Peer Review History
| Original SubmissionOctober 1, 2024 |
|---|
|
PONE-D-24-43598Perish the thawed? EDTA reduces DNA degradation during extraction from frozen tissue.PLOS ONE Dear Dr. Distel, 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 Feb 22 2025 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: 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, Shailender Kumar Verma, Ph.D. Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. 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. To comply with PLOS ONE submissions requirements, in your Methods section, please provide additional information regarding the experiments involving animals and ensure you have included details on (a) methods of sacrifice, (b) methods of anesthesia and/or analgesia, and (c) efforts to alleviate suffering. [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: Yes Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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: 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: 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: The manuscript addresses an important issue in DNA preservation during tissue thawing, offering a potential solution using EDTA. The study's relevance is significant for genomic and genetic research, especially in cryopreserved biological samples. There are several questions. 1. Why was the focus placed specifically on EDTA and ethanol (EtOH)? Were other preservatives considered but excluded, and if so, why? 2. What novel insights does this study add beyond previous research on EDTA in DNA preservation? 3�Explain why authors chose these 10 organisms as target species. 4.Were any controls implemented to account for potential variability in tissue type (muscle vs. visceral mass)? Could tissue composition impact the efficacy of EDTA treatment? 5. Is there variability in tissue degradation across species that could confound the interpretation of EDTA's effectiveness? Would standardized storage conditions for all species improve the reliability of cross-species comparisons? 6. What mechanisms might explain the species-specific variations observed in DNA preservation? Expand on potential biological or chemical factors. 7. How does this study inform protocols for non-marine or plant tissues? Discuss the generalizability of findings to other types of biological samples. Reviewer #2: This study presents a comparative analysis of the effects of EDTA and ethanol on the preservation of high-molecular-weight (HMW) DNA in frozen tissues. The authors hypothesize that EDTA, known for its metal chelation properties, can reduce DNA degradation during the thawing process, which is a common step in DNA extraction that can lead to DNA damage. The study involved ten marine species, with tissues treated with EDTA at pH 10 or ethanol, and then analyzed for HMW DNA recovery. The results indicate that EDTA, particularly at pH 10, significantly improves the recovery of HMW DNA compared with that of ethanol and untreated tissues. These findings suggest that EDTA treatment can be a simple and effective method to increase DNA recovery from frozen tissues, which has implications for genetic and genomic research. Before this manuscript can be published, several questions need to be addressed: 1. Since EDTA is one of the primary active ingredients of DESS, why not compare it with DESS instead of choosing ethanol for comparison? 2. In the Materials and methods section, the authors describe taking 100 mg of tissue and adding EDTA or ethanol, then placing it at 4°C for 12-24 hours before dividing it into 25 mg pieces for DNA extraction. Therefore, what is the purpose of the remaining three 25 mg tissues? If only 25 mg is used for testing, would not it be better to directly immerse the 25 mg tissue into EDTA or ethanol for better protection of DNA? Please provide a detailed explanation. 3. Regarding the above question, does the N=10 in Figure 1 refer to 10 marine fish or 10 marine invertebrate species, or is it 10 samples taken for testing? The S1 Table shows 10 fish, whereas the S2 Table shows 10 measurements for each treatment. 4. Lines 198-200: The authors calculated the concentration of HMW DNA for each sample by subtracting the low molecular weight DNA concentration from the total concentration of DNA present. However, quantitative results of the total DNA concentration and the low molecular weight DNA concentration are lacking. Please supplement more detailed data on how to calculate the concentration of HMW DNA. 5. Lines 195-215 & S2 Table: Table S2 shows only the raw results of the Nanodrop 1000. The %HMW and nY values were calculated from the DNA concentration analyzed via the Agilent Technologies TapeStation 2200 DNA Analyzer. Please provide raw results from Agilent and the detailed data on how to calculate the concentration of HMW DNA. In addition, why are not Agilent's results provided in S2 Fig? 6. Lines 301--304: For four of the five invertebrate species (Amphioctopus sp., H. americanus, M. gigas, and P. vannamei), the %HMW values of DNA extracts from EtOH-thawed tissues were the same as or significantly lower than those from frozen tissues. However, for H. americanus, as shown in Fig. 2, the %HMW value from EtOH-thawed tissues was obviously higher than that from frozen tissues. Please clarify further. 7. Line 159: The samples were stored in preservative for 12 to 24 hours at 4°C. This means that the thawing times of the samples in the preservatives were inconsistent. Therefore, are the data in manuscript accurately compared under the same variable? 8. Lines 147--151: Tissue samples were collected from different tissue parts of different species, such as the musculature posterior to the pectoral fin, tentacles, visceral mass, and mantle. Does the difference between tissue samples affect the determined results and conclusions? ********** 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 |
|
Perish the thawed? EDTA reduces DNA degradation during extraction from frozen tissue. PONE-D-24-43598R1 Dear Dr. Distel, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Shailender Kumar Verma, 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: Authors have provided enough answers for my questions. I think that this manuscript could be accepted. Reviewer #2: The authors have provided a detailed response to my comments, addressing each concern with clarity and justification. Their revisions to the manuscript are substantial and have significantly improved the overall quality and clarity of the research presented. In their response, the authors have effectively addressed the concerns. For instance, they have provided a clear explanation for their choice of EDTA and ethanol (EtOH) as the focus of their study, emphasizing the practicality and relevance of these preservatives in the context of DNA preservation. They have also clarified the experimental design, particularly the use of 100 mg tissue samples for treatment and 25 mg subsamples for DNA extraction, which is a reasonable trade-off between practicality and effectiveness. Overall, the revisions made to the manuscript have addressed the key issues, and the research presented is now more robust and clearly communicated. The study provides valuable insights into the use of EDTA as a preservative for improving HMW DNA recovery from frozen tissues, which has significant implications for genetic and genomic research. ********** 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: Yes: Kaiyu Qian ********** |
| Formally Accepted |
|
PONE-D-24-43598R1 PLOS ONE Dear Dr. Distel, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Shailender Kumar Verma 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 .