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'''» [[MitoEAGLE preprint 2018-02-08]]'''
== Nature Metabolism: NATMETAB-A19071509A Out to Review ==
== Phase 3: [[MitoEAGLE preprint 2018-02-08]] ==
:::: Dear Prof Gnaiger,
* 2018-02-15 [[Gnaiger E]] Version 24.  
:::: Thank you for submitting your manuscript "Mitochondrial respiratory states and rates" to Nature Metabolism. I am pleased to tell you that we are sending your paper out for formal peer review.
[[File:Mt-recovery.png|right|400px|thumb|Fig. 9. Mitochondrial recovery, ''Y<sub>mtE</sub>'', in preparation of isolated mitochondria.]]
:::: If you have not done so already, please alert us to any related manuscripts from your group that are under consideration or in press at other journals, or are being written up for submission to other journals (see www.nature.com/authors/policies/duplicate.html for details).
:::: Towards a shorter version: Old Fig. 9 was removed.  
:::: We are trying to improve the quality of methods and statistics reporting in our papers. To that end, we are asking all life sciences authors to complete two items: an editorial policy checklist that verifies compliance with all required editorial policies and a reporting summary that collects information on experimental design and reagents.
:::: Reporting summary: https://www.nature.com/documents/nr-reporting-summary.pdf
:::: Editorial policy checklist: https://www.nature.com/documents/nr-editorial-policy-checklist.pdf
:::: Please complete the relevant forms and return them within 48 hours. Please note that these forms are dynamic ‘smart pdfs’ and must therefore be downloaded and completed in Adobe Reader. We will then flatten them for ease of use by the reviewers. If you would like to reference the guidance text as you complete the template, please access these flattened versions at www.nature.com/authors/policies/availability.html
:::: All points on the policy checklist must be addressed; if needed, please send me a new version of the manuscript with your completed checklist.
:::: Finally, we would like to inform you that on a case by case basis we coordinate a brief consultation between referees and editors after all referee reports have been received. This is to improve the peer review process and the feedback provided to authors. Referees are given the opportunity to make comments on their peers’ concerns and update their reports to comment on issues raised by the other reviewers. If we feel it would be helpful, we will engage reviewers in this additional consultation with the goal of providing you with the most valuable feedback possible.
:::: We will be in touch again as soon as we have received comments from our referees. In the meantime - the status of your manuscript can be followed in the manuscript tracking system.  
:::: Best regards,
:::: Dr. Christoph Schmitt
:::: Chief Editor
:::: Nature Metabolism


* 2018-02-08 [[Gnaiger E]] Version 22. Change of title: '''Mitochondrial respiratory states and rates''': Building blocks of mitochondrial physiology. Part 1.
:::::: Dear co-authors and MitoEAGLE Network Members:


::::::* New manuscript version 22: www.mitoeagle.org/index.php/M
== Version 5 ==
::::::* Change of title: Mitochondrial respiratory states and rates
::::* 2019-07-24 [[Gnaiger 2019 MitoFit Preprint Arch]]
::::::* Section 3 removed
::::::* Your feedback will be appreciated until Feb 20


:::::: Our MitoEAGLE position statement originally entitled 'The protonmotive force and respiratory control' has been discussed in many meetings and working groups. Many opinions and concerns have been raised about: (''1'') the exploding length; (''2'') the heterogeneity from respiratory states, to protonmotive force, to normalization of respiratory flow and flux; (''3'') the complex thermodynamic treatment in Section 3 of compartmental systems, power and entropy production, exergy, forces, electric and chemical advancement, fluxes, molecular-molar-electrical formats, and motive units; and (''4'') corresponding concerns about the meaning of co-authorship, if an entire section of the manuscript remains a challenge rather than becoming a familiar piece of collaborative work for most participants.


:::::: In the attempt to give a more detailed introduction and provide clarification of some basic principles related to the protonmotive force, I tried to stick to the conventional presentations of electric potential differences, Δ''Ψ'', and chemical potential differences, Δ''μ''<sub>H+</sub>, up to the point of recognizing a physicochemical incompleteness in the formal representation of potential differences. I am highly motivated to share a very simple but fundamental solution of this generally unrecognized problem with you, and want to talk about this at EBEC2018. The physicochemical formalism of potential differences is incomplete and terminologically inconsistent. The protonmotive force is not an electrochemical potential difference, but a difference of 'stoichiometric potentials'. A generalized concept of 'isomorphic forces' is suggested to describe the incomplete although mathematically correct equation defining the protonmotive force more properly. Since this discussion appears to be presently beyond the scope of a MitoEAGLE position statement, '''Section 3 (The protonmotive force, proton flux, and respiratory control) was removed from the new Version 22, the manuscript was updated (see improved Figure 8; extended Table 5), and the title was changed to 'Mitochondrial respiratory states and rates''''.
== Version 5 for discussion ==


:::::: Many co-authors asked about the state of submission and possibilities to further contribute and improve our MitoEAGLE position statement. In this phase 3 towards journal submission, we are asking you and a wider range of experts in the field for '''input preferentially with corresponding references'''. This should allow us without too much further delay ('''deadline: Feb 20''') to incorporate your feedback and contact relevant journal editors for their opinion on implementing our recommendations into their journal policy. We want to proceed with submission to a preprint server and final journal submission. BBA was discussed at MiP2017 as a potentially suitable journal, and we are open for further suggestions.
[[File:MitoFit Preprint Arch pdf.png|left|160px|link=https://www.mitofit.org/index.php/File:Gnaiger_2019_MitoFit_Preprint_Arch_doi_10.26124_mitofit_190001.v5(in_prep).pdf |MitoFit pdf]]  <big><big>'''[https://www.mitofit.org/index.php/File:Gnaiger_2019_MitoFit_Preprint_Arch_doi_10.26124_mitofit_190001.v5(in_prep).pdf Mitochondrial respiratory states and rates]'''</big></big>
<br />
<br />
Version 5 ('''v5''') '''2019-07-12''' [[File:Gnaiger 2019 MitoFit Preprint Arch doi 10.26124 mitofit 190001.v5(in prep).pdf |''Version 5(3) in preparation'']]


:::::: With many thanks for your collaboration, Erich
Version 5 ('''v5''') '''2019-06-24''' [[File:Gnaiger 2019 MitoFit Preprint Arch doi 10.26124 mitofit 190001.v5(in prep).pdf |''Version 5(1) in preparation - changes are marked in the pdf for discussion.'']]


::: '''Relevant changes'''
:::: 2019-07-24 Updates according to feedback from [[Gonzalez-Franquesa A]] and Fig. 1 edited by [[Bravo RF]].
:::: 2019-07-12 [[Gnaiger E |Erich Gnaiger]]: A comment on 'Complex V' is added to Table 8:
:::::: Respiratory ET Complexes are redox proton pumps; Figure 2B; ATP synthase is not a redox proton pump of the ETS, hence the term Complex V should not be used
:::: 2019-06-24 [[Gnaiger E |Erich Gnaiger]]
:::::'''1.'''  ce: The term "Intact cells" has been replaced by "Living cells".
:::::: Rationale: see Table 5.
:::::'''2.''' "Extra-mitochondrial" has been changed to "Extramitochondrial".
:::::: Compare: extracellular.
:::::'''3.''' ""Excess ''E-P'' capacity has been changed to "ET-excess capacity, ''E-P''".
:::::: Rationale: ''E-P'' is the excess capacity of ''E'' over ''P'', but not excess over ''E-P''. 
:::::'''4.''' The symbol "pmf" for ''protonmotive force'' has be replaced by ''pmF''.
:::::: Rationale: (''1'') ''Italics'' are used for symbols of physicochemical quantities. (''2'') ''F'' but not ''f'' is the IUPAC symbol for ''force''.


* 2018-02-06 [[Gnaiger E]] '''[[MitoEAGLE preprint 2017-09-21 |Version 21]]''': Note: Subscript ‘§’ indicates throughout the text those parts, where ''potential differences'' provide a mathematically correct but physicochemically incomplete description and should be replaced by ''stoichiometric potential differences'' ([[Gnaiger 1993 Pure Appl Chem |Gnaiger 1993b]]). A unified concept on vectorial motive transformations and scalar chemical reactions will be derived elsewhere (Gnaiger, in prep.). Appreciation of the fundamental distinction between ''differences of potential'' versus ''differences of stoichiometric potential'' may be considered a key to critically evaluate the arguments presented in Section 3 on the protonmotive force. Since this discussion appears to be presently beyond the scope of a MitoEAGLE position statement, Section 3 will be removed from the [[MitoEAGLE preprint 2018-02-08 |next version]] and final manuscript. This section should become a topic of discussion within [[WG1 MitoEAGLE protocols, terminology, documentation |Working Group 1]] of the MitoEAGLE consortium, following a primary peer-reviewed publication of the concept of stoichiometric potential differences.
::: '''Added reference'''


== Further references ==
:::# Ling C, Rönn T (2019) Epigenetics in human obesity and type 2 diabetes. Cell Metab 29:1028-44. https://doi.org/10.1016/j.cmet.2019.03.009. - [[Ling 2019 Cell Metab |»Bioblast link«]]
::::* [[Bergeson_1981_West_J_Med]]
::::* [[Wheatley_2011_Metrologia]]


::: '''Coauthors''': Version 4: 542; present: 611




== Contacted editors ==
== ICJMD: Defining the role of authors and contributors ==
:: Updated 2018-02-12
::::* '''Biochem J'''
::::* '''Cell Metabolism''': ''J. Estrompa, N. Emambokus''
::::* '''Chemico-Biological Interactions''': ''D. Dietrich''
::::* '''Elsevier '''
:::::: '''Life Sciences''': ''L. Wold''
:::::: '''BBA Bioenergetics - Journal''': ''A. Ruban and S. Arnold''
:::::: '''Platelets''': ''P. Harrison, S.P. Watson''
:::::: '''Pharmacological Research''':'' E. Clementi''
:::::: '''Journal of Physiology and Biochemistry''': ''M.J. Moreno Aliaga''
::::* '''FEBS Journal'''
::::* '''FEBS Lett'''
::::* '''Int. J. Biol. Macromol.''': ''A. Dong''
::::* '''JIMD'''
::::* '''Journal of Experimental Biology''': ''I. Sokolova, H. Hoppeler, A.A. Biewener, R. Suarez, [email protected]''
::::* '''J Physiol''': ''M.C. Hogan, ''
::::* '''Mitochondrion''': K.Singh, ''C. Thorn''
::::* '''Mitochondrial Research''': ''P. Bernardi''
::::* '''PLOSOne''': ''J. Heber''
::::* '''Redox Biology''': ''S. Lamas''


== Phase 3.1: Discussion ==
:::: "Some large multi-author groups designate authorship by a group name, with or without the names of individuals. When submitting a manuscript authored by a group, the corresponding author should specify the group name if one exists, and clearly identify the group members who can take credit and responsibility for the work as authors. The byline of the article identifies who is directly responsible for the manuscript, and MEDLINE lists as authors whichever names appear on the byline. If the byline includes a group name, MEDLINE will list the names of individual group members who are authors or who are collaborators, sometimes called non-author contributors, if there is a note associated with the byline clearly stating that the individual names are elsewhere in the paper and whether those names are authors or collaborators." - [http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html Downloaded from www.icmje.org 2019-01-04]


* 2018-02-21 [[Chinopoulos C]]
::::* In page 10, line 429, please remove “hexokinase”, as this enzyme does not perform a transphosphorylation, it performs only a phosphorylation reaction.
::::: Otherwise, I confirm to have read the newest version of the manuscript and agree to implement the recommendations into my future manuscripts, presentations and teaching materials.
::::: Good luck with the submission!


