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TermAbbreviationDescription
Interlaboratory comparisonAn 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.
Internal flowIi [MU·s-1]Within the system boundaries, irreversible internal flows, Ii,—including chemical reactions and the dissipation of internal gradients of heat and matter—contribute to internal entropy production, diS/dt. In contrast, external flows, Ie, of heat, work, and matter proceed reversibly across the system boundaries (of zero thickness). Flows are expressed in various formats per unit of time, with corresponding motive units [MU], such as chemical [mol], electrical [C], mass [kg]. Flow is an extensive quantity, in contrast to flux as a specific quantity.
Internal-energyU [J]Internal-energy, U [J], can neither be destroyed nor created (first law of thermodynamics: diU/dt = 0). Note that internal (subscript i), as opposed to external (subscript e), must be distinguished from "internal-energy", U, which contrasts with "Helmholtz energy", A, as enthalpy, H, contrasts with Gibbs energy, G.
International Mito Patients (IMP)IMPIMP LOGO.JPGThe International Mito Patients is a network of national patient organizations involved in mitochondrial disease. Mitochondrial disease is a rare disease with a limited number of patients per country. The national patient organizations which are a member of IMP each are active and powerful in their own countries. By joining forces IMP can represent a large group of patients and as such be their voice on an international level.
International Society for Mountain MedicineISMM
ISMM

The International Society for Mountain Medicine is an interdisciplinary society comprising about xx members worldwide. Its purpose is ..

International Society on Oxygen Transport to TissueISOTT
ISOTT LOGO.jpg

The International Society on Oxygen Transport to Tissue is an interdisciplinary society comprising about 250 members worldwide. Its purpose is to further the understanding of all aspects of the processes involved in the transport of oxygen from the air to its ultimate consumption in the cells of the various organs of the body. Founded in 1973, the society has been the leading platform for the presentation of many of the technological and conceptual developments within the field both at the meetings themselves and in the proceedings of the society.

International Standard Serial NumberISSNThe International Standard Serial Number, ISSN, is a code used to identify periodical publications, independent of which media are used (print and/or electronic). - Bioenergetics Communications, BEC: ISSN 2791-4690
International System of UnitsSI

The International System of Units (SI) is the modern form of the metric system of units for use in all aspects of life, including international trade, manufacturing, security, health and safety, protection of the environment, and in the basic science that underpins all of these. The system of quantities underlying the SI and the equations relating them are based on the present description of nature and are familiar to all scientists, technologists and engineers.

The definition of the SI units is established in terms of a set of seven defining constants. The complete system of units can be derived from the fixed values of these defining constants, expressed in the units of the SI. These seven defining constants are the most fundamental feature of the definition of the entire system of units. These particular constants were chosen after having been identified as being the best choice, taking into account the previous definition of the SI, which was based on seven base units, and progress in science (p. 125).

International Union of Pure and Applied Chemistry, IUPACIUPACThe International Union of Pure and Applied Chemistry (IUPAC) celebrated in 2019 the 100th anniversary, which coincided with the International Year of the Periodic Table of Chemical Elements (IYPT 2019). IUPAC {Quote} notes that marking Mendeleev's achievement will show how the periodic table is central to connecting cultural, economic, and political dimensions of global society “through a common language” {end of Quote} (Horton 2019). 2019 is proclaimed as the International Year of the Periodic Table of Chemical Elements (IYPT 2019). For a common language in mitochondrial physiology and bioenergetics, the IUPAC Green book (Cohen et al 2008) is a most valuable resource, which unfortunately is largely neglected in bioenergetics textbooks. Integration of open systems and non-equilibrium thermodynamic approaches remains a challenge for developing a common language (Gnaiger 1993; BEC 2020.1).
International oxygraph courseIOCInternational Oxygraph Course (IOC), see O2k-Workshops.
Internationale Gesellschaft fuer Regenerative Mitochondrien-MedizinIGRMM e.V.

Organizer of

Interpolate pointsSelect Interpolate points in the Mark information window to interpolate all data points in the marked section of the active graph. See also Delete points and Restore points or Recalculate slope.
Intracellular oxygenpO2,iPhysiological, intracellular oxygen pressure is significantly lower than air saturation under normoxia, hence respiratory measurements carried out at air saturation are effectively hyperoxic for cultured cells and isolated mitochondria.
Intrinsic fluorophoresAn Intrinsic flourophore is a naturally occurring fluorophore of which NADH, aromatic amino acids and flavins are examples.
Ion-Selective Electrode TPP+ and Ca2+
Ion-Selective Electrode TPP+ and Ca2+.JPG

Ion-Selective Electrode TPP+ and Ca2+: ISE with 6 mm outer diameter shaft, for Stopper\white PVDF\angular Shaft\side+6.2+2.6 mm Port.

O2k-TPP+ ISE-Module: 2 ISE.

IonomycinImyIonomycin (Imy) is a ionophore used to raise intracellular [Ca2+].
Isocitrate
isocitrate

isocitrate, C6H5O7-3, is a tricarboxylic acid trianion, intermediate of the TCA cycle, obtained by isomerization of citrate. The process is catalyzed by aconitase, forming the enzyme-bound intermediate cis-aconitate.

Isocitrate dehydrogenaseIDHIsocitrate dehydrogenase forms 2-oxoglutarate from isocitrate in the TCA cycle.
Isolated mitochondriaimtIsolated mitochondria, imt, are mitochondria separated from a tissue or cells by breaking the plasma membranes and attachments to the cytoskeleton, followed by centrifugation steps to separate the mitochondria from other components.
Isolated systemThe boundaries of isolated systems are impermeable for all forms of energy and matter. Changes of isolated systems have exclusively internal origins, e.g., internal entropy production, diS/dt, internal formation of chemical species i which is produced in a reaction r, dini/dt = drni/dt. In isolated systems some internal terms are restricted to zero by various conservation laws which rule out the production or destruction of the respective quantity.
IsomorphicThe term isomorphic refers to quantities which have identical or similar form, shape, or structure. In mathematics, an isomorphism defines a one-to-one correspondence between two mathematical sets. In ergodynamics, isomorphic quantities are defined by equations of identical form. If isomorphic quantities are not expressed in identical units, then these quantities are expressed in different formats which can be converted to identical untis. Example: electric force [V=J/C] and chemical force [Jol=J/mol] are ismorphic forces; the electrical format [J/C] can be converted to the chemical format [J/mol] by the Faraday constant. Units not only give meaning to the numerical value of a quantity, but units provide also an abbreviated common language to communicate and compare isomorphic quantities. In irreversible thermodynamics, isomorphic forces are referred to as generalized forces.
Japanese Society of Mitochondrial Research and MedicineJ-mit
J-mit.png

The Japanese Society of Mitochondrial Research and Medicine (J-mit) was founded to share the latest knowledge on mitochondrial research. J-mit is the biggest Asian society of mitochondrial research and medicine and is a member of ASMRM.

JmaxJmaxJmax is the maximum pathway flux (e.g. oxygen flux) obtained at saturating substrate concentration. Jmax is a function of metabolic state. In hyperbolic ADP or oxygen kinetics, Jmax is calculated by extrapolation of the hyperbolic function, with good agreement between the calculated and directly measured fluxes, when substrate levels are >20 times the c50 or p50.
Journal indexingJournal indexing allows publications to be found on search tools/databases. Each database might have different criteria of inclusion.
Journal issueAn issue of a journal or periodical is a number, which typically indicates how many times a volume of the journal has been published in sequence.
Journal publicationIn most cases journal publication {Quote} will not be affected by posting a preprint. However, there are some publishers that do not consider papers that have already appeared online. We strongly recommend that you check all journals that you might submit to in advance {end of Quote}. A list of academic journals by preprint policy is available.
Journal volumeThe volume of a journal or periodical is a number, which in many cases indicates the sequential number of years the journal has been published. Alternatively, the volume number may indicate the current year, independent of the year in which the journal published its first volume. A volume may be subdivided into issues.
KelvinKThe kelvin, symbol K, is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380 649 × 10−23 when expressed in the unit J x-1 K−1.
Keyboard shortcuts - DatLabDatLab provides several keyboard shortcuts to allow for quick access to many functions and settings without using a mouse.
Keywords-MitoPedia in BECKeywords—MitoPedia is the concept to link keywords in articles published in Bioenergetics Communications (BEC) to MitoPedia terms. Authors should consider the message in the selected keywords. Provide consistent definitions of your keywords by linking them to MitoPedia. Extend MitoPedia entries critically by your contributions. The BEC editorial team will hyperlink your keywords with MitoPedia, and a reference to your BEC publication will be generated automatically from the MitoPedia term to your publication. With your contributions, BEC elevates keywords to terms with meaning. Your article gains visibility.
KilogramkgThe kilogram, symbol kg, is the SI unit of mass. It is defined by taking the fixed numerical value of the Planck constant h to be 6.626 070 15 × 10−34 when expressed in the unit J s, which is equal to kg m2 s−1, where the meter and the second are defined in terms of c and ΔνCs.
Korean Society of Mitochondrial Research and MedicineKSMRMThe Korean Society of Mitochondrial Research and Medicine (KSMRM) is a member of ASMRM.
Kynurenine hydroxylaseKynurenine hydroxylase (kynurenine 3-monooxygenase) is located in the outer mitochondrial membrane. Kynurenine hydroxylase catalyzes the chemical reaction: L-kynurenine + NADPH + H+ + O2 ↔ 3-hydroxy-L-kynurenine + NADP+ + H2O Kynurenine hydroxylase belongs to the family of oxidoreductases acting on paired donors, with O2 as oxidant and incorporation or reduction of oxygen. The oxygen incorporated need not be derived from O2 with NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor. This enzyme participates in tryptophan metabolism. It employs one cofactor, FAD.
L/E coupling-control ratioL/ELEAK control ratio The L/E coupling-control ratio is the flux ratio of LEAK respiration over ET capacity, as determined by measurement of oxygen consumption in L and E sequentially. The L/E coupling-control ratio is an index of uncoupling or dyscoupling at constant ET-capacity. L/E increases with uncoupling from a theoretical minimum of 0.0 for a fully coupled system, to 1.0 for a fully uncoupled system.
L/P coupling-control ratioL/PL/P coupling-control ratio The L/P coupling-control ratio or LEAK/OXPHOS coupling-control ratio combines the effects of coupling (L/E) and limitation by the phosphorylation system (P/E); L/P = (L/E) / (P/E) = 1/RCR.
L/R coupling-control ratioL/RL/R coupling-control ratio The L/R coupling-control ratio or LEAK/ROUTINE coupling-control ratio combines the effects of coupling (L/E), physiological control of energy demand, and limitation by the OXPHOS capacity.
LEAK respirationLL.jpg EAK respiration or LEAK oxygen flux L compensating for proton leak, proton slip, cation cycling and electron leak, is a dissipative component of respiration which is not available for performing biochemical work and thus related to heat production. LEAK respiration is measured in the LEAK state, in the presence of reducing substrate(s), but absence of ADP - abbreviated as L(n) (theoretically, absence of inorganic phosphate presents an alternative), or after enzymatic inhibition of the phosphorylation system, which can be reached with the use of oligomycin - abbreviated as L(Omy). The LEAK state is the non-phosphorylating resting state of intrinsic uncoupled or dyscoupled respiration when oxygen flux is maintained mainly to compensate for the proton leak at a high chemiosmotic potential, when ATP synthase is not active. In this non-phosphorylating resting state, the electrochemical proton gradient is increased to a maximum, exerting feedback control by depressing oxygen flux to a level determined mainly by the proton leak and the H+/O2 ratio. In this state of maximum protonmotive force, LEAK respiration, L, is higher than the LEAK component of OXPHOS capacity, P. The conditions for measurement and expression of respiration vary (oxygen flux in the LEAK state, JO2L, or oxygen flow, IO2L). If these conditions are defined and remain consistent within a given context, then the simple symbol L for respiratory rate can be used as a substitute for the more explicit expression for respiratory activity. » MiPNet article
LEAK state with ATPL(T)L.jpg The LEAK state with ATP is obtained in mt-preparations without ATPase activity after ADP is maximally phosphorylated to ATP (State 4; Chance and Williams 1955) or after addition of high ATP in the absence of ADP (Gnaiger et al 2000). Respiration in the LEAK state with ATP, L(T), is distinguished from L(n) and L(Omy).
LEAK state with oligomycinL(Omy)L.jpg The LEAK state with oligomycin is a LEAK state induced by inhibition of ATP synthase by oligomycin. ADP and ATP may or may not be present. LEAK respiration with oligomycin, L(Omy), is distinguished from L(n) and L(T).
LEAK state without adenylatesL(n)L.jpg In the LEAK state without adenylates mitochondrial LEAK respiration, L(n) (n for no adenylates), is measured after addition of substrates, which decreases slowly to the LEAK state after oxidation of endogenous substrates with no adenylates. L(n) is distinguished from L(T) and L(Omy).
Laboratory titration sheetLaboratory titration sheet contains the sequential titrations in a specific Substrate-uncoupler-inhibitor titration (SUIT) protocol. The laboratory titration sheets for different SUIT protocols are incorporated in DatLab (DL7.1): Protocols in DatLab
Lactate dehydrogenaseLDHLactate dehydrogenase is a glycolytic marker enzyme in the cytosol, regenerating NAD+ from NADH and pyruvate, forming lactate.
Laner 2013 Mitochondr Physiol Network MiP2013
Latent mitochondrial dysfunctionThe concept on latent mitochondrial dysfunction presents the working hypothesis that the dynamic mitochondrial stress response provides a more sensitive and integrative marker for degenerative disease-related defects compared to acute mitochondrial dysfunction. The risk for developing a disease may be quantified in terms of a stress response, rather than a static pathophysiological state. Acute and latent mitochondrial dysfunction are studied at baseline and in response to a particular (e.g. oxidative) stress, using a mitochondrial stress resistance test.
Layout - DatLab

DatLab 8: Graph layouts are selected for standardized display of graphs, plots and scaling of axes. When using DL8-Protocols (.dlp8) the recommended initial layout is already loaded according to the specific DL8-Protocol. Layouts can be further selected, modified and managed through the top menu Layout.

DatLab 7: Layout - DatLab 7

Layout - DatLab 7A Layout in DatLab selected in the Layout menu yields a standardized display of graphs and plots displayed with specific scalings. The graph layout defines initial settings, which can be modified for plots [Ctrl+F6] and scaling [F6]. A modified layout can be saved as user layout without changing the standard layouts.
Least squares methodThis method makes use of all of the data points of the spectrum in order to quantify a measured spectrum with a reference spectrum of known concentration using a least squares method to match the measured spectrum with the reference spectrum. The technique results in improved accuracy compared with the use of only a few characteristic wavelengths.
Lengthl [m]Length l is an SI base quantity with SI base unit meter m. Quantities derived from length are area A [m2] and volume V [m3]. Length is an extensive quantity, increasing additively with the number of objects. The term 'height' h is used for length in cases of vertical position (see height of humans). Length of height per object, LUX [m·x-1] is length per unit-entity UX, in contrast to lentgth of a system, which may contain one or many entities, such as the length of a pipeline assembled from a number NX of individual pipes. Length is a quantity linked to direct sensory, practical experience, as reflected in terms related to length: long/short (height: tall/small). Terms such as 'long/short distance' are then used by analogy in the context of the more abstract quantity time (long/short duration).
Level flowEE.jpg Level flow is a steady state of a system with an input process coupled to an output process (coupled system), in which the output force is zero. Clearly, energy must be expended to maintain level flow, even though output is zero (Caplan and Essig 1983; referring to zero output force, while output flow may be maximum).
Light sourceA variety of light sources are available for fluorometry and spectrophotometry. These include deuterium, mercury and xenon arc lamps and quartz halogen bulbs dependent upon the wavelengths required. However, the advent of light emitting diodes has greatly increased the possibilities for the application of fluorometry and spectrophotometry to areas that were previously not practicable, and at a much reduced cost.
Light-emitting diodeLEDA light-emitting diode (LED) is a light source (semiconductor), used in many every-day applications and specifically in fluorometry. LEDs are available for specific spectral ranges across wavelengths in the visible, ultraviolet, and infrared range.
Light-enhanced dark respirationLEDRLight-enhanced dark respiration LEDR is a sharp (negative) maximum of dark respiration in plants in response to illumination, measured immediately after switching off the light. LEDR is supported by respiratory substrates produced during photosynthesis and closely reflects light-enhanced photorespiration (Xue et al 1996). Based on this assumption, the total photosynthetic oxygen flux TP is calculated as the sum of the measured net photosynthetic oxygen flux NP plus the absolute value of LEDR.
LightguidesLightguides consist of optical fibres (either single or in bundles) that can be used to transmit light to a sample from a remote light source and similarly receive light from a sample and transmit it to a remote detector. They have greatly contributed to the range of applications that for which optical methods can be applied. This is particularly true in the fields of medicine and biology.
Limiting oxygen pressureplThe limiting oxygen pressure, pl, is defined as the partial oxygen pressure, pO2, below which anaerobic catabolism is activated to contribute to total ATP generation. The limiting oxygen pressure, pl, may be substantially lower than the critical oxygen pressure, pc, below which aerobic catabolism (respiration or oxygen consumption) declines significantly.
Limiting pO2plimIn the transition from aerobic to anaerobic metabolism, there is a limiting pO2, plim, below which anaerobic energy flux is switched on and CR ratios become more exothermic than the oxycaloric equivalent. plim may be significanlty below the critical pO2.
Linear phenomenological lawsLinear phenomenological laws are at the core of the thermodynamics of irreversible processes TIP, considered to apply near equilibrium but more generally in transport processes (e.g. Fick's law). In TIP, linearity is discussed as the dependence of generalized flows I or fluxes J on generalized forces, J = -L·F, where L is expected to be constant (as a prerequisite for linearity) and must not be a function of the force F (affinity) for Onsager reciprocity to apply. This paradigm is challenged by the ergodynamic concept of fundamentally non-linear isomorphic flux-force relations and is replaced by the generalized isomorphic flux-pressure relations. Flows I [MU·s-1] and forces F [J·MU-1] are conjugated pairs, the product of which yields power, I·F = P [J·s-1 = W]. Flux J is system-size specific flow, such that volume-specific flux times force yields volume-specific power, PV = J·F [W·m-3]. Then vectoral and vectorial transport processes are inherently non-linear flux-force relationships, with L = u·c in continuous transport processes along a gradient (c is the local concentration), or L = u·α (α is the free activity in a discontinuous transport process across a semipermeable membrane) — formally not different from (isomorphic to) scalar chemical reactions.
LinearityLinearity is the ability of the method to produce test results that are proportional, either directly or by a well-defined mathematical transformation, to the concentration of the analyte in samples within a given range. This property is inherent in the Beer-Lambert law for absorbance alone, but deviations occur in scattering media. It is also a property of fluorescence, but a fluorophore may not exhibit linearity, particularly over a large range of concentrations.
Liver mitochondria purificationArmstrong 2010 J Comp Physiol B: This paper describes a method for purification of rodent liver mitochdondria using relatively low-speed centrifugation through discontinuous Percoll gradients.
Living CommunicationsLCWith Living Communications, Bioenergetics Communications (BEC) takes the next step from pre-print to re-print. The concept of Living Communications pursues a novel culture of scientific communication, addressing the conflict between long-term elaboration and validation of results versus sharing without delay improved methods and preliminary findings. Following the preprint concept, updates may be posted on the BEC website of the resource publication. Updated versions of Living Communications are submitted for Open Peer Review with full traceability. In contrast to static papers, evolution of Living Communications is more resourceful and efficient than a ‘new’ publication. Living Communications provide a pathway along the scientific culture of lively debate towards tested and trusted milestones of research, from pre-print to re-print, from initial steps to next steps.
Living cellsceCell 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 (Nce) is the sum of viable cells (Nvce) and dead cells (Ndce). In contrast, the plasma membrane can be permeabilized selectively by mild detergents (digitonin), to obtain the 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.
Loe 2013 PLOS ONE
LuminescenceLuminescence is spontaneous emission of radiation from an electronically or vibrationally excited species not in thermal equilibrium with its environment (IUPC definition). An alternative definition is "Luminescence is emission of light by a substance not resulting from heat." Luminescence comprises many different pehnomena. Luminescence from direct photoexcitation of the emitting species is called photoluminescence. Both fluorescence and phosphorescence are forms of photoluminescence. In biomedical research also forms of chemiluminescence (e.g.the luciferin reaction) are used. In chemiluminescence the emission of radiation results from a chemical reaction. For other forms of luminescence see the IUPAC Gold Book.
MITOEAGLE in MitoGlobalMitoEAGLE
MITOEAGLE-representation.jpg

The objective of the MitoEAGLE network is to improve our knowledge on mitochondrial function in health and disease related to Evolution, Age, Gender, Lifestyle and Environment.

Magnesium GreenMgGMagnesium Green (MgG) is an extrinsic fluorophore that fluoresces when bound to Mg2+ and is used for measuring mitochondrial ATP production in mitochondrial preparations. Determination of mitochondrial ATP production is based on the different dissociation constants of Mg2+ for ADP and ATP, and the exchange of one ATP for one ADP across the mitochondrial inner membrane by the adenine nucleotide translocase (ANT). Using the dissociation constants for ADP-Mg2+ and ATP-Mg2+ and initial concentrations of ADP, ATP and Mg2+, the change in ATP concentration in the medium is calculated, which reflects mitochondrial ATP production.
MalateM
Malic acid

Malic acid, C4H6O5, occurs under physiological conditions as the anion malate2-, M, with pKa1 = 3.40 and pKa2 = 5.20. L-Malate is formed from fumarate in the TCA cycle in the mitochondrial matrix, where it is the substrate of malate dehydrogenase oxidized to oxaloacetate. Malate is also formed in the cytosol. It cannot permeate through the lipid bilayer of membranes and hence requires a carrier (dicarboxylate carrier, tricarboxylate carrier and 2-oxoglutarate carrier). Malate alone cannot support respiration of mt-preparations from most tissues, since oxaloacetate accumulates in the absence of pyruvate or glutamate. Malate is a type N substrate (N) required for the FAO-pathway. In the presence of anaplerotic pathways (e.g., mitochondrial malic enzyme, mtME) the capacity of the FAO-pathway can be overestimated due to a contribution of NADH-linked respiration, F(N) (see SUIT-002).

