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List of results

• Tricarboxylic acid cycle  + (The '''tricarboxylic acid (TCA) cycle''' i … The '''tricarboxylic acid (TCA) cycle''' is a system of enzymes in the mitochondrial matrix arranged in a cyclic metabolic structure, including dehydrogenases that converge in the NADH pool and [[succinate dehydrogenase]] (on the inner side of the inner mt-membrane) for entry into the membrane-bound ET pathway [[Membrane-bound ET pathway|mET pathway]]. [[Citrate synthase]] is a marker enzyme of the TCA cycle, at the gateway into the cycle from [[pyruvate]] via [[acetyl-CoA]]. It is thus the major module of the [[Electron transfer pathway]], upstream of the inner [[Membrane-bound ET pathway|Membrane-bound ET pathway]] (mET-pathway) and downstream of the [[Mitochondrial outer membrane|outer mt-membrane]]. Sections of TCA cycle are required for [[fatty acid oxidation]] (FAO, β-oxidation). [[Anaplerosis|Anaplerotic reactions]] fuel the TCA cycle with other intermediary metabolites. In the cell, the TCA cycle serves also biosynthetic functions by metabolite export from the matrix into the cytosol.e export from the matrix into the cytosol.)
• Uncoupling-control ratio  + (The '''uncoupling-control ratio''' UCR is … The '''uncoupling-control ratio''' UCR is the ratio of ET-pathway/ROUTINE-respiration (''E/R'') in living cells, evaluated by careful [[uncoupler]] titrations ([[Steinlechner-Maran 1996 Am J Physiol Cell Physiol|Steinlechner et al 1996]]). Compare [[ROUTINE-control ratio]] (''R/E'') [[Gnaiger 2008 POS|(Gnaiger 2008)]].[[Gnaiger 2008 POS|(Gnaiger 2008)]].)
• Journal volume  + (The '''volume''' of a journal or periodica … The '''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 [[Journal issue |issues]].[[Journal issue |issues]].)
• Wet mass  + (The '''wet mass''' of a tissue or biological sample, obtained after blotting the sample to remove an arbitrary amount of water adhering externally to the sample.)
• Permeability transition pore  + (The (mitochondrial, mt) permeability trans … The (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]]).[[Hansson 2010 J Biol Chem]]).)
• Search for defective O2k components  + (The 2-chamber design of the O2k helps to '''search for defective O2k components''', by switching components linked to O2k chambers A and B between sides A and B.)
• P»-system  + (The ADP-ATP phosphorylation system or P»-system. ''See'' [[Phosphorylation system]].)
• CDGSH iron-sulfur domain proteins  + (The CDGSH iron-sulfur domain (CISDs) famil … The CDGSH iron-sulfur domain (CISDs) family of proteins uniquely ligate labile 2Fe-2S clusters with a 3Cys-1His motif. CISD1 and CISD3 have been demonstrated to localize to the outer mitochondrial membrane and mitochondrial matrix respectively, however their relationship to mitochondrial physiology remains ill-defined [1]. The best characterized member of the CISD family, CISD1, has been demonstrated to be involved in respiratory capacity, iron homeostasis, and ROS regulationcity, iron homeostasis, and ROS regulation)
• French Group of Bioenergetics  + (The French Group of Bioenergetics...)
• O2k control panel - DatLab  + (The O2k control panel allows for quick acc … The 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.ween O2k control panel and protocol panel.)
• Closed chamber  + (The O2k-chamber can be used as a [[closed system]] or [[open system]]. Gas bubbles must be avoided.)
• OroboPOS-Connector Service  + (The OroboPOS-Connector Service entails routine maintenance and any necessary repairs of the OroboPOS-Connector in the Oroboros electronics workshop (WGT).)
• PC requirements  + (The PC requirements for controlling an O2k and data recording with [[DatLab]] are found [[DatLab installation |here]].)
• Display Power-O2k  + (The Power-O2k number, which is set in the … The Power-O2k number, which is set in the pull-down menu Oroboros O2k \ [[O2k configuration]], is shown in the active graph. To show it in graphs copied to clipboard, the option "Show Oroboros icon in clipboard files" must be enabled in the Graph-menu [[Graph options - DatLab]].[[Graph options - DatLab]].)
• TIP2k - DatLab  + (The Titration-Injection microPump (TIP2k) provides automated injection of liquids into both O2k chambers. It is controlled via DatLab, allowing for programmable titration regimes and feedback control.)
• MtOM  + (The [[Mitochondrial outer membrane| '''mitochondrial outer membrane''']])
• Succinate transport  + (The [[dicarboxylate carrier]] catalyses the electroneutral exchange of succinate^2- for HPO_4-^2-.)