* 2018-02-21 [[Granata C]]
== Comments ==
::::* I have given a thorough read to the latest version of the manuscript as downloaded from the MitoEAGLE webpage.
::::* At the beginning of page 7 (In Box1), it is mentioned the crosstalk between ER and mitochondria. I think it should be included that this interaction plays an important role also in lipid transport and biosynthesis. The second comment regards the mechanisms of respiratory uncoupling and in particular the acoupled respiration described in Fig 3, page 14 and table 2. The acoupled respiration is described as the respiration occurring in “non-compartmental mitochondrial fragments”. May be this concept could be explain further, since I think that acoupled respiration can refer to just fragments of the inner mitochondrial membrane but also mitoplasts (obtained by mitochondria swelling in hypotonic buffer). So, acoupled respiration could refer to cases in which the integrity of either only the outer membrane or both inner and outer membrane is compromised. ~ [[Fontanesi F]]
::::: Please find [http://wiki.oroboros.at/images/c/cb/MitoEAGLE_preprint_2018-02-08-CGranata_feedback.pdf attached] my feedback (you will see a series, not many, of comments, or words typed in RED font, to attract your attention to what I have changed/suggested to change).
::::* I am happy to confirm that the pre-print has no flaws that I could see. It is truly an excellent work, for sure a manuscript of reference. ~ [[Teodoro J]]
It is very polished at this stage and it has come a long way from the first version I reviewed back in summer 2017.
::::* I have been following the MitoEAGLE preprint on mitochondrial respiration, as well as the different comments. First of all, I am really interested in this topic, since as a student I already had troubles comparing different papers with different respiratory states, and this is a great opportunity to finally harmonize all the mitochondrial respiration experiments and publications. Pablo invited me to re-read it and make comments to contribute to the final final version. This would be a great honor, since this will be a reference paper in the future for experimental design and data reporting. .. I think it is a really elegant publication, with a lot of detail, but this is needed for the mitochondrial community to settle bases of nomenclature and harmonization. ~ [[Gonzalez-Franquesa A]]
::::: With this in mind; "I confirm that I read the latest version of the manuscript, and that I have provided feedback/improvements by sending a .pdf revised copy to the corresponding author (Prof. Erich Gnaiger), and that I agree to implement the recommendations into future manuscripts, presentations and teaching materials"
::::* Finally, I took the time to read the “Mitochondria States and Rates” preprint during the flight back home, I have one small comment: at the bottom of page 14, below table I, I get a bit confused all the way in this paragraph, but mostly by the part starting as “Defined coupling states are induced by…” (4 lines from the bottom). Somehow the points 1-4 that follow seem to refer to the states described in Table 1 above. If so, it may be clearer to arrange these points in the same order: seems that uncoupling (point 4) should go before inhibition of phosphorylation pathways (point 3) – I hope I’m not wrong for this? More generally, it might be useful for less advanced reader to relate the different parts of this paragraph to the states described in table I, following the same order given in the table: LEAK, OXPHOS, ET, ROX. As it is this paragraph starts with OXPHOS, then ET, then LEAK, with point 3 in the final description apparently being ROX.  ~ [[Joseph V]]
::::: I would be extremely happy and grateful if I could be upgraded as a "contributing co-author".
:::::: [[Gnaiger E]]: Many thanks for your positive feedback. Your suggestions for the MitoEAGLE white paper are very helpful. See the file (in prep for Version 5) for discussion: See pp. 14-15 for the re-arrangements. I hope that the confusion is now taken away – let me know.


* 2018-02-21 [[Hernansanz-Agustin P]]
::::* Nevertheless [http://www.mitoeagle.org/images/3/30/MitoEAGLE_preprint_2018-02-08_%28Schlattner%29.docx below] some suggestions and remarks from my side, maybe you can use them for a revision. And of course I would be glad to see my favorite proteins mentioned (CK, NDPK, recent reviews attached). ~ [[Schlattner U]]
::::* I have read the manuscript. Again, congratulations for the good job, in my opinion everything is quite clear.
::::* Please find ([http://www.mitoeagle.org/images/7/72/DMunro_-_Comments.docx attached]) my comments. I am glad to be part of this endeavour, which necessity is becoming increasingly clear every years! ~ [[Munro D]]
::::: Just couple of small things, it could be interesting to mention that cardiolipin/phospholipids are necessary for the activity and stability of respiratory complexes and interact with subunits in all of them (i.e. PMID: 25038566; 16388600; 26300339). Also, I have noticed that in the manuscript is on UK english and on page 11 (line 480) the word “channeling” is in US english.
::::* Fantastic initiative with the new mitochondrial physiology preprint server! ~ [[Donnelly C]]
::::* It is quite surprising that the final manuscript was not accepted in BioRvix. I completely agree with MitoFit Preprints. ~ [[Singh BK]]
::::* It will be a pleasure to join the MitoEagle task group publication. ~ [[Laranjinha J]]
::::* I have a small remark : the concept of multiple authors signature started to be contested... By all ETHICS commities everywhere in Europa at least since it overpassed the usual rules... And also altered the signification of the authors impact factor. The regulation will be to form a consortium that is the true entity that will sign the collective work. That is teh best for teh COST since all members are easily identifiables. Overall conmment: This paper has been stanfding to long.... on teh bench! [[Petit PX]]
::::* I just found a minor typo. If you look at the “S” references, they are out of alphabetical order. ~ [[Sparagna GC]]
::::* Please find [http://wiki.oroboros.at/images/c/cd/Gnaiger_2019_MitoFit_Preprint_Arch_doi_10.26124_mitofit_190001_MCKENZIE.pdf attached] manuscript with comments (I have made 5 in total). Feel free to incorporate (or ignore) as you see fit! ~ [[McKenzie M]]
::::::* ''[[Gnaiger E]]'': To address your comment “Interesting that you state saturating O2, as this is only at the start of an experiment? (but is accounted for in the oxygraph calibration with dithionite, so that measured respiration rates are relative to saturating O2?).”, I extended Section 2.1.2: “Kinetically-saturated conditions are evaluated by substrate kinetics to obtain the maximum reaction velocity or maximum pathway flux, in contrast to solubility-saturated conditions.”
:::::: We are in direct contact with Kyle Hoehn to obtain and test their uncouplers.


* 2018-02-21 [[Lee HK]]
:::::: To summarize your comment “So would it be optimal in publications to not only state final flux rates/unit sample (e.g per mg) but also the raw flux rates (per mL) and the mg of sample used?”, I extended Box 3:Box 3: Recommendations for studies with mitochondrial preparations
::::* I am very much honored to be an author of this historical paper. I firmly believe this paper will be a base of new mitochondria based medicine. I had suggested a little for this paper early on and read most of the paper, while I did not grasp some part of it.
:::::: ●  Normalization of respiratory rates should be provided as far as possible:
::::::: A. Sample normalization
:::::::: 1. Object-specific biophysical normalization: on a per organism or per cell basis as O2 flow; this may not be possible when dealing with coenocytic organisms, e.g., filamentous fungi, or tissues without cross-walls separating individual cells, e.g., muscle fibers.
:::::::: 2.  Size-specific cellular normalization: per g protein; per organism-, cell- or tissue-mass as mass-specific O2 flux; per cell volume as cell volume-specific flux.
::::::::3.  Mitochondrial normalization: per mitochondrial marker as mt-specific flux.
::::::: B. Chamber normalization
:::::::: 1. Chamber volume-specific flux, JV [pmol∙s-1∙mL-1], is reported for quality control in relation to instrumental sensitivity and limit of detection of volume-specific flux.
:::::::: 2. Sample concentration in the instrumental chamber is reported as number concentration, mass concentration, or mitochondrial concentration; this is a component of the measuring conditions.
:::::: With information on cell size and the use of multiple normalizations, maximum potential information is available (Renner et al. 2003; Wagner et al. 2011; Gnaiger 2014). Reporting flow in a respiratory chamber [nmol∙s-1] is discouraged, since it restricts the analysis to intra-experimental comparison of relative (qualitative) differences.


* 2018-02-21 [[Orynbayeva Z]]
::::* I am happy to see that we are one step closer to the final publication of the MitoEAGLE manuscript in a journal. ~ [[Komlodi T]]
::::* I will look over the manuscript by the designated deadline.
::::* It is a great step towards the publication of the manuscript and congratulations for creating your own tool to circumvent decisions that can not be easily understood. ~ [[Thierry A]]
::::: Thank you very much
::::* Excellent article and one of its kind too. Please let me how can i help to get it published in a high impact j. Look forward to work in your team. ~ [[Sharma P]]
::::* It's great to see the preprint. The preprint server in the area of mitochondrial physiology is a great idea and definitely will be a success. ~ [[Tomar D]]
::::* First and foremost I would like to express my deepest gratitude and would like to thank you for giving us your time to review our manuscript and be part of us as the co-author. It is a great honour to get you in touch and reply promptly. .. I would like to also thank you for giving me the opportunity to be part of the MitoEAGLE as one of the co-authors and I am happy to be listed in the next version of the preprint. ~ [[Hassan H]]
::::* However - just a note about pre-prints. A significant portion of scientists that I collaborate with feel uncomfortable submitting manuscript on a pre-print server. Is this something that could be addressed maybe in an article regarding the benefits and nuances of pre-print server submission. ~ [[Towheed A]]


* 2018-02-21 [[Pak YK]]
:::* '''FAQ''' - [[Preprint|MitoPedia:Preprint]]
::::* It is my great honor to be a co-author of MitoEAGLE manuscript.
::::: I like the sections of metabolic state of mitochondria and coupling state. I wondered how to and what portion of protonmotive force generate heat for a long time. If you can explain or comment this on section 2.2, it would be great.
::::: Thank you for your effort and dedication to mitochondria research.


