Skip to content
Snippets Groups Projects
Commit 7e9b54cb authored by Jean c's avatar Jean c
Browse files

update system-template.md

parent 5ab8ad83
No related branches found
No related tags found
1 merge request!27Issue #145. Added page template and reviewer guide
Pipeline #115997 passed
Stage: delete-release
Stage: deploy-meilisearch
Stage: update-meilisearch-indexes
Stage: get-meili-key
Stage: build
Stage: deploy
Hide whitespace changes
Inline Side-by-side
helpers/system-template.md
+ 77
− 79
View file @ 7e9b54cb
title: <!--Replace this with Defense system name--> <!-- The following block is th frontmatter that will be used to build the big table -->
tableColumns: ---
article: title: <!--Replace this with Defense system name-->
doi: <!--Replace this with the main article doi--> tableColumns:
abstract: article:
<!--Replace this with the abstract of the main article--> doi: <!--Replace this with the main article doi-->
Sensor: '<!--Fill sensor name here. If it's unknown : Leave it blank -->' abstract:
Activator: ' <!--Fill activator name here. If it's unknown : Leave it blank -->' <!--Replace this with the abstract of the main article-->
Effector: '<!--Fill effector name here. If it's unknown : Leave it blank -->' Sensor: <!--Fill sensor name here. If it's unknown : Leave it blank -->
PFAM: <!--PFXXXXX, PFYYYYY, PFZZZZZ--> Activator: <!--Fill activator name here. If it's unknown : Leave it blank -->
Effector: <!--Fill effector name here. If it's unknown : Leave it blank -->
<!--Markdown syntax in a nutshell--> PFAM: <!--PFXXXXX, PFYYYYY, PFZZZZZ-->
<!--Move it to a dedicated file ?--> relevantAbstracts:
<!--Use # for titles : # Main title ; ## Secondary title ; ### Tertiary title ; etc.--> - doi: 10.xxxx/toto.yyyy.zz
<!--Use * * for italic : *this text will be displayed in italic*--> contributors:
<!--Use ** ** for bold text : **this text will be displayed in bold**--> - John Doe
<!--Use []() for links to external websites : ![This text will be displayed, if you click on it you will be directed to the website](https://url.of.the.website)--> ---
<!--Use ![alt text](path.to.image "Image title") to embed an image. Do we have an 'images' directory in the repo ?-->
<!--That's all folks!--> <!--
Markdown syntax in a nutshell, check other pages for example
# Defense system name
<!--Replace the main title with the name of the defense system Use # for titles : # Main title ; ## Secondary title ; ### Tertiary title ; etc.
Use * * for italic : *this text will be displayed in italic*
Example : # CBASS Use ** ** for bold text : **this text will be displayed in bold**
--> Use []() for links to external websites : ![This text will be displayed, if you click on it you will be directed to the website](https://url.of.the.website)
Use ![alt text](/system/system.svg) to embed an image. The file of the image should be in a folder with the name of the system, located in /public
## Description Use for references : "This is a great results :ref{doi=10.xxxx/toto.yyyy.zz}." it will write "This is a great result (Foo et al, 2023)."
<!--This paragraph contains a short description of the defense system. It should provide the essential information regarding the system at a glance.
- How many proteins compose the defense system ? What are their name and what is their biological function ? That's all folks!
- Optionally, you can quickly state in which model organism the system was tested and against which phages.
Please don't forget to refer to the articles that you will cite at the end of the article. -->
This should be precise but as synthetic as possible (rule of thumb : a dozen of lines maximum).
Example : # Defense system name
"RADAR is comprised of two genes, encoding respectively for an adenosine triphosphatase (RdrA) and a divergent adenosine deaminase (RdrB) [1], which are in some cases associated with a small membrane protein (RdrC or D) [1]. <!--Replace the main title with the name of the defense system
RADAR was found to perform RNA editing of adenosine to inosine during phage infection. Editing sites are broadly distributed on the host transcriptome, which could prove deleterious to the host and explain the observed growth arrest of RADAR upon phage infection."
--> Example : # CBASS
-->
## Molecular mechanism
<!--If the mechanism of action of the defense system is known, please describe it in one short paragraph. If the exact mechanism is not known, simply state it and sum up the information available in the literature. ## Description
This should be precise but as synthetic as possible (rule of thumb : a dozen of lines maximum). This paragraph contains a short description of the defense system. It should provide the essential information regarding the system at a glance.
- How many proteins compose the defense system ? What are their name and what is their biological function ?
Example : - Optionally, you can quickly state in which model organism the system was tested and against which phages.
The exact mechanism of action of the Shango defense system has not yet been characterized, but it was shown that the TerB domain and the catalytic activity of the ATPase and the Helicase are required to provide antiviral defense. The fact that TerB domains are known to be associated to the periplasmic membrane could indicate that Shango might be involved in membrane surveillance [1]. Please don't forget to refer to the articles that you will cite at the end of the article.
--> This should be precise but as synthetic as possible (rule of thumb : a dozen of lines maximum).
## Example of genomic structure Example :
<!--Automatically filled. "RADAR is comprised of two genes, encoding respectively for an adenosine triphosphatase (RdrA) and a divergent adenosine deaminase (RdrB) :ref{doi=10.xxxx/toto.yyyy.zz}. which are in some cases associated with a small membrane protein (RdrC or D) :ref{doi=10.xxxx/toto.yyyy.zz}.
You can optionally describe in more details which proteins compose the system if the Description paragraph did give all the information--> RADAR was found to perform RNA editing of adenosine to inosine during phage infection. Editing sites are broadly distributed on the host transcriptome, which could prove deleterious to the host and explain the observed growth arrest of RADAR upon phage infection."
## Distribution of the system among prokaryotes
<!--Automatically filled--> ## Molecular mechanism
If the mechanism of action of the defense system is known, please describe it in one short paragraph. If the exact mechanism is not known, simply state it and sum up the information available in the literature.
## Structure This should be precise but as synthetic as possible (rule of thumb : a dozen of lines maximum).
<!--Automatically filled-->
Example :
## Experimental validation The exact mechanism of action of the Shango defense system has not yet been characterized, but it was shown that the TerB domain and the catalytic activity of the ATPase and the Helicase are required to provide antiviral defense. The fact that TerB domains are known to be associated to the periplasmic membrane could indicate that Shango might be involved in membrane surveillance :ref{doi=10.xxxx/toto.yyyy.zz}.
<!--Give more information about the experimental validation :
- In which organism was it tested ?
- Against which phages ? ## Example of genomic structure
Please do not forget to cite the papers which provide the information. <!--Automatically filled.
--> You can optionally describe in more details which proteins compose the system if the Description paragraph did give all the information-->
## Relevant abstracts ## Distribution of the system among prokaryotes
::article-doi-list <!--Automatically filled-->
---
items: ## Structure
- doi: <!--replace this with the doi of a relevant abstract--> <!--Automatically filled-->
- doi: <!--replace this with the doi of a second relevant abstract-->
--- ## Experimental validation
:: <!--Give more information about the experimental validation :
- In which organism was it discovered ?
## References - In which organism was it tested ?
<!--Provide here the references mentioned in the wiki page : - Against which phages ?
- Citation in APA style + optionally the DOI in the following format : [doi](doi). - In which paper was this described ?
Or you can try to build the graph with mermaid (see help page or other page)
Example : -->
- Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., ... & Sorek, R. (2022). An expanded arsenal of immune systems that protect bacteria from phages. Cell host & microbe, 30(11), 1556-1569. [https://doi.org/10.1016/j.chom.2022.09.017](https://doi.org/10.1016/j.chom.2022.09.017)
-->
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment