Talk:Gnaiger 2019 MitoFit Preprints

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).

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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

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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

• 2019-07-24 Gnaiger 2019 MitoFit Preprint Arch

Version 5 for discussion

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 ce: The term "Intact cells" has been replaced by "Living cells".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

• FAQ - MitoPedia:Preprint

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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