• Ampere  + (The ampere, symbol A, is the SI unit of el … The ampere, symbol A, is the SI unit of electric current. It is defined by taking the fixed numerical value of the elementary charge ''e'' to be 1.602 176 634 × 10⁻¹⁹ when expressed in the unit C, which is equal to A s, where the second is defined in terms of Δ''ν''_Cs.the second is defined in terms of Δ''ν''_Cs.)
• Isolated system  + (The boundaries of '''isolated system'''s a … The boundaries of '''isolated system'''s are impermeable for all forms of energy and matter. Changes of isolated systems have exclusively internal origins, ''e.g.'', internal entropy production, d_i''S''/d''t'', internal formation of chemical species ''i'' which is produced in a reaction ''r'', d_i''n_i''/d''t'' = d_r''n_i''/d''t''. 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. by various conservation laws which rule out the production or destruction of the respective quantity.)
• Calorespirometric ratio  + (The calorimetric/respirometric or '''calor … The calorimetric/respirometric or '''calorespirometric ratio''' (CR ratio) is the ratio of calorimetrically and respirometrically measured heat and oxygen flux, determinded by [[calorespirometry]]. The experimental CR ratio is compared with the theoretically derived [[oxycaloric equivalent]], and agreement in the range of -450 to -480 kJ/mol O₂ indicates a balanced [[aerobic]] energy budget ([[Gnaiger_1987_PhysiolZool|Gnaiger and Staudigl 1987]]). In the transition from aerobic to [[anaerobic | anaerobic metabolism]], there is a [[Limiting pO2|limiting ''p''_O2]], ''p''_lim, below which CR ratios become more exothermic since anaerobic energy flux is switched on.h CR ratios become more exothermic since anaerobic energy flux is switched on.)
• Candela  + (The candela, symbol cd, is the SI unit of … The candela, symbol cd, is the SI unit of luminous intensity in a given direction. It is defined by taking the fixed numerical value of the luminous efficacy of monochromatic radiation of frequency 540 × 10¹² Hz, ''K''_cd, to be 683 when expressed in the unit lm W⁻¹.;/sub>, to be 683 when expressed in the unit lm W⁻¹.)
• Illumination  + (The chambers of the [[OROBOROS O2k|Oroboros O2k]] … The chambers of the [[OROBOROS O2k|Oroboros O2k]] are illuminated by an internal LED. The '''illumination''' is switched on and off in [[DatLab]] during the experiment by pressing [F10]. This illumination must be distinguished from light introduced into the chambers by LEDs for the purpose of spectrophotometric and fluorometric measurements. For these, the internal illumination must be switched off.nternal illumination must be switched off.)
• Matrix-ETS  + (The component of the electron transfer sys … The 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.s pyruvate, malate, succinate, and others.)
• Affinity of reaction  + (The concept of '''affinity''' and hence ch … The concept of '''affinity''' and hence chemical force is deeply rooted in the notion of '''attraction''' (and repulsion) of alchemy, which was the foundation of chemistry originally, but diverted away from laboratory experiments towards occult secret societies [1].^** Newton's extensive experimental alchemical work and his substantial written track record on alchemy (which he did not publish) is seen today as a key inspiration for his development of the concept of the gravitational force [2-4]. This marks a transition of the meaning of affinity, from the descriptive 'adjacent' (proximity) to the causative 'attractive' (force) [5]. Correspondingly, Lavoisier (1790) equates affinity and force [6]: “''... the degree of force or affinity with which the acid adheres to the base''” [5]. By discussing the influence of electricity and gravity on chemical affinity, Liebig (1844) considers affinity as a force [7]. This leads to Guldberg and Waage's [[mass action ratio]] ('Studies concerning affinity', 1864; see [5]), the free energy and chemical affinity of Helmholtz (1882 [8]), and chemical thermodynamics of irreversible processes [9], where flux-force relations are center stage [10]. </br></br>According to the IUPAC definition, the '''affinity of reaction''', ''A'' [J·mol^-1], equals the negative molar Gibbs energy of reaction [11], which is the negative Gibbs [[force]] of reaction (derivative of [[Gibbs energy]] per [[advancement]] of reaction [12]):</br></br> -''A'' = Δ_r''F'' = ∂''G''/∂_r''ξ''</br></br>The historical account of affinity is summarized by concluding, that today affinity of reaction should be considered as an isomorphic motive '''force''' and be generalized as such. This will help to (''1'') avoid confusing reversals of sign conventions (repulsion = negative attraction; pull = negative push), (''2'') unify symbols across classical and nonequilibrium thermodynamics [12,13], and thus (''3'') facilitate interdisciplinary communication by freeing ourselves from the alchemical, arcane scientific nomenclature.ry communication by freeing ourselves from the alchemical, arcane scientific nomenclature.)