* 2018-02-21 [[Puurand M]]
::: '''Journal submission comments'''
::::* Congratulations on the profound and necessary work in our field.
::::: I read a manuscript versioon 22.
::::: I totally agree with the removal of the chapter about thermodynamics,as we dscussed it at the Mip2017 meeting in Czech Republic.
::::: I have only minor notes. First, Figure 1 shows also AOX. This is correct, but i think that comment  or remark that AOX is absent in mammals should be added to the legend of the figure.
::::: Chapter 3 about normalization is proportionally too comprehensive  and i see possibilities for shortering paper mainly in this chapter. Table 6 can be excluded, if nessesery.


* 2018-02-21 [[Sandi C]]
::::* Cell Metabolism seems like a good first choice. ~ [[Williams C]]
::::* Many thanks for your note. I confirm that I read and approve the ms. for submission. Thanks for the great and important work.
::::* Cell Metabolism, I think this is a good choice. ~ [[Rossiter HB]]
::::* Cell Metabolism seems highly appropriate. ~ [[Newsom SA]]
::::* No preference. Just go ahead. ~ [[Zaugg M]]
::::* I concur with the choice of cell metabolism. ~ [[Pulinilkunnil T]]
::::* I think cell metabolism would be great, but I doubt whether it is realistic. Possibly Molecular Metabolism (very rapid, good reputation, european), Cell and Molecular Life Sciences (many reviews) or BBA- bioenergetics could be alternatives. ~ [[Keijer J]]
::::* Alternatives if Cell Met is not accepting: Nature metabolism or Acta physiologica. ~ [[Amati F]]
::::* And Cell met is a good 1st choice for this publication. ~ [[Zanou N]]
::::* The question is why did Biorxiv reject the manuscript? Before submitting to a prestigious journal like Cell Metabolism all the doubts Biorxiv had should be ruled out. ~ [[Methner A]]
::::* And I think that Cell Metabolism is a good first journal choice for submission of our manuscript. ~ [[Breton S]]
::::* Cell Metabolism is a good option as a first submission. ~ [[Bouitbir J]]
::::* Cell metabolism is a good fit for the manuscript. ~ [[Adiele RC]]
::::* The choice of journal is excellent, although it might be a long shot. ~ [[Oliveira MT]]
::::* I guess that also  TIBs  or Current Biology could be considered. ~ [[Calabria E]]
::::* I am in agreement that the first journal will be Cell Metabolism. ~ [[Victor VM]]
::::* Cell metabolism is an excellent choice. If they are interested that would be wonderfull. Physiological Reviews could be an alternative, in case Cell metabolism declines the manuscript. ~ [[Thierry A]]
::::* I would suggest to try the submission in Cell Metabolism. ~ [[Doerrier C]]
::::* Regarding the future submission of our paper, if there is already a pre-acceptance of the Editor of Cell Metabolism, I believe we should submit there. There are not many journals willing to publish a paper with so many authors, and the reviewing process will not be easy, in my opinion. ~ [[Crisostomo L]]
::::* I think cell metabolism is a good target to submit our article. ~ [[Salin K]]
::::* I would format accurately as a resource manuscript for Cell Metabolism. ~ [[Lavery GG]]
::::* The manuscript is still extremely long. In my modest opinion too long compared to the editorial format limits of many journals. If the manuscript cannot be substantially shortened to the essentials (in my opinion preferable) one strategy is to try to find a journal without such limits. ~ [[Spinazzi M]]
::::* I am happy with Cell Metabolism to start the submission process of this preprint. ~ [[Moisoi N]]


* 2018-02-21 [[Stier A]]
== 2019-07-22 Circular to coauthors ==
::::* The revised version is definitively clearer for non-experts, and my previous comments on the manuscript have been addressed. I’ll implement the recommendations detailed in this paper into future publications and teaching material.
::::: Therefore I am happy to be listed as co-author for the submission to Cell Metab.


* 2018-02-21 [[Tepp K]]
::: '''Re: MitoEAGLE preprint on ‘Mitochondrial respiratory states and rates’'''
::::* First of all, I think that the manuscript gains a lot after splitting it into the two parts. Reader of the text is more focused and do not get tired before the end .
::::: There are some suggestions and thoughts, when reading the article.
::::: In Figure 1 - maybe it is worth to mention that AOX is not present in mammalian cells ?
::::: Table 2 explains very well terms of different coupled states in Figure 3, which are maybe otherwise difficult to distinguish for people who are not familiar with them. I do not know how it appears in the journal but maybe it is better to sum Table 1 and Table 2 so that when you look Figure 3, it is easier to find definition of the a/un/Dys/de-coupled respiration?
::::: It is great news that the editor-in-chief of Cell Metabolism considered our article to be suitable for his journal. If it is necessary to make the article even shorter, 3.6 may be the part in my opinion. Maybe Table 7 is not so necessary as the texts already explains the basic concept.
::::: In general I think the article is with a great importance to have all the basic concepts and definitions in one article and I am honored to be part of it.


* 2018-02-21 [[Wuest RCI]]
:::: Dear coauthors,
::::* I confirm to have read the almost final version of the preprint publication, and agree to implement these recommendations.


:::: The recent MiP/MitoEAGLE Training School in Coimbra provided another excellent opportunity to present the concept of our ‘States and rates’ white paper, to discuss it with several students and scientists who joined as additional coauthors, and to take a decision on journal submission.


* 2018-02-20 [[Breton S]]
:::: 1. Preprint version 5 (in prep) is now available for your evaluation before proceeding with journal submission. At this stage, the MitoFit Preprint version 5 (in prep) has not yet a DOI, to allow final changes to be made according to the immediate feedback received upon this circular. The latest changes are listed on the website, minor changes and improvements are included in the manuscript:  
::::* I confirm that I have read the newest version of the manuscript and agree to implement the recommendations into my future manuscripts, presentations and teaching materials.
::::: Thank you very much


* 2018-02-20 [[Chaurasia B]]
::::» www.mitofit.org/index.php/Talk:Gnaiger_2019_MitoFit_Preprint_Arch
::::* Everything looks and sounds for me.


* 2018-02-20 [[Irving BA]]
:::: 2. Please finally check your personal page for any corrections to be made in your initials and affiliations.
::::* In figure 1A. I believe there are typos in the protons pumped at complex III and IV.
::::: What ends up on the innermembrane side of complex III is 4H+ (or for molecular oxygen 8H+).  Some of which comes from UQH2 and some from the matrix.
::::: What ends up on the innermembrane side of complex IV is 2H+ (or for molecular oxygen 4H+).  Half the protons from the matrix side combine with O2 to form water and don’t make it into the innermembrane space. Please see the [http://wiki.oroboros.at/images/c/cf/MitoEAGLE_Figur_1A_H%2B.pdf attached edit]. Plus a Figure 4.2 from the Brand and Nicholson Text.
::::: If this is not correct, please clarify this issue for me.
::::: Otherwise I agree with the manuscript and to be a co-author. Thank you.


* 2018-02-20 [[Calbet JA]]
:::: 3. Feel free to invite additional colleagues to evaluate our white paper and join as coauthors.
::::* I'm happy with this version of the manuscript. I confirm to have read the newest version of the manuscript and i agree to implement the recommendations into my future manuscripts, presentations and teaching materials.  


* 2018-02-20 [[Chicco AJ]]
:::: 4. We have announced the plan for journal submission for quite some time, but the number of coauthors increased to 612 and many discussions lead to further improvement of the manuscript. Our first goal for submission has been ‘Cell Metabolism’. Since then, the new journal ‘Nature Metabolism’ was launched. Feedback from several coauthors, and the interest of the editor of ‘Nature Metabolism’ in our white paper, has led to a change in the strategy, to submit primarily to the European journal ‘Nature Metabolism’, since the COST Action MitoEAGLE is a European project-with worldwide participation.
::::*It is great to hear that Cell Metabolism is interested. This work is a masterpiece of gentile science with rigorous attention to detail, and is sure to be broadly cited wherever it ends up. I am honored to have contributed as a co-author.  
::::: Best of luck with submission!


* 2018-02-20 [[Genova ML]]
:::: With many thanks for your contributions and for supporting the MitoEAGLE project,  
::::* I am working at a couple of new short comments that I would like to submit to your attention as my additional contribution to  the improvement of the current version of the manuscript. I hope that I will be able to send you my notes within a few days.
::::: Meanwhile, as a contributing co-author, I confirm "to have read the newest version of the manuscript and to have made additions or suggestions for improvement". I also agree to implement the recommendations into my future manuscripts, presentations and teaching materials.


* 2018-02-20 [[Gorr TA]]
:::: Erich
::::* No further suggestions. I confirm to have read the newest version of the manuscript and to have made a suggestion for improvement


* 2018-02-20 [[Iyer S]]
:::: Erich Gnaiger, Ph.D.
::::* I have had an opportunity to review the contents of the manuscript and agree to implement the recommendations into our future manuscripts, presentations and teaching materials.  
:::: Chair COST Action MitoEAGLE
::::: I am excited at the opportunity to present this article to the broader community and hope this gets accepted in ‘Cell Metabolism’. I once again thank you for your leadership in this regard, and look forward to our next meeting.
:::: [email protected].at | www.mitoeagle.org


* 2018-02-20 [[Jang DH]]
::::* Thank-you for listing me. Happy to help in any other way


* 2018-02-20 [[Kappler L]]
== 2019-03-12 Circular to coauthors ==
::::* I´ve read the latest version and everything is to my satisfaction, my suggestion have been considered. I will implement this in my future papers, presentations and lectures. Best wishes and good luck with the submission.


