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Getting started - DatLab + (Users have to enter their user details the first time they use DatLab 8 on a specific computer. As well, entering some basic settings is required when connecting DatLab 8 with an O2k for the first time.)
Valinomycin + (Valinomycin catalyzes electrogenic K+ transport down the electrochemical transmembrane gradient (150 ng.mg-1 protein).)
Smoothing + (Various methods of '''smoothing''' can be … Various methods of '''smoothing''' can be applied to improve the [[signal-to-noise ratio]]. For instance, data points recorded over time [s] or over a range of wavelengths [nm] can be smoothed by averaging ''n'' data points per interval. Then the average of the ''n'' points per smoothing interval can be taken for each successively recorded data point across the time range or range of the spectrum to give a ''n''-point moving average smoothing. This method decreases the [[noise]] of the signal, but clearly reduces the time or wavelength [[resolution]]. More advanced methods of smoothing are applied to retain a higher [[time resolution]] or wavelength resolution.[[time resolution]] or wavelength resolution.)
Hydrogenion flux + (Volume-specific '''hydrogenion flux''' or … Volume-specific '''hydrogenion flux''' or H+ flux is measured in a closed system as the time derivative of H+ concentration, expressed in units [pmol·s-1·mL-1]. H+ flux can be measured in an open system at steady state, when any acidification of the medium is compensated by external supply of an equivalent amount of base. The extracellular acidification rate (ECAR) is the change of pH in the incubation medium over time, which is zero at steady state. Volume-specific H+ flux is comparable to volume-specific [[oxygen flux]] [pmol·s-1·mL-1], which is the (negative) time derivative of oxygen concentration measured in a closed system, corrected for instrumental and chemical background.[[pH]] is the negative logarithm of hydrogen ion activity. Therefore, ECAR is of interest in relation to acidification issues in the incubation buffer or culture medium. The physiologically relevant metabolic H+ flux, however, must not be confused with ECAR.e incubation buffer or culture medium. The physiologically relevant metabolic H+ flux, however, must not be confused with ECAR.)
Different O2 fluxes in left and right chamber + (What are potential causes for '''different O2 fluxes in the left and right chamber'''?)
Transmittance + (When light enter a sample, '''transmittance''' (''T'') is the fraction of the intensity (''I'') of the light emerging from the sample compared with the incident light intensity (''I''''0''): ''T'' = ''I''/''I''''0''.)
Absorption + (When light enters a sample and emerges wit … When light enters a sample and emerges with an intensity (''I''), '''absorption''' (''Abs'') is the fraction of the light absorbed by the sample compared with the [[incident light]] intensity (''I''''0''): ''Abs'' = 1-''I''/''I''''0''. Absorption can also be expressed as ''Abs'' = 1-''T'', where ''T'' is the [[transmittance]].[[transmittance]].)
Absorbance spectrum + (When light enters a sample, the amount of … When light enters a sample, the amount of light that it absorbs is dependent upon the wavelength of the incident light. The '''absorbance spectrum''' is the curve derived by plotting the measured [[absorbance]] against the wavelength of the light emerging from the sample over a given [[wavelength range]]. An [[absorbance spectrum]] may be characterised by peaks and troughs (absorbance maxima and minima) that can be used to identify, and sometimes quantify, different absorbing substances present in a sample. absorbing substances present in a sample.)
O2k-MultiSensor + (When one (or more) analytical parameters a … When 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.tions require the standard black stoppers.)
TIP2k syringe blocked + (When the '''TIP2k syringe is blocked''', it must not be used with the TIP2k, and specific cleaning instructions should be followed.)
Living Communications + (With '''Living Communications''', [https:/ … With '''Living Communications''', [https://www.bioenergetics-communications.org/index.php/bec 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.e-print, from initial steps to next steps.)
Internal flow + (Within the system boundaries, irreversible … Within the system boundaries, irreversible '''internal flows''', ''I''i,—including chemical reactions and the dissipation of internal gradients of heat and matter—contribute to internal entropy production, di''S''/d''t''. In contrast, [[external flow]]s, ''I''e, of heat, work, and matter proceed reversibly across the system boundaries (of zero thickness). Flows are expressed in various [[format]]s per unit of time, with corresponding [[motive unit]]s [MU], such as chemical [mol], electrical [C], mass [kg]. Flow is an [[extensive quantity]], in contrast to [[flux]] as a [[specific quantity]].ecific quantity]].)
Liver mitochondria purification + ([[Armstrong 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.)
File:MitoFitPreprints and BEC manuscript template.docx + ([[Bioenergetics Communications]] and [[MitoFit Preprints]] manuscript template.)
ET-pathway competent state + ([[Electron transfer pathway]] competent state, ''see'' '''[[Electron-transfer-pathway state]]'''.)
Duroquinol + ([[Electron-transfer-pathway state |ET-path … [[Electron-transfer-pathway state |ET-pathway level 2]] is supported by '''duroquinol''' DQ feeding electrons into Complex III (CIII) with further electron transfer to CIV and oxygen. Upstream pathways are inhibited by rotenone and malonic acid in the absence of other substrates linked to ET-pathways with entry into the Q-junction.T-pathways with entry into the Q-junction.)
Fluorometric dyes + ([[Extrinsic fluorophores]]; fluorescent markers.)
SUIT-014 + ([[File: 1GM;2D;3P;4S;5U;6Rot-.png|400px]])
O2k-sV-Module + ([[File:11200-01.jpg|180px|right]] The ''' … [[File:11200-01.jpg|180px|right]] 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.the delivery of this revolutionary module.)
SUIT-033 + ([[File:1D.1;2PGM;3D2.5-.png|450px]])
SUIT-038 O2 mt D091 + ([[File:1D;2M.1;2H2O;2c;3M.2;3M.5;3M1;3M2;4P;5G;6S10;6S50;7Gp;8U;9Rot;10Ama.png|400px]])
SUIT-041 O2 mt D096 + ([[File:1D;2M.1;3AC;3c;4M2;5P;6S;7Rot;8Ama.png|400px]])
SUIT-037 O2 mt D090 + ([[File:1D;2M.1;3Oct;3c;4M.2;4M.5;4M1;4M2;5P;6G;7S10;7S50;8Gp;9U;10Rot;11Ama.png|400px]])
SUIT-002 O2 mt D005 + ([[File:1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px]])
SUIT-025 + ([[File:1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Rot-.png|600px]])
SUIT-025 O2 mt D057 + ([[File:1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Rot;9Ama.png|600px]])
SUIT-002 + ([[File:1D;2M.1;3Oct;4M2;5P;6G;7S;8Gp;9U;10Rot-.png|400px]])
SUIT-036 O2 mt D089 + ([[File:1D;2M.1;3Pal;3c;4M.2;4M.5;4M1;4M2;5P;6G;7S10;7S50;8Gp;9U;10Rot;11Ama.png|400px]])
SUIT-040 O2 mt D094 + ([[File:1D;2M.1;3Pal;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama.png|400px]])
SUIT-040 O2 pfi D095 + ([[File:1D;2M.1;3Pal;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama.png|400px]])
SUIT-039 O2 mt D092 + ([[File:1D;2M.1;3Pal;3c;4M2;5P;6G;7S;8U;9Rot;10Ama.png|400px]])
SUIT-039 O2 pfi D093 + ([[File:1D;2M.1;3Pal;3c;4M2;5P;6G;7S;8U;9Rot;10Ama.png|400px]])
SUIT-007 + ([[File:1G;2D;3M;4U-.png|300px]])
SUIT-014 O2 pfi D042 + ([[File:1GM;2D;2c;3P;4S;5U;6Rot;7Ama.png|400px]])
SUIT-021 O2 mt D035 + ([[File:1GM;2D;2c;3S;4Rot;5Omy;6U;7Ama.png|300px]])
SUIT-011 O2 pfi D024 + ([[File:1GM;2D;2c;3S;4U;5Rot;6Ama.png|400px]])
SUIT-021 + ([[File:1GM;2D;3S;4Rot;5Omy;6U-.png|400px]])
SUIT-021 Fluo mt D036 + ([[File:1GM;2D;3S;4Rot;5Omy;6U;7Ama.png|300px]])
SUIT-011 + ([[File:1GM;2D;3S;4U;5Rot-.png|400px|SUIT-011]])
SUIT-018 + ([[File:1GMS;2D-.png|300px|SUIT-018]])
SUIT-018 O2 mt D054 + ([[File:1GMS;2D;2c;3Ama.png|290px]])
SUIT-018 AmR mt D031 + ([[File:1GMS;2D;3Ama.png|290px]])
SUIT-018 AmR mt D041 + ([[File:1GMS;2D;3Ama.png|290px]])
SUIT-018 AmR mt D040 + ([[File:1GMS;2D;3Ama.png|290px|SUIT-018]])
SUIT-027 + ([[File:1M;2D;3M;4P;5G-.png|400px]])
SUIT-017 + ([[File:1OctM;2D;2c;3G;4S;5U;6Rot-.png |355px]])
SUIT-017 O2 pfi D049 + ([[File:1OctM;2D;2c;3G;4S;5U;6Rot;7Ama.png|350px]])
SUIT-005 O2 pfi D011 + ([[File:1OctM;2D;2c;3P;4S;5U;6Rot;7Ama;8AsTm;9Azd.png|450px]])
SUIT-017 O2 mt D046 + ([[File:1OctM;2D;3G;3c;4S;5U;6Rot;7Ama.png |350px]])
SUIT-015 + ([[File:1OctM;2D;3G;4P;5S;6U;7Rot-.png|451px]])
SUIT-015 O2 pti D043 + ([[File:1OctM;2D;3G;4P;5S;6U;7Rot;8Ama.png|450px]])
SUIT-016 + ([[File:1OctM;2D;3G;4S;5Rot;6Omy;7U-.png|420px]])
SUIT-016 O2 pfi D044 + ([[File:1OctM;2D;3G;4S;5Rot;6Omy;7U;7c-8Ama.jpg|400px]])
SUIT-005 + ([[File:1OctM;2D;3P;4S;5U;6Rot-.png|300px]])
1OctM;2D;3PG;4S;5U;6Rot- + ([[File:1OctM;2D;3PG;4S;5U;6Rot-.png|300px]])
1PGM;2D;3S;4Rot;5U- + ([[File:1PGM;2D;3S;4Rot;5U-.png|300px]])
SUIT-028 + ([[File:1PGM;2D;3S;4U;5Rot-.png|400px|SUIT-028]])
1PGM;2D;3U;4S;5Rot- + ([[File:1PGM;2D;3U;4S;5Rot-.png|300px]])
SUIT-020 O2 mt D032 + ([[File:1PM;2D;2c;3G;4S;5Rot;6Omy;7U;8Ama.png|500px]])
SUIT-008 O2 pfi D014 + ([[File:1PM;2D;2c;3G;4S;5U;6Rot;7Ama;8AsTm;9Azd.png|400px]])
SUIT-008 O2 mt D026 + ([[File:1PM;2D;2c;3G;4S;5U;6Rot;7Ama;8AsTm;9Azd.png|600px]])
SUIT-012 O2 mt D027 + ([[File:1PM;2D;2c;3G;4U;5Ama.png|300px]])
SUIT-006 O2 mt D047 + ([[File:1PM;2D;2c;3Omy;4U;5Ama.png|300px]])
SUIT-031 O2 mt D075 + ([[File:1PM;2D;2c;3S;4Rot;5U;6Ama.png|400px]])
SUIT-001 + ([[File:1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp-.png|400px|SUIT-001]])
SUIT-004 O2 pfi D010 + ([[File:1PM;2D;2c;3U;4S;5Rot;6Ama;7AsTm;8Azd.png|450px]])
SUIT-006 MgG mt D055 + ([[File:1PM;2D;3Cat;4U;5Ama.png|300px]])
