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This page provides a simple browsing interface for finding entities described by a property and a named value. Other available search interfaces include the page property search, and the ask query builder.

List of results

Elasticity + (According to David Fell, "Elasticities are … According to David Fell, "Elasticities are properties of individual enzymes and not the metabolic system. The elasticity of an enzyme to a metabolite is related to the slope of the curve of the enzyme's rate plotted against metabolite concentration, taken at the metabolite concentrations found in the pathway in the metabolic state of interest. It can be obtained directly as the slope of the logarithm of the rate plotted against the logarithm of the metabolic concentration. The elasticity will change at each point of the curve (s,v) and must be calculated for the specific concentration of the metabolite (s) that will give a specific rate (r) of the enzyme activity" (See Figure).[[File:Elasticity_Measurement.jpg]][[File:Elasticity_Measurement.jpg]])
O2k control - DatLab 7 + (After selection of an O2k setup in the '''O2k control''' [F7] window, followed by a left-click '''Send to O2k''', only the following control functions are routinely required during experimental operations.)
Amperometric,Amp + (After selection of the Amperometric, Amp c … 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.ometric measurement is routinely required.)
Connection window + (After starting [[DatLab]] either the '''Connection window''' opens automatically by default or open [[O2k control]] by pressing [F7] and select the communication port.)
Absorbance + (Also known as attenuation or extinction, ' … Also known as attenuation or extinction, '''absorbance''' (''A'') is a measure of the difference between the [[incident light]] intensity (''I''0) and the intensity of light emerging from a sample (''I''). It is defined as:''A'' = log (''I''0/''I'') is defined as: ''A'' = log (''I''0/''I''))
Intrinsic fluorophores + (An '''Intrinsic flourophore''' is a naturally occurring [[fluorophore]] of which [[NADH]], aromatic amino acids and flavins are examples.)
Absorption spectrum + (An '''absorption spectrum''' is similar to an [[absorbance spectrum]] of a sample, but plotted as a function of [[absorption]] against wavelength.)
Entity + (An '''entity''' of type ''X'' is something … An '''entity''' of type ''X'' is something that can measured as an [[extensive quantity]] or counted as an [[elementary entity]]. The term entity with symbol ''X'', therefore, has a general meaning, including but not limited to elementary entities ''U''''X''. The distinction can be emphasized by using the term entity-type ''X'', to avoid confusion of an entity ''X'' with the more restricted definition of elementary entity ''U''''X'' as a ''single'' countable object or event.ub>''X'' as a ''single'' countable object or event.)
Events - DatLab + (An '''event''' in [[DatLab]] … An '''event''' in [[DatLab]] is a defined point in time, labelled by a name (1 to 10 characters). An event applies to all plots of the selected O2k-Chamber. The event is shown by a vertical line in the graph and the label of the event is shown on the top (DatLab 6 and lower: on the bottom). The default name is the sequential number of the event. It is recommended to edit event labels with a minimum number of characters, and to explain the abbreviation in the 'Definition' box. The final concentration and titration volume can be entered into the corresponding boxes, if the event relates to the titration of a substance. A short comment can be entered to describe the event in detail. '''Set events''' - Manual events are entered (real-time, connected to the O2k) by pressing [F4] at the time of the event (e.g. to indicate a manual titration into the chamber). An event belongs either to chamber A, chamber B, or both. Instrumental events are added automatically, e.g. when the stirrer (A or B) or illumination (both chambers) is switched on or off.After setting a new event the Edit event window pops up. Pressing F4 defines the time point of the event. Full attention can then be paid to the experiment. Edit the event later, as it is possible to insert an event at any chosen moment of the plotted record of the experiment by placing the cursor anywhere in the graph at the selected time point by pressing Ctrl and clicking the left mouse button.'''Edit event''' - Left click on the name of an existing event to open the Edit event window to edit or Delete event.In events obtained from a selected [[DL-Protocols |protocol]], the entire sequence of consecutive events is defined with event names, definitions, concentrations and titration volumes.'''Name''' - Enter an event name of 1 to 10 characters. Short names (e.g. O instead of Open) are recommended.''' Comment''' - Further information can be entered into the text field.Select O2k-chamber A, B or both. The Event will be shown on plots for both or one selected chamber.»[[DL-Protocols#DL-Protocol_principles|Protocol events]][DL-Protocols#DL-Protocol_principles|Protocol events]])
Examination + (An '''examination''' is a set of operations having the object of determining the value or characteristics of a property. In some disciplines (e.g. microbiology) an examination is the total activity of a number of tests, observations or measurements.)
