Property:Description

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[[File:1OctM;2D;3PG;4S;5U;6Rot-.png|300px]]  +
[[File:1PGM;2D;3S;4Rot;5U-.png|300px]]  +
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'''2-Deoxyglucose''', also known as 2-deoxy-D-glucose is a glucose derivative which has the 2-hydroxyl group replaced by hydrogen. It competitively inhibits glycolysis by blocking hexokinase and phosphohexoseisomerase .  +
Reduction of [[oxoglutarate]] (2OG or alpha-ketoglutarate) to '''2-hydroxyglutarate''' (2HG) is driven by NADPH. 2HG is also formed in side reactions of [[lactate dehydrogenase]] and [[malate dehydrogenase]]. Millimolar 2HG concentrations are found in some cancer cells compared to , whereas side activities of lactate and malate dehydrogenase form submillimolar s-2-hydroxyglutarate (s-2HG). However, even wild-type IDH1 and IDH2, notably under shifts toward reductive carboxylation glutaminolysis or changes in other enzymes, lead to “intermediate” 0.01–0.1 mM 2HG levels, for example, in breast carcinoma compared with nanomolar concentrations in benign cells. 2HG is considered an important player in reprogramming metabolism of cancer cells.  +
'''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
'''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]].  +
'''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.  +
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.  +
'''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''' 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''' 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).  +
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'')  +
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.  +
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]].  +
An '''absorption spectrum''' is similar to an [[absorbance spectrum]] of a sample, but plotted as a function of [[absorption]] against wavelength.  +
In chemistry or physics, '''abundance''' or '''natural abundance''' refers to the amount of a chemical element isotope existing in nature. The abundance of an isotope on the Earth may vary depending on the place, but remains relatively constant in time (on a short-term scale). In a chemical reaction, the reactant is in abundance when the quantity of a substance is enough (or high) and constant during the reaction. '''Relative abundance''' represents the percentage of the total amount of all isotopes of the element. The relative abundance of each isotope in a sample can be identified using mass spectrometry.  +
'''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''' is an immediate time scale adaptation expressing pheotypic plasticity in response to changes of a single variable under controlled laboratory conditions.  +
'''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.  +
The '''accuracy''' of a method is the degree of agreement between an individual test result generated by the method and the true value.  +
[[File:Acetyl coenzyme A 700.png|left|200px|acetyl-CoA]]'''Acetyl-CoA''', C<sub>23</sub>H<sub>38</sub>N<sub>7</sub>O<sub>17</sub>P<sub>3</sub>S, is a central piece in metabolism involved in several biological processes, but its main role is to deliver the acetyl group into the [[TCA cycle]] for its oxidation. It can be synthesized in different pathways: (i) in glycolysis from [[pyruvate]], by pyruvate dehydrogenase, which also forms NADH; (ii) from fatty acids β-oxidation, which releases one acetyl-CoA each round; (iii) in the catabolism of some amino acids such as leucine, lysine, phenylalanine, tyrosine and tryptophan. <br>In the mitochondrial matrix, acetyl-CoA is condensed with [[oxaloacetate]] to form [[citrate]] through the action of [[citrate synthase]] in the [[tricarboxylic acid cycle]]. Acetyl-CoA cannot cross the mitochondrial inner membrane but citrate can be transported out of the mitochondria. In the cytosol, citrate can be converted to acetyl-CoA and be used in the synthesis of fatty acid, cholesterol, ketone bodies, acetylcholine, and other processes.  +
[[File:Aconitase.jpg|right|500px|aconitase]]'''Aconitase''' is a [[TCA cycle]] enzyme that catalyzes the reversible isomerization of [[citrate]] to [[isocitrate]]. Also, an isoform is also present in the cytosol acting as a trans-regulatory factor that controls iron homeostasis at a post-transcriptional level.<br>  +
The '''activity''' (relative activity) is a dimensionless quantity related to the concentration or partial pressure of a dissolved substance. The activity of a dissolved substance B equals the [[concentration]], ''c''<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. In general, the relative activity is defined by the [[chemical potential]], ''µ''<sub>B</sub> ''a''<sub>B</sub> = exp[(''µ''<sub>B</sub>-''µ''°)/''RT'']  +
'''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''' is an evolutionary time scale expression of phenotypic plasticity in response to selective pressures prevailing under various habitat conditions.  +
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 fluorescent 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), [[phosphoenolpyruvate 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.  +
'''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.  +
'''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''' (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''' 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.  +
'''Artemisinin''' and various derivatives are potent anti-malaria drugs which have additionally anti-tumorigenic effects, particularly when targeted at mitochondria. The anti-malaria effect is associated with artemisinin's action on heme. Mitochondria are involved in the synthesis of heme, and may play additional roles in the anti-tumorigenic effect of artemisinin.  +
In respiratory assays for cytochrome ''c'' oxidase activity ([[Complex IV|Complex IV, CIV]]), '''ascorbate''' is added as regenerating system to maintain [[TMPD]] in a reduced state. It has to be titrated into the respiration medium prior to the addition of TMPD, otherwise the [[autoxidation]] reaction velocity is permanently elevated.  +
[[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.  +
'''Aspirin''' is a widely applied drug that requires dosage adjusted to individual body mass. It is a non-selective COX inhibitor and exerts an effect on long-chain fatty acid transport into mitochondria.  +
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''' 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.  +
Many cell types are grown in culture as '''attached cells''', such as endothelial or neuronal cells in a monolayer.  +
'''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''' (AF) is a gold complex which inhibites thioredoxin reductase (TrxR).  +
'''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''' zooms in or out of the selected period with [[Autoscale time axis]], [[Autoscale Y1 (Y2) axes]] and [[Automatic pan]].  +
'''Autoscale Y1 (Y2) axes''': Autoscaling the measured values (full data range) on the Y1 (Y2) axis in the selected [[plot]].  +
'''Autoscale time axis''' gives an overview of the entire experimental period.  +
''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.  +
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.  +
[[File:Table Physical constants.png|left|400px|thumb|]] {Quote} The '''Avogadro constant''' ''N''<sub>A</sub> is a proportionality constant between the quantity [[amount]] of substance (with unit [[mole]]) and the quantity for [[count |counting entities]] ... One mole contains exactly 6.022 140 76 × 10<sup>23</sup> elementary [[entity |entities]]. This number is the fixed numerical value of the Avogadro constant, ''N''<sub>A</sub>, when expressed in the unit mol<sup>−1</sup> and is called the Avogadro number {[[Bureau International des Poids et Mesures 2019 The International System of Units (SI)]] end of quote}. Thus the Avogadro constant ''N''<sub>A</sub> has the SI unit 'per mole' [mol<sup>-1</sup>], but more strictly the unit for counting entities per amount is 'units per mole' [x·mol<sup>-1</sup>] (compare [[elementary charge]]). Therefore, ''N''<sub>A</sub> is 'count per amount' with units 'counting units per mole'. The Avogadro constant times elementary charge is the [[Faraday constant]].  +
'''Sodium azide''' is an inhbitor of [[Complex IV|cytochrome c oxidase]] (COX, CcO).  +
B
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.  +
Obesity is defined as a disease associated with an excess of body fat with respect to a healthy reference condition. Cutoff points for [[body mass excess]], '''BME cutoff points''', define the critical values for underweight (-0.1 and -0.2), overweight (0.2), and various degrees of obesity (0.4, 0.6, 0.8, and above). BME cutoffs are calibrated by crossover-points of BME with established BMI cutoffs.  +
The '''background state''' Y (background rate ''Y<sub>X</sub>'') is the non-activated or inhibited respiratory state at background rate, which is low in relation to the higher rate ''Z<sub>X</sub>'' in the [[reference state]] Z. The transition from the background state to the reference state is a step change. A [[metabolic control variable]] ''X'' (substrate, activator) is added to the background state to stimulate flux to the level of the reference state. Alternatively, the metabolic control variable ''X'' is an inhibitor, which is present in the background state Y, but absent in the reference state Z. The background state is the baseline of a single step in the definition of the [[flux control efficiency]]. In a sequence of step changes, the common [[baseline state]] is the state of lowest flux in relation to all steps, which can be used as a [[baseline correction]].  +
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''' 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''', ''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>O<sub>2</sub></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 (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''' 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''']]  +
'''[[Template:Base quantities and count]]'''  +
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]].  +
