Talk:WikiJournal of Science/Structural Model of Bacteriophage T4

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Article information

Author: Victor Padilla-Sanchez[a][i]ORCID iD.svg 

Victor Padilla-Sanchez (5 August 2021), "Structural Model of Bacteriophage T4", WikiJournal of Science, 4 (1): 5, doi:10.15347/WJS/2021.005, ISSN 2470-6345, Wikidata Q100272642




 


Plagiarism check

Artículo bueno.svg Pass. Report from WMF copyvios tool: 0% Plagiarism detected. T.Shafee(Evo﹠Evo)talk 22:47, 2 November 2020 (UTC)[reply]

Peer review 1


Review by anonymous peer reviewer , Senior Researcher of Bacteriophage T4

These assessment comments were submitted on , and refer to this previous version of the article

The interest in studying bacteriophage T4 is growing year-by-year. I would appreciate the authors’ effort in creating a complete atomistic structure of phage T4 to be used in future teaching and research areas. However, I have a few comments on the image and the body of the article:

1. The text should be grammatically revised. Also, some sentences are not clear and well-written.

2. In the Abstract “Bacteriophage T4 is a virus that infects Escherichia coli with dimensions of 90 nm wide and 200 nm long…”, the authors should clarify what are these numbers? Do they refer to the size of whole phage T4 including head, tail assembly, and the fibers? They also should emphasize in the text that these numbers are the dimensions of phage T4 in the extended state (?). Please also add related references for these numbers.

3. In the Abstract, “that has been studied for a century by many important virologists including Watson and Crick who elucidated the structure of DNA.”. I believe this sentence is not very informative and required for the readers! Why would it be important for readers that “ important virologists including Watson and Crick “ studied phage T4?! The authors instead should focus on the main purpose of the article that is the structure of phage T4.

4. Generally, the Abstract requires revision in both language and the content. My suggestion is to include a summary of phage T4 components such as head, tail assembly, and fibers, and in doing so, prepare the reader’s mind for the atomistic structure described in the body.

5. The authors should completely explain the source of the protein composition of different components of phage T4. They should cite the related papers and corresponding PDB sources that they have used to create this model. “There are approximately 50 structural proteins that assemble the virus constructed with protein databank (pdb) structures”; it would be very useful for many readers if the authors create a list of all components and cite their corresponding PDB structures and reference papers and directly link them to their PDB files on RCSB.org or any other related website.

6. I appreciate the authors’ effort in preparing a complete structural model of phage T4, however, the sentence “it is the best reconstruction of the entire organism…” is a claim without any direct proof! The authors are expected to highlight how their model is advanced to other models or they should ignore this claim.

7. As the authors are expected to know, bacteriophage T4 has two states; extended state and contracted state. I suggest that the authors add the information and the reconstructed model of contracted phage T4 in addition to the extended virus. The authors can then briefly compare those two structures. Otherwise, they should briefly explain that the reconstructed model corresponds to the “extended conformation”. Creating complete models for both states would be a good source for broad audiences.

8. Do similar colors in the figure reflect the similar proteins? For example, the green-colored proteins of fibers are as same as those for the capsid? Please add a direct note on this to the text. If the colors do not reflect the similar proteins, please add a comment in the body, and then, I recommend assigning different colors to each strand of the sheath to show that the sheath is a six helical stranded structure.

Response

I have addressed the comments of the reviewer in the updated version of the article


Review by anonymous peer reviewer ,

These assessment comments were submitted on , and refer to this previous version of the article

Thank you for sharing the revised version of the article. In general, the revision looks nice except for a few minor grammatical errors. For instance, lines 1-3 in Abstract, line 5 in Introduction, and etc., include minor errors.

Peer review 2


Review by Paul Hyman ORCID iD.svgWikidata-logo.svg , Ashland University

These assessment comments were submitted on , and refer to this previous version of the article

While this article doesn’t necessarily say anything totally untrue, it is highly misleading to suggest that the structure of the T4 virion required 3D cryoEM to be determined. CryoEM has been useful in confirming some details and some of the structural changes that occur during infection but the majority of the structural information was developed using standard EM and X-ray crystallography in the 1980s (see references 4-7 in this 2003 review https://pubmed.ncbi.nlm.nih.gov/14625682/).

It is also misleading to say that the entire reconstruction depended on the Chimera visualization tool. This was one of many tools used for the work in the article’s reference 2 but is not mentioned at all in reference 1 although that is a review article so Chimera may have been used for some of the cited work. Overall, it is just one tool, not a key one.

At the end of that same paragraph, the sentence seems to imply that all of the model was developed at Catholic University of America which is certainly not true. Researchers at CUA contributed but this model was developed over decades by researchers at dozens of locations.

A minor point – the “brown ring between the head and tail” (last paragraph of Reconstruction) is called the collar.

Overall, this article does not seem to add significantly useful information to what is found in the Bacteriophage T4 article (https://en.wikipedia.org/wiki/Escherichia_virus_T4#Virus_particle_structure) and has less detail than is found in that article.

Response

I have addressed the comments of the reviewer in the updated version of the article. Notice that I am talking about this particular structural model and not about the previous works that have researched single structural components of T4 virus.


Review by Paul Hyman ORCID iD.svgWikidata-logo.svg ,

These assessment comments were submitted on , and refer to this previous version of the article

I read through the revised text and the science is fine. It badly needs editing for grammar and formatting. For instance, the first sentence is a run-on. It is inconsistent about capitalizing T4 which is always capitalized. There are at least 3 different referencing formats in the text.

Author comments

Response

2021-07-14
Thank you very much to the reviewers and the editor for their comments and suggestions to improve the quality of this Bacteriophage T4 article. The final version was greatly improved addressing the reviewers comments.