' is an amplification factor applied to an input signal to increase the output signal.)
Glutamate-aspartate carrier + (The '''glutamate-aspartate carrier''' cata … The '''glutamate-aspartate carrier''' catalyzes the electrogenic antiport of glutamate- +H+ for aspartate-. It is an important component of the malate-aspartate shuttle in many mitochondria. Due to the symport of glutamate- + +H+, the glutamate-aspartate antiport is not electroneutal and may be impaired by [[uncoupling]]. [[Aminooxyacetate]] is an [[inhibitor]] of the glutamate-aspartate carrier.[[inhibitor]] of the glutamate-aspartate carrier.)
Height of humans + (The '''height of humans''', ''h'', is give … The '''height of humans''', ''h'', is given in SI units in meters [m]. Humans are countable objects, and the symbol and unit of the number of objects is ''N'' [x]. The average height of ''N'' objects is, ''H'' = ''h''/''N'' [m/x], where ''h'' is the heights of all ''N'' objects measured on top of each other. Therefore, the height per human has the unit [m·x-1] (compare [[body mass]] [kg·x-1]). Without further identifyer, ''H'' is considered as the standing height of a human, measured without shoes, hair ornaments and heavy outer garments., measured without shoes, hair ornaments and heavy outer garments.)
Hexokinase + (The '''hexokinase''' catalyzes the phosphorylation of D-glucose at position 6 by ATP to yield D-glucose 6-phosphate as well as the phosphorylation of many other hexoses like D-fructose, D-mannose, D-glucosamine.)
Limiting oxygen pressure + (The '''limiting oxygen pressure''', ''p''& … The '''limiting oxygen pressure''', ''p''l, is defined as the partial oxygen pressure, ''p''O2, below which [[anaerobic]] catabolism is activated to contribute to total ATP generation. The limiting oxygen pressure, ''p''l, may be substantially lower than the '''[[critical oxygen pressure]]''', ''p''c, below which [[aerobic]] catabolism (respiration or oxygen consumption) declines significantly.[[aerobic]] catabolism (respiration or oxygen consumption) declines significantly.)
Membrane-bound ET pathway + (The '''membrane-bound [[electron transfer pathway]] … The '''membrane-bound [[electron transfer pathway]] (mET pathway)''' consists in mitochondria mainly of [[respiratory complexes]] CI, CII, electron transferring flavoprotein complex (CETF), glycerophosphate dehydrogenase complex (CGpDH), and choline dehydrogenase, with [[convergent electron flow]] at the [[Q-junction]] (Coenzyme Q), and the two downstream respiratory complexes connected by cytochrome ''c'', CIII and CIV, with oxygen as the final electron acceptor. The mET-pathway is the terminal (downstream) module of the mitochondrial [[ET pathway]] and can be isolated from the ET-pathway in [[submitochondrial particles]] (SmtP).[[submitochondrial particles]] (SmtP).)
Meter + (The '''meter''', symbol m, is the SI unit … The '''meter''', symbol m, is the SI unit of the SI base quantity [[length]] ''l''. It is defined by taking the fixed numerical value of the speed of light ''c'' in vacuum to be 299 792 458 when expressed in the unit m·s−1, where the second is defined in terms of the caesium frequency Δ''ν''Cs.in terms of the caesium frequency Δ''ν''Cs.)
Mitochondrial ATP-sensitive K+ channel + (The '''mitochondrial ATP-sensitive K+ channel''' (mtKATP or mitoKATP).)
Mitochondrial free radical theory of aging + (The '''mitochondrial free radical theory o … The '''mitochondrial free radical theory of aging''' goes back to Harman (1956) and ranks among the most popular theories of aging. It is based on postulates which are not unequivocally supported by observation (Bratic, Larsson 2013):(i) Mitochondrial ROS production increases with age caused by progressive mitochondrial dysfunction;(ii) antioxidat capacity declines with age;(iii) mutations of somatic mtDNA accumulate during aging;(iv) a vicious cycle occurs of increased ROS production caused by mtDNA mutations and degenerated mt-function, and due to ROS-induced ROS production.on, and due to ROS-induced ROS production.)
