diff --git a/.github/workflows/nuxtjs.yml b/.github/workflows/nuxtjs.yml
new file mode 100644
index 0000000000000000000000000000000000000000..2f05e0db9380e8762b48cfec7d565388b6403853
--- /dev/null
+++ b/.github/workflows/nuxtjs.yml
@@ -0,0 +1,90 @@
+# Sample workflow for building and deploying a Nuxt site to GitHub Pages
+#
+# To get started with Nuxt see: https://nuxtjs.org/docs/get-started/installation
+#
+name: Deploy Nuxt site to Pages
+
+on:
+ # Runs on pushes targeting the default branch
+ push:
+ branches: ["dev"]
+
+ # Allows you to run this workflow manually from the Actions tab
+ workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+ contents: read
+ pages: write
+ id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+ group: "pages"
+ cancel-in-progress: false
+
+jobs:
+ # Build job
+ build:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+ - name: Detect package manager
+ id: detect-package-manager
+ run: |
+ if [ -f "${{ github.workspace }}/yarn.lock" ]; then
+ echo "manager=yarn" >> $GITHUB_OUTPUT
+ echo "command=install" >> $GITHUB_OUTPUT
+ exit 0
+ elif [ -f "${{ github.workspace }}/package.json" ]; then
+ echo "manager=npm" >> $GITHUB_OUTPUT
+ echo "command=ci" >> $GITHUB_OUTPUT
+ exit 0
+ else
+ echo "Unable to determine package manager"
+ exit 1
+ fi
+ - name: Setup Node
+ uses: actions/setup-node@v3
+ with:
+ node-version: "16"
+ cache: ${{ steps.detect-package-manager.outputs.manager }}
+ # - name: Setup Pages
+ # uses: actions/configure-pages@v3
+ # with:
+ # # Automatically inject router.base in your Nuxt configuration file and set
+ # # target to static (https://nuxtjs.org/docs/configuration-glossary/configuration-target/).
+ # #
+ # # You may remove this line if you want to manage the configuration yourself.
+ # static_site_generator: nuxt
+ - name: Restore cache
+ uses: actions/cache@v3
+ with:
+ path: |
+ dist
+ .nuxt
+ key: ${{ runner.os }}-nuxt-build-${{ hashFiles('dist') }}
+ restore-keys: |
+ ${{ runner.os }}-nuxt-build-
+ - name: Install dependencies
+ run: ${{ steps.detect-package-manager.outputs.manager }} ${{ steps.detect-package-manager.outputs.command }}
+ - name: Static HTML export with Nuxt
+ run: ${{ steps.detect-package-manager.outputs.manager }} run generate
+ - name: Upload artifact
+ uses: actions/upload-pages-artifact@v2
+ with:
+ path: ./dist
+
+ # Deployment job
+ deploy:
+ environment:
+ name: github-pages
+ url: ${{ steps.deployment.outputs.page_url }}
+ runs-on: ubuntu-latest
+ needs: build
+ steps:
+ - name: Deploy to GitHub Pages
+ id: deployment
+ uses: actions/deploy-pages@v2
diff --git a/.gitignore b/.gitignore
index 69f6b69d0721455f28a50b8dddc9be72baa8d6c9..6585b4093564aa4322599ea9f860237720f972be 100755
--- a/.gitignore
+++ b/.gitignore
@@ -3,10 +3,8 @@ node_modules
.idea
*.log*
.nuxt
-.vscode
-.DS_Store
-coverage
-dist
-sw.*
-.env
+.nitro
+.cache
.output
+.env
+dist
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7be7f42076f1b90984b433d999fe5f73a6be6dca..565c80416985f9ab346c1ae3b34d6a45fd94693b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -28,6 +28,7 @@ pages:
only:
- main
script:
+ - NUXT_APP_BASE_URL=/wiki npm run generate
- rm -rf public
- mv .output/public public
artifacts:
diff --git a/app.config.ts b/app.config.ts
deleted file mode 100644
index 07ea1fc5b051c9e4962fed817a738ba2c2a7cda8..0000000000000000000000000000000000000000
--- a/app.config.ts
+++ /dev/null
@@ -1,35 +0,0 @@
-export default defineAppConfig({
- docus: {
- title: 'DefenseFinder Wiki',
- description: 'A comprehensive effort to map microbial defense systems against their viruses',
- // image: 'https://user-images.githubusercontent.com/904724/185365452-87b7ca7b-6030-4813-a2db-5e65c785bf88.png',
- socials: {
- twitter: '@MDMlab_Paris',
- github: 'mdmparis',
- },
- aside: {
- level: 0,
- exclude: []
- },
- header: {
- title: 'DefenseFinder Wiki',
- logo: false,
- showLinkIcon: true,
- exclude: []
- },
- footer: {
- credits: {
- text: 'MDM Labs, Paris',
- href: 'https://mdmlab.fr/'
- },
- textLinks: [],
- iconLinks: []
- },
- gitlab: {
- owner: 'defense-finder',
- repo: 'wiki',
- branch: "main",
- edit: true,
- },
- }
-})
diff --git a/app.vue b/app.vue
deleted file mode 100644
index e19315ee54f8fb6ce425eb5ad5397aa0b27fb5e0..0000000000000000000000000000000000000000