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''.  +
The '''bias''' is defined as the difference between the mean of the measurements and the reference value. In general, the measuring instrument calibration procedures should focus on establishing and correcting it.  +
'''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.  +
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]]).  +
[[File:J(E-L).jpg|50 px|link=E-L coupling efficiency |''E-L'' coupling efficiency]] The '''biochemical coupling efficiency''' is the [[E-L coupling efficiency |''E-L'' coupling efficiency]], (''E-L'')/''E'' = 1-''L/E''. This is equivalent to the [[P-L control efficiency |''P-L'' control efficiency]], (''P-L'')/''P'' = 1-''L/P'', only at zero [[E-P excess capacity |''E-P'' excess capacity]], when ''P'' = ''E''). The biochemical coupling efficiency is independent of kinetic control by the phosphorylation system.  +
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 may be caused by microbial growth in the O2k-Chamber or in the experimental medium.  +
'''Biological reference interval''' or reference interval is the central 95% interval of the distribution of reference values.  +
'''Biopsy preservation solution''', for preservation of tissue samples, preparation of muscle fibres, and permeabilization with [[saponin]].  +
In [[fluorometry]] and [[transmission spectrophotometry]] '''blank''' [[cuvettes]] (with no samples in them) are used to carry out the [[balance]].  +
Blebbistatin is a widely used muscle and non-muscle myosin II-specific inhibitor that block contractile activity. Blebbistatin shows selectivity and high affinity for multiple class II myosins. Blebbistatin is commonly employed in respirometric experiments with permeabilized muscle fibers (pfi). Permeabilized muscle fibers are sensitive to low oxygen supply due to diffusion restrictions that limit mitochondrial respiration at the core of the fiber bundle. Therefore, hyperoxic conditions are required to counteract this limitation. Further studies have shown that the addition of blebbistatin in the respiration medium prevents fiber contraction, reduces the oxygen sensitivity and allows the study of ADP kinetics in pfi at normoxic oxygen levels. However, other studies described that the presence of blebbistatin does not prevent the oxygen dependence in pfi. Moreover, several limitations of blebbistatin i.e. low solubility in water, cytotoxicity and phototoxicity have been described.  +
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''' (bcp) is one of the key steps in diagnostic protocols.  +
'''Blood plasma''' is the non-cellular component of the blood. Plasma lacks cellular components of the blood, [[red blood cell]]s, [[white blood cell]]s, and [[platelet]]s. However, there are many proteins in plasma, i.e. fibrinogen, albumin and globulin. Both blood plasma and [[platelet-rich plasma]] maintain clotting activity after whole blood separation.  +
'''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.  +
In the [[healthy reference population]] (HRP), there is zero '''body fat excess''', BFE, and the fraction of excess body fat in the HRP is expressed - by definition - relative to the reference body mass, ''M''°, at any given [[height of humans |height]]. Importantly, body fat excess, BFE, and [[body mass excess]], BME, are linearly related, which is not the case for the body mass index, BMI.  +
The '''body mass''', ''M'', is the mass ([[kilogram]] [kg]) of an individual (object) [x] and is expressed in units [kg/x]. Whereas the body weight changes as a function of gravitational force (you are weightless at zero gravity; your floating weight in water is different from your weight in air), your mass is independent of gravitational force, and it is the same in air and water.  +
The '''body mass excess''', BME, is an index of obesity and as such BME is a lifestyle metric. The BME is a measure of the extent to which your actual [[body mass]], ''M'' [kg/x], deviates from ''M''° [kg/x], which is the reference body mass [kg] per individual [x] without excess body fat in the [[healthy reference population]], HRP. A balanced BME is BME° = 0.0 with a band width of -0.1 towards underweight and +0.2 towards overweight. The BME is linearly related to the [[body fat excess]].  +
The '''body mass index''', BMI, is the ratio of body mass to height squared (BMI=''M''·''H''<sup>-2</sup>), recommended by the WHO as a general indicator of underweight (BMI<18.5 kg·m<sup>-2</sup>), overweight (BMI>25 kg·m<sup>-2</sup>) and obesity (BMI>30 kg·m<sup>-2</sup>). Keys et al (1972; see 2014) emphasized that 'the prime criterion must be the relative independence of the index from height'. It is exactly the dependence of the BMI on height - from children to adults, women to men, Caucasians to Asians -, which requires adjustments of BMI-cutoff points. This deficiency is resolved by the [[body mass excess]] relative to the [[healthy reference population]].  +
[[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>]. ''k'' = ''f''·''e''<sup>-1</sup>, the [[electrochemical constant]] ''f'' times the [[elementary charge]] ''e''. ''k'' = ''R''·''N''<sub>A</sub><sup>-1</sup>, the [[gas constant]] ''R'' divided by the [[Avogadro constant]] ''N''<sub>A</sub>.  +
'''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]].  +
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 is a membane stabilizer, oxygen radical scavenger, and binds Ca<sup>2+</sup> 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.  +
'''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
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).  +
'''CHNO-fuel substrates''' are reduced carbon-hydrogen-nitrogen-oxygen substrates which are oxidized in the [[exergonic]] process of [[cell respiration]]. Mitochondrial pathways are stimulated by CHNO-fuel substrates feeding electrons into the [[ETS]] at different levels of integration and in the presence or absence of inhibitors acting on specific enzymes which are gate-keepers and control various pathway segments.  +
''See'' '''[[N/NS pathway control ratio]]'''  +
''See'' '''[[S/NS pathway control ratio]]'''  +
'''Ca<sup>2+</sup>''' is a major signaling molecule in both prokaryotes and eukaryotes. Its cytoplasmic concentration is tightly regulated by transporters in the plasma membrane and in the membranes of various organelles. For this purpose, it is either extruded from the cell through exchangers and pumps or stored in organelles such as the endoplasmic reticulum and the mitochondria. Changes in the concentration of the cation regulate numerous enzymes including many involved in ATP utilizing and in ATP generating pathways and thus ultimately control metabolic activity of mitochondria and of the entire cell. Measuring changes in Ca<sup>2+</sup> levels is thus of considerable interest in the context of [[high-resolution respirometry]].  +
'''Calcium Green''' denotes a family of [[extrinsic fluorophores]] applied for measurement of Ca<sup>2+</sup> concentration.  +
Calcium retention capacity (CRC) is a measure of the capability of mitochondria to retain calcium, primarily in the form of calcium phosphates, in the mitochondrial matrix. By storing calcium in the form of osmotically inactive precipitates the mitochondria contribute to the buffering of cytosolic free calcium levels and thereby to the regulation of calcium-dependent cellular processes. Alterations of CRC are believed to be important in stress phenomena associated with energy limitation and have also been linked to neurodegenerative diseases [[Starkov 2010 FEBS J |(Starkov 2013 FEBS J).]] Experimentally, CRC has been indirectly assessed by determination of respiratory rates of isolated mitochondria which were exposed to continuously increasing levels of calcium by use of the [[TIP2k-Module| Titration-Injection microPump TIP2k]]. The upper limit of CRC was observed as a sudden decrease of respiration presumed to reflect opening of the permeability transition pore [[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]]  +
The calorimetric/respirometric or '''calorespirometric ratio''' (CR ratio) is the ratio of calorimetrically and respirometrically measured heat and oxygen flux, determinded by [[calorespirometry]]. The experimental CR ratio is compared with the theoretically derived [[oxycaloric equivalent]], and agreement in the range of -450 to -480 kJ/mol O<sub>2</sub> indicates a balanced [[aerobic]] energy budget ([[Gnaiger_1987_PhysiolZool|Gnaiger and Staudigl 1987]]). In the transition from aerobic to [[anaerobic | anaerobic metabolism]], there is a [[Limiting pO2|limiting ''p''<sub>O2</sub>]], ''p''<sub>lim</sub>, below which CR ratios become more exothermic since anaerobic energy flux is switched on.  +
'''Calorespirometry''' is the method of measuring simultaneously metabolic heat flux ([[calorimetry]]) and oxygen flux ([[respirometry]]). The [[calorespirometric ratio]] (CR ratio; heat/oxygen flux ratio) is thus experimentally determined and can be compared with the theoretical [[oxycaloric equivalent]], as a test of the aerobic energy balance.  +
The candela, symbol cd, is the SI unit of luminous intensity in a given direction. It is defined by taking the fixed numerical value of the luminous efficacy of monochromatic radiation of frequency 540 × 10<sup>12</sup> Hz, ''K''<sub>cd</sub>, to be 683 when expressed in the unit lm W<sup>−1</sup>.  +
A '''canonical ensemble''' is the group of compartments enclosed in an isolated system '''H''', with a smaller compartment A<sub>1</sub> in thermal equilibrium with a larger compartment A<sub>2</sub> which is the heat reservoir at temperature ''T''. When A<sub>1</sub> 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.  +
'''Carbohydrates''', also known as '''saccharides''', are molecules composed of carbon, hydrogen and oxygen. These molecules can be divided by size and complexity into monosaccharides, disaccharides, oligosaccharides, and polysaccharides. [[Glucose]] is a monosaccharide considered the primary source of energy in cells and a metabolic intermediate. This carbohydrate undergoes glycolysis, with the generation of [[pyruvate]], that can enter the [[TCA cycle]]. Carbohydrates such as glucose and fructose may also be involved in the [[Crabtree effect]].  +