Mitochondrial inner membrane + (The '''mitochondrial inner membrane''' mtI … The '''mitochondrial inner membrane''' mtIM is the structure harboring the membrane-bound [[electron transfer system]] ETS including the respiratory complexes working as [[hydrogen ion pump]]s, the mt-[[phosphorylation system]] including the hydrogen ion pump [[ATP synthase]], several substrate transporters involved in the [[electron transfer pathway]], and a variety of other ion pumps that carry [[proton]] charge (Ca2+, Mg2+). The [[protonmotive force]] is the electrochemical potential difference across the mtIM generated by the [[hydrogen ion pumps]] of the .[[hydrogen ion pumps]] of the .)
Mitochondrial matrix + (The '''mitochondrial matrix''' (mt-matrix) … The '''mitochondrial matrix''' (mt-matrix) is enclosed by the mt-inner membrane mtIM. The terms mitochondrial matrix space or mitochondrial lumen are used synonymously. The mt-matrix contains the enzymes of the [[tricarboxylic acid cycle]], [[fatty acid oxidation]] and a variety of enzymes that have cytosolic counterparts (e.g. [[glutamate dehydrogenase]], [[malic enzyme]]). Metabolite concentrations, such as the concentrations of fuel substrates, adenylates (ATP, ADP, AMP) and redox systems (NADH), can be very different in the mt-matrix, the mt-intermembrane space, and the cytosol. The finestructure of the gel-like mt-matrix is subject of current research. mt-matrix is subject of current research.)
Mitochondrial membrane potential + (The '''mitochondrial membrane potential''' … The '''mitochondrial membrane potential''' difference, mtMP or Δ''Ψ''p+ = Δel''F''''e''p+, is the electric part of the protonmotive [[force]], Δp = Δm''F''''e''H+.:::: Δel''F''''e''p+ = Δm''F''''e''H+ - Δd''F''''e''H+:::: Δ''Ψ''p+ = Δp - Δ''µ''H+·(''z''H+·''F'')-1Δ''Ψ''p+ is the potential difference across the mitochondrial inner membrane (mtIM), expressed in the electric unit of volt [V]. Electric force of the mitochondrial membrane potential is the electric energy change per ‘motive’ charge or per charge moved across the transmembrane potential difference, with the number of ‘motive’ charges expressed in the unit coulomb [C].t;p+ is the potential difference across the mitochondrial inner membrane (mtIM), expressed in the electric unit of volt [V]. Electric force of the mitochondrial membrane potential is the electric energy change per ‘motive’ charge or per charge moved across the transmembrane potential difference, with the number of ‘motive’ charges expressed in the unit coulomb [C].)
Mitochondrial outer membrane + (The '''mitochondrial outer membrane''' is … The '''mitochondrial outer membrane''' is the incapsulating membrane which is osmotically not active and contains the cytochrome ''b''5 enzyme similar to that found in the endoplasmatic reticulum, the translocases of the outer membrane, monoaminooxidase, the palmitoyl-CoA synthetase and carnytil-CoA transferase 1.lmitoyl-CoA synthetase and carnytil-CoA transferase 1.)
Motive unit + (The '''motive unit''' [MU] is the variable … The '''motive unit''' [MU] is the variable SI unit in which the [[motive entity]] (transformant) of a transformation is expressed, which depends on the energy transformation under study and on the chosen [[format]]. Fundamental MU for electrochemical transformations are:* MU = x, for the particle or molecular format, ''N''* MU = mol, for the chemical or molar format, ''n''* MU = C, for the electrical format, ''e''; For the [[protonmotive force]] the motive entity is the proton with charge number ''z''=1. The protonmotive force is expressed in the electrical or molar format with MU J/C=V or J/mol=Jol, respectively. The conjugated flows, ''I'', are expressed in corresponding electrical or molar formats, C/s = A or mol/s, respectively.The [[charge number]], ''z'', has to be considered in the conversion of motive units (compare Table below), if a change not only of units but a transition between the entity [[elementary charge]] and an entity with charge number different from unity is involved (''e.g.'', O2 with ''z''=4 in a redox reaction). The ratio of elementary charges per reacting O2 molecule (''z''O2=4) is multiplied by the elementary charge (''e'', coulombs per proton), which yields coulombs per O2 [C∙x-1]. This in turn is multiplied with the [[Avogadro constant]], ''N''A (O2 molecules per mole O2 [x∙mol-1]), thus obtaining for ''zeN''A the ratio of elementary charges [C] per amount of O2 [mol-1]. The conversion factor for O2 is 385.94132 C∙mmol-1., thus obtaining for ''zeN''A the ratio of elementary charges [C] per amount of O2 [mol-1]. The conversion factor for O2 is 385.94132 C∙mmol-1.)
