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2-mercaptoacetate +'''2-mercaptoacetate''' is an inhibitor of medium-chain acyl-CoA dehydrogenase, MCAD, the rate-limiting enzyme of [[octanoylcarnitine]] oxidation. 2-mercaptoacetate has been used as an inhibitor of [[fatty acid oxidation]] ([[F-pathway control state]]). In permeabilized rat soleus muscle fibers, pre-incubation with 1 mM 2-mercaptoacetate for 45 min resulted in 58% inhibition of MCAD and decreased [[octanoylcarnitine]]&[[malate]] stimulated respiration by approximately 60% ([[Osiki 2016 FASEB J]]).  +
A
ADP +'''Adenosine diphosphate''' is a nucleotide. In [[OXPHOS]] core metabolism, ADP is a substrate of [[ANT]] and [[ATP synthase]] in the [[phosphorylation system]]. ADP is the discharged or low-energy counterpart of [[ATP]]. ADP can accept chemical energy by regaining a phosphate group to become ATP, in substrate-level phosphorylation (in anaerobic catabolism), at the expense of solar energy (in photosynthetic cells) or chemiosmotic energy (respiration in heterotrophic cells). ADP is added to [[mitochondrial preparations]] at kinetically saturating concentrations to induce the active state for evaluation of [[OXPHOS capacity]].  +
AMPK +'''AMP-activated protein kinase''' is a regulatory protein which acts as crucial cellular energy sensor by sensing AMP, [[ADP]] and/or Ca<sup>2+</sup> levels in response to metabolic stresses or drug administration.  +
ASAPbio +Science only progresses as quickly and efficiently as it is shared. But even with all of the technological capabilities available today, the process of publishing scientific work is taking longer than ever. '''ASAPbio''' (Accelerating Science and Publication in biology) is a scientist-driven nonprofit working to address this problem by promoting innovation and transparency in life sciences communication. In 2015, ASAPbio founder Ron Vale published an analysis of the increasing time to first-author publication among graduate students at UCSF, and proposed a more widespread use of preprints in the life sciences as a potential solution.  +
ATP +'''Adenosine triphosphate''' is a nucleotid and functions as the major carrier of chemical energy in the cells. As it transfers its energy to other molecules, it looses its terminal phosphate group and becomes adenosine diphosphate ([[ADP]]).  +
ATP synthase +'''ATP synthase''' or '''F-ATPase''' (the use of Complex V is discouraged) catalyzes the [[endergonic]] phosphorylation of [[ADP]] to [[ATP]] in an over-all [[exergonic]] process that is driven by proton translocation along the [[protonmotive force]]. The ATP synthase can be inhibited by [[oligomycin]].  +
ATPases +'''ATPases''' are enzymes that hydrolyse [[ATP]], releasing [[ADP]] and [[inorganic phosphate]]. The contamination of isolated mitochondria with ATPases from other organelles and endogenous adenylates can lead to the production of ADP, which can stimulate respiration. This situation would lead to an overestimation of [[LEAK-respiration]] measured in the absence of ADP, ''L''(n) and subsequent inhibition of respiration by oligomycin, ''L''(Omy).  +
Absorbance +Also known as attenuation or extinction, '''absorbance''' (''A'') is a measure of the difference between the [[incident light]] intensity (''I''<sub>0</sub>) and the intensity of light emerging from a sample (''I''). It is defined as: ''A'' = log (''I''<sub>0</sub>/''I'')  +
Absorbance spectrum +When light enters a sample, the amount of light that it absorbs is dependent upon the wavelength of the incident light. The '''absorbance spectrum''' is the curve derived by plotting the measured [[absorbance]] against the wavelength of the light emerging from the sample over a given [[wavelength range]]. An [[absorbance spectrum]] may be characterised by peaks and troughs (absorbance maxima and minima) that can be used to identify, and sometimes quantify, different absorbing substances present in a sample.  +
Absorption +When light enters a sample and emerges with an intensity (''I''), '''absorption''' (''Abs'') is the fraction of the light absorbed by the sample compared with the [[incident light]] intensity (''I''<sub>''0''</sub>): ''Abs'' = 1-''I''/''I''<sub>''0''</sub>. Absorption can also be expressed as ''Abs'' = 1-''T'', where ''T'' is the [[transmittance]].  +
Absorption spectrum +An '''absorption spectrum''' is similar to an [[absorbance spectrum]] of a sample, but plotted as a function of [[absorption]] against wavelength.  +
Acceleration +'''Acceleration''', '''''a''''', is the change of [[velocity]] over time [m·s<sup>-2</sup>]. '''''a''''' = d'''''v'''''/d''t'' The symbol ''g'' is used for acceleration of free fall. The standard acceleration of free fall is defined as ''g''<sub>n</sub> = 9.80665 [m·s<sup>-2</sup>].  +
Acclimation +'''Acclimation''' is an immediate time scale adaptation expressing pheotypic plasticity in response to changes of a single variable under controlled laboratory conditions.  +
Acclimatization +'''Acclimatization''' is an immediate time scale adaptation expressing phenotypic plasticity in response to changes of habitat conditions and life style where several variables may change simultaneously.  +
Accuracy +The '''accuracy''' of a method is the degree of agreement between an individual test result generated by the method and the true value.  +
