Identification and quantification of cassava starch adulteration in different food starches by droplet digital PCR

Jia Chen; Yalun Zhang; Chen Chen; Yan Zhang; Wei Zhou; Yaxin Sang

doi:10.1371/journal.pone.0228624

Peer Review History

Original SubmissionJune 24, 2019
12 Aug 2019 Decision Letter - Evangelia V. Avramidou, Editor PONE-D-19-17769 A quantitative study of the adulteration of cassava components in starch products by droplet digital PCR PLOS ONE Dear Dr. Yaxin Sang 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 Sep 26 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, Evangelia V. Avramidou, PhD 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. In your Methods, please specify the exact source(s) of the cassava and potato extracts used in your study. Additional Editor Comments: Dear Dr. Yaxin Sang, [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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know ****** 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: No 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: Overview: The manuscript presents adequate data to support use of droplet digital PCR to assess the accurate composition of cassava starch when mixed or blended with starch from other sources such as sweet potato, potato and corn. Are there some industry quality standards required for such starch products be of a certain proportion like there is for varietal wines? Is there any reference that can provide documentation of fraud by food processor? Are there health concerns (e.g. associated food allergies)? Authors indicate models were developed but the data only shows target DNA copies and correlations only. Does this count as a model? Otherwise, the science and methodology appear solid. Specific comments: Ln 29-30. Cassava DNA- clarify the linear relationship was with regard cassava dry weight to DNA concentration. Ln 40-43. Recommend rewriting the first five sentences with a reference to cassava adulteration by other starch produces due to economics. Ln 45. Sanitation tests? Ln 53. Digital dPCR (ddPCR) and use ddPCR thereafter in this manuscript. Ln 184-190. Needs a Table or a figure. Ln 196 – Fig. 5 is missing. Table 5 is incoherent without adding what the samples are. The results indicate cassava/sweet potato at different ratios which need to be included in the title or at least foot-noted. Ln 199 maximum relative error 10.2%. Is this shown in Table 5? Reviewer #2: The manuscript entitled ‘A quantitative study of the adulteration of cassava components in starch products by droplet digital PCR’ describes the development of a method aiming to enable the rapid and accurate detection and quantitation of cassava adulteration in starch products by utilizing droplet digital PCR technology (dd PCR). The experiment seems well thought out and carefully executed. However certain points need to be elaborated and explained further. 1. It is not clear what was the basis of selecting the Acc gene for the PCR analysis. In fact there is no information or reference given about this gene. Could more genes be studied? 2. Have there been other studies to detect cassava adulteration previously? Have there been studies employing the other PCR technologies and what were the results? Could a comparison between other PCR technologies and dd PCR be provided? 3. It is not clear how a calculation formula was established between cassava quality, DNA concentration and copy number On line 112 and 113 it is mentioned: “The program for the reaction denaturation was as follows: 95°C, 10 min; 94°C denaturation, 1 min; 56°C annealing, 45 s; 40 cycles; 98°C, 10 min; and 4°C for temporary storage” The step ‘98°C, 10 min;’ refers to which part of the pcr reaction? Why it is 98°C degrees? 4. On line 127: “The experimental system and operating procedures are shown above” It is not clear what it is shown above. 5. On line 141: On line 127: “The experimental system and operating procedures are shown above” It is not clear what it is shown above. 6. Fig 1: The legend of Fig 1 needs more detail 7. Fig. 2: The legend of Fig 2 needs more detailed description 8. Fig. 3: The same. Please provide some minimal explanation of what the figure and graphs depict. 9. Fig. 5: Fig 5 is missing! 10. The Discussion section is really limited. Overall the manuscript describes a good effort towards the employment of a rapid and accurate method to detect and quantify cassava adulteration in different starch sources using an important new technology, ddPCR, and merits to be published for reasons of knowledge transfer to the scientific community. However, the introduction, results and discussion sessions need to be described in a much more detailed and elaborate manner providing the reader with much more information on the topic and on data acquisition, in order to make it a comprehensible publication. ****** 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: Yes: Raymond Yokomi 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 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. Attachments Attachment Submitted filename: PONE-D-19-17769 review.pdf https://doi.org/10.1371/journal.pone.0228624.r001
Revision 1
