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List of results

Hydroxylamine + ('''Hydroxylamine''' is an inhibitor of [[catalase]].)

Hyperoxia + ('''Hyperoxia''' is defined as environmenta … '''Hyperoxia''' is defined as environmental oxygen pressure above the [[normoxic]] reference level. Cellular and intracellular hyperoxia is imposed on isolated cells and isolated mitochondria at air-level oxygen pressures which are higher compared to cellular and intracellular oxygen pressures under tissue conditions in vivo. Hyperoxic conditions may impose oxidative stress and may increase maximum aerobic performance. may increase maximum aerobic performance.)
Hyperthermia + ('''Hyperthermia''' in [[endothermy | endotherms]] … '''Hyperthermia''' in [[endothermy | endotherms]] is a state of stressful up to lethal elevated body core temperature. In humans, the limit of hyperthermia (fever) is considered as >38.3 °C, compared to [[normothermia]] at a body temperature of 36.5 to 37.5 °C.[normothermia]] at a body temperature of 36.5 to 37.5 °C.)
Hyphenation + ('''Hyphenation''' is used to connect two w … '''Hyphenation''' is used to connect two words (compound words) or two parts of a word to clarify the meaning of a sentence. The same two words may be hyphenated or not depending on context. Hyphenation may present a problem when searching for a term such as '[[Steady state]]'. It is helpful to write 'steady-state measurement', to clarify that the measurement is performed at steady state, rather than implying that a state measurement is steady. But this does not imply that hyphenation is applied to the 'measurement performed at steady state'. Thus, the key word is '[[steady state]]'. Compound adjectives should be hyphenated (steady-state measurement), but if the compound adjective follows the term (measurement at steady state), hyphenation does not add any information and should be avoided. Find more examples and guidelines in the [https://www.grammarly.com/blog/hyphen/ grammarly blog on Hyphen] and in [https://apastyle.apa.org/learn/faqs/when-use-hyphen apastyle.apa.org].rn/faqs/when-use-hyphen apastyle.apa.org].)
Hypothermia + ('''Hypothermia''' in [[endothermy | endotherms]] … '''Hypothermia''' in [[endothermy | endotherms]] is a state of stressful up to lethal low body core temperature. In humans, the limit of hypothermia is considered as 35 °C, compared to [[normothermia]] at a body temperature of 36.5 to 37.5 °C. Hypothermia is classified as mild (32–35 °C), moderate (28–32 °C), severe (20–28 °C), and profound (<20 °C). severe (20–28 °C), and profound (<20 °C).)
Hypoxia + ('''Hypoxia''' (hypox) is defined in respir … '''Hypoxia''' (hypox) is defined in respiratory physiology as the state when insufficient O2 is available for respiration, compared to ''environmental'' hypoxia defined as environmental oxygen pressures below the [[normoxic]] reference level. Three major categories of hypoxia are (''1'') environmental hypoxia, (''2'') physiological tissue hypoxia in hyperactivated states (e.g. at ''V''O2max) with intracellular oxygen demand/supply balance at steady state in tissues at environmental normoxia, compared to tissue normoxia in physiologically balanced states, and (''3'') pathological tissue hypoxia including ischemia and stroke, anaemia, chronic heart disease, chronic obstructive pulmonary disease, severe COVID-19, and obstructive sleep apnea. Pathological hypoxia leads to tissue hypoxia and heterogenous intracellular anoxia. Clinical oxygen treatment ('environmental hyperoxia') may not or only partially overcome pathological tissue hypoxia.al hyperoxia') may not or only partially overcome pathological tissue hypoxia.)
ISO 10012:2003 Measurement management systems + ('''ISO 10012:2003 Measurement management s … '''ISO 10012:2003 Measurement management systems — Requirements for measurement processes and measuring equipment''': An effective measurement management system ensures that measuring equipment and measurement processes are fit for their intended use and is important in achieving product quality objectives and managing the risk of incorrect measurement results. The objective of a measurement management system is to manage the risk that measuring equipment and measurement processes could produce incorrect results affecting the quality of an organization’s product. The methods used for the measurement management system range from basic equipment verification to the application of statistical techniques in the measurement process control.niques in the measurement process control.)
ISO 13528:2015 Statistical methods for use in proficiency testing by interlaboratory comparison + ('''ISO 13528:2015 Statistical methods for … '''ISO 13528:2015 Statistical methods for use in proficiency testing by interlaboratory comparison''': Proficiency testing involves the use of interlaboratory comparisons to determine the performance of participants (which may be laboratories, inspection bodies, or individuals) for specific tests or measurements, and to monitor their continuing performance. There are a number of typical purposes of proficiency testing [[ISO/IEC 17043 General requirements for proficiency testing |ISO/IEC 17043:2010]]. These include the evaluation of laboratory performance, the identification of problems in laboratories, establishing effectiveness and comparability of test or measurement methods, the provision of additional confidence to laboratory customers, validation of uncertainty claims, and the education of participating laboratories. The statistical design and analytical techniques applied must be appropriate for the stated purpose(s). be appropriate for the stated purpose(s).)
ISO 15189:2012 Medical laboratories — Particular requirements for quality and competence + ('''ISO 15189:2012 Medical laboratories — P … '''ISO 15189:2012 Medical laboratories — Particular requirements for quality and competence''': This International Standard is for use by medical laboratories in developing their quality management systems and assessing their own competence, and for use by accreditation bodies in confirming or recognising the competence of medical laboratories. While this International Standard is intended for use throughout the currently recognised disciplines of medical laboratory services, those working in other services and disciplines could also find it useful and appropriate.could also find it useful and appropriate.)
ISO 17511:2003 In vitro diagnostic medical devices + ('''ISO 17511:2003 In vitro diagnostic medi … '''ISO 17511:2003 In vitro diagnostic medical devices -- Measurement of quantities in biological samples -- Metrological traceability of values assigned to calibrators and control materials''': For measurements of quantities in laboratory medicine, it is essential that the quantity is adequately defined and that the results reported to the physicians or other health care personel and patients are adequately accurate (true and precise) to allow correct medical interpretation and comparability over time and space.ion and comparability over time and space.)
ISO 9001:2015 Quality management systems - requirements + ('''ISO 9001:2015 Quality management system … '''ISO 9001:2015 Quality management systems - requirements''': The adoption of a quality management system is a strategic decision for an organization that can help to improve its overall performance and provide a sound basis for sustainable development initiatives. Consistently meeting requirements and addressing future needs and expectations poses a challenge for organizations in an increasingly dynamic and complex environment. To achieve this objective, the organization might find it necessary to adopt various forms of improvement in addition to correction and continual improvement, such as breakthrough change, innovation and re-organization.gh change, innovation and re-organization.)
ISO/IEC 17025:2005 Competence of testing and calibration laboratories + ('''ISO/IEC 17025:2005 General requirements … '''ISO/IEC 17025:2005 General requirements for the competence of testing and calibration laboratories''': The use of this International Standard will facilitate cooperation between laboratories and other bodies, and assist in the exchange of information and experience, and in the harmonization of standards and procedures. This International Standard specifies the general requirements for the competence to carry out tests and/or calibrations, including sampling. It covers testing and calibration performed using standard methods, non-standard methods, and laboratory-developed methods.methods, and laboratory-developed methods.)
ISO/IEC 17043:2010 General requirements for proficiency testing + ('''ISO/IEC 17043:2010 Conformity assessmen … '''ISO/IEC 17043:2010 Conformity assessment — General requirements for proficiency testing''': The use of interlaboratory comparisons is increasing internationally. This International Standard provides a consistent basis to determine the competence of organizations that provide proficiency testing.izations that provide proficiency testing.)
Iconic symbols + ('''Iconic symbols''' are used in [[ergodynamics]] … '''Iconic symbols''' are used in [[ergodynamics]] to indicate more explicitely — compared to standard SI or IUPAC symbols — the quantity represented and some boundary conditions. This is particularly the case in normalized quantities (ratios of quantities). Iconic (or canonical) symbols help to clarify the meaning, are based on SI and IUPAC symbols as far as possible, and may be translated into more commonly used, practical symbols. Several ambiguities in SI and IUPAC symbols are eliminated by the systematic structure of iconic symbols, but it may be impossible to avoid all ambiguities, particulary when long (canonical) symbols are abbreviated in a particular context. Clarity is improved always by showing the unit of a quantity together with the symbol of the quantity. Iconic symbols cannot be identical with IUPAC symbols when a different definition is used — this would add to the confusion. For example, the IUPAC symbols ''n''B [mol] and ''V''B [m3] denote amount and volume of B. Consequently, it should be expected, that the symbol ''Q''B indicates charge of B [C]. However, the IUPAC symbol ''Q''B is used for particle charge per ion B [C·x-1]. This prohibits a consistent definition of ''Q''B as a potential iconic symbol for charge carried by a given quantity of ions B with unit [C], instead of particle charge per ion B with unit [C·x-1]. Hence, the conventional ambigous system forces compatible iconic symbols to be more complicated, using ''Q''elB [C] and ''Q''''N''B [C·x-1] to distinguish charge of B from charge per elementary B. ''Q''''n''B [C·mol-1] is charge per molar amount of B.'B [C·x-1] to distinguish charge of B from charge per elementary B. ''Q''''n''B [C·mol-1] is charge per molar amount of B.)
Impact factor + ('''Impact factor''' is a measure of a scie … '''Impact factor''' is a measure of a scientific journal's citations per publication. The Journal Citation Reports, maintained by Clarivate Analytics, provides the calculated impact factors. The IF is frequently used as an indicator of a journal's importance or prestige, which is nowadays increasingly contested. which is nowadays increasingly contested.)
Inorganic phosphate + ('''Inorgnic phosphate''' (Pi) is a salt of phosphoric acid. In solution near physiological pH, the species HPO42- and H2PO4- dominate. ''See also'': [[Phosphate carrier]] (Pic).)
Oxygen flux - instrumental background + ('''Instrumental background oxygen flux''', … '''Instrumental background oxygen flux''', ''J''°O2, in a respirometer is due to oxygen consumption by the [[POS]], and oxygen diffusion into or out of the aqueous medium in the [[O2k-chamber]]. It is a property of the instrumental system, measured in the range of experimental oxygen levels by a standardized instrumental O2 background test. The oxygen regime from air saturation towards zero oxygen is applied generally in experiments with isolated mitochondria, and living or permeabilized cells. To overcome oxygen diffusion limitation in permeabilized fibers and homogenates, an elevated oxygen regime is applied, requiring instrumental background test in the same range of elevated oxygen., requiring instrumental background test in the same range of elevated oxygen.)
Integration time + ('''Integration time''' is the time taken t … '''Integration time''' is the time taken to scan a single full range spectrum using [[photodiode arrays]]. It is equivalent to the exposure time for a camera. The shortest integration time defines the fastest response time of a [[spectrophotometer]]. Increasing the integration time increases the [[sensitivity]] of the device. The [[white balance]] or [[balance]] and subsequent measurements must always be carried out at the same integration time. carried out at the same integration time.)
Internal-energy + ('''Internal-energy''', ''U'' [J], can neit … '''Internal-energy''', ''U'' [J], can neither be destroyed nor created (first law of thermodynamics: di''U''/d''t'' = 0). Note that ''internal'' (subscript i), as opposed to ''external'' (subscript e), must be distinguished from "internal-energy", ''U'', which contrasts with "[[Helmholtz energy]]", ''A'', as [[enthalpy]], ''H'', contrasts with Gibbs energy, ''G''.[[enthalpy]], ''H'', contrasts with Gibbs energy, ''G''.)
International oxygraph course + ('''International Oxygraph Course''' (IOC), see [[O2k-Workshops]].)
Ionomycin + ('''Ionomycin''' (Imy) is a ionophore used to raise intracellular [Ca2+].)
Isocitrate dehydrogenase + ('''Isocitrate dehydrogenase''' forms 2-oxoglutarate from isocitrate in the [[TCA cycle]].)
Isolated mitochondria + ('''Isolated mitochondria''', imt, are mitochondria separated from a tissue or cells by breaking the plasma membranes and attachments to the cytoskeleton, followed by centrifugation steps to separate the mitochondria from other components.)
Journal indexing + ('''Journal indexing''' allows publications to be found on search tools/databases. Each database might have different criteria of inclusion.)
Keywords-MitoPedia in BEC + ('''Keywords—MitoPedia''' is the concept to … '''Keywords—MitoPedia''' is the concept to link keywords in articles published in [[Bioenergetics Communications]] (BEC) to [[MitoPedia]] terms. Authors should consider the message in the selected keywords. Provide consistent definitions of your keywords by linking them to MitoPedia. Extend MitoPedia entries critically by your contributions. The BEC editorial team will hyperlink your keywords with MitoPedia, and a reference to your BEC publication will be generated automatically from the MitoPedia term to your publication. With your contributions, BEC elevates keywords to terms with meaning. Your article gains visibility.th meaning. Your article gains visibility.)
Kynurenine hydroxylase + ('''Kynurenine hydroxylase''' (kynurenine 3 … '''Kynurenine hydroxylase''' (kynurenine 3-monooxygenase) is located in the outer mitochondrial membrane. Kynurenine hydroxylase catalyzes the chemical reaction: L-kynurenine + NADPH + H+ + O2 ↔ 3-hydroxy-L-kynurenine + NADP+ + H2OKynurenine hydroxylase belongs to the family of oxidoreductases acting on paired donors, with O2 as oxidant and incorporation or reduction of oxygen. The oxygen incorporated need not be derived from O2 with [[NADH]] or [[NADPH]] as one donor, and incorporation of one atom of oxygen into the other donor. This enzyme participates in tryptophan metabolism. It employs one cofactor, [[FAD]].FAD]].)
Laboratory titration sheet + ('''Laboratory titration sheet''' contains … '''Laboratory titration sheet''' contains the sequential titrations in a specific Substrate-uncoupler-inhibitor titration (SUIT) protocol. The laboratory titration sheets for different SUIT protocols are incorporated in DatLab (DL7.1): [[Protocols in DatLab]][[Protocols in DatLab]])
Lactate dehydrogenase + ('''Lactate dehydrogenase''' is a glycolytic marker enzyme in the cytosol, regenerating NAD+ from NADH and pyruvate, forming lactate.)
Length + ('''Length''' ''l'' is an SI base quantity … '''Length''' ''l'' is an SI base quantity with SI base unit [[meter]] m. Quantities derived from length are [[area]] ''A'' [m2] and [[volume]] ''V'' [m3]. Length is an extensive quantity, increasing additively with the number of objects. The term 'height' ''h'' is used for length in cases of vertical position (see [[height of humans]]). Length of height per object, ''L''''U''''X'' [m·x-1] is length per unit-entity ''U''''X'', in contrast to lentgth of a system, which may contain one or many entities, such as the length of a pipeline assembled from a number ''N''''X'' of individual pipes. Length is a quantity linked to direct sensory, practical experience, as reflected in terms related to length: long/short (height: tall/small). Terms such as 'long/short distance' are then used by analogy in the context of the more abstract quantity [[time]] (long/short duration).[time]] (long/short duration).)
Light-enhanced dark respiration + ('''Light-enhanced dark respiration''' ''LE … '''Light-enhanced dark respiration''' ''LEDR'' is a sharp (negative) maximum of dark respiration in plants in response to illumination, measured immediately after switching off the light. ''LEDR'' is supported by respiratory substrates produced during photosynthesis and closely reflects light-enhanced [[photorespiration]] (Xue et al 1996). Based on this assumption, the total photosynthetic oxygen flux ''TP'' is calculated as the sum of the measured net photosynthetic oxygen flux ''NP'' plus the absolute value of ''LEDR''.'NP'' plus the absolute value of ''LEDR''.)
Lightguides + ('''Lightguides''' consist of optical fibre … '''Lightguides''' consist of optical fibres (either single or in bundles) that can be used to transmit light to a sample from a remote [[light source]] and similarly receive light from a sample and transmit it to a remote [[detector]]. They have greatly contributed to the range of applications that for which optical methods can be applied. This is particularly true in the fields of medicine and biology.rue in the fields of medicine and biology.)
Linear phenomenological laws + ('''Linear phenomenological laws''' are at … '''Linear phenomenological laws''' are at the core of the thermodynamics of irreversible processes TIP, considered to apply near equilibrium but more generally in transport processes (e.g. Fick's law). In TIP, linearity is discussed as the dependence of generalized flows ''I'' or fluxes ''J'' on generalized forces, ''J'' = -''L''·''F'', where ''L'' is expected to be constant (as a prerequisite for linearity) and must not be a function of the force ''F'' ([[affinity]]) for [[Onsager 1931 Phys Rev |Onsager reciprocity]] to apply. This paradigm is challenged by the [[ergodynamics |ergodynamic concept]] of fundamentally non-linear isomorphic flux-[[force]] relations and is replaced by the generalized isomorphic flux-[[pressure]] relations. Flows ''I'' [MU·s-1] and forces ''F'' [J·MU-1] are conjugated pairs, the product of which yields power, ''I''·''F'' = ''P'' [J·s-1 = W]. Flux ''J'' is system-size specific flow, such that volume-specific flux times force yields volume-specific power, ''P''''V'' = ''J''·''F'' [W·m-3]. Then [[Vector |vectoral]] and [[Discontinuous system |vectorial]] transport processes are inherently non-linear flux-force relationships, with '''''L''''' = '''''u'''''·'''''c''''' in continuous transport processes along a gradient ('''''c''''' is the local concentration), or ''L'' = ''u''·''α'' (''α'' is the [[free activity]] in a discontinuous transport process across a semipermeable membrane) — formally not different from (isomorphic to) [[scalar]] chemical reactions.emical reactions.)
Linearity + ('''Linearity''' is the ability of the meth … '''Linearity''' is the ability of the method to produce test results that are proportional, either directly or by a well-defined mathematical transformation, to the concentration of the analyte in samples within a given range. This property is inherent in the [[Beer-Lambert law]] for [[absorbance]] alone, but deviations occur in [[scattering]] media. It is also a property of [[fluorescence]], but a [[fluorophore]] may not exhibit linearity, particularly over a large range of concentrations.arly over a large range of concentrations.)