Activity +The '''activity''' (relative activity) is a dimensionless quantity related to the concentration or partial pressure of dissolved substances. The activity of a dissolved substance B equals the [[concentration]], ''c''<sub>B</sub> [mol·L<sup>-1</sup>], at high dilution divided by the unit concentration, ''c''° = 1 mol·L<sup>-1</sup>: ''a''<sub>B</sub> = ''c''<sub>B</sub>/''c''° This simple relationship applies frequently to substances at high dilutions <10 mmol·L<sup>-1</sup> (<10 mol·m<sup>-3</sup>). In general, the concentration of a [[solute]] has to be corrected for the activity coefficient (concentration basis), ''γ''<sub>B</sub>, ''a''<sub>B</sub> = ''γ''<sub>B</sub>·''c''<sub>B</sub>/''c''° At high dilution, ''γ''<sub>B</sub> = 1. For a dissolved gas G, the activity is the partial pressure, ''p''<sub>G</sub> [Pa] (strictly: fugacity), divided by the unit partial pressure, ''p''° = 1 Pa. The partial pressure is related to the concentration of the gas by the [[solubility]], ''S''<sub>G</sub> [Pa/mol] (''see'' [[Oxygen solubility]]): ''a''<sub>G</sub> = ''c''<sub>G</sub>·''S''<sub>G</sub>/''p''° In general, the relative activity is defined by the chemical potential, ''µ''<sub>X</sub> ''a''<sub>X</sub> = exp[(''µ''<sub>X</sub>-''µ''°)/''RT'']  +
Acyl-CoA oxidase +'''Acyl-CoA oxidase''' is considered as a rate-limiting step in peroxysomal ''β''-oxidation, which carries out few ''β''-oxidation cycles, thus shortening very-long-chain fatty acids (>C<sub>20</sub>). Electrons are directly transferred from FADH<sub>2</sub> to O<sub>2</sub> with the formation of H<sub>2</sub>O<sub>2</sub>.  +
Adaptation +'''Adaptation''' is an evolutionary time scale expression of phenotypic plasticity in response to selective pressures prevailing under various habitat conditions.  +
Add Graph/Delete bottom graph +The active graph is selected by a left click into the graph. The active graph is highlighted and indicated by the Oroboros logo. '''Add:''' A new graph is added at the bottom of the screen. Select plots for display in the new graph, Ctrl+F6 '''Delete: ''' By clicking '''Delete bottom graph''' in the Graph-menu in [[DatLab]], the bottom graph is deleted, which reappears with the same layout by '''Add'''.  +
Additive effect of convergent electron flow +'''Additivity''' describes the princple of substrate control of mitochondrial respiration with [[convergent electron flow]]. The '''additive effect of convergent electron flow''' is a consequence of electron flow converging at the '''[[Q-junction]]''' from respiratory Complexes I and II ([[NS-linked substrate state |NS or CI<small>&</small>II e-input]]). Further additivity may be observed by convergent electron flow through [[Glycerophosphate_dehydrogenase_complex|glycerophosphate dehydrogenase]] and [[electron-transferring flavoprotein complex]]. Convergent electron flow corresponds to the operation of the [[TCA cycle]] and mitochondrial substrate supply ''in vivo''. Physiological substrate combinations supporting convergent NS e-input are required for reconstitution of intracellular TCA cycle function. Convergent electron flow simultaneously through Complexes I and II into the [[Q-junction]] supports higher [[OXPHOS-capacity]] and [[ET-capacity]] than separate electron flow through either CI or CII. The convergent [[NS]] effect may be completely or partially additive, suggesting that conventional bioenergetic protocols with [[Mitochondrial preparations|mt-preparations]] have underestimated cellular OXPHOS-capacities, due to the gating effect through a single branch. Complete additivity is defined as the condition when the sum of separatly measured respiratory capacities, N + S, is identical to the capacity measured in the state with combined substrates, NS (CI<small>&</small>II). This condition of complete additivity, NS=N+S, would be obtained if electron channeling through supercomplex CI, CIII and CIV does not interact with the pool of redox intermediates in the pathway from CII to CIII and CIV, and if the capacity of the phosphorylation system (≈''P'') does not limit OXPHOS-capacity ([[Excess E-P capacity factor |excess ''E-P'' capacity factor]] is zero). In most cases, however, additivity is incomplete, NS < N+S.  +
Adenine nucleotide translocase +The '''adenine nucleotide translocator''', ANT, exchanges [[ADP]] for [[ATP]] in an electrogenic antiport across the inner mt-membrane. The ANT is inhibited by [[atractyloside]], [[carboxyatractyloside|carboxyatractyloside]] and [[bongkrekik acid]]. The ANT is a component of the [[phosphorylation system]].  +
Adenine nucleotides +'''Adenine nucleotides''', which are also sometimes referred to as adenosines or adenylates, are a group of organic molecules including AMP, [[ADP]] and [[ATP]]. These molecules present the major players of energy storage and transfer.  +
Adenylate kinase +'''Adenylate kinase''', which is also called myokinase, is a phosphotransferase enzyme that is located in the mitochondrial intermembrane space and catalyzes the rephosphorylation of AMP to ADP in the reaction ATP + AMP ↔ ADP + ADP.  +
Advancement +In an isomorphic analysis, any form of [[flow]] is the '''advancement''' of a process per unit of time, expressed in a specific [[motive unit]] [MU∙s<sup>-1</sup>], ''e.g.'', ampere for electric flow or current, ''I''<sub>el</sub> = d<sub>el</sub>''ξ''/d''t'' [A≡C∙s<sup>-1</sup>], watt for thermal or heat flow, ''I''<sub>th</sub> = d<sub>th</sub>''ξ''/d''t'' [W≡J∙s<sup>-1</sup>], and for chemical flow of reaction, ''I''<sub>r</sub> = d<sub>r</sub>''ξ''/d''t'', the unit is [mol∙s­<sup>-1</sup>] ('''extent of reaction''' per time). The corresponding motive [[force]]s are the partial exergy (Gibbs energy) changes per advancement [J∙MU<sup>-1</sup>], expressed in volt for electric force, Δ<sub>el</sub>''F'' = ∂''G''/∂<sub>el</sub>''ξ'' [V≡J∙C<sup>-1</sup>], dimensionless for thermal force, Δ<sub>th</sub>''F'' = ∂''G''/∂<sub>th</sub>''ξ'' [J∙J<sup>-1</sup>], and for chemical force, Δ<sub>r</sub>''F'' = ∂''G''/∂<sub>r</sub>''ξ'', the unit is [J∙mol<sup>-1</sup>], which deserves a specific acronym [Jol] comparable to volt [V]. For chemical