25 Sep 2019 Author Response 3. Have the authors made all data underlying the findings in their manuscript fully available? Response: Raw data has been placed in the support file. Reviewer #1: Overview: The manuscript presents adequate data to support use of droplet digital PCR to assess the accurate composition of cassava starch when mixed or blended with starch from other sources such as sweet potato, potato and corn. Are there some industry quality standards required for such starch products be of a certain proportion like there is for varietal wines? Is there any reference that can provide documentation of fraud by food processor? Are there health concerns (e.g. associated food allergies)? Authors indicate models were developed but the data only shows target DNA copies and correlations only. Does this count as a model? Otherwise, the science and methodology appear solid. Response: 1. There is a national standard for starch products in China (China National Standard for Starch Products GB 2713-2015), and we have cited this standard in the revised manuscript. 2. Starch adulteration has been reported before and we have cited the reference. 3. Food allergies are another concern of starch adulteration, and we have added this concern to the introduction. 4. We used a mixture of sweet potato and cassava starch to model starch adulteration. https://doi.org/10.1371/journal.pone.0228624.r002
23 Oct 2019 Decision Letter - Evangelia V. Avramidou, Editor PONE-D-19-17769R1 A quantitative study of the adulteration of cassava components in starch products by droplet digital PCR PLOS ONE Dear Dr Sang, 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 07 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, Evangelia V. Avramidou, PhD Academic Editor PLOS ONE Additional Editor Comments (if provided): Dear authors, according to reviewers opinion please proceed according to minor revision comments. [Note: HTML markup is below. Please do not edit.] 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: Please see pdf attachment. New edits are suggested to improve clarity of the manuscript. Mass is confusing to this reviewer in the context of this manuscript. It is preferable to use dry weight. ****** 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: Raymond K. Yokomi [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. Attachments Attachment Submitted filename: PONE-D-19-17769-R1 review.pdf https://doi.org/10.1371/journal.pone.0228624.r003
Revision 2
20 Nov 2019 Author Response Dear editor： I have completely revised the revised comments and submitted a modified version. Contact if you have any questions. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0228624.r004
21 Nov 2019 Decision Letter - Evangelia V. Avramidou, Editor PONE-D-19-17769R2 Identification and quantification of cassava starch adulteration in different food starches by droplet digital PCR PLOS ONE Dear Dr Sang, 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 Jan 05 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: 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, Evangelia V. Avramidou, PhD Academic Editor PLOS ONE Additional Editor Comments (if provided): Dear authors, I have checked that you adopted reviewers's comments, but I still have some corrections regarding the manuscript. Please fullfill in line 31 do you mean products by "oducts"?? Furthermore, according also to reviewer's and mine opinion you should substitute word "mass" with "weight" also to tables and figures. Please make tha above corrections in order that your article can be published. With kind regards [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.0228624.r005
Revision 3
17 Jan 2020 Author Response Reply A rebuttal letter Ln 2-3. Article title has been changed Ln 7. Text has been changed Ln 8 The text was changed to weight Ln 12 Text has been changed Ln 13 Text has been changed Ln 22 Text has been changed Ln 24. Text has been changed Ln 26 Text has been changed Ln 30-31. Text has been changed Ln 34 Text has been changed Ln 36 Text has been changed Ln 49. Text has been changed Ln 51 Text has been changed Ln 57 Text has been changed Ln 68. Text has been changed Ln 85 Text has been changed Ln 88 Text has been changed Ln 110 Text has been changed Ln 117. Text has been changed Ln 148. Text has been changed Ln 154 Text has been changed Ln 161 Text has been changed Ln 171-175 Rewritten Ln 224 Text has been changed Ln 227 Text has been changed Ln 297 Text has been changed Ln 299 Text has been changed Ln 301 Text has been changed Ln 303-311. Text has been changed Attachments Attachment Submitted filename: A rebuttal letter.docx https://doi.org/10.1371/journal.pone.0228624.r006
22 Jan 2020 Decision Letter - Evangelia V. Avramidou, Editor Identification and quantification of cassava starch adulteration in different food starches by droplet digital PCR PONE-D-19-17769R3 Dear Dr. Sang, 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, Evangelia V. Avramidou, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0228624.r007
Formally Accepted
28 Jan 2020 Acceptance Letter - Evangelia V. Avramidou, Editor PONE-D-19-17769R3 Identification and quantification of cassava starch adulteration in different food starches by droplet digital PCR Dear Dr. Sang: 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. Evangelia V. Avramidou Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0228624.r008

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 .