Experimental code + (An '''experimental code''' can be entered in the [[Sample - DatLab|Sample]] window, containing up to 10 digits.)
Interlaboratory comparison + (An '''interlaboratory comparison''' is the organization, performance and evaluation of measurements or tests on the same or similar items by two or more laboratories in accordance with predetermined conditions.)
Journal issue + (An '''issue''' of a journal or periodical is a number, which typically indicates how many times a [[Journal volume |volume]] of the journal has been published in sequence.)
Open system + (An '''open system''' is a system with boun … An '''open system''' is a system with boundaries that allow external exchange of energy and matter; the surroundings are merely considered as a source or sink for quantities transferred across the system boundaries ([[external flow]]s, ''I''ext).[[external flow]]s, ''I''ext).)
Outlier + (An '''outlier''' is a member of a set of v … An '''outlier''' is a member of a set of values which is inconsistent with other members of that set. An outlier can arise by chance from the expected population, originate from a different population, or be the result of an incorrect recording or other blunder. Many schemes use the term outlier to designate a result that generates an action signal. This is not the intended use of the term. While outliers will usually generate action signals, it is possible to have action signals from results that are not outliers [SOURCE: ISO 5725‑1:1994, modified].liers [SOURCE: ISO 5725‑1:1994, modified].)
Outlier-skewness index + (An '''outlier-skewness index''' ''OSI'' is … An '''outlier-skewness index''' ''OSI'' is defined for evaluation of the distribution of data sets with outliers including separate clusters or skewness in relation to a normal distribution with equivalence of the average and median. The ''OSI'' is derived from [http://www.statisticshowto.com/pearsons-coefficient-of-skewness/ Pearson’s coefficient of skewness] 2:: Pearson 2 coefficient = 3 · (average-median)/SDThe outlier-skewness index ''OSI'' introduces the absolute value of the arithmetic mean, ''m'' = ABS(average + median)/2, for normalization:: ''OSI'' = (average-median)/(''m'' + SD) : ''OSI'' = (average-median)/[ABS(average+median)/2 + SD]At the limit of a zero value of ''m'', the ''OSI'' equals the Pearson 2 coefficient (without the multiplication factor of 3). At high ''m'' with small standard deviation (SD), the ''OSI'' is effectively the difference between the average and the median normalized for ''m'', (average-median)/''m''.malized for ''m'', (average-median)/''m''.)
Uncoupler + (An '''uncoupler''' is a protonophore ([[CCCP]] … 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. uncoupler-induced inhibition is observed.)
Endothermic + (An [[energy]] … An [[energy]] transformation is '''endothermic''' if the [[enthalpy]] change of a closed system is positive when the process takes place in the forward direction and heat is absorbed from the environment under isothermal conditions (∆e''Q'' > 0) without performance of work (∆e''W'' = 0). The same energy transformation is [[exothermic]] if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are [[exergonic]].ergonic]].)
Exothermic + (An [[energy]] … An [[energy]] transformation is '''exothermic''' if the [[enthalpy]] change of a closed system is negative when the process takes place in the forward direction and heat is lost to the environment under isothermal conditions (∆e''Q'' < 0) without performance of work (∆e''W'' = 0). The same energy transformation is [[endothermic]] if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are [[exergonic]].ergonic]].)
