Property:Description
From Bioblast
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A
'''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 {''End of Quote'': [[Bureau International des Poids et Mesures 2019 The International System of Units (SI)]]}.
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 inhibitor of [[Complex IV]]/cytochrome ''c'' oxidase (CIV, 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''. +
'''Beryllium sulfate''' is used in combination with [[sodium fluoride]] to form beryllium trifluoride (BeF<sup>3−</sup>), to inhibit the [[ATP synthase]] if it is exposed by disruption of the mitochondrial membranes. +
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 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. +