Ordinate + (The '''ordinate''' is the vertical axis ''y'' of a rectangular two-dimensional graph with the [[abscissa]] ''x'' as the horizontal axis. Values ''Y'' are placed vertically from the origin. See [[Ordinary Y/X regression |Ordinary ''Y''/''X'' regression]].)
Oxycaloric equivalent + (The '''oxycaloric equivalent''' is the the … The '''oxycaloric equivalent''' is the theoretically derived enthalpy change of the oxidative catabolic reactions per amount of oxygen respired, Deltak''H''O2, ranging from -430 to -480 kJ/mol O2. The oxycaloric equivalent is used in [[indirect calorimetry]] to calculate the theoretically expected metabolic heat flux from the respirometrically measured metabolic oxygen flux. [[Calorespirometric ratio|Calorimetric/respirometric ratios]] (CR ratios; heat/oxygen flux ratios) are experimentally determined by [[calorespirometry]]. A CR ratio more exothermic than the oxycaloric equivalent of -480 kJ/mol indicates the simultaneous involvement of aerobic and anaerobic mechanisms of energy metabolism.ltaneous involvement of aerobic and anaerobic mechanisms of energy metabolism.)
Oxygen signal + (The '''oxygen signal''' of the [[Oroboros O2k]] … The '''oxygen signal''' of the [[Oroboros O2k]] is transmitted from the electrochemical polarographic oxygen sensor ([[OroboPOS]]) for each of the two O2k-chambers to [[DatLab]]. The primary signal is a current [µA] which is converted into a voltage [V] (raw signal), and calibrated in SI units for amount of substance concentration [µmol·L-1 or µM]. For technical reasons, the raw signal is given in [V] (DatLab 7 and previous) or [µA] (DatLab 8). The value of the raw signal is the same, independent of the displayed unit ([V] or [µA]). In the following sections, only [µA] is used for information on the raw signal, but the same values in [V] apply for the raw signal when using DL7 or previous versions.or the raw signal when using DL7 or previous versions.)
Oxygen solubility factor + (The '''oxygen solubility factor''' of the … The '''oxygen solubility factor''' of the incubation medium, ''F''M, expresses the effect of the salt concentration on [[oxygen solubility]] relative to pure water. In mitochondrial respiration medium [[MiR05]], [[MiR05-Kit]] and [[MiR06]], ''F''M is 0.92 (determined at 30 and 37 °C) and in culture media is 0.89 (at 37 °C). ''F''M varies depending on the temperature and composition of the medium. To determine the FM based on the oxygen concentration, specific methods and equipment are needed (see references Rasmussen HN, Rasmussen UF 2003 in [https://wiki.oroboros.at/index.php/MiPNet06.03_POS-calibration-SOP MiPNet06.03]). For other media, ''F''M may be estimated using Table 4 in [https://wiki.oroboros.at/index.php/MiPNet06.03_POS-calibration-SOP MiPNet06.03]. For this purpose KCl based media can be described as "seawater" of varying salinity. The original data on sucrose and KCl-media (Reynafarje et al 1985), however, have been critizesed as artefacts and the ''F''M of 0.92 is suggested in the temperature range of 10 °C to 40 °C as for MiR05.M of 0.92 is suggested in the temperature range of 10 °C to 40 °C as for MiR05.)
