From 76d9a4d54048fc306ddfb5b6963e319df623c347 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Sat, 16 Dec 2023 13:19:29 +0100
Subject: [PATCH] Fix typo: ref: -> :ref
---
content/3.defense-systems/gabija.md | 2 +-
content/3.defense-systems/nixi.md | 2 +-
content/3.defense-systems/pd-t4-6.md | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/content/3.defense-systems/gabija.md b/content/3.defense-systems/gabija.md
index b8f9aee1..88e5f388 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -24,7 +24,7 @@ relevantAbstracts:
## Description
-Gabija is named after the Lithuanian spirit of fire, protector of home and family. It is a two gene defense system found in 8.5% of the 4360 bacterial and archeal genomes that were initially analyzed :ref{doi=10.1126/science.aar4120}. Both proteins are necessary for defense and are forming a heteromeric octamer complex: GajA forms a central tetramer surrounded by two GajB dimers ref:{doi=10.1101/2023.05.01.538945,10.1093/nar/gkad951}. A phage protein inhibiting Gabija function was described, Gabidja anti defense 1 (Gad1) :ref{doi=10.1101/2023.05.01.538945,10.1101/2023.05.01.538930}.
+Gabija is named after the Lithuanian spirit of fire, protector of home and family. It is a two gene defense system found in 8.5% of the 4360 bacterial and archeal genomes that were initially analyzed :ref{doi=10.1126/science.aar4120}. Both proteins are necessary for defense and are forming a heteromeric octamer complex: GajA forms a central tetramer surrounded by two GajB dimers :ref{doi=10.1101/2023.05.01.538945,10.1093/nar/gkad951}. A phage protein inhibiting Gabija function was described, Gabidja anti defense 1 (Gad1) :ref{doi=10.1101/2023.05.01.538945,10.1101/2023.05.01.538930}.
## Molecular mechanism
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index 6b4704c0..2ae6b2a3 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -20,7 +20,7 @@ relevantAbstracts:
Phage-inducible chromosomal island-like elements (PLEs) are chromosomally-integrated phage parasites described in *Vibrio cholerae* :ref{doi=10.7554/eLife.53200}. PLEs excise in response to infection by phage ICP1 and halt its progeny production. PLE halts ICP1 infection by means of redirecting virion packaging and interfiring with ICP1 genome replication :ref{doi=10.1093/nar/gkz1005}. NixI is a PLE-encoded nuclease that nicks the ICP1 genome at specific sites preventing transition to the rolling circle replication (RCR) :ref{doi=10.1093/nar/gkac002}.
## Molecular mechanisms
-The NixI endonuclease cleaves the ICP1 genome at the GNAANCTT motif :ref{doi=10.1093/nar/gkac002}. It creates nicks and does not cause double stranded breaks ref:{doi=10.1093/nar/gkac002}.
+The NixI endonuclease cleaves the ICP1 genome at the GNAANCTT motif :ref{doi=10.1093/nar/gkac002}. It creates nicks and does not cause double stranded breaks :ref{doi=10.1093/nar/gkac002}.
## Example of genomic structure
diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md
index 5eb31a5e..4748ba2e 100644
--- a/content/3.defense-systems/pd-t4-6.md
+++ b/content/3.defense-systems/pd-t4-6.md
@@ -19,7 +19,7 @@ relevantAbstracts:
# PD-T4-6
## Description
-The PD-T4-6 system is composed of a single protein. It was discovered via a selection screening of 71 *E. coli* strains challenged with diverse phage. The name stands from Phage Defense (PD) and the phage with which the strain was challenge (T4) ref:{doi=10.1038/s41564-022-01219-4}. The system has been identified as an Abortive Infection (Abi) system ref:{doi=10.1038/s41564-022-01219-4,10.1016/j.mib.2023.102312}. The protein was found within a P2-like prophage and contains a predicted Der/Thr kinase domain. Site-specific mutation in the domain reduces phage protection ref:{doi=10.1038/s41564-022-01219-4}.
+The PD-T4-6 system is composed of a single protein. It was discovered via a selection screening of 71 *E. coli* strains challenged with diverse phage. The name stands from Phage Defense (PD) and the phage with which the strain was challenge (T4) :ref{doi=10.1038/s41564-022-01219-4}. The system has been identified as an Abortive Infection (Abi) system :ref{doi=10.1038/s41564-022-01219-4,10.1016/j.mib.2023.102312}. The protein was found within a P2-like prophage and contains a predicted Der/Thr kinase domain. Site-specific mutation in the domain reduces phage protection :ref{doi=10.1038/s41564-022-01219-4}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
--
GitLab