--- a/app.vue
+++ /dev/null
@@ -1,5 +0,0 @@
-<template>
- <AppLayout>
- <NuxtPage />
- </AppLayout>
-</template>
diff --git a/components/EditGitLab.vue b/components/EditGitLab.vue
deleted file mode 100644
index 50fda769789fcdf2f9b9f11114f24ae3b3bc1a74..0000000000000000000000000000000000000000
--- a/components/EditGitLab.vue
+++ /dev/null
@@ -1,22 +0,0 @@
-<template>
- <ProseA :to="path" target="blank">
- <span> Edit this page on GitLab </span>
- </ProseA>
-</template>
-<script setup lang="ts">
-import { ref } from "vue";
-const { page } = useContent();
-const config = useDocus();
-const props = defineProps<{
- owner: string;
- repo: string;
- branch: string;
-}>();
-const baseUrl = ref(new URL("https://gitlab.pasteur.fr"));
-const path = ref(
- new URL(
- `/${props.owner}/${props.repo}/-/edit/${props.branch}/content/${page.value._file}`,
- baseUrl.value
- ).href
-);
-</script>
diff --git a/components/EditGitlab.vue b/components/EditGitlab.vue
new file mode 100644
index 0000000000000000000000000000000000000000..2ccddd60ef7ab490a07e47c860268fd1d80490ff
--- /dev/null
+++ b/components/EditGitlab.vue
@@ -0,0 +1,29 @@
+<template>
+ <v-row>
+ <v-col>
+ <v-btn prepend-icon="mdi-github" variant="text" size="small" :href="path" target="_blank">Edit on github</v-btn>
+ </v-col>
+ </v-row>
+</template>
+<script setup lang="ts">
+import { ref } from "vue";
+const { page } = useContent();
+// const owner = ref("mdm-lab");
+const owner = ref("rplanel");
+// const repo = ref("wiki");
+const repo = ref("defense-finder-wiki-test");
+// const branch = ref("main");
+const branch = ref("dev");
+
+
+// const baseUrl = ref(new URL("https://gitlab.pasteur.fr"));
+const baseUrl = ref(new URL("https://github.com"))
+
+// https://github.com/rplanel/defense-finder-wiki-test/edit/dev/content/1.introduction/0.index.md
+const path = ref(
+ new URL(
+ `/${owner.value}/${repo.value}/edit/${branch.value}/content/${page.value._file}`,
+ baseUrl.value
+ ).href
+);
+</script>
diff --git a/components/Nav/Navbar.vue b/components/Nav/Navbar.vue
new file mode 100644
index 0000000000000000000000000000000000000000..97d9560ccb1091bf2a6392257e6799e7adbfd23f
--- /dev/null
+++ b/components/Nav/Navbar.vue
@@ -0,0 +1,25 @@
+<template>
+ <v-app-bar>
+ <v-app-bar-nav-icon variant="text" @click.stop="drawer = !drawer"></v-app-bar-nav-icon>
+ <v-toolbar-title>DefenseFinder Wiki</v-toolbar-title>
+ <v-btn icon="mdi-theme-light-dark" @click="toggle()">
+ </v-btn>
+ </v-app-bar>
+ <v-navigation-drawer v-model="drawer" :border="0">
+ <v-card flat>
+ <v-list nav density="compact" :lines="false">
+ <NavNavigation :navigation="navigation" />
+ </v-list>
+ </v-card>
+ </v-navigation-drawer>
+</template>
+<script setup lang="ts">
+import { useCustomTheme } from '~/composables/useCustomTheme'
+
+const { toggle } = useCustomTheme()
+
+const { navigation, page, surround, globals } = useContent();
+
+
+const drawer = ref(true);
+</script>
diff --git a/components/Nav/Navigation.vue b/components/Nav/Navigation.vue
new file mode 100644
index 0000000000000000000000000000000000000000..6ead9e06711dddb1b9d3ff36acc4177a0a1e1119
--- /dev/null
+++ b/components/Nav/Navigation.vue
@@ -0,0 +1,23 @@
+<script setup lang="ts">
+const props = defineProps<{
+ navigation: any;
+}>();
+
+// const { navigation } = useContent();
+// console.log(navigation.value);
+</script>
+
+<template>
+ <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" 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" color="primary" exact
+ nav></v-list-item>
+ </template>
+ </template>
+</template>
diff --git a/components/Nav/TableOfContent.vue b/components/Nav/TableOfContent.vue
new file mode 100644
index 0000000000000000000000000000000000000000..45b9639eb3c3921656e60cc169c6be7674c9d049
--- /dev/null
+++ b/components/Nav/TableOfContent.vue
@@ -0,0 +1,32 @@
+<script setup lang="ts">
+import { useDisplay } from "vuetify";
+const props = defineProps<{
+ links: any;
+}>();
+
+const { mobile } = useDisplay();
+
+// const { navigation } = useContent();
+// console.log(navigation.value);
+</script>
+
+<template>
+ <v-navigation-drawer
+ v-if="!mobile"
+ id="app-toc"
+ location="right"
+ :border="0"
+ permanent
+ >
+ <template #prepend>