* 2018-02-20 [[Lerfall J]]
::: '''Re: MitoFit_Preprint_Archives'''
::::* I herby confirm that I have read the last version of the manuscript. I think the manuscript give a clear introduction to terms related to mitocondrial respiratory and I confirm to include them in my lab and in teaching.


* 2018-02-20 [[Malik AN]]
:::: Dear coauthors,
::::* Thanks for your letter re the manuscript. I’d be happy to be included as a co-author and will have a detailed read of it and get back to you in the next few days if i have any comments/suggestions.
::::...thanks for all the hard work.


* 2018-02-20 [[Muntane J]]
:::: We thank you for the feedback received to our previous circular. Here is the summary of 176 answers to the three questions on preprints, which encourages us to proceed with '''MitoFit Preprint Archives''':
::::* I have read the newest version of the manuscript which it is far over my actual knowledge in the field. I have learned during the reading, and consequently I will be implement the concepts into our manuscripts, presentations, as well as teaching materials.
::::::» [[MitoFit_Preprint_Archives#Preprint_questionnaire |Summary on preprint questionnaire]]


* 2018-02-20 [[Menze MA]]
:::: The [[MitoFit_Preprint_Archives#Advisory_Board |Scientific Advisory Board]] has expanded, and we thank all MitoEAGLE members who have joined the International Board. Again we extend our invitation to join the editorial team. In particular, we would like to establish a '''Member Advisory Board''' including scientific organizations and journals which support the concept of '''MitoFit Preprints'''. If you are involved in such an organization, please let us know if joining the 'Member Advisory Board' might be an option for your organization.
::::*I am happy to be upgraded as contributing co-author and I will have a careful read over the current manuscript by Monday.


* 2018-02-20 [[Nemec M]]
:::: Information on next steps for [[Gnaiger_2019_MitoFit_Preprint_Arch#Towards_the_preprint |our manuscript on 'Mitochondrial respiratory states and rates']] will follow soon.
::::* Thank you once more for the opportunity to participate in introducing concepts for the broad scientific community. I have read the newest version of the manuscript and I fully agree with nomenclature of mitochondrial respiratory states and rates. Also, I will try the best to implement the nomencalture in my (or my students) future papers, presentations and materials as I have been trying to do up to now.


* 2018-02-20 [[Patel HH]]
:::: Kind regards,
::::* I have read through the latest version of the manuscript. I do not have any additional suggestions for revision. Thank you for including me as a co-author.
:::: Erich
::::: I agree to implement the recommendations into my future manuscripts, presentations, and teaching materials. Please let me know if anything additional is needed.  
:::: Chair COST Action CA15203 MitoEAGLE
:::: [email protected] | www.mitoeagle.org


* 2018-02-20 [[Petit PX]]
::::* This is fantastic to see the end of this first manuscript.
::::: I hope this will go through.


* 2018-02-20 [[Pirkmajer S]]
== 2019-02-12 Circular to coauthors ==
::::* Thank you for your note and update. I’ve been reading thoroughly and with great interest the latest version (#22) of the manuscript. I do not expect to have any further comments, but in case I have them you will receive them within the deadline


* 2018-02-20 [[Rohlena J]]
:::: Dear coauthors,  
::::* I have read the paper, it is very comprehensive. It struck me it might be perhaps informative to make a more head-on comparison of the new (leak, ET, ROX ) and old (state 1, 2 etc) definitions of the respiratory states, for example in one of the tables, or an addition table. 


* 2018-02-20 [[Sharma V]]
:::: The MitoEAGLE manuscript on ‘Mitochondrial respiratory states and rates’ is now published in MitoFit Preprint Archives as a preprint citable with DOI number with 530 coauthors. The next step will be journal submission:  
::::* I am glad to have this opportunity and happy for selecting me as a Joint collaborator.
:::: » http://wiki.oroboros.at/index.php/MitoFit_Preprint_Arch
::::: However, I go through the manuscript of all the concept of mitochondrial physiology, and previously that book I have already, also helps me a to understand the concept of Mitochondrial Physiology. Here, I am sending you a three answer of your question,  I am bit unfit for reviewing all that concepts in this short span period. Here, I am sending all the explanations which I think, as per my understanding. If any feedback please let me know.
::::: I will also share with my Supervisors and Colleague in further.
::::: ''[[Gnaiger E]]'': Do you recognize a general need for a consensus on nomenclature and standards of reporting in the field of mitochondrial respiratory physiology?
::::: [[Sharma V]]: Respiratory rates and states would be possible to develop a researchers need to choose which effect size provides the best summary and specify which effect size they report. In the end, the choice of an Proton motive force, ETS, ET has play a significant role in effect size calculation depends on the research question and the experimental design. It is important to explicitly stated that which effect size is calculated, and to make a motivated choice about which effect sizes to report. With the current overview, The manuscript have provided a practical concept and consistency to assist researchers in choosing and calculating effect sizes by establishing the link between vectorial and scalar energy transformation and coupling in oxidative phosphorylation in both states.
::::: ''[[Gnaiger E]]'': Can you provide comments and suggestions for the ‘MitoEAGLE preprint: Mitochondrial respiratory states and rates’ from your point of view as an editor?
::::: [[Sharma V]]: As per my suggestion the manuscript explained very well about to do the mechanisms behind observed oxygen consumption, and factors affecting the oxygen consumption rates and consequence of different electron pathway.
::::: However, I would suggest the elaborate of any kind of procedure which will conduct as in vivo method determination of mitochondrial respiratory chain. I am not aware about how to perform such measurements in tissue does anybody have any experience in this topic kindly mentioned.
:::::* Short Classification of Mitochondrial biomarkers with respect to disorders in Respiratory states and Rates. (Healthy and Diseases States)
:::::* Emphasize the abnormal mitochondrial function and positioning alters multiple components of the specific organ physiological system.
::::: ''[[Gnaiger E]]'': Which further steps do you suggest towards implementing a harmonized terminology on mitochondrial states and rates in your editorial policy?
::::: [[Sharma V]]:
:::::* Metabolic programming of immune cell differentiation and proliferation into anti and pro-inflammatory phenotypes, driven by the balance of oxidative phosphorylation (OXPHOS) vs. glycolysis and mitochondrial reactive oxygen species (mtROS).[1]
:::::* Mitochondrial epidemiological studies with reference to particular disease states and rates. [2]
:::::* Modulating the mitochondrial quality with diseases transmission with respect to mitochondrial biomarkers.[3][4]
:::::* Development of simulation studies, based on experimental method for predicting the future perspective of specific mitochondrial disorder.
:::::* Designing of multi-omics experiments and applying on large data sets to develop a precise medicine approach in mitochondrial dysfunction and also helps us to understand the physiological mechanism in different aspects. [3][4]
::::: Reference
::::: 1. Picard, M., D.C. Wallace, and Y. Burelle, The rise of mitochondria in medicine. Mitochondrion, 2016. 30: p. 105-116.
::::: 2. Diot, A., et al., Modulating mitochondrial quality in disease transmission: towards enabling mitochondrial DNA disease carriers to have healthy  children. Biochemical Society Transactions, 2016. 44(4): p. 1091-1100.
::::: 3. Haas, R., et al., Designing and interpreting ‘multi-omic’experiments that may change our understanding of biology. Current Opinion in Systems Biology, 2017. 6: p. 37-45.
::::: 4. Meng, C., et al., A multivariate approach to the integration of multi-omics datasets. BMC bioinformatics, 2014. 15(1): p. 162.


* 2018-02-20 [[Smenes BT]]
:::: Why a new preprint server MitoFit Preprints? – On 2018-12-12 the MitoEAGLE manuscript was submitted to the preprint server www.biorxiv.org/. We are amazed that our manuscript was not accepted:
::::* I have read the manuscript and have no suggestions for further improvements. Let me know if you need any more information from me. I accept the upgrade to contributing co-author.
:::: » http://www.mitoeagle.org/index.php/Talk:MitoEAGLE_preprint_States_and_rates#BIORXIV
:::: Instead of starting a debate with bioRxiv we started MitoFit Preprints (originally MitoFit Preprint Archives) - the Open Access preprint server for mitochondrial physiology


* 2018-02-20 [[Soares FAA]]
:::: The first DOI number was allocated to our MitoEAGLE manuscript.
::::* I read the last version and my group are all studying the manuscript to use it as a “bible” of mitochondria.  
::::: I am ok with the submission to a journal


* 2018-02-20 [[ Sokolova I]]
:::: Your opinion means a lot to us. Therefore we would like to ask you:
::::* I have not yet congratulated and thanked you for putting together this impressive document and for coordinating this whole effort, and I am doing so now. I [http://wiki.oroboros.at/images/8/85/MitoEAGLE_preprint_2018-02-08_IrinaMS.pdf attach] the manuscript with a few comments, all minor and editorial. Good luck with the submission and thanks for involving me in the project!
::::# Are you familiar with the concepts of preprints? '''Y / N'''
::::# Will you consider to submit a manuscript to MitoFit Preprints for publication as a preprint? '''Y / N'''
::::# Which alternative preprint server do you prefer? ___________
:::: The results of this questionnaire will be summarized anonymously on our website (beginning of March).


* 2018-02-20 [[Suravajhala P]]
:::: We thank you for answering these questions in advance and are looking forward to your feedback. In particular, do you have further suggestions for our first journal choice for submission of our manuscript (Cell Metabolism)? 
::::* Thank you.  I have gone through the last version and will go through the latest version and get back asap.
::::: I have read the manuscript again. It’s very solid. This time I only have a couple suggestions which may be implemented:
::::: Page 11, line 480-482:
:::::: “…(4) mitochondrial density (enzyme concentrations and membrane area) and morphology (cristae folding, fission and fusion).”
:::::: Suggested reference to support this sentence: PMID: 24606803
::::: Page 23, line 1018-1019:
“Mitochondria undergo dynamic fission and fusion cycles, and can exist in multiple stages and sizes which may be altered by a range of factors.”
:::::: I suggest to add something like this after the quoted sentence: “Changes in mitochondrial morphology is often associated with alterations in mitochondrial function, and In cultured cells this can be evaluated by quantitative analysis of mitochondrial shape using fluorescence microscopy and image analysis in 2 or 3 dimensions (Ref PMID: 24988307)”
::::: Thanks.


