Property:Description
From Bioblast
This is a property of type Text.
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[[File:Ce1;1Dig;1S;2D;3P;4Rot;5Ama.png|520px|SUIT9]] +
[[File:1S;2D;3P;4Rot;5Ama.png|400px|SUIT-009]] +
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[[File:1S;2D;2c;3P;4Rot;5Ama.png|400px|SUIT9]] +
[[File:ce1;ce2Rot;ce3S;ce4D;1Dig;1c.png|400px|Respirometric test of optimum digitonin concentration ]] +
[[File:ce1;ce2Rot;ce3S;ce4D;1Dig;1c.png|400px|Respirometric test of optimum digitonin concentration ]] +
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[[File:1GMS;2D;3Ama.png|290px|SUIT-018]] +
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A comprehensive library of SUIT protocols including DatLab example traces, instructions, brief explanatory texts, links to relevant pages, representative diagrams and templates for data evaluation can be browsed from inside DatLab 7.4. Click on menu [Protocols]\SUIT: Browse DL-Protocols and templates to open a folder with all the [[MitoPedia: SUIT|SUIT protocols]] provided with the DatLab 7.4. [[Run DL-Protocol/Set O2 limit| DL-Protocols]] (DLP) for different [[MitoPedia: Sample preparations|sample preparations]] can be chosen to assess multiple sequences of respiratory [[Coupling control state|coupling control ]] and [[Electron-transfer-pathway state|ET-pathway ]] states. DL-Protocols posses unique D## codes and comprise a fixed sequence of events and marks which cannot be changed by the user. However, the users can edit titration volumes and concentrations in the Overview window of a DL-protocol, save the overview, and export the file as a [[Export DL-Protocol User (*.DLPU)|user-specific DL-Protocol]] [File / Export / A or B: Export DL-Protocol User (*.DLPU)]. In DatLab 7.4, fixed sequence of events and marks can be changed (Skip/Added) in a SUIT protocol by the user. Moreover, editions of text, instructions, concentrations and titration volumes of injections in a specific DL-Protocol can be edited and saved as [[Export DL-Protocol User (*.DLPU)|user-specific DL-Protocol]] [File]\Export\DL-Protocol User (*.DLPU). For more information, see: [[Enable DL-Protocol editing]]. +
Use the '''SUITbrowser''' to find the substrate-uncoupler-inhibitor-titration ([[SUIT]]) protocol most suitable for addressing your research questions.
<big><big>Open the SUITbrowser: http://suitbrowser.oroboros.at/</big></big>
[[Image:PlayVideo.jpg|50px|link=https://www.youtube.com/watch?v=8T33sp9KkJk]] [https://www.youtube.com/watch?v=8T33sp9KkJk How to find a DL-Protocol (DLP)] +
'''Safranin''' is one of the most established dyes for measuring [[mitochondrial membrane potential]] by [[fluorometry]]. It is an [[extrinsic fluorophores |extrinsic fluorophore]] with an excitation wavelength of 495 nm and emission wavelength of 587 nm. Safranin is a potent inhibitor of [[NADH electron transfer-pathway state |N-linked respiration]] and of the [[phosphorylation system]].
''Synonyms:'' Safranin O, Safranin Y, Safranin T, Gossypimine, Cotton Red, Basic Red2 +
'''Salicylhydroxamic acid''' (SHAM; synonym: 2-Hydroxybenzohydroxamic acid N,2-Dihydroxybenzamide) is an inhibitor of the [[alternative oxidase]] (AOX). When AOX is blocked by SHAM, electrons are forced through the CIII-cytochrome ''c'' oxidase pathway, allowing observation of the operation of the CIII-CIV pathway without AOX activity. +
A '''sample''' is one or more parts taken from an ensemble that is studied. A sample is either stored for later quantification or prepared and possibly separated into subsamples, which are enclosed in a system for qualitative or quantitative investigation. A pure sample S is a pure gas, pure liquid or pure solid of a defined elementary [[entity]]-type. A pure biological sample is a cell type, tissue, or organism without its solid, liquid or gaseous environment. Then the system used to investigate sample S contains only entities of entity-type S, and the [[volume]] ''V''<sub>S</sub> [L] and [[mass]] ''m''<sub>S</sub> [kg] of the pure (sub)sample S are identical to the volume ''V'' and mass ''m'' of the experimental [[system]]. A pure sample S may be mixed with other components to be investigated as a solution, mixture, or suspension, indicated by the symbol s in contrast to the pure sample S. A sample s is obtained in combination with other components, such that the [[volume]] ''V''<sub>s</sub> [L] and [[mass]] ''m''<sub>s</sub> [kg] of the sample s are larger than the volume ''V''<sub>S</sub> and mass ''m''<sub>S</sub> of the pure sample S. For example, the number of cells ''N''<sub>ce</sub> [Mx] can be counted in a sample s of a cell suspension, whereas the mass ''m''<sub>ce</sub> [mg] of cells requires a pure sample S of cells to be measured on a mass-balance. Clarity of statistical representation is improved, if the symbol ''N'' is used for the number of [[primary sample]]s taken from a study group, and the symbol ''n'' is used for the number of subsamples studied as technical repeats. +
'''DatLab 8''': In the window '''Sample and medium''', information is entered and displayed for the sample and medium. Entries can be edited any time during the experiment or during post-experiment analysis. All related results are recalculated instantaneously with the new parameters.
'''DatLab 7''': +
[[File:Sample Holder - 28410-01.jpg|right|180px]] Sample Holder - to protect susceptible samples from being damaged by stirring of the medium in the 2.0 mL O2k-chamber. +
'''Sample mass [[concentration]]''' is ''C''<sub>''m''<sub>s</sub></sub> = ''m''<sub>s</sub>·''V''<sup>-1</sup> [kg·m<sup>-3</sup>]. +
'''Sample size''' is an ambiguous term. (1) Size can be measured as an extensive quantity in terms of [[mass]] ''m''<sub>S</sub> [kg], [[volume]] ''V''<sub>S</sub> [m<sup>3</sup>], or [[energy]] ''E''<sub>S</sub> [J] of a pure [[sample]] S. If the sample consists of countable [[entity |entities]] ''X'', the [[count]] ''N''<sub>''X''</sub> [x] in sample S is an elementary quantity, in contrast to the extensive quantities used as indicators of sample size. (2) In statistics, however, the term 'sample size' does not refer to the individual sample, but indicates on the contrary the number of samples investigated or sampled from a study group. ''N'' is the number of [[sample]]s collected and assayed to obtain representative statistical information on the [[population]]. The population size defines the upper limit of the statistical sample size. +
An experimental '''sample type''' is the object of an [[experiment]]. A sample type is defined by the specifications of the [[population]] and by a specific sample preparation (see [[MitoPedia: Sample preparations]]). +
'''Saponin''' is a mild detergent that [[Permeabilization of plasma membrane|permeabilizes plasma membranes]] completely and selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Applied for [[Permeabilized tissue or cells|permeabilization of muscle fibres]]. +
Low muscle strength is a key characteristic of '''sarcopenia''' due to low muscle quantity and quality, with poor physical performance at severe sarcopenia. Older age may be defined as the age group when sarcopenia becomes a common burden. +
'''Save''' a DatLab file. When disconnected from the O2k, save any changes made under the identical file name overwriting the previous file. Such changes do not affect the raw data of the experiment, but relate to calibrations, experimental protocol, marks, events, and layout. +
'''Save and Disconnect''': Stops data acquisition and disconnects from the O2k (only for DatLab 7) +
'''Save as''' a DatLab file. When disconnected from the O2k, save the file under a different file name, optionally in a different directory. +
A '''scalar''' is a pysicochemical quantity that is fully described by its magnitude. A potential difference, differences of concentration or pressure are scalars, whereas a potential gradient is a [[vector]]. Similarly, the [[protonmotive force]] and metabolic oxygen [[flux]] are scalars, whereas the fundamental [[force]]s of physics and [[velocity]] are vectors. +
'''Scaling''' a graph in [[DatLab]] provides flexibility to vary the display of the plots and create Graph layouts. It allows viewing a data plot in differently scaled graphs, zooming the signal and time scales, and scrolling along the axes of the graph provide maximum information on the current experiment. This does not influence the format of stored data. Different ranges for the axes change the appearance of data dramatically. It is highly recommended to use reference layouts.
»''Compare:'' [[Select plots - DatLab]]. +
'''Scaling factor''' determines the multiplication factor that is applied to the time derivative of the signal. +
Most biological samples do not consist simply of pigments but also particles (e.g. cells, fibres, mitochondria) which scatter the [[incident light]]. The effect of '''scattering''' is an apparent increase in [[absorbance]] due to an increase in pathlength and the loss of light scattered in directions other than that of the detector. Two types of scattering are encountered. For incident light of wavelength ''λ'', Rayleigh scattering is due to particles of diameter < ''λ'' (molecules, sub-cellular particles). The intensity of scatter light is proportional to ''λ''<sup>4</sup> and is predominantly backward scattering. Mie scattering is caused by particles of diameter of the order of or greater than ''λ'' (tissue cells). The intensity of scatter light is proportional to 1/''λ'' and is predominantly forward scattering. +
As per the 2017 UNESCO Recommendation on Science and Scientific Researchers, the term ‘science’ signifies the enterprise whereby humankind, acting individually or in small or large groups, makes an organized attempt, in cooperation and in competition, by means of the objective study of observed phenomena and its validation through sharing of findings and data and through peer review, to discover and master the chain of causalities, relations or interactions; brings together in a coordinated form subsystems of knowledge by means of systematic reflection and conceptualization; and thereby furnishes itself with the opportunity of using, to its own advantage, understanding of the processes and phenomena occurring in nature and society. +
The '''Science Citation Index''' SCI offers bibliographical access to a curated collection of journals across 178 scientific disciplines. The SCI provides gold-standard lists of established journals. +
[[Image:Scissors stainless steel straight Tip sharp.jpg|right|180px]]'''Scissors\stainless steel\straight Tip\sharp'''. +
[[File:24330-02.jpg|right|180px]]'''Screwdriver allen wrench''', a standard component of the [[O2k-FluoRespirometer]] and [[O2k-sV-Module]]. +
The 2-chamber design of the O2k helps to '''search for defective O2k components''', by switching components linked to O2k chambers A and B between sides A and B. +
The second, symbol s, is the SI unit of time. It is defined by taking the fixed numerical value of the caesium frequency ∆''ν''<sub>Cs</sub>, the unperturbed ground-state hyperfine transition frequency of the caesium 133 atom, to be 9 192 631 770 when expressed in the unit Hz, which is equal to s<sup>−1</sup>. +
'''Select O2k - DatLab''' +
In the pull-down menue [Graph], '''Select plots''' opens the Graph layout window 'Plots'. For each graph, the plots shown with the Y1 or Y2 axis can be selected, axis labels and line styles can be defined, the unit for the calibrated signal can be changed, Flux/Slope can be chosen to be displayed as Flux per volume or as normalized specific flux/flow, the background correction can be switched on or off, and the channel can be selectively displayed as the raw signal. Graph layouts can be selected and loaded or a Graph layout may be saved.
