From 93eaf0d8639297b3cd329dca7585fec1365fc98d Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Mon, 18 Sep 2023 14:55:45 +0200
Subject: [PATCH] Fix error links
---
.gitlab-ci.yml | 3 +--
content/2.defense-systems/0.index.md | 18 +-----------------
content/2.defense-systems/brex.md | 4 ++--
content/2.defense-systems/disarm.md | 2 +-
content/2.defense-systems/rst_paris.md | 2 +-
5 files changed, 6 insertions(+), 23 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ec4184c4..ef90f0d3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,6 +16,7 @@ stages:
image: docker:24
variables:
CONTEXT: "."
+ DOCKERFILE: "Dockerfile"
before_script:
- i=0; while [ "$i" -lt 12 ]; do docker info && break; sleep 5; i=$(( i + 1 )) ; done
- docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
@@ -41,9 +42,7 @@ stages:
build:dev:nuxt:
extends: .build
variables:
- DOCKERFILE: "Dockerfile"
IMAGE_NAME: "df-wiki"
- CONTEXT: "./"
rules:
- if: $CI_COMMIT_BRANCH != "main"
diff --git a/content/2.defense-systems/0.index.md b/content/2.defense-systems/0.index.md
index 897d91ad..9d3a6693 100644
--- a/content/2.defense-systems/0.index.md
+++ b/content/2.defense-systems/0.index.md
@@ -11,23 +11,7 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
-::list-systems
----
-systems:
- - system: Paris
- dois:
- - 10.1101/2021.01.21.427644
- - system: AbiE
- dois:
- - 10.1093/nar/gkt1419
- - system: AVAST
- dois:
- - 10.1126/science.aba0372
- - system: RM
- dois:
- - 10.1093/nar/gku734
----
-::
+
diff --git a/content/2.defense-systems/brex.md b/content/2.defense-systems/brex.md
index 640c57d5..7c7338ee 100644
--- a/content/2.defense-systems/brex.md
+++ b/content/2.defense-systems/brex.md
@@ -4,13 +4,13 @@ title: BREX
## Description
-BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/list_defense_systems/RM)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1).
+BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/defense-systems/rm)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1).
BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific (1).
## Molecular mechanism
-*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/list_defense_systems/RM) systems.Â
+*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/defense-systems/rm) systems.Â
However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids (1).Â
diff --git a/content/2.defense-systems/disarm.md b/content/2.defense-systems/disarm.md
index 153d6dde..c24239e8 100644
--- a/content/2.defense-systems/disarm.md
+++ b/content/2.defense-systems/disarm.md
@@ -6,7 +6,7 @@ title: DISARM
DISARM (Defense Island System Associated with Restriction-Modification) is a defense system widespread in prokaryotes, encoded by a 5-gene cassette. DISARM provides broad protection against double-stranded DNA phages, including siphophages, myophages, and podophages (1,3).
-Â It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/list_defense_systems/RM)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2).
+Â It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/defense-systems/rm)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2).
## Molecular mechanism
diff --git a/content/2.defense-systems/rst_paris.md b/content/2.defense-systems/rst_paris.md
index 8422d207..52e9a898 100644
--- a/content/2.defense-systems/rst_paris.md
+++ b/content/2.defense-systems/rst_paris.md
@@ -6,7 +6,7 @@ title: Rst_PARIS
PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1).
-This system relies on an unknown [Abortive infection](/general_concepts/Abi) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3).Â
+This system relies on an unknown [Abortive infection](/general-concepts/abortive-infection) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3).Â
## Example of genomic structure
--
GitLab