SUIT-020 + ([[File:1PM;2D;3G;4S;5Rot;6Omy;7U-.png|400px]])
SUIT-020 Fluo mt D033 + ([[File:1PM;2D;3G;4S;5Rot;6Omy;7U;8Ama.png|450px]])
SUIT-008 O2 pce D25 + ([[File:1PM;2D;3G;4S;5U;6Rot-.png|300px]])
SUIT-008 + ([[File:1PM;2D;3G;4S;5U;6Rot.png|400px]])
SUIT-012 + ([[File:1PM;2D;3G;4U-.png|300px]])
1PM;2D;3G;4U;5S;6Rot- + ([[File:1PM;2D;3G;4U;5S;6Rot-.png|300px]])
SUIT-006 Fluo mt D034 + ([[File:1PM;2D;3Omy;4U;5Ama.png|300px]])
SUIT-006 AmR mt D048 + ([[File:1PM;2D;3Omy;4U;5Ama.png|400px]])
SUIT-031 + ([[File:1PM;2D;3S;4Rot;5U;-.png|400px]])
SUIT-004 + ([[File:1PM;2D;3U;4S;5Rot.png|450px]])
SUIT-029 O2 mt D066 + ([[File:1PM;2T;2D;2c;3Omy;4U;5G;6S;6U;7Rot;8Ama.png|350px]])
SUIT-019 O2 pfi D045 + ([[File:1PalM;2D;2c;3Oct;4P;5G;6U;7S;8Rot;9Ama.png|400px]])
SUIT-019 + ([[File:1PalM;2D;3Oct;4P;5G;6U;7S;8Rot-.png|450px]])
SUIT-009 O2 mt D015 + ([[File:1S;2D;2c;3P;4Rot;5Ama.png|400px|SUIT9]])
SUIT-009 + ([[File:1S;2D;3P;4Rot-.png|400px|SUIT9]])
SUIT-009 AmR mt D021 + ([[File:1S;2D;3P;4Rot;5Ama.png|400px|SUIT-009]])
SUIT-026 O2 mt D063 + ([[File:1S;2Rot;3D;3c;4Ama.png|400px]])
SUIT-026 + ([[File:1S;2Rot;3D;4Ama.png|350px]])
SUIT-006 O2 mt D022 + ([[File:1SRot;2D;2c;3(Omy);4U;5Ama.png|400px]])
SUIT-006 + ([[File:1X;2D;2c;3Omy;4U-.png|450px]])
SUIT-003 O2 ce D009 + ([[File:1ce;2ceOmy;3ceU-.jpg|450px]])
SUIT-003 Ce1;ce2U- + ([[File:1ce;2ceU-.jpg|150px]])
SUIT-003 Ce1;ce3U- + ([[File:1ce;3ceU-.jpg|150px]])
SUIT-032 NADH mt D078 + ([[File:1mt;1PGM;2D;3Anox;4Myx;5Reox.png|300px]])
Oxoglutarate + ([[File:2-Oxoglutaric_acid.jpg|left|100px|2 … [[File:2-Oxoglutaric_acid.jpg|left|100px|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.transaminated to form oxaloacetate+glutamate. Cytosolic malate dehydrogenase converts oxaloacetate+NADH to malate.)
Mitochondria-Targeted Drug Development + ([[File:21640 - Mitochondria Targeted Thera … [[File:21640 - Mitochondria Targeted Therapeutics logo NEW.jpg|200px|left|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.tunities, panel discussions and dedicated roundtables.)
Screwdriver allen wrench + ([[File:24330-02.jpg|right|180px]]'''Screwdriver allen wrench''', a standard component of the [[O2k-FluoRespirometer]] and [[O2k-sV-Module]].)
MultiSensor-Connector + ([[File:30420-24 MultiSensorConnector.JPG|right|180px]] '''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 + ([[File:30430--24 NO-Attachment.JPG|right|180px]] '''MultiSensor-Preamplifier 1/100''': Required only for O2k-Series A-C, for application of NO (or other amperometric) sensors (single chamber mode of application).)
TIP2k-Needle Safety Support with cable guide + ([[File:31330-01 3.jpg|right|280px]] '''TIP2k-Needle Safety Support with cable guide''': for safe storage of TIP2k-needles and MultiSensor Modules cables when not required during the experiment.)
Storage box sV + ([[File:32001-01.jpg|right|180px]]'''Storage box sV''' empty, for storage of [[O2k-sV-Module]] components.)
O2k-Chamber Holder sV + ([[File:32100-01.jpg|right|180px]]'''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]].)
POS-Holder sV + ([[File:32300-01.jpg|right|180px]] '''POS-H … [[File:32300-01.jpg|right|180px]]'''POS-Holder sV''', made from black POM, to be screwed into the copper block of the [[O2k-Main Unit]], guiding the [[OroboPOS|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.inst the angular cut of the glass chamber.)
O2k-Chamber sV + ([[File:33100-01.jpg|right|180px]]'''O2k-Chamber sV''': 12 mm inner diameter, Duran® glass polished, with standard operation volume ''V'' of 0.5 mL.)
Stirrer-Bar sV\white PVDF\11.5x6.2 mm + ([[File:33210-01.jpg|right|180px]]'''Stirre … [[File:33210-01.jpg|right|180px]]'''Stirrer-Bar sV\white [[PVDF]]\11.5x6.2 mm''', operated in the 0.5-mL [[O2k-Chamber sV]] at constant stirring speed (standard is 750 rpm, or 12.5 Hz), to provide optimum mixing of the sample in the aqueous medium and ensure a stable signal of the polarographic oxygen sensor ([[OroboPOS]]) placed in a position of maximum current of the medium.position of maximum current of the medium.)
Stopper sV\black PEEK\conical Shaft\central Port + ([[File:34000-01.jpg|right|180px]]'''Stoppe … [[File:34000-01.jpg|right|180px]]'''Stopper sV\black PEEK\conical Shaft\central Port''': with conical shaft (with PTFE, graphite, carbon fiber) and one central capillary (1.0 mm diameter; 48.9 mm length), [[Volume-Calibration Ring sV]] (A or B) for volume adjustment 0.5 mL; 2 mounted O-rings ([[O-ring sV\Viton\9.5x1 mm]]).[[O-ring sV\Viton\9.5x1 mm]]).)
O-ring sV\Viton\9.5x1 mm + ([[File:34310-02.jpg|right|180px]]'''O-ring sV\[[Viton]]\9.5x1 mm''', for [[Stopper sV\black PEEK\conical Shaft\central Port | PEEK Stopper sV]], 2 are mounted on each PEEK Stopper sV, box of 8 as spares.)
Asia Society for Mitochondrial Research and Medicine + ([[File:ASMRM LOGO.JPG|200px|left]]The '''Asia Society for Mitochondrial Research and Medicine''' (ASMRM) was founded in 2003 to share the latest knowledge on mitochondrial research.)
Acetyl-CoA + ([[File:Acetyl coenzyme A 700.png|left|200p … [[File:Acetyl coenzyme A 700.png|left|200px|acetyl-CoA]]'''Acetyl-CoA''', C23H38N7O17P3S, is a central piece in metabolism involved in several biological processes, but its main role is to deliver the acetyl group into the [[TCA cycle]] for its oxidation. It can be synthesized in different pathways: (i) in glycolysis from [[pyruvate]], by pyruvate dehydrogenase, which also forms NADH; (ii) from fatty acids β-oxidation, which releases one acetyl-CoA each round; (iii) in the catabolism of some amino acids such as leucine, lysine, phenylalanine, tyrosine and tryptophan. In the mitochondrial matrix, acetyl-CoA is condensed with [[oxaloacetate]] to form [[citrate]] through the action of [[citrate synthase]] in the [[tricarboxylic acid cycle]]. Acetyl-CoA cannot cross the mitochondrial inner membrane but citrate can be transported out of the mitochondria. In the cytosol, citrate can be converted to acetyl-CoA and be used in the synthesis of fatty acid, cholesterol, ketone bodies, acetylcholine, and other processes. and be used in the synthesis of fatty acid, cholesterol, ketone bodies, acetylcholine, and other processes.)
Aconitase + ([[File:Aconitase.jpg|right|500px|aconitase … [[File:Aconitase.jpg|right|500px|aconitase]]'''Aconitase''' is a [[TCA cycle]] enzyme that catalyzes the reversible isomerization of [[citrate]] to [[isocitrate]]. Also, an isoform is also present in the cytosol acting as a trans-regulatory factor that controls iron homeostasis at a post-transcriptional level. tasis at a post-transcriptional level. )
Cardiovascular Exercise Research Group + ([[File:CERG.gif|200px|left|CERG]] The '''C … [[File:CERG.gif|200px|left|CERG]]The '''Cardiovascular Exercise Research Group''' (CERG) was established in January 2008 and their research focuses on identifying the key cellular and molecular mechanisms underlying the beneficial effects of physical exercise on the heart, arteries and skeletal muscle in the context of disease prevention and management through experimental, clinical and epidemiological studies. Since 2003 this research group organizes the biennial seminar [http://www.ntnu.edu/cerg/seminar-2013 "Exercise in Medicine"] in Trondheim, Norway.ercise in Medicine"] in Trondheim, Norway.)
Complex II ambiguities + ([[File:CII-ambiguities Graphical abstract. … [[File:CII-ambiguities Graphical abstract.png|300px|left|link=Gnaiger 2023 MitoFit CII]]The current narrative that the reduced coenzymes NADH and FADH2 feed electrons from the tricarboxylic acid (TCA) cycle into the mitochondrial electron transfer system can create ambiguities around respiratory Complex CII. Succinate dehydrogenase or CII reduces FAD to FADH2 in the canonical forward TCA cycle. However, some graphical representations of the membrane-bound electron transfer system (ETS) depict CII as the site of oxidation of FADH2. This leads to the false believe that FADH2 generated by electron transferring flavoprotein (CETF) in fatty acid oxidation and mitochondrial glycerophosphate dehydrogenase (CGpDH) feeds electrons into the ETS through CII. In reality, NADH and succinate produced in the TCA cycle are the substrates of Complexes CI and CII, respectively, and the reduced flavin groups FMNH2 and FADH2 are downstream products of CI and CII, respectively, carrying electrons from CI and CII into the Q-junction. Similarly, CETF and CGpDH feed electrons into the Q-junction but not through CII. The ambiguities surrounding Complex II in the literature call for quality control, to secure scientific standards in current communications on bioenergetics and support adequate clinical applications.nd support adequate clinical applications.)
Complex II + ([[File:CII.png |right|200px|link=Gnaiger 2 … [[File:CII.png |right|200px|link=Gnaiger 2023 MitoFit CII]]'''Complex II''' or '''succinate:quinone oxidoreductase (SQR)''' is the only membrane-bound enzyme in the [[TCA cycle]] and is part of the [[electron transfer pathway]]. The reversible oxidoreduction of succinate and fumarate is catalyzed in a soluble domain and coupled to the reversible oxidoreduction of quinol and quinone in the mitochondrial inner membrane. CII consists in most species of four subunits. The flavoprotein [[succinate dehydrogenase]] is the largest polypeptide of CII, located on the matrix face of the mt-inner membrane. Succinate:quinone oxidoreductases (SQRs, SDHABCD) favour oxidation of succinate and reduction of quinone in the canonical forward direction of the TCA cycle and electron transfer into the [[Q-junction]]. In contrast, quinol:fumarate reductases (QFRs, fumarate reductases, FRDABCD) tend to operate in the reverse direction reducing fumarate and oxidizing quinol.on reducing fumarate and oxidizing quinol.)