»''Compare:'' [[Scaling - DatLab]]. +
'''Selectivity''' is the ability of a sensor or method to quantify accurately and specifically the analyte or analytes in the presence of other compounds. +
'''Semiquinone''' is an unstable free radical derived either from the removal of one hydrogen atom with its electron from [[quinol]] (reduced form), or by the addition of a single hydrogen atom to a [[quinone]] (oxidized form). +
'''Sensitivity''' refers to the response obtained for a given amount of analyte and is often denoted by two factors: the limit of detection and the limit of quantification. +
[[File:SSMFRP.jpg|left|200px]] The '''Serbian Society for Mitochondrial and Free Radical Physiology (SSMFRP)''' was established in 2008 as a national Society and has 150 members who gather research in the fields of molecular biology, biochemistry, medicine, chemistry, agriculture, physics and other related disciplines.
The SSMFRP was founded as a '''voluntary non-governmental and non-profit association''' for researchers whose goal is to support the creative improvement of scientific knowledge about the '''physiology of mitochondria and free radicals''', support for the development of modern research approaches and integration of fundamental research in order to better understand the role of free radicals in pathophysiological states, as well as promoting scientific knowledge in the country and abroad. +
'''Serial port''' describes the connection between O2k and Computer.
With the [[USB-Cable 2.0\Type A-B]] connected, select '''Serial port''' in the [[Connection window]]. Depending on the [[O2k series]], it is possible to connect with a '''Serial port''' or [[USB port]]. +
Create an identifier for your Power O2k instrument. Since it is displayed in the status panel (bottom right) and in axis labels, it should be a short code, any combination of digits and letters is allowed. +
For '''shipping an O2k or parts''', standard operating procedures have to be followed to avoid damage of the instrument and unexpected delays. The [[O2k-Main Unit]] must be shipped only in [[Packing\O2k-Box 1]], without [[O2k-chamber]]s and without [[OroboPOS]]. Two [[O2k-Chamber Holder]]s, two [[OroboPOS-Holder]]s and two [[OroboPOS-Connector]]s are attached to the O2k-Main Unit for transport. +
'''Shredder-Accessory Box''': for storage and shipping of Shredder accessories. +
[[Image:Shredder-Tube Cap Tool.JPG|180px|right|link=http://www.bioblast.at/index.php/Shredder-Tube_Cap_Tool]] '''Shredder-Tube Cap Tool''': component of [[PBI-Shredder_O2k-Set | PBI-Shredder O2k-Set]], not available as a single item. +
[[Image:Shredder-Tube Ram Tool.JPG|right|180px]]'''Shredder-Tube Ram Tool''': component of [[PBI-Shredder_O2k-Set | PBI-Shredder O2k-Set]]. +
[[Image:Shredder-Tube Analyt Biochem.jpg|180px|right]]'''Shredder-Tubes''': consisting of Shredder Tube FT500-PS with Lysis Disk, serrated [[Shredder-Tube_Ram_Tool | Shredder-Tube Ram Tool]] and [[Shredder-Tube_Cap_Tool | Shredder-Tube Cap Tool]], coral colour (Box of 100) and Shredder Tube FT500-PMS with Lysis Disk, serrated [[Shredder-Tube_Ram_Tool | Shredder-Tube Ram Tool]] and [[Shredder-Tube_Cap_Tool | Shredder-Tube Cap Tool]], coral colour (Box of 100). There is no difference between the white and the coral shredder tubes, except that the white tubes are also approved for high pressure. +
There are many '''sides''' of the term 'side' in our language system. Inside and outside are the sides that are separated by the system boundaries of an experimental [[system]]. + and - are the two sides of numbers separated by 0. Pages in books have opposite sides or front sides versus backsides. Many fundamental terms have opposite sides of the meaning, thus spanning the entire message in the space between their apparently contrasting sides, and transforming the paradox as a perspective into the unified whole, the full, the complete. On the other side, such fundamental terms are fully understood only after ''realization'' of the opposite sides of their meaning — treasures discovered in the etymological origins of the word. It makes sense to open all our senses to comprehend the bright side and the dark side of things. Whereas the student sais "I see a black sheep", Zen decides "You see, that one side of the sheep is black". This is the message to consider both sides before choosing sides, besides overcoming a one-sided point of view. Don't rock side-to-side, but get immersed deeply inside things to see the upsides and downsides of every thing or anything, and more so of nothing. Inside is the insight, for insiders and outsiders of the feedback loop of an [[Ouroboros]]. +
see [[O2k signal line]] +
The '''signal to noise ratio''' is the ratio of the power of the signal to that of the noise. For example, in [[fluorimetry]] it would be the ratio of the square of the [[fluorescence]] intensity to the square of the intensity of the background noise. +
'''Sirtuins''' are NAD<sup>+</sup>-dependent deacetylases which play a prominent role as metabolic regulators. Their dependence on intracellular levels of NAD<sup>+</sup> (NAD<sup>+</sup> activates sirtuin activity, whereas NADH inhibits it) makes them suitable as sensors that can detect cellular energy status.
[[Sirtuins#Sirtuin_family |» '''MiPNet article''']] +
The '''slit width''' determines the amount of light entering the [[spectrofluorometer]] or [[spectrophotometer]]. A larger slit reduces the [[signal-to-noise ratio]] but reduces the wavelength [[resolution]]. +
[[Image:SmartFluo.png|200px|right]]'''Smart Fluo-Sensor Blue''': Excitation LED 465 nm (dominant wavelenght) with short pass filter, emission (red) with long pass filter, individual sensors are calibrated with sensor-specific memory and direct input into DatLab 7 to obtain reproducible light intensities with different sensors, including photodiode, [[Filter-Cap]] equipped with [[Filter Set Saf]] for measurement of mitochondrial membrane potential with [[Safranin|safranin]] and [[Rhodamine 123|rhodamine 123]]. [[Filter Set MgG / CaG]] for [[Magnesium green]] and [[Calcium green]] measurements are included. +
[[Image:SmartFluo.png|200px|right]]'''Smart Fluo-Sensor Green''': Excitation LED 525 nm (dominant wavelength) with short pass filter, emission (red) with long pass filter, individual sensors are calibrated with sensor-specific memory and direct input into DatLab 7 to obtain reproducible light intensities with different sensors, including photodiode, [[Filter-Cap]] equipped with [[Filter Set AmR]] for [[Amplex® UltraRed|Amplex UltraRed]] and [[TMRM]] measurements when delivered. +
[[Image:DSC_0491_SmartPOS.jpg|right|180px]]
The '''SmartPOS''' is a [[polarographic oxygen sensor]] (POS), for O2k-Series J and XB onward, with an amperometric mode of operation. The SmartPOS combines the previous [[OroboPOS]] and [[OroboPOS-Connector]] and is automatically recognized by the software DatLab 8. Combination of the previously separated components in one piece, protects the electrical connections. The SmartPOS is, like the [[OroboPOS]], a Clark type polarographic oxygen sensor (POS), which remains the gold standard for measuring dissolved oxygen in biomedical, environmental and industrial applications over a wide dynamic oxygen range. The SmartPOS meets the highest quality criteria in terms of linearity, stability and sensitivity of the signal.
The sensor consists of a gold cathode, a silver/silverchloride anode and a KCl electrolyte reservoir separated from the sample by a 25 µm membrane (FEP). With application of a polarization voltage (0.8 V), a current is obtained as an amperometric signal. +
Various methods of '''smoothing''' can be applied to improve the [[signal-to-noise ratio]]. For instance, data points recorded over time [s] or over a range of wavelengths [nm] can be smoothed by averaging ''n'' data points per interval. Then the average of the ''n'' points per smoothing interval can be taken for each successively recorded data point across the time range or range of the spectrum to give a ''n''-point moving average smoothing. This method decreases the [[noise]] of the signal, but clearly reduces the time or wavelength [[resolution]]. More advanced methods of smoothing are applied to retain a higher [[time resolution]] or wavelength resolution. +
[[File:SHVM.png|100px|left]]The '''Society for Heart and Vascular Metabolism''' (SHVM) The Society for Heart and Vascular Metabolism was founded in 2001, with the intent of providing a forum for the free exchange of ideas by a group of investigators that had a special interest in the multiple roles of intermediary metabolism in the cardiovascular system. An important aim of the Society is to foster interactions between young investigators and senior scientists and our meetings are deliberately designed to maximize these interactions. There is growing recognition across many areas of scientific investigation and in the cardiovascular arena of the importance of metabolic homeostasis. The Society for Heart and Vascular Metabolism intends to remain at the vanguard of this rapidly expanding area. +
[[File:SMRM.JPG|150px|left]]The Society for '''Mitochondria Research and Medicine - India''' (SMRM-India) is a nonprofit organization of scientists, clinicians and academicians. The purpose of SMRM is to foster research on basic science of mitochondria, mitochondrial pathogenesis, prevention, diagnosis and treatment through out India and abroad. +
'''Sodium fluoride (NaF)''' is used in combination with [[beryllium sulfate]] to form beryllium trifluoride (BeF<sup>3−</sup>), to inhibit the [[ATP synthase]] if it is exposed by disruption of the mitochondrial membranes. +
'''Sodium vanadate (Na<sub>3</sub>VO<sub>4</sub>)''' is used as an ATPase inhibitor. +
Sodium phosphate buffer, '''Na-PB''', for [[HRR]] with freeze-dried baker´s yeast. +
The '''solubility''' of a gas, ''S''<sub>G</sub>, is defined as concentration divided by partial pressure, ''S''<sub>G</sub> = ''c''<sub>G</sub>·''p''<sub>G</sub><sup>-1</sup>. +
''The following definition lacks quality control and is not applied as such in the Oroboros QM.''
'''Solution protocols''' contain media, substrates, uncouplers, inhibitors used in [[SUIT|SUIT protocols]], permeabilization agents, etc. +
A '''solution''' is {''Quote''}: A liquid or solid phase containing more than one substance, when for convenience one (or more) substance, which is called the solvent, is treated differently from the other substances, which are called solutes. When, as is often but not necessarily the case, the sum of the mole fractions of solutes is small compared with unity, the solution is called a dilute solution. A superscript attached to the ∞ symbol for a property of a solution denotes the property in the limit of infinite dilution {''end of Quote'': [http://goldbook.iupac.org/S05746.html IUPAC Gold Book]}.