Luminescence + ('''Luminescence''' is spontaneous emission … '''Luminescence''' is spontaneous emission of radiation from an electronically or vibrationally excited species not in thermal equilibrium with its environment (IUPC definition). An alternative definition is "Luminescence is emission of light by a substance not resulting from heat." Luminescence comprises many different pehnomena. Luminescence from direct photoexcitation of the emitting species is called photoluminescence. Both [[fluorescence]] and [[phosphorescence]] are forms of photoluminescence. In biomedical research also forms of chemiluminescence (e.g.the luciferin reaction) are used. In chemiluminescence the emission of radiation results from a chemical reaction. For other forms of luminescence see [http://goldbook.iupac.org/L03641.html the IUPAC Gold Book].upac.org/L03641.html the IUPAC Gold Book].)
Magnesium Green + ('''Magnesium Green''' (MgG) is an [[extrinsic fluorophores|extrinsic fluorophore]] … '''Magnesium Green''' (MgG) is an [[extrinsic fluorophores|extrinsic fluorophore]] that fluoresces when bound to Mg2+ and is used for measuring mitochondrial ATP production by [[mitochondrial preparations]]. Determination of mitochondrial ATP production is based on the different dissociation constants of Mg2+ for [[ADP]] and [[ATP]], and the exchange of one ATP for one ADP across the mitochondrial inner membrane by the [[adenine nucleotide translocase]] (ANT). Using the dissociation constants for ADP-Mg2+ and ATP-Mg2+ and initial concentrations of ADP, ATP and Mg2+, the change in ATP concentration in the medium is calculated, which reflects mitochondrial ATP production. change in ATP concentration in the medium is calculated, which reflects mitochondrial ATP production.)
Malic enzyme + ('''Malic enzyme''' (ME; EC 1.1.1.40) catal … '''Malic enzyme''' (ME; EC 1.1.1.40) catalyzes the oxidative decarboxylation of L-malate to pyruvate with the concomitant reduction of the dinucleotide cofactor NAD+ or NADP+ and a requirement for divalent cations (Mg2+ or Mn2+) as cofactors.NAD(P)+ + L-malate2- <--> NAD(P)H + pyruvate- + CO2Three groups of ME are distinguished (i) NAD+- and (ii) NADP+-dependent ME specific for NAD+ or NADP+, respectively, and (iii) NAD(P)+- dependent ME with dual specificity for NAD+ or NADP+ as cofactor. Three isoforms of ME have been identified in mammals: cytosolic NADP+-dependent ME (cNADP-ME or ME1), mitochondrial NAD(P)+-dependent ME (mtNAD-ME or ME2; with NAD+ or NADP+ as cofactor, preference for NAD+ under physiological conditions), and mitochondrial NADP+-dependent ME (mtNADP-ME or ME3). mtNAD-ME plays an important role in [[anaplerosis]] when glucose is limiting, particularly in heart and skeletal muscle. [[Tartronic acid]] (hydroxymalonic acid) is an inhibitor of ME.[[Tartronic acid]] (hydroxymalonic acid) is an inhibitor of ME.)
Malonate + ('''Malonate''' (malonic acid) is a competitive inhibitor of [[succinate dehydrogenase]] ([[Complex II]]). Malonate is a substrate of [[malonyl-CoA synthase]].)
Malonyl-CoA synthase + ('''Malonyl-CoA synthase''' or ACSF3 protei … '''Malonyl-CoA synthase''' or ACSF3 protein is a mitochondrial fatty-acyl-CoA synthase found in mammals. Traditionally, malonyl-CoA is formed from acetyl-CoA by the action of acetyl-CoA carboxylase. However, Witkowski et al (2011) showed that mammals express malonyl-CoA Synthase (ACSF3) with enzymatic activity in the presence of [[malonate]] (Complex II inhibitor) and methylmalonate.(Complex II inhibitor) and methylmalonate.)
Marks - DatLab + ('''Marks''' in [[DatLab]] … '''Marks''' in [[DatLab]] define sections of a [[plot]] recorded over time. Marks are set by the [[user]] in real-time, or post-experimentally for basic level data analysis. Set Marks to obtain the median, average, standard deviation, [[Outlier index - DatLab |outlier index]] and range of the data within the mark, for calibration of the oxygen signal, flux analysis, or to delete marked data points. Marks are shown by a horizontal bar in the active plot. The default [[Mark names]] are given automatically in numerical sequence, independent for each plot. Rename marks individually by clicking into the horizontal bar, or use corresponding templates for renaming the entire sequence of marks. Several marks can be set on any plot.rks. Several marks can be set on any plot.)
VO2max + ('''Maximum oxygen consumption''', ''V''< … '''Maximum oxygen consumption''', ''V''O2max, is and index of cardiorespiratory fitness, measured by spiroergometry on human and animal organisms capable of controlled physical exercise performance on a treadmill or cycle ergometer. ''V''O2max is the maximum respiration of an organism, expressed as the volume of O2 at [[STPD]] consumed per unit of time per individual object [mL.min-1.x-1]. If normalized per body mass of the individual object, ''M'' [kg.x-1], mass specific maximum oxygen consumption, ''V''O2max/''M'', is expressed in units [mL.min-1.kg-1]. specific maximum oxygen consumption, ''V''O2max/''M'', is expressed in units [mL.min-1.kg-1].)
Melatonin + ('''Melatonin''' (N-acetyl-5-methoxytryptam … '''Melatonin''' (N-acetyl-5-methoxytryptamine, aMT) is a highly conserved molecule present in unicellular to vertebrate organisms. Melatonin is synthesized from tryptophan in the pinealocytes by the pineal gland and also is produced in other organs, tissues and fluids (extrapineal melatonin). Melatonin has lipophilic and hydrophilic nature which allows it to cross biological membranes. Therefore, melatonin is present in all subcellular compartments predominantly in the nucleus and mitochondria. Melatonin has pleiotropic functions with powerful antioxidant, anti-inflammatory and oncostatic effects with a wide spectrum of action particularly at the level of mitochondria. » [[#Melatonin and protection from mitochondrial damage |'''MiPNet article''']][#Melatonin and protection from mitochondrial damage |'''MiPNet article''']])
Mersalyl + ('''Mersalyl''' (C13H17HgNO6) is an inhibitor of the [[Pi symporter]].)
Metformin + ('''Metformin''' (dimethylbiguanide) is mainly known as an important antidiabetic drug which is effective, however, in a wide spectrum of degenerative diseases. It is an inhibitor of [[Complex I]] and [[glycerophosphate dehydrogenase complex]].)
Methylmalonic acid + ('''Methylmalonic acid''' (Mma) is a common intermediate in many catabolic processes. In methylmalonic acidemia mitochondrial dysfunction can be observed, related to accumulation of Mma and associated with neurological symptoms.)
Metrology + ('''Metrology''' is the science of measurement, including all aspects both theoretical and practical with reference to measurements, whatever their uncertainty, and in whatever fields of science or technology they occur [SOURCE: VIM:1993, 2.2].)
Microplates + ('''Microplate''' readers allow large numbe … '''Microplate''' readers allow large numbers of sample reactions to be assayed in well format microtitre plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 µL per well. a wide range of applications involve the use of [[fluorescence]] measurements , although they can also be used in conjunction with [[absorbance]] measurements.[absorbance]] measurements.)
Microxia + ('''Microxia''' (deep hypoxia) is obtained when trace amounts of O2 exert a stimulatory effect on respiration above the level where metabolism is switched to a purely [[anaerobic]] mode.)
MitoFit protocols + ('''MitoFit protocols''' are moderated by t … '''MitoFit protocols''' are moderated by the [[MitoFit moderators]] (MitoFit team), either as protocols with direct reference to publications available to the scientific communicty, or protocols additionally described and made available in Bioblast with full information on authors (including contact details), author contributions, and editor (moderator) in charge. This aims at a comprehensive [[MitoFit data repository]], which will require global input and cooperation.will require global input and cooperation.)
MitoFit registered project + ('''MitoFit registered projects''' are anno … '''MitoFit registered projects''' are announced with reference to [[MitoFit protocols]] as [[publicly deposited protocols]]. Project registration is a two-phase process. Guidelines will be defined. (''1'') Pre-registration of a project requires submission to a MitoFit moderator (editor), including protocol details with reference to MitoPedia protocols, or with submission of protocols for publication (Open Access) in MitoPedia. The MitoFit (Bioblast) editors will edit the submitted protocols (layout) and insert into Bioblast submitted pre-registrations and protocols. (''2'') MitoFit moderators (editors) will set up a [[MitoFit accreditation panel]], in which the registrant will be included (perhaps not in the long run, to avoid conflict of interests) and/or for which the registrant can suggest delegates (compare peer review). Accredited [[MitoFit protocols]] are labelled as [[MitoFit accredited]], and the pre-registered MitoFit project becomes labelled and listed as '''MitoFit registered project''' (MitoFit accredited). This is possible before (advance registration), during progress, and after completion of a study (post-registration). A MitoFit registered project receives a code for feeding data into the [[MitoFit data repository]].[[MitoFit data repository]].)
MitoKit-CII/Malonate-nv + ('''MitoKit-CII/Malonate-nv''' (diacetoxyme … '''MitoKit-CII/Malonate-nv''' (diacetoxymethyl malonate) is a plasma membrane-permeable prodrug (permeable malonate; Mnanv) that diffuses across the plasma membrane. Cleavage of diacetoxymethyl groups is mediated by intracellular esterases, thus releasing [[malonate]] in the intracellular space. Abliva #: 01-161-s2e intracellular space. Abliva #: 01-161-s2)
MitoKit-CII/Succinate-nv + ('''MitoKit-CII/Succinate-nv''' (diacetoxym … '''MitoKit-CII/Succinate-nv''' (diacetoxymethyl succinate) is a plasma membrane-permeable prodrug (permeable succinate; Snv) that diffuses across the plasma membrane. Cleavage of diacetoxymethyl groups is mediated by intracellular esterases, thus releasing [[succinate]] in the intracellular space. Abliva #: 01-118-s4 intracellular space. Abliva #: 01-118-s4)
MitoSOX + ('''MitoSOXTM''' is … '''MitoSOXTM''' is the version of the [[Dihydroethidium|hydroetidine]] designed to target mitochondria in live cells for the detection of [[superoxide]] (O2•-). The oxidation of the compound by O2•- is easily detected in the red spectrum. One of the advantages of MitoSOXTM is its selectivity for O2•- but not for other [[Reactive oxygen species|reactive oxygen species]] or [[Reactive nitrogen species|reactive nitrogen species]]. ::::• Readily '''oxidized by superoxide''' but not by other ROS- or RNS-generating systems::::• '''Absorption/emission maxima''': ~510/580 nm::::• Use for '''live cell imaging'''::::• Rapidly and selectively '''targeted to the mitochondria''''''MitoSOXTM''' has been widely used in life cell imaging but it is not free of problems and should be used cautiously. For example, it has been highlighted that the use of potentiometric dyes which accumulates into the mitochondria due to its moiety with [[Tetraphenylphosphonium]], confers a membrane potential sensitivity that creates a series of artifacts and problems not often considered.hosphonium]], confers a membrane potential sensitivity that creates a series of artifacts and problems not often considered.)
Mitochondria + ('''Mitochondria''' (Greek ''mitos'': threa … '''Mitochondria''' (Greek ''mitos'': thread; ''chondros'': granule) are small structures within cells, which function in cell respiration as powerhouses or batteries. Mitochondria belong to the '''[[bioblasts]]''' of Richard Altmann. Abbreviation: mt, as generally used in mtDNA. Singular: mitochondrion (bioblast); plural: mitochondria (bioblasts).oblast); plural: mitochondria (bioblasts).)
MitoOx1 + ('''Mitochondrial respiration medium, MitoOx1,''' used by the Budapest groups for respirometry und Amplex Red trials.)
MiP-Collection + ('''Mitochondrial Physiology - Historical C … '''Mitochondrial Physiology - Historical Collection''''''Aims'''The growing '''''MiP-Collection''''' aims at preserving scientific instruments that are of historical importance in the field of bioenergetics and mitochondrial physiology. The fast turnover of scientific equipment makes obsolete even comparatively recent instrumentation. The Oroboros O2k was the first commercial mitochondrial respirometer using a computer for data acquisition. Today, [[chart recorder]]s are nearly forgotten. Due to limitations of storage space, unused scientific equipment is disposed of, despite its potential historical value. The disposal of some unique apparatus constitutes an irreversible loss to science and society, and to the continued appreciation of the foundations of our scientific discipline. You may consider to make items of scientific historical interest in mitochondrial physiology available to the ''MiP-Collection''. These items of the ''MiP-Collection'' may specifically include historically valuable * equipment and accessories,* books and symposium proceedings, * reprint collections,* pictures, slides, documents.ollections, * pictures, slides, documents.)
MiP03 + ('''Mitochondrial Preservation Medium, MiP03''', developed for preservation of [[isolated mitochondria]].)
Mitochondrial concentration + ('''Mitochondrial concentration''' is ''CmtE'' = ''mtE''·''V''-1 [mtEU·m-3]. mt-Concentration is an experimental variable, dependent on sample concentration.)
Mitochondrial content + ('''Mitochondrial content''' per object ''X'' is ''mtENX'' = ''mtE''·''NX''-1 [mtEU·x-1].)
Mitochondrial marker enzymes + ('''Mitochondrial marker enzymes''' are enzymes that are specifically present in mitochondria, in the mt-matrix, the inner mt-membrane, the inter-membrane space, or the outer mt-membrane.)
Mitochondrial marker + ('''Mitochondrial marker'''s are structural … '''Mitochondrial marker'''s are structural or functional properties that are specific for mitochondria. A structural mt-marker is the area of the inner mt-membrane or mt-volume determined stereologically, which has its limitations due to different states of swelling. If mt-area is determined by electron microscopy, the statistical challenge has to be met to convert area into a volume. When fluorescent dyes are used as mt-marker, distinction is necessary between mt-membrane potential dependent and independent dyes. mtDNA or cardiolipin content may be considered as a mt-marker. [[Mitochondrial marker enzymes]] may be determined as molecular (amount of protein) or functional properties (enzyme activities). Respiratory capacity in a defined respiratory state of a mt-preparation can be considered as a functional mt-marker, in which case respiration in other respiratory states is expressed as [[flux control ratio]]s. » [[Mitochondrial marker#Mitochondrial markers and expression of mitochondrial respiration| '''MiPNet article''']][Mitochondrial marker#Mitochondrial markers and expression of mitochondrial respiration| '''MiPNet article''']])
Mitochondrial competence + ('''Mitochondrial metabolic competence''' i … '''Mitochondrial metabolic competence''' is the organelle's capacity to provide adequate amounts of ATP in due time, by adjusting the mt-membrane potential, mt-redox states and the ATP/ADP ratio according to the metabolic requirements of the cell.The term '''mitochondrial competence''' is also known in a genetic context: Mammalian mitochondria possess a natural competence for DNA import.'''''[[MitoCom_O2k-Fluorometer]]''''' is a '''Mitochondrial Competence''' network, the nucleus of which is formed by the K-Regio project ''[[MitoCom_O2k-Fluorometer|MitoCom Tyrol]]''.[[MitoCom_O2k-Fluorometer|MitoCom Tyrol]]''.)
Mitochondrial preparations + ('''Mitochondrial preparations''' (mtprep) … '''Mitochondrial preparations''' (mtprep) are isolated mitochondria (imt), tissue homogenate (thom), mechanically or chemically permeabilized tissue (permeabilized fibers, pfi) or permeabilized cells (pce). In mtprep the plasma membranes are either removed (imt) or mechanically (thom) and chemically permeabilized (pfi), while mitochondrial functional integrity and to a large extent mt-structure are maintained in incubation media optimized to support mitochondrial physiological performance. According to this definition, submitochondrial particles (smtp) are not a mtprep, since mitochondrial structure is altered although specific mitochondrial functions are preserved.fic mitochondrial functions are preserved.)
Buffer Z + ('''Mitochondrial respiration medium, Buffer Z''', described by [http://bioblast.at/index.php/Perry_2011_Biochem_J Perry 2011 Biochem J] For composition and comparison see: [[Mitochondrial respiration media: comparison]])
MiR05 + ('''Mitochondrial respiration medium, MiR05 … '''Mitochondrial respiration medium, MiR05''', developed for oxygraph incubations of [[mitochondrial preparations]]. Respiration of [[living cells]] may be assessed in MiR05 by adding pyruvate (P) as an external source. [[MiR06]] = MiR05 + catalase.[[MiR05Cr]] = [[MiR05]] + creatine.[[MiR05]] + creatine.)
MiRK03 + ('''Mitochondrial respiration medium, MiRK03''', modified after a medium described by [[Komary 2010 Biochim Biophys Acta]], intended for use as medium for H2O2 production measurement with Amplex Red.)
MitoOx2 + ('''Mitochondrial respiration medium, MitoO … '''Mitochondrial respiration medium, MitoOx2''', developed for oxygraph incubations of [[mitochondrial preparations]] to measure the H2O2 production. MitoOx2 yields a higher optical sensitivity and lower "drift" (oxidation of the fluorophore precurcor without H2O2 present) for Amplex UltraRed(R) than e.g. [[MiR05|MiR05]].[[MiR05|MiR05]].)
MiR06 + ('''Mitochondrial respiration medium, [[MiPNet14.13 Medium-MiR06|MiR06]]''', developed for oxygraph incubations of [[mitochondrial preparations]]. MiR06 = MiR05 plus [[catalase]]. MiR06Cr = MiR06 plus [[creatine]].)
Molar mass + ('''Molar mass''' ''M'' is the mass of a c … '''Molar mass''' ''M'' is the mass of a chemical compound divided by its amount-of-substance measured in moles. It is defined as ''M''B = ''m''/''n''B, where ''m'' is the total mass of a sample of pure substance and ''n''B is the amount of substance B given in moles. The definition applies to pure substance. The molar mass allows for converting between the mass of a substance and its amount for bulk quantities. It is calculated as the sum of standard atomic weights of all atoms that form one entity of the substance.The appropriate [[SI base units]] is kg·mol-1. However, for historical as well as usability reasons, g·mol-1 is almost always used instead.historical as well as usability reasons, g·mol-1 is almost always used instead.)
