From 2f44c5730e942be6e1a475f0876fd9b65cf64914 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Wed, 6 Sep 2023 14:09:20 +0200
Subject: [PATCH] refactor
---
components/Nav/Navigation.vue | 18 +---
components/content/ListSystems.vue | 19 ++++
content/0.index.md | 2 +-
.../1.introduction/{index.md => 0.index.md} | 44 +---------
content/1.introduction/_dir.yml | 1 -
content/2.defense-systems/_dir.yml | 2 -
.../1.abortive-infection/index.md | 10 +++
content/2.general-concepts/index.md | 10 +++
.../0.index.md | 47 +++++++---
.../1.paris.md} | 2 +-
.../2.AbiE.md => 3.defense-systems/2.abie.md} | 2 +-
.../3.avast.md} | 2 +-
content/3.defense-systems/4.rm.md | 43 +++++++++
content/3.defense-systems/5.viperin.md | 87 +++++++++++++++++++
content/list.json | 14 ---
layouts/article.vue | 21 ++---
nuxt.config.ts | 2 +-
pages/[...slug].vue | 3 +-
pages/list.vue | 27 ------
19 files changed, 222 insertions(+), 134 deletions(-)
create mode 100644 components/content/ListSystems.vue
rename content/1.introduction/{index.md => 0.index.md} (54%)
delete mode 100644 content/1.introduction/_dir.yml
delete mode 100644 content/2.defense-systems/_dir.yml
create mode 100644 content/2.general-concepts/1.abortive-infection/index.md
create mode 100644 content/2.general-concepts/index.md
rename content/{2.defense-systems => 3.defense-systems}/0.index.md (89%)
rename content/{2.defense-systems/1.PARIS.md => 3.defense-systems/1.paris.md} (87%)
rename content/{2.defense-systems/2.AbiE.md => 3.defense-systems/2.abie.md} (99%)
rename content/{2.defense-systems/3.AVAST.md => 3.defense-systems/3.avast.md} (95%)
create mode 100644 content/3.defense-systems/4.rm.md
create mode 100644 content/3.defense-systems/5.viperin.md
delete mode 100644 content/list.json
delete mode 100644 pages/list.vue
diff --git a/components/Nav/Navigation.vue b/components/Nav/Navigation.vue
index 36583b69..6ead9e06 100644
--- a/components/Nav/Navigation.vue
+++ b/components/Nav/Navigation.vue
@@ -11,25 +11,13 @@ const props = defineProps<{
<template v-for="navItem in props.navigation">
<v-list-group v-if="navItem?.children" :value="navItem.title">
<template v-slot:activator="{ props }">
- <v-list-item
- v-bind="props"
- :title="navItem.title"
- active-color="primary"
- exact
- nav
- ></v-list-item>
+ <v-list-item v-bind="props" :title="navItem.title" color="primary" exact nav></v-list-item>
</template>
<Navigation :navigation="navItem.children" />
</v-list-group>
<template v-else>
- <v-list-item
- :title="navItem.title"
- :value="navItem.title"
- :to="navItem._path"
- active-color="primary"
- exact
- nav
- ></v-list-item>
+ <v-list-item :title="navItem.title" :value="navItem.title" :to="navItem._path" color="primary" exact
+ nav></v-list-item>
</template>
</template>
</template>
diff --git a/components/content/ListSystems.vue b/components/content/ListSystems.vue
new file mode 100644
index 00000000..a17b7ca4
--- /dev/null
+++ b/components/content/ListSystems.vue
@@ -0,0 +1,19 @@
+<script setup lang="ts">
+
+const props = defineProps<{
+ systems: any;
+}>();
+
+const headers = ref([{
+ title: "Systems",
+ key: "system"
+}])
+
+</script>
+<template>
+ <v-card>
+ <v-card-text>
+ <v-data-table items-per-page="5" :headers="headers" :items="props.systems" class="elevation-1"></v-data-table>
+ </v-card-text>
+ </v-card>
+</template>
\ No newline at end of file
diff --git a/content/0.index.md b/content/0.index.md
index f04a96e2..415515dc 100755
--- a/content/0.index.md
+++ b/content/0.index.md
@@ -8,7 +8,7 @@ layout: custom
This page corresponds to the `/` route of your website. You can delete it or create another file in the `content/` directory.
-Try to navigate to [/about](/about). These 2 pages are rendered by the `pages/[...slug].vue` component.
