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BEC 2020.1 doi10.26124bec2020-0001.v1

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Bioenergetics Communications        
Gnaiger 2020 BEC MitoPathways
       
Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1.
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Bioenergetics Communications
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Mitochondrial physiology
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Gnaiger E et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. https://doi.org/10.26124/bec:2020-0001.v1

» Bioenerg Commun 2020.1. Open Access pdf published online 2020-05-20

Author affiliations in hyperlinks:, Gnaiger Erich, Aasander Frostner Eleonor, Abdul Karim Norwahidah, Abdel-Rahman Engy Ali, Abumrad Nada A, Acuna-Castroviejo Dario, Adiele Reginald C, Ahn Bumsoo, Alencar Mayke Bezerra, Ali Sameh S, Almeida Angeles, Alton Lesley, Alves Marco G, Amati Francesca, Amoedo Nivea Dias, Amorim Ricardo, Anderson Ethan J, Andreadou Ioanna, Antunes Diana, Arago Marc, Aral Cenk, Arandarcikaite Odeta, Arias-Reyes Christian, Armand Anne-Sophie, Arnould Thierry, Avram Vlad F, Axelrod Christopher L, Bailey Damian M, Bairam Aida, Bajpeyi Sudip, Bajzikova Martina, Bakker Barbara M, Banni Aml, Bardal Tora, Barlow J, Bastos Sant'Anna Silva Ana Carolina, Batterson Philip M, Battino Maurizio, Bazil Jason N, Beard Daniel A, Bednarczyk Piotr, Beleza Jorge, Bello Fiona, Ben-Shachar Dorit, Bento Guida Jose Freitas, Bergdahl Andreas, Berge Rolf K, Bergmeister Lisa, Bernardi Paolo, Berridge Michael V, Bettinazzi Stefano, Bishop David J, Blier Pierre U, Blindheim Dan Filip, Boardman Neoma T, Boetker Hans Erik, Borchard Sabine, Boros Mihaly, Borsheim Elisabet, Borras Consuelo, Borutaite Vilma, Botella Javier, Bouillaud Frederic, Bouitbir Jamal, Boushel Robert C, Bovard Josh, Bravo-Sagua Roberto, Breton Sophie, Brown David A, Brown Guy C, Brown Robert Andrew, Brozinick Joseph T, Buettner Garry R, Burtscher Johannes, Bustos Matilde, Calabria Elisa, Calbet Jose AL, Calzia Enrico, Cannon Daniel T, Cano Sanchez Maria Consolacion, Canto Alvarez Carles, Cardinale Daniele A, Cardoso Luiza HD, Carvalho Eugenia, Casado Pinna Marta, Cassar Samantha, Castelo Rueda Maria Paulina, Castilho Roger F, Cavalcanti-de-Albuquerque Joao Paulo, Cecatto Cristiane, Celen Murat C, Cervinkova Zuzana, Chabi Beatrice, Chakrabarti Lisa, Chakrabarti Sasanka, Chaurasia Bhagirath, Chen Quan, Chicco Adam J, Chinopoulos Christos, Chowdhury Subir Kumar, Cizmarova Beata, Clementi Emilio, Coen Paul M, Cohen Bruce H, Coker Robert H, Collin-Chenot Anne, Coughlan Melinda T, Coxito Pedro, Crisostomo Luis, Crispim Marcell, Crossland Hannah, Dahdah Norma Ramon, Dalgaard Louise T, Dambrova Maija, Danhelovska