* 2018-02-20 [[Ward ML]]
:::: In the spirit of the bottom-up approach of MitoEAGLE, this is an invitation to join the editorial team (Scientific Advisory Board) of MitoFit Preprints.
::::* Thank you for the opportunity to join as a co-author on the manuscript "Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology". I have taken the time to read the latest version, and am favourably impressed with the clarity of the writing and the content. This will be a most useful publication for many different research groups and teachers world-wide.
::::: I did detect one typographical error: Box 1. Line 236/237 Membrane fluidity “exters”…, should I think read “extends”.


* 2018-02-20 [[Wohlwend M]]
:::: Best regards,
::::* I have read the newest version of the manuscript and I think the manuscript looks excellent and I have no more further suggestions.
:::: Erich Gnaiger
:::: Chair COST Action CA15203 MitoEAGLE
:::: [email protected] | www.mitoeagle.org




* 2018-02-19 [[Giovarelli M]]
::::* '''2019-02-12: MitoEAGLE Task Group on 'Mitochondrial resipratory states and rates''''
::::* I'm glad to take part in the discussion of the MitoEAGLE preprint. The new version of the manuscript provides a significant step forward for the approach to mitochondrial metabolism concepts and the terminology harmonization, especially for the young scientists. For my purposes, I found very important the section on the Flux Normalization methods and principles; this point is crucial for the interpretation of the final outcomes and for the results comparison between different labs. The endeavour to find standard protocols and normalization requires time; nonetheless a statistical evaluation of the best mitochondrial marker for different mitochondrial preparation and tissues is needed. This issue is well pointed out in the conclusion section.
[[File:Doi 10.26124 mitofit 190001.PNG|left|1000px|MitoEAGLE: States and rates - the preprint is citable with DOI number and getting ready for journal submission|thumb|link=http://www.mitoeagle.org/index.php/Gnaiger_2019_MitoFit_Preprint_Arch]]
::::: In Classical terminology for isolated mitochondria, the “classical states” of mitochondrial respiration are well presented; I have personally started the study of mitochondrial bioenergetic using the mitochondrial States as references for evaluating my respirometry experiments. Must we consider this terminology out of date or rather a co-existing complementary terminology?


* 2018-02-19 [[Gorr TA]]
[[Image:BB-Bioblast.jpg|left|30px|link=Bioblast:About|Bioblast wiki]]
::::* please find [http://wiki.oroboros.at/images/2/2a/MitoEAGLE_preprint_2018-02-08_Gorr.pdf attached] our position statement manuscript -  with one comment from me, right at the beginning (highlighted yellowed text).
::::: Overall, the text is still not easy to digest. I had to read mnay sections two or three times to understand their intention. Maybe, a professional science writer should work on in to smoothen the tex as much as possible.


* 2018-02-17 [[Liu J]]
== Popular Bioblast page ==
::::* Thank you very much for inviting me to be a coauthor of your masterpiece of mitochondrial history! I will try my best to be qualified for being a contributing co-author
::: [[Gnaiger 2019 MitoFit Preprints]] has been accessed more than
::::: ''[[Gnaiger E]]'': I would be very thankful for receiving your comments and critical evaluation of the present version of our manuscript.
::::* 50,000 times (2019-12-11)
 
::::* 35,000 times (2019-07-22)
* 2018-02-16 [[Gnaiger E]]
::::* Dear Anthony, Pushpa did a great job. Here is a first-level promising answer (see [http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08#Answers here]).
::::: ''[[Molina AJ]]'': That is fantastic!  I have worked with that editor before.  A positive response from her is a promising sign.
 
* 2018-02-16 [[Kaambre T]]
::::* I read the MitoEAGLE paper, and you've done a lot of work with it! It is more compact now, and it's much easier to read. The part of thermodynamics might be a separate article, this would be very important for young scientists and for the education in general in the field of bioenergetics.
::::: May be you could advise me? I have problem with terminology, but I´m not sure, is it the topic of our paper (Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology). It is not clear at all, when the mitochondrial preparations are in vivo, in situ, ex vivo or in vitro. With isolated mitochondria no problem, this mitochondrial preparation is always described as in vitro. But with mitochondria in cell cultures the terminology is very messy. I met various variants like in vivo, in situ and ex vivo in different papers. The story is not better also with permebilized samples and tissue homogenates.
::::: ''[[Gnaiger E]]'': Thank you for your positive feedback. I agree that the thermodynamics part is important. I was reluctant to remove it, but the arguments to reduce the complexity of the present MS were valid.
::::: You make a good point on the terminology of in vivo, in situ, ex vivo, .. I suggest that we ‘make it’ a topic of our paper, since we start with the definition of mitochondrial preparations. I suggest: all mitochondrial preparations are ‘in vitro’ (then we do not need ‘ex vivo’). In contrast to isolated mitochondrial and homogenate preparations, mitochondria can be considered as ‘in situ’ relative to the plasma membrane in permeabilized fibers and permeabilized cells. Do you think that everybody can agree on that? The text is included in the new version as a suggestion:
::::: “Mitochondrial preparations are defined as either isolated mitochondria, or tissue and cellular preparations in which the barrier function of the plasma membrane is disrupted. Since this entails the loss of cell viability, mitochondrial preparations are not studied in vivo. In contrast to isolated mitochondria and tissue homogenate preparations, mitochondria in permeabilized tissues and cells are in situ relative to the plasma membrane.” (I will upload the new version in a few minutes)
::::: Now we were invited by CELL METABOLISM to submit our manuscript for in-depth editorial evaluation.
 
* 2018-02-15 [[Gnaiger E]]
::::* Dear Prof. Liu Shusen, I would be very thankful for receiving your comments and critical evaluation of the present version of our manuscript. Below is the link to our updated version.
::::: ''[[Liu SS]]'': I will give my response as much as possible to you after my finishment of reading it. but, I am not sure every point I could agree with that noted in the manuscript, although, it is very good totally and generally! My main consideration is that biomembrane bioenergetics ,the study on  mitochondrial oxidative phosphorylation is still in the rapid period of development and refinement, not only technically, but also theoritically/conceptionally.  So, I need get time to learn and to read more recent scientific research achievements and progresses, including your manuscript!
 
* 2018-02-15 [[Sharma P]]
::::* I have received a response from "CELL METABOLISM".  Looks like they are interested in our manuscript. Please read their response and advise me what to do next.
::::: ''[[Gnaiger E]]'': Thank you so much for your correspondence with CELL METABOLISM. This sounds like the door is not closed. I propose that I will add the Executive summar into the present pdf file and send the whole manuscript to Nikla Emambokus, Editor-in-Chief, Cell Metabolism. In any case, it will be interesting to receive his response.
::::: [[Sharma P]]: Excellent idea to polish the manuscript and submit to CELL METABOLISM ASAP before editor changes his mind.
::::: ''[[Gnaiger E]]'': Dear Dr. Emambokus, we thank you for your interest in evaluating our manuscript ‘Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology’ in your in-house editorial review system.
::::: A pdf file of the full manuscript is attached. A Task Group of the COST Action MitoEAGLE has been working on this manuscript with Open Access as a ‘MitoEAGLE preprint’ and the ultimate aim of peer-reviewed publication: » http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08
::::: The global MitoEAGLE network made it possible to collaborate with more than 250 co-authors to reach consensus on the present manuscript. Nevertheless, we do not consider scientific progress to be supported by ‘declaration’ statements (other than on ethical or political issues). Our manuscript aims at providing arguments for further debate rather than pushing opinions.  We hope to initiate a much broader process of discussion and want to raise the awareness on the importance of a consistent terminology for the reporting of scientific data in the field of bioenergetics, mitochondrial physiology and pathology. Quality of research requires quality of communication. Some established researchers in the field may not want to re-consider the use of jargon which has become established despite deficiencies of accuracy and meaning. In the long run, superior standards will become accepted. We hope to contribute to this evolutionary process, with an emphasis on harmonization rather than standardization.
::::: The manuscript has not yet been formatted for a specific journal. We will be glad to ensure that-before submission-an updated version conforms to the format guidelines for your journal, should you encourage us to proceed with submission at your EM site.
::::: We are looking forward to hearing your opinion about the timeliness and potential impact of our manuscript, and possibly your suggestions for improvement.
::::: With many thanks for your consideration, and kind regards, Erich Gnaiger
:::::* [http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08#Answers Estrompas answer to Dr. Gnaiger]
 
* 2018-02-15 [[Watala C]]
::::* I have sent the enlosed letter to several jpournals, in which we published during the last 5 years, and which may have something in common with mitochondrial physiology. I have included you as the “to your information” addressee.
::::: ''[[Gnaiger E]]'': Many thanks for your great efforts!
 
* 2018-02-14 [[Wagner BA]]
::::* Dr. Gnaiger, here are some suggestions or items that might need to be double checked. Most of the items are minor. The manuscript looks great
::::: Thank you for your effort.  This manuscript is timely, informative, and clearly sets forth the future: highly educational as well. No single author or smaller group could do what’s been accomplished here. Again, I must Thank you for orchestrating it so well!
::::: I found a couple of things in the manuscript where some items need to be double checked, clarified, or verified that they are not typos or missing characters as posted (Version 22_2018-02-08 ). Hopefully, the below listed comments will aid in the final manuscript and publication. and editing.
:::::: Lines 210-211:  might be better as “enzymes of the tricarboxylic acid and fatty acid oxidation”.
:::::: Lines 219-223:  Possible to many “and’s, not sure if this is a run on sentence or not.   
:::::: Line 404: (10 ug•10-6 cells) is this 10-6 cells or 106 cells, also is the dot the best way to separate the 2 different normalization values?
:::::: 464, 524-525, Figure 3 Note 5 and through the whole manuscript: “superoxide anion radical” could be simply “superoxide” unless the intent is to educate people unfamiliar with this molecule and highlight that it’s a radical and an anion.
:::::: Line 741:  is (CHNO; 2[H]) correct or a typo or missing a character?
::::: ''[[Gnaiger E]]'': Dear Brett, many thanks for your excellent comments and (already earlier) contributions. We have an interesting reply from CELL METABOLISM (see[[MitoEAGLE_preprint_2018-02-08#Answers| here]]). We will send them the MS.
 
 
* 2018-02-13 [[Lemieux H]]
::::* Here are a few additinal comments on the review [http://wiki.oroboros.at/images/a/ae/MitoEAGLE_preprint_2018-02-08-HL_edit.pdf (pages 6, 13, 25)]. I'm still a little bit under the impression that it is very complex for general users to apply properly all the nomenclature. 
::::: About the editors, nobody comes into my mind but I will look if I can find some to send the letter of information too.
 