+
---
diff --git a/content/1.introduction/index.md b/content/1.introduction/0.index.md
similarity index 54%
rename from content/1.introduction/index.md
rename to content/1.introduction/0.index.md
index 1e973aff..31f5cbb2 100644
--- a/content/1.introduction/index.md
+++ b/content/1.introduction/0.index.md
@@ -13,56 +13,18 @@ In response to this evolutionary pressure, bacteria have developed an arsenal of
The first anti-phage defense system was discovered in the early 1950s by two separate teams of researchers (Luria and Human, 1952 ; Bertani and Wiegle 1952). Luria and Human reported a mysterious phenomenon, where one phage was only capable of infecting a specific bacterial strain once. The progeny phages produced by this first round of infection had lost their ability to infect the same strain again, yet remained able to infect other bacterial strains. For them, this could only mean that "the genotype of the host in which a virus reproduces affects the phenotype of the new virus" (Luria and Human, 1952). A similar phenomenon was shortly after described by Bertani and Wiegle.
-Their work was in fact the first report of what would later be named Restriction-Modification ([RM](/list_defense_systems/RM)) system, which is considered to be the first anti-phage defense system discovered.
+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](/list_defense_systems/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 (Barrangou et al., 2007) , 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.
## List of known defense systems
-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).
+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
-The molecular mechanisms responsible for the anti-phage activity of defense systems are diverse. Overall, these molecular mechanisms can be divided into 3 categories (Tal and Sorek, 2022):
-
-- **Degrading phage nucleic acids (either DNA or RNA)**
-
-One or a combination of enzymes will degrade phage nucleic acids upon their injection into the bacterial host.
-
-Target nucleic acid recognition and degradation of the target (often through endonuclease activity) are key functions performed by these defense systems. To avoid collateral damage to the bacterial DNA, these functions are accompanied by mechanisms allowing Self versus Non-Self discrimination.
-
-[RM](/list_defense_systems/RM) and [CRISPR-Cas](/list_defense_systems/CRISPR) systems are the main representants of this type of anti-phage systems.
-
-- **Inhibiting nucleic acid synthesis**
-
-After phage nucleic acids are injected, their replication and/or transcription is inhibited.
-
-This can be achieved by the bacteria through the production of small anti-phage molecules (see [Chemical defense](/general_concepts/Chemical_defense)). For instance, [prokaryotic viperins](/list_defense_systems/viperins) produce chain terminators which, once integrated in a nascent nucleic acid, stop its further elongation.
-
-Another possible strategy is the depletion of cell components essential to viral replication. For instance, some enzymes (like dGTPase) deplete the cytosolic pool of deoxynucleotide triphosphates (dNTPs), which are essential building blocks for nucleic acid synthesis.
-
-- **Abortive infection**
-
-Abortive infection can be described as the suicide of a bacteria when infected by a phage. The premature death of the bacterial host prevents the completion of the phage infection cycle, therefore avoiding the production and release of a multitude of newly formed phages. This represents a widespread strategy for anti-phage defense at the community level in bacterial populations.
-
-Abortive infection usually involves a sensor module responsible for detecting phage infection and activating an effector module, which will in turn mediates cell death.
-
-## Impact and applications of defense systems in diverse fields
-
-The study of anti-phage defense systems has had a significant impact on a striking amount of research and industry fields:
-
-- **molecular biology**
-
-The discovery of the first anti-phage system also marked the discovery of restriction enzymes, which are key elements of RM systems. Through their ability to recognize specific nucleic sequences and cleave nucleic acid, restriction enzymes quickly became invaluable tools for molecular biology. A Nobel Prize was awarded in 1978 to Werner Arber, Daniel Nathans and Hamilton O. Smith ["for the discovery of restriction enzymes and their application to problems of molecular genetics."](/https://www.nobelprize.org/prizes/medicine/1978/summary/)
-
-A few decades later, the discovery of CRISPR-Cas systems also created a major genome editing revolution. The Cas nucleases are major components of CRISPR-Cas, and are able to specifically recognize and bind a given nucleic sequence thanks to an RNA guide. This RNA guide can easily be programmed to target any desired sequence, making CRISPR-Cas derived components extremely powerful tools for researchers. A Nobel prize was awarded in 2020 to Emmanuelle Charpentier and Jennifer A. Doudna ["for the development of a method for genome editing"](/https://www.nobelprize.org/prizes/chemistry/2020/summary/).