Tereza, Darveau Charles-A, Darwin Paula M, Das Anibh Martin, Dash Ranjan K, Davidova Eliska, Davis Michael S, Dayanidhi Sudarshan, De Bem Andreza Fabro, De Goede Paul, De Palma Clara, De Pinto Vito, Dela Flemming, Dembinska-Kiec Aldona, Detraux Damien, Devaux Yvan, Di Marcello Marco, Di Paola Floriana Jessica, Dias Candida, Dias Tania R, Diederich Marc, Distefano Giovanna, Djafarzadeh Siamak, Doermann Niklas, Doerrier Carolina, Dong Lan-Feng, Donnelly Chris, Drahota Zdenek, Duarte Filipe Valente, Dubouchaud Herve, Duchen Michael R, Dumas Jean-Francois, Durham William J, Dymkowska Dorota, Dyrstad Sissel E, Dyson Alex, Dzialowski Edward M, Eaton Simon, Ehinger Johannes K, Elmer Eskil, Endlicher Rene, Engin Ayse Basak, Escames Germaine, Evinova Andrea, Ezrova Zuzana, Falk Marni J, Fell David A, Ferdinandy Peter, Ferko Miroslav, Fernandez-Ortiz Marisol, Fernandez-Vizarra 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Jelena, Stiban Johnny, Stier Antoine, Stocker Roland, Storder Julie, Sumbalova Zuzana, Suomalainen Anu, Suravajhala Prashanth, Svalbe Baiba, Swerdlow Russell H, Swiniuch Daria, Szabo Ildiko, Szewczyk Adam, Szibor Marten, Tanaka Masashi, Tandler Bernard, Tarnopolsky Mark A, Tausan Daniel, Tavernarakis Nektarios, Teodoro Joao Soeiro, Tepp Kersti, Thakkar Himani, Thapa Maheshwor, Thyfault John P, Tomar Dhanendra, Ton Riccardo, Torp May-Kristin, Torres-Quesada Omar, Towheed Atif, Treberg Jason R, Tretter Laszlo, Trewin Adam J, Trifunovic Aleksandra, Trivigno Catherine, Tronstad Karl Johan, Trougakos Ioannis P, Truu Laura, Tuncay Erkan, Turan Belma, Tyrrell Daniel J, Urban Tomas, Urner Sofia, Valentine Joseph Marco, Van Bergen Nicole J, Van der Ende Miranda, Varricchio Frederick, Vaupel Peter, Vella Joanna, Vendelin Marko, Vercesi Anibal E, Verdaguer Ignasi Bofill, Vernerova Andrea, Victor Victor Manuel, Vieira Ligo Teixeira Camila, Vidimce Josif, Viel Christian, Vieyra Adalberto, Vilks Karlis, Villena Josep A, Vincent Vinnyfred, Vinogradov Andrey D, Viscomi Carlo, Vitorino Rui Miguel Pinheiro, Vlachaki Walker Julia, Vogt Sebastian, Volani Chiara, Volska Kristine, Votion Dominique-Marie, Vujacic-Mirski Ksenija, Wagner Brett A, Ward Marie Louise, Warnsmann Verena, Wasserman David H, Watala Cezary, Wei Yau-Huei, Weinberger Klaus M, Weissig Volkmar, White Sarah Haverty, Whitfield Jamie, Wickert Anika, Wieckowski Mariusz R, Wiesner Rudolf J, Williams Caroline M, Winwood-Smith Hugh, Wohlgemuth Stephanie E, Wohlwend Martin, Wolff Jonci Nikolai, Wrutniak-Cabello Chantal, Wuest Rob CI, Yokota Takashi, Zablocki Krzysztof, Zanon Alessandra, Zanou Nadege, Zaugg Kathrin, Zaugg Michael, Zdrazilova Lucie, Zhang Yong, Zhang Yizhu, Zikova Alena, Zischka Hans, Zorzano Antonio, Zujovic Tijana, Zurmanova Jitka, Zvejniece Liga (2020) Bioenerg Commun