'''Carbonyl cyanide m-chlorophenyl hydrazone''', CCCP (U; C<sub>9</sub>H<sub>5</sub>ClN<sub>4</sub>; ''F''<sub>W</sub> = 204.62) is a protonophore (H<sup>+</sup> ionophore) and is used as a potent chemical [[uncoupler]] of [[oxidative phosphorylation]]. Like all uncouplers, CCCP concentrations must be titrated carefully to evaluated the optimum concentration for maximum stimulation of mitochondrial respiration, particularly to avoid inhibition of respiration at higher CCCP concentrations.  +
'''Carboxy SNARF® 1''' is a cell-impermeant pH indicator dye. The pKa of ~7.5 makes it useful for measuring pH in the range of pH 7 to pH 8. The emission shifts from yellow-orange at low pH to deep red fluorescence at high pH. Ratiometric fluorometry, therefore, is applied at two emission wavelengths,such as 580 nm and 640 nm. Relative molecular mass: ''M''<sub>r</sub> = 453.45  +
'''Carboxyatractyloside''', Cat, is a highly selective and potent inhibitor of the [[adenine nucleotide translocator]] (ANT). Cat stabilizes the nucleoside binding site of ANT on the cytoplasmic (positive) side of the inner membrane and blocks the exchange of matrix ATP and cytoplasmic ADP. It causes stabilization of the ''c'' conformation of ANT leading to permeability transition pore (PTP) opening, loss of mitochondrial membrane potential, and apoptosis.  +
'''Cardiolipin''', CL, is a double phospholipid (having 4 fatty acyl chains) in the mitochondrial inner membrane (mtIM) which plays an important role in mitochondrial bioenergetics. CL is involved in the mitochondria-dependent pathway of apoptosis, participates in the function and stabilization of mitochondrial respiratory complexes and supercomplexes and also contributes to mitochondrial integrity. Contributed by [[Sparagna G]] 2016-04-18  +
[[File:CERG.gif|200px|left|CERG]] The '''Cardiovascular Exercise Research Group''' (CERG) was established in January 2008 and their research focuses on identifying the key cellular and molecular mechanisms underlying the beneficial effects of physical exercise on the heart, arteries and skeletal muscle in the context of disease prevention and management through experimental, clinical and epidemiological studies. Since 2003 this research group organizes the biennial seminar [http://www.ntnu.edu/cerg/seminar-2013 "Exercise in Medicine"] in Trondheim, Norway.  +
'''Carnitine''' is an important factor for the transport of long-chain fatty acids bound to carnitine ([[carnitine acyltransferase]]) into the mitochondrial matrix for subsequent β-oxidation. There are two enantiomers: D- and L-carnitine. Only the L-isomer is physiologically active.  +
'''Carnitine O-octanoyltransferase''' is a mitochondrial enzyme that transfers [[carnitine]] to octanoyl-CoA to form [[Coenzyme A]] and [[octanoylcarnitine]]: Octanoyl-CoA + L-carnitine ↔ CoA + L-octanoylcarnitine.  +
'''Carnitine acetyltransferase''' (CrAT) is located in the mitochondrial matrix and catalyses the formation of acetyl-carnitine from acetyl-CoA and L-carnitine and thus regulates the acetyl-CoA/free CoA ratio which is essential for [[pyruvate dehydrogenase]] complex (PDC) activity.  +
'''Carnitine acyltransferases''' mediate the transport of long-chain fatty acids across the inner mt-membrane by binding them to carnitine. First, long-chain fatty acids are activated by an energy-requiring step in which the fatty acid ester of CoA is formed enzymatically at the expense of ATP. The fatty acids then pass through the inner mt-membrane and enter the mitochondria as carnitine esters. The fatty acyl group is then transferred from carnitine to intramitochondrial CoA and the resulting fatty acyl CoA is used as a substrate in the fatty acid oxidation (FAO) cycle in the mt-matrix.  +
'''Carnitine palmitoyltransferase 2''' (CPT-2, also known as carnitine acyltransferase II) is part of the carnitine shuttle which is responsible for the mitochondrial transport of long-chain fatty acids. CPT-2 is located on the inner side of the mtIM and converts the acyl-carnitines (produced in the reaction catalyzed by [[carnitine palmitoyltransferase I]]) to carnitine and acyl-CoAs, which undergo ''ß''-oxidation in the mitochondrial matrix. Free carnitines are transported out of the mitochondrial matrix in exchange for acyl-carnitines via an integral mtIM protein [[carnitine-acylcarnitine translocase]] (CACT). Short- and medium-chain fatty acids do not require the carnitine shuttle for mitochondrial transport.  +
'''Carnitine palmitoyltransferase I''' (CPT 1, also known as carnitine acyltransferase I) is a regulatory enzyme in mitochondrial long-chain acyl-CoA uptake and further oxidation. CPT 1 is associated with the outer mt-membrane and catalyses the formation of acylcarnitines from acyl-CoA and L-carnitine. In the next step, acyl-carnitines are transported to the mitochondrial matrix via [[carnitine-acylcarnitine translocase]] in exchange for free [[carnitine]]. In the inner side of the mtIM [[carnitine palmitoyltransferase 2]] converts the acyl-carnitines to carnitine and acyl-CoAs. There are three enzyme isoforms: CPT 1A (liver type), CPT 1B (muscle type), CPT 1C (brain type). Isoforms have significantly different kinetic and regulatory properties. Malonyl-CoA is an endogenous inhibitor of CPT 1.  +
'''Carnitine-acylcarnitine translocase''' (CACT) is part of the carnitine shuttle which mediates the mitochondrial transport of long-chain fatty acids where the [[fatty acid oxidation]] occurs. CACT is an internal mt-IM protein and transports acyl-carnitines into the mitochondrial matrix in exchange for free [[carnitine]].  +
Most of the nonpolar compounds have to be diluted in organic solvents such as DMSO or acetonitrile in order to use them for the titrations in the SUIT protocols. However, the solvent (carrier) itself could affect the mitochondrial physiology and promote alterations that we need to take into account. For this reason, it is necessary to run in parallel to our treatment experiment a control experiment on which we will add a '''carrier control titration''' to test if it affects our sample or not.  +
'''Catalase''' catalyzes the dismutation of [[hydrogen peroxide]] to water and [[oxygen]]. Perhaps all cells have catalase, but mitochondria of most cells lack catalase. Cardiac mitochondria are exceptional in having mt-catalase activity (rat heart mitochondria: Radi et al 1991; mouse heart mitochondria: Rindler et al 2013). [[Hydroxylamine]] is an inhibitor of catalase, which is also inhibited by [[cyanide]] and [[azide]].  +
'''Catalytic activity''' of an enzyme is measured by an enzyme assay and is expressed in units of katal (kat [mol∙s<sup>-1</sup>]). More commonly (but not conforming to SI units or IUPAC recommendations) enzyme activity is expressed in units U [mol∙min<sup>-1</sup>].  +
Cataplerosis is the exit of TCA cycle intermediates from the mt-matrix space.  +
[[File:SUIT-catg_MitoPathway types.jpg|right|200px]] '''Categories of SUIT protocols''' group [[MitoPedia: SUIT |SUIT protocols]] according to all substrate types involved in a protocol (F, N, S, Gp), independent of the sequence of titrations of substrates and inhibitors which define the [[Electron-transfer-pathway state]]s. The [[N-pathway control |N-type substrates]] are listed in parentheses, independent of the sequence of titrations. ROX states may or may not be included in a SUIT protocol, which does not change its category. Similarly, the [[CIV]] assay may or may not be added at the end of a SUIT protocol, without effect on the category of a SUIT protocol. * '''F''' - ET-pathway-level 5: [[FADH2 |FADH<sub>2</sub>]]-linked substrates (FAO) with obligatory support by the N-linked pathway. * '''N''' - ET-pathway-level 4: [[NADH]]-linked substrates (CI-linked). * '''S''' - ET-pathway-level 3: [[Succinate]] (CII-linked). * '''Gp''' - ET-pathway-level 3: [[Glycerophosphate]] (CGpDH-linked). * '''Y(X)'''- In the SUIT general protocols Y makes reference to the ET-pathway state and X to the combination os substrates added for the corresponding pathway. » [[#Categorization of SUIT protocols: ETS pathway control states |'''MiPNet article''']]  +
[[File:CellSymposiaLogo.jpg|90px]] Organized by the editors of Cell Press's leading journals, '''Cell Symposia''' bring together exceptional speakers and scientists to discuss topics at the forefront of scientific research.  +
The '''cell count''' ''N''<sub>ce</sub> is the number of cells, expressed in the abstract [[unit]] [x] (1 Mx = 10<sup>6</sup> x). The ''elementary entity'' cell ''U''<sub>ce</sub> [x] is the real unit, the 'single individual cell'. A cell count is the multitude or number ''N'' of cells, ''N''<sub>ce</sub> = ''N''·''U''<sub>ce</sub> ([[Gnaiger MitoFit Preprints 2020.4]]). Normalization of respiratory rate by cell count yields oxygen [[flow]] ''I''<sub>O<sub>2</sub></sub> expressed in units [amol·s<sup>-1</sup>·x<sup>-1</sup>] (=10<sup>-18</sup> mol·s<sup>-1</sup>·x<sup>-1</sup>).  +
'''Cell culture media''', like RPMI or DMEM, used for [[HRR]] of living cells.  +
'''Cell respiration''' channels metabolic fuels into the chemiosmotic coupling (bioenergetic) machinery of [[oxidative phosphorylation]], being regulated by and regulating oxygen consumption (or consumption of an alternative final electron acceptor) and molecular redox states, ion gradients, mitochondrial (or microbial) membrane potential, the phosphorylation state of the ATP system, and heat dissipation in response to intrinsic and extrinsic energy demands. See also [[respirometry]]. In internal or '''cell respiration''' in contrast to [[fermentation]], redox balance is maintained by external electron acceptors, transported into the cell from the environment. The chemical potential between electron donors and electron acceptors drives the [[electron transfer pathway]], generating a chemiosmotic potential that in turn drives ATP synthesis.  +
1) Cellular substrates ''in vivo'', endogenous; '''Ce'''. 2) Cellular substrates ''in vivo'', with exogenous substrate supply from culture medium or serum; '''Cm'''.  +