Oxygen solubility + (The '''oxygen solubility''', ''S''<sub& … The '''oxygen solubility''', ''S''O2 [µM/kPa] = [(µmol·L-1)/kPa], expresses the oxygen concentration in solution in equilibrium with the [[oxygen pressure]] in a gas phase, as a function of temperature and composition of the solution. The inverse of oxygen solubility is related to the [[activity]] of dissolved oxygen. The oxygen solubility in solution, ''S''O2(aq), depends on temperature and the concentrations of solutes in solution, whereas the dissolved oxygen concentration at equilibrium with air, ''c''O2*(aq), depends on ''S''O2(aq), barometric pressure and temperature. ''S''O2(aq) in pure water is 10.56 µM/kPa at 37 °C and 12.56 µM/kPa at 25 °C. At standard [[barometric pressure]] (100 kPa), ''c''O2*(aq) is 207.3 µM at 37 °C (19.6 kPa partial oxygen pressure) or 254.7 µM at 25 °C (20.3 kPa partial oxygen pressure). In [[MiR05]] and serum, the corresponding saturation concentrations are lower due to the [[oxygen solubility factor]]: 191 and 184 µM at 37 °C or 234 and 227 µM at 25 °C.lubility factor]]: 191 and 184 µM at 37 °C or 234 and 227 µM at 25 °C.)
PH + (The '''pH value''' or pH is the negative o … The '''pH value''' or pH is the negative of the base 10 logarithm of the [[activity]] of [[proton]]s (hydrogen ions, H+). A [[pH electrode]] reports the pH and is sensitive to the activity of H+. In dilute solutions, the hydrogen ion activity is approximately equal to the hydrogen ion [[concentration]]. The symbol pH stems from the term ''potentia hydrogenii''.[[concentration]]. The symbol pH stems from the term ''potentia hydrogenii''.)
Partial oxygen pressure + (The '''partial oxygen pressure''' ''p''< … The '''partial oxygen pressure''' ''p''O2 [kPa] is the contribution of the O2 gas pressure to the total gas pressure. According to the gas law, the partial oxygen pressure is ''p''O2(g) = ''n''O2(g)·''V''·''RT'', where the [[concentration]] is ''c''O2(g) = ''n''O2(g)·''V''-1 [mol·m-3], ''R'' is the [[gas constant]], and ''T'' is the absolute temperature, and ''RT'' is expressed in units of chemical force [J·mol-1]. In aqueous solutions at equilibrium with a gas phase, the partial O2 pressures are equal in the aqueous phase (aq) and gas phase (g), ''p''O2(aq) = ''p''O2(g) at total [[pressure]]s where the partial pressure equals the fugacity. The O2 concentration in the aqueous phase, however, is much lower than in the gas phase, due to the low [[oxygen solubility]] in water. The activity of dissolved O2 is expressed by the ''p''O2, where the [[solubility]] can be seen as an activity coefficient.ubility]] can be seen as an activity coefficient.)
Particle charge + (The '''particle charge''' ''QN& … The '''particle charge''' ''QNX'' (''QNX'') or charge per elementary entity is the [[charge]] ''Q''el''X'' [C] carried by ions of type ''X'' divided by the count ''NX'' [x]. The particle charge per proton is the [[elementary charge]] or proton charge ''e''.[[elementary charge]] or proton charge ''e''.)
Pascal + (The '''pascal''' [Pa] is the SI unit for [[pressure]] … The '''pascal''' [Pa] is the SI unit for [[pressure]]. [Pa] = [J·m-3] = [N·m-2] = [m-1·kg·s-2].The standard pressure is 100 kPa = 1 bar (105 Pa; 1 kPa = 1000 Pa). Prior to 1982 the standard pressure has been defined as 101.325 kPa or 1 standard atmosphere (1 atm = 760 mmHg).982 the standard pressure has been defined as 101.325 kPa or 1 standard atmosphere (1 atm = 760 mmHg).)
Phosphate carrier + (The '''phosphate carrier''' (PiC) is a pro … The '''phosphate carrier''' (PiC) is a proton/phosphate symporter which transports negatively charged [[inorganic phosphate]] across the inner mt-membrane. The transport can be described either as symport of H+ with Pi, or antiport of hydroxide anion against Pi. The phosphate carrier is a component of the [[phosphorylation system]].[[phosphorylation system]].)