SUIT-007 O2 ce-pce D030 + ([[File:Ce1;1Dig;1G;2D;2c;3M;4U;5Ama.png|400px]])
SUIT-027 O2 ce-pce D065 + ([[File:Ce1;1Dig;1M;2D;3M;4P;5G;6Ama.png|500px]])
SUIT-006 O2 ce-pce D029 + ([[File:Ce1;1Dig;1PM;2D;2c;3Omy;4U;5Ama.png|600px]])
SUIT-031 O2 ce-pce D079 + ([[File:Ce1;1Dig;1PM;2D;2c;3S;4Rot;5U;6Ama.png|400px]])
SUIT-024 + ([[File:Ce1;1Dig;1PM;2T;2D;3Omy-.png|410px]])
SUIT-024 O2 ce-pce D056 + ([[File:Ce1;1Dig;1PM;2T;2D;3Omy;4Ama.png|410px]])
SUIT-031 Q ce-pce D074 + ([[File:Ce1;1Dig;1Q2;1PM;2D;3S;4Rot;5U;6Anox;7Ama.png|400px]])
SUIT-009 O2 ce-pce D016 + ([[File:Ce1;1Dig;1S;2D;2c;3P;4Rot;5Ama.png|520px|SUIT-009]])
SUIT-009 AmR ce-pce D019 + ([[File:Ce1;1Dig;1S;2D;3P;4Rot;5Ama.png|520px|SUIT9]])
SUIT-026 AmR ce-pce D087 + ([[File:Ce1;1Dig;1S;2Rot;3D;4Ama.png|600px]])
SUIT-018 AmR ce-pce D068 + ([[File:Ce1;1Dig;2GMS;3D;4Ama.png|290px]])
SUIT-003 O2 ce D037 + ([[File:Ce1;ce1Glc;ce2(Omy);ce3U;ce4Ama.png|350px]])
SUIT-003 O2 ce-pce D018 + ([[File:Ce1;ce1P;ce2Omy;ce3U;ce4Glc;ce5Rot;ce6S;1Dig;1U;1c;2Ama;3AsTm;4Azd.png|600px]])
SUIT-003 O2 ce D012 + ([[File:Ce1;ce1P;ce2Omy;ce3U;ce4Rot;ce5Ama.png|400px]])
SUIT-003 Ce1;ce1SD;ce3U;ce4Rot;ce5Ama + ([[File:Ce1;ce1SD;ce3U;ce4Rot;ce5Ama.png|200px]])

SUIT-003 + ([[File:Ce1;ce2(Omy);ce3U-.png|250px]] [[File:Ce5S;1Dig;1c-.png|250px]])

SUIT-003 O2 ce D038 + ([[File:Ce1;ce2(Omy);ce3U;ce3Glc;ce3'U;ce4Ama.png|350px]])
SUIT-003 Ce1;ce2U;ce3Rot;ce4S;ce5Ama + ([[File:Ce1;ce2U;ce3Rot;ce4S;ce5Ama.png|200px]])
SUIT-003 Ce1;ce3U;ce4Rot;ce5S;ce6Ama + ([[File:Ce1;ce3U;ce4Rot;ce5S;ce6Ama.png|200px]])
Cell Symposia + ([[File:CellSymposiaLogo.jpg|90px]] Organized by the editors of Cell Press's leading journals, '''Cell Symposia''' bring together exceptional speakers and scientists to discuss topics at the forefront of scientific research.)
Chemical background + ([[File:Chb.png|100px|https://wiki.oroboros … [[File:Chb.png|100px|https://wiki.oroboros.at/index.php/File:Chb.png]] '''Chemical background''' ''Chb'' is due to autooxidation of the reagents. During CIV assays, ascorbate and TMPD are added to maintain cytochrome ''c'' in a reduced state. External cytochrome ''c'' may be included in the CIV assay. The autooxidation of these compounds is linearly oxygen-dependent down to approximately 50 µM oxygen and responsible for the chemical background oxygen flux after the inhibition of CIV. Oxygen flux due to the chemical reaction of autooxidation must be corrected for the [[Oxygen flux - instrumental background|instrumental O2 background]]. The correction for chemical background is necessary to determine CIV activity, in which case the instrumental O2 background and chemical background may be combined in an overall correction term.be combined in an overall correction term.)
Citrate + ([[File:Citrate 300 (1).png|left|100px|citr … [[File:Citrate 300 (1).png|left|100px|citrate]]'''citrate''', C6H5O7-3, is a tricarboxylic acid trianion, intermediate of the TCA cycle, obtained by deprotonation of the three carboxy groups of citric acid. Citrate is formed from [[oxaloacetate]] and acetyl-CoA through the catalytic activity of the [[citrate synthase]]. In the TCA cycle, citrate forms isocitrate by the activity of the [[aconitase]]. Citrate can be transported out of the mitochondria by the tricarboxylate transport, situated in the inner mitochondrial membrane. The transport occurs as an antiport of malate from the cytosol and it is a key process for fatty acid and oxaloacetate synthesis in the cytosol. ol and it is a key process for fatty acid and oxaloacetate synthesis in the cytosol. )
Coenzyme Q2 + ([[File:Coenzyme Q2.png|left|200px|CoQ<s … [[File:Coenzyme Q2.png|left|200px|CoQ2]]'''Coenzyme Q2''' or ubiquinone-2 (CoQ2) is a [[quinone]] derivate composed of a benzoquinone ring with an isoprenoid side chain consisting of two isoprenoid groups, with two methoxy groups, and with one methyl group. In HRR it is used as a Q-mimetic to detect the redox changes of [[coenzyme Q]] at the [[Q-junction]] in conjunction with the [[Q-Module]], since the naturally occurring long-chain coenzyme Q (e.g. CoQ10) is trapped within membrane boundaries. CoQ2 can react both with mitochondrial complexes (e.g. [[CI]], [[CII]] and [[CIII]]) at their quinone-binding sites and with the [[Three-electrode system |detecting electrode]].[[Three-electrode system |detecting electrode]].)
Company of Scientists + ([[File:Company-of-Scientists logo.jpg|left|140px|link=http://www.company-of-scientists.com|Company of Scientists]] The '''Company of Scientists''' evolves as a concept for implementing scientific innovations on the market.)
Unit + ([[File:Count-vs-number.png|right|120px|lin … [[File:Count-vs-number.png|right|120px|link=Elementary entity]]A '''unit''' is defined as 'a single individual thing' in Euclid's ''Elements'' (Book VII). This defines the [[elementary entity]] ''U''''X'' of entity-type ''X'' (thing). The [[International System of Units]] defines the unit as 'simply a particular example of the quantity concerned which is used as a reference'. Then the ''value'' of a quantity ''Q'' is the product of a number ''N'' and a unit ''u''''Q''. The symbols ''U''''X'' and ''u''''Q'' are chosen here with ''U'' and ''u'' for 'unit': ''U''''X'' is the Euclidean or entetic unit ('eunit'), and ''u''''Q'' is the abstract unit ('aunit'). Subscripts ''X'' and ''Q'' for 'entity-type' and 'quantity-type' reflect perhaps even more clearly than words the contrasting meanings of the two fundamental definitions of an entetic versus abstract 'unit'. The term 'unit' with its dual meanings is used and confused in practical language and the scientific literature today. In the elementary entity ''U''''X'', the unit (the 'one') relates to the entity-type ''X'', to the single individual thing (single individual or undivided; the root of the word ''thing'' has the meaning of 'assembly'). The quantity involved in the unit of a single thing is the ''count'', ''N''''X'' = ''N''·''U''''X'' [x]. In contrast to counting, a unit ''u''''Q'' is linked to the measurement of quantities ''Q''''u'' = ''N''·''u''''Q'', such as volume, mass, energy; and these quantities — and hence the units ''u''''Q'' — are abstracted from entity-types, pulled away from the world of real things. The new SI (2019-05-20) has completed this total abstraction of units, from the previous necessity to not only provide a quantitative definition but also a physical realization of a unit in the form of an 'artefact', such as the international prototype (IPK) for the unit kilogram. The new definitions of the base SI units are independent of any physical realization: ''u''''Q'' is separate from ''X''. The classical unit of Euklid is the elementary unit for counting, entirely independent of measuring. Therefore, the quantity [[count]] is unique with respect to two properties: (''1'') in contrast to all other quantities in the metric system, the count depends on quantization of entities ''X''; and (''2'') in the SI, the '''N'''umber 1 is the '''U'''nit of the '''C'''ount of '''entities''' — NUCE.ntrast to all other quantities in the metric system, the count depends on quantization of entities ''X''; and (''2'') in the SI, the '''N'''umber 1 is the '''U'''nit of the '''C'''ount of '''entities''' — NUCE.)
Elementary entity + ([[File:Count-vs-number.png|right|120px|lin … [[File:Count-vs-number.png|right|120px|link=Unit]]An '''elementary entity''' is an [[entity]] of type ''X'', distinguished as a single ''[[unit]]'' of countable objects (''X'' = molecules, cells, organisms, particles, parties, items) or events (''X'' = beats, collisions, emissions, decays, celestial cycles, instances, occurrences, parties). "An elementary entity may be an atom, a molecule, an ion, an electron, any other particle or specified group of particles" ([[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |Bureau International des Poids et Mesures 2019)]]. An elementary entity, therefore, needs to be distinguished from non-countable entities and the general class of entities ''X''. This distinction is emphasized by the term 'elementary' (synonymous with 'elementary entity') with symbol ''U''''X'' and [[unit |elementary unit]] [x].If an object is defined as an assembly of particles (a party of two, a molecule as the assembly of a stoichiometric number of atoms), then the elementary is the assembly but not the assembled particle. A number of defined elementaries ''U''''X'' is a [[count]], ''N''''X'' = ''N''·''U''''X'' [x], where ''N'' is a number, and as such ''N'' is dimensionless, and ''N'' is a ''number'' (stop) and is not 'a number of ..'. Elementaries are added as items to a count. The elementary ''U''''X'' has the [[dimension]] U of the [[count]] ''N''''X''. The elementary ''U''''X'' has the same unit [x] as the count ''N''''X'', or more accurately it gives the count the defining 'counting-unit', which is the 'elementary unit' [x]. From the definition of count as the number (''N'') of elementaries (''U'') of entity type ''X'', it follows that count divided by elementary is a pure number, ''N'' = ''N''''X''·''U''''X''-1. The unit x of a count can neither be the entity ''X'' nor a number. The elementary of type ''X'' defines the identity ''X'' of the elementary ''U''''X'' with the unit 'elementary unit' with symbol [x]. Since a count ''N''''X'' is the number of elementary entities, the elementary ''U''''X'' is not a count (''U''''X'' is not identical with ''N''·''U''''X'').''N''''X'' is the number of elementary entities, the elementary ''U''''X'' is not a count (''U''''X'' is not identical with ''N''·''U''''X'').)