The '''chamber volume''' of the O2k is 2.0 mL or 0.5 mL of aqueous medium with or without sample, excluding the volume of the stirrer and the volume of the capillary of the stopper. A modular extension of the O2k, the [[O2k-sV-Module]], was specifically developed to perform high-resolution respirometry with reduced amounts of biological sample, and all components necessary for the smaller operation volume of 0.5 mL.  +
» See [[O2k signals and output]]  +
'''Charge''' ''Q''<sub>el</sub> is the quantity of electricity expressed in the SI unit coulomb [C]. ''Q''<sub>el''X''</sub> [C] indicates the charge carried by the quantity of a specified ion ''X''.  +
The '''charge number''' of an ion ''X'' or electrochemical reaction with unit stoichiometric number of ''X'' is the [[particle charge]] [C·x<sup>-1</sup>] divided by the [[elementary charge]] [C·x<sup>-1</sup>]. The particle charge ''Q''<sub><u>''N''</u>''X''</sub> is the charge per count of ions ''X'' or per ion ''X'' transferred in the reaction as defined in the reaction equation.  +
The '''chemical potential''' of a substance B, ''µ''<sub>B</sub> [J/mol], is the partial derivative of Gibbs energy, ''G'' [J], per amount of B, ''n''<sub>B</sub> [mol], at constant temperature, pressure, and composition other than that of B, ''µ''<sub>B</sub> = (∂''G''/∂''n''<sub>B</sub>)<sub>''T'',''p'',''n<small>j''≠B</small></sub> The chemical potential of a [[solute]] in solution is the sum of the standard chemical potential under defined standard conditions and a concentration ([[activity]])-dependent term, ''µ''<sub>B</sub> = ''µ''<sub>B</sub>° + ''RT'' ln(''a''<sub>B</sub>) The standard state for the solute is refered to ideal behaviour at standard concentration, ''c''° = 1 mol/L, exhibiting infinitely diluted solution behaviour [1]. ''µ''<sub>B</sub>° equals the standard molar Gibbs energy of formation, Δ<sub>f</sub>''G''<sub>B</sub>° [kJ·mol<sup>-1</sup>]. The formation process of B is the transformation of the pure constituent elements to one mole of substance B, with all substances in their standard state (the most stable form of the element at 100 kPa (1 bar) at the specified temperature) [2].  +
The '''Chinese Society of Mitochondrial Research and Medicine''' (Chinese-Mit) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]].  +
'''Chinese numerals''' The Arabic numeral system used today in China was introduced to China by the Europeans in the early 17<sup>th</sup> century. But the Chinese character-based number systems are still in use. The financial numerals are used only when writing an amount on a form for remitting money at a bank. They function as anti-fraud numerals. The character 零 (zero) appeared very early in ancient Chinese writing. However, at that time, it did not mean "nothing", but "bits and pieces", "not much". 一百零五(105) means in Chinese: In addition to a hundred, there is a fraction of five. With the introduction of the Arabic numerals, 105 is exactly pronounced “one hundred zero five”, the character 零 corresponds exactly to the symbol 0. Thus, the character 零has the meaning of 0. But the character 〇 was one of the Chinese characters created and promulgated by the only empress (with greater achievements than countless emperors) in the history of China in 690 AD (much later than the invention of 0 in India) for the purpose of demonstrating her power. At that time the character 〇 meant “star”, representing a round planet. It is now used as a synonym for the 零 (zero).  +
'''Chloroplasts''' (Greek chloros: green; plastes: the one who forms) are small structures within the cells that conduct [[photosynthesis]]. They are a type of organelle called plastids that are present in eukaryotic plant cells (algae, aquatic and terrestrial plants) and characterized by having two membranes and a high concentration of the pigment Chlorophyll. Like [[mitochondria]], they originated through the endosymbiosis of a cyanobacteria by an early eukaryotic cell and they have their own DNA which replicates during cell division. In addition to photosynthesis, in their internal matrix called stroma they also carry out other metabolic functions within the plant cells such as fatty acid synthesis or amino acid synthesis.  +
'''Chlororespiration''' is the phenomenon by which oxygen is consumed by a putative respiratory electron transfer chain (ETC) within the thylakoid membrane of the [[chloroplasts]] and ATP is produced. It is a process that involves the interaction with the photosynthetic ETC in which the NAD(P)H dehydrogenase enzyme transfers electrons to oxygen molecules with the assistance of the photosynthetic Plastoquinone (PQ), which acts as a non-photochemical redox carrier. Initially described in the unicellular alga ''Chlamydomonas reindhartdii'', chlororespiration was highly disputed for years until the discovery of a NAD(P)H-dehydrogenase (Ndh) complex (plastidic encoded) and plastid terminal oxidase (PTOX) (nuclear encoded) in higher-plant chloroplasts. The PTOX, which is homologous to the plant mitochondrial alternative oxidase, has the role of preventing the over-reduction of the PQ pool while the Ndh complexes provide a gateway for the electrons to form the ETC and consume oxygen. As a result of this process there is a cyclic electron flow around the Photosystem I (PSI) that has been reported to be activated under stress conditions acting as a photoprotection mechanism and could be involved in protecting against any other stress that implies the increase of ROS formation.  +
'''Choline dehydrogenase''' (EC 1.1.99.1) is bound to the inner mt-membrane, oxidizes choline in kidney and liver mitochondria, with electron transfer into the [[Q-junction]], and is thus part of the [[Electron transfer pathway]]. Analogous to [[succinate dehydrogenase]] (CII), electron transfer from choline dehydrogenase is FAD-linked downstream to Q. Choline is an [[ET-pathway substrate types]] 3.  +
[[File:Citrate 300 (1).png|left|100px|citrate]]'''citrate''', C<sub>6</sub>H<sub>5</sub>O<sub>7</sub><sup>-3</sup>, is a tricarboxylic acid trianion, intermediate of the TCA cycle, obtained by deprotonation of the three carboxy groups of citric acid. Citrate is formed from [[oxaloacetate]] and acetyl-CoA through the catalytic activity of the [[citrate synthase]]. In the TCA cycle, citrate forms isocitrate by the activity of the [[aconitase]]. Citrate can be transported out of the mitochondria by the tricarboxylate transport, situated in the inner mitochondrial membrane. The transport occurs as an antiport of malate from the cytosol and it is a key process for fatty acid and oxaloacetate synthesis in the cytosol. <br>  +
Condensation of [[oxaloacetate]] with acetyl-CoA yields citrate as an entry into the [[TCA cycle]]. CS is located in the mt-matrix. CS activity is frequently used as a functional marker of the amount of mitochondria (mitochondrial elementary marker, ''mtE'') for normalization of respiratory flux.  +
'''Citreoviridin''' is an inhibitor of the [[ATP synthase]] which, differently from the FO subunit binding inhibitor oligmycin, binds to the F1 subunit of the ATP synthase.  +
'''Close''' a DLD file. A window '''"Save changes to file?"''' pops up offering the options to close the file after saving the changes, or close the file without saving any modifications on the presently open file.  +
The O2k-chamber can be used as a [[closed system]] or [[open system]]. Gas bubbles must be avoided.  +
A '''closed system''' is a system with boundaries that allow external exchange of energy (heat and work), but do not allow exchange of matter. A limiting case is light and electrons which cross the system boundary when work is exchanged in the form of light or electric energy. If the surroundings are maintained at constant temperature, and heat exchange is rapid to prevent the generation of thermal gradients, then the closed system is isothermal. A frequently considered case are closed isothermal systems at constant pressure (and constant volume with aqueous solutions). Changes of closed systems can be partitioned according to internal and external sources. Closed systems may be [[Homogenous system |homogenous]] (well mixed and isothermal), [[Continuous system |continuous]] with gradients, or [[Compartmental system |discontinuous]] with compartments (heterogenous).  +
'''Coenzyme A''' is a coenzyme playing an essential role in the [[tricarboxylic acid cycle]] (oxidation of [[pyruvate]] to [[acetyl-CoA]]) and [[fatty acid oxidation]]. CoA is a thiol that reacts with carboxylic acids to form CoA-activated thioesters.  +
'''Coenzyme Q''' or ubiquinone (2,3-dimethoxy-5-methyl-6-polyprenyl-1,4-benzoquinone) was discovered in 1957 by the group of Crane. It is a lipid composed of a benzoquinone ring with an isoprenoid side chain, two methoxy groups and one methyl group. The length of the isoprenoid chain varies depending on the species; for example, six isoprenoid units (CoQ6) have been described as the most commonly found CoQ in ''Saccharomyces cerevisiae'', eight units in ''Escherichia coli'', (CoQ8), nine units in ''Caenorhabditis elegans'' and rodents (CoQ9), ten units in humans (CoQ10), and some species have more than one CoQ form, e.g. human and rodent mitochondria contain different proportions of CoQ9 and CoQ10. These redox compounds exist in three different forms: [[quinone]] (oxidized), [[quinol]] (reduced), and an intermediate [[semiquinone]]. ''More details'' » '''[[Q-junction]]'''.  +
[[File:Coenzyme Q2.png|left|200px|CoQ2]] '''Coenzyme Q2''' or ubiquinone-2 or ubiquinone Q2 is a [[quinone]] derivate composed of a benzoquinone ring with an isoprenoid side chain consisting of two isoprenoid groups, with two methoxy groups, and with one methyl group. In HRR it is used to detect the redox changes of the [[Q-junction]] in conjunction with the [[Q-Module]], since CoQ2 can react both with mitochondrial complexes (e.g. [[CI]], [[CII]] and [[CIII]]) at their quinone-binding sites and with the [[Three-electrode system |detecting electrode]].  +