Malate dehydrogenasemtMDHMitochondrial malate dehydrogenase is localized in the mitochondrial matrix and oxidizes malate, generated from fumarate by fumarase, to oxaloacetate, reducing NAD+ to NADH+H+ in the TCA cycle. Malate is added as a substrate in most N-pathway control states.
Malate transport

Carriers for malate:

Malate-anaplerotic pathway control stateM
M

M: Malate alone does not support respiration of mt-preparations if oxaloacetate cannot be metabolized further in the absence of a source of acetyl-CoA. Transport of oxaloacetate across the inner mt-membrane is restricted particularly in liver. Mitochondrial citrate and 2-oxoglutarate (α-ketoglutarate) are depleted by antiport with malate. Succinate is lost from the mitochondria through the dicarboxylate carrier. OXPHOS capacity with malate alone is only 1.3% of that with Pyruvate&Malate in isolated rat skeletal muscle mitochondria. However, many mammalian and non-mammalian mitochondria have a mt-isoform of NADP+- or NAD(P)+-dependent malic enzyme (mtME), the latter being particularly active in proliferating cells. Then the anaplerotic pathway control state with malate alone (aN) supports high respiratory activities comparable to the NADH-linked pathway control states (N) with pyruvate&malate or glutamate&malate substrate combinations (PM-pathway control state, GM-pathway control state).

Malate-aspartate shuttleThe malate-aspartate shuttle involves the glutamate-aspartate carrier and the 2-oxoglutarate carrier exchanging malate2- for 2-oxoglutarate2-. Cytosolic and mitochondrial malate dehydrogenase and transaminase complete the shuttle for the transport of cytosolic NADH into the mitochondrial matrix. It is most important in heart, liver and kidney.
Malic enzymemtME

Malic enzyme (ME; EC 1.1.1.40) catalyzes the oxidative decarboxylation of L-malate to pyruvate with the concomitant reduction of the dinucleotide cofactor NAD+ or NADP+ and a requirement for divalent cations (Mg2+ or Mn2+) as cofactors.

NAD(P)+ + L-malate2- <--> NAD(P)H + pyruvate- + CO2

Three groups of ME are distinguished (i) NAD+- and (ii) NADP+-dependent ME specific for NAD+ or NADP+, respectively, and (iii) NAD(P)+- dependent ME with dual specificity for NAD+ or NADP+ as cofactor. Three isoforms of ME have been identified in mammals: cytosolic NADP+-dependent ME (cNADP-ME or ME1), mitochondrial NAD(P)+-dependent ME (mtNAD-ME or ME2; with NAD+ or NADP+ as cofactor, preference for NAD+ under physiological conditions), and mitochondrial NADP+-dependent ME (mtNADP-ME or ME3). mtNAD-ME plays an important role in anaplerosis when glucose is limiting, particularly in heart and skeletal muscle. Tartronic acid (hydroxymalonic acid) is an inhibitor of ME.

MalonateMnaMalonate (malonic acid) is a competitive inhibitor of succinate dehydrogenase (Complex II). Malonate is a substrate of malonyl-CoA synthase.
Malonyl-CoA synthaseMalonyl-CoA synthase or ACSF3 protein is a mitochondrial fatty-acyl-CoA synthase found in mammals. Traditionally, malonyl-CoA is formed from acetyl-CoA by the action of acetyl-CoA carboxylase. However, Witkowski et al (2011) showed that mammals express malonyl-CoA Synthase (ACSF3) with enzymatic activity in the presence of malonate (Complex II inhibitor) and methylmalonate.
Manage setups and templates - DatLabSetups and templates in DatLab can be renamed or deleted under Manage setups or Manage templates.
Manuscript template for MitoFit PreprintsManuscripts template for MitoFit Preprints and Bioenergetics Communications.
Mark informationMarks» See Marks - DatLab
Mark specifications - DatLabThe function Mark specifications is largely replaced by SUIT DL-Protocols and Instrumental DL-Protocols in DatLab 7.4. Mark specifications allow the user to rename Marks in the active plot and save/recall the settings. Rename marks individually by clicking into the horizontal bar, or use corresponding templates for renaming the entire sequence of marks.
Mark statistics - DatLabF2

DatLab 8: displays the statistical values (e.g. medians) for the marks set on the plots and allows copying and exporting them for data analysis. As default, the window opens and shows the information according to the current active plot and chamber selected.

DatLab 7: Mark statistics

Mark statistics - DatLab 7F2In Mark statistics one Plot is selected as a source for Marks over sections of time. Values (e.g. medians) are displayed for these time sections of the source plot and of all selected plots.
Marks - DatLab

DatLab 8: Marks define sections of a plot set by the user for calibrations, analysis, or to delete marked data points.

DatLab 7: Marks - DatLab 7

Matrix-ETSmatrix-ETSThe component of the electron transfer system located in the mitochondrial matrix (matrix-ETS) is distringuished from the ETS bound to the mt-inner membrane (membrane-ETS). Electron transfer and corresponding OXPHOS capacities are classically studied in mitochondrial preparations as oxygen consumption supported by various fuel substrates undergoing partial oxidation in the mt-matrix, such as pyruvate, malate, succinate, and others.
Measurement processA measurement process or a measurement is a set of operations to determine the value of a quantity.
Measuring equipmentA measuring equipment is a measuring instrument, software, measurement standard, reference material or auxiliary apparatus, or a combination thereof, necessary to realize a measurement process.
Medical deviceA medical device is an instrument, apparatus, implement, machine, contrivance, implant, in vitro reagent, or other similar or related article, including a component part, or accessory which is (1) intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease, in man or other animals, or (2) intended to affect the structure or any function of the body of man or other animals, and which does not achieve any of its primary intended purposes through chemical action within or on the body of man or other animals and which is not dependent upon being metabolized for the achievement of any of its primary intended purposes.
MelatoninaMTMelatonin (N-acetyl-5-methoxytryptamine, aMT) is a highly conserved molecule present in unicellular to vertebrate organisms. Melatonin is synthesized from tryptophan in the pinealocytes by the pineal gland and also is produced in other organs, tissues and fluids (extrapineal melatonin). Melatonin has lipophilic and hydrophilic nature which allows it to cross biological membranes. Therefore, melatonin is present in all subcellular compartments predominantly in the nucleus and mitochondria. Melatonin has pleiotropic functions with powerful antioxidant, anti-inflammatory and oncostatic effects with a wide spectrum of action particularly at the level of mitochondria. » MiPNet article
Membrane-bound ET pathwaymET-pathwayThe membrane-bound electron transfer pathway (mET pathway) consists in mitochondria mainly of respiratory complexes CI, CII, electron transferring flavoprotein complex (CETF), glycerophosphate dehydrogenase complex (CGpDH), and choline dehydrogenase, with convergent electron flow at the Q-junction (Coenzyme Q), and the two downstream respiratory complexes connected by cytochrome c, CIII and CIV, with oxygen as the final electron acceptor. The mET-pathway is the terminal (downstream) module of the mitochondrial ET pathway and can be isolated from the ET-pathway in submitochondrial particles (SmtP).
MersalylMersalyl (C13H17HgNO6) is an inhibitor of the Pi symporter.
Metabolic control analysis

Metabolic control analysis is a science focused on the understanding of metabolic regulation and control. In metabolism, the reductionist approach has allowed us to know which enzymes, metabolites and genes are involved in a metabolic pathway but this is not enough to understand how it is controlled, resulting in poor results from attempts to increase the rates of selected metabolic pathways. The control of the metabolism is the capacity to alter the metabolic state in response to an external signal. With this definition in mind, we will assess the metabolic control in terms of the strength of any of the responses to the external factor without making the assumption about the function or purpose of that response[1].

Bibliography:

1. David Fell. Frontiers in metabolism 2. Understanding the control of metabolism. Portland Press. 1997.
Metabolic control variableXA metabolic control variable X causes the transition between a background state Y (background rate YX) and a reference state Z (reference rate ZX). X may be a stimulator or activator of flux, inducing the step change from background to reference steady state (Y to Z). Alternatively, X may be an inhibitor of flux, absent in the reference state but present in the background state (step change from Z to Y).
MetermThe meter, symbol m, is the SI unit of the SI base quantity length l. It is defined by taking the fixed numerical value of the speed of light c in vacuum to be 299 792 458 when expressed in the unit m·s−1, where the second is defined in terms of the caesium frequency ΔνCs.
MetforminMetformin (dimethylbiguanide) is mainly known as an important antidiabetic drug which is effective, however, in a wide spectrum of degenerative diseases. It is an inhibitor of Complex I and glycerophosphate dehydrogenase complex.
Methylmalonic acidMmaMethylmalonic acid (Mma) is a common intermediate in many catabolic processes. In methylmalonic acidemia mitochondrial dysfunction can be observed, related to accumulation of Mma and associated with neurological symptoms.
MetrologyMetrology is the science of measurement, including all aspects both theoretical and practical with reference to measurements, whatever their uncertainty, and in whatever fields of science or technology they occur [SOURCE: VIM:1993, 2.2].
MiP-CollectionMiP-Collection

Mitochondrial Physiology - Historical Collection

Aims

The growing MiP-Collection aims at preserving scientific instruments that are of historical importance in the field of bioenergetics and mitochondrial physiology. The fast turnover of scientific equipment makes obsolete even comparatively recent instrumentation. The Oroboros O2k was the first commercial mitochondrial respirometer using a computer for data acquisition. Today, chart recorders are nearly forgotten. Due to limitations of storage space, unused scientific equipment is disposed of, despite its potential historical value. The disposal of some unique apparatus constitutes an irreversible loss to science and society, and to the continued appreciation of the foundations of our scientific discipline.

You may consider to make items of scientific historical interest in mitochondrial physiology available to the MiP-Collection. These items of the MiP-Collection may specifically include historically valuable

  • equipment and accessories,
  • books and symposium proceedings,
  • reprint collections,
  • pictures, slides, documents.
MiP03MiP03Mitochondrial Preservation Medium, MiP03, developed for preservation of isolated mitochondria.
MiPMapMiPMap
MiPMap

The project Mitochondrial Physiology Map (MiPMap) is initiated to provide an overview of mitochondrial properties in cell types, tissues and species. As part of Bioblast, MiPMap may be considered as an information synthase for Comparative Mitochondrial Physiology. Establishing a comprehensive database will require global input and cooperation.

A comparative database of mitochondrial physiology may provide the key for understanding the functional implications of mitochondrial diversity from mouse to man, and evaluation of altered mitochondrial respiratory control patterns in health and disease (Gnaiger 2009).

MiPNet-PublicationMiPNetMiPNet is the abbreviation for the OROBOROS Journal Mitochondrial Physiology Network, including chapters of the O2k-Manual, O2k-Procedures, O2k-Workshops, and other announcements, starting with MiPNet 01 in 1996. See also »MiPNet.
MiPSocietyMiP
MiPsociety

The Mitochondrial Physiology Society (MiP) has been founded to organize MiPconferences, MiPschools, and MiPworkshops worldwide. MiP has been founded at the Third Conference on Mitochondrial Physiology (MiP2003, Schroecken, Austria). The MiPsociety is an international organization, based in Europe and operating world-wide.

MiR05MiR05Mitochondrial respiration medium, MiR05, developed for oxygraph incubations of mitochondrial preparations. Respiration of living cells may be assessed in MiR05 by adding pyruvate (P) as an external source. MiR06 = MiR05 + catalase. MiR05Cr = MiR05 + creatine.
MiR05-Kit
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Mitochondrial Respiration Medium - MiR05-Kit, 1 vial; for a final volume of 250 mL

MiR05CrMiR05Cr

Mitochondrial respiration medium, MiR05Cr, developed for oxygraph incubations of mitochondrial preparations - permeabilized muscle fibers.

MiR05Cr = MiR05 + 20 mM creatine.

MiR06MiR06Mitochondrial respiration medium, MiR06, developed for oxygraph incubations of mitochondrial preparations. MiR06 = MiR05 plus catalase. MiR06Cr = MiR06 plus creatine.
MiR06CrMiR06Cr

Mitochondrial respiration medium, MiR06Cr, developed for oxygraph incubations of mitochondrial preparations - permeabilized muscle fibers.

MiR06Cr = MiR06 + 20 mM creatine.

MiRK03MiRK03Mitochondrial respiration medium, MiRK03, modified after a medium described by Komary 2010 Biochim Biophys Acta, intended for use as medium for H2O2 production measurement with Amplex Red.
Microbalance 120 g
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Microbalance max 120 g; 0.01 mg display; particularly for wet weight determination of permeabilized fibres.

Microbalance-Transport Case
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Microbalance transport case, not suitable for shipping

MicroplatesMicroplate readers allow large numbers of sample reactions to be assayed in well format microtitre plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 µL per well. a wide range of applications involve the use of fluorescence measurements , although they can also be used in conjunction with absorbance measurements.
Microsyringe\10 mm3 51/0.13 mm
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Hamilton Microsyringe\10 mm3 51/0.13 mm for manual titrations, 10 mm3 volume; fixed injection needle with rounded tip: 51 mm length, 0.13 mm inner diameter.

Microsyringe\100 mm3 51/0.41 mm
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Hamilton Microsyringe\100 mm3 51/0.41 mm for manual titrations, 100 mm3 volume; fixed needle with rounded tip: 51 mm length, 0.41 mm inner diameter. It is recommended for injections of suspensions of isolated mitochondria.

Microsyringe\200 mm3\TIP2k
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Microsyringe\200 mm3\TIP2k: Microinjection syringe for Titration-Injection microPump, 200 mm3 (µl), fixed injection needle with rounded tip, with spacers.

Microsyringe\25 mm3 51/0.15 mm
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Hamilton Microsyringe\25 mm3 51/0.15 mm for manual titrations, 25 mm3 volume; fixed needle with rounded tip: 51 mm length, 0.15 mm inner diameter.

Microsyringe\50 mm3 51/0.15 mm
Microsyringe 100 mm3 51 0.41 mm - Kopie.JPG

Hamilton Microsyringe\50 mm3 51/0.15 mm for manual titrations, 50 mm3 volume; fixed needle with rounded tip: 51 mm length, 0.15 mm inner diameter.

Microsyringe\500 mm3\TIP2k
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Microsyringe\500 mm3\TIP2k: Microinjection syringe for Titration-Injection microPump, 500 mm3 (µl), fixed injection needle with rounded tip, with spacers.

MicroxiamicroxMicroxia (deep hypoxia) is obtained when trace amounts of O2 exert a stimulatory effect on respiration above the level where metabolism is switched to a purely anaerobic mode.
MitObesity drugsBioactive mitObesity compounds are drugs and nutraceuticals with more or less reproducible beneficial effects in the treatment of diverse preventable degenerative diseases implicated in comorbidities linked to obesity, characterized by common mechanisms of action targeting mitochondria.
MitoActionMitoActionMitoAction.JPGThe mission of MitoAction is to improve quality of life for all who are affected by mitochondrial disorders through support, education and advocacy initiatives.
MitoCanada FoundationmitoCanada
MitoCanada

The MitoCanada Foundation.

The MitoCanada Foundation is Canada’s only not-for-profit organization focused on mitochondrial disease. Since its founding in 2010, MitoCanada has dedicated over $1 million to fund the work of leading Canadian scientists and to support national awareness and support programs.

The MitoCanada Foundation is committed to ensuring that those who live with mitochondrial disease are able to enjoy the best possible quality of life until there is a cure.

MitoFit DOI Data CenterMitoFit DOI DCThe MitoFit DOI Data Center is responsible for the provision of digital identifiers, for the storage and ensuring the persistence of the scientific objects, the provision of access, review process and maintenance of the Metadata, and quality control.
MitoFit PreprintsMitoFit Prep
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MitoFit Preprints is an Open Access preprint server for mitochondrial physiology and bioenergetics.

MitoFit protocolsMitoFit protocols are moderated by the MitoFit moderators (MitoFit team), either as protocols with direct reference to publications available to the scientific communicty, or protocols additionally described and made available in Bioblast with full information on authors (including contact details), author contributions, and editor (moderator) in charge. This aims at a comprehensive MitoFit data repository, which will require global input and cooperation.
MitoFit registered projectMitoFit-RPMitoFit registered projects are announced with reference to MitoFit protocols as publicly deposited protocols. Project registration is a two-phase process. Guidelines will be defined. (1) Pre-registration of a project requires submission to a MitoFit moderator (editor), including protocol details with reference to MitoPedia protocols, or with submission of protocols for publication (Open Access) in MitoPedia. The MitoFit (Bioblast) editors will edit the submitted protocols (layout) and insert into Bioblast submitted pre-registrations and protocols. (2) MitoFit moderators (editors) will set up a MitoFit accreditation panel, in which the registrant will be included (perhaps not in the long run, to avoid conflict of interests) and/or for which the registrant can suggest delegates (compare peer review). Accredited MitoFit protocols are labelled as MitoFit accredited, and the pre-registered MitoFit project becomes labelled and listed as MitoFit registered project (MitoFit accredited). This is possible before (advance registration), during progress, and after completion of a study (post-registration). A MitoFit registered project receives a code for feeding data into the MitoFit data repository.
MitoGlobalPlayer invitation
MitoKit-CII
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Cell permeable prodrugs, composed of MitoKit-CII/Succinate-nv and MitoKit-CII/Malonate-nv, stimulates (Snv) or inhibits (Mnanv) mitochondrial respiration in CI-deficient human blood cells, fibroblasts and heart fibres, acting on Complex II of the electron transfer system.

MitoKit-CII/Malonate-nvMnanvMitoKit-CII/Malonate-nv (diacetoxymethyl malonate) is a plasma membrane-permeable prodrug (permeable malonate; Mnanv) that diffuses across the plasma membrane. Cleavage of diacetoxymethyl groups is mediated by intracellular esterases, thus releasing malonate in the intracellular space. Abliva #: 01-161-s2
MitoKit-CII/Succinate-nvSnvMitoKit-CII/Succinate-nv (diacetoxymethyl succinate) is a plasma membrane-permeable prodrug (permeable succinate; Snv) that diffuses across the plasma membrane. Cleavage of diacetoxymethyl groups is mediated by intracellular esterases, thus releasing succinate in the intracellular space. Abliva #: 01-118-s4
MitoOx1MitoOx1Mitochondrial respiration medium, MitoOx1, used by the Budapest groups for respirometry und Amplex Red trials.
MitoOx2MitoOx2Mitochondrial respiration medium, MitoOx2, developed for oxygraph incubations of mitochondrial preparations to measure the H2O2 production. MitoOx2 yields a higher optical sensitivity and lower "drift" (oxidation of the fluorophore precurcor without H2O2 present) for Amplex UltraRed(R) than e.g. MiR05.
MitoPedia
MitoPedia
MitoPedia: Concepts and methods
MitoPedia: Enzymes
MitoPedia: Ergodynamics
MitoPedia: Fluorometry
MitoPedia: Gentle Science
MitoPedia: Inhibitors
MitoPedia: Media for respirometry
MitoPedia: MiP and biochemistry
MitoPedia: MiP concepts
MitoPedia: O2k hardware
MitoPedia: Oroboros QM
MitoPedia: Permeabilization agents
MitoPedia: Preprints and history
MitoPedia: Respiratory control ratios
MitoPedia: Respiratory states
MitoPedia: Respirometry
MitoPedia: SUIT A
MitoPedia: SUIT B
MitoPedia: SUIT C
MitoPedia: Sample preparations
MitoPedia: Spectrophotometry
MitoPedia: Substrates and metabolites
MitoPedia: Uncouplers
MitoSOX

MitoSOXTM is the version of the hydroetidine designed to target mitochondria in live cells for the detection of superoxide (O2•-). The oxidation of the compound by O2•- is easily detected in the red spectrum. One of the advantages of MitoSOXTM is its selectivity for O2•- but not for other reactive oxygen species or reactive nitrogen species.

• Readily oxidized by superoxide but not by other ROS- or RNS-generating systems
Absorption/emission maxima: ~510/580 nm
• Use for live cell imaging
• Rapidly and selectively targeted to the mitochondria


MitoSOXTM has been widely used in life cell imaging but it is not free of problems and should be used cautiously. For example, it has been highlighted that the use of potentiometric dyes which accumulates into the mitochondria due to its moiety with Tetraphenylphosphonium, confers a membrane potential sensitivity that creates a series of artifacts and problems not often considered.

MitochondriamtMitochondria (Greek mitos: thread; chondros: granule) are small structures within cells, which function in cell respiration as powerhouses or batteries. Mitochondria belong to the bioblasts of Richard Altmann. Abbreviation: mt, as generally used in mtDNA. Singular: mitochondrion (bioblast); plural: mitochondria (bioblasts).
Mitochondria Interest GroupMIG


MIG.gif

The Mitochondria Interest Group (MIG) is an Inter-Institute Interest Group at the National Institutes of Health (NIH), with members worldwide! MIG is concerned with all aspects of the mitochondrion and diseases in which the mitochondrion is involved. We hold monthly meetings, usually on the second Monday of the month (except when it is a Federal holiday or other special exceptions).

MITOCHONDRIA-L@LIST.NIH.GOV is an Email list moderated by Ph.D. Steven Zullo as an interactive information platform, with free subscritpion to this mitochondrial network. List members are reminded of their responsibility to critically evaluate the content of the postings. The information, opinions, data, and statements contained herein are not necessarily those of the U. S. Government, the National Institutes of Health (NIH), or MIG and should not be interpreted, acted on or represented as such.

Mitochondria Research SocietyMRS
MRS LOGO.JPG

The Mitochondria Research Society (MRS) is a nonprofit international organization of scientists and physicians. The purpose of MRS is to find a cure for mitochondrial diseases by promoting research on basic science of mitochondria, mitochondrial pathogenesis, prevention, diagnosis and treatment through out the world.

Mitochondria-Targeted Drug Developmenthansonwade
Mitochondria-Targeted Drug Development

The Mitochondria-Targeted Drug Development Summit was first established in 2021, as an online conference. Due to its success and unmatched focus, the 2nd edition returns to Boston this March 2022. This is the only industry-led meeting that unites key stakeholders under a mutual and ambitious objective of accelerating the discovery and development of novel drugs that target mitochondrial functions for chronic, primary mitochondrial diseases, muscular dystrophy, metabolic disorders, and neurodegenerative diseases. Join our speakers from GenSight Biologics, Abliva, Reneo Pharma, Mito BioPharma, Mitokinin and more with exciting networking opportunities, panel discussions and dedicated roundtables.