Count + ([[File:Count-vs-number.png|right|120px|lin … [[File:Count-vs-number.png|right|120px|link=Number]]'''Count''' ''N''''X'' is the [[number]] ''N'' of elementary entities of [[entity]]-type ''X''. The single [[elementary entity]] ''U''''X'' is a countable object or event. ''N''''X'' is the number of objects of type ''X'', whereas the term 'entity' and symbol ''X'' are frequently used and understood in dual-message code indicating both (''1'') the entity-type ''X'' and (''2'') a count of ''N''''X'' = 1 x for a single elementary entity ''U''''X''. 'Count' is synonymous with 'number of entities' (number of particles such as molecules, or objects such as cells). Count is one of the most fundamental quantities in all areas of physics to biology, sociology, economy and philosophy, including all perspectives of the statics of countable objects to the dynamics of countable events. The term 'number of entities' can be used in short for 'number of elementary entities', since only elementary entities can be counted, and as long as it is clear from the context, that it is not the number of different entity types that are the object of the count.rom the context, that it is not the number of different entity types that are the object of the count.)
Elementary unit + ([[File:Count-vs-number.png|right|120px|lin … [[File:Count-vs-number.png|right|120px|link=Elementary entity]]The '''elementary unit''' [x] is the unit of a [[count]] ''N''''X'' [x]. The [[International System of Units]] defines the unit of a count as 1. Then the '''N'''umber 1 is the '''U'''nit of the '''C'''ount of '''E'''ntities — NUCE. This causes a number of formal inconsistencies which are resolved by introducing the elementary unit [x] as the abstracted unit of Euclid’s unit, which is an [[elementary entity]] ''U''''X'' [x], and as the unit of Euclid’s number, which is a count ''N''''X'' [x].it of Euclid’s number, which is a count ''N''''X'' [x].)
DORA + ([[File:Dorabadge5.png|150px|right]] The Declaration on Research Assessment '''DORA''' recognizes the need to improve the ways in which researchers and the outputs of scholarly research are evaluated.)
Level flow + ([[File:E.jpg |link=ET capacity]] '''Level … [[File:E.jpg |link=ET capacity]] '''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). force, while output flow may be maximum).)
Noncoupled respiration + ([[File:E.jpg |link=ET capacity]] '''Noncou … [[File:E.jpg |link=ET capacity]] '''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]]).» [[#Is_respiration_uncoupled_-_noncoupled_-_dyscoupled.3F |'''MiPNet article''']][#Is_respiration_uncoupled_-_noncoupled_-_dyscoupled.3F |'''MiPNet article''']])
State 3u + ([[File:E.jpg |link=ET capacity]] Noncouple … [[File:E.jpg |link=ET capacity]] Noncoupled state of [[ET capacity]]. '''State 3u''' (u for uncoupled) has been used frequently in bioenergetics, without sufficient emphasis [[Villani 1998 J Biol Chem|(e.g. Villani et al 1998)]] on the fundamental difference between [[OXPHOS capacity]] (''P'', coupled with an uncoupled contribution; State 3) and noncoupled [[ET capacity]] (''E''; State 3u) ([[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]; [[Rasmussen 2000 Mol Cell Biochem|Rasmussen and Rasmussen 2000]]).[[Rasmussen 2000 Mol Cell Biochem|Rasmussen and Rasmussen 2000]]).)
ET capacity + ([[File:E.jpg]] '''T capacity''' is the res … [[File:E.jpg]] '''T capacity''' is the respiratory electron-transfer-pathway capacity ''E'' of mitochondria measured as oxygen consumption in the noncoupled state at optimum [[uncoupler]] concentration. This optimum concentration is obtained by stepwise titration of an established protonophore to induce maximum oxygen flux as the determinant of ET capacity. The experimentally induced noncoupled state at optimum uncoupler concentration is thus distinguished from (''1'') a wide range of uncoupled states at any experimental uncoupler concentration, (''2'') physiological uncoupled states controlled by intrinsic uncoupling (e.g. UCP1 in brown fat), and (''3'') pathological dyscoupled states indicative of mitochondrial injuries or toxic effects of pharmacological or environmental substances. ET capacity in mitochondrial preparations requires the addition of defined fuel substrates to establish an ET-pathway competent state.» [[#Why ET capacity, why not State 3u.3F | '''MiPNet article''']][#Why ET capacity, why not State 3u.3F | '''MiPNet article''']])
EUROMIT + ([[File:EUROMIT.jpg|left|250px]] '''EUROMIT''' is a group based in Europe for organizing '''International Meetings on Mitochondrial Pathology'''.)
Ethanol + ([[File:Ethanol.png|left|80px|Ethanol]] < … [[File:Ethanol.png|left|80px|Ethanol]]<div></div><div>'''Ethanol''' or ethyl alcohol, C2H6O or EtOH, is widely used in the laboratory, particularly as a solvent and cleaning agent. There are different grades of high purity ethanol. Up to a purity of 95.6 % ethanol can be separated from water by destillation. Higher concentrations than 95% require usage of additives that disrupt the azeotrope composition and allow further distillation. Ethanol is qualified as "absolute" if it contains no more than one percent water. Whenever 'ethanol abs.' is mentioned without further specification in published protocols, it refers to ≥ 99 % ethanol a.r. (analytical reagent grade).</div><div></div><div></div>s to ≥ 99 % ethanol a.r. (analytical reagent grade). </div><div> </div><div></div>)
Glutamate-anaplerotic pathway control state + ([[File:G.jpg|left|200px|G]] '''G''': [[Glu … [[File:G.jpg|left|200px|G]] '''G''': [[Glutamate]] is an [[Anaplerotic pathway control state |anaplerotic]] [[Electron-transfer-pathway state |NADH-linked type 4 substrate]] (N). When supplied as the sole fuel substrate in the '''glutamate-anaplerotic pathway control state''', G is transported by the electroneutral glutamate-/OH- exchanger, and is oxidised via mt-[[glutamate dehydrogenase]] in the mitochondrial matrix. The G-pathway plays an important role in [[glutaminolysis]].[[glutaminolysis]].)
GM-pathway control state + ([[File:GM.jpg|left|200px|GM]] '''GM''': [[ … [[File:GM.jpg|left|200px|GM]] '''GM''': [[Glutamate]] & [[Malate]].'''MitoPathway control state:''' [[NADH electron transfer-pathway state]]The '''GM-pathway control state''' (glutamate-malate pathway control state) is established when glutamate&malate are added to isolated mitochondria, permeabilized cells and other mitochondrial preparations. Glutamate and transaminase are responsible for the metabolism of [[oxaloacetate]], comparable to the metabolism with acetyl-CoA and citrate synthase.e metabolism with acetyl-CoA and citrate synthase.)
GMS-pathway control state + ([[File:GMS.jpg|left|200px|GMS]]'''GMS''': … [[File:GMS.jpg|left|200px|GMS]]'''GMS''': [[Glutamate]] & [[Malate]] & [[Succinate]].'''MitoPathway control:''' NSTransaminase catalyzes the reaction from oxaloacetate to 2-oxoglutarate, which then establishes a cycle without generation of citrate. OXPHOS is higher with GS (CI&II) compared to GM (CI) or SRot (CII). 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).ed muscle fibres and isolated mitochondria (Gnaiger 2009).)
Glutamate + ([[File:Glutamic_acid.jpg|left|100px|Glutam … [[File:Glutamic_acid.jpg|left|100px|Glutamic acid]]'''Glutamic acid''', C5H9NO4, is an amino acid which occurs under physiological conditions mainly as the anion '''glutamate-, G''', with ''p''Ka1 = 2.1, ''p''Ka2 = 4.07 and ''p''Ka3 = 9.47. 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 ([[oxoglutarate|2-oxoglutarate]]), representing the [[glutamate-anaplerotic pathway control state]]. Ammonia (the byproduct of the reaction) passes freely through the mitochondrial membrane.[glutamate-anaplerotic pathway control state]]. Ammonia (the byproduct of the reaction) passes freely through the mitochondrial membrane.)
Glycerophosphate shuttle + ([[File:Gp-shuttle.jpg|left|200px|Gp]] The … [[File:Gp-shuttle.jpg|left|200px|Gp]]The '''glycerophosphate shuttle''' makes cytoplasmic NADH available for mitochondrial oxidative phosphorylation. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophosphate dehydrogenase. On the outer face of the inner mitochondrial membrane, [[glycerophosphate dehydrogenase complex]] (mitochondrial glycerophosphate dehydrogenase) oxidizes glycerophosphate back to dihydroxyacetone phosphate, a reaction not generating NADH but reducing a flavin prosthesic group. The reduced flavoprotein transfers its reducing equivalents into the [[Q-junction]], thus representing a [[Electron-transfer-pathway state|ET pathway level 3 control state]].[[Electron-transfer-pathway state|ET pathway level 3 control state]].)
Water + ([[File:H2O.jpg|left|60px|Water]] '''Water' … [[File:H2O.jpg|left|60px|Water]]'''Water''', H2O, is widely used in the laboratory, particularly as a solvent and cleaning agent. Chemically pure water is prepared in various grades of purification: double distilled water (ddH2O) versus distilled water (dH2O or [[aqua destillata]], a.d.) and deionized or demineralized water (diH2O) with various combination purification methods. When H2O is mentioned without further specification in published protocols, it is frequently assumed that the standards of each laboratory are applied as to the quality of purified water. Purification is not only to be controlled with respect to salt content and corresponding electrical conductivity (ultra-pure water: 5.5 μS/m due to H+ and OH- ions), but also in terms of microbial contamination. 5.5 μS/m due to H+ and OH- ions), but also in terms of microbial contamination.)
Hydrogen peroxide + ([[File:H2O2.jpg|left|60px|Hydrogen peroxid … [[File:H2O2.jpg|left|60px|Hydrogen peroxide]]'''Hydrogen peroxide''', H2O2 or dihydrogen dioxide, is one of several reactive oxygen intermediates generally referred to as [[reactive oxygen species]] (ROS). It is formed in various enzyme-catalyzed reactions (''e.g.'', [[superoxide dismutase]]) with the potential to damage cellular molecules and structures. H2O2 is dismutated by [[catalase]] to water and [[oxygen]]. H2O2 is produced as a signaling molecule in aerobic metabolism and passes membranes more easily compared to other ROS. is produced as a signaling molecule in aerobic metabolism and passes membranes more easily compared to other ROS.)
International Mito Patients (IMP) + ([[File:IMP LOGO.JPG|150px]]The '''Internat … [[File:IMP LOGO.JPG|150px]]The '''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. be their voice on an international level.)
IRDiRC + ([[File:IRDiRC.png|150px]] The Internationa … [[File:IRDiRC.png|150px]] The International Rare Diseases Research Consortium (IRDiRC) teams up researchers and organizations investing in rare diseases research in order to achieve two main objectives by the year 2020, namely to deliver 200 new therapies for rare diseases and means to diagnose most rare diseases. and means to diagnose most rare diseases.)
International Society for Mountain Medicine + ([[File:ISMM.jpg|150px|left|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 Tissue + ([[File:ISOTT LOGO.jpg|200px|left]] The ''' … [[File:ISOTT LOGO.jpg|200px|left]]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.ves and in the proceedings of the society.)
Isocitrate + ([[File:Isocitrate.png|left|100px|isocitrat … [[File:Isocitrate.png|left|100px|isocitrate]]'''isocitrate''', C6H5O7-3, is a tricarboxylic acid trianion, intermediate of the [[tricarboxylic acid cycle|TCA cycle]], obtained by isomerization of citrate. The process is catalyzed by [[aconitase]], forming the enzyme-bound intermediate ''cis''-aconitate.[[aconitase]], forming the enzyme-bound intermediate ''cis''-aconitate.)