Monoamine oxidase + ('''Monoamine oxidases''' are enzymes boun … '''Monoamine oxidases''' are enzymes bound to the outer membrane of mitochondria and they catalyze the oxidative deamination of monoamines. Oxygen is used to remove an amine group from a molecule, resulting in the corresponding aldehyde and ammonia. Monoamine oxidases contain the covalently bound cofactor [[FAD]] and are, thus, classified as flavoproteins.nd are, thus, classified as flavoproteins.)
Myxothiazol + ('''Myxothiazol''' Myx is an inhibitor of [[Complex III]] … '''Myxothiazol''' Myx is an inhibitor of [[Complex III]] (CIII). CIII also inhibits [[Complex I|CI]]. Myxothiazol binds to the Qo site of CIII (close to cytochrome ''b''L) and inhibits the transfer of electrons from reduced QH2 to the Rieske iron sulfur protein.ons from reduced QH2 to the Rieske iron sulfur protein.)
N-ethylmaleimide + ('''N-ethylmaleimide''' is an organic compound that is derived from maleic acid and blocks endogenous Pi transport.)
NADH + ('''NAD+''' and '''NADH''': see [[Nicotinamide adenine dinucleotide]].)
NADH calibration - DatLab + ('''NADH calibration''')
NS e-input + ('''NS e-input''' or the [[NS-pathway control state]] … '''NS e-input''' or the [[NS-pathway control state]] is electron input from a combination of substrates for the [[N-pathway control state]] and [[S-pathway control state]] through Complexes [[CI]] and [[CII]] simultaneously into the [[Q-junction]]. NS e-input corresponds to [[TCA cycle]] function ''in vivo'', with [[convergent electron flow]] through the [[Electron transfer pathway]]. In [[Mitochondrial preparations|mt-preparations]], NS e-input requires addition not only of NADH- (N-) linked substrates (pyruvate&malate or glutamate&malate), but of succinate (S) simultaneously, since [[metabolite depletion]] in the absence of succinate prevents a significant stimulation of S-linked respiration. For more details, see: [[Additive effect of convergent electron flow]].[[Additive effect of convergent electron flow]].)
Nagarse + ('''Nagarse''' is a broad specifity proteas … '''Nagarse''' is a broad specifity protease from bacteria used to promote breakdown of the cellular structure of "hard" tissues such as skeletal muscle or heart mucsle that cannot be homogenized easily without treatment with a protease. Nagarse is frequently used in protocols for isolating mitochondria from muscle tissue.isolating mitochondria from muscle tissue.)
Nicotinamide adenine dinucleotide + ('''Nicotinamide adenine dinucleotide''', N … '''Nicotinamide adenine dinucleotide''', NAD+ and NADH (pyridine nucleotide coenzymes, NAD and NADP), is an oxidation-reduction coenzyme (redox cofactor; compare [[FADH2 |FADH2]]). In the [[NADH electron transfer-pathway state]] fuelled by type N-substrates, mt-matrix dehydrogenases generate NADH, the substrate of [[Complex I]] (CI). The reduced N-substrate RH2 is oxidized and NAD+ is reduced to NADH,:::: RH2 + NAD+ → NADH + H+ + RThe mt-NADH pool integrates the activity of the [[TCA cycle]] and various matrix dehydrogenases upstream of CI, and thus forms a junction or funnel of electron transfer to CI, the [[N-junction]] (compare [[F-junction]], [[Q-junction]]). NAD+ and NADH are not permeable through the [[Mitochondrial inner membrane|mt-inner membrane]], mtIM. Therefore, an increase of mitochondrial respiration after the addition of NADH may indicate an alteration of the mtIM integrity. Cytosolic NADH is effectively made available for mitochondrial respiration through the [[malate-aspartate shuttle]] or [[Glycerophosphate_dehydrogenase_Complex|glycerophosphate dehydrogenase Complex]].Glycerophosphate_dehydrogenase_Complex|glycerophosphate dehydrogenase Complex]].)
Nitric oxide synthase + ('''Nitric oxide synthase''', NOS, catalyzes the production of nitric oxide (NO•), which is a [[reactive nitrogen species]]. There are four types of NOS: neuronal NOS (nNOS), endothelial NOS (eNOS), inducible NOS (iNOS) and mitochondrial NOS (mtNOS).)
Normalization of rate + ('''Normalization of rate''' (respiratory r … '''Normalization of rate''' (respiratory rate, rate of hydrogen peroxide production, growth rate) is required to report experimental data. Normalization of rates leads to a diversity of formats. Normalization is guided by physicochemical principles, methodological considerations, and conceptual strategies. The challenges of measuring respiratory rate are matched by those of normalization. Normalization of rates for: (''1'') the number of objects (cells, organisms); (''2'') the volume or mass of the experimental sample; and (''3'') the concentration of mitochondrial markers in the instrumental chamber are sample-specific normalizations, which are distinguished from system-specific normalization for the volume of the instrumental chamber (the measuring system). Metabolic ''flow'', ''I'', per [[Count |countable]] object increases as the size of the object is increased. This confounding factor is eliminated by expressing rate as sample-mass specific or sample-volume specific ''flux'', ''J''. [[Flow]] is an [[extensive quantity]], whereas [[flux]] is a [[specific quantity]]. If the aim is to find differences in mitochondrial function independent of mitochondrial density, then normalization to a [[mitochondrial marker]] is imperative. [[Flux control ratio]]s and [[flux control efficiency |flux control efficiencies]] are based on internal normalization for rate in a reference state, are independent of externally measured markers and, therefore, are statistically robust. and, therefore, are statistically robust.)
Normothermia + ('''Normothermia''' in endotherms is a stat … '''Normothermia''' in endotherms is a state when body core temperature is regulated within standard limits. In humans, normothermia is considered as a body temperature of 36.4 to 37.8 °C. Normothermia, however, has a different definition in the context of [[ectotherms]].» [[Normothermia#Normothermia:_from_endotherms_to_ectotherms | '''MiPNet article''']]Normothermia#Normothermia:_from_endotherms_to_ectotherms | '''MiPNet article''']])
Nuclear respiratory factor 1 + ('''Nuclear respiratory factor 1''' is a transcription factor downstream of [[Peroxisome proliferator-activated receptor gamma coactivator 1-alpha|PGC-1alpha]] involved in coordinated expression of [[nDNA]] and [[mtDNA]].)
O-ring\Viton\12x1 mm + ('''O-ring\[[Viton]] … '''O-ring\[[Viton]]\12x1 mm''', for PVDF or PEEK O2k-Stoppers, box of 4 as spares.Two spare boxes of this product are standard components of the [[O2k-Assembly Kit]] ([[O2k-FluoRespirometer]]) as well as the [[O2k-TPP+ ISE-Module]] and the [[O2k-NO Amp-Module]].[[O2k-NO Amp-Module]].)
O-ring\Viton\16x2 mm + ('''O-ring\[[Viton]]\16x2 mm''', mounted on the [[O2k-Chamber Holder sV]].)
Oxygen calibration - DatLab + ('''O2 calibration''' is the calibration in … '''O2 calibration''' is the calibration in DatLab of the oxygen sensor. It is a prerequisite for obtaining accurate measurements of respiration. Accurate calibration of the oxygen sensor depends on (''1'') equilibration of the incubation medium with air oxygen partial pressure at the temperature defined by the experimenter; (''2'') zero oxygen calibration; (''3'') high stability of the POS signal tested for sufficiently long periods of time; (''4'') linearity of signal output with oxygen pressure in the range between oxygen saturation and zero oxygen pressure; and (''5'') accurate oxygen solubility for aqueous solutions for the conversion of partial oxygen pressure into oxygen concentration. The standard oxygen calibration procedure is described below for high-resolution respirometry with the calibration routine using instrumental calibration DL-Protocols in [[DatLab]].[[DatLab]].)
O2k repair + ('''O2k repair''' of defective hardware may … '''O2k repair''' of defective hardware may require replacement of spare parts. Some electronic or mechanical defects may be solved only by repair of the O2k in the electronics workshop of Oroboros Instruments, ''e.g.'', a defective Peltier unit (temperature control).ective Peltier unit (temperature control).)
O2k status line + ('''O2k status line''' is found above the [[O2k signal line]] … '''O2k status line''' is found above the [[O2k signal line]]. It contains information about the chamber label, O2 calibration, amperometric calibration, potentiometric calibration, the [[block temperature]], the [[illumination]] in chambers, the TIP2k status and the [[Automatic pan]].[[Automatic pan]].)
O2k + ('''O2k''' - [[Oroboros O2k]]: the modular system for [[high-resolution respirometry]].)
O2k-Amperometric OroboPOS Twin-Channel + ('''O2k-Amperometric OroboPOS Twin-Channel' … '''O2k-Amperometric OroboPOS Twin-Channel''': Two-channel variable polarization voltage; current/voltage converter for the polarographic oxygen sensor (POS); amplifyer with digital gain settings (1x, 2x, 4x, 8x); A/D converter; output in the range -10 V to 10 V. Integral component of the [[O2k-Main Unit]].[[O2k-Main Unit]].)
O2k-Barometric Pressure Transducer + ('''O2k-Barometric Pressure Transducer''', … '''O2k-Barometric Pressure Transducer''', A/D converter and digital output to DatLab for continuous recording of [[barometric pressure]] [kPa or mmHg], integrated into the air calibration of the POS ([[MiPNet06.03 POS-calibration-SOP]]). Integral component of the [[O2k-Main Unit]]. The warranty on the accuracy of the signal obtained from the O2k-Barometric Pressure Transducer expires within three years.ure Transducer expires within three years.)
O2k-Electromagnetic Stirrer Twin-Control + ('''O2k-Electromagnetic Stirrer Twin-Contro … '''O2k-Electromagnetic Stirrer Twin-Control''' for smooth rotation of the [[Stirrer-Bar\white PVDF\15x6 mm|stirrer bars]] in the two [[O2k-chamber]]s; with slow-start function to prevent decoupling of the stirrer bar; regulated stirrer speed in the range of 100 to 800 rpm (decoupling may occur at higher stirrer speeds), independent for the two O2k-Chambers; automatic events sent to DatLab when the stirrer is switched on/off or when the rotation seed is changed by the experimenter. Integral component of the [[O2k-Main Unit]].[[O2k-Main Unit]].)
O2k-Main Power Cable + ('''O2k-Main Power Cable''', for connecting the main unit to the power supply.)
O2k-Peltier Temperature Control + ('''O2k-Peltier Temperature Control''': Bui … '''O2k-Peltier Temperature Control''': Built-in electronic thermostat controlling temperature for two [[O2k-chamber]]s in the range of 4 to 47 °C; ±0.002 °C (at room temperature). Continuous recording of the O2k-Copper Block temperature with DatLab. Temperature change from 20 to 30 °C within 15 min; cooling from 30 to 20 °C within 20 min. Integral component of the [[O2k-Main Unit]]. The electronic temperature control of the O2k replaced the conventional water jacket.2k replaced the conventional water jacket.)
Obesity + ('''Obesity''' is a disease resulting from … '''Obesity''' is a disease resulting from excessive accumulation of body fat. In common obesity (non-syndromic obesity) excessive body fat is due to an obesogenic lifestyle with lack of physical exercise ('couch') and caloric surplus of food consumption ('potato'), causing several comorbidities which are characterized as preventable non-communicable diseases. Persistent [[body fat excess]] associated with deficits of physical activity induces a weight-lifting effect on increasing muscle mass with decreasing mitochondrial capacity. Body fat excess, therefore, correlates with [[body mass excess]] up to a critical stage of obesogenic lifestyle-induced [[sarcopenia]], when loss of muscle mass results in further deterioration of physical performance particularly at older age.cal performance particularly at older age.)
OctGM + ('''OctGM''': [[Octanoylcarnitine]] & [[Glutamate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocols:''' [[SUIT-015]], [[SUIT-016]], [[SUIT-017]])
OctGMS + ('''OctGMS''': [[Octanoylcarnitine]] &[[Glutamate]] & [[Malate]]& [[Succinate]]. '''MitoPathway control state:''' [[FNS]] '''SUIT protocols:''' [[SUIT-016]], [[SUIT-017]])
OctM pathway control state + ('''OctM''': [[Octanoylcarnitine]] … '''OctM''': [[Octanoylcarnitine]] & [[Malate]].'''MitoPathway control state:''' F'''SUIT protocols:''' [[SUIT-002]], [[SUIT-015]], [[SUIT-016]], [[SUIT-017]]Respiratory stimulation of the [[Fatty acid oxidation pathway control state| FAO-pathway]], F, by [[fatty acid]] FA in the presence of [[malate]] M. Malate is a [[NADH Electron transfer-pathway state |type N substrate]] (N), required for the F-pathway. In the presence of [[Malate-anaplerotic pathway control state|anaplerotic pathways]] (''e.g.'', [[Malic enzyme|mitochondrial malic enzyme, mtME]]) the F-pathway capacity is overestimated, if there is an added contribution of NADH-linked respiration, F(N) (see [[SUIT-002]]). The FA concentration has to be optimized to saturate the [[Fatty acid oxidation pathway control state| FAO-pathway]], without inhibiting or uncoupling respiration. Low concentration of [[malate]], typically 0.1 mM, does not saturate the [[N-pathway]]; but saturates the [[Fatty acid oxidation pathway control state |F-pathway]]. High concentration of [[malate]], typically 2 mM, saturates the [[N-pathway]].[[N-pathway]].)
OctPGM pathway control state + ('''OctPGM''': [[Octanoylcarnitine]] … '''OctPGM''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]].'''MitoPathway control state:''' [[FN]]'''SUIT protocols:''' [[SUIT-002]]:This substrate combination supports N-linked flux which is typically higher than FAO capacity (F/FN<1 in the OXPHOS state). In SUIT-RP1, PMOct is induced after PM(E), to evaluate any additive effect of adding Oct. In SUIT-RP2, FAO OXPHOS capacity is measured first, testing for the effect of increasing malate concentration (compare [[malate-anaplerotic pathway control state]], M alone), and pyruvate and glutamate is added to compare FAO as the background state with FN as the reference state.O as the background state with FN as the reference state.)
OctPGMS pathway control state + ('''OctPGMS''': [[Octanoylcarnitine]] … '''OctPGMS''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]].'''MitoPathway control state:''' [[FNS]]'''SUIT protocol:''' [[SUIT-001]], [[SUIT-002]], [[SUIT-015]]This substrate combination supports convergent electron flow to the [[Q-junction]].[[Q-junction]].)
OctPGMSGp pathway control state + ('''OctPGMSGp''': [[Octanoylcarnitine]] … '''OctPGMSGp''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]].'''MitoPathway control state:''' FNSGp'''SUIT protocol:''' [[SUIT-002]]This substrate combination supports convergent electron flow to the [[Q-junction]].[[Q-junction]].)
OctPM pathway control state + ('''OctPM''': [[Octanoylcarnitine]] … '''OctPM''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Malate]].'''MitoPathway control state:''' [[FN]]'''SUIT protocol:''' [[SUIT-002]], [[SUIT-005]]This substrate combination supports N-linked flux which is typically higher than FAO capacity (F/FN<0 in the OXPHOS state). In SUIT-RP1, PMOct is induced after PM(E), to evaluate any additive effect of adding Oct. In SUIT-RP2, FAO OXPHOS capacity is measured first, testing for the effect of increasing malate concentration (compare [[malate-anaplerotic pathway control state]], M alone), and pyruvate is added to compare FAO as the background state with FN as the reference state. the background state with FN as the reference state.)
OctPMS + ('''OctPMS''': [[Octanoylcarnitine]] & [[Pyruvate]] & [[Malate]] & [[Succinate]]. '''MitoPathway control state:''' [[FNS]] '''SUIT protocol:''' [[SUIT-005]])
Octanoate + ('''Octanoate''' (octanoic acid). C8H16O2 Common name: Caprylic acid.)
Octanoylcarnitine + ('''Octanoylcarnitine''' is a medium-chain fatty acid (octanoic acid: eight-carbon saturated fatty acid) covalently linked to [[carnitine]], frequently applied as a substrate for [[fatty acid oxidation]] (FAO) in [[mitochondrial preparations]].)
Oligomycin + ('''Oligomycin''' (Omy) is an inhibitor of … '''Oligomycin''' (Omy) is an inhibitor of [[ATP synthase]] by blocking its proton channel (Fo subunit), which is necessary for oxidative phosphorylation of ADP to ATP (energy production). The inhibition of ATP synthesis also inhibits respiration. In OXPHOS analysis, Omy is used to induce a [[LEAK respiration]] state of respiration (abbreviated as ''L''(Omy) to differentiate from ''L''(n), LEAK state in the absence of ADP).L''(n), LEAK state in the absence of ADP).)
Optics + ('''Optics''' are the components that are u … '''Optics''' are the components that are used to relay and focus light through a [[spectrofluorometer]] or [[spectrophotometer]]. These would normally consist of lenses and/or concave mirrors. The number of such components should be kept to a minimum due to the losses of light (5-10%) that occur at each surface. light (5-10%) that occur at each surface.)
Ouabain + ('''Ouabain''' (synonym: G-strophantin octa … '''Ouabain''' (synonym: G-strophantin octahydrate) is a poisonous cardiac glycoside. The classical mechanism of action of ouabain involves its binding to and inhibition of the plasma membrane Na+/K+-ATPase (sodium pump) especially at the higher concentrations. Low (nanomolar and subnanomolar) concentrations of ouabain stimulate the Na-K-ATPase.ions of ouabain stimulate the Na-K-ATPase.)
Overfitting + ('''Overfitting''' in statistics is the act … '''Overfitting''' in statistics is the act of mistaking noise for a signal. Overfitting makes a model look ‘’better’’ on paper but perform ‘’worse’’ in the real world. This may make it easier to get the model published in an academic journal or to sell to a client, crowding out more honest models from the marketplace. But if the model is fitting noise, it has the potential to hurt the science (quoted from [[Silver 2012 Penguin Press]]).nguin Press]]).)