processes of reaction (spontaneous from high-potential substrates to low-potential products) and compartmental diffusion (spontaneous from a high-potential compartment to a low-potential compartment), the advancement is the amount of motive substance that has undergone a compartmental transformation [mol]. The concept was originally introduced by De Donder [1]. Central to the concept of advancement is the [[stoichiometric number]], ''ν''<sub>''i''</sub>, associated with each motive component ''i'' (transformant [2]). In a chemical reaction, r, the motive entity is the stoichiometric amount of reactant, d<sub>r</sub>''n''<sub>''i''</sub>, with stoichiometric number ''ν''<sub>''i''</sub>. The advancement of the chemical reaction, d<sub>r</sub>''ξ'' [mol], is defined as, d<sub>r</sub>''ξ'' = d<sub>r</sub>''n''<sub>''i''</sub>·''ν''<sub>''i''</sub><sup>-1</sup> The flow of the chemical reaction, ''I''<sub>r</sub> [mol·s<sup>-1</sup>], is advancement per time, ''I''<sub>r</sub> = d<sub>r</sub>''ξ''·d''t''<sup>-1</sup> This concept of advancement is extended to compartmental diffusion and the advancement of charged particles [3], and to any discontinuous transformation in compartmental systems [2], :::: [[File:Advancement.png|100px]]  +
Advancement per volume +'''Advancement per volume''' or volume-specific advancement, d<sub>tr</sub>''Y'', is related to [[advancement]] of a transformation, d<sub>tr</sub>''Y'' = d<sub>tr</sub>''ξ''∙''V''<sup>-1</sup> [MU∙L<sup>-1</sup>]. Compare d<sub>tr</sub>''Y'' with the amount of substance ''j'' per volume, ''c''<sub>''j''</sub> ([[concentration]]), related to [[amount]], ''c''<sub>''j''</sub> = ''n''<sub>''j''</sub>∙''V''<sup>-1</sup> [mol∙''V''<sup>-1</sup>]. Advancement per volume is particularly introduced for chemical reactions, d<sub>r</sub>''Y'', and has the dimension of concentration (amount per volume [mol∙L<sup>-1</sup>]). In an [[open system]] at steady-state, however, the concentration does not change as the reaction advances. Only in [[closed system]]s and [[isolated system]]s, specific advancement equals the change in concentration divided by the stoichiometric number, d<sub>r</sub>''Y'' = d''c''<sub>''j''</sub>/''ν''<sub>''j''</sub> (closed system) d<sub>r</sub>''Y'' = d<sub>r</sub>''c''<sub>''j''</sub>/''ν''<sub>''j''</sub> (general) With a focus on ''internal'' transformations (i; specifically: chemical reactions, r), d''c''<sub>''j''</sub> is replaced by the partial change of concentration, d<sub>r</sub>''c''<sub>''j''</sub> (a transformation variable or process variable). d<sub>r</sub>''c''<sub>''j''</sub> contributes to the total change of concentration, d''c''<sub>''j''</sub> (a system variable or variable of state). In open systems at steady-state, d<sub>r</sub>''c''<sub>''j''</sub> is compensated by ''external processes'', d<sub>e</sub>''c''<sub>''j''</sub> = -d<sub>r</sub>''c''<sub>''j''</sub>, exerting an effect on the total concentration change of substance ''j'', d''c''<sub>''j''</sub> = d<sub>r</sub>''c''<sub>''j''</sub> + d<sub>e</sub>''c''<sub>''j''</sub> = 0 (steady state) d''c''<sub>''j''</sub> = d<sub>r</sub>''c''<sub>''j''</sub> + d<sub>e</sub>''c''<sub>''j''</sub> (general)  +
Advantage of preprints +The '''advantages of preprints''', the excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences are discussed by N Bhalla (2016).  +
Aerobic +The '''aerobic''' state of metabolism is defined by the presence of oxygen (air) and therefore the potential for oxidative reactions (ox) to proceed, particularly in [[oxidative phosphorylation]] (OXPHOS). Aerobic metabolism (with involvement of oxygen) is contrasted with [[anaerobic]] metabolism (without involvement of oxygen): Whereas anaerobic ''metabolism'' may proceed in the absence or presence of oxygen (anoxic or oxic ''conditions''), aerobic ''metabolism'' is restricted to oxic ''conditions''. Below the [[critical oxygen pressure]], aerobic ATP production decreases.  +
Affinity of reaction +The concept of '''affinity''' and hence chemical force is deeply rooted in the notion of '''attraction''' (and repulsion) of alchemy, which was the foundation of chemistry originally, but diverted away from laboratory experiments towards occult secret societies [1].<sup>**</sup> Newton's extensive experimental alchemical work and his substantial written track record on alchemy (which he did not publish) is seen today as a key inspiration for his development of the concept of the gravitational force [2-4]. This marks a transition of the meaning of affinity, from the descriptive 'adjacent' (proximity) to the causative 'attractive' (force) [5]. Correspondingly, Lavoisier (1790) equates affinity and force [6]: “''... the degree of force or affinity with which the acid adheres to the base''” [5]. By discussing the influence of electricity and gravity on chemical affinity, Liebig (1844) considers affinity as a force [7]. This leads to Guldberg and Waage's [[mass action ratio]] ('Studies concerning affinity', 1864; see [5]), the free energy and chemical affinity of Helmholtz (1882 [8]), and chemical thermodynamics of irreversible processes [9], where flux-force relations are center stage [10]. According to the IUPAC definition, the '''affinity of reaction''', ''A'' [J·mol<sup>-1</sup>], equals the negative molar Gibbs energy of reaction [11], which is the negative Gibbs [[force]] of reaction (derivative of [[Gibbs energy]] per [[advancement]] of reaction [12]): -''A'' = Δ<sub>r</sub>''F'' = ∂''G''/∂<sub>r</sub>''ξ'' The historical account of affinity is summarized by concluding, that today affinity of reaction should be considered as an isomorphic motive '''force''' and be generalized as such. This will help to (''1'') avoid confusing reversals of sign conventions (repulsion = negative attraction; pull = negative push), (''2'') unify symbols across classical and nonequilibrium thermodynamics [12,13], and thus (''3'') facilitate interdisciplinary communication by freeing ourselves from the alchemical, arcane scientific nomenclature.  +