-
-- **agri-food industries**
-
-- **human health**
-
## References
Barrangou, R. et al. CRISPR provides acquired resistance against viruses in
diff --git a/content/1.introduction/_dir.yml b/content/1.introduction/_dir.yml
deleted file mode 100644
index 9effc99b..00000000
--- a/content/1.introduction/_dir.yml
+++ /dev/null
@@ -1 +0,0 @@
-icon: ic:round-star
\ No newline at end of file
diff --git a/content/2.defense-systems/_dir.yml b/content/2.defense-systems/_dir.yml
deleted file mode 100644
index 24957f0b..00000000
--- a/content/2.defense-systems/_dir.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-title: Defense Systems
-icon: ic:sharp-shield
\ No newline at end of file
diff --git a/content/2.general-concepts/1.abortive-infection/index.md b/content/2.general-concepts/1.abortive-infection/index.md
new file mode 100644
index 00000000..82a892a6
--- /dev/null
+++ b/content/2.general-concepts/1.abortive-infection/index.md
@@ -0,0 +1,10 @@
+---
+title: Abortive Infection
+layout: article
+toc: true
+---
+
+
+## encore
+
+This section is empty. You can help by adding to it.
diff --git a/content/2.general-concepts/index.md b/content/2.general-concepts/index.md
new file mode 100644
index 00000000..08c7522b
--- /dev/null
+++ b/content/2.general-concepts/index.md
@@ -0,0 +1,10 @@
+---
+title: General Concepts
+toc: true
+layout: article
+---
+
+
+## Tzqr
+
+du contenu
\ No newline at end of file
diff --git a/content/2.defense-systems/0.index.md b/content/3.defense-systems/0.index.md
similarity index 89%
rename from content/2.defense-systems/0.index.md
rename to content/3.defense-systems/0.index.md
index d2087bd6..9e4d65b2 100644
--- a/content/2.defense-systems/0.index.md
+++ b/content/3.defense-systems/0.index.md
@@ -1,6 +1,7 @@
---
title: List of defense systems
layout: article
+
---
# List of defense systems
@@ -14,9 +15,9 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
| [AbiE](/defense-systems/abie) | Dy, R.L., Przybilski, R., Semeijn, K., Salmond, G.P.C., Fineran, P.C., 2014. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res 42, 4590–4605. [https://doi.org/10.1093/nar/gkt1419](https://doi.org/10.1093/nar/gkt1419) |
| AbiH | Prévots, F., Daloyau, M., Bonin, O., Dumont, X., Tolou, S., 1996. Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp. lactis biovar. diacetylactis S94. FEMS Microbiol Lett 142, 295–299. [https://doi.org/10.1111/j.1574-6968.1996.tb08446.x](https://doi.org/10.1111/j.1574-6968.1996.tb08446.x) |
| Ago | Garb, J. _et al._ _Multiple phage resistance systems inhibit infection via SIR2-dependent NAD + depletion_. (2021). doi:10.1101/2021.12.14.472415.<br><br>Zeng Z, Chen Y, Pinilla-Redondo R, Shah SA, Zhao F, Wang C, Hu Z, Wu C, Zhang C, Whitaker RJ, She Q, Han W. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. Cell Host Microbe. 2022 Jul 13;30(7):930-943.e6. doi: 10.1016/j.chom.2022.04.015. Epub 2022 May 19. PMID: 35594868. |
-| [AVAST](/list_defense_systems/AVAST) | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
-| [BREX](/list_defense_systems/BREX) | Goldfarb, T., Sberro, H., Weinstock, E., Cohen, O., Doron, S., Charpak-Amikam, Y., Afik, S., Ofir, G., Sorek, R., 2015. BREX is a novel phage resistance system widespread in microbial genomes. The EMBO Journal 34, 169–183. [https://doi.org/10.15252/embj.201489455](https://doi.org/10.15252/embj.201489455) |
-| [BstA](/list_defense_systems/BstA) | Owen, S.V., Wenner, N., Dulberger, C.L., Rodwell, E.V., Bowers-Barnard, A., Quinones-Olvera, N., Rigden, D.J., Rubin, E.J., Garner, E.C., Baym, M., Hinton, J.C.D., 2020. Prophage-encoded phage defence proteins with cognate self-immunity. bioRxiv 2020.07.13.199331. [https://doi.org/10.1101/2020.07.13.199331](https://doi.org/10.1101/2020.07.13.199331) |
+| [AVAST](/defense-systems/avast) | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| BREX | Goldfarb, T., Sberro, H., Weinstock, E., Cohen, O., Doron, S., Charpak-Amikam, Y., Afik, S., Ofir, G., Sorek, R., 2015. BREX is a novel phage resistance system widespread in microbial genomes. The EMBO Journal 34, 169–183. [https://doi.org/10.15252/embj.201489455](https://doi.org/10.15252/embj.201489455) |