Overlay of plots - DatLab + ('''Overlay of plots''' is defined in DatLa … '''Overlay of plots''' is defined in DatLab as selection of graph layouts showing identical plots from the two O2k-chambers in each graph. Overlay of plots is selected in [[Graph layout - DatLab |Graph layout]]. Superimposed traces of flux/flow from chambers A and B are then shown in Graph 1, and of concentration in chambers A and B in Graph 2.There are basically two ways to superimpose traces recorded in different experiments: Export of the graphics via windows metafile or export of the data to e.g. a spreadsheet program.If you export via wmf you also can manipulate the graphics but then usually the lines are broken up in different segments. This can be done in various programs like MS Word, Open Office Draw and even in MSPower Point, though this maybe is the worst program to do this. It is better to manipulate them in a proper program like OO Draw, convert it to an unchangeable picture and then import it to a presentation graphics. Anyway, when you import directly to Power point (or other programs), make sure not to import it as a "picture" but as a metafile. Also in some programs you might afterwards have to "break" it up, or accept a "conversion to a MS Draw object" or other similar linguistic inventions of the software gurus. For this option we suggest to do as much as possible directly in DatLab (setting colors, line widths, ..) using the options in "Plots"/"select plots" and "graph"/"options". The “hardcore“ option is to export the data and import it into e.g. a spreadsheet program (MS Excel , OOCalc). It takes longer to have a simple overlay but gives you far less problems later and its easier to make changes later. To do this you can export your dataset "Export"/"Data to Textfile" and then go from there."Data to Textfile" and then go from there.)
Oxalomalic acid + ('''Oxalomalic acid''' is an inhibitor of a … '''Oxalomalic acid''' is an inhibitor of aconitase (and of cytoplasmic NADP-dependent isocitrate dehydrogenase). Aconitase mediates the isomerization of citrate to isocitrate as the first step in the [[TCA_cycle| TCA cycle]]. Oxalomalic acid has been used at 1 mM concentration and after 45 min of pre-incubation to inhibit aconitase in permeabilized rat Soleus muscle fibres, inhibiting the enzyme by 24% ([[Osiki 2016 FASEB J]]).[[Osiki 2016 FASEB J]]).)
Oxidative stress + ('''Oxidative stress''' results from an imb … '''Oxidative stress''' results from an imbalance between pro-oxidants and antioxidants shifting the equilibrium in favor of the pro-oxidants. This process can be due by an increment in pro-oxidants, by a depletion of antioxidant systems or both. Oxidative stress generates oxidative damage of proteins, lipids and DNA.dative damage of proteins, lipids and DNA.)
Oxoglutarate dehydrogenase + ('''Oxoglutarate dehydrogenase''' (α-ketogl … '''Oxoglutarate dehydrogenase''' (α-ketoglutarate dehydrogenase) is a highly regulated enzyme of the [[tricarboxylic acid cycle]]. It catalyses the conversion of oxoglutarate (alpha-ketoglutarate) to succinyl-CoA, reduces NAD+ to [[NADH]] and thus links to [[Complex I]] in the Electron transfer-pathway. OgDH is activated by low Ca2+ (<20 µM) but inactivated by high Ca2+ (>100 µM). OgDH is an important source of ROS.y high Ca2+ (>100 µM). OgDH is an important source of ROS.)
Oxygen flux + ('''Oxygen flux''', ''J''O<su … '''Oxygen flux''', ''J''O2, is a [[specific quantity]]. Oxygen [[flux]] is [[oxygen flow]], ''I''O2 [mol·s-1 per system] (an [[extensive quantity]]), divided by system size. Flux may be volume-specific (flow per volume [pmol·s-1·mL-1]), mass-specific (flow per mass [pmol·s-1·mg-1]), or marker-specific (flow per mtEU). Oxygen flux (''e.g.'', per body mass, or per cell volume) is distinguished from oxygen flow (per number of objects, such as cells), ''I''O2 [mol·s-1·x-1]. These are different forms of [[normalization of rate]].lization of rate]].)
Oxygen kinetics + ('''Oxygen kinetics''' describes the depend … '''Oxygen kinetics''' describes the dependence of respiration of isolated mitochondria or cells on oxygen partial pressure. Frequently, a strictly hyperbolic kinetics is observed, with two parameters, the oxygen pressure at half-maximum flux, ''p''50, and maximum flux, Jmax. The ''p''50 is in the range of 0.2 to 0.8 kPa for cytochrome ''c'' oxidase, isolated mitochondria and small cells, strongly dependent on ''J''max and coupling state.lls, strongly dependent on ''J''max and coupling state.)
Oxygen pressure + ('''Oxygen pressure''' or partial [[pressure]] of oxygen [kPa], related to oxygen concentration in solution by the [[oxygen solubility]], ''S''O2 [µM/kPa].)
Ap5A + ('''P1,P5-Di(adenosine-5')pentaphosphate (Ap5A)''' is an inhibitor of [[adenylate kinase]] (ADK), the enzyme which rephosphorylates AMP to ADP, consuming ATP (ATP + AMP ↔ 2 ADP).)
PGMSGp pathway control state + ('''PGMSGp''': [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' NSGp '''SUIT protocol:''' [[SUIT-038]] This substrate combination supports convergent electron flow to the [[Q-junction]].)
POS-Service Kit + ('''POS-Service Kit''', in [[O2k-Accessory Box]] including all oxygen sensor service accessories for membrane mounting and service of the [[OroboPOS|POS]].)
PREreview + ('''PREreview''' encourages scientists to p … '''PREreview''' encourages scientists to post their scientific outputs as preprints. PREreview makes it easier to start and run a Preprint Journal Club, or integrate preprint review into conventional journal clubs. PREreview seeks to diversify peer review in the academic community by crowdsourcing pre-publication feedback to improve the quality of published scientific output, and to train early-career researchers (ECRs) in how to review others' scientific work. We want to facilitate a cultural shift in which every scientist posts, reads, and engages with preprints as standard practice in scholarly publishing. We see PREreview as a hub to support and nurture the growth of a community that openly exchanges timely, constructive feedback on emerging scientific outputs. We believe that by empowering ECRs through peer review training programs, thereby increasing the diversity of researchers involved in the peer review process, PREreview will help establish a healthier and more sustainable culture around research dissemination and evaluation. This project was born in April 2017 as a collaboration between Samantha Hindle and Daniela Saderi, scientists and [[ASAPbio]] Ambassadors, with help from Josh Nicholson, at the time working for [https://www.authorea.com/aboutus Authorea].ttps://www.authorea.com/aboutus Authorea].)
Packing\O2k-Box 1+2 + ('''Packing\O2k-Box 1+2''' for shipping the [[O2k-Core]]. O2k-WorldWide delivery, insurance and handling are included in the O2k-Core.)
PalM + ('''PalM''': [[Palmitoylcarnitine]] & [[Malate]]. '''MitoPathway control state:''' [[ F | Fatty acid oxidation pathway control state]] '''SUIT protocols:''' [[SUIT-019]])
PalOctM + ('''PalOctM''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Malate]]. '''MitoPathway control state:''' [[ F | Fatty acid oxidation pathway control state]] '''SUIT protocols:''' [[SUIT-019]])
PalOctPGM + ('''PalOctPGM''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocols:''' [[SUIT-019]])
PalOctPGMS + ('''PalOctPGMS''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]]. '''MitoPathway control state:''' [[FNS]] '''SUIT protocols:''' [[SUIT-019]])
PalOctPM + ('''PalOctPM''': [[Palmitoylcarnitine]] & [[Octanoylcarnitine]] & [[Pyruvate]] & [[Malate]]. '''MitoPathway control state:''' [[FN]] '''SUIT protocols:''' [[SUIT-019]])
PalPGMSGp pathway control state + ('''PalPGMSGp''': [[Palmitoylcarnitine]] … '''PalPGMSGp''': [[Palmitoylcarnitine]] & [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]] & [[Glycerophosphate]].'''MitoPathway control state:''' FNSGp'''SUIT protocol:''' [[SUIT-026]]This substrate combination supports convergent electron flow to the [[Q-junction]].[[Q-junction]].)
Palmitate + ('''Palmitate''' is a term for the salts an … '''Palmitate''' is a term for the salts and esters of palmitic acid (CH3(CH2)14COOH). Palmitic acid is the first fatty acid produced during fatty acid synthesis and the precursor to longer fatty acids. Palmitate negatively feeds back on acetyl-CoA carboxylase (ACC), which is responsible for converting acetyl-CoA to malonyl-CoA, which in turn is used to add to the growing acyl chain, thus preventing further palmitate generation. In order to dissolve the water-insoluble sodium palmitate, [[Bovine serum albumine| BSA]] is needed to form the water-soluble compound called palmitate:BSA.[[Bovine serum albumine| BSA]] is needed to form the water-soluble compound called palmitate:BSA.)
Palmitoyl-CoA + ('''Palmitoyl-CoA''' is a coenzyme A deriva … '''Palmitoyl-CoA''' is a coenzyme A derivative of palmitate formed by acyl-CoA synthase. In contrast to medium- and short-chain acyl-CoA, palmitoyl-CoA cannot freely diffuse into the mitochondrial matrix. Formation of palmitoylcarnitine by CPTI is necessary prior to transfer into mitochondria for further fatty acid oxidation (β-oxidation). To study [[Fatty acid oxidation]] using Palmitoyl-CoA, [[Carnitine]] and low amount of malate is needed on mitochondrial preparations.e is needed on mitochondrial preparations.)
Palmitoylcarnitine + ('''Palmitoylcarnitine''' is an ester deriv … '''Palmitoylcarnitine''' is an ester derivative of [[carnitine]] (long-chain acylcarnitine) involved in the metabolism of fatty acids. Within the cell, palmitoylcarnitine is transported into the mitochondria to deliver palmitate for fatty acid oxidation and energy production.atty acid oxidation and energy production.)
Pathway control efficiency + ('''Pathway control efficiencies''' are [[flux control efficiency |flux control efficiencies]] … '''Pathway control efficiencies''' are [[flux control efficiency |flux control efficiencies]], expressing the relative change of flux in response to a transition between two [[electron-transfer-pathway state]]s due to a change of (''1'') substrate availability or (''2'') inhibition of enzyme steps in the pathway, in a defined [[coupling-control state]].[[coupling-control state]].)
Peer review + ('''Peer reviews''' provide a critical asse … '''Peer reviews''' provide a critical assessment of a manuscript prior to publication. Bioenergetics Communications publishes [https://www.bioenergetics-communications.org/index.php/bec/BECPolicies#Permanency_of_content.2C_peer-review_process.2C_and_Journal.27s_options_for_post-publication_discussions_and_corrections Open Peer Reviews] for transparency of the review process.s] for transparency of the review process.)
PeerJ Preprints 'pre-print' area of PeerJ + ('''PeerJ Preprints''' is the 'pre-print' a … '''PeerJ Preprints''' is the 'pre-print' area of the Open Access journal ''PeerJ''. Similar to preprint servers that already exist (for example arXiv.org), authors can submit draft, incomplete, or final versions of articles they are working on. By using this service, authors establish precedent; they can solicit feedback; and they can work on revisions of their manuscript. Once they are ready, they can submit their preprint article into ''PeerJ'' (although it is not a requirement to do so).''PeerJ Preprints'' was launched in April 2013. It only accepts submissions in the same subject areas as ''PeerJ'' (biological, medical and environmental sciences) and ''PeerJ Computer Science''. In order to submit to ''PeerJ Preprints'', at least the submitting author must have a user account with ''PeerJ''. There is no pre-publication peer-review of submissions; however we do perform basic checks to ensure conformity with our policies. Submissions are made using the same platform as with the peer-reviewed journals, although some of the requirements are less stringent. Articles are not typeset, but we do provide automated conversion into PDF. The default is for a ''PeerJ Preprints'' publication to be fully open to all viewers (what we call a 'public' pre-print).'''PeerJ''' is an Open Access, peer-reviewed, scholarly journal. It considers and publishes research articles in the biological, medical and environmental sciences. It aims for rapid decision making and will publish articles as soon as they are ready. ''PeerJ'' is based in both San Diego, US, and London, UK.sed in both San Diego, US, and London, UK.)
Perfluorooctanoic acid + ('''Perfluorooctanoic acid''' (PFOA) is a metabolically inert perfluorinated fatty acid which activates [[UCP1]] in brown-fat mitochondria. UCP1-dependent respiration can be stimulated with 600 μM PFOA after inhibition of the phosphorylation system.)
Performance Estimation + ('''Performance estimation''')
PBMC + ('''Peripheral blood mononuclear cells''' ( … '''Peripheral blood mononuclear cells''' (PBMC) are a fraction of the leucocyte population in the blood composed by cells with round nucleus. PBMC consist of lymphocytes (T, B and NK cells) and monocytes. During extraction, neutrophils and platelets (PLT) can be found in the PBMC fraction, where PLT are considered as a contamination.ere PLT are considered as a contamination.)
Permeabilized cells + ('''Permeabilized cells''' (pce) are mitoch … '''Permeabilized cells''' (pce) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane (e.g., with [[digitonin]]), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.'''Permeabilized cells''' (pce) are, therefore, not any longer viable or [[living cells]] (ce), since the intactness of cells implies the intactness of the plasma membrane. Any typical quantiative cell viability test (trypan blue etc) evaluating the intactness of the plasma membrane, yields a 100% negative result on fully permeabilized cells.For permeabilizing the cell plasma membranes chemically with [[digitonin]], without damaging the [[mitochondrial|mt]]-membranes, the optimum concentration of digitonin must be previously determinated. The protocol [[SUIT-010]] is designed for the evaluation of optimum digitonin concentration for permeabilizing cells, a requirement to account for differences between cell types, the concentration of cells, and variability between batches of the natural product digitonin. batches of the natural product digitonin.)
Permeabilized muscle fibers + ('''Permeabilized muscle fibers''' (pfi) ar … '''Permeabilized muscle fibers''' (pfi) are used as a mitochondrial preparation in respirometry to access mitochondrial function comparable to [[isolated mitochondria]] (imt). pfi are obtained by selectively permeabilizing the plasma membrane mechanically and chemically ([[saponin]]), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.:» MitoPedia topic: [[Mitochondrial preparations]][Mitochondrial preparations]])
Permeabilized tissue or cells + ('''Permeabilized tissue''' ([[Permeabilized tissue|pti]] … '''Permeabilized tissue''' ([[Permeabilized tissue|pti]], see also [[permeabilized muscle fibers]], pfi) or cells ([[Permeabilized cells|pce]]) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane mechanically or [[permeabilization of plasma membrane|chemically]], for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.'''Permeabilized cells''' (pce) are, therefore, not any longer viable or [[living cells]] (ce), since the intactness of cells implies the intactness of the plasma membrane. Any typical quantiative cell viability test (trypan blue etc) evaluating the intactness of the plasma membrane, yields a 100% negative result on fully permeabilized cells.ative result on fully permeabilized cells.)
Permeabilized tissue + ('''Permeabilized tissue''' (pti, see also … '''Permeabilized tissue''' (pti, see also [[permeabilized muscle fibers]], pfi) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane mechanically or chemically (e.g., with [[saponin]]), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the [[mitochondrial|mt]]-membranes.[[mitochondrial|mt]]-membranes.)
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha + ('''Peroxisome proliferator-activated recep … '''Peroxisome proliferator-activated receptor-γ (PPAR-γ) coactivator-1α''' (PGC-1α) is a protein which functions as an inducible transcriptional coactivator, a coregulator of transcription factors, particularly [[NRF-1]] and [[TFAM]]. PGC-1α was first described in 1998 ([[Puigserver 1998 Cell]]). PGC-1α drives the formation of slow-twich muscle fibres ([[Lin 2002 Nature]]) and is increased upon endurance training ([[Norrbom 2004 J Appl Physiol]]). PGC-1α expression is inhibited by the proinflammatory cytokine tumor necrosis factor α (TNF-α) and high levels of leptin. Upregulation of PGC-1α expression is induced by increased [[eNOS]] activity -> [[MiPNet15.05_NO-manual|NO]] -> [[guanylate cyclase]] -> [[cGMP]] ([[Nisoli 2007 Circ Res]]). AMP-activated protein kinase (AMPK) increases PGC-1α expression through SIRT1 ([[Canto 2009 Nature]]).9 Nature]]).)
Phenylsuccinate + ('''Phenylsuccinate''' is a competitive inhibitor of succinate transport (20 mM).)
Phosphocreatine + ('''Phosphocreatine''' is a high energy compound in the skeletal muscle of vertebrates and is present in 4 to 5 times the concentration of ATP.)
Phosphoenolpyruvate carboxykinase + ('''Phosphoenolpyruvate carboxykinase''' (P … '''Phosphoenolpyruvate carboxykinase''' (PEPCK) catalyzes the anabolic reaction of [[oxaloacetate]] (Oxa) to [[phosphoenolpyruvate]] at the expense of GTP. PEPCK is a cytoplasmatic enzyme involved in gluconeogenesis in mouse and rat liver, but 'is found in the mitochondria in the rabbit and chicken, and in both cytoplasm and mitochondria in the guinea pig' ([[Lehninger 1970 Worth Publishers |Lehninger 1970]]). In many anoxia-resistant animals, PEPCK plays an important catabolic role under severe hypoxia and anoxia at the PEPCK branchpoint ([[Hochachka 2002 Oxford Univ Press |Hochachka, Somero 2002)]], feeding malate into the reversed TCA cycle: malate is dismutated to pyruvate catalyzed by [[malic enzyme]] in the oxidative direction, and to fumarate in the reductive direction, leading to formation of succinate and ATP under anoxia ([[Gnaiger 1977 Invertebrate anoxibiosis |Gnaiger 1977]]).[[Gnaiger 1977 Invertebrate anoxibiosis |Gnaiger 1977]]).)
Phosphorescence + ('''Phosphorescence''' is a similar phenome … '''Phosphorescence''' is a similar phenomenon to [[fluorescence]]. However, instead of the electron returning to its original energy state following excitation, it decays to an intermediate state (with a different spin value) where it can remain for some time (minutes or even hours) before decaying to its original state. Phosphorescence is one form of [[Luminescence]], especially Photoluminescence.[[Luminescence]], especially Photoluminescence.)