E-L coupling efficiency + ([[File:J(E-L).jpg|50 px|E-L coupling effic … [[File:J(E-L).jpg|50 px|E-L coupling efficiency]] The '''''E-L'' coupling efficiency''', ''jE-L'' = (''E-L'')/''E'' = 1-''L/E'', is 0.0 at zero coupling (''L''=''E'') and 1.0 at the limit of a fully coupled system (''L''=0). The background state is the [[LEAK respiration|LEAK]] state which is stimulated to flux in the [[electron transfer pathway]] reference state by [[uncoupler]] titration. LEAK states ''L''N or ''L''T may be stimulated first by saturating ADP (rate ''P'' in the OXPHOS state) with subsequent uncoupler titration to the ET state with maximum rate ''E''. The ''E-L'' coupling efficiency is based on measurement of a [[coupling-control ratio]] ([[LEAK-control ratio]], ''L/E''), whereas the thermodynamic or [[ergodynamic efficiency]] of coupling between ATP production (phosphorylation of ADP to ATP) and oxygen consumption is based on measurement of the output/input flux ratio (P»/O2 ratio) and output/input force ratio (Gibbs force of phosphorylation/Gibbs force of oxidation). The [[biochemical coupling efficiency]] expressed as the ''E-L'' coupling efficiency is independent of kinetic control by the ''E-P'' control efficiency, and is equal to the [[P-L control efficiency |''P-L'' control efficiency]] if ''P=E'' as evaluated in a [[coupling-control protocol]].» [[#Biochemical_coupling_efficiency:_from_0_to_.3C1 | '''MiPNet article''']]#Biochemical_coupling_efficiency:_from_0_to_.3C1 | '''MiPNet article''']])
Biochemical coupling efficiency + ([[File:J(E-L).jpg|50 px|link=E-L coupling … [[File:J(E-L).jpg|50 px|link=E-L coupling efficiency |''E-L'' coupling efficiency]] The '''biochemical coupling efficiency''' is the [[E-L coupling efficiency |''E-L'' coupling efficiency]], (''E-L'')/''E'' = 1-''L/E''. This is equivalent to the [[P-L control efficiency |''P-L'' control efficiency]], (''P-L'')/''P'' = 1-''L/P'', only at zero [[E-P excess capacity |''E-P'' excess capacity]], when ''P'' = ''E''). The biochemical coupling efficiency is independent of kinetic control by the phosphorylation system.tic control by the phosphorylation system.)
E-P control efficiency + ([[File:J(E-P).jpg|50 px|E-P control effici … [[File:J(E-P).jpg|50 px|E-P control efficiency]] The '''''E-P'' control efficiency''', ''jE-P'' = (''E-P'')/''E'' = 1-''P/E'', is an expression of the relative limitation of [[OXPHOS capacity]] by the capacity of the [[phosphorylation system]]. It is the normalized ''E-P'' excess capacity. ''jE-P'' = 0.0 when OXPHOS capacity is not limited by the phosphorylation system at zero ''E-P'' excess capacity, ''P''=''E'', when the phosphorylation system does not exert any control over OXPHOS capacity. ''jE-P'' increases with increasing control of the phosphorylation system over OXPHOS capacity. ''jE-P'' = 1 at the limit of zero phosphorylation capacity. The [[OXPHOS]] state of mt-preparations is stimulated to [[electron transfer pathway]] capacity ''E'' by [[uncoupler]] titration, which yields the [[E-P excess capacity |''E-P'' excess capacity]].[[E-P excess capacity |''E-P'' excess capacity]].)
P-L control efficiency + ([[File:J(P-L).jpg|50 px|P-L control effici … [[File:J(P-L).jpg|50 px|P-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'' 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.» [[#Cell ergometry: OXPHOS-control and ET-coupling efficiency |'''MiPNet article''']][#Cell ergometry: OXPHOS-control and ET-coupling efficiency |'''MiPNet article''']])
R-L control efficiency + ([[File:J(R-L).jpg|50 px|R-L ROUTINE-coupli … [[File:J(R-L).jpg|50 px|R-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 |''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 respiration|LEAK]] state, and the flux control variable is stimulation to ROUTINE respiration by physiologically controlled ATP turnover in living cells.ration by physiologically controlled ATP turnover in living cells.)
Japanese Society of Mitochondrial Research and Medicine + ([[File:J-mit.png|100px|left]]The '''Japane … [[File:J-mit.png|100px|left]]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]].[[ASMRM]].)
State 4 + ([[File:L.jpg |link=LEAK respiration]] '''S … [[File:L.jpg |link=LEAK respiration]] '''State 4''' is the [[respiratory state]] obtained in isolated mitochondria after [[State 3]], when added [[ADP]] is phosphorylated maximally to [[ATP]] driven by electron transfer from defined respiratory substrates to O2 ([[Chance 1955 JBC-III|Chance and Williams, 1955]]). State 4 represents [[LEAK respiration]], ''L''T (''L'' for [[LEAK respiration]]; T for ATP), or an overestimation of LEAK respiration if [[ATPase]] activity prevents final accumulation of ATP and maintains a continuous stimulation of respiration by recycled ADP. This can be tested by inhibition of ATP synthase by [[oligomycin]]; ''L''Omy). In the [[LEAK state]] (state of non-phosphorylating resting respiration; static head), oxygen flux is decreased to a minimum (corrected for [[ROX]]), and the [[mt-membrane potential]] is increased to a maximum for a specific substrate or substrate combination.] is increased to a maximum for a specific substrate or substrate combination.)
Static head + ([[File:L.jpg |link=LEAK respiration]] '''S … [[File:L.jpg |link=LEAK respiration]] '''Static head''' is a [[steady state]] of a system with an input process coupled to an output process (coupled system), in which the output force is maximized at constant input or driving force up to a level at which the conjugated output flow is reduced to zero. ''In an incompletely coupled system, energy must be expended to maintain static head, even though the output is zero'' (Caplan and Essig 1983; referring to output flow at maximum output force). [[LEAK respiration]] is a measure of input flow at static head, when the output flow of phosphorylation (ADP->ATP) is zero at maximum phosphorylation potential (Gibbs force of phosphorylation; [[Gnaiger_1993_Hypoxia|Gnaiger 1993a]]). In a completely coupled system, not only the output flux but also the input flux are zero at static head, which then is a state of ''[[ergodynamic equilibrium]]'' ([[Gnaiger_1993_Pure_Appl_Chem |Gnaiger 1993b]]). Whereas the output force is maximum at ergodynamic equilibrium compensating for any given input force, all forces are zero at ''[[thermodynamic equilibrium]]''. Flows are zero at both types of equilibria, hence entropy production or power (power = flow x force) are zero in both cases, i.e. at thermodynamic equilibrium in general, and at ergodynamic equilibrium of a completely coupled system at static head.f a completely coupled system at static head.)
LEAK state without adenylates + ([[File:L.jpg |link=LEAK respiration]] In t … [[File:L.jpg |link=LEAK respiration]] 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).istinguished from ''L''(T) and ''L''(Omy).)
LEAK state with ATP + ([[File:L.jpg |link=LEAK respiration]] The … [[File:L.jpg |link=LEAK respiration]] 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 2000 Proc Natl Acad Sci U S A |Gnaiger et al 2000]]). Respiration in the LEAK state with ATP, ''L''(T), is distinguished from ''L''(n) and ''L''(Omy).istinguished from ''L''(n) and ''L''(Omy).)
LEAK state with oligomycin + ([[File:L.jpg |link=LEAK respiration]] The … [[File:L.jpg |link=LEAK respiration]] 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). distinguished from ''L''(n) and ''L''(T).)
LEAK respiration + ([[File:L.jpg]] '''EAK respiration''' or LE … [[File:L.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 [[Uncoupler|uncoupled]] or [[Dyscoupled respiration|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, ''J''O2''L'', or [[oxygen flow]], ''I''O2''L''). 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.» [[LEAK respiration#LEAK respiration: concept-linked terminology of respiratory states |'''MiPNet article''']][LEAK respiration#LEAK respiration: concept-linked terminology of respiratory states |'''MiPNet article''']])
Malate-anaplerotic pathway control state + ([[File:M.jpg|left|200px|M]] '''M''': [[Mal … [[File:M.jpg|left|200px|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 [[PM |Pyruvate&Malate]] in isolated rat skeletal muscle mitochondria. However, many mammalian and non-mammalian mitochondria have a mt-isoform of NADP+- or NAD(P)<big>+</big>-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]]).[GM-pathway control state]]).)
PM-pathway control state + ([[File:M.jpg|left|200px|PM]] '''PM''': [[P … [[File:M.jpg|left|200px|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).ate) is formed from isocitrate (isocitrate dehydrogenase).)
MITOEAGLE in MitoGlobal + ([[File:MITOEAGLE-representation.jpg|150px|left]] 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.)
MitoKit-CII + ([[File:MITOKIT-CII.jpg|right|180px]]'''Cel … [[File:MITOKIT-CII.jpg|right|180px]]'''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.omplex II of the electron transfer system.)
Rare New England + ([[File:MNE.jpg|left|110px|MNE]] MNE has tr … [[File:MNE.jpg|left|110px|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.isease and living in the New England area.)
Mitochondria Research Society + ([[File:MRS LOGO.JPG|250px|left]] The '''Mi … [[File:MRS LOGO.JPG|250px|left]]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.nosis and treatment through out the world.)
Malate + ([[File:Malic_acid.jpg|left|100px|Malic aci … [[File:Malic_acid.jpg|left|100px|Malic acid]]'''Malic acid''', C4H6O5, occurs under physiological conditions as the anion '''malate2-, M''', with p''K''a1 = 3.40 and p''K''a2 = 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 [[Mitochondrial preparations|mt-preparations]] from most tissues, since oxaloacetate accumulates in the absence of [[pyruvate]] or [[glutamate]].Malate is a [[NADH electron transfer-pathway state |type N substrate]] (N) required for the [[Fatty acid oxidation pathway control state| FAO-pathway]]. In the presence of [[Malate-anaplerotic pathway control state|anaplerotic pathways]] (''e.g.'', [[Malic enzyme|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]]).[[SUIT-002]]).)
Mitochondrial European Education Training + ([[File:Meet.jpg|200px|left]] The '''Mitoch … [[File:Meet.jpg|200px|left]] 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.tment of mitochondria-related pathologies.)
MiPMap + ([[File:MiPMap Publication.jpg|left|240px|M … [[File:MiPMap Publication.jpg|left|240px|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 Int J Biochem Cell Biol|Gnaiger 2009]]).[[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]).)
MiR05-Kit + ([[File:MiR05-Kit.jpg|right|180px]] Mitochondrial Respiration Medium - MiR05-Kit, 1 vial; for a final volume of 250 mL)
MitoCanada Foundation + ([[File:Mito Canada logo tag web2.png|200px … [[File:Mito Canada logo tag web2.png|200px|left|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.ble quality of life until there is a cure.)
Mitochondrial Research Guild + ([[File:Mito-Reseach-Guild.JPG|200px|left]] … [[File:Mito-Reseach-Guild.JPG|200px|left]]'''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.eatening effects of mitochondrial disease.)
European Bioenergetics Conference + ([[File:Mito-and-Chlora EBEC.png|270px]] '''EBEC''' is a group based in Europe that organizes the '''European Bioenergetics Conference'''.)