+| BstA | Owen, S.V., Wenner, N., Dulberger, C.L., Rodwell, E.V., Bowers-Barnard, A., Quinones-Olvera, N., Rigden, D.J., Rubin, E.J., Garner, E.C., Baym, M., Hinton, J.C.D., 2020. Prophage-encoded phage defence proteins with cognate self-immunity. bioRxiv 2020.07.13.199331. [https://doi.org/10.1101/2020.07.13.199331](https://doi.org/10.1101/2020.07.13.199331) |
| Cas | Bernheim, A., Bikard, D., Touchon, M., Rocha, E.P.C., 2020. Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements. Nucleic Acids Res 48, 748–760. [https://doi.org/10.1093/nar/gkz1091](https://doi.org/10.1093/nar/gkz1091) |
| CBASS | Millman, A., Melamed, S., Amitai, G., Sorek, R., 2020. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nature Microbiology 5, 1608–1615. [https://doi.org/10.1038/s41564-020-0777-y](https://doi.org/10.1038/s41564-020-0777-y) |
| DarTG | LeRoux, M., Srikant, S., Littlehale, M.H., Teodoro, G., Doron, S., Badiee, M., Leung, A.K.L., Sorek, R., Laub, M.T., 2021. The DarTG toxin-antitoxin system provides phage defense by ADP-ribosylating viral DNA. bioRxiv 2021.09.27.462013. [https://doi.org/10.1101/2021.09.27.462013](https://doi.org/10.1101/2021.09.27.462013) |
@@ -27,7 +28,7 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
| DRT | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
| Druantia | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
| Dsr | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
-| [Gabija](/list_defense_systems/Gabija) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Gabija | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
| Gao_ApeA | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
| Gao_Her | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
| Gao_Hhe | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
@@ -40,19 +41,19 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
| Gao_Tmn | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
| Gao_Upx | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
| GasderMIN | Johnson, A.G., Wein, T., Mayer, M.L., Duncan-Lowey, B., Yirmiya, E., Oppenheimer-Shaanan, Y., Amitai, G., Sorek, R., Kranzusch, P.J., 2021. Bacterial gasdermins reveal an ancient mechanism of cell death. bioRxiv 2021.06.07.447441. [https://doi.org/10.1101/2021.06.07.447441](https://doi.org/10.1101/2021.06.07.447441) |
-| [Hachiman](/list_defense_systems/Hachiman) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Hachiman | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
| Kiwa | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
-| [Lamassu](/list_defense_systems/Lamassu) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Lamassu | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
| Lit | Uzan, M., Miller, E.S., 2010. Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation. Virology Journal 7, 360. [https://doi.org/10.1186/1743-422X-7-360](https://doi.org/10.1186/1743-422X-7-360) |
| Nhi | Bari, S.M.N., Chou-Zheng, L., Cater, K., Dandu, V.S., Thomas, A., Aslan, B., Hatoum-Aslan, A., 2019. A unique mode of nucleic acid immunity performed by a single multifunctional enzyme. bioRxiv 776245. [https://doi.org/10.1101/776245](https://doi.org/10.1101/776245) |
| NixI | LeGault, K.N., Barth, Z.K., DePaola, P., Seed, K.D., 2021. A phage parasite deploys a nicking nuclease effector to inhibit replication of its viral host. bioRxiv 2021.07.12.452122. [https://doi.org/10.1101/2021.07.12.452122](https://doi.org/10.1101/2021.07.12.452122) |
-| [PARIS](/list_defense_systems/PARIS) | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| [PARIS](/defense-systems/paris) | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
| Pif | Cram, D., Ray, A., Skurray, R., 1984. Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage. Mol Gen Genet 197, 137–142. [https://doi.org/10.1007/BF00327934](https://doi.org/10.1007/BF00327934) |
| PrrC | Uzan, M., Miller, E.S., 2010. Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation. Virology Journal 7, 360. [https://doi.org/10.1186/1743-422X-7-360](https://doi.org/10.1186/1743-422X-7-360) |
-| [RADAR](/list_defense_systems/RADAR) | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| RADAR | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