Mitochondrial ATP-sensitive K+ channelmtKATPThe mitochondrial ATP-sensitive K+ channel (mtKATP or mitoKATP).
Mitochondrial European Education TrainingMEET
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The Mitochondrial European Education Training (MEET)

MEET is a project started on January 2013. MEET network is composed by a multi-partner project that intends to mobilize the critical mass of expertise, by linking partners from 8 different countries, among which 8 world-leading basic science and clinical centers of excellence, an 1 SME with direct interest in mitochondrial medicine and 3 associated partners that provide for all trainees no-scientific training. MEET is training 11 ESRs and 3 ERs coming from all over the world supervised in their research by 15 mentors and by their collaborators. MEET combine the efforts of leading clinicians with those of more basic oriented groups and will have important implications for the comprehension and treatment of mitochondria-related pathologies.

Mitochondrial Medicine SocietyMMS
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The Mitochondrial Medicine Society (MMS) was founded in 2000 and represents an international group of physicians, researchers and clinicians working towards the better diagnosis, management, and treatment of mitochondrial diseases.

Mitochondrial Physiology NetworkMitochondr physiol network, MiPNetThe Mitochondrial Physiology Network is the on-line Oroboros journal.
Mitochondrial Research Guild
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The Mitochondrial Research Guild is a special interest guild of Seattle Children's Hospital. The guild was founded by a group of families in the Seattle area that are working together to raise awareness, promote research, and improve the quality of medical care that is available to children that are dealing with the devastating and potentially life threatening effects of mitochondrial disease.

Mitochondrial competencemt-competence; MitoCom

Mitochondrial metabolic competence is the organelle's capacity to provide adequate amounts of ATP in due time, by adjusting the mt-membrane potential, mt-redox states and the ATP/ADP ratio according to the metabolic requirements of the cell.

The term mitochondrial competence is also known in a genetic context: Mammalian mitochondria possess a natural competence for DNA import.

MitoCom_O2k-Fluorometer is a Mitochondrial Competence network, the nucleus of which is formed by the K-Regio project MitoCom Tyrol.

Mitochondrial concentrationCmtEMitochondrial concentration is CmtE = mtE·V-1 [mtEU·m-3]. mt-Concentration is an experimental variable, dependent on sample concentration.
Mitochondrial contentmtENXMitochondrial content per object X is mtENX = mtE·NX-1 [mtEU·x-1].
Mitochondrial densityDmtESpecific mitochondrial density is DmtE = mtE·mX-1 [mtEU·kg-1]. If the amount of mitochondria, mtE, is expressed as mitochondrial mass, then DmtE is the mass fraction of mitochondria in the sample. If mtE is expressed as mitochondrial volume, Vmt, and the mass of sample, mX, is replaced by volume of sample, VX, then DmtE is the volume fraction of mitochondria in the sample.
Mitochondrial free radical theory of agingMFRTAThe mitochondrial free radical theory of aging goes back to Harman (1956) and ranks among the most popular theories of aging. It is based on postulates which are not unequivocally supported by observation (Bratic, Larsson 2013): (i) Mitochondrial ROS production increases with age caused by progressive mitochondrial dysfunction; (ii) antioxidat capacity declines with age; (iii) mutations of somatic mtDNA accumulate during aging; (iv) a vicious cycle occurs of increased ROS production caused by mtDNA mutations and degenerated mt-function, and due to ROS-induced ROS production.
Mitochondrial inner membranemtIMThe mitochondrial inner membrane mtIM is the structure harboring the membrane-bound electron transfer system ETS including the respiratory complexes working as hydrogen ion pumps, the mt-phosphorylation system including the hydrogen ion pump ATP synthase, several substrate transporters involved in the electron transfer pathway, and a variety of other ion pumps that carry proton charge (Ca2+, Mg2+). The protonmotive force is the electrochemical potential difference across the mtIM generated by the hydrogen ion pumps of the .
Mitochondrial markermt-markerMitochondrial markers are structural or functional properties that are specific for mitochondria. A structural mt-marker is the area of the inner mt-membrane or mt-volume determined stereologically, which has its limitations due to different states of swelling. If mt-area is determined by electron microscopy, the statistical challenge has to be met to convert area into a volume. When fluorescent dyes are used as mt-marker, distinction is necessary between mt-membrane potential dependent and independent dyes. mtDNA or cardiolipin content may be considered as a mt-marker. Mitochondrial marker enzymes may be determined as molecular (amount of protein) or functional properties (enzyme activities). Respiratory capacity in a defined respiratory state of a mt-preparation can be considered as a functional mt-marker, in which case respiration in other respiratory states is expressed as flux control ratios. » MiPNet article
Mitochondrial marker enzymesMitochondrial marker enzymes are enzymes that are specifically present in mitochondria, in the mt-matrix, the inner mt-membrane, the inter-membrane space, or the outer mt-membrane.
Mitochondrial matrixmt-matrixThe mitochondrial matrix (mt-matrix) is enclosed by the mt-inner membrane mtIM. The terms mitochondrial matrix space or mitochondrial lumen are used synonymously. The mt-matrix contains the enzymes of the tricarboxylic acid cycle, fatty acid oxidation and a variety of enzymes that have cytosolic counterparts (e.g. glutamate dehydrogenase, malic enzyme). Metabolite concentrations, such as the concentrations of fuel substrates, adenylates (ATP, ADP, AMP) and redox systems (NADH), can be very different in the mt-matrix, the mt-intermembrane space, and the cytosol. The finestructure of the gel-like mt-matrix is subject of current research.
Mitochondrial membrane potentialmtMP, ΔΨp+, ΔelFep+ [V]

The mitochondrial membrane potential difference, mtMP or ΔΨp+ = ΔelFep+, is the electric part of the protonmotive force, Δp = ΔmFeH+.

ΔelFep+ = ΔmFeH+ - ΔdFeH+
ΔΨp+ = Δp - ΔµH+·(zH+·F)-1

ΔΨp+ is the potential difference across the mitochondrial inner membrane (mtIM), expressed in the electric unit of volt [V]. Electric force of the mitochondrial membrane potential is the electric energy change per ‘motive’ charge or per charge moved across the transmembrane potential difference, with the number of ‘motive’ charges expressed in the unit coulomb [C].

Mitochondrial outer membranemtOMThe mitochondrial outer membrane is the incapsulating membrane which is osmotically not active and contains the cytochrome b5 enzyme similar to that found in the endoplasmatic reticulum, the translocases of the outer membrane, monoaminooxidase, the palmitoyl-CoA synthetase and carnytil-CoA transferase 1.
Mitochondrial preparationsmtprepMitochondrial preparations (mtprep) are isolated mitochondria (imt), tissue homogenate (thom), mechanically or chemically permeabilized tissue (permeabilized fibers, pfi) or permeabilized cells (pce). In mtprep the plasma membranes are either removed (imt) or mechanically (thom) and chemically permeabilized (pfi), while mitochondrial functional integrity and to a large extent mt-structure are maintained in incubation media optimized to support mitochondrial physiological performance. According to this definition, submitochondrial particles (smtp) are not a mtprep, since mitochondrial structure is altered although specific mitochondrial functions are preserved.
Mitochondrial respirationIntegrative measure of the dynamics of complex coupled metabolic pathways, including metabolite transport across the mt-membranes, TCA cycle function with electron transfer through dehydrogenases in the mt-matrix, membrane-bound electron transfer mET-pathway, the transmembrane proton circuit, and the phosphorylation system.
Mitochondrial respiration media: comparisonMiRMitochondrial respiratory capacity and control are compared in different mitochondrial respiration media, MiRs, to evaluate the quality of MiRs in preserving mitochondrial function and to harmonize results obtained in various studies using different MiRs. In some cases alterations of the formulation are incorporated to optimize conditions for the simultaneous measurement of multiple parameters, e.g. respiration and ROS production.
Mitochondrial states and rates - terminology beyond MitoEAGLE 2020States and rates666 coauthors of the 'MitoEAGLE white paper' [1] collaborated to reach a consensus on terminology related to mitochondrial respiratory states and rates. This page is intended to prepare a questionnaire and follow-up publication.
Mitochondrial transcription factor ATFAMThe transcription factor A is a gene that encodes a mitochondrial transcription factor that is a key activator of mitochondrial transcription as well as a participant in mitochondrial genome replication. TFAM is downstream of PGC-1alpha.
MitophagyAutophagy (self-eating) in general is viewed as a degradation process which removes non-essential or damaged cellular constituents. » MiPNet article
ModelA model regarding databases is the representation of a real world object in a computer understandable language. A model can be defined by the structure of its dataset and the relations to other models.
Molar massM [kg·mol-1]; [g·mol-1]

Molar mass M is the mass of a chemical compound divided by its amount-of-substance measured in moles. It is defined as MB = m/nB, where m is the total mass of a sample of pure substance and nB is the amount of substance B given in moles. The definition applies to pure substance. The molar mass allows for converting between the mass of a substance and its amount for bulk quantities. It is calculated as the sum of standard atomic weights of all atoms that form one entity of the substance.

The appropriate SI base units is kg·mol-1. However, for historical as well as usability reasons, g·mol-1 is almost always used instead.

MolemolThe mole [mol] is the SI base unit for the amount of substance of a system that contains 6.02214076·1023 specified elementary entities (see Avogadro constant). The elementary entities must be specified and may be atoms, molecules, ions, electrons, other particles, or specified groups of such particles.
Monoamine oxidaseMAOMonoamine oxidases are enzymes bound to the outer membrane of mitochondria and they catalyze the oxidative deamination of monoamines. Oxygen is used to remove an amine group from a molecule, resulting in the corresponding aldehyde and ammonia. Monoamine oxidases contain the covalently bound cofactor FAD and are, thus, classified as flavoproteins.
Motic Microscope
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Motic Microscope SMZ-171 TLED: for preparation of permeabilized fibres; compact and light stereo microscope, Greenough optical system, switching power supply for use worldwide (100-240V); including auxiliary ESD objective 2.0X(38.6mm).

Motive entityXtr [MU]
From Gnaiger 2020 BEC MitoPathways

.

A motive entity Xtr is an entity involved in a transformation including spacial transfer. Motive entities (transformants) are expressed in different motive units [MU] depending on the energy transformation under study and the chosen format. Flows are defined as advancement in terms of stoichiometric motive entities per time. Isomorphic forces are partial derivatives of Gibbs energy per advancement. Ions carrying a positive charge (cations) or negative charge (anions) may be considered as a paradigm of motive entities, since Faraday did not coin but introduced the term 'ion', which is old Greek for 'going' — advancing to the cathode or anode and thus generating an electric current.

Motive unitMU

The motive unit [MU] is the variable SI unit in which the motive entity (transformant) of a transformation is expressed, which depends on the energy transformation under study and on the chosen format. Fundamental MU for electrochemical transformations are:

  • MU = x, for the particle or molecular format, N
  • MU = mol, for the chemical or molar format, n
  • MU = C, for the electrical format, e;

For the protonmotive force the motive entity is the proton with charge number z=1. The protonmotive force is expressed in the electrical or molar format with MU J/C=V or J/mol=Jol, respectively. The conjugated flows, I, are expressed in corresponding electrical or molar formats, C/s = A or mol/s, respectively.

The charge number, z, has to be considered in the conversion of motive units (compare Table below), if a change not only of units but a transition between the entity elementary charge and an entity with charge number different from unity is involved (e.g., O2 with z=4 in a redox reaction). The ratio of elementary charges per reacting O2 molecule (zO2=4) is multiplied by the elementary charge (e, coulombs per proton), which yields coulombs per O2 [C∙x-1]. This in turn is multiplied with the Avogadro constant, NA (O2 molecules per mole O2 [x∙mol-1]), thus obtaining for zeNA the ratio of elementary charges [C] per amount of O2 [mol-1]. The conversion factor for O2 is 385.94132 C∙mmol-1.

Mouse control: MarkCtrl+M

The mark mode is active by default, can be selected in the menu or by [Ctrl+M]. If Mouse control: Mark is enabled, specific sections of the experiment can be marked in each plot. Usually, marks are set on the plot for oxygen concentration for calibration, whereas marks on the plot for oxygen flux are set for exporting the median or average of flux to a table.

»More details: Marks - DatLab.

Mouse control: ZoomCtrl+ZSelect Mouse Control: Zoom in the Graph-menu or press [Ctrl+Z].
MtOMmtOMThe mitochondrial outer membrane
MultiSensor-Connector
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MultiSensor-Connector: for separate reference electrode and ISE; only for O2k-Series B and Series C with MultiSensor electronic upgrading before 2011.

MultiSensor-Preamplifier 1/100
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MultiSensor-Preamplifier 1/100: Required only for O2k-Series A-C, for application of NO (or other amperometric) sensors (single chamber mode of application).

Multicomponent analysisSimilarly to the least squares method, multicomponent analysis makes use of all of the data points of the spectrum in order to analyse the concentration of the component parts of a measured spectrum. To do this, two or more reference spectra are combined using iterative statistical techniques in order to achieve the best fit with the measured spectrum.
MyxothiazolMyxMyxothiazol Myx is an inhibitor of Complex III (CIII). CIII also inhibits CI. Myxothiazol binds to the Qo site of CIII (close to cytochrome bL) and inhibits the transfer of electrons from reduced QH2 to the Rieske iron sulfur protein.
N-ethylmaleimideNemN-ethylmaleimide is an organic compound that is derived from maleic acid and blocks endogenous Pi transport.
N-junction
N-junction

The N-junction is a junction for convergent electron flow in the electron transfer pathway (ET-pathway) from type N substrates (further details »N-pathway control state) through the mt-NADH pool to Complex I (CI), and further transfer through the Q-junction to Complex III (CIII). Representative type N substrates are pyruvate (P), glutamate (G) and malate (M). The corresponding dehydrogenases (PDH, GDH, MDH) and some additional TCA cycle dehydrogenases (isocitrate dehydrogenase, oxoglutarate dehydrogenase generate NADH, the substrate of Complex I (CI). The concept of the N-junction and F-junction provides a basis for defining categories of SUIT protocols based on Electron-transfer-pathway states.

N/NS pathway control ratioN/NSThe N/NS pathway control ratio is obtained when succinate is added to N-linked respiration in a defined coupling state. N and NS are abbreviations for respiration in the N-pathway control state (with pyruvate, glutamate, malate, or other ETS competent N-linked substrate combinations) and the NS-pathway control state (N in combination with succinate). NS indicates respiration with a cocktail of substrates supporting the N- and S-pathways.
N/S pathway control ratioN/SThe N/S pathway control ratio is obtained from SUIT protocols when the N-pathway flux and S-pathway flux are measured in the same coupling control state. The N/S pathway control ratio may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The S-pathway control state may be selected preferentially as reference state, if mitochondria are studied with respect to N-pathway injuries.
NADHNADHNAD+ and NADH: see Nicotinamide adenine dinucleotide.
NADH calibration - DatLabNADH calibration
NADH electron transfer-pathway stateN
N-junction

The NADH electron transfer-pathway state (N) is obtained by addition of NADH-linked substrates (CI-linked), feeding electrons into the N-junction catalyzed by various mt-dehydrogenases. N-supported flux is induced in mt-preparations by the addition of NADH-generating substrate combinations of pyruvate (P), glutamate (G), malate (M), oxaloacetate (Oa), oxoglutarate (Og), citrate, hydroxybutyrate. These N-junction substrates are (indirectly) linked to Complex I by the corresponding dehydrogenase-catalyzed reactions reducing NAD+ to NADH+H+ + H+. The most commonly applied N-junction substrate combinations are: PM, GM, PGM. The malate-anaplerotic pathway control state (M alone) is a special case related to malic enzyme (mtME). The glutamate-anaplerotic pathway control state (G alone) supports respiration through glutamate dehydrogenase (mtGDH). Oxidation of tetrahydrofolate is a NAD(P)H linked pathway with formation of formate. In mt-preparations, succinate dehydrogenase (SDH; CII) is largely substrate-limited in N-linked respiration, due to metabolite depletion into the incubation medium. The residual involvement of S-linked respiration in the N-pathway control state can be further suppressed by the CII-inhibitor malonic acid). In the N-pathway control state ET pathway level 4 is active.

NADH fluorescenceReduced nicotinamide adenine dinucleotide (NADH) is amongst the intrinsic fluorophores and can be used as an intracellular indicator of hypoxia. The excitation wavelength is 340 nm and emission is at 460 nm.
NADH-Module
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The NADH-Module, is a component of the NextGen-O2k for simultaneous measurement of oxygen consumption and NAD(P)H autofluorescence. NAD(P)H autofluorescence is used to evaluate the redox state of the NAD(P)H-pool. The NADH-Module incorporates an UV light and NADH-Sensors which include a photodiode and specific filters.

NADH-Sensor
NADH sesnor 003.png

The NADH-Sensor has been developed as a part of the NADH-Module for simultaneous monitoring of oxygen consumption and NADH redox state. The NADH-Sensor is composed of a photodiode and equipped with three supergel R370 Italian blue filters (Rosco, US).

NCD-RisC 2017 Lancet
NS e-inputNS, CI&IINS e-input or the NS-pathway control state is electron input from a combination of substrates for the N-pathway control state and S-pathway control state through Complexes CI and CII simultaneously into the Q-junction. NS e-input corresponds to TCA cycle function in vivo, with convergent electron flow through the Electron transfer pathway. In mt-preparations, NS e-input requires addition not only of NADH- (N-) linked substrates (pyruvate&malate or glutamate&malate), but of succinate (S) simultaneously, since metabolite depletion in the absence of succinate prevents a significant stimulation of S-linked respiration. For more details, see: Additive effect of convergent electron flow.
NS-N pathway control efficiencyjNS-N; jCI&II-CIThe NS-N pathway control efficiency, jNS-N = 1-N/NS, expresses the fractional change of flux when succinate is added to the N-pathway control state in a defined coupling-control state.
NS-S pathway control efficiencyjNS-S

The NS-S pathway control efficiency expresses the relative stimulation of succinate supported respiration (S) by NADH-linked substrates (N), with the S-pathway control state as the background state and the NS-pathway control state as the reference state. In typical SUIT protocols with type N and S substrates, flux in the NS-pathway control state NS is inhibited by rotenone to measure flux in the S-pathway control state, S(Rot) or S. Then the NS-S pathway control efficiency in the ET-coupling state is

j(NS-S)E = (NSE-SE)/NSE

The NS-S pathway control efficiency expresses the fractional change of flux in a defined coupling-control state when inhibition by rotenone is removed from flux under S-pathway control in the presence of a type N substrate combination. Experimentally rotenone Rot is added to the NS-state. The reversed protocol, adding N-substrates to a S-pathway control background does not provide a valid estimation of S-respiration with succinate in the absence of Rot, since oxaloacetate accumulates as a potent inhibitor of succinate dehydrogenase CII.

NS-pathway control stateNS, CI&II
NS-pathway control

NS-pathway control is exerted in the NS-linked substrate state (flux in the NS-linked substrate state, NS; or Complex I&II, CI&II-linked substrate state). NS-OXPHOS capacity provides an estimate of physiologically relevant maximum mitochondrial respiratory capacity. NS is induced in mt-preparations by addition of NADH-generating substrates (N-pathway control state in combination with succinate (Succinate pathway; S). Whereas NS expresses substrate control in terms of substrate types (N and S), CI&II defines the same concept in terms of convergent electron transfer to the Q-junction (pathway control). NS is the abbreviation for the combination of NADH-linked substrates (N) and succinate (S). This physiological substrate combination is required for partial reconstitution of TCA cycle function and convergent electron-input into the Q-junction, to compensate for metabolite depletion into the incubation medium. NS in combination exerts an additive effect of convergent electron flow in most types of mitochondria.

NSGpNSGp
Convergent electron flow

MitoPathway control state: NSGp

Pyruvate &/or Glutamate & Malate & Succinate & Glycerophosphate.

SUIT protocol: SUIT-038

This substrate combination supports convergent electron flow to the Q-junction.

NagarseNagarse is a broad specifity protease from bacteria used to promote breakdown of the cellular structure of "hard" tissues such as skeletal muscle or heart mucsle that cannot be homogenized easily without treatment with a protease. Nagarse is frequently used in protocols for isolating mitochondria from muscle tissue.
National Academies of Sciences, Engineering, and Medicine 2023 BMI and beyond
National Academies of Sciences, Engineering, and Medicine 2024 Body composition and obesity
National Standards BodyA National Standards Body is the national member of the International Organization for Standardization (ISO).
Natoms Onatoms O0.5 nmol O2; in bioenergetics a variety of expressions is used for units of amount of half a nmol molecular oxygen (natoms oxygen; natoms O; ng.atom O; nmol O), with the identical meaning: 0.5 nmol O2.
Net P/E control ratio(P-L)/Enet P/E control ratio The net P/E control ratio, (P-L)/E, expresses the OXPHOS capacity (corrected for LEAK respiration) as a fraction of ET capacity. The net P/E control ratio remains constant, if dyscoupling is fully compensated by an increase of OXPHOS capacity and net OXPHOS capacity P-L, P-L, is maintained constant.
Net R/E control ratio(R-L)/Enet R/E control ratio The net R/E control ratio, (R-L)/E, expresses phosphorylation-related respiration (corrected for LEAK respiration) as a fraction of ET capacity. The net R/E control ratio remains constant, if dyscoupling is fully compensated by an increase of ROUTINE respiration and R-L net ROUTINE capacity, R-L, is maintained constant.
NeuroconNeurocon
Neurocon LOGO.JPG

Neurocon is an Indian society organizing international conferences on neurodegenerative and neurodevelopmental diseases.