Should we used a '''comma for separating a term and its abbreviation''' in the text? The SI Brochure frequently does not use a comma. The comma might be added, if it helps to clarify the distinction between the term and its abbreviation. The example “reduced Q fraction, ''Q''<sub>r</sub>” – the sequence of Q and ''Q''<sub>r</sub> may be confusing without comma. There will always be examples, where it is not clear, if a comma is needed.  +
'''Comorbidities''' are common in obesogenic lifestyle-induced early aging. These are preventable, non-communicable diseases with strong associations to obesity. In many studies, cause and effect in the sequence of onset of comorbidities remain elusive. Chronic degenerative diseases are commonly obesity-induced. The search for the link between obesity and the etiology of diverse preventable diseases lead to the hypothesis, that mitochondrial dysfunction is the common mechanism, summarized in the term 'mitObesity'.  +
[[File:Company-of-Scientists logo.jpg|left|140px|link=http://www.company-of-scientists.com|Company of Scientists]] The '''Company of Scientists''' evolves as a concept for implementing scientific innovations on the market.  +
The '''comparison of respirometric methods''' provides the basis to evaluate different instrumental platforms and different [[mitochondrial preparations]], as a guide to select the best approach and to critically evaluate published results.  +
'''Complex I''', '''NADH:ubiquinone oxidoreductase''' (EC 1.6.5.3), is an enzyme complex of the [[Electron transfer pathway]], a [[proton pump]] across the inner mt-membrane, responsible for electron transfer to [[ubiquinone]] from [[NADH]] formed in the mt-matrix. CI forms a [[supercomplex]] with [[Complex III]].  +
''See'' '''[[NS-pathway control state]]''' (previous: CI<small>&</small>II-linked)  +
''See'' '''[[N-pathway control state]] (previous: CI-linked)  +
'''Complex II''' or '''succinate:quinone oxidoreductase (SQR)''' is the only membrane-bound enzyme in the [[TCA cycle]] and is part of the [[Electron transfer pathway]]. The flavoprotein [[succinate dehydrogenase]] is the largest polypeptide of CII, located on the matrix face of the mt-inner membrane. Following succinate oxidation, the enzyme transfers electrons directly to the quinone pool.  +
''See'' '''[[S-pathway control state]] (previous: CII-linked)  +
'''Complex III''' or coenzyme Q : cytochrome c - oxidoreductase, sometimes also called the cytochrome ''bc''<sub>1</sub> complex is a complex of the [[electron transfer pathway]]. It catalyzes the reduction of cytochrome ''c'' by oxidation of [[coenzyme Q]] (CoQ) and the concomitant [[Proton pump|pumping of 4 protons]] from the cathodic (negative) mitochondrial matrix to the anodic (positive) intermembrane space.  +
'''Complex IV''' or '''cytochrome ''c'' oxidase''' is the terminal oxidase of the mitochondrial [[electron transfer system]], reducing [[oxygen]] to [[water]], with reduced [[cytochrome c |cytochrome ''c'']] as a substrate. Concomitantly to that, CIV [[Proton pump|pumps protons]] against the electrochemical protonmotive force. CIV is frequently abbreviated as COX or CcO. It is the 'ferment' (Atmungsferment) of Otto Warburg, shown to be related to the cytochromes discovered by David Keilin.  +
'''Concentration''' [mol·L<sup>-1</sup>] is a volume-specific quantity for diluted [[sample]]s s. In a concentration, the sample is expressed in a variety of [[format]]s: [[count]], amount, [[charge]], [[mass]], [[energy]]. In solution chemistry, amount concentration is [[amount of substance]] ''n''<sub>B</sub> per volume ''V'' of the solution, ''c''<sub>B</sub> = [B] = ''n''<sub>B</sub>·''V''<sup>-1</sup> [mol·dm<sup>-3</sup>] = [mol·L<sup>-1</sup>]. The standard concentration, ''c''°, is defined as 1 mol·L<sup>-1</sup> = 1 M. [[Count]] concentration ''C<sub>X</sub>'' = ''N<sub>X</sub>''·''V''<sup>-1</sup> [x·L<sup>-1</sup>] is the concentration of the number ''N<sub>X</sub>'' of elementary entities ''X'', for which the less appropriate term 'number concentration' is used by [[Cohen 2008 IUPAC Green Book |IUPAC]]. If the sample is expressed as volume ''V''<sub>s</sub> (''e.g.'', ''V''<sub>O<sub>2</sub></sub>), then the 'volume-concentration' of ''V''<sub>s</sub> in ''V'' is termed '[[volume fraction]]', ''Φ''<sub>s</sub> = ''V''<sub>s</sub>·''V''<sup>-1</sup> (''e.g.'', volume fraction of O<sub>2</sub> in dry air, ''Φ''<sub>O<sub>2</sub></sub>) = 0.20946). [[Density]] is the mass concentration in a volume ''V''<sub>S</sub> of pure sample S. A ''change'' of concentration, d''c''<sub>X</sub>, in isolated or closed [[system]]s at constant [[pressure]] is due to internal transformations ([[advancement per volume]]) only. In closed compressible systems (with a gas phase), the concentration of the gas changes, when pressure-volume work is performed on the system. In open systems, a change of concentration can additionally be due to [[external flow]] across the system boundaries.  +
'''Connect to O2k''' connects DatLab with the O2k. Select the [[USB port]] (or [[Serial port]]) with the corresponding cable connecting your PC to the O2k. Select the subdirectory for saving the [[DatLab data file| DLD file]]. Then data recording starts with experimental time set at zero.  +
After starting [[DatLab]] either the '''Connection window''' opens automatically by default or open [[O2k control]] by pressing [F7] and select the communication port.  +
[[Image:SUIT-catg_FNSGp.jpg|right|300px|Convergent electron flow]] '''Convergent electron flow''' is built into the metabolic design of the [[Electron transfer pathway]]. The glycolytic pathways are characterized by important ''divergent branchpoints'': phosphoenolpyruvate (PEPCK) branchpoint to pyruvate or oxaloactetate; pyruvate branchpoint to (aerobic) acetyl-CoA or (anaerobic) lactate or alanine. The mitochondrial Electron transfer pathway, in contrast, is characterized by ''convergent junctions'': (1) the [[N-junction]] and [[F-junction]] in the [[mitochondrial matrix]] at ET-pathway level 4, with dehydrogenases (including the TCA cycle) and ß-oxidation generating NADH and FADH<sub>2</sub> as substrates for [[Complex I]] and [[electron-transferring flavoprotein complex]], respectively, and (2) the [[Q-junction]] with inner mt-membrane respiratory complexes at ET-pathway level 3, reducing the oxidized ubiquinone and partially reduced semiquinone to the fully reduced ubiquinol, feeding electrons into [[Complex III]].  +
In '''Copy marks''', [[Marks - DatLab |Marks in DatLab]] are copied from a seleted [[Plot - DatLab |Plot]] to the active plot.  +
In DatLab '''Copy to clipboard''' can be used to copy selected graphs or values and to paste them to your preferred program or file (e.g. Word, Excel).  +
{Quote} All preprints are posted with a Creative Commons CC BY 4.0 license, ensuring that authors retain '''copyright''' and receive credit for their work, while allowing anyone to read and reuse their work. {end of Quote}  +
[[File:Count-vs-number.png|right|120px|link=Number]] '''Count''' ''N''<sub>''X''</sub> is the [[number]] ''N'' of elementary entities of [[entity]]-type ''X''. The single [[elementary entity]] ''U''<sub>''X''</sub> is a countable object or event. ''N''<sub>''X''</sub> is the number of objects of type ''X'', whereas the term 'entity' and symbol ''X'' are frequently used and understood in dual-message code indicating both (''1'') the entity-type ''X'' and (''2'') a count of ''N''<sub>''X''</sub> = 1 x for a single elementary entity ''U''<sub>''X''</sub>. 'Count' is synonymous with 'number of entities' (number of particles such as molecules, or objects such as cells). Count is one of the most fundamental quantities in all areas of physics to biology, sociology, economy and philosophy, including all perspectives of the statics of countable objects to the dynamics of countable events. The term 'number of entities' can be used in short for 'number of elementary entities', since only elementary entities can be counted, and as long as it is clear from the context, that it is not the number of different entity types that are the object of the count.  +
'''Coupled respiration''' drives oxidative phosphorylation of the diphosphate [[ADP]] to the triphosphate [[ATP]], mediated by proton pumps across the inner mitochondrial membrane. Intrinsically [[uncoupled respiration]], in contrast, does not lead to phosphorylation of ADP, despite of protons being pumped across the inner mt-membrane. Coupled respiration, therefore, is the coupled part of respiratory oxygen flux that pumps the fraction of protons across the inner mt-membrane which is utilized by the phosphorylation system to produce ATP from ADP and Pi. In the OXPHOS state, mitochondria are in a partially coupled state, and the corresponding coupled respiration is the [[free OXPHOS capacity]]. In the state of ROUTINE respiration, coupled respiration is the [[free ROUTINE activity]].  +
'''Coupling-control efficiencies''' are [[flux control efficiency |flux control efficiencies]] ''j<sub>Z-Y</sub>'' at a constant [[ET-pathway competent state]].  +
A '''coupling-control protocol CCP''' induces different [[coupling control state]]s at a constant [[electron-transfer-pathway state]]. [[Residual oxygen consumption]] (''Rox'') is finally evaluated for ''Rox'' correction of flux. The CCP may be extended, when further respiratory states (e.g. cell viability test; CIV assay) are added to the coupling control module consisting of three coupling control states. The term '''phosphorylation control protocol''', PCP, has been introduced synonymous for CCP. » [[Coupling_control_protocol#From_PCP_to_CCP |'''MiPNet article''']]  +
'''Coupling-control ratios''' ''CCR'' are [[flux control ratio]]s ''FCR'' at a constant mitochondrial [[pathway-control state]]. In mitochondrial preparations, there are three well-defined coupling states of respiration: [[LEAK respiration]], [[OXPHOS]], and [[Electron transfer pathway |Electron-transfer-pathway state]] (ET state). In these states, the corresponding respirtory rates are symbolized as ''L'', ''P'', and ''E''. In living cells, the OXPHOS state cannot be induced, but in the [[ROUTINE]] state the respiration rate is ''R''. A reference rate ''Z'' is defined by taking ''Z'' as the maximum flux, i.e. flux ''E'' in the ET-state, such that the lower and upper limits of the ''CCR'' are defined as 0.0 and 1.0. Then there are two mitochondrial ''CCR'', [[L/E |''L/E'']] and [[P/E |''P/E'']], and two ''CCR'' for living cells, [[L/E |''L/E'']] and [[ROUTINE-control ratio |''R/E'']].  +