| Retron | Mestre, M.R., González-Delgado, A., Gutiérrez-Rus, L.I., MartÃnez-Abarca, F., Toro, N., 2020. Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. Nucleic Acids Res 48, 12632–12647. [https://doi.org/10.1093/nar/gkaa1149](https://doi.org/10.1093/nar/gkaa1149) <br><br>Millman, A., Bernheim, A., Stokar-Avihail, A., Fedorenko, T., Voichek, M., Leavitt, A., Oppenheimer-Shaanan, Y., Sorek, R., 2020. Bacterial Retrons Function In Anti-Phage Defense. Cell 183, 1551-1561.e12. [https://doi.org/10.1016/j.cell.2020.09.065](https://doi.org/10.1016/j.cell.2020.09.065) |
| RexAB | Parma, D.H., Snyder, M., Sobolevski, S., Nawroz, M., Brody, E., Gold, L., 1992. The Rex system of bacteriophage lambda: tolerance and altruistic cell death. Genes Dev 6, 497–510. [https://doi.org/10.1101/gad.6.3.497](https://doi.org/10.1101/gad.6.3.497) |
-| [RM](/defense_systems/RM) | Oliveira, P.H., Touchon, M., Rocha, E.P.C., 2014. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Research 42, 10618. [https://doi.org/10.1093/nar/gku734](https://doi.org/10.1093/nar/gku734) |
+| [RM](/defense-systems/rm) | Oliveira, P.H., Touchon, M., Rocha, E.P.C., 2014. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Research 42, 10618. [https://doi.org/10.1093/nar/gku734](https://doi.org/10.1093/nar/gku734) |
| Rst_2TM_1TM_TIR | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
| Rst_3HP | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
| Rst_DprA-PPRT | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
@@ -67,13 +68,33 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
| Shedu | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
| SspBCDE | Wang, S., Wan, M., Huang, R., Zhang, Y., Xie, Y., Wei, Y., Ahmad, M., Wu, D., Hong, Y., Deng, Z., Chen, S., Li, Z., Wang, L., n.d. SspABCD-SspFGH Constitutes a New Type of DNA Phosphorothioate-Based Bacterial Defense System. mBio 12, e00613-21. [https://doi.org/10.1128/mBio.00613-21](https://doi.org/10.1128/mBio.00613-21) |
| Stk2 | Depardieu, F., Didier, J.-P., Bernheim, A., Sherlock, A., Molina, H., Duclos, B., Bikard, D., 2016. A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages. Cell Host & Microbe 20, 471–481. [https://doi.org/10.1016/j.chom.2016.08.010](https://doi.org/10.1016/j.chom.2016.08.010) |
-| [Thoeris](/list_defense_systems/Thoeris) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
-| [Viperin](/list_defense_systems/viperins) | Bernheim, A., Millman, A., Ofir, G., Meitav, G., Avraham, C., Shomar, H., Rosenberg, M.M., Tal, N., Melamed, S., Amitai, G., Sorek, R., 2021. Prokaryotic viperins produce diverse antiviral molecules. Nature 589, 120–124. [https://doi.org/10.1038/s41586-020-2762-2](https://doi.org/10.1038/s41586-020-2762-2) |
+| Thoeris | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| [Viperin](/defense-systems/viperin) | Bernheim, A., Millman, A., Ofir, G., Meitav, G., Avraham, C., Shomar, H., Rosenberg, M.M., Tal, N., Melamed, S., Amitai, G., Sorek, R., 2021. Prokaryotic viperins produce diverse antiviral molecules. Nature 589, 120–124. [https://doi.org/10.1038/s41586-020-2762-2](https://doi.org/10.1038/s41586-020-2762-2) |
| Wadjet | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
-| Zorya | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Zorya | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120)
+
+
+
+
+ |
**From** **_Tesson et al., 2022_**
+
+
+::list-systems
+---
+systems:
+ - system: Paris
+ - system: Abie
+---
+::
+
## References
-Florian Tesson, Alexandre Hervé, Marie Touchon, Camille d’Humières, Jean Cury, Aude Bernheim, bioRxiv 2021.09.02.458658; doi: https://doi.org/10.1101/2021.09.02.458658
+::references-list
+---
+items:
+ - 10.1101/2021.09.02.458658
+---
+::
\ No newline at end of file
diff --git a/content/2.defense-systems/1.PARIS.md b/content/3.defense-systems/1.paris.md
similarity index 87%
rename from content/2.defense-systems/1.PARIS.md
rename to content/3.defense-systems/1.paris.md
index ec087763..fc6d7898 100644
--- a/content/2.defense-systems/1.PARIS.md
+++ b/content/3.defense-systems/1.paris.md
@@ -8,7 +8,7 @@ layout: article
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).
