Peer Review History
| Original SubmissionJune 2, 2020 |
|---|
|
PONE-D-20-16607 The plasma lipidome of the Quaker parrot (Myiopsitta monachus) PLOS ONE Dear Dr. Beaufrere, 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. I think there is a fair bit of work to be done here but you should be able to address many of the reviewer's comments in a revised version of the manuscript. I am not too concerned about Reviewer 1's comment 5 regarding the sum of the fatty acid composition as I realize this is probably the best resolution you could get. Please submit your revised manuscript by Sep 24 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, Robin D Clugston, 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 Methods section, please provide additional details regarding the birds used in your study and ensure you have described the source. For more information regarding PLOS' policy on materials sharing and reporting, see https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-materials. 3. We note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 3 in your text; if accepted, production will need this reference to link the reader to the Table. [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: Yes ********** 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: Yes Reviewer #2: Yes ********** 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: Yes Reviewer #2: Yes ********** 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: This is an observational study using target and untargeted lipidome to characterize the lipidome of young male and female healthy Quaker parrots considering them as representative of psittacine birds. Due to advantages of lipidome characterization as base for further study of dyslipidemia and other metabolic dysfunction on these birds the study is an important effort to advance the scientific field. The study presented a small population sample of 6 males and 6 females’ birds that were used for the lipidome profile. A set of 6 samples (3 male and 3 female) were sent to one center for performance of target lipidome and another set of 6 birds to another center for performance of the untargeted lipidome, as well as for targeted panels for bile acids, sterols, non-esterified fatty acids, acyl carnitines, and sphingolipids. The authors recognized that although their lipidomic methods could detect free fatty acids and lipids containing only one fatty acid as lysolipids and acylcarnitines and cholesteryl esters, there is a critical limitation of identification of the fatty acid composition of lipids containing two or more fatty acids. The use of target and untargeted lipidome methods put together to characterize the Quaker parrots lipidome present some issues that need to be clarified, as well as the use of such small sample. The acquisition of only 1 milliliter of blood probably is also a limitation of the study, since the 500 µL appears not enough to divide for shipping for two different samples, and rather the authors divided the sample population (from 12 parrots, 6 were sent to one center and 6 to other). Major issues: 1- On line 354 the authors state that Identified abundant species in untargeted lipidome did not necessarily correspond to lipid found to be abundant on targeted panels. The untargeted lipidome is presented only on Table 4 and does not appear to add much information to the study, since the other tables on the manuscript appears to come from the target analysis. The authors discussed this issue, but it is not clear the benefit of it for the characterization of the lipidome. 2- The presentation of specific lipids species that were under the limit of detection (LOD) appears to add a lack of accuracy to the lipid characterization proposed. In a few cases as in Table 17 the specie Cer(d18:1/18:1) and Cer(d18:1/20:4) values are presented as LOD although their percentage are 13.1 and 21.0 respectively. An explanation of the importance to show these lipids species should be stated in the discussion. 3- The comparison of gender presents some concerns on the aspect of the power of the analysis. The authors mentioned that only 2 lipids reached the threshold to be considered statistically significant, although the criteria are not specified. This lack of power is probably to the fact of only 3 males and 3 females were compared. However, the multivariate analysis present clear separation of the gender. This creates a problem, since if a sex bias exists in the lipidome, the abundance and relative concentration of the lipidome presented on the several tables of the study must be very influenced by the gender bias and should be explored. Again, the small sample size becomes a problem for a univariate analysis. 4- The hierarchical cluster analysis also shows a clear difference between sexes. It must be stated when presenting this analysis that although a t-test was used to select the 50 more important features that classify the genders, none of them reach statistical significance. To present the result as 50 significant lipids is confusing at the minimum. 5- The use of the sum of the fatty acid composition to represent the lipids is a limitation of the methodology that does not give enough information to the purpose of characterization of the metabolic profile of the Quaker parrots. Minor issues: 1) Although the authors address some of the major issues on discussion section, all justification related to limitation of the study should be clustered on a Limitation session. Overall assessment: The issues with the study creates enough problems that are out of the objective of the authors to find metabolic profile of the lipidome of the Quaker parrots, and therefore, the manuscript does not add important information for the advance of the field. Reviewer #2: The article by Beaufrere, et. al., presents a descriptive and semi-quantitative lipidomic profile of captive Quaker parrot plasma with the goal of establishing the baseline data for future studies. The analytical methods used are highly robust and the authors clearly identified limitations of the study. Because of the descriptive nature of the study, it is understandable that the authors have little scope to draw conclusions with respect to dyslipidemia and lipid accumulation disorders in these birds at this time. More experimental details are needed in the absence of published references. While the methods used were comprehensive and the data presented is extensive, several minor corrections would help improve the manuscript. 1. Some of the methods need to include more details or appropriate references. For example, what are the deuterated standards of bile acids used, what are the chromatographic conditions, and how well are the closely related compounds resolved on the column as well as the mass spectrometric conditions for their detection? This comment applies to all method descriptions where a published procedure is not cited. 2. Description of the preparation of standards to generate standard curves, details about the use of linear regression, etc., can be consolidated in the general methods rather than repeating the same text for each analytical method. 3. Description and definition of lipidomics presented in the third paragraph of the Introduction could be minimized by citing appropriate references. While relatively new, lipidomics is quite an established field to warrant such detailed introduction. 4. Data table descriptions consistently reminded the reader about concentrations as ‘µmol/L’. While this is not inaccurate, the more appropriate designation would be ‘µM’! 5. What is the ‘3-NOH’ in line 218? ********** 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: Yes: Krishna Rao Maddipati [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 |
|
The plasma lipidome of the Quaker parrot (Myiopsitta monachus) PONE-D-20-16607R1 Dear Dr. Beaufrere, 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, Robin D Clugston, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): 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 #1: All comments have been addressed Reviewer #2: 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 #1: Yes Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? 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. 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: The authors have addressed the major and minor issues found in the previous submission adequately and have edited the tables and point out in the discussion the limitations of the analysis when dealing with a small sample size study. Due to the novelty of the characterization of the Quaker parrots lipidome and the satisfactory answers to my questions I suggest the publication of the manuscript. Reviewer #2: The authors addressed all my concerns. The study provides basis for additional work in avian biology, especially to improve captive bird management. ********** 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: Yes: Daniel Contaifer Junior Reviewer #2: Yes: Krishna Rao Maddipati |
| Formally Accepted |
|
PONE-D-20-16607R1 The plasma lipidome of the Quaker parrot (Myiopsitta monachus) Dear Dr. Beaufrere: 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. Robin D Clugston 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 .