Nicotinamide adenine dinucleotideNADHNicotinamide adenine dinucleotide, NAD+ and NADH (pyridine nucleotide coenzymes, NAD and NADP), is an oxidation-reduction coenzyme (redox cofactor; compare FADH2). In the NADH electron transfer-pathway state fuelled by type N-substrates, mt-matrix dehydrogenases generate NADH, the substrate of Complex I (CI). The reduced N-substrate RH2 is oxidized and NAD+ is reduced to NADH,:::: RH2 + NAD+ → NADH + H+ + RThe mt-NADH pool integrates the activity of the TCA cycle and various matrix dehydrogenases upstream of CI, and thus forms a junction or funnel of electron transfer to CI, the N-junction (compare F-junction, Q-junction). NAD+ and NADH are not permeable through the mt-inner membrane, mtIM. Therefore, an increase of mitochondrial respiration after the addition of NADH may indicate an alteration of the mtIM integrity. Cytosolic NADH is effectively made available for mitochondrial respiration through the malate-aspartate shuttle or glycerophosphate dehydrogenase Complex.
NigericinNigericin is a H+/K+ antiporter, which allows the electroneutral transport of these two ions in opposite directions across the mitochondrial inner membrane following the K+ concentration gradient. In the presence of K+, nigericin decreases pH in the mitchondrial matrix, thus, almost fully collapses the transmembrane ΔpH, which leads to the compensatory increase of the electric mt-membrane potential. Therefore, it is ideal to use to dissect the two components of the protonmotive force, ΔpH and mt-membrane potential. It is recommended to use the lowest possible concentration of nigericin, which creates a maximal mitochondrial hyperpolarization. In the study of Komlodi 2018 J Bioenerg Biomembr, 20 nM was applied on brain mitochondria isolated from guinea-pigs using 5 mM succinate in the LEAK state which caused maximum hyperpolarisation, but did not fully dissipate the transmembrane ΔpH. Other groups (Selivanov et al 2008; Lambert et al 2004), however, used 100 nM nigericin, which in their hands fully collapsed transmembrane ΔpH using succinate as a respiratory substrate on isolated rat brain and skeletal muscle in the LEAK state.
Nitric oxide synthaseNOSNitric oxide synthase, NOS, catalyzes the production of nitric oxide (NO•), which is a reactive nitrogen species. There are four types of NOS: neuronal NOS (nNOS), endothelial NOS (eNOS), inducible NOS (iNOS) and mitochondrial NOS (mtNOS).
NoiseIn fluorometry and spectrophotometry, noise can be attributed to the statistical nature of the photon emission from a light source and the inherent noise in the instrument’s electronics. The former causes problems in measurements involving samples of analytes with a low extinction coefficient and present only in low concentrations. The latter becomes problematic with high absorbance samples where the light intensity emerging from the sample is very small.
Noncoupled respirationE

E.jpg Noncoupled respiration is distinguished from general (pharmacological or mechanical) uncoupled respiration, to give a label to an effort to reach the state of maximum uncoupler-activated respiration without inhibiting respiration. Noncoupled respiration, therefore, yields an estimate of ET capacity. Experimentally uncoupled respiration may fail to yield an estimate of ET capacity, due to inhibition of respiration above optimum uncoupler concentrations or insufficient stimulation by sub-optimal uncoupler concentrations. Optimum uncoupler concentrations for evaluation of (noncoupled) ET capacity require inhibitor titrations (Steinlechner-Maran 1996 Am J Physiol Cell Physiol; Huetter 2004 Biochem J; Gnaiger 2008 POS).

Noncoupled respiration is maximum electron flow in an open-transmembrane proton circuit mode of operation (see ET capacity). » MiPNet article

NormA norm is a rule that is enforced by members of a community.
Normalization of rateNormalization of rate (respiratory rate, rate of hydrogen peroxide production, growth rate) is required to report experimental data. Normalization of rates leads to a diversity of formats. Normalization is guided by physicochemical principles, methodological considerations, and conceptual strategies. The challenges of measuring respiratory rate are matched by those of normalization. Normalization of rates for: (1) the number of objects (cells, organisms); (2) the volume or mass of the experimental sample; and (3) the concentration of mitochondrial markers in the instrumental chamber are sample-specific normalizations, which are distinguished from system-specific normalization for the volume of the instrumental chamber (the measuring system). Metabolic flow, I, per countable object increases as the size of the object is increased. This confounding factor is eliminated by expressing rate as sample-mass specific or sample-volume specific flux, J. Flow is an extensive quantity, whereas flux is a specific quantity. If the aim is to find differences in mitochondrial function independent of mitochondrial density, then normalization to a mitochondrial marker is imperative. Flux control ratios and flux control efficiencies are based on internal normalization for rate in a reference state, are independent of externally measured markers and, therefore, are statistically robust.
NormothermiaNormothermia in endotherms is a state when body core temperature is regulated within standard limits. In humans, normothermia is considered as a body temperature of 36.4 to 37.8 °C. Normothermia, however, has a different definition in the context of ectotherms. » MiPNet article
Normoxianormox
Oxia

Normoxia is a reference state, frequently considered as air-level oxygen pressure at sea level (c. 20 kPa in water vapor saturated air) as environmental normoxia. Intracellular tissue normoxia is variable between organisms and tissues, and intracellular oxygen pressure is frequently well below air-level pO2 as a result of cellular (mainly mitochondrial) oxygen consumption and oxygen gradients along the respiratory cascade. Oxygen pressure drops from ambient normoxia of 20 kPa to alveolar normoxia of 13 kPa, while extracellular normoxia may be as low as 1 to 5 kPa in solid organs such as heart, brain, kidney and liver. Pericellular pO2 of cells growing in monolayer cell cultures may be hypoxic compared to tissue normoxia when grown in ambient normoxia (95 % air and 5 % CO2) and a high layer of culture medium causing oxygen diffusion limitation at high respiratory activity, but pericellular pO2 may be effectively hyperoxic in cells with low respiratory rate with a thin layer of culture medium (<2 mm). Intracellular oxygen levels in well-stirred suspended small cells (5 - 7 mm diameter; endothelial cells, fibroblasts) are close to ambient pO2 of the incubation medium, such that matching the experimental intracellular pO2 to the level of intracellular tissue normoxia requires lowering the ambient pO2 of the medium to avoid hyperoxia.

Notified BodyA Notified Body is an organisation designated by an EU country to assess the conformity of certain products before being placed on the market.
Nuclear receptorsNRsNuclear receptors are ligand-dependent transcription factors.
Nuclear respiratory factor 1NRF-1Nuclear respiratory factor 1 is a transcription factor downstream of PGC-1alpha involved in coordinated expression of nDNA and mtDNA.
NumberNA number N is a count NX [x] divided by the elementary entity UX [x]. X must represent the same entity in both occurences. The elementary unit [x] cancels in the division by simplification, such that numbers (for example, numbers 8 or 24) are abstracted from the counted entity X. The concept of number is tightly entangled with units, counts and entities.
NumeralA numeral is the symbol representing a specific number. A numeral is the figure of a number, with different notation types used as a figure (VIII and 8 for Roman and Arabic numerals; 八 and 捌 for practical and financial Chinese). A numeral may consist of one or more characters or digits. 60 and 60.00 are different numerals consisting of two and four digits, respectively, which represent the same number sixty. Sixty is the name of the number 60, with the meaning 'number 60'. N is not a numeral but a symbol representing the entity 'number'. The equation N=60 assignes the numerical value 60 to the entity 'number'. The numeral 60 is a symbol for a pure number that equals 6 times 10 (or 2 times 30; or 1 times 60).
O-ring sV\Viton\9.5x1 mm
34310-02.jpg

O-ring sV\Viton\9.5x1 mm, for PEEK Stopper sV, 2 are mounted on each PEEK Stopper sV, box of 8 as spares.

O-ring\Viton\12.5x1 mm
O-ringViton12.5x1 mm.jpg

O-ring\Viton\12.5x1 mm, for PVDF or PEEK O2k-Stoppers (2-mL O2k-Chamber), box of 8 as spares.

O-ring\Viton\16x2 mmO-ring\Viton\16x2 mm, mounted on the O2k-Chamber Holder sV.
O-ring\Viton\18x2 mm
Viton O-ring 18x2.jpg

O-ring\Viton\18x2 mm, mounted on the O2k-Chamber Holder.

O-ring\Viton\6x1 mm
POS O-ring for sensor head or POS mounting tool.jpg

O-ring\Viton\6x1 mm for POS-Mounting Tool.

O-ring\Viton\8x1 mm
POS O-ring for sensor head or POS mounting tool.jpg

O-ring\Viton\8x1 mm: for OroboPOS sensor head. Replaces the

O-ring\Viton\9x1 mm

O2 background correction - DatLab
O2-Zero Powder
O2-Zero Powder.jpg

O2-Zero Powder, dithionite (Na2S2O4), for zero-oxygen calibration of the OroboPOS.

O2kO2kO2k - Oroboros O2k: the modular system for high-resolution respirometry.
O2k chamber volume calibrationThe O2k-chamber volume calibration has to be done before getting started with the Oroboros O2k to guarantee a standard chamber volume of 2.0 mL.
O2k channel labels - DatLab 7Default 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.
O2k configuration

Configure or modify the settings for the O2k sensors

In 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-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 windows.

O2k control (active)F7

DatLab 8: Change settings of the connected O2k and current measurement.

DatLab 7 : to modify instrumental settings: O2k control; to modify settings of specific channels: O2k configuration.

O2k control - DatLab 7F7After 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.
O2k control panel - DatLabThe O2k control panel allows for quick access of O2k instrument settings. It covers the right side of the graphical user interface of DatLab 8. If a DatLab protocol is active, the protocol panel ist shown instead, a tab at the right side allows to switch between O2k control panel and protocol panel.
O2k info (view)Ctrl+F7O2k info (view) displays the experimental settings from the selected file, but does not allow modification. The only exception is the O2 sensor number, that can be modified by clicking on the edit button below the field. If the sensor number is modified after the recording, a warning appears next to the field, for quality control, informing that it has been changed. If more previously recorded files are open while running a measurement, O2k control (active) will always show the settings of the active recording, while O2k info (view) will show the settings of the selected file. The O2k info (view) option is disabled when the current recording file is selected.
O2k repairO2k repair of defective hardware may require replacement of spare parts. Some electronic or mechanical defects may be solved only by repair of the O2k in the electronics workshop of Oroboros Instruments, e.g., a defective Peltier unit (temperature control).
O2k series
The serial number of each O2k is shown on a sticker at the rear of the O2k.

The O2k series is specified as the capital letter in the O2k serial number of the Oroboros O2k. A serial number G-#### or H-#### denotes an Oxygraph from the G or H series, while A-#### denotes an O2k from the A series. With DatLab running real-time connected to the O2k, the serial number of the currently connected O2k is displayed: (1) in the right corner of the status line, besides the DatLab version number (bottom), and (2) in windows O2k control [F7] and O2k configuration.

O2k signal lineThe O2k signal line is underneath the O2k status line. It shows, depending on the O2k series, on the left side the O2k number, the time of the experiment, the oxygen raw signal of each chamber, the block temperature, the barometric pressure, the Peltier power, the recorded amperometric and potentiometric raw signal, the enviromental (room) temperature and the signal from internal sensors recording the humidity and temperature of the electronics. On the right side of the O2k signal line the current user, the DatLab version and the O2k serial number are displayed.
O2k signals and outputThree electronic channel types are available in the O2k-MultiSensor system. All channels are available twofold (dual-data), for O2k-Chambers A (left) and B (right), based on numerical signals sent at a fixed data sampling time interval (default: 2 s; range 0.2 s to >10 s).
O2k status lineO2k status line is found above the O2k signal line. It contains information about the chamber label, O2 calibration, amperometric calibration, potentiometric calibration, the block temperature, the illumination in chambers, the TIP2k status and the Automatic pan.
O2k-Accessory BoxThe O2k-Accessory Box contains components of the POS-Service Kit and the O2k-Assembly Kit and is shipped with the O2k.
O2k-Amperometric OroboPOS Twin-ChannelO2k-Amperometric OroboPOS Twin-Channel: Two-channel variable polarization voltage; current/voltage converter for the polarographic oxygen sensor (POS); amplifyer with digital gain settings (1x, 2x, 4x, 8x); A/D converter; output in the range -10 V to 10 V. Integral component of the O2k-Main Unit.
O2k-Assembly KitThe O2k-Assembly Kit is a component of the Oroboros O2k, consisting of 2 PVDF Stirrer-Bars, 2 PEEK O2k-Stoppers, OroboPOS-Connectors for O2k-series A-I and NextGen-O2k series XA (attached to the O2k-Main Unit) and cables (power supply, USB-connection). Several components of the O2k-Assembly Kit are included in the O2k-Accessory Box either for shipment or for storage.
O2k-Barometric Pressure TransducerO2k-Barometric Pressure Transducer, A/D converter and digital output to DatLab for continuous recording of barometric pressure [kPa or mmHg], integrated into the air calibration of the POS (MiPNet06.03 POS-calibration-SOP). Integral component of the O2k-Main Unit. The warranty on the accuracy of the signal obtained from the O2k-Barometric Pressure Transducer expires within three years.
O2k-Catalogue: Microbalance Mettler-Toledo
Microbalance Set.jpg

Microbalance Mettler-Toledo

O2k-Chamber Holder
Chamber holder PVDF Stopper.jpg

O2k-Chamber Holder (blue POM) for PVDF or PEEK stoppers (2-mL O2k-chamber), with O-ring\Viton\18x2 mm and V-ring\30-35-4.5 mm. Two units of this item are standard components mounted on the O2k-Main Unit.

O2k-Chamber Holder sV
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O2k-Chamber Holder sV (black POM) for PVDF or PEEK stoppers (0.5-mL O2k-chamber), with O-ring\Viton\16x2 mm and V-ring\30-35-4.5 mm.

O2k-Chamber sV
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O2k-Chamber sV: 12 mm inner diameter, Duran® glass polished, with standard operation volume V of 0.5 mL.

O2k-Dissection Set
O2k-Dissection-Set.jpg

O2k-Dissection Set: for tissue preparation, set of 4 pairs of stainless steel, antimagnetic forceps and a pair of scissors.

O2k-Electromagnetic Stirrer Twin-ControlO2k-Electromagnetic Stirrer Twin-Control for smooth rotation of the stirrer bars in the two O2k-chambers; with slow-start function to prevent decoupling of the stirrer bar; regulated stirrer speed in the range of 100 to 800 rpm (decoupling may occur at higher stirrer speeds), independent for the two O2k-Chambers; automatic events sent to DatLab when the stirrer is switched on/off or when the rotation seed is changed by the experimenter. Integral component of the O2k-Main Unit.
O2k-Fluo LED2-Module
Fluorescence-Control Unit lettered.jpg

The O2k-Fluo LED2-Module is a component of the O2k-Fluorometer (O2k-Series D to G). It is an amperometric add-on module to the O2k-Core (O2k-Series D to G), adding a new dimension to high-resolution respirometry. Optical sensors are inserted through the front window of the O2k-glass chambers, for measurement of hydrogen peroxide production (Amplex® UltraRed), ATP production (Magnesium Green™), mt-membrane potential (Safranin, TMRM, Rhodamine 123), Ca2+ (Calcium Green™), and numerous other applications open for O2k-user innovation.

O2k-Fluo Smart-Module

The O2k-Fluo Smart-Module is an amperometric add-on module to the O2k-Respirometer, adding a new dimension to high-resolution respirometry. Optical sensors are inserted through the front window of the O2k-glass chambers, for measurement of hydrogen peroxide production (Amplex® UltraRed), ATP production (Magnesium Green™), mt-membrane potential (Safranin, TMRM), Ca2+ (Calcium Green™), and numerous other applications open for O2k-user innovation.

» MiPNet28.09 O2k-Fluo Smart-Module manual
O2k-FluoRespirometer
O2k-FluoRespirometer

The Oroboros O2k-FluoRespirometer - the experimental system complete for high-resolution respirometry (HRR), including fluorometry, the TIP2k and the O2k-sV-Module allowing simultaneous monitoring of oxygen consumption together with either ROS production (AmR), mt-membrane potential (TMRM, Safranin and Rhodamine 123), Ca2+ (CaG) or ATP production (MgG).

The O2k-FluoRespirometer supports all add-on O2k-Modules: O2k-TPP+ ISE-Module, O2k-pH ISE-Module, O2k-NO Amp-Module, enabling measurement of mt-membrane potential with ion sensitive electrodes (ISE for TPP+ or TPMP+) or pH.

O2k-Fluorometer Series G
O2k-Fluorometer Series G

O2k-Fluorometer Series G - Former Series (up to 2017-July) - the experimental system complete for high-resolution respirometry (HRR) combined with fluorometry. The O2k-Fluorometer includes the O2k-Core, O2k-Fluo LED2-Module and TIP2k, and supports all other add-on O2k-Modules of the Oroboros O2k.

The O2k is a sole source apparatus with no other instruments meeting its test experiments on O2k-Specifications.

O2k-Fuse Power Plug\M2.5 A\5x20 mm
Fuses mains.jpg

O2k-Fuse Power Plug\M2.5 A\5x20 mm: This item is a standard component of the O2k-Assembly Kit (O2k-FluoRespirometer), mounted on the socket for the O2k-Main Power Cable, at the rear panel of the O2k-Main Unit.

O2k-Main Basic

The O2k-Main Basic is an integral element of the O2k-Main Unit. The Oroboros O2k Main Basic has the following components:

  • Stainless-Steel Housing
  • Switching power supply
  • Microprocessor for integrated control, A/D converters and data handling
  • Copper-Block with windows to 2 O2k-Chambers
  • 2 Amperometric OroboPOS Plugs
  • TIP2k socket, providing the basis for add-on of the TIP2k
  • 2 Potentiometric Plugs for ion sensitive electrodes (ISE: TPP+, Ca2+; pH), providing the basis for add-on of the O2k-MultiSensor Modules
  • 2 Amperometric Plugs, providing the basis for add-on of the O2k-Fluo LED2-Module or NO (H2S) sensors.
  • USB-Port for connection with DatLab (PC or laptop not included)
O2k-Main Power CableO2k-Main Power Cable, for connecting the main unit to the power supply.
O2k-Main Power Cable\120 V\US-CA
O2k-Main Power Cable 120 V US-CA.JPG

O2k-Main Power Cable\120 V\US-CA, USA and Canada (120 V).

O2k-Main Power Cable\230 V\AU-NZ
O2k-Main Power Cable 230 V AU-NZ.JPG

O2k-Main Power Cable\AU-NZ, Australia and New Zealand (230 V).

O2k-Main Power Cable\230 V\Europe
O2k-Main Power Cable 230 V Europe.JPG

O2k-Main Power Cable\230 V\Europe.

O2k-Main UnitThe O2k-Main Unit is a component of the O2k-Core. The O2k-Main Unit consists of functionally defined, integral elements, the (O2k-Main Basic, O2k-Peltier Temperature Control, two O2k-Electromagnetic Stirrer Twin-Control units, two O2k-Amperometric OroboPOS Twin-Channels, O2k-Barometric Pressure Transducer), which cannot be obtained separately.
O2k-MultiSensorWhen one (or more) analytical parameters are monitored simultaneously with oxygen concentration and oxygen flux, this is an O2k-MultiSensor application of the Oroboros O2k-technology. The NextGen-O2k supports all O2k-MultiSensor Modules, while the O2k does not provide for the Q- and NADH-Redox-Modules. For some O2k-MultiSensor applications it is necessary to introduce one or more additional sensors into the chamber through a MultiSensor stopper. Optical applications require the standard black stoppers.
O2k-NO Amp-Module
O2k-NO Amp-Module.jpg

O2k-NO Amp-Module: NO-sensor compatability pack an amperometric add-on for O2k-MultiSensor application The NO sensor is not included.

O2k-Network Reference LaboratoryO2k-Network Lab
O2k-Network Reference Laboratory

O2k-Network Reference Laboratories build a WorldWide network on high-resolution respirometry and mitochondrial physiology, the Oroboros O2k-Network.

O2k-Open Support agreementO2k-Open Support aims at providing expert help quickly. Please, help us sharing our support communication openly with the scientific community.
O2k-Peltier Temperature ControlO2k-Peltier Temperature Control: Built-in electronic thermostat controlling temperature for two O2k-chambers in the range of 4 to 47 °C; ±0.002 °C (at room temperature). Continuous recording of the O2k-Copper Block temperature with DatLab. Temperature change from 20 to 30 °C within 15 min; cooling from 30 to 20 °C within 20 min. Integral component of the O2k-Main Unit. The electronic temperature control of the O2k replaced the conventional water jacket.
O2k-Publications: Exercise physiology;nutrition;life style
O2k-Publications: Obesity
O2k-Specifications
O2k-Info.png

O2k versus multiwell respirometer: O2k stands for Oroboros O2k and high-resolution respirometry, meeting powerful quality criteria securing high output and pioneering state-of-the-art comprehensive OXPHOS analysis of substrate control and coupling control of mitochondrial function. 'High throughput' stands for disposable multiwell systems - expensive, with limited scope and extremely high running costs. In respirometry, high throughput is not equivalent to high output. If you’re using a biased instrument, it doesn’t matter how many measurements you take – you’re aiming at the wrong target (Silver 2012 Penguin Press).

O2k-TPP+ ISE-Module
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O2k-TPP+ ISE-Module: Potentiometric ion-selective electrodes for measurement of mitochondrial membrane potential

O2k-Titration Set
O2k-Titration Set.JPG

The O2k-Titration Set consists of Hamilton microsyringes (6 x 10 mm3 and 3 spare plungers, 6 x 25 mm3, 1 x 50 mm3, 1 x 100 mm3, 1 x 500 mm3; fixed needles with rounded tips), provided in the Syringe Storage Box with Syringe Labels, a set of two Syringe Racks with Syringe Collars, and a set of two Tube Racks.

O2k-USB Flash Drive
Oroboros-USB-flash-drive.JPG

The O2k-USB Flash Drive is a component of the Oroboros O2k containing: DatLab, O2k-Manual, O2k-Protocols, O2k-Publications, and info on O2k-Workshops.

O2k-Virtual SupportO2k-Virtual support includes 8 individual hours. Via a live video link, Oroboros experts guide you step-by-step on topics of your choice, such as O2k instrumental setup and service of the polarographic oxygen sensors (POS) for instrumental quality control, an essential component of HRR. This offers the opportunity to analyze and discuss your experimental DatLab files obtained with your O2k with the bioenergetics experts of Oroboros. It offers flexibility to participants and gives the option to choose virtual sessions that best fit individual needs.
O2k-Window Frame
O2k-Window Frame.JPG

O2k-Window Frame: blue POM, with thread for fixation on the O2k-Main Unit, to be removed only for rare cleaning purposes and for front fixation of the Fluorescence-Control Unit, using the O2k-Window Tool.

O2k-Window Tool
O2k-Window Tool.jpg

O2k-Window Tool for removing the blue O2k-Window Frame from the O2k-Main Unit, for rare cleaning purposes and for front fixation of the Fluorescence-Control Unit.

O2k-chamber
O2k-Chamber.jpg

O2k-Chamber: Duran® glass polished, with standard operation volumes (V) of 2.0 mL (O2k-nV, nominal volume, 16 mm inner diameter) or 0.5 mL (O2k-sV, small volume in the O2k-sV-Module, 12 mm inner diameter). The optical properties of Duran® allow application of fluorometric sensors (Duran® optical properties).