* 2018-02-13 [[Velika B]]
::::* I think, the letter to the editor you sent is it's really nicely written, with all needed information.
 
* 2018-02-13 [[Victor VM]]
::::* Thank you very much for your collaboration adn invitation. I think that it is a very nice article.
::::: I will send it to the editors.
::::: In fact, this afternoon I have a meeting with Santiago Lamas who is an associate editor of redox Biology,and I can talk about the article.
 
* 2018-02-13 [[Villena JA]]
::::: ''[[Gnaiger E]]'':May I ask you to send a letter with the information contained in the template (feel free to modify) to relevant editors whom you know.
::::* Thanks, Erich. I will do so.
 
* 2018-02-12 [[Battino M]]
::::* I deeply appreciate your efforts to make the text more affordable also for not-experts in the field: I agree with you and I am convinced that this help to better widespread the message inside and to gain much more visibility and an enhanced number of potential reader will be reached.
::::: BTW, I am preparing to send the letter you suggested to some EiC but I think it would be useful to avoid any overlapping in this task: therefore I am suggesting you make available a list of EiC/journals already contacted in order it could be easier to resend the same letter to the same EiC.
::::: Moreover, before sending the letter, the sender should advise you for a continuous update of the list.
::::: You can also prepare a doodle/surveymonkey or similar where each contributor could add by his/her own the journal contacted.
 
* 2018-02-12 [[Buettner GR]]
::::* I offer some suggestions.
::::: ''[[Gnaiger E]]'': Many thanks for your excellent comments and (already earlier) contributions. We have an interesting reply from CELL METABOLISM (see [http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08#Answers Dr.Sharma]). We will send them the MS.
::::: ''[[Buettner GR]]'': This manuscript has had a rigorous “internal” review.  Thus, a journal’s review would not be expected to add too much. 
::::: I think you are in the driver’s seat, as many journals would welcome this work. I would not bend too much to a specific journal’s demands.  Bargain hard if the editor(s) want changes in format, length etc. 
::::: To ensure the work gets into PubMed Central (12 mo from publication), I assume an author(s) must have NIH grant support.  I have such support.  Others may as well.  Thus, this may need consideration.  ::::: I have done this for other collaborative works; obviously it helps me justify my grant -- showing productively and progress, but most important it assists with long-term accessibility. 
::::: The goal is to get easy and wide distribution to all researchers whose research touches on this area. 
::::: ''[[Stocker R]]'': I completely agree with Garry. Accessibility is going to be a key determinator whether this project will be a success and result in broad adherence to the guidelines provided.
 
* 2018-02-12 [[Calabria E]]
::::* Dear Erich, thanks a lot. I think this is a great idea. I sent the message contained in the attachment to three editors I’ve been in contact with and their colleagues.
 
* 2018-02-12 [[Chen Q]]
::::* I would suggest you to contact Prof. Liu Shusen for his comments. I copy this message to him so that he may be helpful.
::::: ''[[Gnaiger E]]'': Many thanks for reaching out to Prof. Liu Shusen. I have gladly added you to the list of co-authors of our MitoEAGLE Position Statement.
::::: We recieved an interesting reply from CELL METABOLISM (see preprints main page). We will send them the MS.
 
* 2018-02-12 Jadiya P
::::* I have gone through the preprint version and its really nice compilation of our current understanding of the mitochondrial physiology as well as related terminology. In the Box1, Line 229, it would be great to add one sentence for the endoplasmic reticulum and mitochondrial contacts as these contact sites involved in metabolites transfer as well as mitochondrial dynamics regulation.
::::: "The crosstalk between mitochondria and endoplasmic reticulum are involved in the regulation of various cellular functions, such as calcium homeostasis, cell division, autophagy, differentiation, anti-viral signaling, and others (Murley and Nunnari 2016)".
::::: Ref: Murley A, Nunnari J (2016) The Emerging Network of Mitochondria-Organelle Contacts. Mol Cell 61(5):648-653.
::::: ''[[Gnaiger E]]'': Many thanks for your contribution, which I added according to your suggestion (line 217). Thanks for joining our initiative as a co-author.
 
* 2018-02-12 [[Keijer J]]
::::* I has become a balanced and high quality document. Nevertheless still some comments. Please find these [http://www.mitoeagle.org/images/b/b0/Comments_jaap_keijer_preprint_20180208.pdf attached] (written in the scan and I added only the pages with comments). Please find also an alternative [http://www.mitoeagle.org/index.php/File:Keijer_Abstract_suggestion.docx abstract], which is slightly altered (improved) over the one pasted in the scan.
::::: ''[[Gnaiger E]]'': Thank you very much, your input is much appreciated and largely included in the new ms version. We have an interesting reply from CELL METABOLISM (see[[MitoEAGLE_preprint_2018-02-08#Answers| here]]). We will send them the MS.
 
* 2018-02-12 [[Spinazzi M]]
::::* I believe there is strong need for such armonization procedure.
::::: A detail regarding it. I would personally propose to redefine the electron transfer capacity as ETC rather than ETS –it is less confusing.
 
* 2018-02-12 [[Trougakos IP]]
::::* Thank you for the email and the attached paper.
::::: I found the paper really very informative and as discussed before the initiative is very much needed and timely.
::::: At this point I have no further input; we do have some papers in Revision and if we get them through I will send the citations for adding in this Review paper.
::::: ''[[Gnaiger E]]:'' On ET- versus ETS-capacity. I also like ETS better. BUT: There is the OXPHOS system, and we do not say ‘OXPHOS system capacity’. There is the ET system – we should say ET-capacity.
 
* 2018-02-12 [[Vyssokikh MY]]
::::* It's a pleasure to participate in such interesting project for me, thank You for invitation!
 
* 2018-02-10 [[Coen PM]]
::::* A suggestion is to post something similar to relevant sections at the American Physiological Society. (http://connect.the-aps.org/home). You could probably sent this to all sections, but I’m pretty sure there would be interest from members of the endocrinology and metabolism and exercise physiology sections.
 
* 2018-02-10 [[Tretter L]]
::::* I would send it to the editor in Chief of Mitochondrion. Is it OK?
::::: ''[[Gnaiger E]]'':Excellent – thanks
 
* 2018-02-09 [[Arnould T]]
::::* the demand specifies to send the information to Editors of Journals that I know. I could do that for J. Cellular Physiology but do not you expect a higher and more poweful journal to publish this excellent paper ? In addition, the timing....would be bfore you submit or after...
 
* 2018-02-09 [[Dias T]]
::::* I want to congratulate you and all the co-authors for the excellent work. The manuscript has highly improved since my last reading. I am sending some minor suggestions annotated in the [http://www.mitoeagle.org/images/2/25/MitoEAGLE_preprint_2018-02-08_TRD.pdf attached pdf file]. Thank you very much for the collaboration,
::::: ''[[Gnaiger E]]'': Thank you for your kind feedback and for the careful reading with excellent improvements – obviously you are a professional science writer. I have incorportated your suggestions in the new version 24.
 
* 2018-02-09 [[Keijer J]]
::::* I think Cell Metabolism is hardly possible. Did you consider JBC (with John Demu as editor for mitochondria) or Nature Communications? Maybe also Molecular Metabolism, but that may be too little physiological.
 
* 2018-02-09 [[Koopman WJ]]
::::* Will have a look.
 
* 2018-02-09 [[Lerfall J]]
::::* Off course! I can prepare a letter and forward this message to actual editors whom I know.
 
* 2018-02-09 [[Pardo Andreu GL]]
::::* Sure Erich. I will send it to a couple of editors. I will keep you informed.
 
* 2018-02-09 [[Saada A]]
::::* OK- I sent the letter to an editor of JIMD
 
* 2018-02-09 [[Valentine JM]]
::::* The manuscript looks fantastic and I am very excited about it. Just a couple of comments. In the section on standardization. It is well outlined how proper standardization should be conducted; however in the manuscript we do not say, which method of standardization to use. For instance, flux can be normalized to wet weight or dry weight of the tissue (for permeabilized fibers) but we do not say which to use and the flux per mass values are very different depending on which you use. There is a lot more variability in weight wet measurements due to how much drying researcher does. Also, most scales are not accurate enough for measuring 1-2mg pieces of tissue and weighing the sample three times can give much more consistent values. If measurements are off by just one or even less than one mg when weighing a 1mg piece of muscle, then values can have double or half the respiration rates when normalizing to mass. Also, I recommend in the paper suggesting all raw data should be published in a supplemental table. This way anyone can access and compare values. Also, while the limitations of the normalizing factors are discussed in detail, we should specify which marker of mitochondrial content (CS activity mtDNA copy number) to use for normalizing. It may be important to explain that when phosphorylation is not limiting oxygen consumption such as in mouse permeabilized muscle fibers the addition of uncouplers does not increase oxygen flux; therefore, when generating flux control ratios using CI+CII_E to normalize to becomes confusing because CI+CII_P will also equal 1.
::::: As far as journals go, I think that diabetes would be a good journal to submit to if cell metabolism does not work out. Although it is limited to this one metabolic disorder nearly every researcher studying mitochondrial physiology have published in this journal.
::::: Another possible journal is EMBO as the word mitochondria turns up over 1500 articles and is a well read journal.
::::: ''[[Gnaiger E]]'': Thank you for your valuable comments. I agree with you, that recommendations on wet weight versus dry weight should be given. In fact, a MitoEAGLE Task Group is working on this to provide a comparative experimental basis for evaluation and a corresponding recommendation. This will be summarized in a separate MitoEAGLE position paper. Similarly, a recommendation on the ‘best’ mt-marker would be helpful, if such a best marker does exist. The present MS may contribute to make us more aware on the importance of paying critical attention to mt-markers. A insufficiently substantiated recommendation, however, would not help and weaken the impact of our manuscript.
::::: Ps: We are working on nomenclature of the pathway states. I regret to have introduced the CI+II nomenclature (but CI+CII is different), hence we replaced it with a less difficult terminology:
::::::* Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers. Sci Rep 7:2840, DOI:10.1038/s41598-017-02789-8. - http://www.bioblast.at/index.php/Lemieux_2017_Sci_Rep
::::: [[Valentine JM]]: I agree and I am excited to contribute to this critical work in any way possible. Please let me know what I can do!!! Thank you for the reference paper. 
 