• Latent mitochondrial dysfunction  + (The concept on '''latent mitochondrial dys … The 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.ng a mitochondrial stress resistance test.)

• Mark specifications - DatLab  + (The function '''Mark specifications''' is … The function '''Mark specifications''' is largely replaced by [[SUIT: Browse DL-Protocols and templates |SUIT DL-Protocols]] and [[Instrumental: Browse DL-Protocols and templates |Instrumental DL-Protocols]] in [https://www.oroboros.at/index.php/product/datlab/ DatLab 7.4]. Mark specifications allow the user to rename [[Marks - DatLab| 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.for renaming the entire sequence of marks.)
• Hydride  + (The hydride anion is the species H⁻.)
• Illumination on/off  + (The illumination in both chambers is switched on/off.)
• Kelvin  + (The 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.)
• Kilogram  + (The kilogram, symbol kg, is the SI unit of … The 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 Δ''ν''_Cs.he meter and the second are defined in terms of ''c'' and Δ''ν''_Cs.)
• Malate-aspartate shuttle  + (The malate-aspartate shuttle involves the … The malate-aspartate shuttle involves the glutamate-aspartate carrier and the 2-oxoglutarate carrier exchanging malate^2- for 2-oxoglutarate^2-. 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.chondrial matrix. It is most important in heart, liver and kidney.)
• Mouse control: Mark  + (The mark mode is active by default, can be … 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. </br>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.</br></br>»More details: [[Marks - DatLab]].[Marks - DatLab]].)
• Wavelength range  + (The minimum and the maximum wavelengths ov … The minimum and the maximum wavelengths over which an [[absorbance spectrum]] is measured are described in terms of the [[wavelength range]]. It is determined mainly by the specifications of the [[spectrophotometer]] and the type of [[light source]] used, and the characteristic [[absorbance spectrum]] of the sample being investigated.[[absorbance spectrum]] of the sample being investigated.)
• Ergodynamics  + (The mission of '''ergodynamics''' is the r … The mission of '''ergodynamics''' is the revelation of relations of general validity. "''Thermodynamics deals with relationships between properties of systems at equilibrium and with differences in properties between various equilibrium states. It has nothing to do with time. Even so, it is one of the most powerful tools of physical chemistry''" [1]. '''Ergodynamics''' is the theory of exergy changes (from the Greek word 'erg' which means [[work]]). Ergodynamics includes the fundamental aspects of thermodynamics ('[[heat]]') and the thermodynamics of irreversible processes (TIP; nonequilibrium thermodynamics), and thus links thermodynamics to kinetics. In its most general scope, ergodynamics is the science of [[energy]] transformations. Classical thermodynamics includes [[open system]]s, yet as a main focus it describes [[closed system]]s. This is reflected in a nomenclature that is not easily applicable to the more general case of open systems [2]. At present, IUPAC recommendations [3] fall short of providing adequate guidelines for describing energy transformations in open systems.ng energy transformations in open systems.)
• Creatine kinase  + (The mitochondrial '''creatine kinase''', also known as phosphocreatine kinase (CPK), facilitates energy transport with [[creatine]] and [[phosphocreatine]] as diffusible intermediates.)
• Respiratory chain  + (The mitochondrial '''respiratory chain''' … The mitochondrial '''respiratory chain''' (RC) consists of enzyme complexes arranged to form a metabolic system of convergent pathways for [[oxidative phosphorylation]]. In a general sense, the RC includes (1) the [[electron transfer pathway]] (ET-pathway), with transporters for the exchange of reduced substrates across the inner mitochondrial membrane, enzymes in the matrix space (particularly dehydrogenases of the tricarboxylic acid cycle), inner membrane-bound electron transfer complexes, and (2) the inner membrane-bound enzymes of the [[phosphorylation system]].[[phosphorylation system]].)
• Mole  + (The mole [mol] is the SI base unit for the … The mole [mol] is the SI base unit for the [[amount |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.ther particles, or specified groups of such particles.)
• Pyruvate carrier  + (The monocarboxylic acid [[pyruvate]]^- is exchanged electroneutrally for OH^- by the '''pyruvate carrier'''. H⁺/anion symport is equivalent to OH^-/anion antiport.)
• Drift  + (The most common cause of '''drift''' is variation in the intensity of the [[light source]]. The effect of this can be minimised by carrying out a [[balance]] at frequent intervals.)
• DatLab oxygen flux: performance and data analysis  + (The quality of the results are strongly affected by the performance and data analysis. Therefore, we provide guidelines for performing and evaluating respirometric assays.)
