PONE-D-20-00611

Physico-chemical Characterization and Topological Analysis of Pathogenesis-related Proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches

PLOS ONE

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Diego F. Gomez-Casati, PhD

Academic Editor

PLOS ONE

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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

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: No

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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

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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: No

Reviewer #2: Yes

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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: Literature review was too shallow and it rarely referenced from pools of already published relevant research. This should be rewritten. The analysis was done without adequate statistical packages to bring home the point. The conclusion contains flying general statements without concluding in specific terms on the results. This conclusion should be rewritten. The entire manuscript should be subjected to editing by native speaker of English language

Reviewer #2: I the view of reviewing manuscript “Physico-chemical Characterization and Topological Analysis of Pathogenesis-related Proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches ” has been looked thoroughly and observed following points.

1. Author justify that Arabidopsis thaliana and Oryza sativa are different family member of plant so that why compere these of PR proteins.

2. Compare the physico-chemical properties of 12 PR proteins 6 PRs of Arabidopsis

thaliana and 6 PRs of Oryza sativa .while as table no 1, 2 and 3 mentioned only 6 PRs in both Arabidopsis and Oryza PR1, PR2, PR5, PR9, PR10 , PR12 remaining are Figures 1, 2 and 3 why not all 12 PRs mentioned both table and Figures?

3. In introduction section line no.31 Reactive Oxygen Plants (ROS) : Reactive Oxygen Species (ROS).

4. Line no 40-41. many phytohormones like JA, SA and ET: write the full name of JA, SA and ET first time in manuscript.

5. Line No 55- 60 : include appropriate references in introduction section.

6. In table no 1 all entries of At are bold and Os are bold this demarcation pattern create confusion of readers like bold letter have other scientific meaning but this not view of author only differentiate to At and Os. So that table column may shadow.

7. In table no 1. II value of PR 9 and PR10 not stable disused.

8. In table no 2 . Cello, Euloc and Wolfpsort data are not presenting Subcellular localization of PR proteins predicting uniform result .

9. In table no 3. Comparative topological analysis of PR proteins presence or absence of transmembrane domains homogenious resu;t are showing such as TMHMM of PR12 At (1) and Os (0) why.

10. Conclusion should elaborate . Present conclusion no such pin pointing.

11. 5) Kaur A, Pati PK, Pati AM, Nagpal AK . In-silico analysis of cis-acting regulatory elements of

pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PLoS ONE. 2017; 12(9):

e0184523. https://doi.org/10.1371/journal.pone.0184523. Page no Missing.

12. Hofmann K, Stoffel W. TMbase - A database of membrane spanning proteins segments. Biological Chemistry Hoppe-Seyler. 1993; 374:166. doi: citeulike-article-id:9087200. Vol. missing

13. Shen H, Chou JJ. MemBrain: Improving the Accuracy of Predicting Trans membrane Helices. PLoS

ONE. 2008; 3(6): e2399. doi:10.1371/journal.pone.0002399. Page no Missing.

14. No any such current year 2019 and 2020 are present in this manuscript. May some refrences should be add.

15. All figure are not self explainer specially fig. no 3.

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Reviewer #1: No

Reviewer #2: No

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Physico-chemical Characterization and Topological Analysis of Pathogenesis-related Proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches

PONE-D-20-00611R1

Dear Dr. Nagpal,

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.

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Kind regards,

Diego F. Gomez-Casati, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The manuscript was properly corrected and the authors took into account the suggestions made by the reviewers.

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 #2: All comments have been addressed

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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 #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

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 #2: Yes

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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 #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 #2: Author compliances of all my 15 comments and reviewer satisfied with all, specially origin of PR proteins , table formation and rewrite of discussion.

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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 #2: No