+ <div class="text-h6 font-weight-medium mt-4 mb-2 ms-4">Contents</div>
+ </template>
+ <ul class="px-2 py-2">
+ <NavTableOfContentItem :links="props.links" /></ul
+ ></v-navigation-drawer>
+</template>
+<style scoped>
+#app-toc ul {
+ list-style-type: none;
+}
+</style>
diff --git a/components/Nav/TableOfContentItem.vue b/components/Nav/TableOfContentItem.vue
new file mode 100644
index 0000000000000000000000000000000000000000..a244aabeccd435294210aa0ef6114b8320fc19d1
--- /dev/null
+++ b/components/Nav/TableOfContentItem.vue
@@ -0,0 +1,47 @@
+<script setup lang="ts">
+import { useTheme } from "vuetify";
+
+const theme = useTheme();
+console.log(theme);
+const route = useRoute();
+
+const props = defineProps<{
+ links: any;
+}>();
+</script>
+<template>
+ <template v-for="link in props.links">
+ <li
+ :title="link.text"
+ :value="link.id"
+ :class="[
+ `ps-${(link.depth - 1) * 3}`,
+ {
+ 'text-primary': route.hash === `#${link.id}`,
+ 'text-medium-emphasis': route.hash !== `#${link.id}`,
+ },
+ ]"
+ :style="{
+ 'border-left':
+ route.hash === `#${link.id}`
+ ? `2px solid ${theme.current.value.colors.primary}`
+ : '2px solid #e5e5e5',
+ }"
+ >
+ <NuxtLink
+ :to="`#${link.id}`"
+ class="text-decoration-none"
+ style="color: inherit"
+ >{{ link.text }}</NuxtLink
+ >
+ </li>
+ <template v-if="link?.children?.length > 0">
+ <NavTableOfContentItem :links="link.children" />
+ </template>
+ </template>
+</template>
+<style scoped>
+li {
+ border-left: 2px solid #e5e5e5;
+}
+</style>
diff --git a/components/content/ListSystems.vue b/components/content/ListSystems.vue
new file mode 100644
index 0000000000000000000000000000000000000000..b65364664eb34cae57db3bb8b876bc0107fffb14
--- /dev/null
+++ b/components/content/ListSystems.vue
@@ -0,0 +1,35 @@
+<script setup lang="ts">
+
+const props = defineProps<{
+ systems: any;
+}>();
+const itemsPerParge = ref(25)
+const search = ref('')
+const sortBy = ref([{ key: 'system', order: 'asc' }])
+const headers = ref([{
+ title: "Systems",
+ key: "system"
+}, { title: "Articles", key: "dois" }
+])
+
+</script>
+<template>
+ <v-card flat color="transparent" class="my-5">
+ <v-toolbar>
+ <v-toolbar-title>Defense Systems</v-toolbar-title>
+
+ <v-text-field v-model="search" density="compact" variant="underlined" append-inner-icon="mdi-magnify" label="Search"
+ single-line hide-details class="mx-2"></v-text-field>
+ </v-toolbar>
+ <v-data-table :items-per-page="itemsPerParge" v-model:sort-by="sortBy" :headers="headers" :items="props.systems"
+ :search="search">
+ <template #[`item.system`]="{ item }">
+ <v-chip variant="text" link :to="`/defense-systems/${item.columns.system.toLowerCase()}`">{{
+ item.columns.system }}</v-chip>
+ </template>
+ <template #[`item.dois`]="{ item }">
+ <ReferencesList :items="item.columns.dois"></ReferencesList>
+ </template>
+ </v-data-table>
+ </v-card>
+</template>
\ No newline at end of file
diff --git a/components/content/ProseH1.vue b/components/content/ProseH1.vue
new file mode 100644
index 0000000000000000000000000000000000000000..23edff067437132bd264725632dc2406a4422e1c
--- /dev/null
+++ b/components/content/ProseH1.vue
@@ -0,0 +1,30 @@
+<template>
+ <span :id="id" class="anchor"></span>
+ <h1 class="text-h3 font-weight-bold my-6">
+ <a v-if="id && generate" :href="`#${id}`" class="text-decoration-none">
+ <slot />
+ </a>
+ <slot v-else />
+ </h1>
+</template>
+
+<script setup lang="ts">
+import { useRuntimeConfig } from "#imports";
+defineProps<{ id?: string }>();
+const heading = 1;
+const { anchorLinks } = useRuntimeConfig().public.content;
+
+const generate =
+ anchorLinks?.depth >= heading && !anchorLinks?.exclude.includes(heading);
+</script>
+<style scoped>
+a {
+ color: inherit;
+}
+anchor {
+ display: block;
+ position: relative;
+ top: -64px;
+ visibility: hidden;
+}
+</style>
diff --git a/components/content/ProseH2.vue b/components/content/ProseH2.vue
new file mode 100644
index 0000000000000000000000000000000000000000..6461c9ced25a8bffed38b5be9eebc5bb5402d7ee
--- /dev/null
+++ b/components/content/ProseH2.vue
@@ -0,0 +1,29 @@
+<template>
+ <span :id="id" class="anchor"></span>
+ <h2 class="text-h4 font-weight-bold my-4">
+ <a v-if="id && generate" :href="`#${id}`" class="text-decoration-none">
+ <slot />
+ </a>
+ <slot v-else />
+ </h2>