• Improvement score  + (The relative improvement score, ''RIS'', p … The relative improvement score, ''RIS'', provides a measure of improvement of a trait from a value measured at baseline, ''B'', to a value measured after treatment, ''T'', expressing the total improvement, ''T-B'', in relation to the theoretical scope of improvement and the level of the trait observed at baseline. '''RIS'' incorporates the concept of diminishing returns and consideres maintaining a high value of a trait as an improvement relative to the potential loss.mprovement relative to the potential loss.)
• Reproducibility crisis  + (The reproducibility crisis is alarming.< … The reproducibility crisis is alarming.¹ An experiment or study is ''reproducible'' or ''replicable'' when subsequent experiments confirm the results. This is [[research |re-search]]. However, we can define different types of reproducibility depending on the conditions that we use to replicate the previous work or in the information available. Our aim is to focus mostly on two different kinds²: '''1. Direct:''' is when we obtaining the same results using the same experimental conditions, materials, and methods as described in the original experiment. This would be the ideal reproducibility of an experiment. However, it requires a very accurate description of how the original experiment was performed. Some journals are trying to resolve the '''reproducibility crisis''' improving the rigor and the excellence on the reported methods and results (e.g. [https://www.cell.com/star-authors-guide STAR Methods in Cell Press]). '''2. Systematical:''' refers to obtaining the same results, but under different conditions; for example, using another cell line or mouse strain or humman study, or inhibiting a gene pharmacologically instead of genetically. This opens the door to subsequent studies to find the conditions under which an initial finding holds.udies to find the conditions under which an initial finding holds.)
• Second  + (The second, symbol s, is the SI unit of ti … The second, symbol s, is the SI unit of time. It is defined by taking the fixed numerical value of the caesium frequency ∆''ν''_Cs, the unperturbed ground-state hyperfine transition frequency of the caesium 133 atom, to be 9 192 631 770 when expressed in the unit Hz, which is equal to s⁻¹.ssed in the unit Hz, which is equal to s⁻¹.)
• Stoichiometric number  + (The sign of the '''stoichiometric number'' … The sign of the '''stoichiometric number''' ''ν''_X is determined by the nonspatial direction of the transformation (positive for products, negative for substrates), and the magnitude of ''ν''_X is determined by the stoichiometric form. For instance, ''ν''_A=-1 in the reaction 0 = -1 A + 2 B (-1 glucose converted to +2 lactate), but ''ν''_A=-1/6 in the reaction 0 = -1/6 A - 1 B + 1 C (-1/6 glucose and -1 O₂ converted to +1 H₂CO₃).1 B + 1 C (-1/6 glucose and -1 O₂ converted to +1 H₂CO₃).)
• Dithionite  + (The sodium salt of '''Dithionite''' Na< … The sodium salt of '''Dithionite''' Na₂S₂O₄ (Dit) is the 'zero oxygen solution powder' used for [[Oxygen calibration - DatLab |calibration of oxygen sensors]] at [[Zero calibration | zero oxygen concentration]], or for stepwise reduction of oxygen [[concentration]]s in [[MiPNet14.06 Instrumental O2 background |instrumental O₂ background tests]]. It is not recommended to use dithionite in experiments with biological samples or several multisensor approaches, for these see [[Setting the oxygen concentration]].[[Setting the oxygen concentration]].)
• Install Oroboros protocol package  + (The standard '''Instrumental and SUIT DL-P … The standard '''Instrumental and SUIT DL-Protocols''' package is automatically implemented with the simple DatLab programme installation. We recommend a 'clean install': rename your previous DatLab programme subdirectory (''e.g.'' C:\DatLab_OLD).</br>Updates and newly developed DL protocols can be simply downloaded by clicking on [Protocols]\Install Oroboros protocol package.tocols]\Install Oroboros protocol package.)
• Flux analysis - DatLab  + (The strategy of '''Flux analysis''' using … The strategy of '''Flux analysis''' using DatLab depends on the research question and the corresponding settings applied in DatLab when recording the data with the O2k. Usng [[MitoPedia: SUIT |SUIT protocols]], a sequence of respiratory steady-states is measured, marks are set, and numerical data are summarized in [[Mark statistics - DatLab|Mark statistics]] (F2). An AI approach is kept in mind when describing guidelines for evaluation of steady-states during data recording and analysis.states during data recording and analysis.)
• %  + (The symbol '''%''' indicates 'per cent' (per hundred). {''Quote''} The internationally recognized symbol % (per cent) may be used with the SI. When it is used, a space separates the number and the symbol %. {''end of Quote''}.)
• ≡  + (The symbol '''≡''' indicates (numerical) [[equivalence]], in contrast to = as the symbol for (physicochemical) [[equality]].)
• Open chamber  + (The 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]].)