* 2018-02-08 [[Ahn B]]
::::* I am happy to send a letter to editors. I came up with four editors from their Cell Metab website. They are Martin Brand, Michael Murphy, Nils-Goran Larsson, and Varnsi Mootha. I wanted to see if you suggest anyone else who I might include in the email as this will have an impact on our paper. I am happy with your template and will send it as is. I would also like to confirm that you want me to use the email address of [email protected] instead of individual emails of relevant editors.
* 2018-02-08 [[Battino M]]
::::* I'll do it with pleasure
 
* 2018-02-08 [[Casado Pinna M]]
::::* Of course that I will send the letter to the known editors. I would appreciate if you would confirm if the idea is to send to Cell Metabolism or any journal that you know that includes studies of mitochondria such as Sci report, Hepatology, BBA, etc.
 
* 2018-02-08 [[Genova ML]]
::::* As you requested, I will think of possible Journal Editors (e.g. I am familiar with U. Brandt-BBA bioenergetis, but I suppose that you already asked him; if not, please let me know). Meanwhile, I wonder if you would like to consider also the possibility of submitting the same inquiry to the "Scientific Committee of the World Mitochondria Society", whose annual conference will be held as usual in Berlin (next date: October 2018 - https://www.targeting-mitochondria.com/)
 
* 2018-02-08 [[Labieniec-Watala M]]
::::* I have just looked at the preprint very quickly and I see many changes 😊 Wow! Very, very good job! During next days I will be reading it carefully. Now I am thinking about the journal where this review could be sent. So, in my opinion, this manuscript is excellent and you may consider to send it i.e. here ? :) ... Nature Methods, IF >25; of course earlier writing to editor
 
* 2018-02-08 [[Leeuwenburgh C]]
::::* Will do and send to other editors. I am the editor of experimental gerontology. Have you considered to publish this in a methods journal?
 
* 2018-02-08 [[Muntane J]]
::::* Thank you very much, I will send the input of the editors.
 
* 2018-02-08 [[Procaccio V]]
::::* Great initiative. I will send the letter to the editors I know and will come back to you. Again thanks again for your efforts
 
* 2018-02-08 [[Tomar D]]
::::* Many thanks for the information. I will disseminate the information.
::::: '''sent to ''': [email protected]
 
* 2018-02-08 [[Tronstad KJ]]
::::* I know Keshav K Singh, Editor-in-chief of “Mitochondrion”, but I guess he might have been contacted  already?
 
* 2018-02-08 [[Ventura N]]
::::* Id be happy to forward the letter to Editors
 
* 2018-02-08 [[Wei YH]]
::::* Thank you very much for your great effort in revising the manuscript and for sending me the revised version of this article that we have co-authored last year! It has been greatly improved!
 
* 2018-02-08 [[Zullo S]]
::::* Yes, thanks for this and the preprint earlier. I will try to get it done by early next week.
 
 
* MitoEAGLE preprint 2018-02-08 Version 22

Latest revision as of 23:44, 25 January 2021

Nature Metabolism: NATMETAB-A19071509A Out to Review

Dear Prof Gnaiger,
Thank you for submitting your manuscript "Mitochondrial respiratory states and rates" to Nature Metabolism. I am pleased to tell you that we are sending your paper out for formal peer review.
If you have not done so already, please alert us to any related manuscripts from your group that are under consideration or in press at other journals, or are being written up for submission to other journals (see www.nature.com/authors/policies/duplicate.html for details).
We are trying to improve the quality of methods and statistics reporting in our papers. To that end, we are asking all life sciences authors to complete two items: an editorial policy checklist that verifies compliance with all required editorial policies and a reporting summary that collects information on experimental design and reagents.
Reporting summary: https://www.nature.com/documents/nr-reporting-summary.pdf
Editorial policy checklist: https://www.nature.com/documents/nr-editorial-policy-checklist.pdf
Please complete the relevant forms and return them within 48 hours. Please note that these forms are dynamic ‘smart pdfs’ and must therefore be downloaded and completed in Adobe Reader. We will then flatten them for ease of use by the reviewers. If you would like to reference the guidance text as you complete the template, please access these flattened versions at www.nature.com/authors/policies/availability.html
All points on the policy checklist must be addressed; if needed, please send me a new version of the manuscript with your completed checklist.
Finally, we would like to inform you that on a case by case basis we coordinate a brief consultation between referees and editors after all referee reports have been received. This is to improve the peer review process and the feedback provided to authors. Referees are given the opportunity to make comments on their peers’ concerns and update their reports to comment on issues raised by the other reviewers. If we feel it would be helpful, we will engage reviewers in this additional consultation with the goal of providing you with the most valuable feedback possible.
We will be in touch again as soon as we have received comments from our referees. In the meantime - the status of your manuscript can be followed in the manuscript tracking system.
Best regards,
Dr. Christoph Schmitt
Chief Editor
Nature Metabolism


Version 5


Version 5 for discussion

MitoFit pdf

Mitochondrial respiratory states and rates



Version 5 (v5) 2019-07-12 File:Gnaiger 2019 MitoFit Preprint Arch doi 10.26124 mitofit 190001.v5(in prep).pdf

Version 5 (v5) 2019-06-24 File:Gnaiger 2019 MitoFit Preprint Arch doi 10.26124 mitofit 190001.v5(in prep).pdf

Relevant changes
2019-07-24 Updates according to feedback from Gonzalez-Franquesa A and Fig. 1 edited by Bravo RF.
2019-07-12 Erich Gnaiger: A comment on 'Complex V' is added to Table 8:
Respiratory ET Complexes are redox proton pumps; Figure 2B; ATP synthase is not a redox proton pump of the ETS, hence the term Complex V should not be used
2019-06-24 Erich Gnaiger
1. ce: The term "Intact cells" has been replaced by "Living cells".
Rationale: see Table 5.
2. "Extra-mitochondrial" has been changed to "Extramitochondrial".
Compare: extracellular.
3. ""Excess E-P capacity has been changed to "ET-excess capacity, E-P".
Rationale: E-P is the excess capacity of E over P, but not excess over E-P.
4. The symbol "pmf" for protonmotive force has be replaced by pmF.
Rationale: (1) Italics are used for symbols of physicochemical quantities. (2) F but not f is the IUPAC symbol for force.
Added reference
  1. Ling C, Rönn T (2019) Epigenetics in human obesity and type 2 diabetes. Cell Metab 29:1028-44. https://doi.org/10.1016/j.cmet.2019.03.009. - »Bioblast link«
Coauthors: Version 4: 542; present: 611


ICJMD: Defining the role of authors and contributors

"Some large multi-author groups designate authorship by a group name, with or without the names of individuals. When submitting a manuscript authored by a group, the corresponding author should specify the group name if one exists, and clearly identify the group members who can take credit and responsibility for the work as authors. The byline of the article identifies who is directly responsible for the manuscript, and MEDLINE lists as authors whichever names appear on the byline. If the byline includes a group name, MEDLINE will list the names of individual group members who are authors or who are collaborators, sometimes called non-author contributors, if there is a note associated with the byline clearly stating that the individual names are elsewhere in the paper and whether those names are authors or collaborators." - Downloaded from www.icmje.org 2019-01-04