Air calibration +'''Air calibration''' of an oxygen sensor (polarographic oxygen sensor) is performed routinely on any day before starting a respirometric experiment. The volume fraction of oxygen in dry air is constant. An aqueous solution in equilibrium with air has the same partial pressure as that in water vapour saturated air. The water vapour is a function of temperature only. The partial oxygen pressure in aqueous solution in equilibrium with air is, therefore, a function of total barometric pressure and temperature. Bubbling an aqueous solution with air generates deviations from barometric pressure within small gas bubbles and is, therefore, not recommended. To equilibrate an aqueous solution ata known partial pressure of oxygen [kPa], the aqueous solution is stirred rigorously in a chamber enclosing air at constant temperature. The concentration of oxygen, ''c''<sub>O2</sub> [µM], is obtained at any partial pressure by multiplying the partial pressure by the oxygen solubility, ''S''<sub>O2</sub> [µM/kPa]. ''S''<sub>O2</sub> is a function of temperature and composition of the salt solution, and is thus a function of the experimental medium. The [[Oxygen_solubility_factor|solubility factor]] of the medium, ''F''<sub>M</sub>, expresses the oxygen solubility relative to pure water at any experimental temperature. ''F''<sub>M</sub> is 0.89 in serum (37 °C) and 0.92 in [[MiR06]] or [[MiR05]] (30 °C and 37 °C).  +
Alternative oxidase +The alternative oxidase is a membrane-bound enzyme capable of supporting [[cyanide| cyanide]]-and [[Antimycin_A| antimycin A]]-resistant mitochondrial respiration. It catalyzes the oxidation of ubiquinol and the reduction of oxygen to water in a four-electron process. As this bypasses several proton-translocating steps, induction of this alternative pathway is associated with a dramatic reduction of ATP production. AOX is found in most plants (including microalgae), many fungi and protists, but is not expressed in animals. AOX is inhibited by [[salicylhydroxamic acid]] (SHAM). Expression and activity of the enzyme are modified by environmental conditions such as temperature, oxidative stress, nutrient availability, and pathogens such as viruses.  +
Ammonia solution concentrated +'''Concentrated ammonia solution''' (25%-30% ammonium hydroxide solution, ammonia) is used for the service of the polarographic oxygen sensor OroboPOS. After opening the commercial solution, the concentration of ammonia may decline during storage and may render the ammonia stock ineffective for sensor service. '''Source:''' A commercially available solution from a drugstore is sufficient for this cleaning purpose  +
Amount of substance +The '''amount of substance''', ''n'', is a base physical quantity, and the corresponding SI unit is the [[mole]] [mol]. Amount of substance (sometimes abbreviated as 'amount' or 'chemical amount') is proportional to the number of specified elementary entities, ''N''<sub>''i''</sub> of that substance ''i'', and the universal proportionality constant is the reciprocal value of the [[Avogadro constant]] [1], ''n''<sub>''i''</sub> = ''N''<sub>''i''</sub>/''N''<sub>A</sub> ''n''<sub>''i''</sub> contained in a system can change due to internal and external transformations, d''n''<sub>''i''</sub> = d<sub>i</sub>''n''<sub>''i''</sub> + d<sub>e</sub>''n''<sub>''i''</sub> In the absence of nuclear reactions, the amount of any atom is conserved, ''e.g.'', for carbon d<sub>i</sub>''n''<sub>C</sub> = 0. This is different for chemical substances or ionic species which are produced or consumed during the [[advancement]] of a reaction, r, :::: [[File:Amount dn.png|100px]] A change in the amount of ''i'', d''n''<sub>''i''</sub>, in an open system is due to both the internal formation in chemical transformations, d<sub>r</sub>''n''<sub>''i''</sub>, and the external transfer, d<sub>e</sub>''n''<sub>''i''</sub>, across the system boundaries. d''n''<sub>''i''</sub> is positive if ''i'' is formed as a product of the reaction within the system. d<sub>e</sub>''n''<sub>''i''</sub> is negative if ''i'' flows out of the system and appears as a product in the surroundings [2].  +
Amp calibration - DatLab +'''Amp calibration''' indicates the calibration of the amperometric O2k-channel.  +
Ampere +The ampere, symbol A, is the SI unit of electric current. It is defined by taking the fixed numerical value of the elementary charge ''e'' to be 1.602 176 634 × 10<sup>−19</sup> when expressed in the unit C, which is equal to A s, where the second is defined in terms of Δ''ν''<sub>Cs</sub>.  +
Amplex UltraRed +'''Amplex UltraRed''' (AmR) is used as an [[extrinsic fluorophores |extrinsic fluorophore]] for measurement of [[hydrogen peroxide]] production ([[ROS]]) by cells or mitochondrial preparations. The reaction of H<sub>2</sub>O<sub>2</sub> and AmR is catalyzed by [[horseradish peroxidase]] to produce the red fluorescent compound [[resorufin]] (excitation wavelength 563 nm, emission 587 nm). The change of emitted fluorescence intensity is directly proportional to the concentration of H<sub>2</sub>O<sub>2</sub> added, whereby the H<sub>2</sub>O<sub>2</sub> is consumed.  +
Amplitude +The '''amplitude''' of the [[absorbance spectrum]] can be described in terms of the [[absorbance]] differences between the characteristic peaks (absorbance maxima) and troughs (absorbance minima) (see [[absorbance spectrum]]) for substances present in the sample.  +