PhotoBiology + ('''PhotoBiology''' is the science of the e … '''PhotoBiology''' is the science of the effect of light on biological processes. This includes [[photosynthesis]], photochemistry, photophysics, photomorphogenesis, vision, bioluminescence, circadian rhythms and photodynamic therapy. Phototoxicity results from non-ionizing radiation (i.e. ultraviolet, visible and infrared radiation). Non-ionizing radiation is any type of electromagnetic radiation that does not carry enough energy per quantum (photon energy below 10 eV) to completely remove an electron from an atom or molecule. When photons interact with molecules, the molecules can absorb the photon energy and become excited, reacting with surrounding molecules and stimulating "photochemical" and "photophysical" changes. Respiration may be affected by light during photosynthesis or in dark respiration, with the transient response of [[light-enhanced dark respiration]].[[light-enhanced dark respiration]].)
Photodecomposition + ('''Photodecomposition''' or photodegradati … '''Photodecomposition''' or photodegradation is the process of decay of organic material induced by increasing light intensity. Under aerobic conditions, the enhancement of photodecomposition by light intensity can be quantified by oxygen consumption in a controlled light regime. consumption in a controlled light regime.)
Photodiode arrays + ('''Photodiode arrays''' are two dimensiona … '''Photodiode arrays''' are two dimensional assemblies of [[photodiodes]]. They are frequently used in conjunction with charge coupled devices (CCDs) for digital imaging. They can be used in combination with [[dispersion devices]] to detect wavelength dependent light intensities in a [[spectrofluorometer]] or [[spectrophotometer]].[[spectrophotometer]].)
Photodiodes + ('''Photodiodes''' are photodetectors that … '''Photodiodes''' are photodetectors that convert [[incident light]] into a current or voltage dependent on their configuration. They have replaced photomultiplier tubes for most applications. For fluorometric measurements that do not require spectral data, a single photodiode with suitable [[filters]] can be used. Due to their larger detection area, they are more sensitive than [[photodiode arrays]].[[photodiode arrays]].)
Photorespiration + ('''Photorespiration''' is the process by w … '''Photorespiration''' is the process by which the enzyme RuBisCo oxygenates ribulose biphosphate (RuBP) instead of carboxylating it as part of the Calvin-Benson cycle, creating phosphoglycolate, a product that cannot be used within this cycle, thus dissipating the energy in [[photosynthesis]]. It is estimated that approximately 25 % of RuBisCo reactions are photorespiration, meaning a potential 25 % reduction in photosynthetic output due to the carbon fixed by photorespiration being released as carbon dioxide and nitrogen as ammonia, while the other product, 3-phosphoglycerate (G3P), requires a higher metabolic cost. This process involves a complex network of enzymes and metabolite exchanges between the chloroplasts, peroxisomes and mitochondria. It is also known as the oxidative photosynthetic carbon cycle or C2 photosynthesis. Environmental conditions tend to affect it, such as temperature and partial pressure of oxygen and carbon dioxide. C4 plants, CAM plants and algae have biochemical and biophysical mechanisms to overcome the photosynthetic losses due to photorespiration making them more photosynthetically efficient than C3 plants. [https://www.biotechniques.com/molecular-biology/new-photorespiratory-pathways-the-key-to-humanitys-survival/ Recent plant biotechnology advances] focuse on increasing plant photosynthetic carbon fixation by reducing photorespiration loses.asing plant photosynthetic carbon fixation by reducing photorespiration loses.)
Photosynthesis + ('''Photosynthesis''' is the process that c … '''Photosynthesis''' is the process that converts light energy into chemical energy which is subsequently transformed to the physiological energy demand. Photosynthesis has a light-dependent and light-independent (dark) phase. In plants, algae, and cynobacteria, light energy is absorbed during the light phase by the pigment chlorophyll and used to split water and generate adenosine triphosphate (ATP) and reducing power - nicotinamide adenine dinucleotide phosphate (NADPH), with the net production of O2 as a waste product. During the dark phase ATP and NADPH are used to synthesize carbohydrates from CO2 through the metabolic pathway called Calvin-Benson cycle. Oxygenic photosynthesis is responsible for producing and maintaining the oxygen concentration of the Earth’s atmosphere. In bacteria such as cyanobacteria, photosynthesis involves the plasma membrane and the cytoplasm. In eukaryotic cells (plants and algae), photosynthesis takes place in the chloroplasts.plants and algae), photosynthesis takes place in the chloroplasts.)
Piericidin + ('''Piericidin''' C25 … '''Piericidin''' C25H37NO4 is an antibiotic (isolated from ''Streptomyces mobaraensis'') showing similarity with ubiquinone structure which has a potent and competitive inhibitory effect of [[Complex I |CI]] (it competes with endogenous and partially with exogenous Q for binding sites). CI inhibitors have been divided (''1'') depending of the site of action (functional classification): quinone antagonists (e.g. piericidin A, first site), semiquinone antagonists (piericidin A, second site; piericidin B; [[Rotenone| rotenone]] and quinol antagonists (myxothiazol; stigmatellin), and (''2'') depending on their effect on ROS production: inducing ROS production (e.g. rotenone, piericidin A, Rolliniastatin-1 and -2) and preventing ROS production (e.g. stigmatellin, capsaicin, mucidin and coenzyme Q2). In plants, pieridicin A inhibits photosystem II.in, mucidin and coenzyme Q2). In plants, pieridicin A inhibits photosystem II.)
Plan S + ('''Plan S''' is an initiative for [[Open Access]] … '''Plan S''' is an initiative for [[Open Access]] publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. According to [https://www.scienceeurope.org/our-priorities/open-access Science Europe], "Plan S requires that recipients of research funding from cOAlition S organisations make the resulting publications available immediately (without embargoes) and under open licences, either in quality Open Access platforms or journals or through immediate deposit in open repositories that fulfil the necessary conditions."ies that fulfil the necessary conditions.")
Platelet-rich plasma + ('''Platelet-rich plasma''' (PRP) is obtain … '''Platelet-rich plasma''' (PRP) is obtained as the upper layer at low-speed centrifugation (around 150-200 ''g''), when white and red blood cells sediment and thus get separated from plasma containing the [[platelet]]s. For further details see [[blood cell preparation]].[[blood cell preparation]].)
Platelet + ('''Platelets''' or '''thrombocytes''' (PLT) are cell fragments derived from megakaryocytes with hemostatic function in the blood stream. PLT are anucleated but contain functioning mitochondria that play a critical role in PLT activation.)
Poicilotherms + ('''Poicilotherms''' are [[ectotherms]] whose body temperatures conform to the temperature of the milieu in a thermally variable environment.)
Redox poise + ('''Poise'''=A state of balance. '''Redox p … '''Poise'''=A state of balance. '''Redox poise''' in electron transport occurs when each electron-carrying intermediate is present in both its oxidized state and its reduced state, in order for that component both to accept and to donate electrons or hydrogen atoms. Redox poise is likely to be essential in the Q-cycle, where the plastosemiquinone participates in one-electron transfer with cytochrome ''b'', despite its tendency to transfer its single electron to oxygen, generating superoxide. When applied to noncyclic electron transport, ''redox poise'' indicates a position of optimal redox state where the activity of components are such that their effective redox potentials favor physiologically useful electron transfer. physiologically useful electron transfer.)
Polarographic oxygen sensor + ('''Polarographic oxygen sensors''' (POS) a … '''Polarographic oxygen sensors''' (POS) are operated with a polarization voltage between the cathode and anode, connected by an electrolyte. Cathode, anode and electrolyte are separated from the analyte by an oxygen-permeable membrane. Oxygen is reduced at the cathode such that the local oxygen concentration is maintained at zero, and diffuses along the concentration gradient from the stirred medium to the cathode, resulting in a linear calibration between oxygen partial pressure and electric current [Amp] (amperometric mode of operation). The [[OroboPOS]] is the POS applied in the [[Oroboros O2k]].[[Oroboros O2k]].)
Polyether ether ketone + ('''Polyether ether ketone (PEEK)''' is a s … '''Polyether ether ketone (PEEK)''' is a semicrystalline organic polymer thermoplastic, which is chemically very resistant, with excellent mechanical properties. PEEK is compatible with ultra-high vacuum applications, and its resistance against oxygen diffusion make it an ideal material for high-resolution respirometry ([[POS]] insulation; coating of stirrer bars; stoppers for closing the O2k-Chamber).rs; stoppers for closing the O2k-Chamber).)
Polyvinylidene fluoride + ('''Polyvinylidene fluoride (PVDF)''' is a … '''Polyvinylidene fluoride (PVDF)''' is a pure thermoplastic fluoropolymer, which is chemically very resistant, with excellent mechanical properties. ''It is used generally in applications requiring the highest purity, strength, and resistance to solvents, acids, bases and heat'' ([http://en.wikipedia.org/wiki/Polyvinylidene_fluoride Wikipedia]). PVDF is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (coating of stirrer bars; stoppers for closing the O2k-Chamber).rs; stoppers for closing the O2k-Chamber).)
Post-examination procedures + ('''Post-examination procedures''', in the … '''Post-examination procedures''', in the postanalytical phase, are processes following the examination including systematic review, formatting and interpretation, authorization for release, reporting and transmission of the results, and storage of samples of the examinations.nd storage of samples of the examinations.)
Potentiometry + ('''Potentiometry''' is the general term gi … '''Potentiometry''' is the general term given to the method of measuring the electric potential difference between two electrodes connected by an electrolytic solution. The potential of the reference electrode is constant. The other electrode is called the indicator electrode. If this is an ion-selective electrode which is in equilibrium with the solution, the measured electric potential difference is proportional to the (negative) logarithm of the activity of a specific ion in the solution. Examples are the pH glass electrode for measurement of pH, and the TPP+ electrode for measurement of pTPP and calculation of mt-membrane potential.ment of pTPP and calculation of mt-membrane potential.)
Power + ('''Power''' ''P'' [W = J·s-1< … '''Power''' ''P'' [W = J·s-1] is [[exergy]] per time, or [[force]] times [[flow]], which cannot be created internally yet is not conserved but is dissipated (''P'' < 0) in irreversible energy transformations at constant temperature and (barometric) pressure, ''T'',''p''. Metabolic power and heat flux of irreversible processes are distinguished as the time rate of Gibbs energy and enthalpy changes, respectively. rate of Gibbs energy and enthalpy changes, respectively.)
Pre-examination procedures + ('''Pre-examination procedures''', in the p … '''Pre-examination procedures''', in the preanalytical phase, are steps starting, in chronological order, from the clinician’s request and including the examination requisition, preparation of the patient, collection of the primary sample, and transportation to and within the laboratory, and ending when the analytical examination procedure begins.e analytical examination procedure begins.)
PrePubMed + ('''PrePubMed''' indexes preprints from [[ArXiv preprint server |arXiv q-bio]] … '''PrePubMed''' indexes preprints from [[ArXiv preprint server |arXiv q-bio]], [[PeerJ Preprints 'pre-print' area of PeerJ |PeerJ Preprints]], [[BioRxiv preprint server for biology |bioRxiv]], [[F1000Research]], [[Preprints multidisciplinary preprint platform |preprints.org]], The Winnower, Nature Precedings, and Wellcome Open Research. Articles are not stored on PrePubMed, but you will be linked to the article at the respective site.ked to the article at the respective site.)
Precision + ('''Precision of measurement''' is the clos … '''Precision of measurement''' is the closeness of agreement between independent results of measurements obtained under stipulated conditions [SOURCE: ISO 3534-1:1993, 3.14]. Precision of measurement cannot be given a numerical value in terms of the [[measurand]], only descriptions such as 'sufficient' or 'insufficient' for a stated purpose. The degree of precision is usually expressed numerically by the statistical measures of imprecision of measurements, such as standard deviation and coefficient of variation, that are inversely related to precision. "Precision" of a given measurement procedure is subdivided according to the specified precision conditions. "[[Repeatability]]" relates to essentially unchanged conditions and is often termed "withinserial" or "within-run precision". "[[Reproducibility]]" relates to changes in conditions, e.g. time, different laboratories, operators, and measuring systems (including different calibrations and reagent batches).fferent calibrations and reagent batches).)
Preparation of SUIT chemicals + ('''Preparation of SUIT chemicals''' describes the preparation of chemicals used in Substrate-Uncoupler-Inhibitor Ttitration (SUIT) protocols.)
Preprints multidisciplinary preprint platform + ('''Preprints''' is a platform dedicated to … '''Preprints''' is a platform dedicated to making early versions of research outputs permanently available and citable. We post original research articles and comprehensive reviews, and papers can be updated by authors at any time. Content on ''Preprints'' is not peer-reviewed and can receive feedback from readers. ''Preprints'' focuses on original research articles and comprehensive reviews. Editorials, discussion papers, and commentary are usually not suitable. Preprints is fully owned and funded by MDPI, an open access journal publisher. It is run on a non-profit basis. You do not need to submit to an MDPI journal in order to post a preprint here, any work is welcome. If you do submit to an MDPI journal, you will be invited to submit to Preprints.org during the submission process. ''Preprints'' has the following features: ''Multidisciplinary'': We cover all research disciplines. ''Open access'': 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. '' Citation via Crossref DOI'': Each preprint has a unique digital object identifier issued by Crossref. This makes them instantly citable and provides a permanent link to the article, even if the URL on our platform changes. New versions of preprints receive a different DOI. ''Comment on any article'': Authors can receive public or private feedback from readers directly from the preprint abstract page. ''Simple submission process'': Submitting a preprint only requires basic information, our team of editors will do the rest and post your preprint as soon as possible. MDPI.com is a platform for peer-reviewed, scientific open-access journals operated by MDPI, based in Basel, Switzerland (since 1996). MDPI is a member of the Committee on Publication Ethics ([https://publicationethics.org/ COPE]). To verify the originality of content submitted to our journals, we use [http://www.ithenticate.com/ iThenticate] to check submissions against previous publications. MDPI works with [https://publons.com/about/home/ Publons] to provide reviewers with credit for their work.vide reviewers with credit for their work.)
Pressure + ('''Pressure''' is a fundamental quantity e … '''Pressure''' is a fundamental quantity expressing energy per volume. The SI unit of pressure is generally pascal [Pa] = [J·m-3]. The term 'stress' (mechanical stress) is used as a synonym for pressure ([[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |SI]]). Pressure is known in physics as mechanical pressure, which is force per area, ''p'' = ''F''·''A''-1 [Pa] = [N·m-2]. In physical chemistry, gas pressure is defined as ''p'' = ''n''·''V''-1·''RT'', where the [[concentration]] is ''c'' = ''n''·''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]. van't Hoff's osmotic pressure assumes the same form applied to dissolved substances diffusing across a semipermeable membrane, but concentrations should be replaced by [[activity |activities]]. The activity of dissolved gases is expressed by the [[partial pressure]], where the [[solubility]] can be seen as an activity coefficient. Pressure appears explicitely or implicitely in all chapters of physics and physical chemistry. In contrast to the universal counterparts energy and force, however, the general connections between various isomorphic expressions of pressure remain poorly understood: Pressure is the concentration of the [[force]] at the point of [[action]]. More generally, pressure is the force times concentration at the interphase of interaction.]]. More generally, pressure is the force times concentration at the interphase of interaction.)
Temperature plot empty + ('''Problem:''' Layout "01 Calibration Exp. … '''Problem:''' Layout "01 Calibration Exp. Gr3-Temp" is selected, a third plot is displayed on the screen but it remains empty (no plot is shown). Newer versions of [[DatLab]] include pre-installed layouts which do not recognize some channel designations from older O2k series.hannel designations from older O2k series.)
Proficiency test + ('''Proficiency testing''' PT is an evaluat … '''Proficiency testing''' PT is an evaluation of participant performance against pre-established criteria by means of interlaboratory comparisons. Some PT providers in the medical area use the term “External Quality Assessment (EQA)” for their proficiency testing schemes, or for their broader programmes, or both. Internal PT strategies may be implemented into laboratory science as practical steps towards PT to achieve reproducibility.eps towards PT to achieve reproducibility.)
Proline dehydrogenase + ('''Proline dehydrogenase''' (ProDH), L-pro … '''Proline dehydrogenase''' (ProDH), L-proline:quinone oxidoreductase, is located on the inner side of the [[mtIM]], oxidizing [[proline]] to delta-1-pyrroline-5-carboxylate, with reduction of FAD to FADH2 and direct entry into the [[Q-junction]], exerting an additive effect of convergent pathways. ProDH is widely distributed in a variety of organisms, is a source of ROS, and may play a role in carcinogenesis. source of ROS, and may play a role in carcinogenesis.)
Proton slip + ('''Proton slip''' is a property of the pro … '''Proton slip''' is a property of the proton pumps (Complexes CI, CIII, and CIV) when the [[proton]] slips back to the matrix side within the proton pumping process. Slip is different from the [[proton leak]], which depends on Δ''p'' and is a property of the inner mt-membrane (including the boundaries between membrane-spanning proteins and the lipid phase). Slip is an uncoupling process that depends mainly on flux and contributes to a reduction in the [[biochemical coupling efficiency]] of ATP production and oxygen consumption. Together with proton leak and cation cycling, proton slip is compensated for by [[LEAK respiration]] or LEAK oxygen flux, ''L''. Compare: [[Proton leak]].[Proton leak]].)
PubMed + ('''PubMed''' is a free search tool for articles in the life sciences field.)
Publication efficiency + ('''Publication efficiency''' is the fracti … '''Publication efficiency''' is the fraction ''F''r,a/p of reproducible publications ''N''r which are among the number ''N''a of publications that receive attention and meaningful interpretation, per total count ''N''p of all published communications. Publication efficiency ''F''r,a/p = ''F''r/p·''F''a/p is low due to (''1'') the reproducibility crisis expressed as low reproducibility efficiency ''F''r/p = ''N''r/''N''p, and (''2'') the inflation crisis expressed as low attention efficiency ''F''a/p = ''N''a/''N''p. Estimates of these partial efficiencies vary from field to field. With ''F''r/p=0.15 and ''F''a/p=0.05, the current publication efficiency is as low as 0.0075, or only 0.75 % of all presently published communictions are reproducible and receive attention and meaningful interpretation. Reduction of the number of irreproducible zero-value publications is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.ons is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.)