MitoAction + ([[File:MitoAction.JPG|230px]]The mission of '''MitoAction''' is to improve quality of life for all who are affected by mitochondrial disorders through support, education and advocacy initiatives.)
MitoFit Preprints + ([[File:MitoFit Preprints.png|left|200px|link=MitoFit Preprints]] '''MitoFit Preprints''' is an Open Access preprint server for mitochondrial physiology and bioenergetics.)
Mitochondrial Medicine Society + ([[File:Mitochondrial Medicine Society.jpg| … [[File:Mitochondrial Medicine Society.jpg|200px|left]]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., and treatment of mitochondrial diseases.)
Motic Microscope + ([[File:Motic Microscope.jpg|right|180px]]' … [[File:Motic Microscope.jpg|right|180px]]'''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).ding auxiliary ESD objective 2.0X(38.6mm).)
Motive entity + ([[File:Motive entities.png|right|300px|Fro … [[File:Motive entities.png|right|300px|From [[Gnaiger 2020 BEC MitoPathways]]]].A '''motive entity''' ''X''tr is an entity involved in a transformation including spacial transfer. Motive entities (transformants) are expressed in different [[motive unit]]s [MU] depending on the energy transformation under study and the chosen [[format]]. [[Flow]]s are defined as advancement in terms of stoichiometric motive entities per time. Isomorphic [[force]]s 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]].current]].)
SUIT-033 NADH mt D081 + ([[File:Mt;1D.1;2PGM;3D2.5;4Anox;5Myx;6Reox.png|400px]])
SUIT-033 O2 mt D110 + ([[File:Mt;1D.1;2PGM;3D2.5;4Myx.png|400 px]])
SUIT-034 NADH mt D082 + ([[File:Mt;1D.1;2PGM;3D2.5;4U;5Anox;6Myx;7Reox.png|400px]])
SUIT-034 O2 mt D111 + ([[File:Mt;1D.1;2PGM;3D2.5;4U;5Myx.png|400px]])
SUIT-032 O2 mt D109 + ([[File:Mt;1PGM;2D;3Myx.png|300 px]])
SUIT-001 O2 mt D001 + ([[File:Mt;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd .png|400px|SUIT-RP1]])
SUIT-031 Q mt D072 + ([[File:Mt;1Q2;1PM;2D;3S;4Rot;5U;6Anox;7Ama.png|400px]])
The North American Mitochondrial Disease Consortium + ([[File:NAMDC.JPG|200px|left]] '''The North … [[File:NAMDC.JPG|200px|left]]'''The North American Mitochondrial Disease Consortium (NAMDC)''' was established to create a network of all clinicians and clinical investigators in North America (US and Canada, with the hope of including Mexico in the future) who follow sizeable numbers of patients with mitochondrial diseases and are involved or interested in mitochondrial research. The NAMDC has created a clinical registry for patients, in the hopes of standardizing diagnostic criteria, collecting important standardized information on patients, and facilitating the participation of patients in research on mitochondrial diseases.For the study of any rare disease, the collection of specimens is a major challenge. The '''NAMDC''' is establishing a repository for specimens and DNA from patients with mitochondrial diseases, in order to make materials easily available to consortium researchers.Finally, the '''NAMDC''' will conduct clinical trials and other kinds of research. The consortium makes biostatisticians, data management experts, and specialists in clinical research available to participating physicians, so that experiments conducted through the NAMDC can make the most efficient and innovative use of the generous participation of patients.of the generous participation of patients.)
Neurocon + ([[File:Neurocon LOGO.JPG|200px|left]] '''Neurocon''' is an Indian society organizing international conferences on neurodegenerative and neurodevelopmental diseases.)
Oroboros O2k-technology + ([[File:NextGen-O2k All-in-one 2023.jpg|300 … [[File:NextGen-O2k All-in-one 2023.jpg|300px|right|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 |DatLab]], with high flexibility for extension by add-on [https://www.oroboros.at/index.php/product-category/products/o2k-modules/ O2k-Modules]. All O2k-Modules are supported by the [[NextGen-O2k]]. The [https://www.oroboros.at/index.php/product/q-module/ O2k-Q-Module] and the [https://www.oroboros.at/index.php/product/nadh-module/ 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 [https://www.oroboros.at/index.php/product/nextgen-o2k-redox/ 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.al physiology and pathology, extended to PhotoBiology.)
O-ring\Viton\12.5x1 mm + ([[File:O-ringViton12.5x1 mm.jpg|right|180px]]'''O-ring\[[Viton]]\12.5x1 mm''', for PVDF or PEEK O2k-Stoppers (2-mL O2k-Chamber), box of 8 as spares.)
Superoxide + ([[File:O2-.jpg|left|60px|Superoxide anion] … [[File:O2-.jpg|left|60px|Superoxide anion]]'''Superoxide anion''', O2•-, is a free radical formed in a one-electron reduction of molecular [[oxygen]] (red bullet in the figure), yielding a negatively charged molecule with a single unpaired electron (blue bullet on the left). It is highly reactive with organic compounds, and its intracellular concentration is kept under control by [[superoxide dismutase]].superoxide dismutase]].)
Oxygen + ([[File:O2.jpg|left|60px|Dioxygen]] '''Mole … [[File:O2.jpg|left|60px|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, ''M''r,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.sub>2 forming the covalent bond, and one electron in each atom is unpaired.)
O2k-chamber + ([[File:O2k-Chamber.jpg|right|180px]] '''O2 … [[File:O2k-Chamber.jpg|right|180px]]'''O2k-Chamber''': Duran® glass polished, with standard operation volumes (''V'') of 2.0 mL or 0.5 mL (small chamber volume in the [[O2k-sV-Module]], 12 mm inner diameter). The optical properties of Duran® allow application of fluorometric sensors ([http://www.duran-group.com/en/about-duran/duran-properties/optical-properties-of-duran.html Duran® optical properties]).f-duran.html Duran® optical properties]).)
Open Science + ([[File:Open Access logo.png |20px |left]] … [[File:Open Access logo.png |20px |left]] 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.pen dialogue with other knowledge systems.)
Open Access + ([[File:Open Access logo.png |20px |left]] … [[File:Open Access logo.png |20px |left]] '''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."or use them for any other lawful purpose.")
O2k-USB Flash Drive + ([[File:Oroboros-USB-flash-drive.JPG|right|120px]] 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.)
Oxaloacetate + ([[File:Oxaloacetic_acid.jpg|left|100px|Oxa … [[File:Oxaloacetic_acid.jpg|left|100px|Oxaloacetic acid]]'''Oxaloacetic acid''', C4H4O5, occurs under physiological conditions as the anion '''oxaloacetate2-, Oa'''. Oxaloacetate is formed from malate by [[Malate dehydrogenase|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 [[mitochondrial|mt]]-membrane of various tissues. Oa is a potent inhibitor of [[succinate dehydrogenase]].[[succinate dehydrogenase]].)
Normoxia + ([[File:Oxia terms.png|right|300px|link=htt … [[File:Oxia terms.png|right|300px|link=https://www.oroboros.at/index.php/product/oxia/|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 ''p''O2 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 ''p''O2 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 ''p''O2 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 ''p''O2 of the incubation medium, such that matching the experimental intracellular ''p''O2 to the level of intracellular tissue normoxia requires lowering the ambient ''p''O2 of the medium to avoid hyperoxia.O2 to the level of intracellular tissue normoxia requires lowering the ambient ''p''O2 of the medium to avoid hyperoxia.)
Oxidative phosphorylation + ([[File:P.jpg |link=OXPHOS capacity]] '''Ox … [[File:P.jpg |link=OXPHOS capacity]] '''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).[residual oxygen consumption]] (ROX).)
State 3 + ([[File:P.jpg |link=OXPHOS capacity]] '''St … [[File:P.jpg |link=OXPHOS capacity]] '''State 3''' respiration is the ADP stimulated respiration of isolated coupled mitochondria in the presence of high ADP and Pi concentrations, supported by a defined substrate or substrate combination at saturating oxygen levels [[Chance_1955_JBC-III|(Chance and Williams, 1955]]). State 3 respiration can also be induced in [[Permeabilized tissue or cells|permeabilized cells]], including permeabilized tissue preparations and tissue homogenates. ADP concentrations applied in State 3 are not necessarily saturating, whereas [[OXPHOS capacity]] is measured at saturating concentrations of ADP and Pi (OXPHOS state). For instance, non-saturating ADP concentrations are applied in State 3 in pulse titrations to determine the [[P/O ratio]] in State 3→4 (D→T) transitions, when saturating ADP concentrations would deplete the oxygen concentration in the closed oxygraph chamber before [[State 4]] is obtained ([[Gnaiger 2000 Proc Natl Acad Sci U S A|Gnaiger et al 2000]]; [[Puchowicz_2004_Mitochondrion|Puchowicz et al 2004]]). Respiration in the OXPHOS state or in State 3 is well [[coupled respiration|coupled]], and partially [[uncoupled respiration|uncoupled]] (physiological) or partially [[dyscoupled respiration|dyscoupled]] (pathological). A high [[mt-membrane potential]] provides the driving force for oxidative phosphorylation, to phosphorylate ADP to ATP and to transport ADP and ATP across the mitochondrial inner membrane (mtIM) through the [[adenine nucleotide translocase]] (ANT). The mt-membrane potential is reduced, however, in comparison to the [[LEAK state]] of respiration, whereas the cytochromes are in a more oxidized redox state.ation, whereas the cytochromes are in a more oxidized redox state.)
OXPHOS capacity + ([[File:P.jpg]] '''OXPHOS capacity''' ''P'' … [[File:P.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. and defined reduced CHNO-fuel substrates.)
PGM-pathway control state + ([[File:PGM.jpg|left|200px|PGM]] '''PGM''': … [[File:PGM.jpg|left|200px|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 ([[oxoglutarate | 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.tate and glutamate by the transaminase, and from glutamate by the glutamate dehydrogenase.)
PGMS-pathway control state + ([[File:PGMS.png|left|200px|PGMS]] '''PGMS' … [[File:PGMS.png|left|200px|PGMS]] '''PGMS''': [[Pyruvate]] & [[Glutamate]] & [[Malate]] & [[Succinate]].'''MitoPathway control state:''' [[NS|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&succinatercle with external pyruvate&malate&glutamate&succinate)
O2k-pH ISE-Module + ([[File:PH new.jpg|right|180px]]'''O2k-pH ISE-Module''': two pH electrodes and reference electrodes and accessories)
PMS-pathway control state + ([[File:PMS.jpg|left|200px|PMS]]'''PMS''': … [[File:PMS.jpg|left|200px|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). permeabilized muscle fibres and isolated mitochondria (Gnaiger 2009).)
O-ring\Viton\8x1 mm + ([[File:POS O-ring for sensor head or POS mounting tool.jpg|right|180px]]'''O-ring\Viton\8x1 mm''': for [[OroboPOS]] sensor head. Replaces the O-ring\Viton\9x1 mm)
O-ring\Viton\6x1 mm + ([[File:POS O-ring for sensor head or POS mounting tool.jpg|right|180px]]'''O-ring\Viton\6x1 mm''' for [[POS-Mounting Tool]].)
POS-Membrane Ring + ([[File:POS membrane holder ring.jpg|right|180px|link=]]'''POS-Membrane Ring''', [[PEEK]], holds the membrane against the inner O-ring on the POS housing.)