[[Solutions#Stock-.2C_storage-_and_working-solutions:_How_do_they_differ.3F |» '''MiPNet article''']] +
'''Specific quantities''' are obtained when the [[extensive quantity]] is divided by system size, in contrast to [[intensive quantity|intensive quantities]]. ''The adjective'' specific ''before the name of an extensive quantity is often used to mean divided by mass'' ([[Cohen 2008 IUPAC Green Book |Cohen et al 2008]]). A mass-specific quantity (''e.g.'', mass-specific flux is flow divided by mass of the system) is independent of the extent of non-interacting homogenous subsystems. If mass-specific oxygen flux is constant and independent of system size (expressed as mass), then there is no interaction between the subsystems. The well-established scaling law in respiratory physiology reveals a strong interaction of oxygen consumption and body mass by the fact that mass-specific basal metabolic rate (oxygen flux) does not increase proportionally and linearly with body mass. Maximum mass-specific oxygen flux, ''V''<sub>O2max</sub>, is less mass-dependent across a large range of body mass of different mammalian species (Weibel and Hoppeler 2005). +
A '''spectrofluorometer''' makes use of a [[spectrometer]] to measure and analyse the fluorescent emission spectra from a [[fluorophore]]. It will typically differ from an [[absorbance]] [[spectrophotometer]] in that it will have a larger [[slit width]] (to increase [[sensitivity]]) and use a longer [[integration time]]. The configuration of the illuminating and receiving optics also differ from [[spectrophotometry]] in that the excitation source is directed perpendicularly to the position of the emission [[detector]] so that the intensity of the excitation signal reaching the [[detector]] is minimised. +
A '''spectrophotometer''' is an instrument that consists of an entrance slit, a dispersion device (see [[dispersion devices]] and a [[detector]] for the purpose of measuring the intensity of light emerging from a sample across a given wavelength range. A [[light source]] is also necessary in order for the instrument to function, and this may be located within the instrument or from an external source using [[lightguides]] or other [[optics]]. +
'''Spectrophotometry''' is the use of a [[spectrophotometer]] to measure the transmittance, reflectance or remittance of a material as a function of wavelength. See [[transmission spectrophotometry]], [[reflectance spectrophotometry]] and [[remission spectrophotometry]]. +
'''Spectroscopy''' is a broader term than [[spectrophotometry]] in that it is concerned with the investigation and measurement of spectra produced when matter interacts with or emits any form electromagnetic radiation. +
'''Speed''', ''v'' [m·s<sup>-1</sup>], is the [[distance]], ''s'' [m], covered by a particle per unit time, irrespective of geometrical direction in space. Therefore, speed is not a [[vector]], in contrast to [[velocity]].
''v'' = d''s''/d''t'' [m·s<sup>-1</sup>] +
'''Spermidine''' is a polycationic bioactive polyamine mainly found in wheat germ, soybean and various vegetables, involved in the regulation of mitophagy, cell growth and cell death. Like other caloric restriction mimetics, spermidine is effective in cardioprotection, neuroprotection and anticancer immunosuppression by preserving mitochondrial function and control of autophagy. +
Some [[spectrofluorometer]] or [[spectrophotometer]] software offers the possibility of '''spline''' interpolation of the spectral data points. This makes use of a polynomial (the number of '''spline''' points is entered by the user) to interpolate the curve between the data points. +
'''Stability''' determines the accuracy of intensity and [[absorbance]] measurements as a function of time. Instability (see [[drift]] introduces systematic errors in the [[accuracy]] of [[fluorescence]] and [[absorbance]] measurements. +
A '''Stand alone application''' is computer software that can work offline, i.e. does not necessarily require network connection to function or does not even provide the possibility to connect to a network. +
A '''standard''' is an established [[norm]] or [[requirement]] in regard to a defined system. It can consist of a formal document that establishes uniform criteria, methods, processes and practices.See also [[Harmonized standard]]. +
''The following definition is incomplete.''
'''Standard operating procedures''' are a set of step-by-step instructions to achieve a predictable, standardized, desired result often within the context of a longer overall process. +
In DatLab 8, the start recording window allows to select protocols or settings before starting recording a file. +
[[Image:Startup O2k-Respirometer notitle.png|200px|right]]'''Startup O2k-Respirometer''' - the experimental system complete for basic [[high-resolution respirometry]] (HRR). The O2k-Respirometer includes the [[O2k-Main Unit]] with stainless steel housing, [[O2k-Assembly Kit]], two [[OroboPOS]] (polarographic oxygen sensors) and [[OroboPOS-Service Kit]], [[DatLab]] software, the [[ISS-Integrated Suction System]], the [[O2k-Titration Set]], and for performing high-resolution respirometry with reduced amounts of biological sample the [[O2k-sV-Module]].
The O2k is a sole source apparatus with no other instruments meeting its [[MiPNet06.05 Test Experiments on O2k-Specifications | specifications]]. +
'''State 1''' is the first respiratory state in an oxygraphic protocol described by [[Chance_1955_JBC-III|Chance and Williams (1955)]], when isolated mitochondria are added to mitochondrial respiration medium containing oxygen and inorganic phosphate, but no ADP and no reduced respiratory substrates. In State 1, [[LEAK respiration]] may be supported to some extent by undefined endogenous substrates, which are oxidized and slowly exhausted. After oxidation of endogenous substrates, only residual oxygen consumption remains ([[ROX]]). +
[[File:ROX.jpg |link=Residual oxygen consumption]] Substrate limited state of [[residual oxygen consumption]], after addition of [[ADP]] to isolated mitochondria suspended in mitochondrial respiration medium in the absence of reduced substrates (ROX<sub>D</sub>). Residual endogenous substrates are oxidized during a transient stimulation of oxygen flux by ADP. The peak – supported by endogenous substrates – is, therefore, a pre-steady state phenomenon preceding State 2. Subsequently oxygen flux declines to a low level (or zero) at the steady '''State 2''' ([[Chance_1955_JBC-III|Chance and Williams 1955]]). ADP concentration (D) remains high during ROX<sub>D</sub>. +
[[File:P.jpg |link=OXPHOS capacity]] '''State 3''' respiration is the ADP stimulated respiration of isolated coupled mitochondria in the presence of high ADP and P<sub>i</sub> concentrations, supported by a defined substrate or substrate combination at saturating oxygen levels [[Chance_1955_JBC-III|(Chance and Williams, 1955]]). State 3 respiration can also be induced in [[Permeabilized tissue or cells|permeabilized cells]], including permeabilized tissue preparations and tissue homogenates. ADP concentrations applied in State 3 are not necessarily saturating, whereas [[OXPHOS capacity]] is measured at saturating concentrations of ADP and P<sub>i</sub> (OXPHOS state). For instance, non-saturating ADP concentrations are applied in State 3 in pulse titrations to determine the [[P/O ratio]] in State 3→4 (D→T) transitions, when saturating ADP concentrations would deplete the oxygen concentration in the closed oxygraph chamber before [[State 4]] is obtained ([[Gnaiger 2000 Proc Natl Acad Sci U S A|Gnaiger et al 2000]]; [[Puchowicz_2004_Mitochondrion|Puchowicz et al 2004]]). Respiration in the OXPHOS state or in State 3 is well [[coupled respiration|coupled]], and partially [[uncoupled respiration|uncoupled]] (physiological) or partially [[dyscoupled respiration|dyscoupled]] (pathological). A high [[mt-membrane potential]] provides the driving force for oxidative phosphorylation, to phosphorylate ADP to ATP and to transport ADP and ATP across the mitochondrial inner membrane (mtIM) through the [[adenine nucleotide translocase]] (ANT). The mt-membrane potential is reduced, however, in comparison to the [[LEAK state]] of respiration, whereas the cytochromes are in a more oxidized redox state. +
[[File:E.jpg |link=ET capacity]] Noncoupled state of [[ET capacity]]. '''State 3u''' (u for uncoupled) has been used frequently in bioenergetics, without sufficient emphasis [[Villani 1998 J Biol Chem|(e.g. Villani et al 1998)]] on the fundamental difference between [[OXPHOS capacity]] (''P'', coupled with an uncoupled contribution; State 3) and noncoupled [[ET capacity]] (''E''; State 3u) ([[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]; [[Rasmussen 2000 Mol Cell Biochem|Rasmussen and Rasmussen 2000]]). +
[[File:L.jpg |link=LEAK respiration]] '''State 4''' is the [[respiratory state]] obtained in isolated mitochondria after [[State 3]], when added [[ADP]] is phosphorylated maximally to [[ATP]] driven by electron transfer from defined respiratory substrates to O<sub>2</sub> ([[Chance 1955 JBC-III|Chance and Williams, 1955]]). State 4 represents [[LEAK respiration]], ''L''<sub>T</sub> (''L'' for [[LEAK respiration]]; T for ATP), or an overestimation of LEAK respiration if [[ATPase]] activity prevents final accumulation of ATP and maintains a continuous stimulation of respiration by recycled ADP. This can be tested by inhibition of ATP synthase by [[oligomycin]]; ''L''<sub>Omy</sub>). In the [[LEAK state]] (state of non-phosphorylating resting respiration; static head), oxygen flux is decreased to a minimum (corrected for [[ROX]]), and the [[mt-membrane potential]] is increased to a maximum for a specific substrate or substrate combination. +
'''State 5''' is the [[respiratory state]] obtained in a protocol with isolated mitochondria after a sequence of [[State 1]] to [[State 4]], when the concentration of O<sub>2</sub> is depleted in the closed oxygraph chamber and zero oxygen (the anaerobic state) is reached ([[Chance 1955 JBC-III|Chance and Williams, 1955]]; Table I).
State 5 is defined in the original publication in two ways: ''State 5 may be obtained by antimycin A treatment or by anaerobiosis'' (Chance and Williams, 1955; page 414). [[Antimycin A]] treatment yields a State 5 equivalent to a state for measurement of [[residual oxygen consumption]], ROX (which may also be induced by [[rotenone]]+[[myxothiazol]]; [[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]). Setting State 5 equivalent to ROX or anoxia (Chance and Williams 1955) can be rationalized only in the context of measurement of cytochrome redox states, whereas in the context of respiration State 5 is usually referred to as [[anoxic]]. +
[[File:L.jpg |link=LEAK respiration]] '''Static head''' is a [[steady state]] of a system with an input process coupled to an output process (coupled system), in which the output force is maximized at constant input or driving force up to a level at which the conjugated output flow is reduced to zero. ''In an incompletely coupled system, energy must be expended to maintain static head, even though the output is zero'' (Caplan and Essig 1983; referring to output flow at maximum output force). [[LEAK respiration]] is a measure of input flow at static head, when the output flow of phosphorylation (ADP->ATP) is zero at maximum phosphorylation potential (Gibbs force of phosphorylation; [[Gnaiger_1993_Hypoxia|Gnaiger 1993a]]).