+</template>
+
+<script setup lang="ts">
+import { useRuntimeConfig } from "#imports";
+defineProps<{ id?: string }>();
+const heading = 2;
+const { anchorLinks } = useRuntimeConfig().public.content;
+const generate =
+ anchorLinks?.depth >= heading && !anchorLinks?.exclude.includes(heading);
+</script>
+<style scoped>
+a {
+ color: inherit;
+}
+.anchor {
+ display: block;
+ position: relative;
+ top: -64px;
+ visibility: hidden;
+}
+</style>
diff --git a/components/content/ProseH3.vue b/components/content/ProseH3.vue
new file mode 100644
index 0000000000000000000000000000000000000000..5d1e79450e5a1b531fbeba0fdb767fdd428c56b9
--- /dev/null
+++ b/components/content/ProseH3.vue
@@ -0,0 +1,29 @@
+<template>
+ <span :id="id" class="anchor"></span>
+ <h3 class="text-h6 font-weight-bold my-3">
+ <a v-if="id && generate" :href="`#${id}`" class="text-decoration-none">
+ <slot />
+ </a>
+ <slot v-else />
+ </h3>
+</template>
+
+<script setup lang="ts">
+import { useRuntimeConfig } from "#imports";
+defineProps<{ id?: string }>();
+const heading = 3;
+const { anchorLinks } = useRuntimeConfig().public.content;
+const generate =
+ anchorLinks?.depth >= heading && !anchorLinks?.exclude.includes(heading);
+</script>
+<style scoped>
+a {
+ color: inherit;
+}
+.anchor {
+ display: block;
+ position: relative;
+ top: -64px;
+ visibility: hidden;
+}
+</style>
diff --git a/components/content/ProseImg.vue b/components/content/ProseImg.vue
new file mode 100644
index 0000000000000000000000000000000000000000..55d8d853479ad6733b7c79f1f5d6c285375dc03d
--- /dev/null
+++ b/components/content/ProseImg.vue
@@ -0,0 +1,38 @@
+<template>
+ <v-img :src="refinedSrc" :alt="alt" :width="width" :height="height"></v-img>
+</template>
+
+<script setup lang="ts">
+import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
+import { useRuntimeConfig, computed } from '#imports'
+
+const props = defineProps({
+ src: {
+ type: String,
+ default: ''
+ },
+ alt: {
+ type: String,
+ default: ''
+ },
+ width: {
+ type: [String, Number],
+ default: undefined
+ },
+ height: {
+ type: [String, Number],
+ default: undefined
+ }
+})
+
+const refinedSrc = computed(() => {
+ if (props.src?.startsWith('/') && !props.src.startsWith('//')) {
+ const _base = withLeadingSlash(withTrailingSlash(useRuntimeConfig().app.baseURL))
+ if (_base !== '/' && !props.src.startsWith(_base)) {
+ return joinURL(_base, props.src)
+ }
+ }
+ return props.src
+})
+</script>
+
\ No newline at end of file
diff --git a/components/content/ProseOl.vue b/components/content/ProseOl.vue
new file mode 100644
index 0000000000000000000000000000000000000000..4c630ffc26d746493b81182b6b04483ab2a5ec75
--- /dev/null
+++ b/components/content/ProseOl.vue
@@ -0,0 +1,9 @@
+<template>
+ <v-card flat color="transparent">
+ <v-card-text>
+ <ol>
+ <slot />
+ </ol>
+ </v-card-text>
+ </v-card>
+</template>
diff --git a/components/content/ProseP.vue b/components/content/ProseP.vue
new file mode 100644
index 0000000000000000000000000000000000000000..7a5ac19cb50edb8dc7175be986d6de72eec8fd3b
--- /dev/null
+++ b/components/content/ProseP.vue
@@ -0,0 +1,6 @@
+<template>
+ <!-- <v-card flat color="transparent">
+ <v-card-text class="px-0 py-2"><slot /></v-card-text>
+ </v-card> -->
+ <p><slot /></p>
+</template>
diff --git a/components/content/ProseUl.vue b/components/content/ProseUl.vue
new file mode 100644
index 0000000000000000000000000000000000000000..c11821543890eaaee2505d2181b09a4b5f4b1715
--- /dev/null
+++ b/components/content/ProseUl.vue
@@ -0,0 +1,9 @@
+<template>
+ <v-card flat color="transparent">
+ <v-card-text>
+ <ul>
+ <slot />
+ </ul>
+ </v-card-text>
+ </v-card>
+</template>
diff --git a/components/content/ReferencesList.vue b/components/content/ReferencesList.vue
index f72d87d53ba4bbb14412bc0ef339868d93c265d6..4f9b0868743a1c33f790774d7af819d77f3c62c3 100644
--- a/components/content/ReferencesList.vue
+++ b/components/content/ReferencesList.vue
@@ -1,25 +1,36 @@
<template>
<ClientOnly fallback-tag="span" fallback="Loading references...">
- <ProseOl v-if="computedItems.length > 0">
- <ProseA
- v-for="item in computedItems"
- :key="item.DOI"
- :href="item.href"
- target="blank"
- >
- <ProseLi class="refArticle">
- <div class="ref-title">{{ item.title }}.</div>