SUIT-002 O2 pfi D006 + ([[File:Pfi;1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd.png|400px|SUIT-RP2]])
SUIT-001 O2 pfi D002 + ([[File:Pfi;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd.png|400px|SUIT-RP1]])
Phosphorylation pathway + ([[File:Phosphorylation system.jpg|thumb|le … [[File:Phosphorylation system.jpg|thumb|left|250px|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 channel]]s. Since substrate-level phosphorylation is involved in the TCA-cycle, the P»-system includes [[succinyl-CoA ligase]] (GDP to GTP or ADP to ATP).ccinyl-CoA ligase]] (GDP to GTP or ADP to ATP).)
Pipette\Plastic\1 ml ungraded + ([[File:Pipette Plastic 1 ml-ungraded.JPG|180px|right]]'''Pipette\Plastic\1 mL ungraded''', for filling electrolyte into the reservoir of the [[OroboPOS]].)
Power O2k Numbers + ([[File:Power O2k Numbers.JPG|right|180px]]'''Power O2k Numbers''': Single number to label the O2k in a Power O2k-Lab.)
Proline + ([[File:Proline.png|left|100px|Proline]] '' … [[File:Proline.png|left|100px|Proline]]'''Proline''' (Pro), C5H9NO2, is an amino acid which occurs under physiological conditions mainly in the nonpolar form, with ''p''Ka1 = 1.99 ''p''Ka2 = 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.[[glutamate]] by 1-pyrroline-5-carboxylate dehydrogenase.)
Pyruvate + ([[File:Pyruvic_acid.jpg|left|80px|Pyruvic … [[File:Pyruvic_acid.jpg|left|80px|Pyruvic acid]]'''Pyruvic acid''', C3H4O3, is an alpha-keto monocarboxylic acid which occurs under physiological conditions mainly as the anion '''pyruvate-, P''', with ''p''Ka = 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 ''K''m' 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 [[Complex IV | cytochrome ''c'' oxidase]] by [[cyanide]]. Pyruvate is an antioxidant reacting with [[hydrogen peroxide]].[[hydrogen peroxide]].)
ROUTINE respiration + ([[File:R.jpg]] In the living cell, '''ROUT … [[File:R.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'', ''J''O2''R'' or [[oxygen flow]] in state ''R'', ''I''O2''R''). 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. apparent ROUTINE respiration or total cellular oxygen consumption of cells including ROX.)
State 2 + ([[File:ROX.jpg |link=Residual oxygen consu … [[File:ROX.jpg |link=Residual oxygen consumption]] Substrate limited state of [[residual oxygen consumption]], after addition of [[ADP]] to isolated mitochondria suspended in mitochondrial respiration medium in the absence of reduced substrates (ROXD). Residual endogenous substrates are oxidized during a transient stimulation of oxygen flux by ADP. The peak – supported by endogenous substrates – is, therefore, a pre-steady state phenomenon preceding State 2. Subsequently oxygen flux declines to a low level (or zero) at the steady '''State 2''' ([[Chance_1955_JBC-III|Chance and Williams 1955]]). ADP concentration (D) remains high during ROXD.concentration (D) remains high during ROXD.)
Residual oxygen consumption + ([[File:ROX.jpg|100px|link=https://wiki.oro … [[File:ROX.jpg|100px|link=https://wiki.oroboros.at/images/3/30/ROX.jpg]] '''Residual oxygen consumption''' ''Rox'' — respiration in the ROX state — is due to oxidative side reactions remaining after inhibition of the [[electron transfer pathway]] (ET pathway) in [[mitochondrial preparation]]s or living cells. Different conditions designated as ROX states (different combinations of inhibitors of CI, CII, CIII and CIV) may result in consistent or significantly different levels of oxygen consumption. Hence the best quantitative estimate of ''Rox'' has to be carefully evaluated. Mitochondrial respiration is frequently corrected for ''Rox'' as the [[baseline state]]. Then, total [[ROUTINE]], [[LEAK respiration]], [[OXPHOS]] or [[Electron transfer pathway |ET]] (''R'', ''L'', ''P'' and ''E'') respiration are distinguished from the corresponding ''Rox''-corrected, mitochondrial (ET-pathway linked) fluxes: ''R''(mt), ''L''(mt), ''P''(mt) and ''E''(mt). Alternatively, ''R'', ''L'', ''P'' and ''E'' are defined as ''Rox''-corrected rates, in contrast to total rates ''R''´, ''L''´, ''P''´ and ''E''´. When expressing ''Rox'' as a fraction of ET capacity ([[flux control ratio]]), total flux ''E''´ (not corrected for ''Rox''), should be taken as the reference. ''Rox'' may be related to, but is of course different from [[ROS]] production.In previous editions, (including [[Gnaiger 2020 BEC MitoPathways]]), the [[REN]] state was not distinguished from the ROX state. However, in novel applications (Q-Module and NADH-Module), a distinction of these states is necessary. Care must be taken when assuming ''Ren'' as a substitute of ''Rox'' correction of mitochondrial respiration.' correction of mitochondrial respiration.)
Ambiguity crisis + ([[File:Rabbit or duck.jpg|right|300px|thum … [[File:Rabbit or duck.jpg|right|300px|thumb|'''Graphical ambiguity:''' ''Fliegende Blätter'' (1892-10-23): Perception versus interpretation (Ludwig Wittgenstein) or paradigm shift (Thomas Kuhn)]]The '''ambiguity crisis''' is a contemporary crisis comparable to the credibility or [[reproducibility crisis]] in the biomedical sciences. The term 'crisis' is rooted etymologically in the Greek word ''krinein'': meaning to 'separate, decide, judge'. In this sense, science and communication in general are a continuous crisis at the edge of separating clarity or certainty from confusing double meaning, or obscure 'alchemical' gibberish, or even fake-news. Reproducibility relates to the condition of repeating and confirming calculations or experiments presented in a published resource. While ambiguity is linked to relevant issues of reproducibility, it extends to the communications space of terminological and graphical representations of concepts. Type 1 ambiguities are the inevitable consequence of conceptual evolution, in the process of which ambiguities are replaced by experimentally and theoretically supported paradigm shifts to clear-cut theorems. In contrast, type 2 ambiguities are traced in publications that reflect merely a disregard and ignorance of established concepts without an attempt to justify the inherent deviations from high-quality science. There are many shades of grey between these types of ambiguity. of grey between these types of ambiguity.)
Residual endogenous substrates + ([[File:Ren.png|100px|link=https://wiki.oro … [[File:Ren.png|100px|link=https://wiki.oroboros.at/index.php/File:Ren.png]] Oxygen consumption due to '''residual endogenous substrates'''. ''Ren'' is the respiration in the REN state. It is due to oxidative reactions in [[mt-preparation]]s incubated without addition of fuel substrates in the absence or presence of ADP (in the presence of ADP to stimulate the consumption of endogenous fuel substrates: [[State 2]]). ''Ren'' values may be used as technical replicates when obtained from the same mt-preparation in different protocols. ''Ren'' may be higher than ''Rox''. Correspondingly, Q and NAD are not fully oxidized in the REN state compared to the ROX state. In previous editions (including [[Gnaiger 2020 BEC MitoPathways]]), the REN state was not distinguished from the [[ROX]] state. However, in novel applications (Q-Module and NADH-Module), a distinction of these states is necessary. Care must be taken when assuming ''Ren'' as a substitute of ''Rox'' correction of mitochondrial respiration.' correction of mitochondrial respiration.)
Society for Heart and Vascular Metabolism + ([[File:SHVM.png|100px|left]]The '''Society … [[File:SHVM.png|100px|left]]The '''Society for Heart and Vascular Metabolism''' (SHVM) The Society for Heart and Vascular Metabolism was founded in 2001, with the intent of providing a forum for the free exchange of ideas by a group of investigators that had a special interest in the multiple roles of intermediary metabolism in the cardiovascular system. An important aim of the Society is to foster interactions between young investigators and senior scientists and our meetings are deliberately designed to maximize these interactions. There is growing recognition across many areas of scientific investigation and in the cardiovascular arena of the importance of metabolic homeostasis. The Society for Heart and Vascular Metabolism intends to remain at the vanguard of this rapidly expanding area.e vanguard of this rapidly expanding area.)
Society for Mitochondrial Research and Medicine - India + ([[File:SMRM.JPG|150px|left]]The Society fo … [[File:SMRM.JPG|150px|left]]The Society for '''Mitochondria Research and Medicine - India''' (SMRM-India) is a nonprofit organization of scientists, clinicians and academicians. The purpose of SMRM is to foster research on basic science of mitochondria, mitochondrial pathogenesis, prevention, diagnosis and treatment through out India and abroad.nd treatment through out India and abroad.)
Serbian Society for Mitochondrial and Free Radical Physiology + ([[File:SSMFRP.jpg|left|200px]] The '''Serb … [[File:SSMFRP.jpg|left|200px]] The '''Serbian Society for Mitochondrial and Free Radical Physiology (SSMFRP)''' was established in 2008 as a national Society and has 150 members who gather research in the fields of molecular biology, biochemistry, medicine, chemistry, agriculture, physics and other related disciplines. The SSMFRP was founded as a '''voluntary non-governmental and non-profit association''' for researchers whose goal is to support the creative improvement of scientific knowledge about the '''physiology of mitochondria and free radicals''', support for the development of modern research approaches and integration of fundamental research in order to better understand the role of free radicals in pathophysiological states, as well as promoting scientific knowledge in the country and abroad.tific knowledge in the country and abroad.)
SUIT-003 pH ce D067 + ([[File:SUIT-003 O2 ce D067 diagram.png|350px]])
SUIT-026 AmR mt D064 + ([[File:SUIT-026 AmR mt D064.png|400px]])
SUIT-026 AmR mt D077 + ([[File:SUIT-026 AmR mt D064.png|400px]])
F-junction + ([[File:SUIT-catg F.jpg|right|300px|F-junct … [[File:SUIT-catg F.jpg|right|300px|F-junction]]The '''F-junction''' is a junction for [[convergent electron flow]] in the [[electron transfer pathway]] (ET-pathway) from fatty acids through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]) to [[electron transferring flavoprotein]] (CETF), and further transfer through the [[Q-junction]] to [[Complex III]] (CIII). The concept of the F-junction and [[N-junction]] provides a basis for defining [[categories of SUIT protocols]]. Fatty acid oxidation, in the [[F-pathway control state]], not only depends on electron transfer through the F-junction (which is typically rate-limiting) but simultaneously generates NADH and thus depends on N-junction throughput. Hence FAO can be inhibited completely by inhibition of Complex I (CI). In addition and independent of this source of NADH, the N-junction substrate malate is required as a co-substrate for FAO in mt-preparations, since accumulation of AcetylCoA inhibits FAO in the absence of malate. Malate is oxidized in a reaction catalyzed by malate dehydrogenase to oxaloacetate (yielding NADH), which then stimulates the entry of AcetylCoA into the TCA cycle catalyzed by citrate synthase.e TCA cycle catalyzed by citrate synthase.)