Primary sample + (The '''primary sample''' or '''specimen''' … The '''primary sample''' or '''specimen''' is a set of one or more parts initially taken from an object. In some countries, the term “specimen” is used instead of primary sample (or a subsample of it), which is the sample prepared for sending to, or as received by, the laboratory and which is intended for examination.ory and which is intended for examination.)
Protonmotive force + (The '''protonmotive force''' ∆m … The '''protonmotive force''' ∆m''F''H+ is known as Δp in Peter Mitchell’s chemiosmotic theory [1], which establishes the link between electric and chemical components of energy transformation and coupling in [[oxidative phosphorylation]]. The unifying concept of the ''pmF'' ranks among the most fundamental theories in biology. As such, it provides the framework for developing a consistent theory and nomenclature for mitochondrial physiology and bioenergetics. The protonmotive force is not a vector force as defined in physics. This conflict is resolved by the generalized formulation of isomorphic, compartmental [[force]]s, ∆tr''F'', in energy (exergy) transformations [2]. Protonmotive means that there is a potential for the movement of protons, and force is a measure of the potential for motion.The ''pmF'' is generated in [[oxidative phosphorylation]] by oxidation of reduced fuel substrates and reduction of O2 to H2O, driving the coupled proton translocation from the mt-matrix space across the mitochondrial inner membrane (mtIM) through the proton pumps of the [[electron transfer pathway]] (ETS), which are known as respiratory Complexes CI, CIII and CIV. ∆m''F''H+ consists of two partial isomorphic forces: (''1'') The chemical part, ∆d''F''H+, relates to the diffusion (d) of uncharged particles and contains the chemical potential difference§ in H+, ∆''µ''H+, which is proportional to the pH difference, ∆pH. (''2'') The electric part, ∆el''F''p+ (corresponding numerically to ∆''Ψ'')§, is the electric potential difference§, which is not specific for H+ and can, therefore, be measured by the distribution of any permeable cation equilibrating between the negative (matrix) and positive (external) compartment. Motion is relative and not absolute (Principle of Galilean Relativity); likewise there is no absolute potential, but isomorphic forces are stoichiometric potential differences§.The total motive force (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆m''F''H+. Reading this symbol by starting with the proton, it can be seen as ''pmF'', or the subscript m (motive) can be remembered by the name of Mitchell, ∆m''F''H+ = ∆d''F''H+ + ∆el''F''p+With classical symbols, this equation contains the [[Faraday constant]], ''F'', multiplied implicitly by the charge number of the proton (''z''H+ = 1), and has the form [1] ∆p = ∆''µ''H+∙''F''-1 + ∆''Ψ''A partial electric force of 0.2 V in the electrical [[format]], ∆el''F''''e''H+''a'', is 19 kJ∙mol-1 H+''a'' in the molar format, ∆el''F''''n''p+''a''. For 1 unit of ∆pH, the partial chemical force changes by -5.9 kJ∙mol-1 in the molar format, ∆d''F''''n''H+''a'', and by 0.06 V in the electrical format, ∆d''F''''e''H+''a''. Considering a driving force of -470 kJ∙mol-1 O2 for oxidation, the thermodynamic limit of the H+''a''/O2 ratio is reached at a value of 470/19 = 24, compared to the mechanistic stoichiometry of 20 for the [[N-pathway]] with three coupling sites.)
Protonmotive pressure + (The '''protonmotive pressure''', ∆<sub& … The '''protonmotive pressure''', ∆m''Π''H+ or ''pmP'' [kPa], is an extension of Peter Mitchell’s concept of the [[protonmotive force]] ''pmF'', based on Fick’s law of diffusion and Einstein’s diffusion equation, accounting for osmotic pressure (corresponding to the diffusion term in the ''pmF'') and electric pressure (the electric term or membrane potential in the ''pmF''). The linearity of the generalized flow-pressure relationship explains the non-ohmic flow-force dependence in the proton leak rate as a function of membrane potential.The total motive pressure (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆m''Π''H+, ∆m''Π''H+ = ∆d''Π''H+ + ∆el''Π''p+ub>''Π''H+ = ∆d''Π''H+ + ∆el''Π''p+)
Raw signal of the oxygen sensor + (The '''raw signal''' of the polarographic … The '''raw signal''' of the polarographic oxygen sensor is the [[current]] ''I''el [µA], 1 µA = 10-6 C·s-1, (DatLab 8) or the electric potential difference ([[voltage]]) [V], 1 V = 1 J·C-1, obtained after a current-to-voltage conversion in the O2k (DatLab 7 and previous versions).btained after a current-to-voltage conversion in the O2k (DatLab 7 and previous versions).)
