Peer Review History
Original SubmissionSeptember 10, 2022 |
---|
PONE-D-22-25226Nanoparticulate air pollution disrupts proteostasis in Caenorhabditis elegansPLOS ONE Dear Dr. Kikis, 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. Please submit your revised manuscript by Jan 1, 2023. 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Mahesh Narayan, 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. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels.
In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: "We would like to thank the laboratory of Caleb E. Finch and the University of Southern California for generously providing us with nPM. We would also like to thank members of the Kikis lab, especially Prisha Rajasekaran and Jeremiah Studivant for technical support and also for their careful reading and thoughtful comments and discussion of this manuscript. This research project was supported in part by the Emory University Integrated Cellular Imaging Core and some strains were provided by the CGC, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). The content is solely the responsibility of the authors and does not necessarily reflect the official views of the National Institute of Health." 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: "E.A.K was supported by a Faculty Fellowship from the Appalachian College Association and by two internal grants, a Faculty Development Grant and a Faculty Summer Research Stipend, from the University of the South. B.A.G.M, J.A.P., and C.A.S. were funded by Sewanee Undergraduate Research Fellowships. The CGC, which provides some strains used in this study, and the Emory University Integrated Cellular Imaging Core, which provided microscopy services, were funded by the National Institutes of Health. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Please include your amended statements within your cover letter; we will change the online submission form on your behalf Additional Editor Comments (if provided): Dear Dr. Kikis Please see the reviewers comments and respond accordingly for further consideration of your MS sincerely MN [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript adhere to the experimental procedures and analyses described in the Registered Report Protocol? If the manuscript reports any deviations from the planned experimental procedures and analyses, those must be reasonable and adequately justified. Reviewer #1: Yes Reviewer #2: Yes ********** 2. If the manuscript reports exploratory analyses or experimental procedures not outlined in the original Registered Report Protocol, are these reasonable, justified and methodologically sound? A Registered Report may include valid exploratory analyses not previously outlined in the Registered Report Protocol, as long as they are described as such. Reviewer #1: Yes Reviewer #2: Yes ********** 3. Are the conclusions supported by the data and do they address the research question presented in the Registered Report Protocol? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. The conclusions must be drawn appropriately based on the research question(s) outlined in the Registered Report Protocol and on the data presented. Reviewer #1: Yes Reviewer #2: 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 #1: Yes Reviewer #2: 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 #1: Yes Reviewer #2: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: In the manuscript entitled “Nanoparticulate air pollution disrupts proteostasis in Caenorhabditis elegans”, Manriquez et al. evaluate the impact of environmental risk factors such as air pollution on proteostasis. Using well established C. elegans protein conformation disease (PCD) models, the authors examine protein aggregation using visual and biochemical assays and monitor proteotoxicity using behavioral readouts for movement. Based on this analysis, the authors conclude that nanoparticulate matter (nPM) exacerbates protein aggregation and proteotoxicity in the PCD models and has no impact on stress responses in wild type animals. Taken together, the authors suggest that exposure to environmental air pollution may overwhelm the proteostasis network and worsen symptoms associated with Alzheimer’s disease and dementia. Overall, the manuscript is well organized and well communicated. This reviewer concludes that the manuscript is appropriate for publication in PLOS ONE after addressing the issues outlined below. To support the authors’ conclusions, the following additions to the experimental data are recommended. 1. To better view the visual aggregates that were quantified in Figure 1B, include an inset with higher magnification that depicts the type of aggregate that was scored. Specifically, magnify the area at the end of the arrowheads. 2. It is unclear what the reader should observe in Figure 1C. Addition of arrows to denote what the authors refer to as AB puncta and arrowheads to highlight what the authors refer to as larger aggregates is needed. 3. Supplemental Figure 2 shows the quantification of relative protein levels in each polyQ model. To support the conclusion that protein levels do not change, a representative gel image of the area quantified would be helpful. Specifically, polyglutamine tracts can lead to accumulation of proteins in the stacking gel of SDS PAGE gels. It would be important to note if protein accumulated in the stacking gel and if this was included in the final determination of protein levels. An image of a representative gel/blot to resolve this would be informative. 4. In Supplemental Figure 2, the authors state that there is no statistical difference (text line 241 but do not provide p values. This is relevant for panel C as the relative level between M9 control and nPM look different. 5. Fix line 264. Change AB to polyQ 6. The formatting in Figure 2B and 2C make it difficult to discern the impact of nPM on N2. It appears as though the lines overlap but a statement in the text would help resolve this confusion. 7. In Figure 2B, it is unclear if there is a statistically significant effect of the acute exposure to nPM for strain GMC101. There is an asterisk on the graph but it is unclear what this refers to. Furthermore, this reviewer questions if a t-test is the appropriate statistical analysis for this data set. The authors should clarify since Line 272 does not state if these differences (IT50) were statistically significant. 8. In Figure 3, it is unclear if the high molecular species are normalized to total protein in each lane or to control. Or are the values determined only by comparing intensity of the HMW species vs monomers for each strain. This reviewer recommends calculating relative amounts of HMW in total for each strain. 9. In Supplemental Figure 4, the figure legend states that protein was collected for the Q40 strain immediately instead of after 72 hours, which was the procedure for aggregate counting. Is there a rationale for why the treatment with nPM was not similar to the procedure for aggregate counting? 10. Supplemental Figure 4 shows the quantification of high molecular weight species in the Q40 and Q44 models. A representative native gel image highlighting the area quantified would be beneficial. The recommendations above ask for additional data and further analysis of the data to strengthen the authors conclusions. This reviewer offers additional suggestions to address within the text to further strengthen the manuscripts conclusion. 1. Have the authors examined the impact of nPM on stress responses in PCD models? The authors demonstrate no impact on N2 animals but the extra challenge of expressing a misfolded disease protein along with the nPM may lead to activation of a stress response. 2. In Supplemental Figure 1A, nPM leads to an unexpected decrease in Q40 aggregates. To explain this surprising result, the authors state that Q35 is a “better sensor” than Q40. The authors should also consider that the treatments are done at different times in the developmental cycle of the worm, which may affect proteostasis demands. 3. In the conclusions section, it would be helpful if the authors offer their insight into why nPM that exacerbates protein misfolding in body wall muscles can suggest deficiencies in protein folding of AB species in neurons leading to dementia. Reviewer #2: The paper by Garcia Manriquez et al is a well written report that describes a study in C.elegans models to assess the proteotoxicity of nanoparticulates associated with air pollution. The study is technically sound. The methods used appear appropriate and appropriate statistical methods were used to assess the data. One short-coming of the study is uncertainty regarding the potential exposure in vulnerable neurons of human brain relative to the dose of nanoparticulates that the worms were exposed to. The only technical comment I have is that in Fig 1C, the authors should indicate the number of replicates that were examined to produce the representative images. ********** 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 #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 |
Nanoparticulate air pollution disrupts proteostasis in Caenorhabditis elegans PONE-D-22-25226R1 Dear Dr. Kikis, 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, Mahesh Narayan, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-22-25226R1 Nanoparticulate air pollution disrupts proteostasis in Caenorhabditis elegans Dear Dr. Kikis: 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 Dr. Mahesh Narayan Academic Editor PLOS ONE |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .