Peer Review History
| Original SubmissionMarch 5, 2020 |
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PONE-D-20-06479 Stress-Dependent Conformational Changes of Artemin: Effects of Heat and Oxidant PLOS ONE Dear Dr. H. Sajedi, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. After careful evaluation of your manuscript and based on the comments received from the potential reviewers, I decided to give your manuscript a further chance. Please consider all the comments/suggestions, especially those of the reference 1. Also, it is necessary to improve the language of your manuscript to an acceptable level. Please submit your revised manuscript by Aug 02 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Reza Yousefi, Ph.D Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: "This work was supported by the research council of Tarbiat Modares University and Ministry of Sciences, Researches, and Technology, Iran." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The author(s) received no specific funding for this work." 4. Thank you for stating the following in the Competing Interests section: "NO authors have competing interests" We note that one or more of the authors are employed by a commercial company: Mah Behin Gene Gostaran Company. 4.1. Please provide an amended Funding Statement declaring this commercial affiliation, as well as a statement regarding the Role of Funders in your study. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study. You can update author roles in the Author Contributions section of the online submission form. Please also include the following statement within your amended Funding Statement. “The funder provided support in the form of salaries for authors [insert relevant initials], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.” If your commercial affiliation did play a role in your study, please state and explain this role within your updated Funding Statement. 4.2. Please also provide an updated Competing Interests Statement declaring this commercial affiliation along with any other relevant declarations relating to employment, consultancy, patents, products in development, or marketed products, etc. Within your Competing Interests Statement, please confirm that this commercial affiliation does not alter your adherence to all PLOS ONE policies on sharing data and materials by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests) . If this adherence statement is not accurate and there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Please include both an updated Funding Statement and Competing Interests Statement in your cover letter. We will change the online submission form on your behalf. Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests 5. Please ensure that you refer to Figure 'Graphical Abstract' in your text as, if accepted, production will need this reference to link the reader to the figure. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: No Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: N/A ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No Reviewer #2: No ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: No Reviewer #2: No ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Sajed et al. present results on the effect of heat and H2O2 on artemin, a protein from Artemia involved in survival of neurons. Despite the large number of experimental tools, there is a lack of experimental and interpretative rigor in the techniques used. For these reasons, some of which are detailed below, the conclusions reported in the text are not supported by the experimental results. In addition to these observations, the novelty of the work is not clear. What is really the applied outcome of the work? The current work has added additional information to artemin knowledge or not. In conclusion, it is not possible to recommend acceptance of the manuscript. Majors: -What is the quality/state of the produced protein? Is the protein folded (include circular dichroism spectra)? Is the protein aggregated (include gel filtration information)? Is there a SDS-PAGE of the preparation that can be evaluated? The second (Fig 2A) and seventh (Fig. 2B) lanes are likely to refer to the produced protein. It seems to show the presence of monomer, dimer and a very large aggregate. Is it possible to separate those species by gel filtration chromatography? In this case, are the species states reversible? Why are the bands at very high concentration SDS-resistant? -Have the authors considered aggregation/precipitation as a function of temperature-induced unfolding-refolding, and also after H2O2 treatment? See for instance: 1)Fig2A: samples at 70 and 80C have much less protein than the other lanes (authors need to use a software tool such as ImageJ to evaluate protein quantity in each lane). 2)Fig.2B: same ´protein missing problem´; samples DTT+GA- and DTT-GA+ have much less proteins than the others. 3)Figs 5 and 7 have the same problem. Same ´protein missing problem´ in many lanes. 4)Fig.3. Distributions ate 70 and 80C are so thin that it may indicate protein precipitated that was not recovered. This is a very important issue because it may explain the decrease in fluorescence in Figs1A and 4A (protein precipitated that was not recovered). -Fluorescence. 1)An amino acid sequence should be added to help quantify the amount of Tyr and Trp. Authors state that Fig1A refers to ´Trp fluorescence emission´ but Tyr residues, if present, also contribute to emitted fluorescence. 2)The intensity of Trp fluorescence is temperature-dependent. Any study of heat-induced unfolding followed by Trp fluorescence has to present a curve control using N-acetyl-tryptophanamide (NATA) at the same buffer (there are plenty of book chapter and reviews about the topic). The authors need to comment on that. 3)Figs. 4A and 6A: Trp fluorescence is quenched by hydrogen peroxide. Is there a control to the experiments? 