Assay + (An experimental '''assay''' is a method to … 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.uires subsampling from homogenous samples.)
Sample type + (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]]).)
Science - the concept + (As per the 2017 UNESCO Recommendation on S … 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.phenomena occurring in nature and society.)
Conflict of interest + (As stated on the [https://www.bioenergetic … As stated on the [https://www.bioenergetics-communications.org/index.php/bec/BECPolicies#Journal_policies_on_conflicts_of_interest_.2F_competing_interests Bioenergetics Communications' policy], a '''conflict of interest''' may be of non-financial or financial nature. Examples of conflicts of interest include (but are not limited to)::::* Individuals receiving funding, salary or other forms of payment from an organization, or holding stocks or shares from a company, whose financial situation might be influenced by the publication of the findings;:::* Individuals, their funding organization or employer holding (or applying for) related patents;:::* Official affiliations and memberships with interest groups relating to the content of the publication;:::* Political, religious, or ideological competing interests.For authors, any conflict of interest is declared at the time of submission and included in the published manuscript. For editors and reviewers, conflicts should be taken into account before accepting an assignment.to account before accepting an assignment.)
STPD + (At '''standard temperature and pressure dr … At '''standard temperature and pressure dry''' (STPD: 0 °C = 273.15 K and 1 atm = 101.325 kPa = 760 mmHg), the molar volume of an ideal gas, ''V''m, and ''V''m,O2 is 22.414 and 22.392 L∙mol-1, respectively. Rounded to three decimal places, both values yield the conversion factor of 0.744 from units used in spiroergometry (''V''O2max [mL O2·min-1]) to SI units [µmol O2·s-1]. For comparison at normal temperature and pressure dry (NTPD: 20 °C), ''V''m,O2 is 24.038 L∙mol-1. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol-1 and 22.689 L∙mol-1 for O2.;/sup>. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol-1 and 22.689 L∙mol-1 for O2.)
Copyright + (Authors retain the copyright for the conte … Authors retain the copyright for the contents of their manuscripts published in [[Bioenergetics Communications]]. {''Quote''} All preprints are posted with a Creative Commons CC BY 4.0 license, ensuring that authors retain '''copyright''' and receive credit for their work, while allowing anyone to read and reuse their work. {''end of Quote''}d and reuse their work. {''end of Quote''})

(Authors retain the copyright for the contents of their manuscripts publi)

Mitophagy + (Autophagy (self-eating) in general is viewed as a degradation process which removes non-essential or damaged cellular constituents. » [[Mitophagy#Mitochondrial_mitophagy | '''MiPNet article''']])
Barth Syndome + (Barth Syndome (BTHS) is an X-linked geneti … 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[[Sparagna GC]] 2016-04-24)
Biological contamination + (Biological contamination may be caused by microbial growth in the O2k-Chamber or in the experimental medium.)
Bovine serum albumin + (Bovine serum albumin is a membrane stabili … Bovine serum albumin is a membrane stabilizer, oxygen radical scavenger, and binds Ca2+ and free fatty acids, hence the rather expensive essentially free fatty acid free BSA is required in mitochondrial isolation and respiration media. Sigma A 6003 fraction V.lation and respiration media. Sigma A 6003 fraction V.)
Full screen + (By clicking/enabling '''Full screen''' in … By clicking/enabling '''Full screen''' in the Graph-menu in DatLab the currently selected graph is shown alone on the full screen (On) or together with the other defined graphs (Off). Full screen is particularly useful for a single channel overview and for Copy to clipboard [ALT+G B].rview and for Copy to clipboard [ALT+G B].)