- <div class="ref-authors">{{ item.authorsString }}</div>
- <div>{{ item?.containerTitle }}</div>
- </ProseLi>
- </ProseA>
- </ProseOl>
+ <v-list v-if="computedItems.length > 0">
+ <v-list-item v-for="item in computedItems" :key="item.title" :title="item.title" lines="three" :href="item.href"
+ :target="item.target">
+ <template #title="{ title }">
+ <span class="font-weight-bold">{{ title }}</span>
+ </template>
+ <template #prepend>
+ <v-avatar>
+ <v-icon>{{ item.prependIcon }}</v-icon>
+ </v-avatar>
+ </template>
+ <template #subtitle>
+ <div>{{ item.subtitle }}</div>
+ <div>{{ item.containerTitle }} ({{ item.year }})</div>
+ </template>
+ <v-card flat color="transparent" class="text-justify my-2">
+ {{ item.abstract }}
+ </v-card>
+ </v-list-item>
+
+
+ </v-list>
</ClientOnly>
</template>
<script setup lang="ts">
import { computed, ref } from "vue";
import { useFetch as useFetchVueUse } from "@vueuse/core";
+
+// import { select, selectAll } from 'unist-util-select';
+
const props = defineProps<{
items: string[];
}>();
@@ -38,6 +49,9 @@ const fetchedDoi = ref(
"container-title-short": string;
"container-title": string;
abstract: string;
+ published: {
+ "date-parts": string[];
+ };
};
}>(url)
.get()
@@ -47,7 +61,7 @@ const fetchedDoi = ref(
)
);
const computedItems = computed(() => {
- return fetchedDoi.value.map((doi) => {
+ return fetchedDoi.value.map((doi, i) => {
if (doi) {
const {
DOI,
@@ -55,15 +69,25 @@ const computedItems = computed(() => {
"container-title-short": cts,
"container-title": ct,
abstract,
+ published,
...rest
} = doi.message;
+ console.log(abstract)
+ let sanitizedAbstract = abstract
+ if (sanitizedAbstract) {
+ sanitizedAbstract = /\<jats\:p\>(.*)\<\/jats\:p\>/.exec(sanitizedAbstract)?.[1] ?? ''
+ }
+ console.log(sanitizedAbstract)
return {
DOI,
title: title[0],
- authorsString: toAuthorsString(doi?.message?.author ?? []),
+ subtitle: toAuthorsString(doi?.message?.author ?? []),
containerTitle: cts?.length > 0 ? cts[0] : ct?.length > 0 ? ct[0] : "",
- abstract,
+ abstract: sanitizedAbstract,
+ year: published["date-parts"][0][0],
href: getReferenceUrl(DOI),
+ target: "_blank",
+ prependIcon: "mdi-newspaper-variant-outline",
};
} else {
return {};
@@ -83,16 +107,3 @@ function getReferenceUrl(doi) {
return new URL(doi, doiBaseUrl.value).href;
}
</script>
-
-<style lang="ts">
-css({
- '.refArticle': {
- 'margin-top': '{space.4}',
-},
-'.ref-title': {
- fontWeight: '{fontWeight.bold}',
-},
-'.ref-authors': {
- fontSize: '{fontSize.sm}',
-}})
-</style>
diff --git a/components/docs/DocsPageBottom.vue b/components/docs/DocsPageBottom.vue
deleted file mode 100644
index 16271c6220812a431094d914dc47d041abf1ee3b..0000000000000000000000000000000000000000
--- a/components/docs/DocsPageBottom.vue
+++ /dev/null
@@ -1,49 +0,0 @@
-<script setup lang="ts">
-const { page } = useContent();
-const { config, tree } = useDocus();
-</script>
-
-<template>
- <div v-if="page" class="docs-page-bottom">
- <div v-if="config?.gitlab?.edit" class="edit-link">
- <Icon name="uil:edit" />
- <EditGitLab
- :owner="config.gitlab.owner"
- :repo="config.gitlab.repo"
- :branch="config?.gitlab?.branch"
- />
- </div>
-
- <!-- Need to be supported by @nuxt/content -->
- <span v-if="page?.mtime"
- >Updated on
- <b>{{
- new Intl.DateTimeFormat("en-US").format(Date.parse(page.mtime))
- }}</b></span
- >
- </div>
-</template>
-
-<style scoped lang="ts">
-css({
- '.docs-page-bottom': {
- display: 'flex',
- alignItems: 'center',
- justifyContent: 'space-between',
- flexDirection: 'row',
- gap: '{space.4}',
- marginTop: '{space.8}',
- fontSize: '{fontSize.sm}',
- color: '{color.gray.500}',
- '@dark': {
- color: '{color.gray.400}'
- },
- '.edit-link': {
- flex: 1,
- display: 'flex',
- alignItems: 'center',
- gap: '{space.2}'
- }
- }
-})
-</style>
diff --git a/composables/useCustomTheme.ts b/composables/useCustomTheme.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7a44c724e9553eb0081ebb52ba1cc0d980ddf4cc
--- /dev/null
+++ b/composables/useCustomTheme.ts
@@ -0,0 +1,17 @@
+// composables/useCustomTheme.ts
+export function useCustomTheme() {
+ const { $vuetify } = useNuxtApp()
+
+ const isDark = useDark({
+ valueDark: 'dark',
+ valueLight: 'light',
+ initialValue: 'auto',
+ onChanged: (dark: boolean) => {