Pyruvate carboxylase + ('''Pyruvate carboxylase''' synthesizes [[oxaloacetate]] … '''Pyruvate carboxylase''' synthesizes [[oxaloacetate]] from [[pyruvate]] and CO2 as an [[anaplerosis |anaplerotic reaction]] in the mitochondrial matrix of the liver and kidney of higher animals, representing an alternative to the [[malic enzyme]] pathway to oxaloacetate or the [[phosphoenolpyruvate carboxykinase]] reaction (compare glyoxylate cycle in plants and microorganisms). Carboxylation of pyruvate to oxaloacetate requires Mg-ATP. Acetyl CoA is a strong positive modulator. PC can form pyruvate from oxaloacetate to remove an excess of oxaloacetate which inhibits succinate dehydrogenase.f oxaloacetate which inhibits succinate dehydrogenase.)
Pyruvate dehydrogenase + ('''Pyruvate dehydrogenase''' is the first … '''Pyruvate dehydrogenase''' is the first component enzyme of the [[pyruvate dehydrogenase complex]], which catalyzes oxidative decarboxylation of [[pyruvate]] in the mt-matrix, and yields [[acetyl-CoA]]. PDH is known as the mitochondrial gatekeeper in the core energy pathway of electron flow into the tricarboxylic acid cycle.on flow into the tricarboxylic acid cycle.)
Q calibration - DatLab + ('''Q calibration''')
Q-cycle + ('''Q-cycle''' refers to the sequential oxi … '''Q-cycle''' refers to the sequential oxidation and reduction of the electron carrier Coenzyme Q (CoQ or [[ubiquinone]]) in mitochondria or plastoquinones in the photosynthetic system. Originally, the concept of the Q-cycle was proposed by [[Mitchell P|Peter D Mitchell]]. Following several modifications, the Q-cycle is established, describing how [[CIII]] translocates hydrogen ions against the protonmotive force. The reduced CoQ ([[quinol |ubiquinol]] QH2) binds to the Qo site of CIII, while the oxidized CoQ ([[ubiquinone]] Q) to the Qi site of CIII. First, QH2 reduces the iron-sulfur protein and feeds cytochrome ''c''1 with one electron. The other electron is transferred to the ''b''L heme and reduces the ''b''H heme, which transfers the electron to ubiquinone at the Qi-site which is reduced to a [[semiquinone]]. A second QH2 is required to fully reduce semiquinone to ubiquinol. At the end of the Q-cycle, four protons leave the mt-matrix and enter the intermembrane space, and the reduced cytochrome ''c'' transfers electrons to CIV. The ubiquinol generated at the Qi-site can be reused by binding to the Qo-site of CIII.chrome ''c'' transfers electrons to CIV. The ubiquinol generated at the Qi-site can be reused by binding to the Qo-site of CIII.)
Quenching + ('''Quenching''' is the name given to any p … '''Quenching''' is the name given to any process that reduces [[fluorescence]] intensity. Molecular oxygen is a [[fluorescence]] and [[phosphorescence]] quencher for some substances – a phenomenon that has been made use of in constructing optical probes for measuring oxygen.cting optical probes for measuring oxygen.)
Quinol + ('''Quinol''' is a class of ''reduced'' org … '''Quinol''' is a class of ''reduced'' organic compounds derived from quinone (oxidized form) by two-electron and two-proton reduction. In the mitochondrial electron transfer system, ubiquinol or reduced [[coenzyme Q]] can be found, while in the photosynthetic systems plastoquinols (particularly PQ9) are common. These redox compounds exist in three different redox states: [[quinone]] (oxidized), quinol (reduced), and an intermediate [[semiquinone]].[[semiquinone]].)
Quinone + ('''Quinone''' is a class of ''oxidized'' o … '''Quinone''' is a class of ''oxidized'' organic compounds with a fully conjugated cyclic dione structure derived from aromatic compounds. [[Ubiquinone]] or coenzmye Q is the naturally occurring quinone in the mitochondrial [[ETS]], while in the photosynthetic system plastoquinones are common. The quinone is reduced either to an unstable semiquinone by one hydrogen atom or to a quinol by two electrons and two protons.a quinol by two electrons and two protons.)
Rapamycin + ('''Rapamycin''' is an inhibitor of the mam … '''Rapamycin''' is an inhibitor of the mammalian/mechanistic target of rapamycin, complex 1 (mTORC1). Rapamycin induces autophagy and dyscouples mitochondrial respiration. Rapamycin delays senescence in human cells, and extends lifespan in mice without detrimental effects on mitochondrial fitness in skeletal muscle. mitochondrial fitness in skeletal muscle.)
Reactive nitrogen species + ('''Reactive nitrogen species''', RNS, are nitric oxide-derived oxidants. The main source of RNS is [[nitric oxide]] (NO•). NO• plays an important role in cell signaling and in oxidative-nitrosative stress.)
Reactive oxygen species + ('''Reactive oxygen species''', ROS, are mo … '''Reactive oxygen species''', ROS, are molecules derived from molecular [[oxygen]], including free oxygen radicals, which are more reactive than O2. Physiologically and pathologically important ROS include [[superoxide]], the [[hydroxyl radical]] and [[hydroxide ion]], [[hydrogen peroxide]] and other [[peroxides]]. These are important in cell signalling, oxidative defence mechanisms and [[oxidative stress]].[[oxidative stress]].)
Reference material + ('''Reference material''' (RM) is material … '''Reference material''' (RM) is material or substance one or more of whose property values are sufficiently homogeneous and well established to be used for the calibration of an apparatus, the assessment of a measurement procedure, or for assigning values to materials (adapted from VIM: 1993, 6.13). The adjective 'homogeneous' refers to the physical homogeneity between macroscopic parts of the material, not to any microheterogeneity between molecules of the analyte.'''Primary reference material''' is reference material having the highest metrological qualities and whose value is determined by means of a primary reference measurement procedure. The concept "primary calibrator" is subordinate to "calibrator" (see 3.7) and to "primary reference material". 3.7) and to "primary reference material".)
References in BEC https-format + ('''References in BEC https-format''' show … '''References in BEC https-format''' show (''1'') the list of authors, (''2'') the year of publication in parentheses, (''3'') the title of the publication, and (''4'') the https://doi.org/ link. Removing all the unnecessary detail of journal name and pages, the focus is on authors, year, and title of the reference, which is a concept in line with [[DORA]]. The https-link then does the full job. In exceptional cases when there is no such link, the following formats would apply: a https://pubmed.ncbi.nlm.nih.gov/ link, a link directly to an Open Access pdf, or the old conventional format for the reference. Scientific journals apply ''yesterday's concepts'' in the various formats of references with bewildering abbreviations of journals, volumes, issues, page numbers. We can do ''today's job'' much better using the BEC https-format: # Arese Lucini F, Morone F, Tomassone MS, Makse HA (2021) Diversity increases the stability of ecosystems. https://doi.org/10.1371/journal.pone.0228692# Begley CG, Ioannidis JPA (2015) Reproducibility in science: improving the standard for basic and preclinical research. https://doi.org/10.1161/CIRCRESAHA.114.303819. # Buranyi S (2017) Is the staggeringly profitable business of scientific publishing bad for science? https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science # Cardoso LHD, Doerrier C, Gnaiger E (2021) Magnesium Green for fluorometric measurement of ATP production does not interfere with mitochondrial respiration. https://doi.org/10.26124/bec:2021-0001 # Day S, Rennie S, Luo D, Tucker JD (2020) Open to the public: paywalls and the public rationale for open access medical research publishing. https://doi.org/10.1186/s40900-020-0182-y# Gnaiger E (2001) Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. https://doi.org/10.1016/S0034-5687(01)00307-3 # ….Compare with a conventional reference format in: Gnaiger E (2021) Beyond counting papers – a mission and vision for scientific publication. https://doi.org/10.26124/bec:2021-0005ic publication. https://doi.org/10.26124/bec:2021-0005)
Reliability + ('''Reliability''' relates the magnitude of … '''Reliability''' relates the magnitude of the measurement error in observed measurements (i.e., precision or intermediate precision) to the inherent variability in the ‘error-free’, ‘true’, or underlying level of the quantity between subjects. The value of the reliability takes a value between 0 and 1. When the variability value is zero, indicates that all the variability in the measurements is due to measurement error. And, on the contrary, when the value is 1 indicates that there is a zero error in the measurement error. It is also known as the intraclass correlation, as it equals the correlation between any two measurements made on the same subject.two measurements made on the same subject.)
Repetitions + ('''Repetitions''' of an [[experiment]] … '''Repetitions''' of an [[experiment]] or [[assay]] are designed to obtain statistical information on the methodological [[precision]] of the measurements. A number of repetitions, ''n'', of measurements are performed on the same sample, applying an identical experimental protocol to subsamples, without providing any information on variability between samples.nformation on variability between samples.)
Replica + ('''Replica''' are designed in scientific [[study |studies]] … '''Replica''' are designed in scientific [[study |studies]] to evaluate the effect of uncontrolled variability on a result obtained from an [[experiment]] on a single [[sample]], to describe the variability and distribution of experimental results, and to obtain statistical information such as the median or average for a defined [[sample size]]. It may be useful to make a terminological distinction between ''replica'' of experiments, ''N'', designed to obtain statistical information on the [[population]], and ''[[repetitions]]'' of [[experiment]]s or [[assay]]s, ''n'', designed to obtain statistical information on the methodological [[precision]] of the measurements. The terms [[study]], [[experiment]] and [[assay]] have to be defined carefully in this context.e to be defined carefully in this context.)
Research + ('''Research''' is a term composed of '''se … '''Research''' is a term composed of '''search''' and '''re'''. What does this tell us? The best comparison of the English with a German word is ''Untersuchung'', composed of ''suchung'' (search) and ''unter'' (below). The term ''search'' (suchen) is straightforward to understand and comparable in both languages. The prefix ''re'' and ''unter'' are more difficult to reconcile, yet in both languages these perfixes reveal complementary if not nearly identical messages. ''re'' means {''Quote''} back to the original place; again, anew, once more {''end of Quote''} [1], whereas ''unter'' means ''below'' or ''underneath''. Re-search, therefore, is not simply the search or investigation of some topic or problem, it means essentially doing the search again and again (re -> re-producibility) and penetrating ''below'' a simple search by reaching out for an underlying level of the search. The ''re'' in re-search and re-producibility has to be extended ultimately from a single re-search group to inter-laboratory re-investigation. This tells us, therefore, that while ''search'' is valuable, ''re-search'' provides the necessary validation. This re-evaluation of confirmative re-search should be re-cognized as the most important strategy to address the [[reproducibility crisis]].[[reproducibility crisis]].)
Resorufin + ('''Resorufin''' is a fluorescence probe us … '''Resorufin''' is a fluorescence probe used in various biological assays. Among others, it is the product obtained in the [[Horseradish_peroxidase| Horseradish peroxidase]]-catalyzed assay using [[Amplex_red| Amplex Red]] for the measurement of [[Hydrogen_peroxide| H2O2]] production.[[Hydrogen_peroxide| H2O2]] production.)
Respiratory complexes + ('''Respiratory Complexes''' are membrane-bound enzymes consisting of several subunits which are involved in energy transduction of the respiratory system. [[Respiratory Complexes#Respiratory Complexes - more than five |» '''MiPNet article''']])
Respiratory state + ('''Respiratory states''' of [[mitochondrial preparations]] … '''Respiratory states''' of [[mitochondrial preparations]] and [[living cells]] are defined in the current literature in many ways and with a diversity of terms. Mitochondrial respiratory states must be defined in terms of both, the [[coupling-control state]] and the [[electron-transfer-pathway state]].[[electron-transfer-pathway state]].)
Respirometry + ('''Respirometry''' is the quantitative mea … '''Respirometry''' is the quantitative measurement of respiration. ''Respiration is therefore a combustion, a very slow one to be precise'' (Lavoisier and Laplace 1783). Thus the ''basic idea of using calorimetry to explore the ''sources'' and ''dynamics'' of heat changes were present in the origins of bioenergetics'' ([[Gnaiger_1983_J Exp Zool|Gnaiger 1983]]). Respirometry provides an ''indirect'' calorimetric approach to the measurement of metabolic heat changes, by measuring oxygen uptake (and carbon dioxide production and nitrogen excretion in the form of ammonia, urea, or uric acid) and converting the oxygen consumed into an [[enthalpy]] change, using the [[oxycaloric equivalent]]. Liebig (1842) showed that the substrate of oxidative respiration was protein, carbohydrates, and fat. ''The sum of these chemical changes of materials under the influence of living cells is known as [[metabolism]]'' (Lusk 1928). The amount (volume STP) of carbon dioxide expired to the amount (volume STP) of oxygen inspired simultaneously is the respiratory quotient, which is 1.0 for the combustion of carbohydrate, but less for lipid and protein. Voit (1901) summarized early respirometric studies carried out by the ''Munich school'' on patients and healthy controls, concluding that ''the metabolism in the body was not proportional to the combustibility of the substances outside the body, but that protein, which burns with difficulty outside, metabolizes with the greatest ease, then carbohydrates, while fats, which readily burns outside, is the most difficultly combustible in the organism.'' Extending these conclusions on the ''sources'' of metabolic heat changes, the corresponding ''dynamics'' or respiratory control was summarized (Lusk 1928): ''The absorption of oxygen does not cause metabolism, but rather the amount of the metabolism determines the amount of oxygen to be absorbed. .. metabolism regulates the respiration.''.. metabolism regulates the respiration.'')
Resting metabolic rate + ('''Resting respiration''' or '''resting me … '''Resting respiration''' or '''resting metabolic rate''' (RMR) is measured under standard conditions of an 8–12-h fast and a 12-h abstinence from exercise. In an exemplary study ([[Haugen 2003 Am J Clin Nutr]]), "subjects rested quietly in the supine position in an isolated room with the temperature controlled to 21–24° C. RMR was measured for 15–20 min. Criteria for a valid RMR was a minimum of 15 min of steady state, determined as a <10% fluctuation in oxygen consumption and <5% fluctuation in respiratory quotient". The main difference between RMR and BMR ([[basal metabolic rate]]) is the position of the subject during measurement. Resting metabolic rate is the largest component of the daily energy budget in most human societies and increases with physical training state ([[Speakman 2003 Proc Nutr Soc]]).man 2003 Proc Nutr Soc]]).)
Resveratrol + ('''Resveratrol''' is a natural bioactive phenol prouced by several plants with antioxidant and anti-inflammatory effects. Dietary intake as nutraceutical is discussed for targeting mitochondria with a wide spectrum of action in degenerative diseases.)
Risk management + ('''Risk management''' is the identification, assessment, and prioritization of risks.)
Rotenone + ('''Rotenone''' is an inhibitor of [[Complex I]] (CI) and thus inhibits NADH oxidation. It inhibits the transfer of electrons from iron-sulfur clusters in CI to ubiquinone via binding to the ubiquinone binding site of CI. See also [[Succinate pathway]].)
Ruthenium red + ('''Ruthenium red''' (synonym: ammoniated r … '''Ruthenium red''' (synonym: ammoniated ruthenium oxychloride) inhibits the mitochondrial Ca2+ uniporter. However, in addition it has been shown to interact with and inhibit a large number of other proteins, including ion channels particularly of the Transient Receptor Potential Vanilloid (TRPV) family [1], Ca2+-ATPases, and, importantly, the voltage-dependent anion channel (VDAC) [2]. and, importantly, the voltage-dependent anion channel (VDAC) [2].)
SF6847 + ('''SF6847''' (C18H& … '''SF6847''' (C18H22N2O), also known as tyrphostin A9 or malonoben, is a protonophore and a very potent [[uncoupler]] of [[oxidative phosphorylation]], being used in the nM range. Like all uncouplers, SF6847 concentrations must be titrated carefully to evaluate the [[Uncoupler#Optimum_uncoupler_concentration|optimum concentration]] for maximum stimulation of mitochondrial respiration, particularly to avoid inhibition of respiration at higher concentrations.ion, particularly to avoid inhibition of respiration at higher concentrations.)
SGp-pathway control state + ('''SGp''': [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' SGp; obtained with OctPGMSGp(Rot) '''SUIT protocol:''' [[SUIT-001]] and ((SUIT-002)
SUIT + ('''SUIT''' is the abbreviation for '''S''' … '''SUIT''' is the abbreviation for '''S'''ubstrate-'''U'''ncoupler-'''I'''nhibitor '''T'''itration. SUIT protocols are used with mt-preparations to study respiratory control in a sequence of coupling and pathway control states induced by multiple titrations within a single experimental assay. These studies use biological samples economically to gain maximum information with a minimum amount of cells or tissue. with a minimum amount of cells or tissue.)
Safranin + ('''Safranin''' is one of the most establis … '''Safranin''' is one of the most established dyes for measuring [[mitochondrial membrane potential]] by [[fluorometry]]. It is an [[extrinsic fluorophores |extrinsic fluorophore]] with an excitation wavelength of 495 nm and emission wavelength of 587 nm. Safranin is a potent inhibitor of [[NADH electron transfer-pathway state |N-linked respiration]] and of the [[phosphorylation system]].''Synonyms:'' Safranin O, Safranin Y, Safranin T, Gossypimine, Cotton Red, Basic Red2nin T, Gossypimine, Cotton Red, Basic Red2)
Salicylhydroxamic acid + ('''Salicylhydroxamic acid''' (SHAM; synony … '''Salicylhydroxamic acid''' (SHAM; synonym: 2-Hydroxybenzohydroxamic acid N,2-Dihydroxybenzamide) is an inhibitor of the [[alternative oxidase]] (AOX). When AOX is blocked by SHAM, electrons are forced through the CIII-cytochrome ''c'' oxidase pathway, allowing observation of the operation of the CIII-CIV pathway without AOX activity.the CIII-CIV pathway without AOX activity.)
Sample mass concentration + ('''Sample mass [[concentration]]''' is ''C''''m''s = ''m''s·''V''-1 [kg·m-3].)
Sample size + ('''Sample size''' is an ambiguous term. (1 … '''Sample size''' is an ambiguous term. (1) Size can be measured as an extensive quantity in terms of [[mass]] ''m''S [kg], [[volume]] ''V''S [m3], or [[energy]] ''E''S [J] of a pure [[sample]] S. If the sample consists of countable [[entity |entities]] ''X'', the [[count]] ''N''''X'' [x] in sample S is an elementary quantity, in contrast to the extensive quantities used as indicators of sample size. (2) In statistics, however, the term 'sample size' does not refer to the individual sample, but indicates on the contrary the number of samples investigated or sampled from a study group. ''N'' is the number of [[sample]]s collected and assayed to obtain representative statistical information on the [[population]]. The population size defines the upper limit of the statistical sample size.[[population]]. The population size defines the upper limit of the statistical sample size.)