Reference state + (The '''reference state''' Z (reference rat … The '''reference state''' Z (reference rate ''ZX'') is the respiratory state with high flux in relation to the [[background state]] Y with low background flux ''YX''. The transition between the background state and the reference state is a step brought about by a [[metabolic control variable]] ''X''. If ''X'' stimulates flux (ADP, fuel substrate), it is present in the reference state but absent in the background state. If ''X'' is an inhibitor of flux, it is absent in the reference state but present in the background state. The reference state is specific for a single step to define the [[flux control efficiency]]. In contrast, in a sequence of multiple steps, the common reference state is frequently taken as the state with the highest flux in the entire sequence, as used in the definition of the [[flux control ratio]].[[flux control ratio]].)
Respiratory acceptor control ratio + (The '''respiratory acceptor control ratio' … The '''respiratory acceptor control ratio''' (''RCR'') is defined as [[State 3]]/[[State 4]] [1]. If State 3 is measured at saturating [ADP], ''RCR'' is the inverse of the OXPHOS control ratio, ''[[L/P]]'' (when State 3 is equivalent to the OXPHOS state, ''P''). ''RCR'' is directly but non-linearly related to the [[P-L control efficiency |''P-L'' control efficiency]], ''j''''P-L'' = 1-''L/P'', with boundaries from 0.0 to 1.0. In contrast, ''RCR'' ranges from 1.0 to infinity, which needs to be considered when performing statistical analyses. In living cells, the term ''RCR'' has been used for the ratio [[State 3u]]/[[State 4o]], i.e. for the inverse ''[[L/E]]'' ratio [2,3]. Then for conceptual and statistical reasons, ''RCR'' should be replaced by the [[E-L coupling efficiency |''E-L'' coupling efficiency]], 1-''L/E'' [4].[[E-L coupling efficiency |''E-L'' coupling efficiency]], 1-''L/E'' [4].)
Signal-to-noise ratio + (The '''signal to noise ratio''' is the ratio of the power of the signal to that of the noise. For example, in [[fluorimetry]] it would be the ratio of the square of the [[fluorescence]] intensity to the square of the intensity of the background noise.)
Slit width + (The '''slit width''' determines the amount of light entering the [[spectrofluorometer]] or [[spectrophotometer]]. A larger slit reduces the [[signal-to-noise ratio]] but reduces the wavelength [[resolution]].)
Solubility + (The '''solubility''' of a gas, ''S''G, is defined as concentration divided by partial pressure, ''S''G = ''c''G·''p''G-1.)
SUIT reference protocol + (The '''substrate-uncoupler-inhibitor titra … The '''substrate-uncoupler-inhibitor titration ([[SUIT]]) reference protocol''', SUIT RP, provides a common baseline for comparison of mitochondrial respiratory control in a large variety of species, tissues and cell types, mt-preparations and laboratories, for establishing a database on comparative mitochondrial phyisology. The SUIT RP consists of two [[harmonized SUIT protocols]] ([[SUIT-001]] - RP1 and [[SUIT-002]] - RP2). These are coordinated such that they can be statistically evaluated as replicate measurements of [[cross-linked respiratory states]], while additional information is obtained when the two protocols are conducted in parallel. Therefore, these harmonized SUIT protocols are complementary with their focus on specific respiratory coupling and pathway control aspects, extending previous strategies for respirometrc OXPHOS analysis.: [[SUIT-001]] (RP1): 1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10Tm;11Azd: [[SUIT-002]] (RP2): 1D;2OctM;2c;3P;4G;5S;6Gp;7U;8Rot;9Ama;10Tm;11AzdtM;2c;3P;4G;5S;6Gp;7U;8Rot;9Ama;10Tm;11Azd)
Mitochondrial transcription factor A + (The '''transcription factor A''' is a gene … The '''transcription factor A''' is a gene that encodes a mitochondrial transcription factor that is a key activator of mitochondrial transcription as well as a participant in mitochondrial genome replication. TFAM is downstream of [[Peroxisome proliferator-activated receptor gamma coactivator 1-alpha|PGC-1alpha]].[[Peroxisome proliferator-activated receptor gamma coactivator 1-alpha|PGC-1alpha]].)