+ $vuetify.theme.global.name.value = dark ? 'dark' : 'light'
+ },
+ })
+
+ const toggle = useToggle(isDark)
+
+ return { isDark, toggle }
+ }
\ No newline at end of file
diff --git a/content/0.index.md b/content/0.index.md
old mode 100755
new mode 100644
index c8dac7ea31f13538ac66a0c4378e79d3ef5683a5..e3f719072563d44c32a167cc648008bae902189f
--- a/content/0.index.md
+++ b/content/0.index.md
@@ -1,20 +1,66 @@
---
title: DefenseFinder Wiki
-navigation: false
-layout: page
+layout: article
---
+## 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.
-::block-hero
+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.
+
+## History
+
+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](/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).
+
+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).
+
+## 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.
+
+
+::references-list
---
-cta:
- - Get Started
- - /introduction
-secondary:
- - Open on GitLab →
- - https://gitlab.pasteur.fr/rplanel/docus-test
+items:
+ - 10.1126/science.1138140
+ - 10.1038/nmicrobiol.2017.92
+ - 10.1128/jb.65.2.113-121.1953
+ - 10.1126/science.aar4120
+ - 10.1126/science.aba0372
+ - 10.1038/s41586-019-1894-8
+ - 10.1128/jb.64.4.557-569.1952
---
+<<<<<<< HEAD
+::
+=======
#title
DefenseFinder Wiki
@@ -52,3 +98,4 @@ What's included
Enjoy the ease and simplicity of Markdown and discover MDC syntax.
::
::
+>>>>>>> main
diff --git a/content/1.general-concepts/0.index.md b/content/1.general-concepts/0.index.md
new file mode 100644
index 0000000000000000000000000000000000000000..e172046eb3f3596722e1cf783e73ed022206d6dc
--- /dev/null
+++ b/content/1.general-concepts/0.index.md
@@ -0,0 +1,8 @@
+---
+title: General Concepts
+toc: true
+layout: article
+---
+
+
+This section is empty. You can help by adding to it.
\ No newline at end of file
diff --git a/content/1.general-concepts/1.abortive-infection.md b/content/1.general-concepts/1.abortive-infection.md
new file mode 100644
index 0000000000000000000000000000000000000000..11d861e589200b1c27367545f8b5737c30951dff
--- /dev/null
+++ b/content/1.general-concepts/1.abortive-infection.md
@@ -0,0 +1,8 @@
+---
+title: Abortive Infection
+layout: article
+toc: true
+---
+
+
+This section is empty. You can help by adding to it.
diff --git a/content/1.general-concepts/2.defense-islands.md b/content/1.general-concepts/2.defense-islands.md
new file mode 100644
index 0000000000000000000000000000000000000000..82062efe0566465413112ad668982411428d4ae4
--- /dev/null
+++ b/content/1.general-concepts/2.defense-islands.md
@@ -0,0 +1,6 @@
+---
+title: Defense Islands
+---
+
+
+This section is empty. You can help by adding to it.
\ No newline at end of file
diff --git a/content/1.introduction/_dir.yml b/content/1.introduction/_dir.yml
deleted file mode 100644
index 9effc99b81b5efae1a879e43d3ef7ad204a88961..0000000000000000000000000000000000000000
--- 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/1.introduction/index.md b/content/1.introduction/index.md
deleted file mode 100644
index e9d1fb1b773310f4b87d1af9d62a040d2b8c2cb7..0000000000000000000000000000000000000000
--- a/content/1.introduction/index.md
+++ /dev/null
@@ -1,86 +0,0 @@
----
-title: Introduction
----
-
-# 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.
-
-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.
-
-# History
-
-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.
-
-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).
-
-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).
-
-## 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
-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.
-
-
diff --git a/content/2.defense-systems/0.index.md b/content/2.defense-systems/0.index.md
index b602c6a202bc5cdd493694ace6c16a54e16ccafd..1b1e188fe77724cfd688423ab0293fa4a7b1b318 100644
--- a/content/2.defense-systems/0.index.md
+++ b/content/2.defense-systems/0.index.md
@@ -1,78 +1,43 @@
---
title: List of defense systems
+layout: article
+
---
# List of defense systems
The knowledge of anti-phage defense systems is ever expanding. The spectacular increase of the number of known systems in the past years suggests that many of them are still to be discovered. As of april 2022, 63 defense systems have been described.