Saponin + ('''Saponin''' is a mild detergent that [[Permeabilization of plasma membrane|permeabilizes plasma membranes]] … '''Saponin''' is a mild detergent that [[Permeabilization of plasma membrane|permeabilizes plasma membranes]] completely and selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Applied for [[Permeabilized tissue or cells|permeabilization of muscle fibres]].[[Permeabilized tissue or cells|permeabilization of muscle fibres]].)
Save and Disconnect + ('''Save and Disconnect''': Stops data acquisition and disconnects from the O2k (only for DatLab 7))
Save as - DatLab + ('''Save as''' a DatLab file. When disconnected from the O2k, save the file under a different file name, optionally in a different directory.)
Save - DatLab + ('''Save''' a DatLab file. When disconnecte … '''Save''' a DatLab file. When disconnected from the O2k, save any changes made under the identical file name overwriting the previous file. Such changes do not affect the raw data of the experiment, but relate to calibrations, experimental protocol, marks, events, and layout.ental protocol, marks, events, and layout.)
Scaling factor + ('''Scaling factor''' determines the multiplication factor that is applied to the time derivative of the signal.)
Scaling - DatLab + ('''Scaling''' a graph in [[DatLab]] … '''Scaling''' a graph in [[DatLab]] provides flexibility to vary the display of the plots and create Graph layouts. It allows viewing a data plot in differently scaled graphs, zooming the signal and time scales, and scrolling along the axes of the graph provide maximum information on the current experiment. This does not influence the format of stored data. Different ranges for the axes change the appearance of data dramatically. It is highly recommended to use reference layouts. »''Compare:'' [[Select plots - DatLab]].[Select plots - DatLab]].)
Select O2k - DatLab + ('''Select O2k - DatLab''')
Selectivity + ('''Selectivity''' is the ability of a sensor or method to quantify accurately and specifically the analyte or analytes in the presence of other compounds.)
Semiquinone + ('''Semiquinone''' is an unstable free radical derived either from the removal of one hydrogen atom with its electron from [[quinol]] (reduced form), or by the addition of a single hydrogen atom to a [[quinone]] (oxidized form).)
Sensitivity + ('''Sensitivity''' refers to the response obtained for a given amount of analyte and is often denoted by two factors: the limit of detection and the limit of quantification.)
Serial port + ('''Serial port''' describes the connection … '''Serial port''' describes the connection between O2k and Computer. With the [[USB-Cable 2.0\Type A-B]] connected, select '''Serial port''' in the [[Connection window]]. Depending on the [[O2k series]], it is possible to connect with a '''Serial port''' or [[USB port]].[[USB port]].)
Shredder-Accessory Box + ('''Shredder-Accessory Box''': for storage and shipping of Shredder accessories.)
Sirtuins + ('''Sirtuins''' are NAD++-dependent deacetylases which play a prominent role as metabolic regulators. Their dependence on intracellular levels of NAD+ (NAD+ activates sirtuin activity, whereas NADH inhibits it) makes them suitable as sensors that can detect cellular energy status.[[Sirtuins#Sirtuin_family |» '''MiPNet article''']][[Sirtuins#Sirtuin_family |» '''MiPNet article''']])
Azide + ('''Sodium azide''' is an inhibitor of [[Complex IV]]/cytochrome ''c'' oxidase (CIV, COX, CcO).)
Sodium fluoride + ('''Sodium fluoride (NaF)''' is used in combination with [[beryllium sulfate]] to form beryllium trifluoride (BeF3−), to inhibit the [[ATP synthase]] if it is exposed by disruption of the mitochondrial membranes.)
Sodium orthovanadate + ('''Sodium vanadate (Na3VO4)''' is used as an ATPase inhibitor.)
Specific quantity + ('''Specific quantities''' are obtained whe … '''Specific quantities''' are obtained when the [[extensive quantity]] is divided by system size, in contrast to [[intensive quantity|intensive quantities]]. ''The adjective'' specific ''before the name of an extensive quantity is often used to mean divided by mass'' ([[Cohen 2008 IUPAC Green Book |Cohen et al 2008]]). A mass-specific quantity (''e.g.'', mass-specific flux is flow divided by mass of the system) is independent of the extent of non-interacting homogenous subsystems. If mass-specific oxygen flux is constant and independent of system size (expressed as mass), then there is no interaction between the subsystems. The well-established scaling law in respiratory physiology reveals a strong interaction of oxygen consumption and body mass by the fact that mass-specific basal metabolic rate (oxygen flux) does not increase proportionally and linearly with body mass. Maximum mass-specific oxygen flux, ''V''O2max, is less mass-dependent across a large range of body mass of different mammalian species (Weibel and Hoppeler 2005).ifferent mammalian species (Weibel and Hoppeler 2005).)
Spectrophotometry + ('''Spectrophotometry''' is the use of a [[spectrophotometer]] … '''Spectrophotometry''' is the use of a [[spectrophotometer]] to measure the transmittance, reflectance or remittance of a material as a function of wavelength. See [[transmission spectrophotometry]], [[reflectance spectrophotometry]] and [[remission spectrophotometry]].[[remission spectrophotometry]].)
Spectroscopy + ('''Spectroscopy''' is a broader term than [[spectrophotometry]] in that it is concerned with the investigation and measurement of spectra produced when matter interacts with or emits any form electromagnetic radiation.)
Speed + ('''Speed''', ''v'' [m·s-1</s … '''Speed''', ''v'' [m·s-1], is the [[distance]], ''s'' [m], covered by a particle per unit time, irrespective of geometrical direction in space. Therefore, speed is not a [[vector]], in contrast to [[velocity]]. ''v'' = d''s''/d''t'' [m·s-1][velocity]]. ''v'' = d''s''/d''t'' [m·s-1])
Spermidine + ('''Spermidine''' is a polycationic bioacti … '''Spermidine''' is a polycationic bioactive polyamine mainly found in wheat germ, soybean and various vegetables, involved in the regulation of mitophagy, cell growth and cell death. Like other caloric restriction mimetics, spermidine is effective in cardioprotection, neuroprotection and anticancer immunosuppression by preserving mitochondrial function and control of autophagy.ondrial function and control of autophagy.)
Stability + ('''Stability''' determines the accuracy of intensity and [[absorbance]] measurements as a function of time. Instability (see [[drift]] introduces systematic errors in the [[accuracy]] of [[fluorescence]] and [[absorbance]] measurements.)
State 1 + ('''State 1''' is the first respiratory sta … '''State 1''' is the first respiratory state in an oxygraphic protocol described by [[Chance_1955_JBC-III|Chance and Williams (1955)]], when isolated mitochondria are added to mitochondrial respiration medium containing oxygen and inorganic phosphate, but no ADP and no reduced respiratory substrates. In State 1, [[LEAK respiration]] may be supported to some extent by undefined endogenous substrates, which are oxidized and slowly exhausted. After oxidation of endogenous substrates, only residual oxygen consumption remains ([[ROX]]).[[ROX]]).)
State 5 + ('''State 5''' is the [[respiratory state]] … '''State 5''' is the [[respiratory state]] obtained in a protocol with isolated mitochondria after a sequence of [[State 1]] to [[State 4]], when the concentration of O2 is depleted in the closed oxygraph chamber and zero oxygen (the anaerobic state) is reached ([[Chance 1955 JBC-III|Chance and Williams, 1955]]; Table I).State 5 is defined in the original publication in two ways: ''State 5 may be obtained by antimycin A treatment or by anaerobiosis'' (Chance and Williams, 1955; page 414). [[Antimycin A]] treatment yields a State 5 equivalent to a state for measurement of [[residual oxygen consumption]], ROX (which may also be induced by [[rotenone]]+[[myxothiazol]]; [[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]). Setting State 5 equivalent to ROX or anoxia (Chance and Williams 1955) can be rationalized only in the context of measurement of cytochrome redox states, whereas in the context of respiration State 5 is usually referred to as [[anoxic]].[[anoxic]].)
Stirrer power + ('''Stirrer power''' is switched on and off during operation of the [[Oroboros O2k]] in [[DatLab]] by pressing [F11] (left chamber) and [F12] (right chamber), respectively. This is functional only with a stirrer bar added to each O2k chamber.)
Stopper-Shaft conical\white PVDF\central Port + ('''Stopper-Shaft conical\white [[PVDF]] … '''Stopper-Shaft conical\white [[PVDF]]\central Port''': PVDF shaft with one central capillary and conical base, receptacle on the top for collecting excess medium during closing the O2k-Chamber and during titration; component of [[Stopper\white PVDF\conical Shaft\central Port]].'''Discontinued'''[[Stopper\white PVDF\conical Shaft\central Port]]. '''Discontinued''')
Stray light + ('''Stray light''' is defined as the detect … '''Stray light''' is defined as the detected light of any wavelength that lies outside the [[bandwidth]] of the selected wavelength. In the presence of '''stray light''' of intensity ''I''''s'', the equation for [[transmittance]] (''T'') becomes ''T'' = (''I'' + ''I''''s'')/(''I''''0'' + ''I''''s'') where ''I''''0'' is the incident light intensity and ''I'' is the transmitted light intensity. Clearly, the lower the value of ''I'', the more dominant becomes the '''stray light''' term and so can cause errors in the quantification of low [[fluorescence]] signals or at high levels of [[absorbance]].[[absorbance]].)
Strobilurin + ('''Strobilurin''': {''Quote''} Strobilurin … '''Strobilurin''': {''Quote''} Strobilurins are a group of chemical compounds used in agriculture as fungicides. They are part of the larger group of QoI inhibitors, which act to inhibit {''end of Quote'': [http://en.wikipedia.org/wiki/Strobilurin]} respiratory [[Complex III]].[[Complex III]].)
Submitochondrial particles + ('''Submitochondrial particles''' (smtp) co … '''Submitochondrial particles''' (smtp) consist of membrane fragments which retain most of the enzymatic machinery required in electron transfer and [[oxidative phosphorylation]]. Such membrane fragments are continuous closed vesicles formed by resealing of mt-membrane fragments after disruption of the mitochondrial structure. smtp are used to isolate the inner-[[membrane-bound ET pathway]] (mETS) from the upstream modules of the [[Electron transfer pathway]] (ETS) which are located in the mt-matrix and outer mt-membrane (transporters). smtp are obtained by treatment of mitochondria with membrane-dispersing agents such as digitonin at high concentration or by sonic irradiation.igh concentration or by sonic irradiation.)
Subsample + ('''Subsamples''' can be obtained (1) from … '''Subsamples''' can be obtained (1) from a homogenous [[sample]] (e.g. cell suspension, tissue homogenate, isolated mitochondria), (2) as subsamples obtained by splitting a sample into comparable parts (e.g. permeabilized muscle fibres from a biopsy split into different chambers for repeated measurements), or (3) repetitive sampling (e.g. taking multiple biopsies) at a single time point. Subsamples may be used for (i) application of different types of [[assay]] (e.g. for measurement of respiration and enzyme activities), and (ii) a number of [[repetitions]], ''n'', of the same assay on the same sample.n'', of the same assay on the same sample.)
Subscripts in physical chemistry + ('''Subscripts in physical chemistry''' are … '''Subscripts in physical chemistry''' are used to differentiate symbols of different quantities. While these subscripts need to be short to be readable, they have to be distinct and well defined. Several subscripts relate to fundamental terms and concepts, summarized in a list below. and concepts, summarized in a list below.)
Pathway control ratio + ('''Substrate control ratios''' are [[flux control ratio]] … '''Substrate control ratios''' are [[flux control ratio]]s ''FCR'', at a constant mitochondrial [[coupling-control state]]. Whereas there are only three well-defined coupling-control states of mitochondrial respiration, ''L'', ''P'', ''E'' ([[LEAK respiration]], [[OXPHOS]], [[Electron transfer pathway]]), numerous [[Electron-transfer-pathway state]]s are possible. Careful selection of the reference state, ''J''ref, is required, for which some guidelines may be provided without the possibility to formulate general rules. ''FCR'' are best defined by taking ''J''ref as the maximum flux (e.g. [[NS |NS''E'']]), such that flux in various other respiratory states, ''Ji'', is smaller or equal to ''J''ref. However, this is not generally possible with ''FCR''. For instance, the [[N/S pathway control ratio]] (at constant coupling-control state) may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The [[S-pathway control state]] may be selected preferentially as ''J''ref, if mitochondria with variable [[N]]-linked injuries are studied. In contrast, the [[reference state]], ''Z'', is strictly defined for [[flux control efficiency]].[[flux control efficiency]].)
Succinate dehydrogenase + ('''Succinate dehydrogenase''' is a [[TCA cycle]] … '''Succinate dehydrogenase''' is a [[TCA cycle]] enzyme converting [[succinate]] to [[fumarate]] while reducing FAD to FADH2. SDH is the largest component of the mt-inner membrane [[Complex II]] (CII) and thus part of the TCA cycle and [[electron transfer pathway]].[[electron transfer pathway]].)
Succinyl-CoA ligase + ('''Succinyl-CoA ligase''' (SUCLA or SUCLG) … '''Succinyl-CoA ligase''' (SUCLA or SUCLG) is a TCA cycle enzyme converting succinyl-CoA + ADP or (GDP) + Pi to [[succinate]] + ATP (GTP). Two different isoforms exsist: SUCLA (EC: 6.2.1.5) is the ATP-forming isoenzyme, SUCLG (EC: 6.2.1.4) is the GTP-forming isoenzyme. Both reactions are reversible. This reaction is attributed to mitochondrial substrate-level phosphorylation, which is considered as an alternative way of ATP synthesis because it is partially independent from the respiratory chain and from the mitochondrial proton motive force.rom the mitochondrial proton motive force.)
Sulfide quinone reductase + ('''Sulfide quinone reductase''' (SQR) is i … '''Sulfide quinone reductase''' (SQR) is involved in electron transfer from sulfide which is used as a hydrogen donor by the mitochondrial respiratory system. SQR is associated with a [[dioxygenase]] and a [[sulfur transferase]] to release thiosulfate (H2S2O3).(H2S2O3).)
Sulfite oxidase + ('''Sulfite oxidase''' (SO) is a dimeric en … '''Sulfite oxidase''' (SO) is a dimeric enzyme, located in the intermembrane space of mitochondria, with each monomer containing a single Mo cofactor and cyt b5-type heme [1]. SO catalyzes the oxidation of sulfite to sulfate as the terminal step in the metabolism of sulfur amino acids and is vital for human health. Inherited mutations in SO result in severe neurological problems, stunted brain growth, and early death [2]. Function: SO catalyzes the terminal reaction in the oxidative degradation of sulfur amino acids with the formation of a sulfate, electrons pass to cytochrom ''c'' and are further utilized in the respiratory system.Sulfite + O2 + H2O --> Sulfate + H2O2 Localization: The level of expression of SO differs in various tissues with main predominant localization in liver, kidney, skeletal muscle, heart, placenta, and brain in humans and liver, kidney, heart, brain, and lung in rats [3]. Deficiency: SO is vital for metabolic pathways of sulfur amino acids (cysteine and methionine). Complete lack of this enzyme, typically caused by gene mutation, leads to lethal disease called sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.ed sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.)
Synchronous time axes + ('''Synchronous time axes''' sets, if ticked, the time axes of all graphs at an identical range and offset, which is particularly useful while panning.)
T-Shirt: Oroboros black/organic cotton + ('''T-Shirt Oroboros black/organic cotton''': An Oroboros on the front.)
TIP2k and O2k-upgrade\B + ('''TIP2k and O2k-Upgrade\B''': Titration-Injection microPump TIP2k, including the electronic upgrade of the O2k-main unit returned to workshop (Series B-D). '''Discontinued''')
TIP2k cooling box + ('''TIP2k-Cooling Box''': Cooling box for TIP2k syringes. '''Discontinued''')
TIP2k-Needle Safety Support + ('''TIP2k-Needle Safety Support''': for safe storage of TIP2k-needles when not required during the experiment. This item is a standard component of the [[TIP2k-Module]].)
TMRM + ('''TMRM''' (tetramethylrhodamine methyl es … '''TMRM''' (tetramethylrhodamine methyl ester) is an [[extrinsic fluorophores|extrinsic fluorophore]] used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. TMRM is a lipophilic cation that is accumulated in the mitochondrial matrix in proportion to Δ''ψ''mt. Upon accumulation of the dye it exhibits a red shift in its absorption and fluorescence emission spectrum. The fluorescence intensity is quenched when the dye is accumulated in the mitochondrial matrix.en the dye is accumulated in the mitochondrial matrix.)
Tetrahydrofolate + ('''Tetrahydrofolate''', THF, is the substrate in mitochondrial folate-mediated 1C metabolism, an [[NADH-linked pathway]] leading to the formation of formate which is exported to the cytosol.)
Tetraphenylphosphonium + ('''Tetraphenylphosphonium''' (TPP+). A lipophilic molecular probe in conjunction with an ion selective electrode (ISE) for [[Mitochondrial membrane potential | measuring the mitochondrial membrane potential]].)
Thenoyltrifluoroacetone + ('''Thenoyltrifluoroacetone''' TTFA is a noncompetitive inhibitor of CII binding on the quinone-binding (SDHC/SDHD).)
Thioredoxin reductase + ('''Thioredoxin reductase''' (TrxR) is a family of enzymes able to reduce thioredoxin in mammals.)
Time resolution + ('''Time resolution''' in respirometric measurements is influenced by three parameters: the [[response time of the POS]], the data sampling interval and the number of points used for flux calculation.)
Traceability + ('''Traceability''' is the property of the … '''Traceability''' is the property of the result of a measurement or the value of a standard whereby it can be related to stated references, usually national or international standards, through an unbroken chain of comparisons all having stated uncertainties [SOURCE: VIM:1993, definition 6.10].nties [SOURCE: VIM:1993, definition 6.10].)
