Talk:WikiJournal Preprints/C10orf71

From Wikiversity
Jump to navigation Jump to search

WikiJournal Preprints logo.svg

WikiJournal Preprints
Open access • Publication charge free • Public peer review

WikiJournal User Group is a publishing group of open-access, free-to-publish, Wikipedia-integrated academic journals. <seo title=" Wikiversity Journal User Group, WikiJournal Free to publish, Open access, Open-access, Non-profit, online journal, Public peer review "/>

<meta name='citation_doi' value=>

Article information

Author: Lydia Hamel[a][i], et al.

Hamel, L; et al.. 




Plagiarism check[edit]

Artículo bueno.svg Pass. WMF copyvio tool using TurnItIn. Fully unique content. --Marshallsumter (discusscontribs) 16:34, 6 February 2019 (UTC)

Editorial comments[edit]

Comments by Marshall Sumter
These comments were submitted on , and refer to this previous version of the article

  1. I searched Google Scholar using C10orf71 and 76 articles resulted. While some may be mentioning C10orf71 as a control or a nearby gene, others seem to be including C10orf71 in their study. Should some of these be included in this review? --Marshallsumter (discusscontribs) 04:13, 7 February 2019 (UTC)
  2. C10orf71 is aka cardiac-enriched FHL2-interacting protein (CEFIP), which exhibits a heart and skeletal muscle–specific expression profile. CEFIP is located at the z-disc and is upregulated in several models of cardiomyopathy. Per Franziska Dierck, Christian Kuhn, Claudia Rohr, Susanne Hille, Julia Braune, Samuel Sossalla, Sibylle Molt, Peter F. M. van der Ven, Dieter O. Fürst, and Norbert Frey, The cardiac z-disc protein CEFIP regulates cardiomyocyte hypertrophy by modulating calcineurin signaling, J. Biol. Chem. 292 (37) 15180. --Marshallsumter (discusscontribs) 16:56, 9 February 2019 (UTC)
  3. Using 'CEFIP' and 'cardiac' as two search concepts on Google Scholar produced about 173 apparently related articles, some of which may be a great way to expand and perhaps improve this preprint. --Marshallsumter (discusscontribs) 17:42, 10 February 2019 (UTC)

Comments by Thomas Shafee
These comments were submitted on , and refer to this previous version of the article

Given that some of the information in this article is generated by the author, a short methods section will be necessary. It would also be useful to copy the relevant sections of those methods into the image description pages so that the information is included there (e.g. at File:Tree_for_PS2.jpg)

Response

So this gene was analyzed for the length of six months. How specific in detail would a methods section need to be? Is it only for the diagrams/tables or how exactly would this methods section need to be constructed?

In the domains and motifs section, what do the orange regions correspond to if they are not also DUFs? Are they known domains? The predicted structure of the next diagram would suggest so, but it is unclear what the domain is, and how many repeats there are.

Response

This cartoon represents the basic layout of C10orf71 protein. The overall protein is represented by the orange/red rectangles, which represent that it’s located in the nucleus. DUF4585 is represented by the blue pentagon and the vacuolar motif is represented by the green skinny oval. Nuclear localization signals are represented by the gray diamonds projecting from the gene and the N-glycosylation sites are represented by the red diamonds projecting off of the top of the gene cartoon. This cartoon was constructed using MyDomains on PROsite. is cartoon represents the basic layout of C10orf71 protein. The overall protein is represented by the orange/red rectangles, which represent that it’s located in the nucleus. DUF4585 is represented by the blue pentagon and the vacuolar motif is represented by the green skinny oval. Nuclear localization signals are represented by the gray diamonds projecting from the gene and the N-glycosylation sites are represented by the red diamonds projecting off of the top of the gene cartoon. This cartoon was constructed using MyDomains on PROsite.

The text stated that "A secondary structure was constructed with a 6.1% confidence level". Is this referring to the i-tasser figure? If so, itasser is a tertiary structure prediction program. Was the structure predicted by i-tasser de novo, or based on an already characterised homolog as a template (if so, what was the homolog)? Is a 6.1% confidence level meaningful in this case? The diagram would be better with a white background if possible, as well as cropped and oriented with C-ter on the left, N-ter on the right since it seems to be a string of repeating domains. It will also be needed in higher resolution in order to see any information.

Response

The secondary structure mentioned in the text was created/predicted with Phyre2. In regards to the iTasser result, this is provided on the black background and I don't believe there is a way for me to put it on a white background.

What was the technique used (NJ/ML/Bayesian etc). The phylogeny will also require bootstraps in order to interpret.

Please check that references have easily interpret-able names. e.g. current reference 1 has the title "Home - Gene - NCBI", when a more useful title would be something like C10orf71 (Gene ID: 118461)".

Response

I will look into the reference names and try and change them accordingly. Thank you.