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B
'''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 albumin is a membrane 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''' 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]]''' +
'''COPE core practices for research''' are applicable to all involved in publishing scholarly literature. +
'''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'''<sup>TM</sup> (CaG) denotes a family of [[extrinsic fluorophores]] applied for measurement of Ca<sup>2+</sup> concentration with [[mitochondrial preparations]]. This dye fluoresces when bound to Ca<sup>2+</sup>. When measuring mitochondrial calcium uptake it is possible to observe the increase of the CaG signal upon calcium titration, followed by the decrease of CaG signal due to the uptake. +
Calcium retention capacity (CaRC) is a measure of the capability of mitochondria to retain calcium (Ca<sup>2+</sup>), 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 Ca<sup>2+</sup> levels and thereby to the regulation of calcium-dependent cellular processes. Alterations of CaRC are important in stress phenomena associated with energy limitation and have been linked to neurodegenerative diseases [[Starkov 2010 FEBS J |(Starkov 2013 FEBS J).]]
Experimentally, CaRC has been indirectly assessed by determination of respiratory rates of isolated mitochondria which were exposed to continuously increasing doses of Ca<sup>2+</sup> by use of the [[TIP2k-Module| Titration-Injection microPump TIP2k]]. The upper limit of CaRC was observed as a sudden decrease of respiration presumed to reflect opening of the permeability transition pore [[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]] +
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 ([[acylcarnitine]]s). 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 I''' (CPT-I, also known as carnitine acyltransferase I) is a regulatory enzyme in mitochondrial long-chain acyl-CoA uptake and further oxidation. CPT-I is associated with the mt-outer membrane mtOM and catalyses the formation of [[acylcarnitine]]s 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 II]] 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-I. +
'''Carnitine palmitoyltransferase II''' (CPT-II, 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-II is located on the inner side of the mtIM and converts the [[acylcarnitine]]s (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-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 [[acylcarnitine]]s 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]].
Mitochondrial respiration medium [[MiR05]] was developed considering the intracellular conditions of mitochondria in living cells. In mitochondrial preparations, enzymes and substrates present in the cytosol (such as catalase) are diluted when the plasma membrane is removed. Therefore, the addition of catalase is recommended when working with mitochondrial preparations, to consume any H<sub>2</sub>O<sub>2</sub> generated during the assay. +
'''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'''.
* ''This page needs an update.'' +
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 (see: [[Cell count and normalization in HRR]]). 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. +
'''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. +
'''Check for updates''' in the Help pull-down menu of DatLab 8 and follow the simple installation instruction if your computer (Linux or Windows) running DatLab is connected to the internet. Alternatively, use a different computer connected to the internet, download the [https://www.oroboros.at/index.php/download-update-datlab-8-for-linux/ update for Linux], and transfer it to the computer operating DatLab by USB. Check regularly for updates. +
[[File:Chb.png|100px|https://wiki.oroboros.at/index.php/File:Chb.png]] '''Chemical background''' ''Chb'' is due to autooxidation of the reagents. During CIV assays, ascorbate and TMPD are added to maintain cytochrome ''c'' in a reduced state. External cytochrome ''c'' may be included in the CIV assay. The autooxidation of these compounds is linearly oxygen-dependent down to approximately 50 µM oxygen and responsible for the chemical background oxygen flux after the inhibition of CIV. Oxygen flux due to the chemical reaction of autooxidation must be corrected for the [[Oxygen flux - instrumental background|instrumental O2 background]]. The correction for chemical background is necessary to determine CIV activity, in which case the instrumental O2 background and chemical background may be combined in an overall correction term. +
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. +
In '''chlororespiration''' oxygen is consumed by a putative respiratory electron transfer system (ETS) within the thylakoid membrane of the [[chloroplasts]] and ATP is produced. It is a process that involves the interaction with the photosynthetic ETS in which NAD(P)H dehydrogenase transfers electrons to oxygen with the assistance of the photosynthetic plastoquinone (PQ), which acts as a non-photochemical redox carrier. Initially described in the unicellular alga ''Chlamydomonas reindhartdii'', chlororespiration was highly disputed for years until the discovery of a NAD(P)H-dehydrogenase (NDH) complex (plastidic encoded) and plastid terminal oxidase (PTOX) (nuclear encoded) in higher-plant chloroplasts. PTOX is homologous to the plant mitochondrial alternative oxidase and has the role of preventing the over-reduction of the PQ pool while the NDH complexes provide a gateway for the electrons to form the ETS and consume oxygen. As a result of this process there is a cyclic electron flow around Photosystem I (PSI) that is activated under stress conditions acting as a photoprotection mechanism and could be involved in protecting against oxidative stress. +
'''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 and delete file'''. The decision to delete a DatLab file containing no useful data can be made most easily when viewing the traces. Only available when disconnected from the O2k. +