5)What is the rational for the bis-ANS concentration used? Is there a bis-ANS titration experiment to be evaluated? -SDS-PAGE figures are of low quality and have little information about protein quantity. See that even the loaded marker has a band of very high molecular mass (Fig. 7 is the worse). Additionally, authors need to use a software tool such as ImageJ to evaluate protein quantity in each lane. -Chaperone activity. Data seem to have some potential but it measures no refolding, maybe it probes protection against aggregation. To probe refolding, authors need to show that lysozyme regain its folded state (CD, NMR, enzymology, other). But even protection against aggregation seem to be minor, 20% or less. Minors: -Protein concentration should be given in micromolar to facilitate understanding of the amount of additives used. -Material and Methods description lack some information, as for instance the temperature of some experiments. Reviewer #2: This study examined the effects of temperature and an oxidizing agent (hydrogen peroxide) on the structure and chaperoning capacity of the brine shrimp protein artemin. This molecular chaperone has received a great deal of study in the past, and the present work is thus built on a large foundation of information. The principal contribution of these new data is the demonstration of how changes in oligomerization of artemin are driven by temperature and oxidative state, and how these structural changes lead to influences on chaperone potential. Activation of artemin relies chiefly on temperature-induced alterations in conformation that favor dimerization of the protein. Disulfide bridges between artemin monomers are shown to play important roles in the dimerization process. The work involves a large and diverse set of experiments, but the conclusions are nicely summarized in the two “schemes” the authors provide. The experimental work appears to have been done carefully and the interpretations of the findings are well-supported by the results. The writing is generally clear, but there are dozens of errors in syntax and grammar that need to be corrected. My main criticism of the paper is that the authors make no effort to link these in vitro findings to the biology of the organism itself. For example, they provide no information on the temperatures that the cysts of the shrimp experience under natural field conditions. Thus, it is not possible to determine whether the experimental conditions used with the isolated protein resemble the thermal conditions found in nature. I am concerned that some of the effects on the protein that were manifested under extremes of stress, notably some of the highest experimental temperatures, would never occur in the actual organism. In summary, whereas the in vitro biochemistry here is of high quality and yields interesting results, there is no way of determining whether these results, notably the stress-driven changes in dimerization state, actually occur in nature. The authors should try to link their in vitro findings to in vivo phenomena. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 1 |
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PONE-D-20-06479R1 Stress-dependent conformational changes of artemin: effects of heat and oxidant PLOS ONE Dear Dr. Sajedi, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. ============================== Your article will be accepted if the following changes are applied correctly. 1. The numbers identifying the affiliations of authors are not used correctly. 2. The language of this manuscript still needs significant improvement. Below please find some examples of typo grammatical errors which must be fixed. Abstract section, lines 3-6, the sentence needs amending. Pg.4, line 2: moderates should be replaced with modulates. Pg.6, line 5: Microtubule must be corrected as micro tube. 3. Length of the final conclusion needs to be greatly shortened and additional and repetitive explanations must to be avoided. 4. While drawing the GA and Scheme 1, if more than one color is used, it will probably be easier for readers to understand the messages. .============================== Please submit your revised manuscript by Dec 03 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Reza Yousefi, Ph.D Academic Editor PLOS ONE Additional Editor Comments (if provided): Your article will be accepted if the following changes are applied correctly. 1) The numbers identifying the affiliations of authors are not used correctly. 2) The language of this manuscript still needs significant improvement. Below please find some examples of typo grammatical errors which must be fixed. Abstract section, lines 3-6, the sentence needs amending. Pg.4, line 2: moderates should be replaced with modulates. Pg.6, line 5: Microtubule must be corrected as micro tube. 3) Length of the final conclusion needs to be greatly shortened and additional and repetitive explanations must to be avoided. 4) While drawing the GA and Scheme 1, if more than one color is used, it will probably be easier for readers to understand their messages. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #3: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #3: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #3: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #3: No comment. In my opinion, all of the points raised in the first revision were addressed by the authors. Accordingly, the manuscript is acceptable for publication in PLOS ONE. ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #3: Yes: Mohsen Asghari [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 2 |
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Stress-dependent conformational changes of artemin: effects of heat and oxidant PONE-D-20-06479R2 Dear Professor Sajedi, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Reza Yousefi, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-20-06479R2 Stress-dependent conformational changes of artemin: effects of heat and oxidant Dear Dr. Sajedi: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Professor Reza Yousefi Academic Editor PLOS ONE |
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