'''Coupling-control states''' are defined in [[mitochondrial preparations]] (isolated mitochondria, permeabilized cells, permeabilized tissues, homogenates) as [[LEAK respiration]], [[OXPHOS]], and [[ET-pathway |ET]] states, with corresponding respiration rates (''L, P, E'') in any [[electron-transfer-pathway state]] which is competent for electron transfer. These coupling states are induced by titration of ADP and uncouplers, and application of specific inhibitors of the [[phosphorylation pathway]]. In [[living cells]], the coupling-control states are [[LEAK respiration]], [[ROUTINE]], and [[ET pathway |ET]] states of respiration with corresponding rates ''L, R, E'', using membrane-permeable inhibitors of the [[phosphorylation system]] (e.g. [[oligomycin]]) and [[uncoupler]]s (e.g. [[CCCP]]). [[Coupling-control protocol]]s induce these coupling-control states sequentially at a constant [[electron-transfer-pathway state]].  +
[[File:SUIT-nomenclature.jpg|300px|right|SUIT protocols]] '''Coupling/pathway control diagrams''' illustrate the respiratory '''states''' obtained step-by-step in substrate-uncoupler-inhibitor titrations in a [[SUIT protocol]]. Each step (to the next state) is defined by an initial state and a [[metabolic control variable]], ''X''. The respiratory states are shown by boxes. ''X'' is usually the titrated substance in a SUIT protocol. If ''X'' ([[ADP]], [[uncoupler]]s, or inhibitors of the [[phosphorylation system]], e.g. oligomycin) exerts '''coupling control''', then a transition is induced between two [[coupling-control state]]s. If ''X'' (fuel substrates, e.g. pyruvate and succinate, or [[Electron transfer pathway]] inhibitors, e.g. rotenone) exerts '''pathway control''', then a transition is induced between two [[Electron-transfer-pathway state]]s. The type of metabolic control (''X'') is shown by arrows linking two respiratory states, with vertical arrows indicating coupling control, and horizontal arrows indicating pathway control. [[Marks - DatLab |Marks]] define the section of an experimental trace in a given [[respiratory state]] (steady state). [[Events - DatLab |Events]] define the titration of ''X'' inducing a transition in the SUIT protocol. The specific sequence of coupling control and pathway control steps defines the [[SUIT protocol pattern]]. The coupling/pathway control diagrams define the [[categories of SUIT protocols]] (see Figure).  +
[[Image:Cover-Slip_black.JPG|180px|right]] A '''Cover-Slip''' should be placed on top of the O2k-Stopper to minimize contamination and evaporation of liquid extruding from the capillary of the stopper. The Cover-Slips do not exert any direct effect on oxygen backdiffusion into the [[O2k-chamber]]. Use the the '''Cover-Slip\black''' to avoid light penetration and disturbance of fluorescence signals and generally for optical measurements in the O2k.  +
The '''Crabtree effect''' describes the observation that respiration is frequently inhibited when high concentrations of glucose or fructose are added to the culture medium - a phenomenon observed in numerous cell types, particularly in proliferating cells, not only tumor cells but also bacteria and yeast. The Pasteur effect (suppression of glycolysis by oxygen) is the converse of the Crabtree effect (suppression of respiration by high concentration of glucose or fructose).  +
'''Creatine''' is a nitrogenous organic acid that occurs naturally in vertebrates and helps primarily muscle cells to supply energy by increasing the formation of adenosine triphosphate ([[ATP]]).  +
The mitochondrial '''creatine kinase''', also known as phosphocreatine kinase (CPK), facilitates energy transport with [[creatine]] and [[phosphocreatine]] as diffusible intermediates.  +
Open Access preprints (not peer-reviewed) and articles (peer-reviewed) distributed under the terms of the '''Creative Commons Attribution License''' allow unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. © remains with the authors, who have granted the publisher license in perpetuity.  +
The '''critical oxygen pressure''', ''p''<sub>c</sub>, is defined as the partial oxygen pressure, ''p''<sub>O2</sub>, below which [[aerobic]] catabolism (respiration or oxygen consumption) declines significantly. If [[anaerobic]] catabolism is activated simultaneously to compensate for lower aerobic ATP generation, then the '''[[limiting oxygen pressure]]''', ''p''<sub>l</sub>, is equal to the ''p''<sub>c</sub>. In many cases, however, the ''p''<sub>l</sub> is substantially lower than the ''p''<sub>c</sub>.  +
Coordinated respiratory [[SUIT|SUIT protocols]] are designed to include '''cross-linked respiratory states''', which are common to these protocols. Different SUIT protocols address a variety of respiratory control steps which cannot be accomodated in a single protocol. Cross-linked respiratory states are included in each individual coordinated protocol, such that these states can be considered as replicate measurements, which also allow for harmonization of data obtained with these different protocols.  +
'''Curcumin''' has been shown to possess significant anti-inflammatory, anti-oxidant, anti-carcinogenic, anti-mutagenic, anti-coagulant and anti-infective effects. The protective effects of curcumin on rat heart mitochondrial injuries induced by in vitro anoxia–reoxygenation were evaluated by [http://www.ncbi.nlm.nih.gov/pubmed/23984717 Xu et al 2013]. It was found that curcumin added before anoxia or immediately prior to reoxygenation exhibited remarkable protective effects against anoxia–reoxygenation induced oxidative damage to mitochondria.  +
A '''Custom label''' can be entered in this box to rename the axis label. Two lines are available for the axis name and unit.  +
Stoppers can be custom-made for applications with user-specific sensors according to customer specifications.  +
'''Cuvettes''' are used in [[fluorometry]] and [[transmission spectrophotometry]] to contain the samples. Use of the term 'cells' for cuvettes is discouraged, to avoid confusion with 'living cells'. Traditionally cuvettes have a square cross-section (10 x 10 mm). For many applications they are made of transparent plastic. Glass cells are used where samples may contain plastic solvents, and for some applications requiring measurements below 300 nm, quartz glass or high purity fused silica cuvettes may be necessary.  +
'''Cyanide''' (usually added as KCN) is a competitive inhibitor of [[Complex_IV| cytochcrome ''c'' oxidase (CIV)]]. Inhibition is reversed by pyruvate and high oxygen levels.  +
'''Cyclic voltammetry''' (CV) is a type of electrochemical measurement which is applied with the [[Q-Module]] as quality control to (''1'') determine the oxidation and reduction peak potentials of [[Coenzyme Q]] in the specific experimental condition, (2) check the quality of the [[Q-Sensor]], and (''3'') test the interference of chemicals used in the HRR assay with the Q-Sensor. In CV, the [[Q-Sensor]] with the [[three-electrode system]] is used to obtain information about the analyte ([[Coenzyme Q|CoQ]]) by measuring the current (''I'') as the electric potential (''V'') between two of the electrodes is varied. In CV the electric potential between the glassy carbon (GC) and the Ag/AgCl reference electrode changes linearly versus time in cyclical phases, while the current is detected between GC and platinum electrode (Pt). The detected current is plotted versus the applied voltage to obtain the typical cyclic voltammogram trace (Figure 1). The presence of substances that are oxidized/reduced will result in current between GC and Pt, which can be seen as characteristic peaks in the voltammogram at a defined potential. The oxidation or the reduction peak potential values are used to set the GC (integrated into the [[Q-Sensor]]) for a separate experiment to measure the [[Q redox state]] of a biological sample. The oxidation and reduction peak potentials can be influenced by 1) the respiration medium, 2) the type of [[Coenzyme Q | CoQ]], 3) the polarization window, 4) the scan speed, 5) the number of cycles, 6) the concentration of the analyte (CoQ), and 7) the initial polarization voltage. <be> :::-''See'': [[MiPNet24.12 NextGen-O2k: Q-Module]].  +
'''Cyclosporin A''' (CsA) is a cyclic undecapeptide from an extract of soil fungi that binds the cyclophilin D and thus preventing the formation of the mitochondrial [[PTP|permeability transition pore]]. The interaction of CsA with the cyclophilin D is phosphate mediated but the full mechanism of interaction is not well understood. For example, the deficiency of cyclophilin D in KO models does not prevent mitochondria from permeability transition and from CsA inhibition. Moreover, it is also a is a calcineurin inhibitor and potent immunosuppressive agent used largely as a means of prophylaxis against cellular rejection after solid organ transplantation.  +
'''Cytochrome ''c''''' is a component of the Electron transfer-pathway ([[Electron transfer pathway]]) in mitochondria. It is a small heme protein loosely associated with the outer side of the inner mitochondrial membrane. The heme group of cytochrome ''c'' transfers electrons from [[Complex III]] to [[Complex IV]]. The release of cytochrome ''c'' into the cytoplasm is associated with apoptosis. Cytochrome ''c'' is applied in [[HRR]] to test the integrity of the [[mitochondrial outer membrane]] ([[cytochrome c control efficiency]]).  +
The '''cytochrome ''c'' control efficiency''' expresses the control of respiration by externally added [[cytochrome c | cytochrome ''c'']], c, as a fractional change of flux from substrate state CHNO to CHNOc. In this [[flux control efficiency]], CHNOc is the [[reference state]] with stimulated flux; CHNO is the [[background state]] with CHNO substrates, upon which c is added: ''j''<sub>c</sub> = (''J''<sub>CHNOc</sub>-''J''<sub>CHNO</sub>)/''J''<sub>CHNOc</sub>. [[MiPNet19.20 Cytochrome c control efficiency |» '''MiPNet article''']]  +
