Talk:Gnaiger 2019 MitoFit Preprints

» MitoEAGLE preprint 2018-02-08

Phase 3: MitoEAGLE preprint 2018-02-08

• 2018-02-15 Gnaiger E Version 24.

Fig. 9. Mitochondrial recovery, Y_mtE, in preparation of isolated mitochondria.

Towards a shorter version: Old Fig. 9 was removed.

• 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
• Change of title: Mitochondrial respiratory states and rates
• 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, ΔΨ, and chemical potential differences, Δμ_H+, 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'.

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.

With many thanks for your collaboration, Erich

• 2018-02-06 Gnaiger E 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 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 next version and final manuscript. This section should become a topic of discussion within Working Group 1 of the MitoEAGLE consortium, following a primary peer-reviewed publication of the concept of stoichiometric potential differences.

Further references

• Bergeson_1981_West_J_Med
• Wheatley_2011_Metrologia

Contacted editors

Updated 2018-02-12

• Biochem J
• Cell Metabolism
• Elsevier

Life Sciences

BBA Bioenergetics - Journal

Platelets

Pharmacological Research

Journal of Physiology and Biochemistry

• FEBS Journal
• FEBS Lett
• Int. J. Biol. Macromol.
• Journal of Experimental Biology
• J Physiol
• Mitochondrion: Keshav K. Singh
• PLOSOne

Phase 3.1: Discussion

• 2018-02-17 Liu J

• 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 E: I would be very thankful for receiving your comments and critical evaluation of the present version of our manuscript.

• 2018-02-16 Gnaiger E

• Dear Anthony, Pushpa did a great job. Here is a first-level promising answer (see 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

• [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 here). We will send them the MS.

• 2018-02-13 Lemieux H

• Here are a few additinal comments on the review (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 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 attached (written in the scan and I added only the pages with comments). Please find also an alternative 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 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.

• 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 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