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 (well mixed and isothermal), continuous with gradients, or [[Discontinuous system|discontinuous]] with compartments (heterogenous). +
A '''coenzyme''' or cosubstrate is a [[cofactor]] that is attached loosely and transiently to an enzyme, in contrast to a [[prosthetic group]] that is attached permanently and tightly. The coenzyme is required by the corresponding enzyme for its activity (IUPAC definition). A coenzyme is 'a low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons' (IUPAC definition). +
'''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 (CoQ<sub>6</sub>) is the most commonly found CoQ in ''Saccharomyces cerevisiae'', eight units in ''Escherichia coli'' (CoQ<sub>8</sub>), nine units in ''Caenorhabditis elegans'' and rodents (CoQ<sub>9</sub>), ten units in humans (CoQ<sub>10</sub>), and some species have more than one CoQ form, e.g. human and rodent mitochondria contain different proportions of CoQ<sub>9</sub> and CoQ<sub>10</sub>. 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|CoQ<sub>2</sub>]]'''Coenzyme Q<sub>2</sub>''' or ubiquinone-2 (CoQ<sub>2</sub>) 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 as a Q-mimetic to detect the redox changes of [[coenzyme Q]] at the [[Q-junction]] in conjunction with the [[Q-Module]], since the naturally occurring long-chain coenzyme Q (e.g. CoQ<sub>10</sub>) is trapped within membrane boundaries. CoQ<sub>2</sub> 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]]. +
A '''cofactor''' is 'an organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely ([[coenzyme]]) or tightly ([[prosthetic group]])' (IUPAC definition). +
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. +
Mitochondria and the patient: communication between patients, medical professionals, scientists, and the public +
'''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]]. There is a widespread ambiguity on the 'lonely H<sup>+</sup> (the lonely [[hydron]])' surrounding Complex I: [[Ambiguity crisis - NAD and H+ |CI ambiguities]]. +
''See'' '''[[NS-pathway control state]]''' (previous: CI<small>&</small>II-linked) +
''See'' '''[[N-pathway control state]]''' (previous: CI-linked) versus '''[[Complex I]]''' +
[[File:CII.png |right|200px|link=Gnaiger 2023 MitoFit CII]]
'''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 reversible oxidoreduction of succinate and fumarate is catalyzed in a soluble domain and coupled to the reversible oxidoreduction of quinol and quinone in the mitochondrial inner membrane. CII consists in most species of four subunits. The flavoprotein [[succinate dehydrogenase]] is the largest polypeptide of CII, located on the matrix face of the mt-inner membrane. Succinate:quinone oxidoreductases (SQRs, SDHABCD) favour oxidation of succinate and reduction of quinone in the canonical forward direction of the TCA cycle and electron transfer into the [[Q-junction]]. In contrast, quinol:fumarate reductases (QFRs, fumarate reductases, FRDABCD) tend to operate in the reverse direction reducing fumarate and oxidizing quinol. +
[[File:CII-ambiguities Graphical abstract.png|300px|left|link=Gnaiger 2023 MitoFit CII]]The current narrative that the reduced coenzymes NADH and FADH2 feed electrons from the tricarboxylic acid (TCA) cycle into the mitochondrial electron transfer system can create ambiguities around respiratory Complex CII. Succinate dehydrogenase or CII reduces FAD to FADH2 in the canonical forward TCA cycle. However, some graphical representations of the membrane-bound electron transfer system (ETS) depict CII as the site of oxidation of FADH2. This leads to the false believe that FADH2 generated by electron transferring flavoprotein (CETF) in fatty acid oxidation and mitochondrial glycerophosphate dehydrogenase (CGpDH) feeds electrons into the ETS through CII. In reality, NADH and succinate produced in the TCA cycle are the substrates of Complexes CI and CII, respectively, and the reduced flavin groups FMNH2 and FADH2 are downstream products of CI and CII, respectively, carrying electrons from CI and CII into the Q-junction. Similarly, CETF and CGpDH feed electrons into the Q-junction but not through CII. The ambiguities surrounding Complex II in the literature call for quality control, to secure scientific standards in current communications on bioenergetics and support adequate clinical applications. +
''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 [[volume]] 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. +
As stated on the [https://www.bioenergetics-communications.org/index.php/bec/BECPolicies#Journal_policies_on_conflicts_of_interest_.2F_competing_interests Bioenergetics Communications' policy], a '''conflict of interest''' may be of non-financial or financial nature. Examples of conflicts of interest include (but are not limited to):
:::* Individuals receiving funding, salary or other forms of payment from an organization, or holding stocks or shares from a company, whose financial situation might be influenced by the publication of the findings;
:::* Individuals, their funding organization or employer holding (or applying for) related patents;
:::* Official affiliations and memberships with interest groups relating to the content of the publication;
:::* Political, religious, or ideological competing interests.
For authors, any conflict of interest is declared at the time of submission and included in the published manuscript. For editors and reviewers, conflicts should be taken into account before accepting an assignment. +
'''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). +
Authors retain the copyright for the contents of their manuscripts published in [[Bioenergetics Communications]]. {''Quote''} All preprints are posted with a Creative Commons CC BY 4.0 license, ensuring that authors retain '''copyright''' and receive credit for their work, while allowing anyone to read and reuse their work. {''end of Quote''} +
[[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]]. +