D
'''D number''' is the unique code given for each [[SUIT]] protocol. In the same [[MitoPedia: SUIT |SUIT protocol]] family (SUIT-###), there might be different protocols, specifically designed for different [[sample]] type (''e.g.'', different [[mitochondrial preparations]]) or for different applications (''e.g.'', O2, [[AmR]], [[Mitochondrial membrane potential|Fluo]], [[MgG]]). Since the use of different kinds of sample or application may result in slightly different steps, each protocol receives a different D-number.  +
'''DTPA''' (Diethylenetriamine-N,N,N',N,N-pentaacetic acid, pentetic acid,(Carboxymethyl)imino]bis(ethylenenitrilo)-tetra-acetic acid) is a polyaminopolycarboxylic acid (like EDTA) chelator of metal cations. DTPA wraps around a metal ion by forming up to eight bounds, because each COO- group and and N-center serves a center for chelation. With transition metals the number of bounds is less than eight. The compound is not cell membrane permeable. In general, it chelates multivalent ions stronger than EDTA.  +
[[Image:Logo OROBOROS-DatLab.jpg|200px|right|DatLab]]'''DatLab''' is the O2k-Software for Data Acquisition & Analysis, specifically developed for [[high-resolution respirometry]] with the [[O2k-FluoRespirometer]]. The newest DatLab version is '''DatLab 7.4''', included in the [[O2k-FluoRespirometer]]. The minimum computer requirements are Intel-Core-2 or equivalent CPU, 2GB RAM and Windows XP. However, we recommend Intel i5 or equivalent CPU, 4GB RAM, Windows 10 and SSD. For the proper display of DatLab on your computer, please make sure the “Language settings” are set to English.  +
'''[[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).  +
This is a brief summary of steps to be taken for performing a high-resolution respirometry experiment with '''[[SUIT protocols]]''' using the OROBOROS [[Oroboros O2k]] and '''[[DatLab]]''' software. (1) Search for a specific [[SUIT protocol name]] (go to [[MitoPedia:_SUIT#SUIT_protocols |MitoPedia: SUIT]]). The list of MitoPedia SUIT protocols can be sorted by [[categories of SUIT protocols]] (sorting by SUIT protocol name), which is listed as the 'abbreviation' of the SUIT protocol name. (2) Copy the template for [[Mark names]] into your DatLab subdirectory: DatLab\APPDATA\MTEMPLAT. (3) Copy the [[DatLab-Analysis templates |DatLab-Analysis template]] for this SUIT protocol. (4) Follow the link to the corresponding publication or MiPNet communication, where the pdf file describing the SUIT protocol is available. (5) A DatLab demo file may be available providing an experimental example. After each sequential titration, a mark is set on the plot for flux or flow. After having set all marks, pull down the 'Mark names' menu, select the corresponding SUIT protocol for mark names, and rename all marks. The Mark names template also provides standard values of the titration volume preceding each mark. (6) Go to 'Mark statistics' [F2], copy to clipboard, and paste into the sample tab in the DatLab-Analysis template. : Example: :* SUIT protocol name: [[SUIT-011]] :* Mark names in DatLab: 1GM;2D;2c;3S;4U;5Rot- :* DatLab-Analysis template: SUIT_NS(GM)01.xlsx :* MiPNet communciation: [[MiPNet12.23 FibreRespiration]] :* DatLab demo file: MiPNet12.23 FibreRespiration.DLD  +
The file type generated by [[DatLab]] is *.DLD.  +
Common '''DatLab error messages''' and according actions and solutions are listed here.  +
[[Image:Logo OROBOROS-DatLab.jpg|left|60px||link=http://wiki.oroboros.at/index.php/DatLab |DatLab]] We recommend a 'clean install' for '''DatLab installation''': rename your previous DatLab programme subdirectory (''e.g.'' C:\DatLab_OLD). The standard '''Instrumental and SUIT DL-Protocols''' package is automatically implemented with the simple DatLab programme installation.  +
The quality of the results are strongly affected by the performance and data analysis. Therefore, we provide guidelines for performing and evaluating respirometric assays.  +
'''DatLab templates''' can be imported for O2k-setups, graph layouts, mark names, TIP2k setups and marks statistics configurations. :::: See also » [[Manage setups and templates - DatLab|Manage setups and templates]]  +
Go in DatLab to [[Mark statistics - DatLab|Mark statistics]] (F2), select which type of marks you want to export ("All marks in plot" or "DL-Protocol marks", with 3 possibilities each), then click on [Copy to clipboard] to copy selected values and paste them to a '''DatLab-Analysis template''' for numerical and graphical data analysis.  +
DatLab-Upgrading to DatLab 6: including free follow-up updates for DatLab 6 for the next two years  +
'''DatLab-Upgrading\4.1-5.2''': Upgrading DatLab 4.x to 5.2, incl. O2k-Manual, with free follow-up updates of DatLab 5.2. '''Discontinued''': see higher [[DatLab]] version.  +
The '''data recording interval''' is the time interval at which data is sampled with an instrument. In [[DatLab]] the data recording interval is set in the [[O2k control]] window. The system default value is 2 s. A lower data recording interval is selected for kinetic experiments, and when the volume-specific oxygen flux is high (>300 pmol O<sub>2</sub>·s<sup>-1</sup>·ml<sup>-1</sup>).<br/>Technically, the O2k instrument (hardware) measures the sensor signal every 10ms (which is NOT the „data recording interval“). By the given data recording interval from DatLab (software) a discrete number of sensor signal points are taken to calculate an average value in the O2k (e.g. a data recording interval of 2 s can take 200 sensor signal points; a data recording interval of 0.5 s can take 50 sensor signal points). This average value is sent to DatLab and is recorded as a raw data point. However, there is a defined threshold: the O2k does not apply more than 200 sensor signal points to calculate the average for the raw data point. For example a data recording interval of 3 s could take 300 sensor signal points but only the 200 most recent sensor signal points are used for averaging.  +
A '''dataset''' is a collection of data. In the context of databases a dataset represents the collection of entries in a database-table. In this table columns represent [[Attribute|attributes]] and rows display the according values of the entries.  +
A '''decimal marker''' is used to separate the integral part of numbers from the decimal part. The SI recommends: "the symbol for the decimal marker shall be either the point on the line or the comma on the line". In English language versions, the dot (point on the line) should be used uniquely as the decimal marker. To avoid ambiguities, BEC follows the SI recommendation that “Numbers may be divided in groups of three in order to facilitate reading; neither dots nor commas are ever inserted in the spaces between groups” (pages 183-184).  +
The '''Default label''' is the system default value for the axis label. These labels are changed automatically, according to the selected channel and unit. To change this label enter a [[Custom label]].  +
'''Delete''' a DLD file. The decision to delete a file containing no useful data can be made most easily when viewing the traces. Only available when disconnected from the O2k.  +
Select '''Delete points''' in the [[Marks - DatLab |Mark information]] window to remove all data points in the marked section of the active plot. See also [[Interpolate points]] and [[Restore points]] or [[Recalculate slope]].  +
'''Density''', mass density ''ρ'' = ''m''·''V''<sup>-1</sup> [kg·m<sup>-3</sup>], is mass ''m'' divided by volume ''V''. Surface density ''ρ''<sub>A</sub> = ''m''·''A''<sup>-1</sup> [kg·m<sup>-2</sup>] ([[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |SI]]). For a pure [[sample]] S, the mass density ''ρ''<sub>S</sub> = ''m''<sub>S</sub>·''V''<sub>S</sub><sup>-1</sup> [kg·m<sup>-3</sup>] is the [[mass]] ''m'' of pure sample S per [[volume]] ''V''<sub>S</sub> of the pure sample. With density ''ρ'' thus defined, the 'amount density' of substance B is ''ρ''<sub>B</sub> = ''n''<sub>B</sub>·''V''<sub>B</sub><sup>-1</sup> [mol·m<sup>-3</sup>]. This is not a commonly used expression, but the inverse is defined as the [[molar volume]] of a pure substance ([[Cohen 2008 IUPAC Green Book |IUPAC]]), ''V''<sub>m,B</sub> = ''V''<sub>B</sub>·''n''<sub>B</sub><sup>-1</sup> [m<sup>3</sup>·mol<sup>-1</sup>]. The pure sample is a pure gas, pure liquid or pure solid of a defined elementary entity. The amount [[concentration]], ''c''<sub>B</sub> = ''n''<sub>B</sub>·''V''<sup>-1</sup> [mol·m<sup>-3</sup>] is the amount ''n''<sub>B</sub> of substance B divided by the volume ''V'' of the mixture ([[Cohen 2008 IUPAC Green Book |IUPAC]]), and this is not called an 'amount density'. The term 'amount density' is reserved for an amount of substance per volume ''V''<sub>S</sub> of the pure substance. This explicit distinction between 'density' related to the volume of the ''sample'' and 'concentration' related to the total volume of the ''mixture'' is very helpful to avoid confusion. Further clarification is required in cases, when the mass density ''ρ''<sub>s</sub> of the sample in the mixture differs from the mass density ''ρ''<sub>S</sub> of the pure sample before mixing. Think of a sample S of pure ethanol with a volume of 1 L at 25 °C, which is mixed with a volume of 1 L of pure water at 25 °C: after the temperature of the mixture has equilibrated to 25 °C, the total volume of the mixture is less than 2 L, such that the volume ''V''<sub>S</sub> of 1 L pure ethanol has diminished to a smaller volume ''V''<sub>s</sub> of ethanol in the mixture; the density of ethanol in the mixture is higher than the density of pure ethanol (this is incomplete [[additivity]]). The volume ''V''<sub>s</sub> of sample s in a mixture is by definition smaller than the total volume ''V'' of the mixture. Sample volume ''V''<sub>S</sub> and system volume ''V'' are identical, but this applies only to the case of a ''pure'' sample. ''Concentration'' is related to samples s per total volume ''V'' of the mixture, whereas ''density'' is related to samples S or s per volume ''V''<sub>S</sub> = ''V'' or ''V''<sub>s</sub> < ''V'', respectively ([[BEC 2020.1]]).  