In a completely coupled system, not only the output flux but also the input flux are zero at static head, which then is a state of ''[[ergodynamic equilibrium]]'' ([[Gnaiger_1993_Pure_Appl_Chem |Gnaiger 1993b]]). Whereas the output force is maximum at ergodynamic equilibrium compensating for any given input force, all forces are zero at ''[[thermodynamic equilibrium]]''. Flows are zero at both types of equilibria, hence entropy production or power (power = flow x force) are zero in both cases, i.e. at thermodynamic equilibrium in general, and at ergodynamic equilibrium of a completely coupled system at static head. +
It is advisable to replace levels of '''statistical significance''' (*, **, ***) by simply stating the actual ''p''-values. +
see [[O2k status line]] +
A [[system]] is in a '''steady state''' if the state variables of a dynamic system do not change over time due to exchange processes with the environment, which compensate for internal dissipative transformations — such as chemical reactions or diffusion — and thus prevent any changes of the system and externalize dissipative changes to the environment. The dynamic nature of the steady state differentiates it from the thermodynamic equilibrium state. {''Quote''} Steady states can be obtained only in [[open system]]s, in which changes by internal transformations, ''e.g.'', O<sub>2</sub> consumption, are instantaneously compensated for by external fluxes across the system boundary, ''e.g.'', O<sub>2</sub> supply, thus preventing a change of O<sub>2</sub> concentration in the system (Gnaiger 1993). Mitochondrial [[respiratory states]] monitored in [[closed system]]s satisfy the criteria of pseudo-steady states for limited periods of time, when changes in the system ([[concentration]]s of O<sub>2</sub>, fuel substrates, ADP, P<sub>i</sub>, H<sup>+</sup>) do not exert significant effects on metabolic fluxes (respiration, phosphorylation). Such pseudo-steady states require respiratory media with sufficient buffering capacity and substrates maintained at kinetically-saturating concentrations, and thus depend on the kinetics of the processes under investigation. {''end of Quote'': [[BEC 2020.1]]}. Whereas fluxes may change at a steady state over time, concentrations are maintained constant. The 'respiratory steady state' (Chance and Williams 1955) is characterized by constant fluxes (O<sub>2</sub> flux, H<sub>2</sub>O<sub>2</sub> flux) and measured variables of state (cytochrome redox states, Q redox state, NADH redox state, mitochondrial membrane potential). [[High-resolution respirometry]] allows for the measurement of several parameters (''e.g.'' O<sub>2</sub> flux, H<sub>2</sub>O<sub>2</sub> flux, mitochondrial membrane potential) at pseudo-steady states, when changes of [[concentration]]s in the [[closed system]] do not exert any control on fluxes. Combination with the [[TIP2k-Module| Titration-Injection microPump (TIP2k)]] allows operation with programmable titration regimes at steady-state ADP concentration (Gnaiger 2001), oxygen concentration (oxystat mode; Gnaiger et al 2000, Harrison et al 2015) or steady-state pH (pH-stat more), yielding an expanded flexibility in experimental design by combining the technical advantages of closed and [[open system]]s approaches.
Toggles between stirrer on/off in the left O2k-chamber, returning to the pre set stirrer speed. +
Toggles between stirrer on/off in the right O2k-chamber, returning to the pre set stirrer speed. +
'''Stirrer power''' is switched on and off during operation of the [[Oroboros O2k]] in [[DatLab]] by pressing [F11] (left chamber) and [F12] (right chamber), respectively. This is functional only with a stirrer bar added to each O2k chamber. +
A '''stirrer test''' is performed in the [[Oroboros O2k]] for quick evaluation of the performance of the [[OroboPOS]] and for [[POS calibration - dynamic|dynamic calibration]]. Stirring is stopped in both chambers and restarted after a selected period. The default period is 30 s, for experiments at 37 °C. At lower experimental temperature, this period should be prolonged (60 s at 25 °C). In the [[O2k-Open Support#O2k_Quality_Control |SOP (O2k Quality Control)]] for the [[O2k-Open_Support#1._O2_sensor_test|O<sub>2</sub> sensor test]], the stirrer test is performed in the 'open' chamber in conjunction with [[Air calibration]]. In general, the stirrer test can be performed equally with an open or closed chamber. Upon automatic re-start of the stirrer (On), the increase of the oxygen signal should be rapid and monoexponential. +
[[File:33210-01.jpg|right|180px]]'''Stirrer-Bar sV\white [[PVDF]]\11.5x6.2 mm''', operated in the 0.5-mL [[O2k-Chamber sV]] at constant stirring speed (standard is 750 rpm, or 12.5 Hz), to provide optimum mixing of the sample in the aqueous medium and ensure a stable signal of the polarographic oxygen sensor ([[OroboPOS]]) placed in a position of maximum current of the medium. +
[[Image:Stirrer-Bar black PEEK15x6 mm.JPG|right|180px]]'''Stirrer-Bar\black [[PEEK]]\15x6 mm''', for 2-mL O2k-Chamber, for specific optical applications to minimize optical interference. +
[[Image:Stirrer bar PVDF.jpg|right|180px]]'''Stirrer-Bar\white [[PVDF]]\15x6 mm''', operated in the 2-mL [[O2k-chamber]] at constant stirring speed (standard is 750 rpm, or 12.5 Hz), to provide optimum mixing of the sample in the aqueous medium and ensure a stable signal of the polarographic oxygen sensor ([[OroboPOS]]) placed in a position of maximum current of the medium. +
The sign of the '''stoichiometric number''' ''ν''<sub>X</sub> is determined by the nonspatial direction of the transformation (positive for products, negative for substrates), and the magnitude of ''ν''<sub>X</sub> is determined by the stoichiometric form. For instance, ''ν''<sub>A</sub>=-1 in the reaction 0 = -1 A + 2 B (-1 glucose converted to +2 lactate), but ''ν''<sub>A</sub>=-1/6 in the reaction 0 = -1/6 A - 1 B + 1 C (-1/6 glucose and -1 O<sub>2</sub> converted to +1 H<sub>2</sub>CO<sub>3</sub>). +
[[File:34000-01.jpg|right|180px]]'''Stopper sV\black PEEK\conical Shaft\central Port''': with conical shaft (with PTFE, graphite, carbon fiber) and one central capillary (1.0 mm diameter; 48.9 mm length), [[Volume-Calibration Ring sV]] (A or B) for volume adjustment 0.5 mL; 2 mounted O-rings ([[O-ring sV\Viton\9.5x1 mm]]). +
[[Image:Stopper-Needle.JPG|180px|right]]'''Stopper-Needle''': Short needle for bubble extrusion from port of the [[Stopper\white PVDF\angular Shaft\side+6.2+2.6 mm Port|ISE-stopper]]. +
'''Stopper-Shaft conical\white [[PVDF]]\central Port''': PVDF shaft with one central capillary and conical base, receptacle on the top for collecting excess medium during closing the O2k-Chamber and during titration; component of [[Stopper\white PVDF\conical Shaft\central Port]].
'''Discontinued''' +
[[Image:Gas spacer for Stopper.jpg|right|180px]]'''Stopper-Spacer''' (or '''gas spacer''') to set the O2k-Stopper into a standard position for a fixed gas phase above the aqueous phase in the 2-mL [[O2k-chamber]], during air calibration or for injection of nitrogen, argon or oxygen into the gas phase; Stopper-Spacer thickness of 4mm (a deviation of +/- 10% possible). +
[[File:Stopper black PEEK angular Shaft side+6.2+2.6 mm Port.JPG|180px|right]]'''Stopper\black PEEK\angular Shaft\side+6.2+2.6 mm Port''', for application with [[ISE]]; side titration port and two additional holes (6.2 mm and 2.6 mm); angular bottom; including [[Volume-Calibration Ring]] (A or B); 2 mounted O-rings, with 8 spare O-rings ([[O-ring\Viton\12.5x1 mm]]). +
[[Image:Stopper black PEEK conical Shaft central Port.JPG|right|180px]]'''Stopper\black PEEK\conical Shaft\central Port''': with conical shaft (with PTFE, graphite, carbon fiber) and one central capillary (1.3 mm diameter; 50.6 mm length), [[Volume-Calibration Ring]] (A or B) for volume adjustment 1.5 to 3.2 ml; 2 mounted O-rings, with 8 spare O-rings ([[O-ring\Viton\12.5x1 mm]]). The black PEEK stoppers are required for optical O2k-MultiSensor Modules. +
[[Image:Stopper black PEEK conical Shaft central Port peripheral 2.3 mm Port.JPG|right|180px]]'''Stopper\black PEEK\conical Shaft\central+peripheral 2.3 mm Port''': for potentiometric [[O2k-MultiSensor]] applications (NO, H<sub>2</sub>S, H<sub>2</sub>O<sub>2</sub>); 1 additional port (2.3 mm); central titration port; conical bottom; including [[Volume-Calibration Ring]] (A or B); 2 mounted O-rings, with 8 spare O-rings ([[O-ring\Viton\12.5x1 mm]]). +
[[File:Stopper black PEEK conical Shaft central+2.3+2.6 mm Port.JPG|180px|right]]'''Stopper\black PEEK\conical Shaft\central+2.3+2.6 mm Port''': for pH and reference electrode, central titration port and two additional ports (2.3 mm and 2.6 mm); conical bottom; including Volume-Calibration Ring (A or B), 2 mounted O-rings, with 8 spare O-rings ([[O-ring\Viton\12.5x1 mm]]). +
[[Image:Stopper_white_PVDF_angular_Shaft_side+6.2+2.6_mm_Port.JPG|180px|right]]'''Stopper\white PVDF\angular Shaft\side+6.2+2.6 mm Port''', for application with [[ISE]]; side titration port and two additional holes (6.2 mm and 2.6 mm); angular bottom; including [[Volume-Calibration Ring]] (A or B); 2 mounted O-rings ([[O-ring\Viton\12x1 mm]]).
'''Discontinued''' +
[[Image:30221-24 PVDF Stopper.jpg|right|180px]] '''Stopper\white PVDF\conical Shaft\central Port''': for closing the 2-mL [[O2k-chamber]], with one capillary and conical basis; including [[Volume-Calibration Ring]] (A or B) for volume adjustment (1.5 to 3.2 mL); 2 mounted O-rings ([[O-ring\Viton\12x1 mm]]).