Tricarboxylate carrier + (The '''tricarboxylate carrier''' in the inner mt-membrane exchanges malate2- for citrate3- or isocitrate3-, with co-transport of H+.)
Tricarboxylic acid cycle + (The '''tricarboxylic acid (TCA) cycle''' i … The '''tricarboxylic acid (TCA) cycle''' is a system of enzymes in the mitochondrial matrix arranged in a cyclic metabolic structure, including dehydrogenases that converge in the NADH pool and [[succinate dehydrogenase]] (on the inner side of the inner mt-membrane) for entry into the membrane-bound ET pathway [[Membrane-bound ET pathway|mET pathway]]. [[Citrate synthase]] is a marker enzyme of the TCA cycle, at the gateway into the cycle from [[pyruvate]] via [[acetyl-CoA]]. It is thus the major module of the [[Electron transfer pathway]], upstream of the inner [[Membrane-bound ET pathway|Membrane-bound ET pathway]] (mET-pathway) and downstream of the [[Mitochondrial outer membrane|outer mt-membrane]]. Sections of TCA cycle are required for [[fatty acid oxidation]] (FAO, β-oxidation). [[Anaplerosis|Anaplerotic reactions]] fuel the TCA cycle with other intermediary metabolites. In the cell, the TCA cycle serves also biosynthetic functions by metabolite export from the matrix into the cytosol.e export from the matrix into the cytosol.)
Uncoupling-control ratio + (The '''uncoupling-control ratio''' UCR is … The '''uncoupling-control ratio''' UCR is the ratio of ET-pathway/ROUTINE-respiration (''E/R'') in living cells, evaluated by careful [[uncoupler]] titrations ([[Steinlechner-Maran 1996 Am J Physiol Cell Physiol|Steinlechner et al 1996]]). Compare [[ROUTINE-control ratio]] (''R/E'') [[Gnaiger 2008 POS|(Gnaiger 2008)]].[[Gnaiger 2008 POS|(Gnaiger 2008)]].)
Journal volume + (The '''volume''' of a journal or periodica … The '''volume''' of a journal or periodical is a number, which in many cases indicates the sequential number of years the journal has been published. Alternatively, the volume number may indicate the current year, independent of the year in which the journal published its first volume. A volume may be subdivided into [[Journal issue |issues]].[[Journal issue |issues]].)
Wet mass + (The '''wet mass''' of a tissue or biological sample, obtained after blotting the sample to remove an arbitrary amount of water adhering externally to the sample.)
Permeability transition pore + (The (mitochondrial, mt) permeability trans … The (mitochondrial, mt) permeability transition pore (PTP) is an unspecific pore presumed to involve components of both the inner and outer mt membrane which upon opening induces a massive increase of the inner mt membrane permeability for solutes up to 1.5 kDa. It is crucially involved in cell death induction in response to, among other stimuli, radical stress and/or calcium overload and may cause necrosis or apoptosis. It plays an important role in neurodegenerative diseases, cardiac ischemia-reperfusion injury and possibly various other diseases. Previously considered essential molecular constituents such as the voltage-dependent anion channel (VDAC), the adenine nucleotide translocator (ANT) and cyclophilin D (CypD) have all been shown to be important regulators of mtPTP opening, but the molecular entities actually forming the pore are still unknown at present. The opening of the pore can be prevented using [[cyclosporin A]], a compound that binds cyclophilin D avoiding the formation of the pore. In respirometry, mtPTP opening may be observed as a sudden decrease of respiration of isolated mitochondria ([[Hansson 2010 J Biol Chem]]).[[Hansson 2010 J Biol Chem]]).)
Search for defective O2k components + (The 2-chamber design of the O2k helps to '''search for defective O2k components''', by switching components linked to O2k chambers A and B between sides A and B.)