Expressional artifact caused by a co-injection marker rol-6 in C. elegans

HoYong Jin; Scott W. Emmons; Byunghyuk Kim

doi:10.1371/journal.pone.0224533

Peer Review History

Original SubmissionOctober 14, 2019
6 Nov 2019 Decision Letter - Denis Dupuy, Editor PONE-D-19-28634 Expressional artifact caused by a co-injection marker rol-6 in C. elegans PLOS ONE Dear Dr. Kim, 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. We would appreciate receiving your revised manuscript by Dec 21 2019 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. 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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, Denis Dupuy, 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 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. We note that Figure(s) [1A] in your submission contain copyrighted images. 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If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only. 3. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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: 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: This manuscript describes a relatively minor finding, but that finding is described in a concise manner. Furthermore, the implications for others working on C. elegans male tail biology are significant and this justifies publication as the information should be in the public domain. It is important to be aware of the presence of a cell specific enhancer in a common transformation marker as this could affect conclusions drawn from experiments. The manuscript is very well put together. A few minor issues are identified below. Line 51. Information on the original genes and the fragments assayed ought to be included perhaps in a supplementary table. Line 94 – 101. Some clarification of the cloning used to identify what part of pRF4 is responsible for driving expression in CP09 is needed in the Results and Discussion text, in addition to that provided in the Materials and Methods section. It is not clear from the general description of sub-cloning of pRF4, if the minimum gfp homology region is in the vector or insert fragment. Also, cloning of the pRF4 vector fragment into pPD95.77, would lead to a repeat of the pUC vector parts in the same plasmid which would be expected to be unstable in E. coli and I would be surprised if this really was achieved. Methods. Restriction enzyme names should include italics. References. Gene and species names should be italicised. Figs. 1 and 2. Reference is to “CP09” throughout the paper apart from in Figs 1 and 2 where it is “CP9”. Fig. 3. Title for panel C is in square brackets and is not needed. ****** 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 [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0224533.r001
Revision 1
14 Nov 2019 Author Response Jin et al. RESPONSE TO REVIEWERS 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 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 We have revised the text to meet the style requirements. 2. We note that Figure(s) [1A] in your submission contain copyrighted images. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: 1. You may seek permission from the original copyright holder of Figure(s) [1A] to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].” We have uploaded the completed Content Permission Form. Also, we have added the text in the figure caption for copyright information. 3. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. As the result was a none-or-all event and negative in a test, we think it can be shown as a simple description without mentioning about data availability. Thus, we have removed the phrase “data not shown”. Review Comments to the Author Reviewer #1: This manuscript describes a relatively minor finding, but that finding is described in a concise manner. Furthermore, the implications for others working on C. elegans male tail biology are significant and this justifies publication as the information should be in the public domain. It is important to be aware of the presence of a cell specific enhancer in a common transformation marker as this could affect conclusions drawn from experiments. The manuscript is very well put together. A few minor issues are identified below. Line 51. Information on the original genes and the fragments assayed ought to be included perhaps in a supplementary table. The original information was described in Experimental Procedures section in our previous paper. To avoid repetition and clearly inform the source of information, we have indicated the source in the text: “for information on the genes and the promoter fragments assayed, see Experimental Procedures section in [ref]”. Line 94 – 101. Some clarification of the cloning used to identify what part of pRF4 is responsible for driving expression in CP09 is needed in the Results and Discussion text, in addition to that provided in the Materials and Methods section. It is not clear from the general description of sub-cloning of pRF4, if the minimum gfp homology region is in the vector or insert fragment. We agree that our description about the minimum gfp homology region was not clear. The minimum homology region is located upstream of the GFP coding region of pPD95.75. In the sub-cloning procedure, the minimum homology region was excluded so that both the vector and rol-6 fragments did not contain the minimum homology sequence. To clarify this, we added the following text in Results and Discussion section: “The minimum homology sequence is located upstream of the GFP coding region of pPD95.75 and included in most promoter::GFP fusion constructs, as this inclusion ensures that an artificial intron is placed in front of the GFP sequence for efficient reporter gene expression [ref].” “…we divided the pRF4 plasmid except for the minimum homology region into two fragments,…” Also, cloning of the pRF4 vector fragment into pPD95.77, would lead to a repeat of the pUC vector parts in the same plasmid which would be expected to be unstable in E. coli and I would be surprised if this really was achieved. We re-checked the sub-cloning of the vector fragment::GFP and found no errors in making it. This construct may be unstable due to the repetition of vector sequences, but we did not find any difficulties to sub-clone and amplify this construct using E. coli. Methods. Restriction enzyme names should include italics. We have revised the text accordingly. References. Gene and species names should be italicised. We have revised the text accordingly. Figs. 1 and 2. Reference is to “CP09” throughout the paper apart from in Figs 1 and 2 where it is “CP9”. We have revised the figures accordingly. Fig. 3. Title for panel C is in square brackets and is not needed. We have removed the title for panel C in Figure 3. Attachments Attachment Submitted filename: Rebuttal letter.docx https://doi.org/10.1371/journal.pone.0224533.r002
15 Nov 2019 Decision Letter - Denis Dupuy, Editor PONE-D-19-28634R1 Expressional artifact caused by a co-injection marker rol-6 in C. elegans PLOS ONE Dear Dr. Kim, Thank you for submitting your revised manuscript to PLOS ONE. This revised version of the manuscript addresses most the points raised during the initial review process. However, it would be preferable if you included the methodological information referenced within this article rather than as a call back : “for information on the genes and the promoter fragments assayed, see Experimental Procedures section in [ref]To avoid repetition and clearly inform the source of information, we have indicated the source in the text: “for information on the genes and the promoter fragments assayed, see Experimental Procedures section in [ref] This would allow readers to access all the pertinent information without juggling between two references. We would appreciate receiving your revised manuscript by Dec 30 2019 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled '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, Denis Dupuy, Ph.D. Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0224533.r003
Revision 2
17 Nov 2019 Author Response Jin et al. RESPONSE TO REVIEWERS Thank you for submitting your revised manuscript to PLOS ONE. This revised version of the manuscript addresses most the points raised during the initial review process. However, it would be preferable if you included the methodological information referenced within this article rather than as a call back : “for information on the genes and the promoter fragments assayed, see Experimental Procedures section in [ref]To avoid repetition and clearly inform the source of information, we have indicated the source in the text: “for information on the genes and the promoter fragments assayed, see Experimental Procedures section in [ref] This would allow readers to access all the pertinent information without juggling between two references. We have added S1 Table to indicate information on the genes and the promoter fragments assayed. Attachments Attachment Submitted filename: Rebuttal letter_v2.docx https://doi.org/10.1371/journal.pone.0224533.r004
20 Nov 2019 Decision Letter - Denis Dupuy, Editor Expressional artifact caused by a co-injection marker rol-6 in C. elegans PONE-D-19-28634R2 Dear Dr. Kim, 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, Denis Dupuy, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0224533.r005
Formally Accepted
25 Nov 2019 Acceptance Letter - Denis Dupuy, Editor PONE-D-19-28634R2 Expressional artifact caused by a co-injection marker rol-6 in C. elegans Dear Dr. Kim: 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. Denis Dupuy Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0224533.r006

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