Peer Review History
Original SubmissionDecember 23, 2019 |
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PONE-D-19-35528 Mechanistic molecular responses of the giant clam Tridacna crocea to Vibrio coralliilyticus challenge PLOS ONE Dear Dr zhiming, 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. 1) Reviewer #1 raised numerous concerns about experimental details. This should be addressed by making appropriate changes to the Material & Methods section and to the text of the Results / Figure legends where appropriate. 2) The concerns about the apoptosis assay in Fig. 1 need to be addressed. While the percentages of cells in the quadrants change upon infection, there is no actual "cell population" coming up which in annexin V positive (and hence early apoptotic) - it appears like a general no specific increase in fluorescence signal. Also the is a considerable number of PI+ cells at t=0 h raising concerns about a large number of cells dying during the cell extraction and purification procedure. Also these cells should likely be PI+ but Annexin V negative; thus there is an apparent issue with the compensation between the fluorescence channels in this experiment ( take a look a the sample plots of the vendor of the kit used: http://www.vazymebiotech.com/products_detail/productId=84.html). One important positive control in this context would be a treatment of the cell with an apoptosis inducing agent (e.g. etoposide).
3) The assembled transcriptome dataset should also be made publicly available such that a consistent gene annotation for this organism can be established for future references. 4) The labeling in heat map shown in Figure 3 is not really helpful - instead of only referring to Cluster XXXX YYYYY, common names should be utilized that give a clear hint on the function of the genes being differentially expressed. 5) The description of the results regarding the GO/ KEGG classification (lines 311-322) is currently meaningless, e.g. it is quite obvious (even without knowing anything about the data) that the majority of genes fall in to classes like "cellular processes", "metabolic processes", "cell", and "cell part". What else should they fall in? I strongly urge the author to use their biological "common sense" to omit this non-useful information (that likely was just copid as the highest ranking scores from a bioinformatics software produces) and rather include information that actually provides some biological insight into the immune system of their model organism. We would appreciate receiving your revised manuscript by Mar 07 2020 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols Please include the following items when submitting your revised manuscript:
Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Sebastian D. Fugmann, 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 http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. In your Methods section, please provide additional information regarding the permits you obtained for collection of Tridacna crocea. Please ensure you have included the full name of the authority that approved the animal collection and, if no permits or approvals were required, a brief statement explaining why. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ [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: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ********** 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 ********** 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 presented here is of interest, well-written and presents new data. My main concern is about the functional demonstration of apoptosis induction by V. coralliilyticus. First, I am not confident in the chosen flow cytometry areas. Can I see your dead and apoptosis-induced controls? For me, PI+ cells should be separated at 102. With such area, I am quite afraid about your control hemocyte mortality (more than 10%?) Secondly, to my opinion, one unique technic (on one sampling point) is not enough to demonstrate apoptosis. Can’t you perform TUNEL assay, caspase dosage, TEM, …? In introduction section, I would appreciate to find more information on the huge diversity of TLR in marine bivalves. Material and method sections lack information - How many individuals were challenges? - Did you check bacterial suspension purity and concentration? - Did you analyze moribund animals to ensure V. coralliilyticus ‘imputability’ in mortality? - What is the difference in the hemolymph sampling explained L138-139 and 141-142 ? - If hemocytes sampled at 0, 3, 6, 12, 24 and 36h, can we see flow cytometry results on all sampling points? - Were the RT-QPCR analyses (L440) and RNA-seq analyses performed on the same biological samples - L150. Triplicate = technical replicates and not biological replicates if I correctly understand what you mean - Can you precise the volume/weight of tissue for RNA extraction L177 - For RNA, 230 nm is also informative (L180) - For qPCR, were the cDNA used diluted or pure? Can you precise it L241? In discussion section, I would recommend to authors to be more careful on the potential bacterial virulence factors that could induce the immune response measured (L485-500). There is a diversity of hemolysins for instance. Even if some hemolysins were described in other models as playing a role in apoptosis, you could not say that ‘some hemolysins […] in the secretome of V. cora […] may be responsible of this phenomena’ (L487). Are they expressed in vivo ? and which hemolysin are we talking about? Except by performing dual-RNAseq, you should be more moderate in this part of your discussion. ********** 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? 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Revision 1 |
Mechanistic molecular responses of the giant clam Tridacna crocea to Vibrio coralliilyticus challenge PONE-D-19-35528R1 Dear Dr. zhiming, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Sebastian D. Fugmann, 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 ********** 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 ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ********** 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 ********** 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: (No Response) ********** 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 |
Formally Accepted |
PONE-D-19-35528R1 Mechanistic molecular responses of the giant clam Tridacna crocea to Vibrio coralliilyticus challenge Dear Dr. zhiming: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Sebastian D. Fugmann Academic Editor PLOS ONE |
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