Fatty acid oxidation pathway control state + ([[File:SUIT-catg F.jpg|right|300px|F-junct … [[File:SUIT-catg F.jpg|right|300px|F-junction]]In the '''fatty acid oxidation pathway control state''' (F- or FAO-pathway), one or several fatty acids are supplied to feed electrons into the [[F-junction]] through fatty acyl CoA dehydrogenase (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting relative to the N-pathway branch), but simultaneously generates FADH2 and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). In addition and independent of this source of NADH, the type N substrate malate is required at low concentration (0.1 mM) as a co-substrate for FAO in mt-preparations, since accumulation of Acetyl-CoA inhibits FAO in the absence of malate. Malate is oxidized in a reaction catalyzed by malate dehydrogenase to oxaloacetate (yielding NADH), which then stimulates the entry of Acetyl-CoA into the TCA cycle catalyzed by citrate synthase. Peroxysomal ''β''-oxidation carries out few ''β''-oxidation cycles, thus shortening very-long-chain fatty acids (>C20) for entry into mitochondrial ''β''-oxidation. Oxygen consumption by peroxisomal [[acyl-CoA oxidase]] is considered as [[residual oxygen consumption]] rather than cell respiration.esidual oxygen consumption]] rather than cell respiration.)
FN + ([[File:SUIT-catg FN.jpg|right|300px|F-junc … [[File:SUIT-catg FN.jpg|right|300px|F-junction]]FN is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]], or CI-linked pathway control) in combination with one or several fatty acids, which are supplied to feed electrons into the [[F-junction]] through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH2 and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). 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. FS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria.[[additive effect of convergent electron flow]] in most types of mitochondria.)
FNS + ([[File:SUIT-catg FNS.jpg|right|300px|F-jun … [[File:SUIT-catg FNS.jpg|right|300px|F-junction]]FNS is induced in mt-preparations by addition of [[NADH]]-generating substrates ([[N-pathway control state]], or CI-linked pathway control) in combination with [[succinate]] ([[S-pathway control state]]; S- or CII-linked) and one or several fatty acids, which are supplied to feed electrons into the [[F-junction]] through [[fatty acyl CoA dehydrogenase]] (reduced form [[FADH2]]), to [[electron transferring flavoprotein]] (CETF), and further through the [[Q-junction]] to [[Complex III]] (CIII). FAO not only depends on electron transfer through the F-junction (which is typically rate-limiting), but simultaneously generates FADH2 and NADH and thus depends on [[N-junction]] throughput. Hence FAO can be inhibited completely by inhibition of [[Complex I]] (CI). 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. FNS in combination exerts an [[additive effect of convergent electron flow]] in most types of mitochondria.[[additive effect of convergent electron flow]] in most types of mitochondria.)
Q-junction + ([[File:SUIT-catg FNSGp.jpg|right|300px|Q-j … [[File:SUIT-catg FNSGp.jpg|right|300px|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 state]]s and [[categories of SUIT protocols]].[[categories of SUIT protocols]].)
Electron-transfer-pathway state + ([[File:SUIT-catg FNSGpCIV.jpg|right|400px] … [[File:SUIT-catg FNSGpCIV.jpg|right|400px]]'''Electron-transfer-pathway states''' are obtained in [[mitochondrial preparations]] (isolated mitochondria, permeabilized cells, permeabilized tissues, tissue homogenate) by depletion of endogenous substrates and addition to the mitochondrial respiration medium of fuel substrates (CHNO) activating specific mitochondrial pathways, and possibly inhibitors of specific pathways. Mitochondrial electron-transfer-pathway states have to be defined complementary to mitochondrial [[coupling-control state]]s. [[Coupling-control state]]s require [[Electron-transfer-pathway state|ET-pathway competent states]], including oxygen supply. [[Categories of SUIT protocols]] are defined according to mitochondrial ET-pathway states.» [[#ET_pathway_states |'''MiPNet article''']][#ET_pathway_states |'''MiPNet article''']])
N-junction + ([[File:SUIT-catg N.jpg|right|300px|N-junct … [[File:SUIT-catg N.jpg|right|300px|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 ([[Pyruvate dehydrogenase |PDH]], [[Glutamate dehydrogenase |GDH]], [[Malate dehydrogenase |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 state]]s.[Electron-transfer-pathway state]]s.)
NADH electron transfer-pathway state + ([[File:SUIT-catg N.jpg|right|300px|N-junct … [[File:SUIT-catg N.jpg|right|300px|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 [[Electron-transfer-pathway state|ET pathway level 4]] is active.[[Electron-transfer-pathway state|ET pathway level 4]] is active.)
NS-pathway control state + ([[File:SUIT-catg NS.jpg|right|300px|NS-pat … [[File:SUIT-catg NS.jpg|right|300px|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.[[additive effect of convergent electron flow]] in most types of mitochondria.)
Glycerophosphate pathway control state + ([[File:SUIT-catg_Gp.jpg|right|300px|Gp-pat … [[File:SUIT-catg_Gp.jpg|right|300px|Gp-pathway]]The '''glycerophosphate pathway control state''' (Gp) is an [[Electron-transfer-pathway state |ET-pathway level 3 control state]], supported by the fuel substrate [[glycerophosphate]] and electron transfer through [[glycerophosphate dehydrogenase Complex]] into the [[Q-junction]]. The [[glycerolphosphate shuttle]] represents an important pathway, particularly in liver and blood cells, of making cytoplasmic [[NADH]] available for mitochondrial [[oxidative phosphorylation]]. Cytoplasmic NADH reacts with dihydroxyacetone phosphate catalyzed by cytoplasmic glycerophos-phate dehydrogenase. On the outer face of the inner mitochondrial membrane, mitochondrial glycerophosphate dehydrogenase oxidises glycerophosphate back to dihydroxyacetone phosphate, a reaction not generating NADH but reducing a flavin prosthesic group. The reduced flavoprotein donates its reducing equivalents to the electron transfer-pathway at the level of [[CoQ]].[[CoQ]].)
Categories of SUIT protocols + ([[File:SUIT-catg_MitoPathway types.jpg|rig … [[File:SUIT-catg_MitoPathway types.jpg|right|200px]]'''Categories of SUIT protocols''' group [[MitoPedia: SUIT |SUIT protocols]] according to all substrate types involved in a protocol (F, N, S, Gp), independent of the sequence of titrations of substrates and inhibitors which define the [[Electron-transfer-pathway state]]s. The [[N-pathway control |N-type substrates]] are listed in parentheses, independent of the sequence of titrations. ROX states may or may not be included in a SUIT protocol, which does not change its category. Similarly, the [[CIV]] assay may or may not be added at the end of a SUIT protocol, without effect on the category of a SUIT protocol.* '''F''' - ET-pathway-level 5: [[FADH2 |FADH2]]-linked substrates (FAO) with obligatory support by the N-linked pathway.* '''N''' - ET-pathway-level 4: [[NADH]]-linked substrates (CI-linked).* '''S''' - ET-pathway-level 3: [[Succinate]] (CII-linked).* '''Gp''' - ET-pathway-level 3: [[Glycerophosphate]] (CGpDH-linked).* '''Y(X)'''- In the SUIT general protocols Y makes reference to the ET-pathway state and X to the combination os substrates added for the corresponding pathway.» [[#Categorization of SUIT protocols: ETS pathway control states |'''MiPNet article''']][#Categorization of SUIT protocols: ETS pathway control states |'''MiPNet article''']])
Succinate pathway + ([[File:SUIT-catg_S.jpg|right|300px|Succina … [[File:SUIT-catg_S.jpg|right|300px|Succinate]]The '''Succinate pathway''' (S-pathway; S) is the [[electron transfer pathway]] that supports succinate-linked respiration (succinate-induced respiratory state; previously used nomenclature: CII-linked respiration; SRot; see [[Gnaiger 2009 Int J Biochem Cell Biol]]). The S-pathway describes the electron flux through [[Complex II]] (CII; see [[succinate dehydrogenase]], SDH) from succinate and FAD to fumarate and CII-bound flavin adenine dinucleotide (FADH2) to the [[Q-junction]].The S-pathway control state is usually induced in mt-preparations by addition of succinate&rotenone. In this case, only [[Complex III]] and [[Complex IV]] are involved in pumping protons from the matrix (positive phase, P-phase) to the negative phase (N-phase) with a P»/O2 of 3.5 (P»/O ratio = 1.75).phase) with a P»/O2 of 3.5 (P»/O ratio = 1.75).)
SUIT protocol names + ([[File:SUIT-nomenclature.jpg|300px|right|S … [[File:SUIT-nomenclature.jpg|300px|right|SUIT protocols]]The '''SUIT protocol name''' starts with (i) the [[Categories of SUIT protocols |SUIT category]] which shows the [[Electron-transfer-pathway state]]s (ET pathway types; e.g. N, S, NS, FNS, FNSGp), independent of the actual sequence of titrations. (ii) A further distinction is provided in the SUIT name by listing in parentheses the substrates applied in the [[N-pathway control state]]s, again independent of the sequence of titrations, e.g. NS(GM), NS(PM), FNSGp(PGM). (iii) A sequentially selected number is added, e.g. SUIT_FNS(PM)01 (see [[Coupling/pathway control diagram]]). The '''systematic name''' of a SUIT protocol starts with the [[Categories of SUIT protocols |SUIT category]], followed by an underline dash and the sequence of titration steps (mark names, #''X'', separated by a comma). The [[Marks in DatLab |Marks]] define the section of a [[respiratory state]] in the SUIT protocol. The [[Mark names in DatLab |Mark name]] contains the sequential number and the [[metabolic control variable]], ''X''. The metabolic control variable is the name of the preceding SUIT [[event]]. The [[MitoPedia: SUIT |MitoPedia list of SUIT protocols]] can be sorted by the short name or the systematic name (hence by SUIT protocol category. The '''[[SUIT protocol pattern]]''' is best illustrated by a [[coupling/pathway control diagram]].[[coupling/pathway control diagram]].)
Coupling/pathway control diagram + ([[File:SUIT-nomenclature.jpg|300px|right|S … [[File:SUIT-nomenclature.jpg|300px|right|SUIT protocols]]'''Coupling/pathway control diagrams''' illustrate the respiratory '''states''' obtained step-by-step in substrate-uncoupler-inhibitor titrations in a [[SUIT protocol]]. Each step (to the next state) is defined by an initial state and a [[metabolic control variable]], ''X''. The respiratory states are shown by boxes. ''X'' is usually the titrated substance in a SUIT protocol. If ''X'' ([[ADP]], [[uncoupler]]s, or inhibitors of the [[phosphorylation system]], e.g. oligomycin) exerts '''coupling control''', then a transition is induced between two [[coupling-control state]]s. If ''X'' (fuel substrates, e.g. pyruvate and succinate, or [[Electron transfer pathway]] inhibitors, e.g. rotenone) exerts '''pathway control''', then a transition is induced between two [[Electron-transfer-pathway state]]s. The type of metabolic control (''X'') is shown by arrows linking two respiratory states, with vertical arrows indicating coupling control, and horizontal arrows indicating pathway control. [[Marks - DatLab |Marks]] define the section of an experimental trace in a given [[respiratory state]] (steady state). [[Events - DatLab |Events]] define the titration of ''X'' inducing a transition in the SUIT protocol. The specific sequence of coupling control and pathway control steps defines the [[SUIT protocol pattern]]. The coupling/pathway control diagrams define the [[categories of SUIT protocols]] (see Figure).[[categories of SUIT protocols]] (see Figure).)
SUIT-013 + ([[File:SUIT013 AmR ce D023.png|300px]])
SUIT-013 AmR ce D023 + ([[File:SUIT013 AmR ce D023.png|400px]])
Sample Holder + ([[File:Sample Holder - 28410-01.jpg|right|180px]] Sample Holder - to protect susceptible samples from being damaged by stirring of the medium in the 2.0 mL O2k-chamber.)