O2k-pH ISE-Module
PH new.jpg

O2k-pH ISE-Module: two pH electrodes and reference electrodes and accessories

O2k-sV-ModuleO2k-sV-Module
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The O2k-sV-Module is the O2k small-volume module, comprised of two Duran® glass chambers of 12 mm inner diameter specifically developed to perform high-resolution respirometry with reduced amounts of biological sample, and all the components necessary for a smaller operation volume V of 0.5 mL. The current DatLab version is included in the delivery of this revolutionary module.

O2k-ticket system

The O2k-ticket system is a customer support platform based on Zammad. This system automatically attributes an unique Ticket number (which is visible on the subject of your e-mail) to each received customer inquiry. For an easy follow-up, all the related correspondence is collected under this Ticket number.

  • Contact us: support@oroboros.at

In order to provide a helpful and reliable support regarding your O2k/equipment, we suggest to include in your inquiries:

  • your affiliation and your O2k-serial number - See: O2k_series
  • DLD file(s) with your reported issue accompanied by a brief explanation.
OSF Preprint serverLeading preprint service providers use OSF Preprints as an open source infrastructure to support their communities. You should upload your preprint to whichever preprint server best fits your topic and the community that you would like to reach. If there isn’t a community-driven preprint server for your discipline, OSF Preprints is available for any discipline. Currently, you can only share your preprint on one community preprint server. It’s on our roadmap to allow users to submit a preprint to multiple community preprint servers. However, to improve discoverability across communities, all preprints shared on OSF Preprints and community preprint servers are indexed and searchable via osf.io/preprints. Right now, it is not possible to add subjects. However, you can add tags with additional subject areas or keywords to improve discoverability. COS supports communities operating their own branded community preprint services using OSF Preprints as the backend.OSF is based in Charlottesville, VA, USA.
OXPHOS InternationalThe OXPHOS International web portal is a repository of information useful to scholars studying mitochondria. The site is operated as a private "special interests" community hub.
OXPHOS capacityPP.jpg OXPHOS capacity P is the respiratory capacity of mitochondria in the ADP-activated state of oxidative phosphorylation, at saturating concentrations of ADP and inorganic phosphate (which may not be the case in State 3), oxygen, and defined reduced CHNO-fuel substrates.
ObesityObesity is a disease resulting from excessive accumulation of body fat. In common obesity (non-syndromic obesity) excessive body fat is due to an obesogenic lifestyle with lack of physical exercise ('couch') and caloric surplus of food consumption ('potato'), causing several comorbidities which are characterized as preventable non-communicable diseases. Persistent body fat excess associated with deficits of physical activity induces a weight-lifting effect on increasing muscle mass with decreasing mitochondrial capacity. Body fat excess, therefore, correlates with body mass excess up to a critical stage of obesogenic lifestyle-induced sarcopenia, when loss of muscle mass results in further deterioration of physical performance particularly at older age.
OctGMOctGM

OctGM: Octanoylcarnitine & Glutamate & Malate.

MitoPathway control state: FN

SUIT protocols: SUIT-015, SUIT-016, SUIT-017

OctGMSOctGMS

OctGMS: Octanoylcarnitine &Glutamate & Malate& Succinate.

MitoPathway control state: FNS

SUIT protocols: SUIT-016, SUIT-017

OctM pathway control stateOctM

OctM: Octanoylcarnitine & Malate.

MitoPathway control state: F

SUIT protocols: SUIT-002, SUIT-015, SUIT-016, SUIT-017

Respiratory stimulation of the FAO-pathway, F, by fatty acid FA in the presence of malate M. Malate is a type N substrate (N), required for the F-pathway. In the presence of anaplerotic pathways (e.g., mitochondrial malic enzyme, mtME) the F-pathway capacity is overestimated, if there is an added contribution of NADH-linked respiration, F(N) (see SUIT-002). The FA concentration has to be optimized to saturate the FAO-pathway, without inhibiting or uncoupling respiration. Low concentration of malate, typically 0.1 mM, does not saturate the N-pathway; but saturates the F-pathway. High concentration of malate, typically 2 mM, saturates the N-pathway.

OctPGM pathway control stateOctPGM

OctPGM: Octanoylcarnitine & Pyruvate & Glutamate & Malate.

MitoPathway control state: FN

SUIT protocols: SUIT-002

This substrate combination supports N-linked flux which is typically higher than FAO capacity (F/FN<1 in the OXPHOS state). In SUIT-RP1, PMOct is induced after PM(E), to evaluate any additive effect of adding Oct. In SUIT-RP2, FAO OXPHOS capacity is measured first, testing for the effect of increasing malate concentration (compare malate-anaplerotic pathway control state, M alone), and pyruvate and glutamate is added to compare FAO as the background state with FN as the reference state.
OctPGMS pathway control stateOctPGMS

OctPGMS: Octanoylcarnitine & Pyruvate & Glutamate & Malate & Succinate.

MitoPathway control state: FNS

SUIT protocol: SUIT-001, SUIT-002, SUIT-015

This substrate combination supports convergent electron flow to the Q-junction.

OctPGMSGp pathway control stateOctPGMSGp

OctPGMSGp: Octanoylcarnitine & Pyruvate & Glutamate & Malate & Succinate & Glycerophosphate.

MitoPathway control state: FNSGp

SUIT protocol: SUIT-002

This substrate combination supports convergent electron flow to the Q-junction.

OctPM pathway control stateOctPM

OctPM: Octanoylcarnitine & Pyruvate & Malate.

MitoPathway control state: FN

SUIT protocol: SUIT-002, SUIT-005

This substrate combination supports N-linked flux which is typically higher than FAO capacity (F/FN<0 in the OXPHOS state). In SUIT-RP1, PMOct is induced after PM(E), to evaluate any additive effect of adding Oct. In SUIT-RP2, FAO OXPHOS capacity is measured first, testing for the effect of increasing malate concentration (compare malate-anaplerotic pathway control state, M alone), and pyruvate is added to compare FAO as the background state with FN as the reference state.

OctPMSOctPMS

OctPMS: Octanoylcarnitine & Pyruvate & Malate & Succinate.

MitoPathway control state: FNS

SUIT protocol: SUIT-005

OctanoateOcaOctanoate (octanoic acid). C8H16O2 Common name: Caprylic acid.
OctanoylcarnitineOctOctanoylcarnitine is a medium-chain fatty acid (octanoic acid: eight-carbon saturated fatty acid) covalently linked to carnitine, frequently applied as a substrate for fatty acid oxidation (FAO) in mitochondrial preparations.
OligomycinOmyOligomycin (Omy) is an inhibitor of ATP synthase by blocking its proton channel (Fo subunit), which is necessary for oxidative phosphorylation of ADP to ATP (energy production). The inhibition of ATP synthesis also inhibits respiration. In OXPHOS analysis, Omy is used to induce a LEAK respiration state of respiration (abbreviated as L(Omy) to differentiate from L(n), LEAK state in the absence of ADP).
Open - DatLabCtrl+OOpen a previously recorded DatLab file.
Open AccessOA
Open Access logo.png

Open Access (OA) academic articles comprise all different forms of published research that are distributed online, free of charge and with an open license to facilitate the distribution and reuse. The open access repositories serve as the perfect vehicle to transmit free knowledge, including but not limited to peer-reviewed and non-peer-reviewed academic journal articles, conference papers, theses, book chapters and monographs. Driven by the problems of social inequality caused by restricting access to academic research, the Open Access movement changes the funding system of published literature allowing for more readers and thus increased access to scientific knowledge, as well as addressing the economic challenges and unsustainability of academic publishing. In addition to being free to read (gratis), open access articles may also be free to use (libre) where the copyright is held by the authors and not the publisher.

Definition by the Directory of Open Access Journals (DOAJ): "We define these as journals where the copyright holder of a scholarly work grants usage rights to others using an open license (Creative Commons or equivalent) allowing for immediate free access to the work and permitting any user to read, download, copy, distribute, print, search, or link to the full texts of articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose."

Open ScienceOS
Open Access logo.png

Building on the essential principles of academic freedom, research integrity and scientific excellence, open science sets a new paradigm that integrates into the scientific enterprise practices for reproducibility, transparency, sharing and collaboration resulting from the increased opening of scientific contents, tools and processes. Open science is defined as an inclusive construct that combines various movements and practices aiming to make multilingual scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation and communication to societal actors beyond the traditional scientific community. It comprises all scientific disciplines and aspects of scholarly practices, including basic and applied sciences, natural and social sciences and the humanities, and it builds on the following key pillars: open scientific knowledge, open science infrastructures, science communication, open engagement of societal actors and open dialogue with other knowledge systems.

Open chamberOThe term "open O2k-chamber" refers to a situation in which the liquid phase is allowed to equilibrate with a gas phase, but the stopper is partially inserted using the Stopper-Spacer.
Open systemAn 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 flows, Iext).
OpticsOptics are the components that are used to relay and focus light through a spectrofluorometer or spectrophotometer. These would normally consist of lenses and/or concave mirrors. The number of such components should be kept to a minimum due to the losses of light (5-10%) that occur at each surface.
Ordinatey

The ordinate is the vertical axis y of a rectangular two-dimensional graph with the abscissa x as the horizontal axis. Values Y are placed vertically from the origin.

See Ordinary Y/X regression.

OroboPOS
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The OroboPOS is a polarographic oxygen sensor (POS), with an amperometric mode of operation. The OroboPOS meets the highest quality criteria in terms of linearity, stability and sensitivity of the signal. The Clark type polarographic oxygen sensor (POS) remains the gold standard for measuring dissolved oxygen in biomedical, environmental and industrial applications over a wide dynamic oxygen range.

It consists of a gold cathode, a silver/silverchloride anode and a KCl electrolyte reservoir separated from the sample by a 25 µm membrane (FEP). The main body of the OroboPOS is made of PEEK. With application of a polarization voltage (0.8 V), a current is obtained as an amperometric signal, which is converted to a voltage.

OroboPOS-Connector
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OroboPOS-Connector (blue POM), with male connection to OroboPOS head (POS) and with cable and male plug fitting into O2k-Main Unit.

OroboPOS-Connector ServiceThe OroboPOS-Connector Service entails routine maintenance and any necessary repairs of the OroboPOS-Connector in the Oroboros electronics workshop (WGT).
Oroboros Instruments Corp
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Oroboros Instruments distributes the gold standard O2k-technology for high-resolution respirometry - HRR - world-wide. The Oroboros Company is a scientifically oriented organization, with emphasis on continuous innovation. The extension of the Oroboros O2k to the O2k-FluoRespirometer sets a new standard. Its modular design provides the flexibility for add-on O2k-Modules (see Oroboros O2k-Catalogue). The O2k is established internationally, with »4294 O2k-Publications in the scientific literature covering areas ranging from fundamental bioenergetics to the analysis of mitochondrial and metabolic diseases, advancing the rapidly growing field of preventive mitochondrial medicine. The Oroboros science team actively participates in science and research (see: publications). Moreover, the Oroboros O2k-Laboratory frequently host international researchers (visiting scientists). Oroboros Instruments organizes international O2k-Workshops on a regular basis. The O2k-Network includes and connects 744 reference laboratories worldwide. The NextGen-O2k extends HRR to include a Q-redox sensor and PhotoBiology module.
Oroboros O2k-Core (O2k-Series D - G)
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Oroboros O2k-Core - Former Series (O2k-Series D - G) - the experimental system complete for basic high-resolution respirometry (HRR). The O2k-Core 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 and the O2k-Titration Set. The O2k-Core supports all add-on O2k-Modules of the O2k.

On-line display of oxygen flux (rate of respiration) is provided in addition to the conventional 'oxygraphic' plot of oxygen concentration over time. Highest signal stability minimizes the required amounts of biological sample, and provides the basis for resolution in the extreme low-oxygen range. Peltier temperature control provides a thermal stability at ±0.002 °C in the range of 4 °C to 47 °C at typical constant room temperature. Electronically controlled PVDF or PEEK stirrers are integrated in the two-chamber design of the O2k, and a barometric pressure transducer enables automatic oxygen calibrations implemented in the DatLab software.

The O2k is a sole source apparatus with no other instruments meeting its specifications.

Oroboros O2k-technology
NextGen-O2k all-in-one

The Oroboros O2k-technology provides modular systems for high-resolution respirometry (HRR) for mitochondria and cell research. Oroboros delivers the O2k-technology for high-resolution respirometry in mitochondria and cell research. The O2k-tecnology allows the measurement of respiration at controlled oxygen levels, combined with redox biology (NADH and CoQ), ROS production, mitochondrial membrane potential, ATP production, Ca2+, or pH. HRR expands to HRPB: High-Resolution PhotoBiology.

Small amounts of biological samples can be used for bioenergetic and OXPHOS analysis, ranging from isolated mitochondria, permeabilized tissues and permeabilized cells to living cells and tissues slices.

The modular O2k-concept is supported by DatLab, with high flexibility for extension by add-on O2k-Modules. All O2k-Modules are supported by the NextGen-O2k. The O2k-Q-Module and the O2k-NADH-Module are exclusively supported by the NextGen-O2k, whereas the O2k (Series-J) provides the basis for all other HRR application but cannot be upgraded to the NextGen-O2k Redox. The globally tested and trusted high-resolution O2k-technology prioritizes both quality and scientific research output in the field of mitochondrial physiology and pathology, extended to PhotoBiology.

Oroboros USB-flash driveThe Oroboros USB-flash drive is delivered with the Oroboros O2k. Copy the folder "Oroboros O2k-Course on HRR" from the Oroboros USB-flash drive to your computer. This folder contains the DatLab installation program as well as tools to find topics, O2k-manuals and O2k-protocols with corresponding DatLab demo files and templates for training with DatLab.
OuabainOuaOuabain (synonym: G-strophantin octahydrate) is a poisonous cardiac glycoside. The classical mechanism of action of ouabain involves its binding to and inhibition of the plasma membrane Na+/K+-ATPase (sodium pump) especially at the higher concentrations. Low (nanomolar and subnanomolar) concentrations of ouabain stimulate the Na-K-ATPase.
OutlierAn 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].
Outlier index threshold - DatLabSet a lab-specific or session-specific threshold (Lab-default or Session value) for the Outlier index different from the System default.
Outlier-skewness indexOSI, OI

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 Pearson’s coefficient of skewness 2:

Pearson 2 coefficient = 3 · (average-median)/SD

The 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.


The outlier index in DatLab: Outlier index threshold

OverfittingOverfitting in statistics is the act of mistaking noise for a signal. Overfitting makes a model look ‘’better’’ on paper but perform ‘’worse’’ in the real world. This may make it easier to get the model published in an academic journal or to sell to a client, crowding out more honest models from the marketplace. But if the model is fitting noise, it has the potential to hurt the science (quoted from Silver 2012 Penguin Press).
OxaloacetateOa
Oxaloacetic acid

Oxaloacetic acid, C4H4O5, occurs under physiological conditions as the anion oxaloacetate2-, Oa. Oxaloacetate is formed from malate by MDH. Oa reacts with acetyl-CoA through citrate synthase to form citrate, or with glutamate through transaminase to form oxoglutarate and aspartate. Oa transport is restricted across the inner mt-membrane of various tissues. Oa is a potent inhibitor of succinate dehydrogenase.

Oxalomalic acidOxalomalic acid is an inhibitor of aconitase (and of cytoplasmic NADP-dependent isocitrate dehydrogenase). Aconitase mediates the isomerization of citrate to isocitrate as the first step in the TCA cycle. Oxalomalic acid has been used at 1 mM concentration and after 45 min of pre-incubation to inhibit aconitase in permeabilized rat Soleus muscle fibres, inhibiting the enzyme by 24% (Osiki 2016 FASEB J).
Oxia
Oxia.png

Oxia - HyperOxia to HypOxia: The Oxia generates gaseous oxygen and hydrogen by electrolysis of water using a proton exchange membrane (PEM). O2 and H2 gas can be used to control the O2 regime in the Oroboros O2k (Setting_the_oxygen_concentration) using the 10 mL Gas-Injection Syringes. Low oxygen concentrations (<50 µM) are used to mimic tissue normoxia or hypoxia. Hyperoxic conditions above air saturation (250-600 µM O2) are routinely used for high-resolution respirometry of permeabilized muscle fibers or to induce oxidative stress in cells and mitochondrial preparations.

Oxidative phosphorylationOXPHOSP.jpg Oxidative phosphorylation (OXPHOS) is the oxidation of reduced fuel substrates by electron transfer to oxygen, chemiosmotically coupled to the phosphorylation of ADP to ATP (P») and accompanied by an intrinsically uncoupled component of respiration. The OXPHOS state of respiration provides a measure of OXPHOS capacity (P), which is frequently corrected for residual oxygen consumption (ROX).
Oxidative stressOxidative stress results from an imbalance between pro-oxidants and antioxidants shifting the equilibrium in favor of the pro-oxidants. This process can be due by an increment in pro-oxidants, by a depletion of antioxidant systems or both. Oxidative stress generates oxidative damage of proteins, lipids and DNA.
OxoglutarateOg
2-Oxoglutaric acid

2-Oxoglutaric acid or alpha-ketoglutaric acid, C5H6O5, occurs under physiological conditions as the anion 2-Oxoglutarate2-, Og. 2-Oxoglutarate (alpha-ketoglutarate) is formed from isocitrate as a product of isocitrate dehydrogenase (IDH) in the TCA cycle, and is a substrate of oxoglutarate dehydrogenase (OgDH). The 2-oxoglutarate carrier exchanges malate2- for 2-oxoglutarate2- as part of the malate-aspartate shuttle. In the cytosol, oxoglutarate+aspartate are transaminated to form oxaloacetate+glutamate. Cytosolic malate dehydrogenase converts oxaloacetate+NADH to malate.

Oxoglutarate dehydrogenaseOgDHOxoglutarate dehydrogenase (α-ketoglutarate dehydrogenase) is a highly regulated enzyme of the tricarboxylic acid cycle. It catalyses the conversion of oxoglutarate (alpha-ketoglutarate) to succinyl-CoA, reduces NAD+ to NADH and thus links to Complex I in the Electron transfer-pathway. OgDH is activated by low Ca2+ (<20 µM) but inactivated by high Ca2+ (>100 µM). OgDH is an important source of ROS.
Oxycaloric equivalentDeltakHO2The oxycaloric equivalent is the theoretically derived enthalpy change of the oxidative catabolic reactions per amount of oxygen respired, DeltakHO2, ranging from -430 to -480 kJ/mol O2. The oxycaloric equivalent is used in indirect calorimetry to calculate the theoretically expected metabolic heat flux from the respirometrically measured metabolic oxygen flux. Calorimetric/respirometric ratios (CR ratios; heat/oxygen flux ratios) are experimentally determined by calorespirometry. A CR ratio more exothermic than the oxycaloric equivalent of -480 kJ/mol indicates the simultaneous involvement of aerobic and anaerobic mechanisms of energy metabolism.
OxygenO2
Dioxygen

Molecular oxygen, O2 or dioxygen, has two atoms of oxygen, O, which is the chemical element with atomic number 8. The relative molecular mass of O2, Mr,O2, is 32 (or 31.9988). The element O has 8 protons, 8 neutrons and 8 electrons. In the figure, the two electrons in the first electron shell are not shown. Of the six electrons in the outer shell (blue bullets), one electron from each of the two atoms is shared in O2 forming the covalent bond, and one electron in each atom is unpaired.