Abstract: BEC.png doi:10.26124/bec:2020-0001.v1

Versions (v1) 2020-05-20 - »Link to all versions«

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery.

Bioblast editor: Gnaiger E

Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1

Keywords—MitoPedia

Cell countCoupling-control ratioElectron transfer pathwayFlowFluxFlux control ratioIUPACLEAK respirationMitochondrial markerMitochondrial preparationsRespiratory statesNormalization of rateOxidative phosphorylationOxygenPhosphorylation efficiencyProtonmotive forceResidual oxygen consumptionSI - The International System of UnitsUncoupling



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MitoPedia Keywords—MitoPedia - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>

Keywords—MitoPedia, including Table 8. Terms, symbols, and units. SI base units are used, except for the liter [L = dm3]. SI refers to ref. [11].

Term Link to MitoPedia term Symbol Unit Links and comments
adenosine diphosphate ADP ADP - Tab. 1; Fig. 1, 2, 5
adenosine monophosphate AMP AMP - 2 ADP ↔ ATP+AMP
adenosine triphosphate ATP ATP - Fig. 2, 5
adenylates Adenine nucleotides AMP, ADP, ATP - Section 2.5.1
alternative quinol oxidase Alternative oxidase AOX - Fig. 1B
amount of substance B Amount nB or n(B) [mol] SI; amount nB of B versus count NB of B
ATP yield per O2 ATP yield YP»/O2 1 P»/O2 ratio measured in any respiratory state
catabolic rate of respiration Cell respiration JkO2; IkO2 varies Fig. 1, 3; flux J versus flow I
catabolic reaction Cell respiration k - Fig. 1, 3
cell count Count Nce [x] Tab. 4; Fig. 5; see number of cells; countable object s=ce
cell-count concentration Concentration Cce [x∙L­-1] Tab. 4; Cce = NceV-1; count concentration C versus amount concentration c; subscript ce indicates the entity type: concentration of ce. But it does not signal 'per entity', which would be written as 'per cell' Xce.
cell mass Body mass mce [kg] Tab. 5; Fig. 5; mass of cells m versus mass per cell (per single entity cell) MXce
cell mass, mass per cell Body mass MXce [kg∙x­-1] Tab. 5; Fig. 5; mass per single cell MXce; upper case M and subscript X signal 'per count', subscript ce signals the entity s=ce; in a context restricted to cells or molecules or a particular organism such as humans, the abbreviated symbol M [kg∙x­-1] provides a sufficiently informative signal, particularly in combination with the explicit unit.
cell-mass concentration in chamber Concentration Cmce [kg∙L­-1] see Cms: Tab. 4; Cmce = mceV-1; upper case C alone would signal 'count concentration' (CN is more explicit), whereas the signal for 'mass concentration' is in the combination Cm.
cell viability index Cell viability VI - VI = NvceNce­-1 = 1 - NdceNce­-1
charge number per entity XB Charge number zB 1 zB = QB·e-1 (IUPAC); Tab. 6; zO2 = = QO2·e-1 = 4; IUPAC uses the term 'charge number of an ion' which should be changed to 'charge number per ion', or more clearly to 'charge number per ion number'. The symbol z carries the message 'number of elementary charges per number', and the subscript carries the message on the type of entity X.
Complexes I to IV Complex I CI to CIV - respiratory ET Complexes are redox proton pumps; Fig. 1B; F1FO-ATPase is not a redox proton pump of the ETS, hence the term CV is not recommended
concentration of B, amount Concentration cB = NB-1 [mol∙L­-1] SI: amount of substance concentration Cohen 2008 IUPAC Green Book; the molar and count formats are distinguished as nB and NB, respectively.
concentration of O2, amount Concentration cO2 = nO2-1 [mol∙L­-1] Box 2; [O2]