Comments

  • At the beginning of page 7 (In Box1), it is mentioned the crosstalk between ER and mitochondria. I think it should be included that this interaction plays an important role also in lipid transport and biosynthesis. The second comment regards the mechanisms of respiratory uncoupling and in particular the acoupled respiration described in Fig 3, page 14 and table 2. The acoupled respiration is described as the respiration occurring in “non-compartmental mitochondrial fragments”. May be this concept could be explain further, since I think that acoupled respiration can refer to just fragments of the inner mitochondrial membrane but also mitoplasts (obtained by mitochondria swelling in hypotonic buffer). So, acoupled respiration could refer to cases in which the integrity of either only the outer membrane or both inner and outer membrane is compromised. ~ Fontanesi F
  • I am happy to confirm that the pre-print has no flaws that I could see. It is truly an excellent work, for sure a manuscript of reference. ~ Teodoro J
  • I have been following the MitoEAGLE preprint on mitochondrial respiration, as well as the different comments. First of all, I am really interested in this topic, since as a student I already had troubles comparing different papers with different respiratory states, and this is a great opportunity to finally harmonize all the mitochondrial respiration experiments and publications. Pablo invited me to re-read it and make comments to contribute to the final final version. This would be a great honor, since this will be a reference paper in the future for experimental design and data reporting. .. I think it is a really elegant publication, with a lot of detail, but this is needed for the mitochondrial community to settle bases of nomenclature and harmonization. ~ Gonzalez-Franquesa A
  • Finally, I took the time to read the “Mitochondria States and Rates” preprint during the flight back home, I have one small comment: at the bottom of page 14, below table I, I get a bit confused all the way in this paragraph, but mostly by the part starting as “Defined coupling states are induced by…” (4 lines from the bottom). Somehow the points 1-4 that follow seem to refer to the states described in Table 1 above. If so, it may be clearer to arrange these points in the same order: seems that uncoupling (point 4) should go before inhibition of phosphorylation pathways (point 3) – I hope I’m not wrong for this? More generally, it might be useful for less advanced reader to relate the different parts of this paragraph to the states described in table I, following the same order given in the table: LEAK, OXPHOS, ET, ROX. As it is this paragraph starts with OXPHOS, then ET, then LEAK, with point 3 in the final description apparently being ROX. ~ Joseph V
Gnaiger E: Many thanks for your positive feedback. Your suggestions for the MitoEAGLE white paper are very helpful. See the file (in prep for Version 5) for discussion: See pp. 14-15 for the re-arrangements. I hope that the confusion is now taken away – let me know.
  • Nevertheless below some suggestions and remarks from my side, maybe you can use them for a revision. And of course I would be glad to see my favorite proteins mentioned (CK, NDPK, recent reviews attached). ~ Schlattner U
  • Please find (attached) my comments. I am glad to be part of this endeavour, which necessity is becoming increasingly clear every years! ~ Munro D
  • Fantastic initiative with the new mitochondrial physiology preprint server! ~ Donnelly C
  • It is quite surprising that the final manuscript was not accepted in BioRvix. I completely agree with MitoFit Preprints. ~ Singh BK
  • It will be a pleasure to join the MitoEagle task group publication. ~ Laranjinha J
  • I have a small remark : the concept of multiple authors signature started to be contested... By all ETHICS commities everywhere in Europa at least since it overpassed the usual rules... And also altered the signification of the authors impact factor. The regulation will be to form a consortium that is the true entity that will sign the collective work. That is teh best for teh COST since all members are easily identifiables. Overall conmment: This paper has been stanfding to long.... on teh bench! Petit PX
  • I just found a minor typo. If you look at the “S” references, they are out of alphabetical order. ~ Sparagna GC
  • Please find attached manuscript with comments (I have made 5 in total). Feel free to incorporate (or ignore) as you see fit! ~ McKenzie M
  • Gnaiger E: To address your comment “Interesting that you state saturating O2, as this is only at the start of an experiment? (but is accounted for in the oxygraph calibration with dithionite, so that measured respiration rates are relative to saturating O2?).”, I extended Section 2.1.2: “Kinetically-saturated conditions are evaluated by substrate kinetics to obtain the maximum reaction velocity or maximum pathway flux, in contrast to solubility-saturated conditions.”
We are in direct contact with Kyle Hoehn to obtain and test their uncouplers.
To summarize your comment “So would it be optimal in publications to not only state final flux rates/unit sample (e.g per mg) but also the raw flux rates (per mL) and the mg of sample used?”, I extended Box 3:Box 3: Recommendations for studies with mitochondrial preparations
● Normalization of respiratory rates should be provided as far as possible:
A. Sample normalization
1. Object-specific biophysical normalization: on a per organism or per cell basis as O2 flow; this may not be possible when dealing with coenocytic organisms, e.g., filamentous fungi, or tissues without cross-walls separating individual cells, e.g., muscle fibers.
2. Size-specific cellular normalization: per g protein; per organism-, cell- or tissue-mass as mass-specific O2 flux; per cell volume as cell volume-specific flux.
3. Mitochondrial normalization: per mitochondrial marker as mt-specific flux.
B. Chamber normalization
1. Chamber volume-specific flux, JV [pmol∙s-1∙mL-1], is reported for quality control in relation to instrumental sensitivity and limit of detection of volume-specific flux.
2. Sample concentration in the instrumental chamber is reported as number concentration, mass concentration, or mitochondrial concentration; this is a component of the measuring conditions.
With information on cell size and the use of multiple normalizations, maximum potential information is available (Renner et al. 2003; Wagner et al. 2011; Gnaiger 2014). Reporting flow in a respiratory chamber [nmol∙s-1] is discouraged, since it restricts the analysis to intra-experimental comparison of relative (qualitative) differences.
  • I am happy to see that we are one step closer to the final publication of the MitoEAGLE manuscript in a journal. ~ Komlodi T
  • It is a great step towards the publication of the manuscript and congratulations for creating your own tool to circumvent decisions that can not be easily understood. ~ Thierry A
  • Excellent article and one of its kind too. Please let me how can i help to get it published in a high impact j. Look forward to work in your team. ~ Sharma P
  • It's great to see the preprint. The preprint server in the area of mitochondrial physiology is a great idea and definitely will be a success. ~ Tomar D
  • First and foremost I would like to express my deepest gratitude and would like to thank you for giving us your time to review our manuscript and be part of us as the co-author. It is a great honour to get you in touch and reply promptly. .. I would like to also thank you for giving me the opportunity to be part of the MitoEAGLE as one of the co-authors and I am happy to be listed in the next version of the preprint. ~ Hassan H
  • However - just a note about pre-prints. A significant portion of scientists that I collaborate with feel uncomfortable submitting manuscript on a pre-print server. Is this something that could be addressed maybe in an article regarding the benefits and nuances of pre-print server submission. ~ Towheed A
Journal submission comments
  • Cell Metabolism seems like a good first choice. ~ Williams C
  • Cell Metabolism, I think this is a good choice. ~ Rossiter HB
  • Cell Metabolism seems highly appropriate. ~ Newsom SA
  • No preference. Just go ahead. ~ Zaugg M
  • I concur with the choice of cell metabolism. ~ Pulinilkunnil T
  • I think cell metabolism would be great, but I doubt whether it is realistic. Possibly Molecular Metabolism (very rapid, good reputation, european), Cell and Molecular Life Sciences (many reviews) or BBA- bioenergetics could be alternatives. ~ Keijer J
  • Alternatives if Cell Met is not accepting: Nature metabolism or Acta physiologica. ~ Amati F
  • And Cell met is a good 1st choice for this publication. ~ Zanou N
  • The question is why did Biorxiv reject the manuscript? Before submitting to a prestigious journal like Cell Metabolism all the doubts Biorxiv had should be ruled out. ~ Methner A
  • And I think that Cell Metabolism is a good first journal choice for submission of our manuscript. ~ Breton S
  • Cell Metabolism is a good option as a first submission. ~ Bouitbir J
  • Cell metabolism is a good fit for the manuscript. ~ Adiele RC
  • The choice of journal is excellent, although it might be a long shot. ~ Oliveira MT
  • I guess that also TIBs or Current Biology could be considered. ~ Calabria E
  • I am in agreement that the first journal will be Cell Metabolism. ~ Victor VM
  • Cell metabolism is an excellent choice. If they are interested that would be wonderfull. Physiological Reviews could be an alternative, in case Cell metabolism declines the manuscript. ~ Thierry A
  • I would suggest to try the submission in Cell Metabolism. ~ Doerrier C
  • Regarding the future submission of our paper, if there is already a pre-acceptance of the Editor of Cell Metabolism, I believe we should submit there. There are not many journals willing to publish a paper with so many authors, and the reviewing process will not be easy, in my opinion. ~ Crisostomo L
  • I think cell metabolism is a good target to submit our article. ~ Salin K
  • I would format accurately as a resource manuscript for Cell Metabolism. ~ Lavery GG
  • The manuscript is still extremely long. In my modest opinion too long compared to the editorial format limits of many journals. If the manuscript cannot be substantially shortened to the essentials (in my opinion preferable) one strategy is to try to find a journal without such limits. ~ Spinazzi M
  • I am happy with Cell Metabolism to start the submission process of this preprint. ~ Moisoi N

2019-07-22 Circular to coauthors

Re: MitoEAGLE preprint on ‘Mitochondrial respiratory states and rates’
Dear coauthors,
The recent MiP/MitoEAGLE Training School in Coimbra provided another excellent opportunity to present the concept of our ‘States and rates’ white paper, to discuss it with several students and scientists who joined as additional coauthors, and to take a decision on journal submission.
1. Preprint version 5 (in prep) is now available for your evaluation before proceeding with journal submission. At this stage, the MitoFit Preprint version 5 (in prep) has not yet a DOI, to allow final changes to be made according to the immediate feedback received upon this circular. The latest changes are listed on the website, minor changes and improvements are included in the manuscript:
» www.mitofit.org/index.php/Talk:Gnaiger_2019_MitoFit_Preprint_Arch
2. Please finally check your personal page for any corrections to be made in your initials and affiliations.
3. Feel free to invite additional colleagues to evaluate our white paper and join as coauthors.
4. We have announced the plan for journal submission for quite some time, but the number of coauthors increased to 612 and many discussions lead to further improvement of the manuscript. Our first goal for submission has been ‘Cell Metabolism’. Since then, the new journal ‘Nature Metabolism’ was launched. Feedback from several coauthors, and the interest of the editor of ‘Nature Metabolism’ in our white paper, has led to a change in the strategy, to submit primarily to the European journal ‘Nature Metabolism’, since the COST Action MitoEAGLE is a European project-with worldwide participation.
With many thanks for your contributions and for supporting the MitoEAGLE project,
Erich
Erich Gnaiger, Ph.D.
Chair COST Action MitoEAGLE
[email protected] | www.mitoeagle.org


2019-03-12 Circular to coauthors

Re: MitoFit_Preprint_Archives
Dear coauthors,
We thank you for the feedback received to our previous circular. Here is the summary of 176 answers to the three questions on preprints, which encourages us to proceed with MitoFit Preprint Archives:
» Summary on preprint questionnaire
The Scientific Advisory Board has expanded, and we thank all MitoEAGLE members who have joined the International Board. Again we extend our invitation to join the editorial team. In particular, we would like to establish a Member Advisory Board including scientific organizations and journals which support the concept of MitoFit Preprints. If you are involved in such an organization, please let us know if joining the 'Member Advisory Board' might be an option for your organization.
Information on next steps for our manuscript on 'Mitochondrial respiratory states and rates' will follow soon.
Kind regards,
Erich
Chair COST Action CA15203 MitoEAGLE
[email protected] | www.mitoeagle.org


2019-02-12 Circular to coauthors

Dear coauthors,
The MitoEAGLE manuscript on ‘Mitochondrial respiratory states and rates’ is now published in MitoFit Preprint Archives as a preprint citable with DOI number with 530 coauthors. The next step will be journal submission:
» http://wiki.oroboros.at/index.php/MitoFit_Preprint_Arch
Why a new preprint server MitoFit Preprints? – On 2018-12-12 the MitoEAGLE manuscript was submitted to the preprint server www.biorxiv.org/. We are amazed that our manuscript was not accepted:
» http://www.mitoeagle.org/index.php/Talk:MitoEAGLE_preprint_States_and_rates#BIORXIV
Instead of starting a debate with bioRxiv we started MitoFit Preprints (originally MitoFit Preprint Archives) - the Open Access preprint server for mitochondrial physiology
The first DOI number was allocated to our MitoEAGLE manuscript.
Your opinion means a lot to us. Therefore we would like to ask you:
  1. Are you familiar with the concepts of preprints? Y / N
  2. Will you consider to submit a manuscript to MitoFit Preprints for publication as a preprint? Y / N
  3. Which alternative preprint server do you prefer? ___________
The results of this questionnaire will be summarized anonymously on our website (beginning of March).
We thank you for answering these questions in advance and are looking forward to your feedback. In particular, do you have further suggestions for our first journal choice for submission of our manuscript (Cell Metabolism)?
In the spirit of the bottom-up approach of MitoEAGLE, this is an invitation to join the editorial team (Scientific Advisory Board) of MitoFit Preprints.
Best regards,
Erich Gnaiger
Chair COST Action CA15203 MitoEAGLE
[email protected] | www.mitoeagle.org


  • 2019-02-12: MitoEAGLE Task Group on 'Mitochondrial resipratory states and rates'
MitoEAGLE: States and rates - the preprint is citable with DOI number and getting ready for journal submission
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