'''Discontinued ''' +
[[File:32001-01.jpg|right|180px]]'''Storage box sV''' empty, for storage of [[O2k-sV-Module]] components. +
'''Stray light''' is defined as the detected light of any wavelength that lies outside the [[bandwidth]] of the selected wavelength. In the presence of '''stray light''' of intensity ''I''<sub>''s''</sub>, the equation for [[transmittance]] (''T'') becomes ''T'' = (''I'' + ''I''<sub>''s''</sub>)/(''I''<sub>''0''</sub> + ''I''<sub>''s''</sub>) where ''I''<sub>''0''</sub> is the incident light intensity and ''I'' is the transmitted light intensity. Clearly, the lower the value of ''I'', the more dominant becomes the '''stray light''' term and so can cause errors in the quantification of low [[fluorescence]] signals or at high levels of [[absorbance]]. +
'''Strobilurin''': {''Quote''} Strobilurins are a group of chemical compounds used in agriculture as fungicides. They are part of the larger group of QoI inhibitors, which act to inhibit {''end of Quote'': [http://en.wikipedia.org/wiki/Strobilurin]} respiratory [[Complex III]]. +
[[MitoFit Preprints]] manuscript template and submission form. +
'''Submitochondrial particles''' (smtp) consist of membrane fragments which retain most of the enzymatic machinery required in electron transfer and [[oxidative phosphorylation]]. Such membrane fragments are continuous closed vesicles formed by resealing of mt-membrane fragments after disruption of the mitochondrial structure. smtp are used to isolate the inner-[[membrane-bound ET pathway]] (mETS) from the upstream modules of the [[Electron transfer pathway]] (ETS) which are located in the mt-matrix and outer mt-membrane (transporters). smtp are obtained by treatment of mitochondria with membrane-dispersing agents such as digitonin at high concentration or by sonic irradiation. +
'''Subsamples''' can be obtained (1) from a homogenous [[sample]] (e.g. cell suspension, tissue homogenate, isolated mitochondria), (2) as subsamples obtained by splitting a sample into comparable parts (e.g. permeabilized muscle fibres from a biopsy split into different chambers for repeated measurements), or (3) repetitive sampling (e.g. taking multiple biopsies) at a single time point. Subsamples may be used for (i) application of different types of [[assay]] (e.g. for measurement of respiration and enzyme activities), and (ii) a number of [[repetitions]], ''n'', of the same assay on the same sample. +
'''Subscripts in physical chemistry''' are used to differentiate symbols of different quantities. While these subscripts need to be short to be readable, they have to be distinct and well defined. Several subscripts relate to fundamental terms and concepts, summarized in a list below. +
IUPAC distinguishes three definitions of 'substrate': (1) The chemical entity whose conversion to a [[product]] or products is catalysed by one or several enzymes. (2) A solution or dry mixture containing all ingredients which are necessary for the growth of a microbial culture or for product formation. (3) Component in the nutrient medium, supplying the organisms with carbon (C-substrate), nitrogen (N-substrate), etc.
A substrate in a chemical reaction has a negative [[stoichiometric number]] since it is consumed, whereas a product has a positive stoichiometric number since it is produced. +
''See'' '''[[Pathway control efficiency]]''' +
''See'' '''[[Pathway control ratio]]''' +
See '''[[Electron-transfer-pathway state]]''' +
Mitochondrial '''Substrate-uncoupler-inhibitor titration''' ('''SUIT''') [[MitoPedia: SUIT |protocols]] are used with [[mitochondrial preparations]] to study respiratory control in a sequence of coupling and substrates states induced by multiple titrations within a single experimental [[assay]]. +
'''[[Substrate]]s as electron donors''' are reduced fuel compounds ''S''<sub>red</sub> that are oxidized to an oxidized product ''P''<sub>ox</sub> during H<sup>+</sup>-linked electron transfer, ''S''<sub>red</sub> → ''P''<sub>ox</sub> + 2{H<sup>+</sup> + e<sup>-</sup>}. Mitochondrial respiration depends on a continuous flow of electron-supplying substrates across the mitochondrial membranes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers. +
[[File:Succinic_acid.jpg|left|100px|Succinic acid]]
'''Succinic acid''', C<sub>4</sub>H<sub>6</sub>O<sub>4</sub>, (butanedioic acid) is a dicarboxylic acid which occurs under physiological conditions as the anion '''succinate<sup>2-</sup>, S''', with ''p''K<sub>a1</sub> = 4.2 and ''p''K<sub>a2</sub> = 5.6. Succinate is formed in the [[TCA cycle]], and is a substrate of [[Complex II |CII]], reacting to [[fumarate]] and feeding electrons into the [[Q-junction]]. Succinate (CII-linked) and NADH (CI-linked) provide convergent electron entries into the Q-junction. Succinate is transported across the inner mt-membrane by the [[dicarboxylate carrier]]. The plasma membrane of many cell types is impermeable for succinate (but see [[Zhunussova 2015 Am J Cancer Res]] for an exception). Incubation of mt-preparations by succinate alone may lead to accumulation of [[oxaloacetate]], which is a potent inhibitor of Complex II (compare [[Succinate and rotenone]]). High activities of mt-[[Malic enzyme]] (mtME) prevent accumulation of oxaloacetate in incubations with succinate without rotenone. +
'''Succinate dehydrogenase''' is a [[TCA cycle]] enzyme converting [[succinate]] to [[fumarate]] while reducing FAD to FADH<sub>2</sub>. SDH is the largest component of the mt-inner membrane [[Complex II]] (CII) and thus part of the TCA cycle and [[electron transfer pathway]]. +
[[File:SUIT-catg_S.jpg|right|300px|Succinate]]
The '''Succinate pathway''' (S-pathway; S) is the [[electron transfer pathway]] that supports succinate-linked respiration (succinate-induced respiratory state; previously used nomenclature: CII-linked respiration; SRot; see [[Gnaiger 2009 Int J Biochem Cell Biol]]). The S-pathway describes the electron flux through [[Complex II]] (CII; see [[succinate dehydrogenase]], SDH) from succinate and FAD to fumarate and CII-bound flavin adenine dinucleotide (FADH<sub>2</sub>) to the [[Q-junction]].
The S-pathway control state is usually induced in mt-preparations by addition of succinate&rotenone. In this case, only [[Complex III]] and [[Complex IV]] are involved in pumping protons from the matrix (positive phase, P-phase) to the negative phase (N-phase) with a P»/O<sub>2</sub> of 3.5 (P»/O ratio = 1.75). +
The [[dicarboxylate carrier]] catalyses the electroneutral exchange of succinate<sup>2-</sup> for HPO<sub>4-</sub><sup>2-</sup>. +
'''Succinyl-CoA ligase''' (SUCLA or SUCLG) is a TCA cycle enzyme converting succinyl-CoA + ADP or (GDP) + Pi to [[succinate]] + ATP (GTP). Two different isoforms exsist: SUCLA (EC: 6.2.1.5) is the ATP-forming isoenzyme, SUCLG (EC: 6.2.1.4) is the GTP-forming isoenzyme. Both reactions are reversible. This reaction is attributed to mitochondrial substrate-level phosphorylation, which is considered as an alternative way of ATP synthesis because it is partially independent from the respiratory chain and from the mitochondrial proton motive force. +
'''Sulfide quinone reductase''' (SQR) is involved in electron transfer from sulfide which is used as a hydrogen donor by the mitochondrial respiratory system. SQR is associated with a [[dioxygenase]] and a [[sulfur transferase]] to release thiosulfate (H<sub>2</sub>S<sub>2</sub>O<sub>3</sub>). +
'''Sulfite oxidase''' (SO) is a dimeric enzyme, located in the intermembrane space of mitochondria, with each monomer containing a single Mo cofactor and cyt b5-type heme [1]. SO catalyzes the oxidation of sulfite to sulfate as the terminal step in the metabolism of sulfur amino acids and is vital for human health. Inherited mutations in SO result in severe neurological problems, stunted brain growth, and early death [2].
Function: SO catalyzes the terminal reaction in the oxidative degradation of sulfur amino acids with the formation of a sulfate, electrons pass to cytochrom ''c'' and are further utilized in the respiratory system.
Sulfite + O<sub>2</sub> + H<sub>2</sub>O --> Sulfate + H<sub>2</sub>O<sub>2</sub>
Localization: The level of expression of SO differs in various tissues with main predominant localization in liver, kidney, skeletal muscle, heart, placenta, and brain in humans and liver, kidney, heart, brain, and lung in rats [3].