Amytal +'''Amytal''' sodium salt (synonym: amobarbital; 5-Ethyl-5-isoamylbarbituric acid) is a barbiturate drug and an inhibitor of [[Complex I]].  +
Anaerobic +'''Anaerobic''' metabolism takes place without the use of molecular oxygen, in contrast to '''[[aerobic]]''' metabolism. The capacity for energy assimilation and growth under '''[[anoxic]]''' conditions is the ultimate criterion for '''facultative anaerobiosis'''. Anaerobic ''metabolism'' may proceed not only under [[anoxic]] ''conditions'' or ''states'', but also under [[hyperoxic]] and [[normoxic]] conditions ('''aerobic glycolysis'''), and under [[hypoxic]] and [[microxic]] conditions below the [[limiting oxygen pressure]].  +
Anaplerosis +'''Anaplerosis''' is the process of formation of intermediates of the [[tricarboxylic acid cycle]]. [[Malic enzyme]] (mtME), phosphoenopyruvate carboxykinase (PEPCK), propionyl-CoA carboxylase, pyruvate carboxylase and [[proline dehydrogenase]] play important roles in anaplerosis.  +
Anaplerotic pathway control state +'''Anaplerotic pathway control states''' are fuelled by single substrates which are transported into the mitochondrial matrix and increase the pool of intermediates of the [[tricarboxylic acid cycle]]. [[Malic enzyme]] (mtME), phosphoenopyruvate carboxykinase (PEPCK), propionyl-CoA carboxylase, and pyruvate carboxylase play important roles in [[anaplerosis]]. The [[glutamate anaplerotic pathway control state]] and [[malate anaplerotic pathway control state]] are the most important anaplerotic substrate control states (aN).  +
Anoxic +Ideally the term '''anoxic''' (anox, without oxygen) should be restricted to conditions where molecular oxygen is strictly absent. Practically, effective anoxia is obtained when a further decrease of experimental oxygen levels does not elicit any physiological or biochemical response. The practical definition, therefore, depends on (i) the techiques applied for oxygen removal and minimizing oxygen diffusion into the experimental system, (ii) the sensitivity and limit of detection of analytical methods of measuring oxygen (O<sub>2</sub> concentration in the nM range), and (iii) the types of diagnostic tests applied to evaluate effects of trace amounts of oxygen on physiological and biochemical processes. The difficulties involved in defining an absolute limit between anoxic and [[microxic]] conditions are best illustrated by a logarithmic scale of oxygen pressure or oxygen concentration. In the '''''anoxic state''''' ([[State 5]]), any aerobic type of metabolism cannot take place, whereas '''''[[anaerobic]] metabolism''''' may proceed under oxic or anoxic conditions.  +
Antimycin A +'''Antimycin A''' is an inhibitor of [[Complex III]] (CIII). It binds to the Qi site of CIII and inhibits the transfer of electrons from heme ''b''<sub>H</sub> to oxidized Q (Qi site inhibitor). High concentrations of antimycin A also inhibit acyl-CoA oxidase and D-amino acid oxidase.  +
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).  +
Aqua destillata +'''Aqua destillata''' (a.d.) is the Latin name for '''distilled [[water]]''', H<sub>2</sub>O. When a.d. is used in various solution protocols, it may indicate that water with the highest possible quality or lowest possible level of impurities should be used, as may be reached not only with distilled water but also with high-purity deionised water.  +
ArXiv preprint server +'''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.  +
Ascorbate +In respiratory assays for cytochrome ''c'' oxidase activity ([[Complex IV|Complex IV, CIV]]), '''ascorbate''' is added as regenerating system for maintaining [[TMPD]] in a reduced state. As has to be titrated into the respiration medium prior to the addition of TMPD, otherwise the reaction velocity of [[autoxidation]] is permanently elevated.  +
Asia Society for Mitochondrial Research and Medicine +[[File:ASMRM LOGO.JPG|200px|left]]The '''Asia Society for Mitochondrial Research and Medicine''' (ASMRM) was founded in 2003 to share the latest knowledge on mitochondrial research.  +
Assay +An experimental '''assay''' is a method to obtain a measurement with a defined instrument on a [[sample]] or [[subsample]]. Multiple assay types may be applied on the same sample or subsample, if the measurement does not destroy it. For instance, the wet weight of a permeabilized muscle fibre preparation can be determined based on a specific laboratory protocol (gravimetric assay), maintaining the functional integrity of the sample, which then can be used in a respirometric assay, followed by a spectrophotometric assay for measurement of protein content. The experimental design determines which types of assays have to be applied for a complete experiment. Destructive assays, such as determination of protein content or dry weight, can be applied on a sample only after performing a respirometric assay, or on a separate subsample. The experimental variability is typically dominated by the assay with the lowest [[resolution]] or signal to noise ratio. The signal to noise ratio may be increased by increasing the number, ''n'', of [[repetitions]] of measurements on subsamples. Evaluation of procedural variation ('experimental noise') due to instrumental resolution and handling requires subsampling from homogenous samples.  +
Atractyloside +'''Atractyloside''' is an inhibitor of the [[Adenine nucleotide translocator|adenine nucleotide translocator (ANT)]]. It is an extremely toxic glycoside that inhibits oxidative phosphorylation by blocking the transfer of adenosine nucleotides through the mitochondrial membrane.  +
Attached cells +Many cell types are grown in culter as '''attached cells''', such as endothelial or neuronal cells in a monolayer.  +