concentration of s, count Concentration Cs = Ns-1 [x∙L-1] Tab. 4 (number concentration Cohen 2008 IUPAC Green Book); the signal for count concentration is given by the upper case C in contrast to c for amount concentration. In both cases, the subscript X indicates the entity type, not to be confused with a number of entities.
count format Format N [x] Tab. 4, 5; Fig. 5
count of Xs Count Ns [x] SI; see number of entities Xs
coupling control Coupling-control ratio CCR - Section 2.4.1
coupling control state Coupling control state CCS - Section 2.4.1
dead cells Cell viability dce - Tab. 5
electrical format Format e [C] Tab. 6
electron transfer pathway Electron transfer pathway ET pathway - Overview; Fig. 1
electron transfer, state Electron transfer pathway ET - Tab. 1; Fig. 2B, 4 (State 3u)
electron transfer system Electron transfer pathway ETS - Fig. 2B, 4 (electron transport chain)
elementary entity Entity Xs [x] single countable object of sample type s; Tab. 4
ET capacity ET capacity E varies rate; Tab. 1; Fig. 2
ET-excess capacity ET capacity E-P varies Fig. 2
flow, for O2 Flow IO2 [mol∙s-­1] system-related extensive quantity; Fig. 5
flux, for O2 Flux JO2 varies size-specific quantity; Fig. 5
flux control ratio Flux control ratio FCR 1 background/reference flux; Fig. 5
hyphenation Hyphenation - - Updates in comparison to Gnaiger 2019 MitoFit Preprints
inorganic phosphate Phosphate Pi - Fig. 1C
inorganic phosphate carrier Phosphate carrier PiC - Fig. 1C
International Union of Pure and Applied Chemistry, IUPAC IUPAC IUPAC - Cohen 2008 IUPAC Green Book
International System of Units International System of Units SI - Cohen 2008 IUPAC Green Book
isolated mitochondria Isolated mitochondria imt - [11]
LEAK state LEAK respiration LEAK - Tab. 1; Fig. 2 (compare State 4)
LEAK respiration LEAK respiration L varies rate; Tab. 1; Fig. 2
living cells Living cells ce - Tab. 5 (intact cells)
mass, dry mass Body mass md [kg] Fig. 5 (dry weight)
mass, wet mass Body mass mw [kg] Fig. 5 (wet weight)
mass concentration of sample s in chamber Concentration Cms [kg∙L-1] Tab. 4
mass format Format m [kg] Tab. 4
mass of sample s in a mixture Mass ms [kg] SI: mass of pure sample mS
mass per single object Body mass MNX [kg∙x­1] Fig. 5; Tab. 4; SI: m(X); compare molar mass M(X)
MITOCARTA MITOCARTA
mitochondria or mitochondrial Mitochondria mt - Box 1
mitochondrial concentration Mitochondrial marker, Concentration CmtE = mtEV-1 [mtEU∙L-1] Tab. 4
mitochondrial content per X Mitochondrial marker mtENX [mtEU∙x­-1] mtENX = mtENX-1; Tab. 4
mitochondrial density per ms Mitochondrial marker, Density DmtE/ms [mtEU∙kg­-1] DmtE/ms=mtEms-1; Tab. 4
mitochondrial density per Vs Mitochondrial marker, Density DmtE/Vs [mtEU∙kg­-1] DmtE/Vs=mtEVs-1; Tab. 4
mitochondrial DNA Mitochondria mtDNA - Box 1
mitochondrial elementary marker Mitochondria mtE [mtEU] quantity of mt-marker; Tab. 4
mitochondrial elementary unit Mitochondria mtEU varies specific units for mt-marker; Tab. 4
mitochondrial inner membrane Mitochondrial inner membrane mtIM - Fig. 1; Box 1 (MIM)
mitochondrial outer membrane Mitochondrial outer membrane mtOM - Fig. 1; Box 1 (MIM)
mitochondrial preparations Mitochondrial preparations mt-prep - Tab. 5
mitochondrial recovery Mitochondrial recovery YmtE 1 fraction of mtE recovered from the tissue sample in imt-stock
mitochondrial yield Mitochondrial yield YmtE/ms [mtEU∙kg-1] mt-yield in imt-stock per mass of tissue sample; YmtE/ms=YmtEDmtE
MitoPedia MitoPedia, MitoPedia: Respiratory states
molar format Format n [mol] Tab. 6
molar mass Molar mass MB [kg∙mol-1] compare MNB [kg∙x-1]; SI M(X)
negative Protonmotive force neg - Fig. 4