Deficiency: SO is vital for metabolic pathways of sulfur amino acids (cysteine and methionine). Complete lack of this enzyme, typically caused by gene mutation, leads to lethal disease called sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy. +
[[File:O2-.jpg|left|60px|Superoxide anion]]
'''Superoxide anion''', O<sub>2</sub><sup>•-</sup>, is a free radical formed in a one-electron reduction of molecular [[oxygen]] (red bullet in the figure), yielding a negatively charged molecule with a single unpaired electron (blue bullet on the left). It is highly reactive with organic compounds, and its intracellular concentration is kept under control by [[superoxide dismutase]]. +
Mammalian '''superoxide dismutase''' (SOD) exists in three forms, of which the Mn-SOD occurs in mitochondria (mtSOD, SOD2; 93 kD homotetramer) and many bacteria, in contrast to the Cu-Zn forms of SOD (cytosolic SOD1, extracellular SOD3 anchored to the extracellular matrix and cell surface). [[Superoxide]] anion (O<sub>2</sub><sup>•-</sup>) is a major [[reactive oxygen species]] (ROS) which is dismutated by SOD to [[oxygen]] and [[hydrogen peroxide | H<sub>2</sub>O<sub>2</sub>]]. +
'''Synchronous time axes''' sets, if ticked, the time axes of all graphs at an identical range and offset, which is particularly useful while panning. +
[[Image:Syringe Collars.JPG|right|180px]]'''Syringe Collars''' (package of 20) for Hamilton microsyringes: for correctly storing the microsyringes in the [[Syringe Racks]]. +
[[File:Syringe Labels_2017.JPG|right|180px]]'''Syringe Labels''': set of labels with standard abbreviations (see [[MiPNet09.12_O2k-Titrations | O2k-Titrations]]). +
[[File:Syringe Racks.JPG|right|180px]]'''Syringe Racks''': stainless steel; for proper placement of eight Hamilton microsyringes in HRR experiments; package of two (for a total of 16 microsyringes). +
[[File:Syringe Storage Box.jpg|right|180px]]'''Syringe Storage Box''': for storing the Hamilton microsyringes; includes [[Syringe Labels]]. +
[[Image:Gas injection syringe.jpg|right|180px]]'''Syringe\10 mL\Gas-Injection''', 10 mL, with spacer and stainless steel needle, flat tip, for gas injection into the [[O2k-chamber]]. 2 syringes are supplied with [[Oxia]]. +
[[File:Syringe 500 mm3 51 0.41 mm.JPG |right|180px]]Hamilton '''Syringe\500 mm<sup>3</sup> 51/0.41 mm''' for manual titrations, 500 mm<sup>3</sup> volume; fixed needle with rounded tip: 51 mm length, 0.41 mm inner diameter; for injections of suspensions of isolated mitochondria and filling of the [[Microsyringe\200 mm3\TIP2k]]. +
[[Image:Gas injection syringe.jpg|right|180px]]'''Syringe\60 mL\Gas-Injection''', 60 mL, with spacer and stainless steel needle, flat tip, for gas injection into the [[O2k-chamber]]. +
The term '''system''' has a variety of meanings and dictionary definitions in different contexts, ''e.g.'', the [[International System of Units]] (SI), MKSA system, data management system, biological or mechanical system, redox system, [[Electron transfer system]], loosely or completely coupled system, instrumental system. In thermodynamics and [[ergodynamics]], the '''system''' is considered as an experimental system (experimental chamber), separated from the environment as an isolated, adiabatic, closed, or open system. {''Quote'' } The internal domain of any system is separated from the external domain (the surroundings) by a boundary. In theory, energy transformations outside the system can be ignored when describing the system. The surroundings are merely considered as a source or sink for quantities transferred across the system boundary. According to the transfer properties of the boundary, three types of thermodynamic systems are distinguished. (''1'') The boundaries of '''''isolated systems''''' are impermeable for all forms of [[energy]] and matter. Isolated systems do not interact with the surroundings. Strictly, therefore, internal changes of isolated systems cannot be observed from outside since any observation requires interaction. (''2'') The boundaries of '''''closed systems''''' are permeable for [[heat]] and [[work]], but impermeable for [[matter]]. A limiting case is electrons which cross the system boundary when work is exchanged in the form of electric energy [''added'': and light]. The volume of a closed system may be variable. (''3'') The boundaries of '''''open systems''''' allow for the transfer of heat, work and matter. Changes of isolated systems have exclusively internal origins, whereas changes of closed and open systems can be partitioned according to internal and external sources. Production and destruction of a quantity within the system are ''internal'' changes, whereas changes of heat, work and matter due to transfer across the system boundaries are labelled ''extenal''. (External) transfer is thus contrasted with (internal) production or destruction. {''end of Quote'': [[Gnaiger 1993 Pure Appl Chem]]}
A system may be treated as a black box. In the analysis of [[Continuous system|continuous]] or [[Discontinuous system |discontinuous system]]s, however, information is implied on the internal structure of the system.
T
[[File:Tshirt MitoFit OROBOROS.jpg|right|180px]] '''T-Shirt MitoFit''': Oroboros Logo on front, MitoFit Logo on back. +
'''T-Shirt Oroboros black/organic cotton''': An Oroboros on the front. +
The Titration-Injection microPump (TIP2k) provides automated injection of liquids into both O2k chambers. It is controlled via DatLab, allowing for programmable titration regimes and feedback control. +
[[Image:TIP2k Filter Papers.JPG|right|180px]]'''TIP2k Filter Papers''' (package of 10) to be used for the stoppers during TIP2k titration for Instrumental oxygen background correction to avoid constant manual siphoning off of extruded liquid. +
'''TIP2k and O2k-Upgrade\B''': Titration-Injection microPump TIP2k, including the electronic upgrade of the O2k-main unit returned to workshop (Series B-D). '''Discontinued''' +
'''TIP2k-Cooling Box''': Cooling box for TIP2k syringes. '''Discontinued''' +
When the '''TIP2k syringe is blocked''', it must not be used with the TIP2k, and specific cleaning instructions should be followed. +
[[File:TIP2k with 200 mm3 microsyringe.JPG|180px|right]]'''TIP2k-Module''' - Titration-Injection microPump (TIP2k) for two-channel operation with the [[O2k-FluoRespirometer]] with automatic control by [[DatLab]] of programmable titration regimes and feedback control (oxystat, pH-stat). +
'''TIP2k-Needle Safety Support''': for safe storage of TIP2k-needles when not required during the experiment.
This item is a standard component of the [[TIP2k-Module]]. +
[[File:31330-01 3.jpg|right|280px]] '''TIP2k-Needle Safety Support with cable guide''': for safe storage of TIP2k-needles and MultiSensor Modules cables when not required during the experiment. +
[[Image:80600-24 Spacers f. TIP2k needle.JPG|right|180px]]'''TIP2k-Needle Spacers''' for microinjection TIP2k needle, silicone stops (200/Pkg.) with mounting tool. +
'''''N,N,N',N'''-Tetramethyl-''p''-phenylenediamine dihydrochloride, TMPD''', is applied as an artificial substrate for reducing [[cytochrome c|cytochrome ''c'']] in the respirometric assay for [[Complex IV|cytochrome ''c'' oxidase]] (CIV) activity. It is maintained in a reduced state by [[ascorbate]] and undergoes [[autoxidation]] as a function of [[oxygen pressure]], TMPD, ascorbate and cytochrome ''c'' concentration. +
'''TMRM''' (tetramethylrhodamine methyl ester) is an [[extrinsic fluorophores|extrinsic fluorophore]] used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. TMRM is a lipophilic cation that is accumulated in the mitochondrial matrix in proportion to Δ''ψ''<sub>mt</sub>. Upon accumulation of the dye it exhibits a red shift in its absorption and fluorescence emission spectrum. The fluorescence intensity is quenched when the dye is accumulated in the mitochondrial matrix. +
A major task in establishing a procedure for measurement of [[mitochondrial membrane potential]] using probe molecules is the evaluation of inhibitory concentrations of the probe molecule on the activity of respiration. The '''TPP<sup>+</sup> inhibitory effect''' (this also applies to TPMP<sup>+</sup> and other indicator molecules) is frequently ignored. Accurate knowledge of a threshold concentration is required to evaluate the necessary limit of detection of TPP<sup>+</sup>, and for restriction of experimental TPP<sup>+</sup> concentrations below the inhibitory range. +
The '''Taiwan Society for Mitochondrial Research and Medicine''' (TSMRM) is a member of [[Asian Society for Mitochondrial Research and Medicine|ASMRM]]. +
Tartronic acid (hydroxymalonic acid, C3H4O5; molecular weight 120.06) is an inhibitor of [[malic enzyme]]. +
Taurine, or 2-Aminoethan sulfonic acid, is one of the most abundant low-molecular-weight organic constituents in animals and humans. It has a multitude of functions in different types of tissue, one of which is the stabilization of membranes. Because of this and its antioxidative effect, taurine is a component of the respiration media MiR05 and MiR06 to preserve mitochondrial function. +
'''Problem:''' Layout "01 Calibration Exp. Gr3-Temp" is selected, a third plot is displayed on the screen but it remains empty (no plot is shown). Newer versions of [[DatLab]] include pre-installed layouts which do not recognize some channel designations from older O2k series. +
'''4,5,6,7-Tetrachloro-2-trifluoromethylbenzimidazole''' is a protonophore or [[uncoupler]] of oxidative phosphorylation. +
'''Tetrahydrofolate''', THF, is the substrate in mitochondrial folate-mediated 1C metabolism, an [[NADH-linked pathway]] leading to the formation of formate which is exported to the cytosol. +
'''Tetraphenylphosphonium''' (TPP<sup>+</sup>). A lipophilic molecular probe in conjunction with an ion selective electrode (ISE) for [[Mitochondrial membrane potential | measuring the mitochondrial membrane potential]]. +
[[File:NAMDC.JPG|200px|left]]
'''The North American Mitochondrial Disease Consortium (NAMDC)''' was established to create a network of all clinicians and clinical investigators in North America (US and Canada, with the hope of including Mexico in the future) who follow sizeable numbers of patients with mitochondrial diseases and are involved or interested in mitochondrial research. The NAMDC has created a clinical registry for patients, in the hopes of standardizing diagnostic criteria, collecting important standardized information on patients, and facilitating the participation of patients in research on mitochondrial diseases.
For the study of any rare disease, the collection of specimens is a major challenge. The '''NAMDC''' is establishing a repository for specimens and DNA from patients with mitochondrial diseases, in order to make materials easily available to consortium researchers.