Attribute +'''Attribute''' in general is a characteristic or property. In databases an attribute describes a column in a table. Rows then represent the according attribute values.  +
Auranofin +'''Auranofin''' (AF) is a gold complex which inhibites thioredoxin reductase (TrxR).  +
Automatic pan - DatLab +'''Automatic pan''' (only for real-time data recording) toggles automatic panning on/off by clicking in the [[O2k status line]]. If it is on (green), the time range is maintained while the time axis always shows the currently recorded data, i.e. the value of the offset (minimum value) increases as experimental time proceeds. If it is off (yellow), the time axis is static. This allows for manually panning backwards to observe previous sections of the experiment at a given time range. In this mode, the actual experimental time may be off-scale. Toggle between "Pan auto" and "Pan off" by a left-click on the text. It does not influence continuous data recording. It is recommended to maintain automatic panning on during the experiment, except for specifically viewing earlier sections of the experiment.  +
Autoscale +'''Autoscale''' zooms in or out of the selected period with [[Autoscale time axis]], [[Autoscale Y1 (Y2) axes]] and [[Automatic pan]].  +
Autoscale Y1 (Y2) axes +'''Autoscale Y1 (Y2) axes''': Autoscaling the measured values (full data range) on the Y1 (Y2) axis in the selected [[plot]].  +
Autoscale time axis +'''Autoscale time axis''' gives an overview of the entire experimental period.  +
Autoxidation +''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.  +
Averaging +In order to improve the [[signal-to-noise ratio]] a number of sequential spectra may be averaged over time. The number of spectra to be averaged can be set prior to carrying out the measurements, or afterwards during data analysis.  +
Avogadro constant +[[File:Table Physical constants.png|left|400px|thumb|]] The '''Avogadro constant''', ''N''<sub>A</sub>, has the SI unit [mol<sup>-1</sup>] (IUPAC), but more strictly the units for particles per amount is [x·mol<sup>-1</sup>] (compare [[Elementary charge]]). Therefore, the reciprocal of the Avogadro constant is the proportionality factor between the amount of substance and the number of specified elementary entities of that substance. The Avogadro constant times elementary charge is the [[Faraday constant]].  +
Azide +'''Sodium azide''' is an inhbitor of [[Complex IV|cytochrome c oxidase]] (COX, CcO).  +
B
BAM15 +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 H<sub>2</sub>O<sub>2</sub>, to leave cellular membrane potential unaffected, and to ultimately exert less cytotoxicity.  +
BME cutoff points +Cutoff points for [[body mass excess]], '''BME cutoff points''', define the critical values for underweight, overweight, obesity and various degrees of obesity. BME cutoffs are calibrated by crossover-points of BME with established BMI cutoffs. The underweight and severe underweight cutoff points are BME = -0.1 and -0.2. The overweight cutoff is BME = 0.2. Increasing degrees of obesity are defined by BME cutoffs of 0.4, 0.6, 0.8, and above.  +
Background state +The '''background state''', ''Y'', is the non-activated or inhibited respiratory state at background flux, which is low in relation to the higher flux in the [[reference state]], ''Z''. The transition from the background state to the reference state is a step change. A [[metabolic control variable]], ''X'' (substrate, activator), is added to the background state to stimulate flux to the level of the reference state. Alternatively, the metabolic control variable, ''X'', is an inhibitor, which is present in the background state, ''Y'', but absent in the reference state, ''Z''. The background state is the baseline of a single step in the definition of the [[flux control factor]]. In a sequence of step changes, the common [[baseline state]] is the state of lowest flux in relation to all steps, which can be used as a [[baseline correction]].  +
Balance +In transmission spectrophotometry [[blank]] [[cuvettes]] are used to record the [[incident light]] intensity (''I''<sub>''0''</sub>) prior to absorbance measurements. (See [[white balance]] for [[reflectance spectrophotometry]], [[remittance spectrophotometry]]).  +
Bandwidth +'''Bandwidth''' is measured in nanometers in terms of the full width half maximum of a peak. This is the portion of the peak that is greater than half of the maximum intensity of that peak.  +
Barometric pressure +'''Barometric pressure''', ''p''<sub>b</sub>, is an important variable measured for calibration of oxygen sensors in solutions equilibrated with air. The atm-standard pressure (1 atm = 760 mmHg = 101.325 kPa) has been replaced by the SI standard pressure of 100 kPa. The partial pressure of oxygen, ''p''<sub>O2</sub>, in air is a function of barometric pressure, which changes with altitude and locally with weather conditions. The partial oxygen pressure declines by 12% to 14% per 1,000 m up to 6,000 m altitude, and by 15% to 17% per 1,000 m between 6,000 and 9,000 m altitude. The [[O2k-Barometric Pressure Transducer]] is built into the Oroboros O2k as a basis for accurate air calibrations in high-resolution respirometry. For highest-level accuracy of calculation of oxygen pressure, it is recommended to compare at regular intervals the barometric pressure recording provided by the O2k with a calibrated barometric pressure recording at an identical time point and identical altitude. The concept of gas pressure or barometric pressure can be related to the generalized concept of isomorphic [[pressure]].  +
