Property:Description
From Bioblast
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A
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<sup>®</sup> 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<sup>®</sup> UltraRed which has a 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 terms '''anoxia''' and 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. +
'''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 {''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]]. +
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