Update 0.index.md

MR new system template

This is a guide to help you review an article of the wiki. Please check that all the following criteria are met to consider that a page is complete and correct.

• The article is correctly structured. It should contain :
  1. Header with the following fields (please pay attention to block indentation)

---
title: 
tableColumns: 
  article:
    doi: 
    abstract: 
  Sensor: 
  Activator: 
  Effector: 
  PFAM: 
contributors: 
  - Firstname Lastname
relevantAbstracts:
  - doi: my-doi
---

2. The following paragraphs - Description - Molecular mechanisms - Example of genomic structure - Distribution of the system among prokaryotes - Structure - Experimental validation - References with the following syntax : :ref{doi=my-doi}.

• The header contains all the required information. The information provided in the header is required to display the list of defense systems.
  • The mandatory fields are :
    • title:
    • article
    • doi
    • abstract
    • PFAM
  • Optional fields are :
    • Sensor
    • Activator
    • Effector.
  • Main title is correct. For a defense system, it should simply be the name of the system.
  • All the information is provided, correct and understandable. Rule of thumb : As a newcommer in the field, does the page provide the essential information in a clear way regarding the system ?
    • Short description of the system
    • Composition of the system
    • Mechanism of action if it is known
    • References to the literature to further explore the defense system
  • Links with the database are working.
    • Distribution of the system among prokaryotes
    • Structure display
  • At least one relevant abstract is provided.

content/0.index.md

@@ -4,12 +4,22 @@ layout: article
 navigation:
   icon: 'md:home'
 relevantAbstracts:
+  - doi: 10.1126/science.1138140
   - doi: 10.1038/nmicrobiol.2017.92
+  - doi: 10.1128/jb.65.2.113-121.1953
+  - doi: 10.1126/science.aar4120
+  - doi: 10.1126/science.aba0372
+  - doi: 10.1038/s41586-019-1894-8
+  - doi: 10.1128/jb.64.4.557-569.1952
+  - doi: 10.1128/JB.05535-11
+  - doi: 10.1016/j.cell.2021.12.029
+  
+
 ---
 
 ## Introduction
 
-Bacteriophages, or phages for short, are viruses that infect bacteria and hijack bacterial cellular machinery to reproduce themselves. Phages are extremely abundant entities, and could be responsible for up to 20-40% of bacterial mortality daily (Hampton et al., 2020). Therefore, phage infection constitutes a very strong evolutionary pressure for bacteria.
+Bacteriophages, or phages for short, are viruses that infect bacteria and hijack bacterial cellular machinery to reproduce themselves. Phages are extremely abundant entities, and could be responsible for up to 20-40% of bacterial mortality daily :ref{doi=10.1038/s41586-019-1894-8}. Therefore, phage infection constitutes a very strong evolutionary pressure for bacteria.
 
 In response to this evolutionary pressure, bacteria have developed an arsenal of anti-phage defense systems. The term "defense system" here designates either a single gene or a set of genes, which expression provides the bacteria with some level of resistance against phage infection.
 
@@ -19,7 +29,7 @@ The first anti-phage defense system was discovered in the early 1950s by two sep
 
 Their work was in fact the first report of what would later be named Restriction-Modification ([RM](/defense-systems/rm)) system, which is considered to be the first anti-phage defense system discovered.
 
-The sighting of a second defense system occured more than 40 years later, in the late 1980s, when several teams around the world observed arrays containing short, palindromic DNA repeats clustered together on the bacterial genome (Barrangou et al., 2017). Yet, the biological function of these repeats was only elucidated in 2007, when a team of researchers demonstrated that these repeats were part of a new anti-phage defense systems (Barrangou et al., 2007) , known as [CRISPR-Cas system](https://en.wikipedia.org/wiki/CRISPR).
+The sighting of a second defense system occured more than 40 years later, in the late 1980s, when several teams around the world observed arrays containing short, palindromic DNA repeats clustered together on the bacterial genome (Barrangou et al., 2017). Yet, the biological function of these repeats was only elucidated in 2007, when a team of researchers demonstrated that these repeats were part of a new anti-phage defense systems :ref{doi=10.1126/science.1138140}, known as [CRISPR-Cas system](https://en.wikipedia.org/wiki/CRISPR).
 
 Following these two major breakthroughs, knowledge of anti-phage systems remained scarce for some years. Yet, in 2011, Makarova and colleagues revealed that anti-phage systems tend to colocalize on the bacterial genome in defense-islands. This led to a guilt-by-association hypothesis : if a gene or a set of genes is frequently found in bacterial genomes in close proximity to known defense systems, such as RM or CRISPR-Cas systems, then it might constitute a new defense system. This concept had a large role in the discovery of an impressive diversity of defense systems in a very short amount of time. To date, more than 60 defense systems have been described.
 
@@ -28,40 +38,3 @@ Following these two major breakthroughs, knowledge of anti-phage systems remaine
 To date, more than 60 anti-phage defense systems have been described. An exhaustive list of the systems with experimentally validated anti-phage activity can be found [here](/defense-systems).
 
 ## Molecular mechanisms
-
-## References
-
-Barrangou, R. et al. CRISPR provides acquired resistance against viruses in
-prokaryotes. Science 315, 1709–1712 (2007)
-
-Barrangou R, Horvath P. A decade of discovery: CRISPR functions and applications. Nat Microbiol. 2017 Jun 5;2:17092. doi: 10.1038/nmicrobiol.2017.92. PMID: 28581505
-
-BERTANI, G, and J J WEIGLE. “Host controlled variation in bacterial viruses.” Journal of bacteriology vol. 65,2 (1953): 113-21. doi:10.1128/jb.65.2.113-121.1953
-
-Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R. Systematic discovery of antiphage defense systems in the microbial pangenome. Science. 2018 Mar 2;359(6379):eaar4120. doi: 10.1126/science.aar4120. Epub 2018 Jan 25. PMID: 29371424; PMCID: PMC6387622.
-
-Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372
-
-Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020)
-
-LURIA SE, HUMAN ML. A nonhereditary, host-induced variation of bacterial viruses. J Bacteriol. 1952;64(4):557-569. doi:10.1128/jb.64.4.557-569.1952
-
-Makarova KS, Wolf YI, Snir S, Koonin EV. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol. 2011 Nov;193(21):6039-56. doi: 10.1128/JB.05535-11. Epub 2011 Sep 9. PMID: 21908672; PMCID: PMC3194920.
-
-Tal N, Sorek R. SnapShot: Bacterial immunity. Cell. 2022 Feb 3;185(3):578-578.e1. doi: 10.1016/j.cell.2021.12.029. PMID: 35120666.
-
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1126/science.1138140
-      abstract: |
-        Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophages. We found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences. Removal or addition of particular spacers modified the phage-resistance phenotype of the cell. Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.
-    - doi: 10.1038/nmicrobiol.2017.92
-    - doi: 10.1128/jb.65.2.113-121.1953
-    - doi: 10.1126/science.aar4120
-    - doi: 10.1126/science.aba0372
-    - doi: 10.1038/s41586-019-1894-8
-    - doi: 10.1128/jb.64.4.557-569.1952
----
-::