Calcium retention capacity + (Calcium retention capacity (CaRC) is a mea … Calcium retention capacity (CaRC) is a measure of the capability of mitochondria to retain calcium (Ca2+), primarily in the form of calcium phosphates, in the mitochondrial matrix. By storing calcium in the form of osmotically inactive precipitates the mitochondria contribute to the buffering of cytosolic free Ca2+ levels and thereby to the regulation of calcium-dependent cellular processes. Alterations of CaRC are important in stress phenomena associated with energy limitation and have been linked to neurodegenerative diseases [[Starkov 2010 FEBS J |(Starkov 2013 FEBS J).]]Experimentally, CaRC has been indirectly assessed by determination of respiratory rates of isolated mitochondria which were exposed to continuously increasing doses of Ca2+ by use of the [[TIP2k-Module| Titration-Injection microPump TIP2k]]. The upper limit of CaRC was observed as a sudden decrease of respiration presumed to reflect opening of the permeability transition pore [[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]][[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]])
POS calibration - dynamic + (Calibration of the sensor response time. See also [[POS calibration - static]].)
Cataplerosis + (Cataplerosis is the exit of TCA cycle intermediates from the mt-matrix space.)
Living cells + (Cell viability in '''living cells''' shoul … Cell viability in '''living cells''' should be >95 % for various experimental investigations, including cell respirometry. Viable cells (vce) are characterized by an intact plasma membrane barrier function. The total cell count (''N''ce) is the sum of viable cells (''N''vce) and dead cells (''N''dce). In contrast, the plasma membrane can be permeabilized selectively by mild detergents ([[digitonin]]), to obtain the [[Mitochondrial preparations |mt-preparation]] of [[permeabilized cells]] used for [[cell ergometry]]. Living cells are frequently labelled as ''intact cells'' in the sense of the total cell count, but ''intact'' may suggest dual meanings of ''viable'' or unaffected by a disease or mitochondrial injury.t dual meanings of ''viable'' or unaffected by a disease or mitochondrial injury.)
Exit - DatLab 7 + (Close DatLab files and '''quit''' the program.)
Close and delete file - DatLab + (Close and delete a file.)
DatLab error messages + (Common '''DatLab error messages''' and according actions and solutions are listed here.)
Citrate synthase + (Condensation of [[oxaloacetate]] … Condensation of [[oxaloacetate]] with acetyl-CoA yields citrate as an entry into the [[TCA cycle]]. CS is located in the mt-matrix. CS activity is frequently used as a functional marker of the amount of mitochondria (mitochondrial elementary marker, ''mtE'') for normalization of respiratory flux.'') for normalization of respiratory flux.)
O2k configuration + (Configure or modify the settings for the O … Configure or modify the settings for the O2k sensorsIn '''O2k configuration''', channels (amperometric and potentiometric) can be switched on/off by selecting the according tick box. The Power-O2k number (P1, P2, ..) and numbers for O2 sensors, Amp sensors, pX electrodes and pX reference electrodes are entered or edited here. With the [[O2k-FluoRespirometer]] (O2k-Series H and higher), the serial numbers of the [[Smart Fluo-Sensor|Smart Fluo-Sensors]] are shown automatically under [Amperometric, Amp]. The O2k configuration window pops up when DatLab starts and "Connect to O2k" is pressed for the first time. It is also accessible from the menu "Oroboros O2k" and from within the [[O2k control]] and [[Mark statistics - DatLab|Mark statistics]] windows.[[Mark statistics - DatLab|Mark statistics]] windows.)
Cross-linked respiratory states + (Coordinated respiratory [[SUIT|SUIT protocols]] … Coordinated respiratory [[SUIT|SUIT protocols]] are designed to include '''cross-linked respiratory states''', which are common to these protocols. Different SUIT protocols address a variety of respiratory control steps which cannot be accomodated in a single protocol. Cross-linked respiratory states are included in each individual coordinated protocol, such that these states can be considered as replicate measurements, which also allow for harmonization of data obtained with these different protocols.a obtained with these different protocols.)
Energy metabolism + (Core '''energy metabolism''' is the integr … Core '''energy metabolism''' is the integrated biochemical process supplying the cell with ATP, utilizing ATP for various forms of work including biogenesis, maintaining ion and redox balance, and in specific organisms or tissues dissipating heat for temperature regulation.ssipating heat for temperature regulation.)