-| | |
-| ------------------------------------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| **System** | **Article** |
-| Abi2 | Chopin, M.-C., Chopin, A., Bidnenko, E., 2005. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473–479. [https://doi.org/10.1016/j.mib.2005.06.006](https://doi.org/10.1016/j.mib.2005.06.006) |
-| [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) |
-| 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) |
-| dCTPdeaminase | Tal, N., Millman, A., Stokar-Avihail, A., Fedorenko, T., Leavitt, A., Melamed, S., Yirmiya, E., Avraham, C., Amitai, G., Sorek, R., 2021. Antiviral defense via nucleotide depletion in bacteria. bioRxiv 2021.04.26.441389. [https://doi.org/10.1101/2021.04.26.441389](https://doi.org/10.1101/2021.04.26.441389) |
-| dGTPase | Tal, N., Millman, A., Stokar-Avihail, A., Fedorenko, T., Leavitt, A., Melamed, S., Yirmiya, E., Avraham, C., Amitai, G., Sorek, R., 2021. Antiviral defense via nucleotide depletion in bacteria. bioRxiv 2021.04.26.441389. [https://doi.org/10.1101/2021.04.26.441389](https://doi.org/10.1101/2021.04.26.441389) |
-| DISARM | Ofir, G., Melamed, S., Sberro, H., Mukamel, Z., Silverman, S., Yaakov, G., Doron, S., Sorek, R., 2018. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat Microbiol 3, 90–98. [https://doi.org/10.1038/s41564-017-0051-0](https://doi.org/10.1038/s41564-017-0051-0) |
-| Dnd | Wang, L., Chen, S., Xu, T., Taghizadeh, K., Wishnok, J.S., Zhou, X., You, D., Deng, Z., Dedon, P.C., 2007. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 3, 709–710. [https://doi.org/10.1038/nchembio.2007.39](https://doi.org/10.1038/nchembio.2007.39) |
-| 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) |
-| 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) |
-| Gao_Iet | 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_Mza | 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_Ppl | 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_Qat | 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_RL | 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_TerYP | 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_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) |
-| 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) |
-| 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) |
-| 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) |
-| 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) |
-| 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) |
-| Rst_DUF4238 | 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_gop_beta_cll | 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_HelicaseDUF2290 | 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_Hydrolase-Tm | 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_Old_Tin | 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_Retron-Tm | 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_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) |
-| Septu | 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) |
-| 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) |
-| 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) |
-**From** **_Tesson et al., 2022_**
+
+
+::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
+---
+::
+
+
+
+
## 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/2.AbiE.md b/content/2.defense-systems/2.AbiE.md
deleted file mode 100644
index 633777a57803ae76da6cedacd5b9e67568a862b7..0000000000000000000000000000000000000000
--- a/content/2.defense-systems/2.AbiE.md
+++ /dev/null
@@ -1,99 +0,0 @@
----
-title: AbiE
----
-
-# AbiE system
-
-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.
-
-## Mechanism
-
-AbiE systems are encoded by two mandatory genes, abiEi and abiEii (1,2).  The latter encodes for AbiEii, a GTP-binding nucleotidyltransferase (NTase) which expression induce a reversible growth arrest.  On the other hand, abiEi encodes for a AbiEi a transcriptional autorepressor that  binds to the promoter of the abiE operon.
-
-Based on this mechanisms, AbiE systems are classified as Type IV Toxin-Antitoxin system, where the antitoxin and toxin are both proteins that do not directly interact with each other.
-
-## Relevant Abstracts
-
-
-::card{icon="ooui:article-ltr"}
-#title
-Garvey P, Fitzgerald GF, Hill C. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl Environ Microbiol. 1995 Dec;61(12):4321-8. doi: 10.1128/aem.61.12.4321-4328.1995. PMID: 8534099; PMCID: PMC167743.
-#description
-The lactococcal plasmid pNP40, from Lactococcus lactis subsp. lactis biovar diacetylactis DRC3, confers complete resistance to the prolate-headed phage phi c2 and the small isometric-headed phage phi 712 in L. lactis subsp. lactis MG1614. A 6.0-kb NcoI fragment of pNP40 cloned in the lactococcal Escherichia coli shuttle vector pAM401 was found to confer partial resistance to phi 712. Subcloning and deletion analysis of the recombinant plasmid pPG01 defined a 2.5-kb ScaIHpaI fragment as conferring phage insensitivity. Sequence analysis of this region confirmed the presence of two overlapping open reading frames (ORFs). Further subcloning of pNP40 to characterize the resistance determinant active against phi c2 identified a 5.6-kb EcoRV fragment of pNP40 which, when cloned in pAM401, conferred partial resistance to both phi c2 and phi 712. Subcloning and deletion analysis of the recombinant plasmid pCG1 defined a 3.7-kb EcoRV-XbaI fragment as encoding phage insensitivity. DNA sequence analysis of this region revealed the presence of a single complete ORF. The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity. The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively. Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication, while AbiE had little effect on phage DNA replication, suggesting a later target of inhibition. The predicted protein product of abiF shows significant homology to the products of two other lactococcal abortive infection genes, abiD and abiD1
-::
-
-<br/>
-
-::card{icon="ooui:article-ltr"}
-#title
-Tangney M, Fitzgerald GF. Effectiveness of the lactococcal abortive infection systems AbiA, AbiE, AbiF and AbiG against P335 type phages. FEMS Microbiol Lett. 2002 Apr 23;210(1):67-72. doi: 10.1111/j.1574-6968.2002.tb11161.x. PMID: 12023079.