normalization of rate Normalization of rate - - Tab. 4; Fig. 5
number of cells Count Nce [x] total cell count of living cells, Nce = Nvce + Ndce; Tab. 4, 5
number of dead cells Cell viability Ndce [x] non-viable cell count, loss of plasma membrane barrier function; Tab. 5
number of entities B Count NB [x] Tab. 4 Cohen 2008 IUPAC Green Book
number of entities X; count Count NX [x] ‘count’ is an SI quantity [11], but the counting unit [x] is not in the SI [95]; Tab. 4; Fig. 5
number of viable cells Cell viability Nvce [x] viable cell count, intact plasma membrane barrier function; Tab. 5
organisms Organism org - Tab. 5
oxidative phosphorylation Oxidative phosphorylation OXPHOS - Tab. 1
OXPHOS-capacity OXPHOS-capacity P varies rate; Tab. 1; Fig. 2
OXPHOS state OXPHOS-capacity OXPHOS - Tab. 1; Fig. 2; OXPHOS-state distinguished from the process OXPHOS (State 3 at kinetically-saturating [ADP] and [Pi])
oxygen concentration Oxygen concentration cO2 = nO2-1 [mol∙L­-1] [O2]; Section 3.2
oxygen solubility Oxygen solubility SO2 [µmol·kPa-1] Section 2.6.3
oxygen flux, in reaction r Oxygen flux JrO2 varies Overview
pathway control state Pathway control state PCS - Section 2.2
permeability transition Permeability transition mtPT - Fig. 3; Section 2.4.3 (MPT)
permeabilized cells Permeabilized cells pce - experimental permeabilization of plasma membrane; Tab. 5
permeabilized muscle fibers Permeabilized muscle fibers pfi - Tab. 5
permeabilized tissue Permeabilized tissue pti - Tab. 5
phosphorylation of ADP to ATP Oxidative phosphorylation - Tab. 1, 2; Fig. 1, 4
phosphorylation efficiency Ergodynamic efficiency ε 1 Section 2.4.1
P»/O2 ratio Oxidative phosphorylation P»/O2 1 mechanistic YP»/O2, calculated from pump stoichiometries; Fig. 1c
positive positive Protonmotive force - Fig. 4
proton in the neg compartment Protonmotive force H+neg [x] Fig. 4
proton in the pos compartment proton in the positive compartment H+pos [x] Fig. 4
protonmotive force protonmotive force pmF [V] Overview; Tab. 1; Fig 1a, 2, 4
publication efficiency publication efficiency Harmonization of nomenclature; Executive summary
quantities, symbols, and units Quantities, symbols, and units - - An explanation of symbols and unit [x]
rate in ET state Electron transfer pathway E varies ET capacity; Tab. 1; Fig. 2, 4
rate in LEAK state LEAK respiration L varies Tab. 1: L(n), L(T), L(Omy); Fig. 2, 4
rate in OXPHOS-state OXPHOS-capacity P varies OXPHOS-capacity; Tab.1; Fig. 2, 4
rate in ROX state Residual oxygen consumption Rox varies Overview; Tab. 1
residual oxygen consumption Residual oxygen consumption ROX; Rox - state ROX; rate Rox; Tab. 1
respiration Respirometry JrO2 varies rate of reaction r; Overview
respiratory state MitoPedia: Respiratory states - - Tab. 1, 3; Fig. 2, 4
respiratory supercomplex Supercomplex SCInIIInIVn - supramolecular assemblies with variable copy numbers (n) of CI, CIII and CIV; Box 1
sample in a mixture Sample s - diluted sample; Tab. 4, 5
steay state Steady state - - Section 2.5.6
substrate concentration at half-maximal rate Concentration c50 [mol∙L­-1] Section 2.1.2
substrate-uncoupler-inhibitor-titration Substrate-uncoupler-inhibitor titration SUIT - Section 2.2
system System - - Fig. 5
tissue homogenate Tissue homogenate thom - Tab. 5
unit elementary entity Entity UX [x] single countable object; Tab. 4, 5
uncoupling Uncoupler titrations - - Tab 2; Fig. 3
viable cells Viable cells vce - Tab. 5
volume format Format V [L] Tab. 6
volume of experimental chamber Volume V [L] liquid volume V including the sample s; Tab. 4, 7; Fig. 5
volume of sample s in a mixture Volume Vs [L] Tab. 5; Fig. 5


Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1

Authors: MitoEAGLE Task Group

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Erich Gnaiger
Chair COST Action CA15203 MitoEAGLE
T +43 512 566796 15, F +43 512 566796 20
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Acknowledgements

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  • We thank Marija Beno for management assistance, and Peter R Rich for valuable discussions. This publication is based upon work from COST Action CA15203 MitoEAGLE, supported by COST (European Cooperation in Science and Technology), in cooperation with COST Actions CA16225 EU-CARDIOPROTECTION and CA17129 CardioRNA; K-Regio project MitoFit funded by the Tyrolian Government, and project NextGen-O2k which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 859770 and partially funded printing and international dissemination of the publication.
  • Several investigators were funded by Short-Term Scientific Missions MitoEAGLE.
  • Authors were funded by their individual projects.


Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1

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Overview. Internal and external respiration. (mt) Mitochondrial catabolic respiration JkO2 is the O2 consumption in the oxidation of fuel substrates (electron donors) and reduction of O2 catalysed by the electron transfer system ETS, which drives the protonmotive force pmF. JkO2 excludes mitochondrial residual oxygen consumption, mt-Rox.


Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1

Discussion — updates — versions

On a Comment in Nature Metabolism

Gnaiger Erich 2020-07-28
One month ago one of our coauthors (Pablo M Garcia-Roves) sent me the reference to a Comment on metabolic terminology published on 2020-05-15 in Nature Metabolism. The present Bioenergetics Communication is deeply concerned about terminology and communication of concepts. Control and regulation (Section 2.7) is profoundly covered in a contribution by coauthor David Fell (our ref [43]). My expertise in thermodynamics (as a former member of an IUPAC Steering Committee; see also ref [50]) motivated me to the statement: "Thus mitochondria are elementary components of energy transformation. Energy is a conserved quantity and cannot be lost or produced in any internal process (First Law of Thermodynamics). Open and closed systems can gain or lose energy only by external fluxes—by exchange with the environment. Therefore, energy can neither be produced by mitochondria, nor is there any internal process without energy conservation (page 12, Section 2.4.1. Coupling).
In the Nature Metabolism Comment, some statements on control and regulation are followed by: "More striking are the frequently made statements that mitochondria ‘create’ or ‘produce’ energy, which are fundamentally incorrect, given that energy can neither be created or destroyed (according to the first law of thermodynamics)" (Nature Metabolism 2, June 2020, p 476). The two authors of this Comment are not known for covering thermodynamics in their publication record, although this is not really needed for such a general statement. What is more interesting are the following coincidences, which cannot be interpreted due to lack of a statistically relevant sample of observations.
  1. One of the 'Comment'-authors joined as a coauthor of the MitoEAGLE manuscript 'States and rates' after Version 2018-10-17(44), which included already our comment on energy conservation.
  2. The preprint Version 6 (Gnaiger E, Aasander Frostner E, Abdul Karim N, Abdel-Rahman EA, Abumrad NA, Acuna-Castroviejo D, Adiele RC, et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001.v6) was the basis of manuscript submission to Nature Metabolism already last year.
  3. The preprint was not cited by the 'Comment'-authors, despite quite obvious overlap of concerns on terminology. If one of our coauthors claims, that she was not aware of the contents in the preprint 'States and rates' (now the present BEC 'Mitochondrial physiology'), this should be an issue of questioning coauthorship in the BEC paper.
  4. Is there any reason to be concerned about fair citation in such a broad context of the First Law of Thermodynamics? This is my question, and I am open for professional answers (considering Gentle Science and mentoring early career investigators). For some further priming, the following points are added.
  5. It remains unclear to me, why our original wording "energy can neither be produced by mitochondria, nor is there any internal process without energy conservation" was changed in the 'Comment' to the suggestion that there are "frequently made statements that mitochondria ‘create’ or ‘produce’ energy". According to my knowledge of the literature, 'mitochondria create energy' is not a frequently made statement. With close to 370000 publications listed in PubMed on the search term 'mitochondr*' (see Publication efficiency), however, I cannot be sure. I doubt it, but this questionable statement on 'creation of energy' is a matter of proof to be made by the 'Comment'-authors. The only rare example I can come up with is the phrase 'using oxygen to create energy' in a journalist's 'educational' www.nature.com website (https://www.nature.com/scitable/topicpage/mitochondria-14053590/). Skip the 'create' with its rather Godly connotation, and the original "energy can neither be produced" phrase is actually relevant (I try to keep religious and pseudoscientific terminology out of my scientific writing).
  6. "How Mitochondria Produce Energy" is a marvellous video full of art (https://www.youtube.com/watch?v=39HTpUG1MwQ), and "Mitochondria and energy production" is another enjoyable video (https://www.youtube.com/watch?v=eOB_M7a9iZ0). A sloppy use of the term 'energy production' is very common in the scientific literature, as is the term 'generation of energy' (but luckily not 'creation'!). Some discussions on the use or abuse of these terms make a rather helpless impression (https://www.researchgate.net/post/Isnt_it_wrong_to_say_that_mitochondria_generate_or_produce_energy).
  7. Reference to internal energy transformation (First Law of Thermodynamics) versus external energy transfer in open systems (exchange with the environment) provides the necessary conceptual framework for clarification. This was not really understood by at least one of our coauthors, and neither by the involved reviewers and editors of Nature Metabolism.
  8. "We hope that this Comment will stimulate further discussion" — is the comment in the Nature Metabolism Comment. My comment: The discussion could have and should have been made openly before the Nature Metabolism Comment publication — but too many scientists just 'create' publications, without taking the time for quality discussions.
Reference: Harper Mary-Ellen, Patti Mary-Elizabeth (2020) Metabolic terminology: what’s in a name? Nat Metab 2:476-7.
SI-units.png

SI units

One year ago, on World Metrology Day (2019-May-20) the redefinition of the SI units came into force. Science faced one of the largest overhauls in history of scientific units. How to commemorate this event of groundbreaking innovation better than with the online publication of Mitochondrial physiology and with the launch of an innovative journal — Bioenergetics Communications.

Versions from MitoFit preprint to BEC reprint

»Versions
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This BEC article was communicated as a preprint in MitoFit Preprints
» Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC, et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001.v4. - »Bioblast link«

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Labels: MiParea: Respiration, mt-Awareness 



Preparation: Permeabilized cells, Permeabilized tissue, Homogenate, Isolated mitochondria  Enzyme: Marker enzyme  Regulation: Coupling efficiency;uncoupling, Flux control, mt-Membrane potential, Uncoupler  Coupling state: LEAK, OXPHOS, ET  Pathway: F, N, S, Gp, DQ, CIV, NS, Other combinations, ROX  HRR: O2k-Protocol 

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