DatLab data file + (DatLab 8: The file type generated is *.dld8. DatLab 7: The file type generated is *.DLD.)
Keyboard shortcuts - DatLab + (DatLab provides several keyboard shortcuts to allow for quick access to many functions and settings without using a mouse.)
DatLab-Upgrading to DatLab 6 + (DatLab-Upgrading to DatLab 6: including free follow-up updates for DatLab 6 for the next two years)
O2k channel labels - DatLab 7 + (Default channel labels can now be changed, … Default channel labels can now be changed, and new labels set by the user. E.g., rename the Amperometric channel, Amp, to 'H2O2' for H2O2 measurements by fluorometry; rename the potentiometric channel, pX, to TPP+ for mitochondrial membrane measurements with the O2k-pH ISE-Module.For changing the label, go to menu [Oroboros O2k]\O2k channel labels and set the new channel label as desired. and set the new channel label as desired.)
Q-pools + (Different '''Q-pools''' are more or less c … Different '''Q-pools''' are more or less clearly distinguished in the cell, related to a variety of models describing degress of Q-pool behavior. (''1'') [[CoQ]]-pools are distinguished according to their compartmentation in the cell: mitochondrial CoQ (mtCoQ) and CoQ in other organelles versus plasma-membrane CoQ. (''2'') The total mitochondrial CoQ-pool mtCoQ is partitioned into an [[ETS]]-reactive Q-pool, Qra, and an inactive mtCoQ-pool, Qia. (''2a'') The Qra-pool is fully reduced in the form of quinol QH2 under anoxia, and fully oxidized in the form of quinone in aerobic [[mitochondrial preparations]] incubated without [[CHNO-fuel substrate]]s. Intermediate redox states of Qra are sensitive to pathway control and coupling control of mitochondrial electron transfer and [[OXPHOS]]. (''2b'') The Qia-pool remains partially reduced and oxidized independent of aerobic-anoxic transitions. The redox state of Qia is insensitive to changes in mitochondrial respiratory states. (''3'') The Qra-pool is partitioned into Q with Q-pool behavior according to the fluid-state model (synonymous: random-collision model) and Q tightly bound to supercomplexes according to the solid-state model. The two models describe the extremes in a continuum of homogenous or heterogenous Q-pool behavior. The CII-Q-CIII segment of the [[S-pathway]] is frequently considered to follow homogenous Q-pool behavior participating in the Qhom-pool, whereas the CI-Q-CIII segment of the [[N-pathway]] indicates [[supercomplex]] organization and metabolic channeling with different degrees of Q-pool heterogeneity contributing to the Qhet-pool.[[supercomplex]] organization and metabolic channeling with different degrees of Q-pool heterogeneity contributing to the Qhet-pool.)
Dilution effect + (Dilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber.)
Biochemical threshold effect + (Due to threshold effects, even a large defect diminishing the velocity of an individual enzyme results in only minor changes of pathway flux.)
Electron leak + (Electrons that escape the [[electron transfer pathway]] … Electrons that escape the [[electron transfer pathway]] without completing the reduction of oxygen to water at cytochrome ''c'' oxidase, causing the production of [[Reactive_oxygen_species |ROS]]. The rate of electron leak depends on the topology of the complex, the redox state of the moiety responsible of electron leakiness and usually on the protonmotive force ([[Protonmotive force|Δ''p'']]). In some cases, the [[Protonmotive force|Δ''p'']] dependance relies more on the ∆pH component than in the ∆''Ψ''.e on the ∆pH component than in the ∆''Ψ''.)
Proton leak + (Flux of protons driven by the protonmotive … Flux of protons driven by the protonmotive force across the inner mt-membrane, bypassing the [[ATP synthase]] and thus contributing to [[LEAK respiration]]. Proton leak-flux depends non-linearly (non-ohmic) on the protonmotive [[force]]. Compare: [[Proton slip]].[[Proton slip]].)