Oxygen calibration - DatLabO2 calibration is the calibration in DatLab of the oxygen sensor. It is a prerequisite for obtaining accurate measurements of respiration. Accurate calibration of the oxygen sensor depends on (1) equilibration of the incubation medium with air oxygen partial pressure at the temperature defined by the experimenter; (2) zero oxygen calibration; (3) high stability of the POS signal tested for sufficiently long periods of time; (4) linearity of signal output with oxygen pressure in the range between oxygen saturation and zero oxygen pressure; and (5) accurate oxygen solubility for aqueous solutions for the conversion of partial oxygen pressure into oxygen concentration. The standard oxygen calibration procedure is described below for high-resolution respirometry with the calibration routine using instrumental calibration DL-Protocols in DatLab.
Oxygen flowIO2 [mol·s-1] or [mol·s-1·x-1]Respiratory oxygen flow is the oxygen consumption per total system, which is an extensive quantity. Flow is advancement of a transformation in a system per time [mol·s-1], when 'system' is defined as the experimental system (e.g. an open or closed chamber). Flow is distinguished from the size-specific quantity flux obtained by normalization of flow per volume of the experimental system [mol·s-1·m-3]. An experimental object, e.g. a living cell, may be considered as the 'experimental system'. Then oxygen flow per cell has the unit [mol·s-1·x-1], where [x] is the elementary unit for a count. Oxygen flow or respiration per cell [amol·s-1·x-1] = [pmol·s-1·Mx-1] is normalized for the cell count, distinguished from oxygen flux (e.g. per mg protein or wet mass). These are different forms of normalization of rate.
Oxygen fluxJO2Oxygen flux, JO2, is a specific quantity. Oxygen flux is oxygen flow, IO2 [mol·s-1 per system] (an extensive quantity), divided by system size. Flux may be volume-specific (flow per volume [pmol·s-1·mL-1]), mass-specific (flow per mass [pmol·s-1·mg-1]), or marker-specific (flow per mtEU). Oxygen flux (e.g., per body mass, or per cell volume) is distinguished from oxygen flow (per number of objects, such as cells), IO2 [mol·s-1·x-1]. These are different forms of normalization of rate.
Oxygen flux - instrumental backgroundJ°O2Instrumental background oxygen flux, J°O2, in a respirometer is due to oxygen consumption by the POS, and oxygen diffusion into or out of the aqueous medium in the O2k-chamber. It is a property of the instrumental system, measured in the range of experimental oxygen levels by a standardized instrumental O2 background test. The oxygen regime from air saturation towards zero oxygen is applied generally in experiments with isolated mitochondria, and living or permeabilized cells. To overcome oxygen diffusion limitation in permeabilized fibers and homogenates, an elevated oxygen regime is applied, requiring instrumental background test in the same range of elevated oxygen.
Oxygen kineticsOxygen kinetics describes the dependence of respiration of isolated mitochondria or cells on oxygen partial pressure. Frequently, a strictly hyperbolic kinetics is observed, with two parameters, the oxygen pressure at half-maximum flux, p50, and maximum flux, Jmax. The p50 is in the range of 0.2 to 0.8 kPa for cytochrome c oxidase, isolated mitochondria and small cells, strongly dependent on Jmax and coupling state.
Oxygen pressurepO2 [kPa]Oxygen pressure or partial pressure of oxygen [kPa], related to oxygen concentration in solution by the oxygen solubility, SO2 [µM/kPa].
Oxygen sensor testPOS testThe O2 sensor test is an important component of Oroboros Quality Management. The OroboPOS test is described in detail in MiPNet06.03 POS-calibration-SOP, is performed after switching on the Oroboros O2k, and is required as a basis of technical service of the instrument.
Oxygen signalThe oxygen signal of the Oroboros O2k is transmitted from the electrochemical polarographic oxygen sensor (OroboPOS) for each of the two O2k-chambers to DatLab. The primary signal is a current [µA] which is converted into a voltage [V] (raw signal), and calibrated in SI units for amount of substance concentration [µmol·L-1 or µM]. For technical reasons, the raw signal is given in [V] (DatLab 7 and previous) or [µA] (DatLab 8). The value of the raw signal is the same, independent of the displayed unit ([V] or [µA]). In the following sections, only [µA] is used for information on the raw signal, but the same values in [V] apply for the raw signal when using DL7 or previous versions.
Oxygen solubilitySO2 [µM/kPa]The oxygen solubility, SO2 [µM/kPa] = [(µmol·L-1)/kPa], expresses the oxygen concentration in solution in equilibrium with the oxygen pressure in a gas phase, as a function of temperature and composition of the solution. The inverse of oxygen solubility is related to the activity of dissolved oxygen. The oxygen solubility in solution, SO2(aq), depends on temperature and the concentrations of solutes in solution, whereas the dissolved oxygen concentration at equilibrium with air, cO2*(aq), depends on SO2(aq), barometric pressure and temperature. SO2(aq) in pure water is 10.56 µM/kPa at 37 °C and 12.56 µM/kPa at 25 °C. At standard barometric pressure (100 kPa), cO2*(aq) is 207.3 µM at 37 °C (19.6 kPa partial oxygen pressure) or 254.7 µM at 25 °C (20.3 kPa partial oxygen pressure). In MiR05 and serum, the corresponding saturation concentrations are lower due to the oxygen solubility factor: 191 and 184 µM at 37 °C or 234 and 227 µM at 25 °C.
Oxygen solubility factorFMThe oxygen solubility factor of the incubation medium, FM, expresses the effect of the salt concentration on oxygen solubility relative to pure water. In mitochondrial respiration medium MiR05, MiR05-Kit and MiR06, FM is 0.92 (determined at 30 and 37 °C) and in culture media is 0.89 (at 37 °C). FM varies depending on the temperature and composition of the medium. To determine the FM based on the oxygen concentration, specific methods and equipment are needed (see references Rasmussen HN, Rasmussen UF 2003 in MiPNet06.03). For other media, FM may be estimated using Table 4 in MiPNet06.03. For this purpose KCl based media can be described as "seawater" of varying salinity. The original data on sucrose and KCl-media (Reynafarje et al 1985), however, have been critizesed as artefacts and the FM of 0.92 is suggested in the temperature range of 10 °C to 40 °C as for MiR05.
P-L control efficiencyjP-LP-L control efficiency The P-L control efficiency (P-L flux control efficiency) is defined as jP-L = (P-L)/P = 1-L/P. OXPHOS capacity corrected for LEAK respiration is the P-L net OXPHOS capacity, P-L. The P-L control efficiency is the ratio of net to total OXPHOS capacity, which is equal to the biochemical E-L coupling efficiency, if P=E. jP-L = 1.0 for a fully coupled system (when RCR approaches infinity); jP-L = 0.0 (RCR=1) for a system with zero respiratory phosphorylation capacity (P-L=0) or zero E-L coupling efficiency (E-L=0 when L=P=E). If State 3 is measured at saturating concentrations of ADP and Pi (State 3 = P), then the respiratory acceptor control ratio RCR equals P/L. Under these conditions, the respiratory control ratio and P-L control efficiency are related by a hyperbolic function, jP-L = 1-RCR-1. » MiPNet article
P-L net OXPHOS capacityP-LP-L net OXPHOS capacity The P-L net OXPHOS capacity is the OXPHOS capacity corrected for LEAK respiration. P-L is the scope for ADP stimulation, the respiratory capacity potentially available for phosphorylation of ADP to ATP. Oxygen consumption in the OXPHOS state, therefore, is partitioned into P-L, strictly coupled to phosphorylation , and nonphosphorylating LEAK respiration, LP, compensating for proton leaks, slip and cation cycling: P = P-L+LP. It is frequently assumed that LEAK respiration L as measured in the LEAK state, overestimates the LEAK component of respiration, LP, as measured in the OXPHOS state, particularly if the protonmotive force is not adjusted to equivalent levels in L and LP. However, if the LEAK component increases with enzyme turnover during P, the low enzyme turnover during L may counteract the effect of the higher pmF.
P/E control ratioP/EOXPHOS-control ratio The P/E control ratio (OXPHOS/ET pathway; phosphorylation system control ratio) is an expression of the limitation of OXPHOS capacity by the phosphorylation system. The relative limitation of OXPHOS capacity by the capacity of the phosphorylation system is better expressed by the E-P control efficiency, jE-P = 1-P/E. The P/E control ratio increases with increasing capacity of the phosphorylation system up to a maximum of 1.0 when it matches or is in excess of ET capacity. P/E also increases with uncoupling. P/E increases from the lower boundary set by L/E (zero capacity of the phosphorylation system), to the upper limit of 1.0, when there is no limitation of P by the phosphorylation system or the proton backpressure (capacity of the phosphorylation system fully matches the ET capacity; or if the system is fully uncoupled). It is important to separate the kinetic effect of ADP limitation from limitation by enzymatic capacity at saturating ADP concentration. » MiPNet article
P/O ratioP/O ratioP/O ratio stands for phosphate to atomic oxygen ratio, where P indicates phosphorylation of ADP to ATP (or GDP to GTP).
P50p50p50 is the oxygen partial pressure at which (a) respiratory flux is 50% of maximum oxygen flux, Jmax, at saturating oxygen levels. The oxygen affinity is indirectly proportional to the p50. The p50 depends on metabolic state and rate. (b) p50 is the oxygen partial pressure at which oxygen binding (on myoglobin, haemoglobin) is 50%, or desaturation is 50%.
PB Light Source
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The PhotoBiology Light Source (PBLS) has been designed as a part of the PB-Module to provide with an external source of light. This enables experiments for evaluating the production of O2 in the presence of light. The PBLS consists of one LED and one photodiode mounted on the PBLS head protected by a PMMA plastic cover. Three pairs of PBLS (white, blue, and red) are provided with the PB-Module. The light intensity can be regulated from 0 to 2750 µmol·s-1·m-2 (red PBLS), from 0 to 3000 µmol·s-1·m-2 (blue PBLS), from 0 to 3500 µmol·s-1·m-2 (white PBLS). An integrated photodiode provides real-time measurement of the light intensity allowing for continuous adjustment to the desired value.

PB-Module
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The PB-Module has been developed for conducting measurements of PhotoBiology, including photosynthesis. It consists of the PB Light Source and electronic components which are an integral part of the NextGen-O2k. Measurements are recorded and evaluated with the DatLab 8 software.

PBI-Shredder O2k-Set
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PBI-Shredder O2k-Set: Auxiliary O2k-Tool for tissue homogenate preparation

PBI-Shredder SG3
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PBI-Shredder SG3 for tissue homogenate preparation, heavy duty high torque SG3 driver with convertible handle, SG3 base with 3 position force setting lever (FSL), battery charger and two lithium ion batteries. The PBI-Shredder SG3 is included in the PBI-Shredder O2k-Set. Select 230 V or 120 V.

Oroboros Instruments: world-wide distributor.

PBMCPBMCPeripheral blood mononuclear cells (PBMC) are a fraction of the leucocyte population in the blood composed by cells with round nucleus. PBMC consist of lymphocytes (T, B and NK cells) and monocytes. During extraction, neutrophils and platelets (PLT) can be found in the PBMC fraction, where PLT are considered as a contamination.
PC requirementsThe PC requirements for controlling an O2k and data recording with DatLab are found here.
PGM-pathway control statePGM
PGM

PGM: Pyruvate & Glutamate & Malate.

MitoPathway control state: NADH electron transfer-pathway state

Pyruvate (P) is oxidatively decarboxylated to acetyl-CoA and CO2, yielding NADH catalyzed by pyruvate dehydrogenase. Malate (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). Glutamate&malate is a substrate combination supporting an N-linked pathway control state, when glutamate is transported into the mt-matrix via the glutamate-aspartate carrier and reacts with oxaloacetate in the transaminase reaction to form aspartate and oxoglutarate. Glutamate as the sole substrate is transported by the electroneutral glutamate-/OH- exchanger, and is oxidized in the mitochondrial matrix by glutamate dehydrogenase to α-ketoglutarate ( 2-oxoglutarate), representing the glutamate-anaplerotic pathway control state. 2-oxoglutarate (α-ketoglutarate) is formed from isocitrate (isocitrate dehydrogenase, from oxaloacetate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase.

PGMS-pathway control statePGMS
PGMS

PGMS: Pyruvate & Glutamate & Malate & Succinate.

MitoPathway control state: NS-pathway control state

2-oxoglutarate is produced through the citric acid cycle from citrate by isocitrate dehydrogenase, from oxaloacetate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase. If the 2-oxoglutarate carrier does not outcompete these sources of 2-oxoglutarate, then the TCA cycle operates in full circle with external pyruvate&malate&glutamate&succinate

PGMSGp pathway control statePGMSGp

PGMSGp: Pyruvate & Glutamate & Malate & Succinate & Glycerophosphate.

MitoPathway control state: NSGp

SUIT protocol: SUIT-038

This substrate combination supports convergent electron flow to the Q-junction.

PHpHThe pH value or pH is the negative of the base 10 logarithm of the activity of protons (hydrogen ions, H+). A pH electrode reports the pH and is sensitive to the activity of H+. In dilute solutions, the hydrogen ion activity is approximately equal to the hydrogen ion concentration. The symbol pH stems from the term potentia hydrogenii.
PH calibration bufferspH calibration buffers are prepared to obtain two or more defined pH values for calibration of pH electrodes and pH indicator dyes.
PH combination electrode 150/6 mm

pH combination electrode, 150 mm shaft, 6 mm diameter, incl. connection cable with BNC plug. Discontinued

PH combination electrode 70/5 mm

pH-Combination Electrode\70/5 mm, 70 mm shaft, 5 mm diameter, for 30251-24 stopper. Discontinued

PH-Glass electrode
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pH-Glass electrode with BNC plug.

PM-pathway control statePM
PM

PM: Pyruvate & Malate.

MitoPathway control state: NADH Electron transfer-pathway state


Upstream of the NAD-junction, Pyruvate (P) is oxidatively decarboxylated to acetyl-CoA and CO2, yielding NADH catalyzed by pyruvate dehydrogenase. Malate (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). 2-oxoglutarate (α-ketoglutarate) is formed from isocitrate (isocitrate dehydrogenase).

PMS-pathway control statePMS
PMS

PMS: Pyruvate & Malate & Succinate.

MitoPathway control: CI&II

Pyruvate (P) is oxidatively decarboxylated to acetyl-CoA and CO2, yielding NADH catalyzed by pyruvate dehydrogenase. Malate (M) is oxidized to oxaloacetate by mt-malate dehydrogenase located in the mitochondrial matrix. Condensation of oxaloacate with acetyl-CoA yields citrate (citrate synthase). This documents an additive effect of convergent CI&II electron flow to the Q-junction, with consistent results obtained with permeabilized muscle fibres and isolated mitochondria (Gnaiger 2009).

POS calibration - dynamicCalibration of the sensor response time. See also POS calibration - static.
POS calibration - staticF5Two-point calibration of the polarographic oxygen sensor, comprising Air calibration and Zero calibration. See also POS calibration - dynamic.
POS-Electrolyte Powder
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POS-Electrolyte Powder, KCl.

The powder is dissolved in 10 ml distilled water to yield a 1 M KCl solution.

POS-Holder
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The POS-Holder, made from blue POM, is screwed into the copper block of the O2k-Main Unit, guiding theguiding the POS to the 2-mL O2k-chamber, and keeping the SmartPOS/OroboPOS-Connector in a fixed position for sealing the O2k-chamber with the POS-Seal Tip. In addition, the POS-Holder fixes the O2k-Chamber in an accurate rotational position by pressing against the angular cut of the glass chamber.

Two units of this item are standard components mounted on the O2k-Main Unit.

POS-Holder sV
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POS-Holder sV, made from black POM, to be screwed into the copper block of the O2k-Main Unit, guiding the POS to the O2k-Chamber sV, and keeping the SmartPOS/OroboPOS-Connector in a fixed position for sealing the O2k-Chamber sV with the POS-Seal Tip. In addition, the POS-Holder sV fixes the O2k-Chamber sV in an accurate rotational position by pressing against the angular cut of the glass chamber.

POS-Membrane Ring
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POS-Membrane Ring, PEEK, holds the membrane against the inner O-ring on the POS housing.

POS-MembranesFEP-membranes
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POS-Membranes, FEP 25 µm; 40/Pck.

POS-Mounting Tool
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POS-Mounting Tool for application of POS-Membranes. It consists of two parts, (i) the membrane guide (larger diameter) and (ii) the membrane ring holder with O-ring\Viton\6x1 mm for holding the POS-Membrane Ring during membrane application. Since the O2k-Series G-0075 membrane ring holder have a 2 mm extended ridge for a better grip.

POS-Seal Tip
POS seal tip.jpg

POS-Seal Tip, black butyl rubber gasket with 3 mm pore. 4/Pck, for sealing the POS (sensor head) against the O2k-Chamber. Push the wetted POS-Seal Tip over the POS-sensor head, with the pore positioned centrally, not covering any peripheral area of the gold cathode. Do not stretch the gasket across the POS-sensor head.

POS-Service KitPOS-Service Kit, in O2k-Accessory Box including all oxygen sensor service accessories for membrane mounting and service of the POS.
PREreviewPREreview encourages scientists to post their scientific outputs as preprints. PREreview makes it easier to start and run a Preprint Journal Club, or integrate preprint review into conventional journal clubs. PREreview seeks to diversify peer review in the academic community by crowdsourcing pre-publication feedback to improve the quality of published scientific output, and to train early-career researchers (ECRs) in how to review others' scientific work. We want to facilitate a cultural shift in which every scientist posts, reads, and engages with preprints as standard practice in scholarly publishing. We see PREreview as a hub to support and nurture the growth of a community that openly exchanges timely, constructive feedback on emerging scientific outputs. We believe that by empowering ECRs through peer review training programs, thereby increasing the diversity of researchers involved in the peer review process, PREreview will help establish a healthier and more sustainable culture around research dissemination and evaluation. This project was born in April 2017 as a collaboration between Samantha Hindle and Daniela Saderi, scientists and ASAPbio Ambassadors, with help from Josh Nicholson, at the time working for Authorea.
PX calibration - DatLabpX calibration
Packing\O2k-Box 1
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Packing\O2k-Box 1: for shipment of the O2k-Main Unit, with polystyrene inlets. Keep the original packing material safely stored, for any future shipping purposes of the O2k-Main Unit.

Packing\O2k-Box 1+2Packing\O2k-Box 1+2 for shipping the O2k-Core. O2k-WorldWide delivery, insurance and handling are included in the O2k-Core.
Packing\O2k-Box 2
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Packing\O2k-Box 2, for shipment of accessories.

Packing\Peli Case
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Packing\Peli Case: Watertight, crushproof, and dust proof case for safe transportation of the O2k:

Retractable extension handle, Strong polyurethane wheels with stainless steel bearings, Easy open Double Throw latches, Open cell core with solid wall design - strong, light weight, O-ring seal, Automatic Pressure Equalization Valve, Fold down handles, Stainless steel hardware and padlock protectors, 4 level Pick N Pluck™ with convoluted lid foam, Special foam inlets for O2k.

Interior Dimensions: 21.48" x 16.42" x 12.54" (54.5 x 41.7 x 31.8 cm)

PalMPalM

PalM: Palmitoylcarnitine & Malate.

MitoPathway control state: Fatty acid oxidation pathway control state

SUIT protocols: SUIT-019

PalOctMPalOctM

PalOctM: Palmitoylcarnitine & Octanoylcarnitine & Malate.

MitoPathway control state: Fatty acid oxidation pathway control state

SUIT protocols: SUIT-019

PalOctPGMPalOctPGM

PalOctPGM: Palmitoylcarnitine & Octanoylcarnitine & Pyruvate & Glutamate & Malate.

MitoPathway control state: FN

SUIT protocols: SUIT-019

PalOctPGMSPalOctPGMS

PalOctPGMS: Palmitoylcarnitine & Octanoylcarnitine & Pyruvate & Glutamate & Malate & Succinate.

MitoPathway control state: FNS

SUIT protocols: SUIT-019

PalOctPMPalOctPM

PalOctPM: Palmitoylcarnitine & Octanoylcarnitine & Pyruvate & Malate.

MitoPathway control state: FN

SUIT protocols: SUIT-019

PalPGMSGp pathway control statePalPGMSGp

PalPGMSGp: Palmitoylcarnitine & Pyruvate & Glutamate & Malate & Succinate & Glycerophosphate.

MitoPathway control state: FNSGp

SUIT protocol: SUIT-026

This substrate combination supports convergent electron flow to the Q-junction.

PalmitatePaaPalmitate is a term for the salts and esters of palmitic acid (CH3(CH2)14COOH). Palmitic acid is the first fatty acid produced during fatty acid synthesis and the precursor to longer fatty acids. Palmitate negatively feeds back on acetyl-CoA carboxylase (ACC), which is responsible for converting acetyl-CoA to malonyl-CoA, which in turn is used to add to the growing acyl chain, thus preventing further palmitate generation. In order to dissolve the water-insoluble sodium palmitate, BSA is needed to form the water-soluble compound called palmitate:BSA.
Palmitoyl-CoAPa-CoAPalmitoyl-CoA is a coenzyme A derivative of palmitate formed by acyl-CoA synthase. In contrast to medium- and short-chain acyl-CoA, palmitoyl-CoA cannot freely diffuse into the mitochondrial matrix. Formation of palmitoylcarnitine by CPTI is necessary prior to transfer into mitochondria for further fatty acid oxidation (β-oxidation). To study Fatty acid oxidation using Palmitoyl-CoA, Carnitine and low amount of malate is needed on mitochondrial preparations.
PalmitoylcarnitinePalPalmitoylcarnitine is an ester derivative of carnitine (long-chain acylcarnitine) involved in the metabolism of fatty acids. Within the cell, palmitoylcarnitine is transported into the mitochondria to deliver palmitate for fatty acid oxidation and energy production.
Partial oxygen pressurepO2 [kPa]The partial oxygen pressure pO2 [kPa] is the contribution of the O2 gas pressure to the total gas pressure. According to the gas law, the partial oxygen pressure is pO2(g) = nO2(g)·V·RT, where the concentration is cO2(g) = nO2(g)·V-1 [mol·m-3], R is the gas constant, and T is the absolute temperature, and RT is expressed in units of chemical force [J·mol-1]. In aqueous solutions at equilibrium with a gas phase, the partial O2 pressures are equal in the aqueous phase (aq) and gas phase (g), pO2(aq) = pO2(g) at total pressures where the partial pressure equals the fugacity. The O2 concentration in the aqueous phase, however, is much lower than in the gas phase, due to the low oxygen solubility in water. The activity of dissolved O2 is expressed by the pO2, where the solubility can be seen as an activity coefficient.
Particle chargeQNX, QNXThe particle charge QNX (QNX) or charge per elementary entity is the charge QelX [C] carried by ions of type X divided by the count NX [x]. The particle charge per proton is the elementary charge or proton charge e.
PascalPa

The pascal [Pa] is the SI unit for pressure. [Pa] = [J·m-3] = [N·m-2] = [m-1·kg·s-2].

The standard pressure is 100 kPa = 1 bar (105 Pa; 1 kPa = 1000 Pa). Prior to 1982 the standard pressure has been defined as 101.325 kPa or 1 standard atmosphere (1 atm = 760 mmHg).

Pathway and coupling control statesIn mitochondrial respiratory physiology a large number of pathway and coupling control states is encountered, for which a unified system of terms and abbreviations is required. In mitochondrial preparations there is a large number of potentially complex pathway control states, in contrast to only three coupling control states (L, P, E). Therefore, it is practical to use L, P, and E as subscripts attached to the abbreviation of the pathway control state.
Pathway control efficiencyjZ-YPathway control efficiencies are flux control efficiencies, expressing the relative change of flux in response to a transition between two electron-transfer-pathway states due to a change of (1) substrate availability or (2) inhibition of enzyme steps in the pathway, in a defined coupling-control state.
Pathway control ratioFCR

Substrate control ratios are flux control ratios FCR, at a constant mitochondrial coupling-control state. Whereas there are only three well-defined coupling-control states of mitochondrial respiration, L, P, E (LEAK respiration, OXPHOS, Electron transfer pathway), numerous Electron-transfer-pathway states are possible.

Careful selection of the reference state, Jref, is required, for which some guidelines may be provided without the possibility to formulate general rules. FCR are best defined by taking Jref as the maximum flux (e.g. NSE), such that flux in various other respiratory states, Ji, is smaller or equal to Jref. However, this is not generally possible with FCR. For instance, the N/S pathway control ratio (at constant coupling-control state) may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The S-pathway control state may be selected preferentially as Jref, if mitochondria with variable N-linked injuries are studied. In contrast, the reference state, Z, is strictly defined for flux control efficiency.