Finally, the '''NAMDC''' will conduct clinical trials and other kinds of research. The consortium makes biostatisticians, data management experts, and specialists in clinical research available to participating physicians, so that experiments conducted through the NAMDC can make the most efficient and innovative use of the generous participation of patients. +
'''Thenoyltrifluoroacetone''' TTFA is a noncompetitive inhibitor of CII binding on the quinone-binding (SDHC/SDHD). +
'''Thioredoxin reductase''' (TrxR) is a family of enzymes able to reduce thioredoxin in mammals. +
A '''three-electrode system''' is the setup used in the [[Q-Sensor]], which is an integral part of the [[Q-Module]]. This system is used in voltammetry (including [[cyclic voltammetry]]) to study the current as a function of the applied potential using three different electrodes: 1) the working electrode 2) the reference electrode, and 3) the counter electrode. In the [[Q-Sensor]], the working or detecting electrode is a glassy carbon (GC) electrode that is set to a given potential and makes contact with the analyte. The potential of the working electrode is controlled by the constant potential of the a silver/silver chloride (Ag/AgCl) reference electrode, which does not pass any current. The applied potential on the surface of the GC should be sufficient to either oxidize reduced analyte (in this case [[Coenzyme Q]]) or to reduce oxidized analyte. Thus, the counter electrode is a platinum electrode (Pt) that passes a current to counter these redox events by completing the circuit that is rate-limited by electron transfer on the GC. To determine the reduced Q fraction the GC electrode is set at the oxidation peak potential, which can be determined with [[cyclic voltammetry]]. +
'''Time resolution''' in respirometric measurements is influenced by three parameters: the [[response time of the POS]], the data sampling interval and the number of points used for flux calculation. +
A '''tissue homogenate''' (thom) is obtained through mechanical micro-disruption of fresh tissue and the cell membranes are mechanically permeabilized. +
[[Image:O2k-Titration Set.JPG|right|180px]]The '''Titration Set Upgrade''' consists of the new items of the [[O2k-Titration Set]] for upgrading your original set (consisting only of Hamilton microsyringes). The upgrade consists of the [[Syringe Storage Box]] with [[Syringe Labels]], a set of two [[Syringe Racks]] with [[Syringe Collars]], and a set of two [[Tube Racks]] including tubes as well as an additional syringe (1 x 100 mm<sup>3</sup>). +
[[Image:Titration-Injection-microPump.jpg|180px|right]]'''Titration-Injection microPump''' (TIP2k) for two-channel operation with the O2k with automatic control by [[DatLab]] of programmable titration regimes and feedback control (oxystat, pH-stat). +
'''Traceability''' is the property of the result of a measurement or the value of a standard whereby it can be related to stated references, usually national or international standards, through an unbroken chain of comparisons all having stated uncertainties [SOURCE: VIM:1993, definition 6.10]. +
In the transmission mode, the incident light passes through the sample [[cuvettes]] and the emergent light reaches the [[detector]] directly. Before [[absorbance]] measurements can be made, a [[balance]] is carried out. +
When light enter a sample, '''transmittance''' (''T'') is the fraction of the intensity (''I'') of the light emerging from the sample compared with the incident light intensity (''I''<sub>''0''</sub>): ''T'' = ''I''/''I''<sub>''0''</sub>. +
The '''tricarboxylate carrier''' in the inner mt-membrane exchanges malate<sup>2-</sup> for citrate<sup>3-</sup> or isocitrate<sup>3-</sup>, with co-transport of H<sup>+</sup>. +
The '''tricarboxylic acid (TCA) cycle''' is a system of enzymes in the mitochondrial matrix arranged in a cyclic metabolic structure, including dehydrogenases that converge in the NADH pool and [[succinate dehydrogenase]] (on the inner side of the inner mt-membrane) for entry into the membrane-bound ET pathway [[Membrane-bound ET pathway|mET pathway]]. [[Citrate synthase]] is a marker enzyme of the TCA cycle, at the gateway into the cycle from [[pyruvate]] via [[acetyl-CoA]]. It is thus the major module of the [[Electron transfer pathway]], upstream of the inner [[Membrane-bound ET pathway|Membrane-bound ET pathway]] (mET-pathway) and downstream of the [[Mitochondrial outer membrane|outer mt-membrane]]. Sections of TCA cycle are required for [[fatty acid oxidation]] (FAO, β-oxidation). [[Anaplerosis|Anaplerotic reactions]] fuel the TCA cycle with other intermediary metabolites. In the cell, the TCA cycle serves also biosynthetic functions by metabolite export from the matrix into the cytosol. +
Triethyltin bromide (TET) is a lipophilic [1] inhibitor of the mitochondrial [[ATP synthase]] [2] which is used to induce [[LEAK state]] in [[living cells]] of ''Saccharomyces cerevisiae''. +
'''Aluminium trolley''' (700x500x60 mm); carrying capacity 120 kg; incl. packing box; for transport of O2k. '''Discontinued''' +
'''Trueness''' is understood as the lack of [[bias]] and the instrument calibration procedures are the key factor on establishing and correcting it. +
'''Trueness of measurement''' is the closeness of agreement between the average value obtained from a large series of results of measurements and a true value (adapted from ISO 3534-1:1993, definition 3.12). The degree of trueness is usually expressed numerically by the statistical measure bias that is inversely related to trueness and is the difference between the expectation of the results of measurement and a true value of the [[measurand]]. +
[[File:Tube Racks.JPG|right|180px]]'''Tube Racks''': stainless steel, accomodating four 50-ml tubes, for cleaning of microsyringes, cleaning and storage of stoppers during cleaning of the [[O2k-chamber]]s; package of two (for a total of eight tubes). +
U
The '''USB port''' describes the connection between O2k and Computer. With the USB cable connected, select '''USB port''' in the [[Connection window]]. Depending on the O2k series, it is possible to connect with a '''USB port''' or [[Serial port]]. +
[[Image:USB-Cable2.0 Type A-B.JPG|180px|right]]'''USB-Cable 2.0\Type A-B''' for connecting the [[O2k-Main Unit]] (O2k-Series E upwards) to the USB port of a PC or laptop. +
'''USB-RS232 Serial Adapter''', for connecting the [[RS232-Cable]] attached to the [[O2k-Main Unit]] (Series A-D) to the USB port of the PC or laptop. This is not required for O2k-Series E, nor when using a PC or laptop with a serial RS232 port. '''Discontinued''' +
'''Uncertainty of measurement''' is a parameter, associated with the result of a [[measurement]], that characterizes the dispersion of the values that could reasonably be attributed to the [[measurand]]. The parameter can be, for example, a standard deviation (or a given multiple of it), or the half-width of an interval having a stated level of confidence. The components of uncertainty are evaluated experimentally from statistical distributions (Type A) or evaluated from assumed probability distributions based on experience or other information (Type B). All components are expressed as standard uncertainties that are combined into one final expression. +
An '''uncoupler''' is a protonophore ([[CCCP]], [[FCCP]], [[DNP]], [[SF6847]]) which cycles across the inner mt-membrane with transport of protons and dissipation of the electrochemical proton gradient. Mild uncoupling may be induced at low uncoupler concentrations, the noncoupled state of [[ET capacity]] is obtained at optimum uncoupler concentration for maximum flux, whereas at higher concentrations an uncoupler-induced inhibition is observed. +
In '''uncoupler titrations''' various [[uncoupler]]s, such as CCCP, FCCP or DNP are applied to uncouple mitochondrial electron transfer from phosphorylation ([[ATP synthase]], [[ANT]] and [[phosphate carrier]]), particularly with the aim to measure [[ET capacity]]. ET capacity is maximum [[oxygen flux]] measured as [[noncoupled respiration]] with [[optimum uncoupler concentration]]. +
'''Uncoupling protein 1''' (UCP1) is also called thermogenin and is predominantly found in brown adipose tissue (BAT). UCP1 belongs to the gene family of [[uncoupling proteins]]. It is vital for the maintenance of body temperature, especially for small mammals. As the essential component of non-shivering thermogenesis, it possesses the ability to build and open a pore in the inner mitochondrial membrane through which protons may flow along their electrochemical gradient, generated by respiration, bypassing the ATP-producing re-entry site at the F1F0-ATP synthase. Thereby the energy stored in the electrochemical gradient is dissipated as heat. +
'''Uncoupling protein 2''' (UCP2) belongs to the gene family of [[uncoupling proteins]]. Whereas [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]], this may not be the case for UCP2. +
'''Uncoupling proteins''' (UCPs) are mitochondrial anion carrier proteins that can be found in the inner mitochondrial membranes of animals and plants. [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]] by dissipating the electrochemical proton gradient ([[mitochondrial membrane potential]]), generated by the [[electron transfer pathway]] by pumping protons from the mitochondrial matrix to the mitochondrial intermembrane space. +
The '''uncoupling-control ratio''' UCR is the ratio of ET-pathway/ROUTINE-respiration (''E/R'') in living cells, evaluated by careful [[uncoupler]] titrations ([[Steinlechner-Maran 1996 Am J Physiol Cell Physiol|Steinlechner et al 1996]]). Compare [[ROUTINE-control ratio]] (''R/E'') [[Gnaiger 2008 POS|(Gnaiger 2008)]]. +
A back-up power supply may be required to secure '''uninterrupted power supply'''. +
[[File:Count-vs-number.png|right|120px|link=Elementary entity]]
A '''unit''' is defined as 'a single individual thing' in Euclid's ''Elements'' (Book VII). This defines the [[elementary entity]] ''U''<sub>''X''</sub> of entity-type ''X'' (thing). The [[International System of Units]] defines the unit as 'simply a particular example of the quantity concerned which is used as a reference'. Then the ''value'' of a quantity ''Q'' is the product of a number ''N'' and a unit ''u''<sub>''Q''</sub>. The symbols ''U''<sub>''X''</sub> and ''u''<sub>''Q''</sub> are chosen here with ''U'' and ''u'' for 'unit': ''U''<sub>''X''</sub> is the Euclidean or entetic unit ('eunit'), and ''u''<sub>''Q''</sub> is the abstract unit ('aunit'). Subscripts ''X'' and ''Q'' for 'entity-type' and 'quantity-type' reflect perhaps even more clearly than words the contrasting meanings of the two fundamental definitions of an entetic versus abstract 'unit'. The term 'unit' with its dual meanings is used and confused in practical language and the scientific literature today. In the elementary entity ''U''<sub>''X''</sub>, the unit (the 'one') relates to the entity-type ''X'', to the single individual thing (single individual or undivided; the root of the word ''thing'' has the meaning of 'assembly'). The quantity involved in the unit of a single thing is the ''count'', ''N''<sub>''X''</sub> = ''N''·''U''<sub>''X''</sub> [x]. In contrast to counting, a unit ''u''<sub>''Q''</sub> is linked to the measurement of quantities ''Q''<sub>''u''</sub> = ''N''·''u''<sub>''Q''</sub>, such as volume, mass, energy; and these quantities — and hence the units ''u''<sub>''Q''</sub> — are abstracted from entity-types, pulled away from the world of real things. The new SI (2019-05-20) has completed this total abstraction of units, from the previous necessity to not only provide a quantitative definition but also a physical realization of a unit in the form of an 'artefact', such as the international prototype (IPK) for the unit kilogram. The new definitions of the base SI units are independent of any physical realization: ''u''<sub>''Q''</sub> is separate from ''X''. The classical unit of Euklid is the elementary unit for counting, entirely independent of measuring. Therefore, the quantity [[count]] is unique with respect to two properties: (''1'') in contrast to all other quantities in the metric system, the count depends on quantization of entities ''X''; and (''2'') in the SI, the '''N'''umber 1 is the '''U'''nit of the '''C'''ount of '''entities''' — NUCE.
