Property:Description

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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'''.  +
'''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.  +
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''', 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''', 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.  +
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''' 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)  +
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).  +
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.  +
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''' 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).  +
'''Allegations of research misconduct''' are handled with care. Publishers and editors shall take reasonable steps to identify and prevent the publication of papers where research misconduct has occurred, including plagiarism, citation manipulation, and data falsification/fabrication, among others. In no case shall a journal or its editors encourage such misconduct, or knowingly allow such misconduct to take place. In the event that a journal's publisher or editors are made aware of any allegation of research misconduct relating to a published article in their journal, the publisher or editor shall follow [https://publicationethics.org/core-practices COPE's guidelines] (or equivalent) in dealing with allegations.  +
'''Alternative quinol oxidases''' AOX are membrane-bound enzymes capable of supporting [[cyanide]]- and [[antimycin A]]-resistant mitochondrial respiration. AOX 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 reduction of ATP production per oxygen consumed. 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.  +
'''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  +
The '''amount of substance''', ''n'', is a base physical quantity, and the corresponding SI unit is the [[mole]] [mol]. Amount of substance (sometimes abbreviated as 'amount' or 'chemical amount') is proportional to the number ''N''<sub>''X''</sub> of specified elementary entities ''X'', and the universal proportionality constant is the reciprocal value of the [[Avogadro constant]] ([[Bureau International des Poids et Mesures_2019_The International System of Units (SI) |SI]]), ''n''<sub>''X''</sub> = ''N''<sub>''X''</sub>·''N''<sub>A</sub><sup>-1</sup> ''n''<sub>''X''</sub> contained in a system can change due to internal and external transformations, d''n''<sub>''X''</sub> = d<sub>i</sub>''n''<sub>''X''</sub> + d<sub>e</sub>''n''<sub>''X''</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 ''X''<sub>''i''</sub>, 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 ''X''<sub>''i''</sub> is formed as a product of the reaction within the system. d<sub>e</sub>''n''<sub>''i''</sub> is negative if ''X''<sub>''i''</sub> flows out of the system and appears as a product in the surroundings ([[Cohen 2008 IUPAC Green Book]]).  +
'''Amp calibration''' indicates the calibration of the amperometric O2k-channel.  +
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>.  +
After selection of the Amperometric, Amp channel in the '''[[O2k configuration]]''', an Amperometric, Amp tab will appear in the '''O2k control''' [F7] window. Set the desired light intensity (0-1600) in the field ´Fluo intensity´ and the desired amplification of the signal (1-1000) in the field ´Gain for Fluo sensor´in the Amperometric, Amp window followed by a left-click '''Send to O2k'''. Switching off the [[Illumination on/off|illumination]] before each fluorometric measurement is routinely required.  +
'''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 fluorescenet product according to the supplier is called UltroxRed in the case of Amplex UltraRed which has a very similar structure to resorufin). 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.  +
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''' sodium salt (synonym: amobarbital; 5-Ethyl-5-isoamylbarbituric acid) is a barbiturate drug and an inhibitor of [[Complex I]].  +
'''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''' 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 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).  +
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.  +