'''Derivative spectroscopy''' can be used to eliminate interfering artefacts or species. A first order derivative will remove a constant background [[absorbance]] across the spectral range. A second order derivative spectrum will remove a species whose absorbance is linearly dependent upon the wavelength, etc..  +
[[O2k signals and output|Channels]] can be selected/deselected in [[DatLab]] in the [[O2k configuration]]. Deselect all O2k-MultiSensor channels in O2k-Core applications. Select only the specifically used channels in O2k-MultiSensor applications.  +
A '''detector''' is a device that converts the light falling upon it into a current or voltage that is proportional to the light intensity. The most common devices in current use for [[fluorometry]] and [[spectrophotometry]] are [[photodiodes]] and [[photodiode arrays]].  +
'''Diapause''' is a preprogrammed form of developmental arrest that allows animals to survive harsh environmental conditions and may also allow populations to synchronize periods of growth and reproduction with periods of optimal temperatures and adequate water and food. Diapause is ''endogenously'' controlled, and this dormancy typically begins well before conditions become too harsh to support normal growth and development [1,2]. » [[Diapause#Diapause versus quiescence| '''MiPNet article''']]  +
The '''dicarboxylate carrier''' is a transporter which catalyses the electroneutral exchange of [[malate]]<sup>2-</sup> (or [[succinate]]<sup>2-</sup>) for inorganic [[phosphate]], HPO<sub>4</sub><sup>2-</sup>.  +
A '''difference spectrum''' is an [[absorbance spectrum]] obtained by subtracting that of one substance from that of another. For example, a '''difference spectrum''' may be plotted of the [[absorbance spectrum]] obtain ed from reduced [[cytochrome c]] and subtracting the [[absorbance spectrum]] from the same concentration of [[cytochrome c]] in its oxidised state. The [[difference spectrum]] may be used to quantify the amount to which the [[cytochrome c]] is reduced. This can be achieved with the aid of a [[reference spectrum]] (or spectra) and the [[least squares method]].  +
What are potential causes for '''different O<sub>2</sub> fluxes in the left and right chamber'''?  +
'''Diffraction gratings''' are [[dispersion devices]] that are made from glass etched with fine grooves, spaced at the same order of magnitude as the wavelength of the light to be dispersed, and then coated with aluminium to reflect the light to the photodiode array. '''Diffraction gratings''' reflect the light in different orders and [[filters]] need to be incorporated to prevent overlapping.  +
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.  +
'''Digitonin''' is a mild detergent that permeabilizes plasma membranes selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Digitonin is a natural product and thus the effective concentration has to be determined by titrations for every batch. The optimum effective digitonin concentrations for complete plasma membrane permeabilization of cultured cells can be determined directly in a respirometric protocol (see: [[SUIT-010 O2 ce-pce D008]]).  +
'''Dihydro-orotate dehydrogenase''' is an electron transfer complex of the inner mitochondrial membrane, converting dihydro-orotate (Dho) into orotate, and linking electron transfer through the [[Q-junction]] to pyrimidine synthesis and thus to the control of biogenesis.  +
'''Dihydroethidium''' (also called hydroethidine) is a cell permeant fluorescent probe used to analyse superoxide presence. It is a reduced form of ethidium that presents blue fluorescence, and after oxidation by superoxide becomes able to intercalate DNA and emits red fluorescence (excitation wavelength ~518–535 nm, emission ~605–610 nm). It has been used to detect superoxide by HPLC and by fluorescence microscopy.  +
Dilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber.  +
'''Dimensions''' are defined in the SI {quote}: Physical quantities can be organized in a system of dimensions, where the system used is decided by convention. Each of the seven base quantities used in the SI is regarded as having its own dimension. .. All other quantities, with the exception of [[count]]s, are derived quantities, which may be written in terms of base quantities according to the equations of physics. The dimensions of the derived quantities are written as products of powers of the dimensions of the base quantities using the equations that relate the derived quantities to the base quantities. There are quantities ''Q'' for which the defining equation is such that all of the dimensional exponents in the equation for the dimension of ''Q'' are zero. This is true in particular for any quantity that is defined as the ratio of two quantities of the same kind. .. There are also some quantities that cannot be described in terms of the seven base quantities of the SI, but have the nature of a [[count]]. Examples are a number of molecules, a number of cellular or biomolecular entities (for example copies of a particular nucleic acid sequence), or degeneracy in quantum mechanics. Counting quantities are also quantities with the associated unit one. {end of quote: p 136, [[Bureau International des Poids et Mesures 2019 The International System of Units (SI)]]}  +
'''Dimethyl sulfoxide''' is a polar aprotic solvent that dissolves both polar and nonpolar compounds and is miscible in a wide range of organic solvents as well as water. DMSO may also be used as a cryoprotectant, added to cell media to reduce ice formation and thereby prevent cell death during the freezing process.  +
'''Dinitrochlorobenzene (1-chloro-2,4-dinitrobenzene)''' (DNCB) is a glutathione (GSH) inhibitor.  +
'''2,4-dinitrophenole''' (C<sub>6</sub>H<sub>4</sub>N<sub>2</sub>O<sub>5</sub>; M = 184.11 g·mol<sup>-1</sup>) is a protonophore acting as an [[uncoupler]] of [[oxidative phosphorylation]].  +
A '''directive''' is a legal act of the European Union, which requires member states to achieve a particular result without dictating the means of achieving that result.  +
In a '''discontinuous system''', gradients in [[continuous system]]s across the length, ''l'', of the diffusion path [m], are replaced by differences across compartmental boundaries of zero thickness, and the local concentration is replaced by the free activity, ''α'' [mol·dm<sup>-3</sup>]. The length of the diffusion path may not be constant along all diffusion pathways, spacial direction varies (''e.g.'', in a spherical particle surrounded by a semipermeable membrane), and information on the diffusion paths may even be not known in a discontinuous system. In this case (''e.g.'', in most treatments of the [[protonmotive force]]) the diffusion path is moved from the (ergodynamic) isomorphic [[force]] term to the (kinetic) [[mobility]] term. The synonym of a discontinuous system is '''compartmental''' or discretized system. In the first part of the definition of discontinuous systems, three compartments are considered: (1) the source compartment A, (2) the sink compartment B, and (3) the internal barrier compartment with thickness ''l''. In a two-compartmental description, a system boundary is defined of zero thickness, such that the barrier comparment (''e.g.'', a semipermeable membrane) is either part of the system (internal) or part of the environment (external). Similarly, the intermediary steps in a chemical reaction may be explicitely considered in an ergodnamic multi-comparment system; alternatively, the kinetic analysis of all intermediary steps may be collectively considered in the catalytic reaction ''mobility'', reducing the measurement to a two-compartmental analysis of the substrate and product compartments.  +
A '''dispersion device''' diffracts light at different angles according to its wavelength. Traditionally, prisms and [[diffraction gratings]] are used, the latter now being the most commonly used device in a [[spectrofluorometer]] or [[spectrophotometer]].  +
'''Display DatLab help''' In this section, we present some issues that could happen during your data analysis related to the graphs display and how to fix them quickly. Case in which an issue might occur: ::* While analysing your data, trying to close the program while the graph is still being loaded. If you cancel the closing window, the graph will not be loaded at the screen. In the event of a frozen display of the graphs, try the alternatives below: ::* Click on: Graph > Autoscale time axis ::* Click on: Graph > Scaling (F6); then press OK to confirm the scaling and induce the program to reload the graphs (no changes in the graphs are required).  +
The Power-O2k number, which is set in the pull-down menu Oroboros O2k \ [[O2k configuration]], is shown in the active graph. To show it in graphs copied to clipboard, the option "Show Oroboros icon in clipboard files" must be enabled in the Graph-menu [[Graph options - DatLab]].  +
If '''Display numerical value''' the current numerical values are displayed in the graph for the active plots on the Y1 axis and Y2 axis (during data acquisition only).  +
'''Dithionite''' Na<sub>2</sub>S<sub>2</sub>O<sub>4</sub> is the 'zero oxygen solution powder' used for [[Oxygen calibration - DatLab |calibration of oxygen sensors]] at [[Zero calibration | zero oxygen]], or for stepwise reduction of oxygen [[concentration]]s in [[MiPNet14.06 Instrumental O2 background |instrumental O<sub>2</sub> background tests]]. It is not recommended to use dithionite in experiments with biological samples or several multisensor approaches, for these see [[Setting the oxygen concentration]].  +
The most common cause of '''drift''' is variation in the intensity of the [[light source]]. The effect of this can be minimised by carrying out a [[balance]] at frequent intervals.  +
If a sample contains a number of absorbing substances, it is sometimes possible to select discrete pairs of wavelengths at which the change in [[absorbance]] of a particular substance (due to oxidation or reduction, for example) is largely independent of changes in the [[absorbance]] of other substances present. '''Dual wavelength analysis''' can be carried out for [[cytochrome c]] by subtracting the [[absorbance]] at 540 nm from that at 550nm in order to give a measure of the degree of reduction. Similarly, by subtracting the [[absorbance]] at 465 nm from that at 444 nm, an indicator of the [[redox state]] of [[Complex IV | cytochrome ''aa''<sub>3</sub>]] can be obtained.  +
'''Dyscoupled respiration''' is [[LEAK respiration]] distinguished from intrinsically (physiologically) uncoupled and from extrinsic experimentally [[Uncoupler|uncoupled]] respiration as an indication of extrinsic uncoupling (pathological, toxicological, pharmacological by agents that are not specifically applied to induce uncoupling, but are tested for their potential dyscoupling effect). Dyscoupling indicates a mitochondrial dysfunction. In addition to intrinsic uncoupling, dyscoupling occurs under pathological and toxicological conditions. Thus a distinction is made between physiological uncoupling and pathologically defective dyscoupling in mitochondrial respiration.  +
E
E +
» [[elementary charge]] ''e'' = 1.602 176 634∙10<sup>-19</sup> C∙x<sup>-1</sup> » [[Euler's number]] ''e'' ~ 2.718 281 828 459 » [[ET capacity]] ''E''  +