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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)

(DatLab-Upgrading to DatLab 6: including free follow-up updates for DatLa)

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]].)