[[File:UMDF LOGO.JPG|200px|left|UMDF]]
The '''United Mitochondrial Disease Foundation''' (UMDF) was founded in 1996 to promote research and education for the diagnosis, treatment and cure of mitochondrial disorders and to provide support to affected individuals and families. +
'''Units in figures and tables''' are specified together with the numerical values. The ''value'' of a quantity ''Q'' is the product of a [[number]] ''N'' and a [[unit]] ''u''<sub>''Q''</sub>. Abstract units ''u''<sub>''Q''</sub> (such as dm<sup>3</sup>=L, kg, J) are linked to measured quantities (such as volume, mass, energy):
Eq.(1) ''Q''<sub>''u''</sub> = ''N''·''u''<sub>''Q''</sub>
The multiplication in Eq.(1) can be handled like any mathematical equation and re-arranged to the form which indicates the meaning (left) of a number (right):
Eq.(2a) ''Q''<sub>''u''</sub>/''u''<sub>''Q''</sub> = ''N''
Eq.(2b) ''N''<sub>''X''</sub>/x = ''N''
When numbers are given on the axes of figures and in tables, the corresponding labels should be indicated according to Eq.(2), where Eq.(2a) applies to measured quantities, whereas Eq.(2b) relates to the countable quantity, i.e. [[count]] with unit [x]. For example, the axis label for volume-specific oxygen flux may be written as ''J''<sub>''V'',O<sub>2</sub></sub> / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''<sub>O<sub>2</sub></sub> / [amol/(s·x)]. +
Unspecific binding of the probe molecule TPP<sup>+</sup> in the matrix phase of mitochondria is taken into account as a correction for measurement of the [[mitochondrial membrane potential]]. External unspecific binding is the binding outside of the inner mt-membrane or on the outer side of the inner mt-membrane, in contrast to internal unspecific binding. +
A '''Upper O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O<sub>2</sub> concentration rises beyond this limit. +
A user name is +
A '''user''' code or name is entered upon starting [[DatLab]]. This window pops up automatically after opening DatLab. Usernames are connected with personal [[Layout for DatLab graphs |graph layouts]]. +
V
[[File:V-Ring 30-35-4.5.JPG|right|180px]]
'''V-ring\30-35-4.5 mm''', mounted on [[O2k-Chamber Holder]] and [[O2k-Chamber Holder sV]]. +
'''Maximum oxygen consumption''', ''V''<sub>O<sub>2</sub>max</sub>, is and index of cardiorespiratory fitness, measured by spiroergometry on human and animal organisms capable of controlled physical exercise performance on a treadmill or cycle ergometer. ''V''<sub>O<sub>2</sub>max</sub> is the maximum respiration of an organism, expressed as the volume of O<sub>2</sub> at [[STPD]] consumed per unit of time per individual object [mL.min<sup>-1</sup>.x<sup>-1</sup>]. If normalized per body mass of the individual object, ''M'' [kg.x<sup>-1</sup>], mass specific maximum oxygen consumption, ''V''<sub>O<sub>2</sub>max/''M''</sub>, is expressed in units [mL.min<sup>-1</sup>.kg<sup>-1</sup>]. +
Valinomycin catalyzes electrogenic K<sup>+</sup> transport down the electrochemical transmembrane gradient (150 ng<sup>.</sup>mg<sup>-1</sup> protein). +
A '''vector''' is a pysicochemical quantity with magnitude and spatial direction of a [[gradient]]. Symbols for vectors are written in bold face. For example, [[velocity]], '''''v''''', and the fundamental [[force]]s of physics, '''''F''''', are vectors. An infinitesimal area is a vector, d'''''A''''', perpendicular to the plane. +
'''Velocity''', '''''v''''' [m·s<sup>-1</sup>], is the [[speed]] in a defined spatial direction, and as such velocity is a [[vector]]. Velocity is the [[advancement]] in distance per unit time,
'''''v''''' ≡ d'''''z''''' ∙ d''t''<sup>-1</sup> [m·s<sup>-1</sup>] +
'''Viable cells''' vce are characterized by an intact plasma membrane barrier function. The total cell count (''N''<sub>ce</sub>) is the sum of viable cells (''N''<sub>vce</sub>) and dead cells (''N''<sub>dce</sub>). +
Not enough is known about '''viruses and mitochondrial medicine''', although several studies point towards a link between viral infection and mitochondrial dysfunction using high-resolution respirometry, with potential impact on drug development. +
'''Viton'''® is a fluoroelastomer with excellent resistance to aggressive fuels and chemicals. Viton is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (Viton O-rings). +
'''Volume''' ''V'' is a derived quantity based on the SI base quantity [[length]] [m] and is expressed in terms of [[SI base units]] in the derived unit cubic meter [m<sup>3</sup>]. The liter [L = dm<sup>3</sup>] is a conventional unit of volume for concentration and is used for most solution chemical kinetics. The volume ''V'' contained in a system (experimental chamber) is separated from the environment by the system boundaries; this is called the volume of the system, and described in practical language as big/small (derived from [[length]], [[height]]) or voluminous. Systems are defined at constant volume or constant [[pressure]]. For a pure sample S, the volume ''V''<sub>S</sub> of the pure sample equals the volume ''V'' of the system, ''V''<sub>S</sub> = ''V''. For [[sample]] s in a mixture, the ratio ''V''<sub>s</sub>·''V''<sup>-1</sup> is the nondimensional [[volume fraction]] ''Φ''<sub>s</sub> of sample s. Quantities divided by volume are [[concentration]]s of sample s in a mixture, such as [[count]] concentration ''C<sub>X</sub>'' = ''N<sub>X</sub>''·''V''<sup>-1</sup> [x·L<sup>-1</sup>], and amount of substance concentration ''C''<sub>B</sub> = ''n''<sub>B</sub>·''V''<sup>-1</sup> [mol·L<sup>-1</sup>]. Mass concentration is [[density]] ''ρ''<sub>s</sub> = ''m''<sub>s</sub>·''V''<sup>-1</sup> [kg·L<sup>-1</sup>]. In closed compressible systems (with a gas phase), the concentration of the gas increases, when pressure-volume [[work]] is performed on the system. +
Most of the chemicals for SUIT protocol titrations are prepared by weighing the substance on the balance, transferring to a volumetric glass flask and adding solvent until the intended volume is reached. However, for practical reasons some of the chemical compounds are prepared by just adding the solvent instead of adjusting it's volume. For example, this approach is useful if the substance is very toxic. Then an arbitratry amount is taken, its mass determined on the balance without trying to reach a specific value and the necessary amount of solvent is added. Adding the solvent instead of adjusting its volume is also useful if small amounts are needed (e.g. 1 mL) or if the compound has to be prepared directly before using it like Pyruvate. In these cases the volume contributed by the solute was tested. +
[[Image:Volume calibration ring A+B PVDF for Stopper.jpg|right|180px]]'''Volume-Calibration Ring''' (A or B) PVDF for O2k-Stoppers (2-mL [[O2k-chamber]]), white; attached to the [[Stopper\black PEEK\conical Shaft\central Port |stoppers]]. +
[[Image:Volume calibration ring A+B PVDF for Stopper.jpg|right|180px]]'''Volume-Calibration Ring sV''' (A or B), white PVDF, attached to [[Stopper sV\black PEEK\conical Shaft\central Port | PEEK O2k-Stopper sV]]. +
W
Recently, controversies had a renaissance on the much neglected Crabtree effect (aerobic glycolysis in a large range of cells exposed to glucose or fructose, with fully functional mitochondria; Crabtree 1929; Gnaiger and Kemp 1990) versus the '''Warburg effect''' (loss of mitochondrial function inducing cancer and stimulating compensatory aerobic glycolysis in the presence of oxygen; Warburg 1956; see list of references for reviews). Today it is widely accepted that ‘''the Warburg effect is not consistent across all cancer types''’ (Potter et al 2016) and reprogramming of mitochondrial energy metabolism represents a functional adjustment of cancer cells (Schöpf et al 2020). +
[[File:H2O.jpg|left|60px|Water]]
'''Water''', H<sub>2</sub>O, is widely used in the laboratory, particularly as a solvent and cleaning agent. Chemically pure water is prepared in various grades of purification: double distilled water (ddH<sub>2</sub>O) versus distilled water (dH<sub>2</sub>O or [[aqua destillata]], a.d.) and deionized or demineralized water (diH<sub>2</sub>O) with various combination purification methods. When H<sub>2</sub>O is mentioned without further specification in published protocols, it is frequently assumed that the standards of each laboratory are applied as to the quality of purified water. Purification is not only to be controlled with respect to salt content and corresponding electrical conductivity (ultra-pure water: 5.5 μS/m due to H<sup>+</sup> and OH<sup>-</sup> ions), but also in terms of microbial contamination. +
'''Wavelength averaging''' is the averaging of several adjacent data points across the recorded spectrum (spectral [[smoothing]]), to improve the [[signal-to-noise ratio]]. For example, if the instrument recorded 5 data points per nm, the average of the 5 points can be taken for each successive nm across the range of the spectrum to give a 5-point smoothing. This method clearly reduces the wavelength [[resolution]]. +
The minimum and the maximum wavelengths over which an [[absorbance spectrum]] is measured are described in terms of the [[wavelength range]]. It is determined mainly by the specifications of the [[spectrophotometer]] and the type of [[light source]] used, and the characteristic [[absorbance spectrum]] of the sample being investigated. +
A '''Web application''' is a computer software where the [[user interface]] gets accessed by the user through a web browser. +
The '''wet mass''' of a tissue or biological sample, obtained after blotting the sample to remove an arbitrary amount of water adhering externally to the sample. +
In [[reflectance spectrophotometry]] and [[remission spectrophotometry]] a white balance is carried out to determine the intensity of the incident light (''I''<sub>''0''</sub>) for the purpose of quantitative [[absorbance]] measurements. In [[reflectance spectrophotometry]], a mirror can be used whereas in [[remission spectrophotometry]] a standard white tile is more appropriate. +
'''Work''' [J] is a specific form of [[energy]] in the First Law of thermodynamics, and a specific form of [[exergy]] in the Second Law of thermodynamics, performed by a closed or open system on its surroundings (the environment). This is the definition of ''external'' work, which is zero in [[isolated system]]s. The term exergy includes external and internal work. Mechanical work is force [N] times path length [m]. The internal-energy change of a closed system, d''U'', is due to external exchange (e) of work and heat, and external total work (et, including pressure-volume work) is the internal-energy change minus heat,
d<sub>et</sub>''W'' = d''U'' - d<sub>e</sub>''Q'' +
A '''working measurement standard''' is a standard that is used routinely to calibrate or check material measures, measuring instruments or reference materials [SOURCE: VIM:1993, 6.7]. +
Z
Science Europe: "Zenodo is an open source and free repository for storing data, code, materials, and any research artefact. It was created by CERN and launched within the frame of the OpenAIRE project, commissioned by the European Commission. It aims at fostering free and easy access to scientific results, scientific data, software, and publications to all researchers." +
'''Zero calibration''' is, together with [[air calibration]], one of the two steps of the POS calibration. It is performed in the [[closed chamber]] after all the oxygen has been depleted by the addition of [[dithionite]] or by respiration of [[Isolated mitochondria |imt]] or [[Living cells |cells]]. Any incubation medium can be used for zero calibration with dithionite or sample. Unlike air calibration, it is not necessary to perform a zero calibration on each experimental day. After performing a zero calibration, it is recommended not running other experiments on the same day. Even after standard cleaning of the O2k-chambers, there might be residual amounts of reduced dithionite in the chamber, affecting the oxygen flux in subsequent experiments performed on the same day. +
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