Barth Syndome +Barth Syndome (BTHS) is an X-linked genetic condition that is caused by a mutation in the tafazzin gene (taz). This mutation causes cardiolipin abnormalities, cardiomyopathy, neutropenia, muscle weakness, growth delay, and exercise intolerance. [https://www.barthsyndrome.org/about-barth-syndrome/overview-of-barth-syndrome Weblink] Contributed by [[Sparagna GC]] 2016-04-24  +
Basal respiration +'''Basal respiration''' or '''basal metabolic rate''' (BMR) is the minimal rate of metabolism required to support basic body functions, essential for maintenance only. BMR (in humans) is measured at rest 12 to 14 hours after eating in a physically and mentally relaxed state at thermally neutral room temperature. Maintenance energy requirements include mainly the metabolic costs of protein turnover and ion homeostasis. In many aerobic organisms, and particularly well studied in mammals, BMR is fully aerobic, i.e. direct calorimetry (measurement of [[heat dissipation]]) and indirect calorimetry (measurement of oxygen consumption multiplied by the [[oxycaloric equivalent]]) agree within errors of measurement (Blaxter KL 1962. The energy metabolism of ruminants. Hutchinson, London: 332 pp [1]). In many cultured mammalian cells, aerobic glycolysis contributes to total ATP turnover ([[Gnaiger_1990_Biochim Biophys Acta|Gnaiger and Kemp 1990]] [2]), and under these conditions, '[[respiration]]' is not equivalent to '[[metabolic rate]]'. Basal respiration in humans and skeletal muscle mitochondrial function (oxygen kinetics) are correlated ([[Larsen_2011_FASEB J|Larsen et al 2011]] [3]). » [[Basal_respiration#Basal_respiration_in_physiology.2C_cellular_bioenergetics_and_mitochondrial_physiology | '''MiPNet article''']]  +
Baseline state +The '''baseline state''' in a sequence of step changes is the state of lowest flux in relation to all steps, which can be used as a [[baseline correction]]. Correction for [[residual oxygen consumption]], ROX, is an example where ROX is the baseline state. In a single step, the baseline state is equivalent to the [[background state]].  +
Beer-Lambert law +This law states that the [[transmittance]] (''T'') of light though a sample is given by: ''T'' = e<sup>-''εbc''</sup>, where ''ε'' is the molar [[extinction coefficient]], ''b'' is the pathlength of the light through the cuvette (in mm) and ''c'' is the concentration of the pigment in the sample (in mM). Transforming this equation, it can be seen that the [[absorbance]] of light (''A'') is simply given by ''A'' = ''εbc''.  +
BioRxiv preprint server for biology +'''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.  +
Bioblasts +Richard Altmann (1894) defined the 'elementary organisms' as '''Bioblasts'''. He observed granula in cells stained with osmium and viewed ‘the protoplasm as a colony of bioblasts’. "Microorganisms and granula are at an equivalent level and represent elementary organisms, which are found wherever living forces are acting, thus we want to describe them by the common term bioblasts. In the bioblast, that morphological unit of living matter appears to be found." [[Altmann 1894 Verlag Von Veit & Comp|Altmann 1894]]; p. 141. Altmann is thus considered as the discoverer of [[mitochondria]] (the granula), which constitute together with the microorganisms the ''bioblasts'' (the elementary organisms). Bioblasts are the aliens with permanent residence in our cells ([[Bioblasts#Bioblasts_.E2.80.93_the_aliens_with_permanent_residence_in_our_cells|Gnaiger 2010]]).  +
Biochemical coupling efficiency +[[Image:j--P.jpg|50 px|link=OXPHOS coupling efficiency |OXPHOS coupling efficiency]] [[Image:j--E.jpg|50 px|link=ETS coupling efficiency |ET-coupling efficiency]] The '''biochemical coupling efficiency''' may be expressed as the [[OXPHOS coupling efficiency]], ''j<sub>≈P</sub>'' = (''P-L'')/''P'' = 1-''L/P'', or [[ET-coupling efficiency]], ''j<sub>≈E</sub>'' = (''E-L'')/''E'' = 1-''L/E'', which are equivalent at zero [[Excess E-P capacity |excess ''E-P'' capacity]] (''ExP'' = ''E-P'' = 0).  +
Biochemical threshold effect +Due to threshold effects, even a large defect diminishing the velocity of an individual enzyme results in only minor changes of pathway flux.  +
Biological contamination +Biological contamination may be caused by microbial growth in and experimental chamber or in the experimental medium.  +
Biological reference interval +'''Biological reference interval''' or reference interval is the central 95% interval of the distribution of reference values.  +
Biopsy preservation solution +'''Biopsy preservation solution''', for preservation of tissue samples, preparation of muscle fibres, and permeabilization with [[saponin]].  +
Blank +In [[fluorometry]] and [[transmission spectrophotometry]] '''blank''' [[cuvettes]] (with no samples in them) are used to carry out the [[balance]].  +
Block temperature +The '''block temperature''' of the [[Oroboros O2k]] is the continuously measured temperature of the copper block, housing the two glass chambers of the O2k. The block temperature is recorded by [[DatLab]] as one of the O2k system channels.  +
Blood cell preparation +'''Blood cell preparation''' (bcp) is one of the key steps in diagnostic protocols.  +
Blood plasma +'''Blood plasma''' is the non-cellular component of the blood. Plasma lacks cellular components of the blood, RBC, WBC and platelets. However, there are many proteins in plasma, i.e. fibrinogen, albumin and globulin. Both blood plasma and PRP maintain clotting activity after whole blood separation.  +
Blood serum +'''Blood serum''' is a purified plasma in which the coagulant components were removed from the [[blood plasma]]. It contains other substances, i.e. antibodies, antigens and hormones. Serum can be obtained by collecting the liquid phase after blood or plasma coagulation.  +