+This system relies on an unknown 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).
## Relevant abstracts
diff --git a/content/2.defense-systems/2.AbiE.md b/content/3.defense-systems/2.abie.md
similarity index 99%
rename from content/2.defense-systems/2.AbiE.md
rename to content/3.defense-systems/2.abie.md
index 1d7331fa..94a93783 100644
--- a/content/2.defense-systems/2.AbiE.md
+++ b/content/3.defense-systems/2.abie.md
@@ -6,7 +6,7 @@ title: AbiE
AbiE is a family of an anti-phage defense systems. They act through a Toxin-Antitoxin mechanism, and are comprised of a pair of genes, with one gene being toxic while the other confers immunity to this toxicity.
-It is classified as an [Abortive infection](/general_concepts/Abi) system.
+It is classified as an Abortive infection system.
## Mechanism
diff --git a/content/2.defense-systems/3.AVAST.md b/content/3.defense-systems/3.avast.md
similarity index 95%
rename from content/2.defense-systems/3.AVAST.md
rename to content/3.defense-systems/3.avast.md
index 3834f923..a0b7e355 100644
--- a/content/2.defense-systems/3.AVAST.md
+++ b/content/3.defense-systems/3.avast.md
@@ -8,7 +8,7 @@ AVAST (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-ph
AVAST systems are composed of NTPases of the STAND (signal transduction ATPases with numerous associated domains) superfamily (1). Â STAND-NTPases typically contain a C-terminal helical sensor domain that activates the N-terminal effector domain upon target recognition (1).
-In eukaryotes, STAND-NTPases are associated with programmed cell death, therefore Gao and colleagues hypothesized that AVAST might function through an [Abortive infection mechanism.](/general_concepts/Abi)
+In eukaryotes, STAND-NTPases are associated with programmed cell death, therefore Gao and colleagues hypothesized that AVAST might function through an Abortive infection mechanism.
## Relevant abstracts
diff --git a/content/3.defense-systems/4.rm.md b/content/3.defense-systems/4.rm.md
new file mode 100644
index 00000000..98337030
--- /dev/null
+++ b/content/3.defense-systems/4.rm.md
@@ -0,0 +1,43 @@
+# RM
+
+## Example of genomic structure
+
+The RM system have been describe in a total of 5 subsystems.
+
+Here is some example found in the RefSeq database:
+
+<img src="./data/RM_Type_I.svg">
+
+RM\_Type\_I subsystem in the genome of *Aeromonas veronii* (GCF\_014169835.1) is composed of 4 proteins: Type\_I\_MTases (WP\_182963881.1), Type\_I\_MTases (WP\_182963881.1), Type\_I\_S (WP\_182963883.1)and, Type\_I\_REases (WP\_182963884.1).
+
+<img src="./data/RM_Type_II.svg">
+
+RM\_Type\_II subsystem in the genome of *Mannheimia haemolytica* (GCF\_007965905.1) is composed of 2 proteins: Type\_II\_MTases (WP\_006248352.1)and, Type\_II\_REases (WP\_006253295.1).
+
+<img src="./data/RM_Type_IIG.svg">
+
+RM\_Type\_IIG subsystem in the genome of *Spirochaeta africana* (GCF\_000242595.2) is composed of 1 protein: Type\_IIG (WP\_014455422.1).
+
+<img src="./data/RM_Type_III.svg">
+
+RM\_Type\_III subsystem in the genome of *Pannonibacter phragmitetus* (GCF\_001484065.1) is composed of 2 proteins: Type\_III\_MTases (WP\_058898889.1)and, Type\_III\_REases (WP\_058898890.1).
+
+<img src="./data/RM_Type_IV.svg">
+
+RM\_Type\_IV subsystem in the genome of *Clostridioides difficile* (GCF\_018884605.1) is composed of 1 protein: Type\_IV\_REases (WP\_021364579.1).
+
+## Distribution of the system among prokaryotes
+
+The RM system is present in a total of 4699 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 19087 genomes (83.7 %).