Paywall journalismThough often defined from the individual reader's perspective, a paywall can also apply to an institution (such as a library) or the author. Paywall journalism is the opposite of Open Access. Open Science does not accept paywalls with the argument, that the public pays for governmentally funded research, hence research funded by public grants should be published with open access for the public without paywalls. Paywalls are most frequently defined from the perspective of the individual reader, who has to pay for an article or pay a journal subscription as a requisite for obtaining full access to the information that is otherwise hidden behind the paywall (reader-paywall journal). From the perspective of the authors, however, an author-paywall journal is defined as any journal which requests publication charges or page charges from the authors for publishing the manuscript Open Access or publishing it at all. Similarly, an institutional-paywall journal charges an institution – typically university libraries – for granting open access to the members of this institution. As long as paywall journalism prevails in science, at least paywall transparence should be required, to declare for each publication not only the reader-paywall costs but provide the full information on the author-paywall and institutional-paywall expenses.
Peer reviewPeer reviews provide a critical assessment of a manuscript prior to publication. Bioenergetics Communications publishes Open Peer Reviews for transparency of the review process.
PeerJ Preprints 'pre-print' area of PeerJ

PeerJ Preprints is the 'pre-print' area of the Open Access journal PeerJ. Similar to preprint servers that already exist (for example arXiv.org), authors can submit draft, incomplete, or final versions of articles they are working on. By using this service, authors establish precedent; they can solicit feedback; and they can work on revisions of their manuscript. Once they are ready, they can submit their preprint article into PeerJ (although it is not a requirement to do so).

PeerJ Preprints was launched in April 2013. It only accepts submissions in the same subject areas as PeerJ (biological, medical and environmental sciences) and PeerJ Computer Science. In order to submit to PeerJ Preprints, at least the submitting author must have a user account with PeerJ. There is no pre-publication peer-review of submissions; however we do perform basic checks to ensure conformity with our policies. Submissions are made using the same platform as with the peer-reviewed journals, although some of the requirements are less stringent. Articles are not typeset, but we do provide automated conversion into PDF. The default is for a PeerJ Preprints publication to be fully open to all viewers (what we call a 'public' pre-print).

PeerJ is an Open Access, peer-reviewed, scholarly journal. It considers and publishes research articles in the biological, medical and environmental sciences. It aims for rapid decision making and will publish articles as soon as they are ready. PeerJ is based in both San Diego, US, and London, UK.

Pen-Contact Oil
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Pen-Contact Oil, for stable low contact resistance between the OroboPOS head and the OroboPOS-Connector.

Discontinued - The Pen-Contact Oil is not part of our product range anymore as it is not absolutely required for ensuring the functioning of the OroboPOS-Connector and the OroboPOS. The Oroboros experts do not use it anymore.

Perfluorooctanoic acidPFOAPerfluorooctanoic acid (PFOA) is a metabolically inert perfluorinated fatty acid which activates UCP1 in brown-fat mitochondria. UCP1-dependent respiration can be stimulated with 600 μM PFOA after inhibition of the phosphorylation system.
Performance EstimationPerformance estimation
Permeability transition porePTPThe (mitochondrial, mt) permeability transition pore (PTP) is an unspecific pore presumed to involve components of both the inner and outer mt membrane which upon opening induces a massive increase of the inner mt membrane permeability for solutes up to 1.5 kDa. It is crucially involved in cell death induction in response to, among other stimuli, radical stress and/or calcium overload and may cause necrosis or apoptosis. It plays an important role in neurodegenerative diseases, cardiac ischemia-reperfusion injury and possibly various other diseases. Previously considered essential molecular constituents such as the voltage-dependent anion channel (VDAC), the adenine nucleotide translocator (ANT) and cyclophilin D (CypD) have all been shown to be important regulators of mtPTP opening, but the molecular entities actually forming the pore are still unknown at present. The opening of the pore can be prevented using cyclosporin A, a compound that binds cyclophilin D avoiding the formation of the pore. In respirometry, mtPTP opening may be observed as a sudden decrease of respiration of isolated mitochondria (Hansson 2010 J Biol Chem).
Permeabilized cellspce

Permeabilized cells (pce) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane (e.g., with digitonin), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the mt-membranes.

Permeabilized cells (pce) are, therefore, not any longer viable or living cells (ce), since the intactness of cells implies the intactness of the plasma membrane. Any typical quantiative cell viability test (trypan blue etc) evaluating the intactness of the plasma membrane, yields a 100% negative result on fully permeabilized cells.

For permeabilizing the cell plasma membranes chemically with digitonin, without damaging the mt-membranes, the optimum concentration of digitonin must be previously determinated. The protocol SUIT-010 is designed for the evaluation of optimum digitonin concentration for permeabilizing cells, a requirement to account for differences between cell types, the concentration of cells, and variability between batches of the natural product digitonin.

Permeabilized muscle fiberspfi

Permeabilized muscle fibers (pfi) are used as a mitochondrial preparation in respirometry to access mitochondrial function comparable to isolated mitochondria (imt). pfi are obtained by selectively permeabilizing the plasma membrane mechanically and chemically (saponin), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the mt-membranes.

» MitoPedia topic: Mitochondrial preparations
Permeabilized tissueptiPermeabilized tissue (pti, see also permeabilized muscle fibers, pfi) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane mechanically or chemically (e.g., with saponin), for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the mt-membranes.
Permeabilized tissue or cellspti, pce

Permeabilized tissue (pti, see also permeabilized muscle fibers, pfi) or cells (pce) are mitochondrial preparations obtained by selectively permeabilizing the plasma membrane mechanically or chemically, for the exchange of soluble molecules between the cytosolic phase and external medium, without damaging the mt-membranes.

Permeabilized cells (pce) are, therefore, not any longer viable or living cells (ce), since the intactness of cells implies the intactness of the plasma membrane. Any typical quantiative cell viability test (trypan blue etc) evaluating the intactness of the plasma membrane, yields a 100% negative result on fully permeabilized cells.

Peroxisome proliferator-activated receptor gamma coactivator 1-alphaPGC-1αPeroxisome proliferator-activated receptor-γ (PPAR-γ) coactivator-1α (PGC-1α) is a protein which functions as an inducible transcriptional coactivator, a coregulator of transcription factors, particularly NRF-1 and TFAM. PGC-1α was first described in 1998 (Puigserver 1998 Cell). PGC-1α drives the formation of slow-twich muscle fibres (Lin 2002 Nature) and is increased upon endurance training (Norrbom 2004 J Appl Physiol). PGC-1α expression is inhibited by the proinflammatory cytokine tumor necrosis factor α (TNF-α) and high levels of leptin. Upregulation of PGC-1α expression is induced by increased eNOS activity -> NO -> guanylate cyclase -> cGMP (Nisoli 2007 Circ Res). AMP-activated protein kinase (AMPK) increases PGC-1α expression through SIRT1 (Canto 2009 Nature).
PhenylsuccinatePhenylsuccinate is a competitive inhibitor of succinate transport (20 mM).
PhosphatePiSee: Inorganic phosphate
Phosphate carrierPiCThe phosphate carrier (PiC) is a proton/phosphate symporter which transports negatively charged inorganic phosphate across the inner mt-membrane. The transport can be described either as symport of H+ with Pi, or antiport of hydroxide anion against Pi. The phosphate carrier is a component of the phosphorylation system.
PhosphocreatinePCrPhosphocreatine is a high energy compound in the skeletal muscle of vertebrates and is present in 4 to 5 times the concentration of ATP.
Phosphoenolpyruvate carboxykinasePEPCKPhosphoenolpyruvate carboxykinase (PEPCK) catalyzes the anabolic reaction of oxaloacetate (Oxa) to phosphoenolpyruvate at the expense of GTP. PEPCK is a cytoplasmatic enzyme involved in gluconeogenesis in mouse and rat liver, but 'is found in the mitochondria in the rabbit and chicken, and in both cytoplasm and mitochondria in the guinea pig' (Lehninger 1970). In many anoxia-resistant animals, PEPCK plays an important catabolic role under severe hypoxia and anoxia at the PEPCK branchpoint (Hochachka, Somero 2002), feeding malate into the reversed TCA cycle: malate is dismutated to pyruvate catalyzed by malic enzyme in the oxidative direction, and to fumarate in the reductive direction, leading to formation of succinate and ATP under anoxia (Gnaiger 1977).
PhosphorescencePhosphorescence is a similar phenomenon to fluorescence. However, instead of the electron returning to its original energy state following excitation, it decays to an intermediate state (with a different spin value) where it can remain for some time (minutes or even hours) before decaying to its original state. Phosphorescence is one form of Luminescence, especially Photoluminescence.
Phosphorylation pathwayDT
From Gnaiger 2014 MitoPathways

The phosphorylation pathway (phosphorylation system) is the functional unit utilizing the protonmotive force to phosphorylate ADP (D) to ATP (T), and may be defined more specifically as the P»-system. The P»-system consists of adenine nucleotide translocase, phosphate carrier, and ATP synthase. Mitochondrial adenylate kinase, mt-creatine kinase and mt-hexokinase constitute extended components of the P»-system, controlling local AMP and ADP concentrations and forming metabolic channels. Since substrate-level phosphorylation is involved in the TCA-cycle, the P»-system includes succinyl-CoA ligase (GDP to GTP or ADP to ATP).

PhotoBiologyPBPhotoBiology is the science of the effect of light on biological processes. This includes photosynthesis, photochemistry, photophysics, photomorphogenesis, vision, bioluminescence, circadian rhythms and photodynamic therapy. Phototoxicity results from non-ionizing radiation (i.e. ultraviolet, visible and infrared radiation). Non-ionizing radiation is any type of electromagnetic radiation that does not carry enough energy per quantum (photon energy below 10 eV) to completely remove an electron from an atom or molecule. When photons interact with molecules, the molecules can absorb the photon energy and become excited, reacting with surrounding molecules and stimulating "photochemical" and "photophysical" changes. Respiration may be affected by light during photosynthesis or in dark respiration, with the transient response of light-enhanced dark respiration.
PhotodecompositionPDPhotodecomposition or photodegradation is the process of decay of organic material induced by increasing light intensity. Under aerobic conditions, the enhancement of photodecomposition by light intensity can be quantified by oxygen consumption in a controlled light regime.
Photodiode arraysPhotodiode arrays are two dimensional assemblies of photodiodes. They are frequently used in conjunction with charge coupled devices (CCDs) for digital imaging. They can be used in combination with dispersion devices to detect wavelength dependent light intensities in a spectrofluorometer or spectrophotometer.
PhotodiodesPhotodiodes are photodetectors that convert incident light into a current or voltage dependent on their configuration. They have replaced photomultiplier tubes for most applications. For fluorometric measurements that do not require spectral data, a single photodiode with suitable filters can be used. Due to their larger detection area, they are more sensitive than photodiode arrays.
PhotorespirationPhotorespiration is the process by which the enzyme RuBisCo oxygenates ribulose biphosphate (RuBP) instead of carboxylating it as part of the Calvin-Benson cycle, creating phosphoglycolate, a product that cannot be used within this cycle, thus dissipating the energy in photosynthesis. It is estimated that approximately 25 % of RuBisCo reactions are photorespiration, meaning a potential 25 % reduction in photosynthetic output due to the carbon fixed by photorespiration being released as carbon dioxide and nitrogen as ammonia, while the other product, 3-phosphoglycerate (G3P), requires a higher metabolic cost. This process involves a complex network of enzymes and metabolite exchanges between the chloroplasts, peroxisomes and mitochondria. It is also known as the oxidative photosynthetic carbon cycle or C2 photosynthesis. Environmental conditions tend to affect it, such as temperature and partial pressure of oxygen and carbon dioxide. C4 plants, CAM plants and algae have biochemical and biophysical mechanisms to overcome the photosynthetic losses due to photorespiration making them more photosynthetically efficient than C3 plants. Recent plant biotechnology advances focuse on increasing plant photosynthetic carbon fixation by reducing photorespiration loses.
PhotosynthesisPSPhotosynthesis is the process that converts light energy into chemical energy which is subsequently transformed to the physiological energy demand. Photosynthesis has a light-dependent and light-independent (dark) phase. In plants, algae, and cynobacteria, light energy is absorbed during the light phase by the pigment chlorophyll and used to split water and generate adenosine triphosphate (ATP) and reducing power - nicotinamide adenine dinucleotide phosphate (NADPH), with the net production of O2 as a waste product. During the dark phase ATP and NADPH are used to synthesize carbohydrates from CO2 through the metabolic pathway called Calvin-Benson cycle. Oxygenic photosynthesis is responsible for producing and maintaining the oxygen concentration of the Earth’s atmosphere. In bacteria such as cyanobacteria, photosynthesis involves the plasma membrane and the cytoplasm. In eukaryotic cells (plants and algae), photosynthesis takes place in the chloroplasts.
Physiological pathway-control stateSee Electron-transfer-pathway state.
PiericidinPiericidin C25H37NO4 is an antibiotic (isolated from Streptomyces mobaraensis) showing similarity with ubiquinone structure which has a potent and competitive inhibitory effect of CI (it competes with endogenous and partially with exogenous Q for binding sites). CI inhibitors have been divided (1) depending of the site of action (functional classification): quinone antagonists (e.g. piericidin A, first site), semiquinone antagonists (piericidin A, second site; piericidin B; rotenone and quinol antagonists (myxothiazol; stigmatellin), and (2) depending on their effect on ROS production: inducing ROS production (e.g. rotenone, piericidin A, Rolliniastatin-1 and -2) and preventing ROS production (e.g. stigmatellin, capsaicin, mucidin and coenzyme Q2). In plants, pieridicin A inhibits photosystem II.
Pipette\Plastic\1 ml ungraded
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Pipette\Plastic\1 mL ungraded, for filling electrolyte into the reservoir of the OroboPOS.

Plan SSPlan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. According to Science Europe, "Plan S requires that recipients of research funding from cOAlition S organisations make the resulting publications available immediately (without embargoes) and under open licences, either in quality Open Access platforms or journals or through immediate deposit in open repositories that fulfil the necessary conditions."
PlateletPLTPlatelets or thrombocytes (PLT) are cell fragments derived from megakaryocytes with hemostatic function in the blood stream. PLT are anucleated but contain functioning mitochondria that play a critical role in PLT activation.
Platelet-rich plasmaPRPPlatelet-rich plasma (PRP) is obtained as the upper layer at low-speed centrifugation (around 150-200 g), when white and red blood cells sediment and thus get separated from plasma containing the platelets. For further details see blood cell preparation.
Plot - DatLabCtrl+F6A plot in DatLab represents a specific channel in the graph. To change the Layout for DatLab graphs go to [Graph]/Select plots to open the Graph layout window.
Plunger\10 mm3
Plunger 10 mm3.JPG

Plunger\10 mm3 for Microsyringe\10 mm3 51/0.13 mm, spare.

Plunger\25 mm3
Plunger 25 mm3.JPG

Plunger\25 mm3 for Microsyringe\25 mm3 51/0.15 mm, spare. Discontinued

Plunger\50 mm3
Plunger 50 mm3.JPG

Plunger\50 mm3 for Microsyringe\50 mm3 51/0.15 mm, spare. Discontinued

PoicilothermsPoicilotherms are ectotherms whose body temperatures conform to the temperature of the milieu in a thermally variable environment.
Polarization voltageUA polarization voltage of 600 mV to 800 mV is applied between anode and cathode of the polarographic oxygen sensor, resulting in a current when oxygen is consumed. The current is converted by the electronics to a voltage (raw signal) which must not be confused with the polarization voltage.
Polarographic oxygen sensorPOSPolarographic oxygen sensors (POS) are operated with a polarization voltage between the cathode and anode, connected by an electrolyte. Cathode, anode and electrolyte are separated from the analyte by an oxygen-permeable membrane. Oxygen is reduced at the cathode such that the local oxygen concentration is maintained at zero, and diffuses along the concentration gradient from the stirred medium to the cathode, resulting in a linear calibration between oxygen partial pressure and electric current [Amp] (amperometric mode of operation). The OroboPOS is the POS applied in the Oroboros O2k.
Polishing Cloth
POS polishing cloth for cathode cleaning.jpg

Polishing Cloth for cathode cleaning. Replace the Polishing Cloth at intervals. A two-year interval may be considered in cases of intensive use.

Polishing Powder
POS polishing powder for cathode cleaning.jpg

Polishing Powder 0.3 µm and Polishing Powder 0.05 µm for cathode cleaning of OroboPOS and Q-sensors.

Polyether ether ketonePEEKPolyether ether ketone (PEEK) is a semicrystalline organic polymer thermoplastic, which is chemically very resistant, with excellent mechanical properties. PEEK is compatible with ultra-high vacuum applications, and its resistance against oxygen diffusion make it an ideal material for high-resolution respirometry (POS insulation; coating of stirrer bars; stoppers for closing the O2k-Chamber).
Polyvinylidene fluoridePVDFPolyvinylidene fluoride (PVDF) is a pure thermoplastic fluoropolymer, which is chemically very resistant, with excellent mechanical properties. It is used generally in applications requiring the highest purity, strength, and resistance to solvents, acids, bases and heat (Wikipedia). PVDF is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (coating of stirrer bars; stoppers for closing the O2k-Chamber).
PopulationA population (or group) defines the sample type of an experiment, before sample preparation. The population (or group) size represents the upper limit of the sample size, N.
Post-examination proceduresPost-examination procedures, in the postanalytical phase, are processes following the examination including systematic review, formatting and interpretation, authorization for release, reporting and transmission of the results, and storage of samples of the examinations.
PotentiometryPotentiometry is the general term given to the method of measuring the electric potential difference between two electrodes connected by an electrolytic solution. The potential of the reference electrode is constant. The other electrode is called the indicator electrode. If this is an ion-selective electrode which is in equilibrium with the solution, the measured electric potential difference is proportional to the (negative) logarithm of the activity of a specific ion in the solution. Examples are the pH glass electrode for measurement of pH, and the TPP+ electrode for measurement of pTPP and calculation of mt-membrane potential.
PowerP [W]Power P [W = J·s-1] is exergy per time, or force times flow, which cannot be created internally yet is not conserved but is dissipated (P < 0) in irreversible energy transformations at constant temperature and (barometric) pressure, T,p. Metabolic power and heat flux of irreversible processes are distinguished as the time rate of Gibbs energy and enthalpy changes, respectively.
Power O2k Numbers
Power O2k Numbers.JPG

Power O2k Numbers: Single number to label the O2k in a Power O2k-Lab.

Power O2k-FluoRespirometer
Power O2k-FluoRespirometer

Power O2k-FluoRespirometer - optional configuration as additional system for increasing output combined with the O2k-FluoRespirometer (O2k-Series H). The Power O2k-FluoRespirometer includes the TIP2k and the O2k-sV-Module, and supports all add-on O2k-Modules of the Oroboros O2k. It can be added to an existing Oroboros O2k of any O2k-Series. This application does not require an additional ISS-Integrated Suction System and O2k-Titration Set. Furthermore, the OroboPOS-Mounting Tool of the OroboPOS Service Tools can be used from the available O2k and is not included.

Power O2k-Respirometer
Power O2k notext.png

The Power O2k-Respirometer is an economical option for using additional O2k-Units to increase output in high-resolution respirometry.

Pre-examination proceduresPre-examination procedures, in the preanalytical phase, are steps starting, in chronological order, from the clinician’s request and including the examination requisition, preparation of the patient, collection of the primary sample, and transportation to and within the laboratory, and ending when the analytical examination procedure begins.
PrePubMedPrePubMed indexes preprints from arXiv q-bio, PeerJ Preprints, bioRxiv, F1000Research, preprints.org, The Winnower, Nature Precedings, and Wellcome Open Research. Articles are not stored on PrePubMed, but you will be linked to the article at the respective site.
PrecisionPrecision of measurement is the closeness of agreement between independent results of measurements obtained under stipulated conditions [SOURCE: ISO 3534-1:1993, 3.14]. Precision of measurement cannot be given a numerical value in terms of the measurand, only descriptions such as 'sufficient' or 'insufficient' for a stated purpose. The degree of precision is usually expressed numerically by the statistical measures of imprecision of measurements, such as standard deviation and coefficient of variation, that are inversely related to precision. "Precision" of a given measurement procedure is subdivided according to the specified precision conditions. "Repeatability" relates to essentially unchanged conditions and is often termed "withinserial" or "within-run precision". "Reproducibility" relates to changes in conditions, e.g. time, different laboratories, operators, and measuring systems (including different calibrations and reagent batches).
Preparation of SUIT chemicalsPreparation of SUIT chemicals describes the preparation of chemicals used in Substrate-Uncoupler-Inhibitor Ttitration (SUIT) protocols.
PreprintA preprint is {Quote} a way in which a manuscript containing scientific results can be rapidly communicated from one scientist, or a group of scientists, to the entire scientific community {end of Quote}. Preprints are disseminated without peer review, e.g. in the preprint server MitoFit Preprints. In contrast, the journal Bioenergetics Communications publishes peer-reviewed articles, which preferentially are communicated in advance in MitoFit Preprints.
Preprints multidisciplinary preprint platform

Preprints is a platform dedicated to making early versions of research outputs permanently available and citable. We post original research articles and comprehensive reviews, and papers can be updated by authors at any time. Content on Preprints is not peer-reviewed and can receive feedback from readers. Preprints focuses on original research articles and comprehensive reviews. Editorials, discussion papers, and commentary are usually not suitable. Preprints is fully owned and funded by MDPI, an open access journal publisher. It is run on a non-profit basis. You do not need to submit to an MDPI journal in order to post a preprint here, any work is welcome. If you do submit to an MDPI journal, you will be invited to submit to Preprints.org during the submission process.

Preprints has the following features: Multidisciplinary: We cover all research disciplines. Open access: 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. Citation via Crossref DOI: Each preprint has a unique digital object identifier issued by Crossref. This makes them instantly citable and provides a permanent link to the article, even if the URL on our platform changes. New versions of preprints receive a different DOI. Comment on any article: Authors can receive public or private feedback from readers directly from the preprint abstract page. Simple submission process: Submitting a preprint only requires basic information, our team of editors will do the rest and post your preprint as soon as possible.

MDPI.com is a platform for peer-reviewed, scientific open-access journals operated by MDPI, based in Basel, Switzerland (since 1996). MDPI is a member of the Committee on Publication Ethics (COPE). To verify the originality of content submitted to our journals, we use iThenticate to check submissions against previous publications. MDPI works with Publons to provide reviewers with credit for their work.