Body fat excess +Body fat is conventionally expressed as BF%, which is the percentage of body fat mass relative to the total [[body mass]]. In the [[healthy reference population]] (HRP), there is zero [[body fat excess]], and the fraction of excess body fat in the HRP is expressed - by definition - relative to the reference body mass, ''M''°, at any given [[height of humans |height]]. Although ''M''° is identical in females and males at any given height, the fraction of body fat is higher in females than males in the HRP, hence it is reasonable that the body fat excess, BFE, - but not BF% - represents the common risk factor and indicator of obesity. Importantly, body fat excess and [[body mass excess]], BME, are linearly related, which is not the case for the body mass index, BMI.  +
Body mass +The '''body mass''', ''M'', is the mass [kg] of an individual (object) [x] and is expressed in units [kg/x]. The individual (object) is a countable quantity, therefore, the unit [x] is a dimensionless number. The SI unit for mass (of a system), ''m'', is [kg] (1 kg = 1000 g). A system is not a countable quantity and thus is not a number. The SI symbol ''m'' is used to indicate the mass of a system or sample [kg], whereas the symbol ''M'' is used to indicate the mass of an individual (object) [kg·x<sup>-1</sup>]. Both, body mass [kg/x] and mass of a sample [kg] are [[Extensive quantity |extensive quantities]], which depend on the size of the individual or the sample. Whereas the body weight changes as a function of gravitational force (you are weightless at zero gravity; your floating weight in water is different from your weight in air), your mass is independent of gravitational force, and it is the same in air and water. The total body mass is the sum of lean body mass and fat mass, ''M'' = ''M''<sub>L</sub> + ''M''<sub>F</sub>, or the sum of the reference body mass of an individual at a given height in the [[healthy reference population]] and excess body mass, ''M'' = ''M''° + ''M''<sub>E</sub>. The excess body mass, in turn, is the sum of excess lean and [[Body fat excess |fat mass]], ''M''<sub>E</sub> = ''M''<sub>LE</sub> + ''M''<sub>FE</sub>. The [[body mass excess]], BME, is normalized for the reference body mass, BME = ''M''/''M''°.  +
Body mass excess +The '''body mass excess''', BME, is a lifestyle metric. The BME with respect to the [[healthy reference population]], HRP, is defined as BME <big>≝</big> Δ''M''/''M''°. Δ''M'' is the excess body mass exceeding the reference body mass, ''M''°, in the HRP. Thus the BME is a measure of the extent to which your actual [[body mass]], ''M'' [kg/x], deviates from ''M''° [kg/x], which is the reference body mass [kg] per individual [x] without excess body fat. The BME is expressed relative to the reference body mass for your [[Height of humans |height]], ''H'' [m]. A balanced BME is BME° = 0.0 with a band width of -0.1 towards underweight and +0.2 towards overweight. Considering a height of 1.78 m, the balanced body mass is ''M''° = 65.9 kg per individual, and overweight is reached at a weight gain of 20 % or BME = 0.2: (1+0.2)·''M''° = 79 kg per individual (body mass index BMI<sub>0.2</sub> = 24.9 kg/m<sup>2</sup>). At a height of 1.84 m, the balanced body mass is ''M''° = 72.4 kg/x, and obesity is reached at a weight gain of 40 % or BME = 0.4:(1.4·''M''° = 101.4 kg/x (BMI<sub>0.4</sub> = 29.9 kg/m<sup>2</sup>).  +
Boltzmann constant +[[File:Table Physical constants.png|left|400px|thumb|]] The '''Boltzmann constant''', ''k'', has the SI unit [J·K<sup>-1</sup>] (IUPAC), but more strictly the units for energy per particles per temperature is [J·x<sup>-1</sup>·K<sup>-1</sup>] (compare [[Gas constant]]).  +
Bongkrekik acid +'''Bongkrekik acid''' is a selective and potent inhibitor of the [[adenine nucleotide translocator]] (ANT). Bka binds to the matrix (negative) site of ANT, opposite of [[carboxyatractyloside]].  +
Bound energy +The '''bound energy''' change in a closed system is that part of the ''total'' [[energy]] change that is always bound to an exchange of [[heat]], d''B'' = d''U'' - d''A'' [Eq. 1] ∆''B'' = ∆''H'' - ∆''G'' [Eq. 2] The ''free'' energy change (Helmoltz or Gibbs; d''A'' or d''G'') is the ''total'' energy change (total inner energy or enthalpy, d''U'' or d''H'') of a system minus the ''bound'' energy change. Therefore, if a process occurs at [[equilibrium]], when d''G'' = 0 (at constant gas pressure), then d''H'' = d''B'', and at d<sub>e</sub>''W'' = 0 (d''H'' = d<sub>e</sub>''Q'' + d<sub>e</sub>''W''; see [[energy]]) we obtain the definition of the bound energy as the heat change taking place in an equilibrium process (eq), d''B'' = ''T''∙d''S'' = d<sub>e</sub>''Q''<sub>eq</sub> [Eq. 3]  +
Bovine serum albumine +Bovine serum albumine is a membane stabilizer, oxygen radical scavenger, and binds Ca2+ and free fatty acids, hence the rather expensive essentially free fatty acid free BSA is required in mitochondrial isolation and respiration media. Sigma A 6003 fraction V.  +
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]]  +
C
CDGSH iron-sulfur domain proteins +The CDGSH iron-sulfur domain (CISDs) family of proteins uniquely ligate labile 2Fe-2S clusters with a 3Cys-1His motif. CISD1 and CISD3 have been demonstrated to localize to the outer mitochondrial membrane and mitochondrial matrix respectively, however their relationship to mitochondrial physiology remains ill-defined [1]. The best characterized member of the CISD family, CISD1, has been demonstrated to be involved in respiratory capacity, iron homeostasis, and ROS regulation  +
CE +'''CE''' marking is a mandatory conformity marking for certain products sold within the European Economic Area (EEA).  +
CI control ratio +''See'' '''[[N/NS pathway control ratio]]'''  +
CII control ratio +''See'' '''[[S/NS pathway control ratio]]'''  +