Trueness of measurement + ('''Trueness of measurement''' is the close … '''Trueness of measurement''' is the closeness of agreement between the average value obtained from a large series of results of measurements and a true value (adapted from ISO 3534-1:1993, definition 3.12). The degree of trueness is usually expressed numerically by the statistical measure bias that is inversely related to trueness and is the difference between the expectation of the results of measurement and a true value of the [[measurand]].[[measurand]].)
Trueness + ('''Trueness''' is understood as the lack of [[bias]] and the instrument calibration procedures are the key factor on establishing and correcting it.)
USB-RS232 Serial Adapter + ('''USB-RS232 Serial Adapter''', for connec … '''USB-RS232 Serial Adapter''', for connecting the [[RS232-Cable]] attached to the [[O2k-Main Unit]] (Series A-D) to the USB port of the PC or laptop. This is not required for O2k-Series E, nor when using a PC or laptop with a serial RS232 port. '''Discontinued'''th a serial RS232 port. '''Discontinued''')
Uncertainty of measurement + ('''Uncertainty of measurement''' is a para … '''Uncertainty of measurement''' is a parameter, associated with the result of a [[measurement]], that characterizes the dispersion of the values that could reasonably be attributed to the [[measurand]]. The parameter can be, for example, a standard deviation (or a given multiple of it), or the half-width of an interval having a stated level of confidence. The components of uncertainty are evaluated experimentally from statistical distributions (Type A) or evaluated from assumed probability distributions based on experience or other information (Type B). All components are expressed as standard uncertainties that are combined into one final expression.at are combined into one final expression.)
Uncoupling protein 1 + ('''Uncoupling protein 1''' (UCP1) is also … '''Uncoupling protein 1''' (UCP1) is also called thermogenin and is predominantly found in brown adipose tissue (BAT). UCP1 belongs to the gene family of [[uncoupling proteins]]. It is vital for the maintenance of body temperature, especially for small mammals. As the essential component of non-shivering thermogenesis, it possesses the ability to build and open a pore in the inner mitochondrial membrane through which protons may flow along their electrochemical gradient, generated by respiration, bypassing the ATP-producing re-entry site at the F1F0-ATP synthase. Thereby the energy stored in the electrochemical gradient is dissipated as heat.rochemical gradient is dissipated as heat.)
Uncoupling protein 2 + ('''Uncoupling protein 2''' (UCP2) belongs to the gene family of [[uncoupling proteins]]. Whereas [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]], this may not be the case for UCP2.)
Uncoupling proteins + ('''Uncoupling proteins''' (UCPs) are mitoc … '''Uncoupling proteins''' (UCPs) are mitochondrial anion carrier proteins that can be found in the inner mitochondrial membranes of animals and plants. [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]] by dissipating the electrochemical proton gradient ([[mitochondrial membrane potential]]), generated by the [[electron transfer pathway]] by pumping protons from the mitochondrial matrix to the mitochondrial intermembrane space. to the mitochondrial intermembrane space.)
Units in figures and tables + ('''Units in figures and tables''' are spec … '''Units in figures and tables''' are specified together with the numerical values. The ''value'' of a quantity ''Q'' is the product of a [[number]] ''N'' and a [[unit]] ''u''''Q''. Abstract units ''u''''Q'' (such as dm3=L, kg, J) are linked to measured quantities (such as volume, mass, energy): Eq.(1) ''Q''''u'' = ''N''·''u''''Q''The multiplication in Eq.(1) can be handled like any mathematical equation and re-arranged to the form which indicates the meaning (left) of a number (right): Eq.(2a) ''Q''''u''/''u''''Q'' = ''N'' Eq.(2b) ''N''''X''/x = ''N''When numbers are given on the axes of figures and in tables, the corresponding labels should be indicated according to Eq.(2), where Eq.(2a) applies to measured quantities, whereas Eq.(2b) relates to the countable quantity, i.e. [[count]] with unit [x]. For example, the axis label for volume-specific oxygen flux may be written as ''J''''V'',O2 / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''O2 / [amol/(s·x)].s ''J''''V'',O2 / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''O2 / [amol/(s·x)].)
Velocity + ('''Velocity''', '''''v''''' [m·s … '''Velocity''', '''''v''''' [m·s-1], is the [[speed]] in a defined spatial direction, and as such velocity is a [[vector]]. Velocity is the [[advancement]] in distance per unit time, '''''v''''' ≡ d'''''z''''' ∙ d''t''-1 [m·s-1] d'''''z''''' ∙ d''t''-1 [m·s-1])
Viable cells + ('''Viable cells''' vce are characterized by an intact plasma membrane barrier function. The total cell count (''N''ce) is the sum of viable cells (''N''vce) and dead cells (''N''dce).)
Viton + ('''Viton'''® is a fluoroelastomer with excellent resistance to aggressive fuels and chemicals. Viton is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (Viton O-rings).)
Volume + ('''Volume''' ''V'' is a derived quantity b … '''Volume''' ''V'' is a derived quantity based on the SI base quantity [[length]] [m] and is expressed in terms of [[SI base units]] in the derived unit cubic meter [m3]. The liter [L = dm3] is a conventional unit of volume for concentration and is used for most solution chemical kinetics. The volume ''V'' contained in a system (experimental chamber) is separated from the environment by the system boundaries; this is called the volume of the system, and described in practical language as big/small (derived from [[length]], [[height]]) or voluminous. Systems are defined at constant volume or constant [[pressure]]. For a pure sample S, the volume ''V''S of the pure sample equals the volume ''V'' of the system, ''V''S = ''V''. For [[sample]] s in a mixture, the ratio ''V''s·''V''-1 is the nondimensional [[volume fraction]] ''Φ''s of sample s. Quantities divided by volume are [[concentration]]s of sample s in a mixture, such as [[count]] concentration ''CX'' = ''NX''·''V''-1 [x·L-1], and amount of substance concentration ''C''B = ''n''B·''V''-1 [mol·L-1]. Mass concentration is [[density]] ''ρ''s = ''m''s·''V''-1 [kg·L-1]. In closed compressible systems (with a gas phase), the concentration of the gas increases, when pressure-volume [[work]] is performed on the system.is performed on the system.)
Wavelength averaging + ('''Wavelength averaging''' is the averagin … '''Wavelength averaging''' is the averaging of several adjacent data points across the recorded spectrum (spectral [[smoothing]]), to improve the [[signal-to-noise ratio]]. For example, if the instrument recorded 5 data points per nm, the average of the 5 points can be taken for each successive nm across the range of the spectrum to give a 5-point smoothing. This method clearly reduces the wavelength [[resolution]].[[resolution]].)
Work + ('''Work''' [J] is a specific form of [[energy]] … '''Work''' [J] is a specific form of [[energy]] in the First Law of thermodynamics, and a specific form of [[exergy]] in the Second Law of thermodynamics, performed by a closed or open system on its surroundings (the environment). This is the definition of ''external'' work, which is zero in [[isolated system]]s. The term exergy includes external and internal work. Mechanical work is force [N] times path length [m]. The internal-energy change of a closed system, d''U'', is due to external exchange (e) of work and heat, and external total work (et, including pressure-volume work) is the internal-energy change minus heat, det''W'' = d''U'' - de''Q''b>et''W'' = d''U'' - de''Q'')
Zero calibration + ('''Zero calibration''' is, together with [[air calibration]] … '''Zero calibration''' is, together with [[air calibration]], one of the two steps of the POS calibration. It is performed in the [[closed chamber]] after all the oxygen has been depleted by the addition of [[dithionite]] or by respiration of [[Isolated mitochondria |imt]] or [[Living cells |cells]]. Any incubation medium can be used for zero calibration with dithionite or sample. Unlike air calibration, it is not necessary to perform a zero calibration on each experimental day. After performing a zero calibration, it is recommended not running other experiments on the same day. Even after standard cleaning of the O2k-chambers, there might be residual amounts of reduced dithionite in the chamber, affecting the oxygen flux in subsequent experiments performed on the same day.ent experiments performed on the same day.)
DatLab 2 + ('''[[DatLab]] 2''' (DL2) is a MS-DOS programe. DL2 is still used for analysis of [[oxygen kinetics]], after exporting files recorded in recent DatLab versions. A user-friendly O2-kinetics module is in preparation (DL8).)
Substrates as electron donors + ('''[[Substrate]] … '''[[Substrate]]s as electron donors''' are reduced fuel compounds ''S''red that are oxidized to an oxidized product ''P''ox during H+-linked electron transfer, ''S''red → ''P''ox + 2{H+ + e-}. Mitochondrial respiration depends on a continuous flow of electron-supplying substrates across the mitochondrial membranes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.anes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.)
Base quantities and count + ('''[[Template:Base quantities and count]]''')
ArXiv preprint server + ('''arXiv''' is a classic preprint server i … '''arXiv''' is a classic preprint server initiated in 1991 by Paul Ginsparg. {''Quote''} arXiv.org is a highly-automated electronic archive and distribution server for research articles. Covered areas include physics, mathematics, computer science, nonlinear sciences, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. arXiv is maintained and operated by Cornell University with guidance from the arXiv Scientific Advisory Board and the arXiv Member Advisory Board, and with the help of numerous subject moderators. {''end of Quote''}. arXiv rejects abstracts that are submitted without accompanying paper. are submitted without accompanying paper.)
BioRxiv preprint server for biology + ('''bioRxiv''' (pronounced "bio-archive") i … '''bioRxiv''' (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It was launched in 2013 by Cold Spring Harbor Laboratory Press in New York, and is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. bioRxiv is intended for rapid sharing of new research. Some review articles contain new data/analyses and may therefore be deemed appropriate. Reviews that solely summarize existing knowledge are not appropriate and neither are term papers, book excerpts, and undergraduate dissertations.excerpts, and undergraduate dissertations.)
PH calibration buffers + ('''pH calibration buffers''' are prepared to obtain two or more defined pH values for calibration of pH electrodes and pH indicator dyes.)
PH combination electrode 150/6 mm + ('''pH combination electrode''', 150 mm shaft, 6 mm diameter, incl. connection cable with BNC plug. '''Discontinued''' * Replaced by [[O2k-pH ISE-Module]].)
PH combination electrode 70/5 mm + ('''pH-Combination Electrode\70/5 mm''', 70 mm shaft, 5 mm diameter, for 30251-24 stopper. ''' Discontinued ''' * Replaced by [[O2k-pH ISE-Module]].)
PX calibration - DatLab + ('''pX calibration''')
Hydroxybutyrate + ('''β-hydroxybutyrate''' or 3-hydroxybutyrate is a ketone body that can be used as a [[NADH electron transfer-pathway state|NADH-linked substrate]]. The β-hydroxybutyrate dehydrogenase produces acetoacetate while reducing NAD+ to [[NADH]]. )
Complex I-linked substrate state + (''See'' '''[[N-pathway control state]]''' (previous: CI-linked) versus '''[[Complex I]]''')
CI control ratio + (''See'' '''[[N/NS pathway control ratio]]''')
Complex I&II-linked substrate state + (''See'' '''[[NS-pathway control state]]''' (previous: CI&II-linked))
Substrate control efficiency + (''See'' '''[[Pathway control efficiency]]''')
Substrate control ratio + (''See'' '''[[Pathway control ratio]]''')
Complex II-linked substrate state + (''See'' '''[[S-pathway control state]] (previous: CII-linked))
CII control ratio + (''See'' '''[[S/NS pathway control ratio]]''')
Group + (''See'' '''[[population]]'''.)
Phosphate + (''See:'' '''[[Inorganic phosphate]]''')
Standard operating procedures + (''The following definition is incomplete.'' '''Standard operating procedures''' are a set of step-by-step instructions to achieve a predictable, standardized, desired result often within the context of a longer overall process.)
Solution protocols + (''The following definition lacks quality control and is not applied as such in the Oroboros QM.'' '''Solution protocols''' contain media, substrates, uncouplers, inhibitors used in [[SUIT|SUIT protocols]], permeabilization agents, etc.)
Project + (''The following definition lacks quality c … ''The following definition lacks quality control and is not applied as such in the Oroboros QM.''A scientific project is a collection of [[experiment| experiments]] designed to proof or disproof a specific hypothesis. The [[experiment| experiments]] will follow the logic of the scientific discovery [1] on which a hypothesis will support a prediction and this will be tested by experimental [[assay| assays]] (''i.e.'', observations under controlled conditions). The result of these experiments will proof or disproof the specific hypothesis and, usually, provide new hypotheses to test. A scientific project must be carefully designed to obtain relevant statistical information through enough [[replica| data collection]].[1] Popper K (2002) The logic of scientific discovery. Routledge Classics. ISBN: 978-0-415-27843-0outledge Classics. ISBN: 978-0-415-27843-0)
Autoxidation + (''This definition is insufficient and need … ''This definition is insufficient and needs elaboration.''Autoxidation is a slow process implying oxidation of carbohydrates through oxygen in open air, leading to a primary formation of peroxides and hydroperoxides. UV radiation can speed up this process.s. UV radiation can speed up this process.)
Cellular substrates + ((1) Cellular substrates ''in vivo'', endogenous; '''Ce'''. (2) Cellular substrates ''in vivo'', with exogenous substrate supply from culture medium or serum; '''Cm'''. * ''This page needs an update.'')
Natoms O + (0.5 nmol O2; in bioenergetics a variety of expressions is used for units of amount of half a nmol molecular oxygen (natoms oxygen; natoms O; ng.atom O; nmol O), with the identical meaning: 0.5 nmol O2.)
BAM15 + (2-fluorophenyl){6-[(2-fluorophenyl)amino]( … 2-fluorophenyl){6-[(2-fluorophenyl)amino](1,2,5-oxadiazolo[3,4-e]pyrazin-5-yl)}amine ('''BAM15''') is a protonophore or uncoupler of [[Oxidative phosphorylation|oxidative phosphorylation]] detected in a screen for uncoupling agents exerting less toxicity than commonly used uncouplers and first described by [[Kenwood 2013 Mol Metab|Kennwood et al. 2013]]. In their comparison of BAM15 with FCCP it was shown to increase oxygen flux to a similar extent as the classical uncoupler, to display a much broader range of concentrations inducing maximum respiration, to stimulate no formation of H2O2, to leave cellular membrane potential unaffected, and to ultimately exert less cytotoxicity.e potential unaffected, and to ultimately exert less cytotoxicity.)
3-Mercaptopropionic acid + (3-Mercaptopropionic acid (MPA) inhibits long chain [[acyl-CoA dehydrogenase]]s (ACADs).)
Mitochondrial states and rates - terminology beyond MitoEAGLE 2020 + (666 coauthors of the 'MitoEAGLE white paper' [1] collaborated to reach a consensus on terminology related to mitochondrial respiratory states and rates. This page is intended to prepare a questionnaire and follow-up publication.)
Mitochondria Interest Group + ( [[File:MIG.gif|128 px|left]] … [[File:MIG.gif|128 px|left]]The '''Mitochondria Interest Group''' (MIG) is an Inter-Institute Interest Group at the National Institutes of Health (NIH), with members worldwide! MIG is concerned with all aspects of the mitochondrion and diseases in which the mitochondrion is involved. We hold monthly meetings, usually on the second Monday of the month (except when it is a Federal holiday or other special exceptions). [email protected] is an Email list moderated by Ph.D. Steven Zullo as an interactive information platform, with free subscritpion to this mitochondrial network. List members are reminded of their responsibility to critically evaluate the content of the postings. The information, opinions, data, and statements contained herein are not necessarily those of the U. S. Government, the National Institutes of Health (NIH), or MIG and should not be interpreted, acted on or represented as such.be interpreted, acted on or represented as such.)
Custom label + (A '''Custom label''' can be entered in this box to rename the axis label. Two lines are available for the axis name and unit.)
Digital Object Identifier + (A '''Digital Object Identifier''', DOI, is … A '''Digital Object Identifier''', DOI, is a persistent identifier used to uniquely identify online publications in order to ensure they remain traceable, searchable and citable over the long term. Compared to other types of persistent identifiers, the DOI system is widespread and well established in the life sciences arena, and it provides widely accepted visible proof that a publication is citable.sible proof that a publication is citable.)
Layout for DatLab graphs + (A '''Layout''' in [[DatLab]] … A '''Layout''' in [[DatLab]] selected in the Layout menu yields a standardized display of graphs and [[Plot - DatLab |plots]] displayed with specific [[Scaling - DatLab|scalings]]. The graph layout defines initial settings, which can be modified for plots [Ctrl+F6] and scaling [F6]. A modified layout can be saved as user layout without changing the standard layouts.out without changing the standard layouts.)
Lower O2 limit - DatLab + (A '''Lower O2 limit [µM]''' can be defined … A '''Lower O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O2 concentration drops below this limit. It reminds the user that re-oxygenation of the O2k-chamber may be required. For the lower O2 concentration limit, the [[critical oxygen pressure |critical oxygen concentration]] should be considered, which differs between isolated mitochondria, large cells, and permeabilized muscle fibers. A higher limit should be chosen when high oxygen flux is expected, e.g. prior to uncoupler titration. A lower limit is acceptable prior to inhibition of respiration causing low oxygen flux.ptable prior to inhibition of respiration causing low oxygen flux.)
National Standards Body + (A '''National Standards Body''' is the national member of the [[International Organization for Standardization]] (ISO).)
Notified Body + (A '''Notified Body''' is an organisation designated by an EU country to assess the conformity of certain products before being placed on the market.)
Quality audit + (A '''Quality Audit''' is the process of systematic examination of a quality system carried out by an internal or external quality auditor or an audit team.)
Stand alone application + (A '''Stand alone application''' is computer software that can work offline, i.e. does not necessarily require network connection to function or does not even provide the possibility to connect to a network.)
Upper O2 limit - DatLab + (A '''Upper O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O2 concentration rises beyond this limit.)
Web application + (A '''Web application''' is a computer software where the [[user interface]] gets accessed by the user through a web browser.)
Canonical ensemble + (A '''canonical ensemble''' is the group of … A '''canonical ensemble''' is the group of compartments enclosed in an isolated system '''H''', with a smaller compartment A1 in thermal equilibrium with a larger compartment A2 which is the heat reservoir at temperature ''T''. When A1 is large in the canonical sense, if its state can be described in terms of macroscopic thermodynamic quantities of ''V'', ''T'', and ''p'' merging with the state described as a probability distribution.T'', and ''p'' merging with the state described as a probability distribution.)