Pressurep, P, Π [Pa]Pressure is a fundamental quantity expressing energy per volume. The SI unit of pressure is generally pascal [Pa] = [J·m-3]. The term 'stress' (mechanical stress) is used as a synonym for pressure (SI). Pressure is known in physics as mechanical pressure, which is force per area, p = F·A-1 [Pa] = [N·m-2]. In physical chemistry, gas pressure is defined as p = n·V-1·RT, where the concentration is c = n·V-1 [mol·m-3], R is the gas constant, and T is the absolute temperature, and RT is expressed in units of chemical force [J·mol-1]. van't Hoff's osmotic pressure assumes the same form applied to dissolved substances diffusing across a semipermeable membrane, but concentrations should be replaced by activities. The activity of dissolved gases is expressed by the partial pressure, where the solubility can be seen as an activity coefficient. Pressure appears explicitely or implicitely in all chapters of physics and physical chemistry. In contrast to the universal counterparts energy and force, however, the general connections between various isomorphic expressions of pressure remain poorly understood: Pressure is the concentration of the force at the point of action. More generally, pressure is the force times concentration at the interphase of interaction.
Primary sampleThe primary sample or specimen is a set of one or more parts initially taken from an object. In some countries, the term “specimen” is used instead of primary sample (or a subsample of it), which is the sample prepared for sending to, or as received by, the laboratory and which is intended for examination.
ProductA product in a chemical reaction has a positive stoichiometric number since it is produced, whereas a substrate has a negative stoichiometric number since it is consumed.
Proficiency testPTProficiency testing PT is an evaluation of participant performance against pre-established criteria by means of interlaboratory comparisons. Some PT providers in the medical area use the term “External Quality Assessment (EQA)” for their proficiency testing schemes, or for their broader programmes, or both. Internal PT strategies may be implemented into laboratory science as practical steps towards PT to achieve reproducibility.
Project

The following definition lacks quality control and is not applied as such in the Oroboros QM.

A scientific project is a collection of experiments designed to proof or disproof a specific hypothesis. The experiments will follow the logic of the scientific discovery [1] on which a hypothesis will support a prediction and this will be tested by experimental assays (i.e., observations under controlled conditions). The result of these experiments will proof or disproof the specific hypothesis and, usually, provide new hypotheses to test. A scientific project must be carefully designed to obtain relevant statistical information through enough data collection.

[1] Popper K (2002) The logic of scientific discovery. Routledge Classics. ISBN: 978-0-415-27843-0

ProlinePro
Proline

Proline (Pro), C5H9NO2, is an amino acid which occurs under physiological conditions mainly in the nonpolar form, with pKa1 = 1.99 pKa2 = 10.96. Proline is an anaplerotic substrate that supports both the proline pathway control state and the glutamate-anaplerotic pathway control state. Proline is used as a single substrate or in combination with carbohydrate-derived metabolites in mitochondria particularly of flight muscle of many (but not all) insects. Proline is oxidized to delta-1-pyrroline-5-carboxylate by the mtIM L-proline:quinone oxidoreductase (proline dehydrogenase, ProDH), with reduction of FAD to FADH2 and direct entry into the Q-junction. delta-1-pyrroline-5-carboxylate is converted to glutamate by 1-pyrroline-5-carboxylate dehydrogenase.

Proline dehydrogenaseProDHProline dehydrogenase (ProDH), L-proline:quinone oxidoreductase, is located on the inner side of the mtIM, oxidizing proline to delta-1-pyrroline-5-carboxylate, with reduction of FAD to FADH2 and direct entry into the Q-junction, exerting an additive effect of convergent pathways. ProDH is widely distributed in a variety of organisms, is a source of ROS, and may play a role in carcinogenesis.
Prosthetic group

A prosthetic group is a cofactor that is attached permanently and tightly or even covalently to an enzyme and that is regenerated in each enzymatic turnover. Thus a prostethic group is distinguished from a coenzyme or cosubstrate that is attached loosely and transiently. Like a coenzyme, the prosthetic group is required by an enzyme for its activity. A prosthetic group is 'a tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity' (IUPAC definition).

FMN/FMNH2 and FAD/FADH2 are prosthetic groups of Complex I and Complex II, respectively.

Protocol editor - DatLab
Protonp+, pThe terms proton p and hydrogen ion H+ are used synonymously in chemistry. In particle physics, a proton is a subatomic particle with a positive electric charge. Protons and neutrons are collectively referred to as nucleons. The proton is a bare charge with only about 1/64 000 of the radius of a hydrogen atom, and so the free proton is extremely reactive chemically. Therefore, the free proton has an extremely short lifetime in aqueous solutions where it forms the hydronium ion, H3O+, which in turn is further solvated by water molecules in clusters such as H5O2+ and H9O4+.
Proton leakFlux 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 pumpMitochondrial proton pumps are large enzyme complexes (CI, CIII, CIV, CV) spanning the inner mt-membrane, partially encoded by mtDNA. CI, CIII and CIV are proton pumps that drive protons against the electrochemical protonmotive force, driven by electron transfer from reduced substrates to oxygen. In contrast, ATP synthase (also known as CIV) is a proton pump that utilizes the energy of proton flow along the protonmotive force to drive phosphorylation of ADP to ATP.
Proton slipProton slip is a property of the proton pumps (Complexes CI, CIII, and CIV) when the proton slips back to the matrix side within the proton pumping process. Slip is different from the proton leak, which depends on Δp and is a property of the inner mt-membrane (including the boundaries between membrane-spanning proteins and the lipid phase). Slip is an uncoupling process that depends mainly on flux and contributes to a reduction in the biochemical coupling efficiency of ATP production and oxygen consumption. Together with proton leak and cation cycling, proton slip is compensated for by LEAK respiration or LEAK oxygen flux, L. Compare: Proton leak.
Protonmotive forcepmF, ∆mFH+, Δp [J·MU-1]

The protonmotive forcemFH+ is known as Δp in Peter Mitchell’s chemiosmotic theory [1], which establishes the link between electric and chemical components of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the pmF ranks among the most fundamental theories in biology. As such, it provides the framework for developing a consistent theory and nomenclature for mitochondrial physiology and bioenergetics. The protonmotive force is not a vector force as defined in physics. This conflict is resolved by the generalized formulation of isomorphic, compartmental forces, ∆trF, in energy (exergy) transformations [2]. Protonmotive means that there is a potential for the movement of protons, and force is a measure of the potential for motion.

The pmF is generated in oxidative phosphorylation by oxidation of reduced fuel substrates and reduction of O2 to H2O, driving the coupled proton translocation from the mt-matrix space across the mitochondrial inner membrane (mtIM) through the proton pumps of the electron transfer pathway (ETS), which are known as respiratory Complexes CI, CIII and CIV. ∆mFH+ consists of two partial isomorphic forces: (1) The chemical part, ∆dFH+, relates to the diffusion (d) of uncharged particles and contains the chemical potential difference§ in H+, ∆µH+, which is proportional to the pH difference, ∆pH. (2) The electric part, ∆elFp+ (corresponding numerically to ∆Ψ)§, is the electric potential difference§, which is not specific for H+ and can, therefore, be measured by the distribution of any permeable cation equilibrating between the negative (matrix) and positive (external) compartment. Motion is relative and not absolute (Principle of Galilean Relativity); likewise there is no absolute potential, but isomorphic forces are stoichiometric potential differences§.

The total motive force (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆mFH+. Reading this symbol by starting with the proton, it can be seen as pmF, or the subscript m (motive) can be remembered by the name of Mitchell,

mFH+ = ∆dFH+ + ∆elFp+

With classical symbols, this equation contains the Faraday constant, F, multiplied implicitly by the charge number of the proton (zH+ = 1), and has the form [1]

∆p = ∆µH+F-1 + ∆Ψ

A partial electric force of 0.2 V in the electrical format, ∆elFeH+a, is 19 kJ∙mol-1 H+a in the molar format, ∆elFnp+a. For 1 unit of ∆pH, the partial chemical force changes by -5.9 kJ∙mol-1 in the molar format, ∆dFnH+a, and by 0.06 V in the electrical format, ∆dFeH+a. Considering a driving force of -470 kJ∙mol-1 O2 for oxidation, the thermodynamic limit of the H+a/O2 ratio is reached at a value of 470/19 = 24, compared to the mechanistic stoichiometry of 20 for the N-pathway with three coupling sites.

Protonmotive pressurepmP, ∆mΠH+ [kPa]

The protonmotive pressure, ∆mΠH+ or pmP [kPa], is an extension of Peter Mitchell’s concept of the protonmotive force pmF, based on Fick’s law of diffusion and Einstein’s diffusion equation, accounting for osmotic pressure (corresponding to the diffusion term in the pmF) and electric pressure (the electric term or membrane potential in the pmF). The linearity of the generalized flow-pressure relationship explains the non-ohmic flow-force dependence in the proton leak rate as a function of membrane potential.

The total motive pressure (motive = electric + chemical) is distinguished from the partial components by subscript ‘m’, ∆mΠH+,

mΠH+ = ∆dΠH+ + ∆elΠp+
PubMedPubMed is a free search tool for articles in the life sciences field.
Publication efficiencyFr,a/pPublication efficiency is the fraction Fr,a/p of reproducible publications Nr which are among the number Na of publications that receive attention and meaningful interpretation, per total count Np of all published communications. Publication efficiency Fr,a/p = Fr/p·Fa/p is low due to (1) the reproducibility crisis expressed as low reproducibility efficiency Fr/p = Nr/Np, and (2) the inflation crisis expressed as low attention efficiency Fa/p = Na/Np. Estimates of these partial efficiencies vary from field to field. With Fr/p=0.15 and Fa/p=0.05, the current publication efficiency is as low as 0.0075, or only 0.75 % of all presently published communictions are reproducible and receive attention and meaningful interpretation. Reduction of the number of irreproducible zero-value publications is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.
Publicly deposited protocolsPDPResearchers need to be introduced into adhering to publicly deposited protocols. Prespecified and time-stamped protocols that are publicly deposited may help to save Millions of Euros that may otherwise be wasted on research that is lacking coherent standards.
PyruvateP
Pyruvic acid

Pyruvic acid, C3H4O3, is an alpha-keto monocarboxylic acid which occurs under physiological conditions mainly as the anion pyruvate-, P, with pKa = 2.5. Pyruvate is formed in glycolysis from phosphoenolpyruvate. In the cytosol, pyruvate is a substrate of lactate dehydrogenase. Pyruvate enters the mitochondrial matrix via a specific low Km' H+/monocarboxylate cotransporter known as the pyruvate carrier. Similarly, the plasma membrane of many cell types has H+/monocarboxylate cotransporter activity and pyruvate can thus be added as a substrate to living cells. In the mt-matrix the oxidative decarboxylation of pyruvate is catalyzed by pyruvate dehydrogenase and yields acetyl-CoA. Pyruvate competitively reverses the inhibition of cytochrome c oxidase by cyanide. Pyruvate is an antioxidant reacting with hydrogen peroxide.

Pyruvate carboxylasePCPyruvate carboxylase synthesizes oxaloacetate from pyruvate and CO2 as an anaplerotic reaction in the mitochondrial matrix of the liver and kidney of higher animals, representing an alternative to the malic enzyme pathway to oxaloacetate or the phosphoenolpyruvate carboxykinase reaction (compare glyoxylate cycle in plants and microorganisms). Carboxylation of pyruvate to oxaloacetate requires Mg-ATP. Acetyl CoA is a strong positive modulator. PC can form pyruvate from oxaloacetate to remove an excess of oxaloacetate which inhibits succinate dehydrogenase.
Pyruvate carrierThe monocarboxylic acid pyruvate- is exchanged electroneutrally for OH- by the pyruvate carrier. H+/anion symport is equivalent to OH-/anion antiport.
Pyruvate dehydrogenasePDHPyruvate dehydrogenase is the first component enzyme of the pyruvate dehydrogenase complex, which catalyzes oxidative decarboxylation of pyruvate in the mt-matrix, and yields acetyl-CoA. PDH is known as the mitochondrial gatekeeper in the core energy pathway of electron flow into the tricarboxylic acid cycle.
Pyruvate dehydrogenase complexPDHCOxidative decarboxylation of pyruvate is catalyzed by the pyruvate dehydrogenase complex in the mt-matrix, and yields acetyl-CoA.
P»-systemP»systemThe ADP-ATP phosphorylation system or P»-system. See Phosphorylation system.
QQ

Multiple meanings of Q

» Coenzyme Q Q
» Charge Q, Qel
» Heat Q, Qth
Q calibration - DatLabQ calibration
Q-ModuleQ-Module
Q-box 002.jpg

The Q-Module, developed for measuring the Q redox state and cyclic voltammetry, is supported by the NextGen-O2k and consists of the Q-Sensor, integrated electronic components in the O2k, and the DatLab software.

Q-Sensor
Q stopper.jpg

The Q-Sensor has been designed as a part of the Q-Module for measurements with cyclic voltammetry and voltammetry, allowing for analysis of the Q redox state. The Q-Stopper with the reference electrode is called Q-Sensor, which is plugged in the NextGen-O2k. A three-electrode system is used to detect the Q redox state. Two of the three electrodes (glassy carbon and platinum electrode) are built into the Q-Stopper, while the reference electrode is removable (Reference-Electrode\2.4 mm).

Q-cycleQQ-cycle refers to the sequential oxidation and reduction of the electron carrier Coenzyme Q (CoQ or ubiquinone) in mitochondria or plastoquinones in the photosynthetic system. Originally, the concept of the Q-cycle was proposed by Peter D Mitchell. Following several modifications, the Q-cycle is established, describing how CIII translocates hydrogen ions against the protonmotive force. The reduced CoQ (ubiquinol QH2) binds to the Qo site of CIII, while the oxidized CoQ (ubiquinone Q) to the Qi site of CIII. First, QH2 reduces the iron-sulfur protein and feeds cytochrome c1 with one electron. The other electron is transferred to the bL heme and reduces the bH heme, which transfers the electron to ubiquinone at the Qi-site which is reduced to a semiquinone. A second QH2 is required to fully reduce semiquinone to ubiquinol. At the end of the Q-cycle, four protons leave the mt-matrix and enter the intermembrane space, and the reduced cytochrome c transfers electrons to CIV. The ubiquinol generated at the Qi-site can be reused by binding to the Qo-site of CIII.
Q-junction
Q-junction

The Q-junction is a junction for convergent electron flow in the Electron transfer pathway (ET-pathway) from type N substrates and mt-matrix dehydrogenases through Complex I (CI), from type F substrates and FA oxidation through electron-transferring flavoprotein Complex (CETF), from succinate (S) through Complex II (CII), from glycerophosphate (Gp) through glycerophosphate dehydrogenase Complex (CGpDH), from choline through choline dehydrogenase, from dihydro-orotate through dihydro-orotate dehydrogenase, and other enzyme Complexes into the Q-cycle (ubiquinol/ubiquinone), and further downstream to Complex III (CIII) and Complex IV (CIV). The concept of the Q-junction, with the N-junction and F-junction upstream, provides the rationale for defining Electron-transfer-pathway states and categories of SUIT protocols.

Q-poolsQDifferent 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 substrates. 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.
Q-redox state

The Q-redox state reflects the redox status of the Q-junction in the mitochondrial or chloroplast electron transfer system (ETS). Coenzyme Q (CoQ or Q, ubiquinone) is a mobile redox component located centrally in the mitochondrial ETS, while plastoquinones are essential mobile components in the photosynthetic system with a similar function. The Q-redox state depends on the balance between reducing capacities of convergent electron entries from fuel substrates into the Q-junction and oxidative capacities downstream of Q to the electron acceptor oxygen. Therefore, deficiencies in the mitochondrial ETS, originating from e.g. the malfunction of respiratory Complexes, can be detected by measuring the changes of the Q-redox state with respect to the respiratory activity.

A three-electrode system was implemented into the NextGen-O2k to monitor the Q-redox state continuously and simultaneously with respiratory oxygen consumption. Added CoQ2 reflects the mitochondrial Q-redox state when equilibrating both with the detecting electrode and the biological sites (e.g. Complexes I, II and III).

Quality auditA Quality Audit is the process of systematic examination of a quality system carried out by an internal or external quality auditor or an audit team.
Quantities, symbols, and unitsIn the context of quantities, symbols, and units, a code is required to convert terms defining physicochemical quantities into symbols (encoding) and to decode symbols as used in equations, text, and figures. Then symbols and abbreviations gain meaning. Simple symbols — such as Q or N — are used with different meanings depending on context (think of Q for heat and Q for electric charge; or N for number of cells and N for number of O2 molecules). The context provides the code. When the context is extended, the symbols have to be expanded too, including more detail to avoid confusion (Qth versus Qel; Nce versus NO2). Then symbols may appear too complicated, loosing the function of sending their message quickly. There is no single best way to design the right symbol or to replace meaningful symbols (Qel) by ambiguous abbreviations (Q) — all depends on context. We need to use the adequate medium (words, symbols, and abbreviations; equations, text, and figures; videos and slide presentations) and provide the code to achieve communication. The medium is the message, the message is the meaning — from Marshall McLuhan to Hofstadter.
QuantityQA quantity is the attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively. A dimensional quantity is a number (variable, parameter, or constant) connected to its dimension, which is different from 1. {Quote} The value of a quantity is generally expressed as the product of a number and a unit. The unit is simply a particular example of the quantity concerned which is used as a reference, and the number is the ratio of the value of the quantity to the unit. {end of Quote: Bureau International des Poids et Mesures 2019 The International System of Units (SI), p. 127)}.
QuenchingQuenching is the name given to any process that reduces fluorescence intensity. Molecular oxygen is a fluorescence and phosphorescence quencher for some substances – a phenomenon that has been made use of in constructing optical probes for measuring oxygen.
QuinolQuinol is a class of reduced organic compounds derived from quinone (oxidized form) by two-electron and two-proton reduction. In the mitochondrial electron transfer system, ubiquinol or reduced coenzyme Q can be found, while in the photosynthetic systems plastoquinols (particularly PQ9) are common. These redox compounds exist in three different redox states: quinone (oxidized), quinol (reduced), and an intermediate semiquinone.
QuinoneQuinone is a class of oxidized organic compounds with a fully conjugated cyclic dione structure derived from aromatic compounds. Ubiquinone or coenzmye Q is the naturally occurring quinone in the mitochondrial ETS, while in the photosynthetic system plastoquinones are common. The quinone is reduced either to an unstable semiquinone by one hydrogen atom or to a quinol by two electrons and two protons.
Quit - DatLab

DatLab 8: Close DatLab files and quit the program.

DatLab 7 : Exit

R-L control efficiencyjR-LR-L ROUTINE-coupling efficiency The R-L control efficiency, jR-L = (R-L)/R = 1-L/R, is the fraction of ROUTINE respiration coupled to phosphorylation in living cells. ROUTINE respiration is corrected for LEAK respiration to obtain the R-L net ROUTINE capacity. The flux control efficiency jR-L is the R-L net ROUTINE capacity normalized for the reference rate R. The background state is the LEAK state, and the flux control variable is stimulation to ROUTINE respiration by physiologically controlled ATP turnover in living cells.
R-L net ROUTINE capacityR-LR-L net ROUTINE capacity The R-L net ROUTINE capacity is ROUTINE respiration corrected for LEAK respiration. R-L is the respiratory capacity available for phosphorylation of ADP to ATP. Oxygen consumption in the ROUTINE state of respiration measured in living cells, therefore, is partitioned into the R-L net ROUTINE capacity, strictly coupled to phosphorylation , and nonphosphorylating LEAK respiration, LR, compensating for proton leaks, slip and cation cycling: R = R-L+LR. It is frequently assumed that LEAK respiration L, as measured in the LEAK state, overestimates the LEAK component of respiration, LR, as measured in the ROUTINE state, particularly if the protonmotive force is not adjusted to equivalent levels in L and LR. However, if the LEAK component increases with enzyme turnover during R, the low enzyme turnover during L may counteract the effect of the higher pmF.
R/E control ratioR/ER/E control ratio The R/E control ratio is the ratio of (partially coupled) ROUTINE respiration R and (noncoupled) ET capacity E. The R/E control ratio is an expression of how close ROUTINE respiration operates to ET capacity.
ROUTINE respirationRR.jpg In the living cell, ROUTINE respiration (R) or ROUTINE activity in the physiological coupling state is controlled by cellular energy demand, energy turnover and the degree of coupling to phosphorylation (intrinsic uncoupling and pathological dyscoupling). The conditions for measurement and expression of respiration vary (oxygen flux in state R, JO2R or oxygen flow in state R, IO2R). If these conditions are defined and remain consistent within a given context, then the simple symbol R for respiratory state can be used to substitute the more explicit expression for respiratory activity. R and growth of cells is supported by exogenous substrates in culture media. In media without energy substrates, R depends on endogenous substrates. R cannot be measured in permeabilized cells or isolated mitochondria. R is corrected for residual oxygen consumption (ROX), whereas R´ is the uncorrected apparent ROUTINE respiration or total cellular oxygen consumption of cells including ROX.
RS232-Cable
RS232-Cable.JPG

RS232 0-modem-Cable for connecting the O2k-Main Unit to the PC or laptop with DatLab installed. When using DatLab 5, this cable is replaced by USB-Cable 2.0\Type A-B for O2k-Series E upwards.

Discontinued

RTRT versus RT

RT indicates room temperature or 25 °C.

RT is the gas constant R [kJ/mol] multiplied by absolute temperature T [K]. This is the motive force quantum in the amount format (Gnaiger 2020 BEC MitoPathways).

RapamycinRapamycin is an inhibitor of the mammalian/mechanistic target of rapamycin, complex 1 (mTORC1). Rapamycin induces autophagy and dyscouples mitochondrial respiration. Rapamycin delays senescence in human cells, and extends lifespan in mice without detrimental effects on mitochondrial fitness in skeletal muscle.
Rare New England
MNE

MNE has transitioned into RNE (Rare New England). Rare New England is an organization providing access to support groups, gatherings, events and resources for those affected by Rare Disease and living in the New England area.

Raw signal of the oxygen sensorRThe raw signal of the polarographic oxygen sensor is the current Iel [µA], 1 µA = 10-6 C·s-1, (DatLab 8) or the electric potential difference (voltage) [V], 1 V = 1 J·C-1, obtained after a current-to-voltage conversion in the O2k (DatLab 7 and previous versions).
Reactive nitrogen speciesRNSReactive nitrogen species, RNS, are nitric oxide-derived oxidants. The main source of RNS is nitric oxide (NO•). NO• plays an important role in cell signaling and in oxidative-nitrosative stress.
Reactive oxygen speciesROSReactive oxygen species, ROS, are molecules derived from molecular oxygen, including free oxygen radicals, which are more reactive than O2. Physiologically and pathologically important ROS include superoxide, the hydroxyl radical and hydroxide ion, hydrogen peroxide and other peroxides. These are important in cell signalling, oxidative defence mechanisms and oxidative stress.
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