+
+<img src="./data/Distribution_RM.svg" width=800px>
+
+*Proportion of genome encoding the RM system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+
+## Relevant abstracts
+
+**Oliveira, P. H., Touchon, M. & Rocha, E. P. C. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res 42, 10618-10631 (2014).**
+The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
+
diff --git a/content/3.defense-systems/5.viperin.md b/content/3.defense-systems/5.viperin.md
new file mode 100644
index 00000000..3e8196ab
--- /dev/null
+++ b/content/3.defense-systems/5.viperin.md
@@ -0,0 +1,87 @@
+---
+title: Viperin
+layout: article
+---
+
+## Description
+
+Viperins, for “Virus Inhibitory Protein, Endoplasmic Reticulum-associated, INterferon-inducibleâ€, are antiviral enzymes whose expression is stimulated by interferons in eukaryotic cells. They are important components of eukaryotic innate immunity, and present antiviral activity against a wide diversity of viruses, including double-stranded DNA viruses, single-strand RNA viruses and retroviruses (1).
+
+Recently, Viperin-like enzymes were found in prokaryotes (pVips). Strikingly, like their eukaryotic counter-part with eukaryotic viruses, pVips provide clear protection against phage infection to their host, and therefore constitute a new defense system (2). Like eukaryotic Viperins, pVips produce modified nucleotides that block phage transcription, acting as chain terminators. They constitute a form of chemical defense. A recent study reported that pVips can be found in around 0.5% of prokaryotic genomes (3).
+
+## Molecular mechanism
+
+
+Fig.1: Catalytic activity of human Viperin generates ddhCTP (Ebrahimi et al. al., 2020)
+
+Viperins are members of the radical S-adenosylmethionine (rSAM) superfamily. This group of enzymes use a \[4Fe-4S\] cluster to cleave S-adenosylmethionine (SAM) reductively, generating a radical which is generally transferred to a substrate. It was demonstrated that through their \[4Fe-4S\] cluster catalytic activity, eukaryotic viperins convert a ribonucleotide, the cytidine triphosphate (CTP) into a modified ribonucleotide, the 3′-deoxy-3′,4′-didehydro-CTP (ddhCTP) (4,5).
+
+Prokaryotic Viperins also convert ribonucleotides triphosphate into modified ribonucleotides, but contrary to their eukaryotic counterparts can use a diversity of substrates to produce ddhCTP, or ddh-guanosine triphosphate (ddhGTP), or ddh-uridine triphosphate (ddhUTP), or several of these nucleotides for certain pVips (2).
+
+Compared to the initial ribonucleotide triphosphate, the modified ddh-nucleotide product of Viperins lacks a hydroxyl group at the 3′ carbon of the ribose (Fig.1). The ddh-nucleotides produced by Viperins can be used as substrates by some viral RNA polymerases. Because of their lost hydroxyl group at the 3’carbon of the ribose, once incorporated into the newly forming viral RNA chain, these ddh-nucleotides act as chain terminators. By preventing further polymerization of the viral RNA chain, ddh-nucleotides can inhibit viral replication (2,4,5).
+
+## Example of genomic structure
+
+The Viperin system is composed of one protein: pVip.
+
+Here is an example found in the RefSeq database:
+
+<img src="./data/Viperin.svg">
+
+Viperin system in the genome of *Moritella yayanosii* is composed of 1 protein: pVip (WP\_112711942.1).
+
+## Distribution of the system among prokaryotes
+
+The Viperin system is present in a total of 85 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 118 genomes (0.5 %).
+
+<img src="./data/Distribution_Viperin.svg" width=800px>
+
+*Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+
+## Experimental validation
+
+Viperin systems were experimentally validated using:
+
+Subsystem pVip6 with a system from *Selenomonas ruminatium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip7 with a system from *Fibrobacter sp. UWT3* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip9 with a system from *Vibrio porteresiae* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip12 with a system from *Ruegeria intermedia* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip15 with a system from *Coraliomargarita akajimensis* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip21 with a system from *Lewinella persica* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip32 with a system from *Phormidium sp. OSCR GFM* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip34 with a system from *Cryomorphaceae bacterium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip37 with a system from *Shewanella sp. cp20* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip39 with a system from *Burkholderiales-76 (UID4002)* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip44 with a system from *Chondromyces crocatus* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip46 with a system from *Photobacterium swingsii* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip57 with a system from *Flavobacterium lacus* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip58 with a system from *Pseudoalteromonas ulvae* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip60 with a system from *Lacinutrix sp. JCM 13824* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip61 with a system from *Euryarchaeota archaeon SCGC AG-487_M08* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip62 with a system from *Fibrobacteria bacterium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+Subsystem pVip63 with a system from *Pseudoalteromonas sp. XI10* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
+
+## Relevant abstracts
+
+**Bernheim, A. et al. Prokaryotic viperins produce diverse antiviral molecules. Nature 589, 120-124 (2021).**
+Viperin is an interferon-induced cellular protein that is conserved in animals1. It has previously been shown to inhibit the replication of multiple viruses by producing the ribonucleotide 3?-deoxy-3?,4?-didehydro (ddh)-cytidine triphosphate (ddhCTP), which acts as a chain terminator for viral RNA polymerase2. Here we show that eukaryotic viperin originated from a clade of bacterial and archaeal proteins that protect against phage infection. Prokaryotic viperins produce a set of modified ribonucleotides that include ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). We further show that prokaryotic viperins protect against T7 phage infection by inhibiting viral polymerase-dependent transcription, suggesting that it has an antiviral mechanism of action similar to that of animal viperin. Our results reveal a class of potential natural antiviral compounds produced by bacterial immune systems.
+
diff --git a/content/list.json b/content/list.json
deleted file mode 100644
index 929167e1..00000000
--- a/content/list.json
+++ /dev/null
@@ -1,14 +0,0 @@
-[
- {
- "system": "Abi2",
- "article": [
- "rererere"
- ]
- },
- {
- "system": "PARIS",
- "article": [
- "rererere"
- ]
- }
-]
\ No newline at end of file
diff --git a/layouts/article.vue b/layouts/article.vue
index 9a20d659..962fabd0 100644
--- a/layouts/article.vue
+++ b/layouts/article.vue
@@ -1,5 +1,8 @@
<script setup lang="ts">
const { page, surround } = useContent();
+console.log(page)
+console.log("surround object!!!!!")
+console.log(surround)
</script>
<template>
<v-card>
@@ -14,20 +17,10 @@ const { page, surround } = useContent();
</v-card> -->
<EditGitlab />
<v-row justify="space-between">
- <v-col
- v-for="(surroundPage, i) in surround"
- :key="surroundPage?._id"
- cols="auto"
- >
- <v-btn
- v-if="surroundPage"
- :prepend-icon="i === 0 ? 'mdi-arrow-left' : undefined"
- :append-icon="i === 1 ? 'mdi-arrow-right' : undefined"
- variant="outlined"
- color="primary"
- :to="surroundPage?._path"
- >{{ surroundPage?.title }}</v-btn
- >
+ <v-col v-for="(surroundPage, i) in surround" :key="surroundPage?._id" cols="auto">
+ <v-btn v-if="surroundPage" :prepend-icon="i === 0 ? 'mdi-arrow-left' : undefined"
+ :append-icon="i === 1 ? 'mdi-arrow-right' : undefined" variant="outlined" color="primary"
+ :to="surroundPage?._path">{{ surroundPage?.title }}</v-btn>
</v-col>
</v-row>
</v-container>
diff --git a/nuxt.config.ts b/nuxt.config.ts
index 7fb59efe..aa69e690 100644
--- a/nuxt.config.ts
+++ b/nuxt.config.ts
@@ -3,7 +3,7 @@ export default defineNuxtConfig({
modules: ['@nuxt/content', 'vuetify-nuxt-module'],
content: {
documentDriven: {
- injectPage: false
+ injectPage: false,
}
},
vuetify: {
diff --git a/pages/[...slug].vue b/pages/[...slug].vue
index d77e6e39..e0c2b132 100644
--- a/pages/[...slug].vue
+++ b/pages/[...slug].vue
@@ -4,7 +4,6 @@
<v-card flat color="transparent" max-width="1280">
<v-card-text>
<ContentDoc />
- </v-card-text> </v-card
- ></v-col>
+ </v-card-text> </v-card></v-col>
</v-row>
</template>
diff --git a/pages/list.vue b/pages/list.vue
deleted file mode 100644
index bde32a9c..00000000
--- a/pages/list.vue
+++ /dev/null
@@ -1,27 +0,0 @@
-<script setup lang="ts">
-definePageMeta({
- documentDriven: false
-})
-const { path } = useRoute()
-const headers = ref([{
- title: "Systems",
- key: "system"
-}])
-const { data } = await useAsyncData(`content-${path}`, () => {
- return queryContent().where({ _path: path }).findOne()
-
-})
-console.log(data)
-</script>
-<template>
- <v-card v-if="data?.body" class="mt-5" flat>
- <ul>
- <li v-for="e in data.body" :key="e.system">
- {{ e.system }}
- </li>
- </ul>
- <v-card-text>
- <v-data-table items-per-page="5" :headers="headers" :items="data.body" class="elevation-1"></v-data-table>
- </v-card-text>
- </v-card>
-</template>
\ No newline at end of file
--
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