-#description
-Four lactococcal abortive infection mechanisms were introduced into strains which were sensitive hosts for P335 type phages and plaque assay experiments performed to assess their effect on five lactococcal bacteriophages from this family. Results indicate that AbiA inhibits all five P335 phages tested, while AbiG affects φP335 itself and φQ30 but not the other P335 species phages. AbiA was shown to retard phage Q30 DNA replication as previously reported for other phages. It was also demonstrated that AbiG, previously shown to act at a point after DNA replication in the cases of c2 type and 936 type phages, acts at the level of, or prior to phage Q30 DNA replication. AbiE and AbiF had no effect on the P335 type phages examined.
-::
-
-<br/>
-
-::card{icon="ooui:article-ltr"}
-#title
-Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res. 2014;42(7):4590-4605. doi:10.1093/nar/gkt1419
-#description
-Bacterial abortive infection (Abi) systems are ‘altruistic’ cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin–antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase β family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins
-::
-
-<br/>
-
-::card{icon="ooui:article-ltr"}
-#title
-Li Z, Song Q, Wang Y, Xiao X, Xu J. Identification of a functional toxin-antitoxin system located in the genomic island PYG1 of piezophilic hyperthermophilic archaeon Pyrococcus yayanosii. Extremophiles. 2018 May;22(3):347-357. doi: 10.1007/s00792-018-1002-2. Epub 2018 Jan 15. PMID: 29335804.
-
-#description
-Toxin-antitoxin (TA) system is bacterial or archaeal genetic module consisting of toxin and antitoxin gene that be organized as a bicistronic operon. TA system could elicit programmed cell death, which is supposed to play important roles for the survival of prokaryotic population under various physiological stress conditions. The phage abortive infection system (AbiE family) belongs to bacterial type IV TA system. However, no archaeal AbiE family TA system has been reported so far. In this study, a putative AbiE TA system (PygAT), which is located in a genomic island PYG1 in the chromosome of Pyrococcus yayanosii CH1, was identified and characterized. In Escherichia coli, overexpression of the toxin gene pygT inhibited its growth while the toxic effect can be suppressed by introducing the antitoxin gene pygA in the same cell. PygAT also enhances the stability of shuttle plasmids with archaeal plasmid replication protein Rep75 in E. coli. In P. yayanosii, disruption of antitoxin gene pygA cause a significantly growth delayed under high hydrostatic pressure (HHP). The antitoxin protein PygA can specifically bind to the PygAT promoter region and regulate the transcription of pygT gene in vivo. These results show that PygAT is a functional TA system in P. yayanosii, and also may play a role in the adaptation to HHP environment.
-::
-
-<br/>
-
-::card{icon="ooui:article-ltr"}
-#title
-Hampton HG, Jackson SA, Fagerlund RD, Vogel AIM, Dy RL, Blower TR, Fineran PC. AbiEi Binds Cooperatively to the Type IV abiE Toxin-Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. J Mol Biol. 2018 Apr 13;430(8):1141-1156. doi: 10.1016/j.jmb.2018.02.022. Epub 2018 Mar 6. PMID: 29518409.
-
-#description
-Bacteria resist phage infection using multiple strategies, including CRISPR-Cas and abortive infection (Abi) systems. Abi systems provide population-level protection from phage predation, via "altruistic" cell suicide. It has recently been shown that some Abi systems function via a toxin-antitoxin mechanism, such as the widespread AbiE family. The Streptococcus agalactiae AbiE system consists of a bicistronic operon encoding the AbiEi antitoxin and AbiEii toxin, which function as a Type IV toxin-antitoxin system. Here we examine the AbiEi antitoxin, which belongs to a large family of transcriptional regulators with a conserved N-terminal winged helix-turn-helix domain. This winged helix-turn-helix is essential for transcriptional repression of the abiE operon. The function of the AbiEi C-terminal domain is poorly characterized, but it contributes to transcriptional repression and is sufficient for toxin neutralization. We demonstrate that a conserved charged surface on one face of the C-terminal domain assists sequence-specific DNA binding and negative autoregulation, without influencing antitoxicity. Furthermore, AbiEi binds cooperatively to two inverted repeats within the abiE promoter and bends the DNA by 72°. These findings demonstrate that the mechanism of DNA binding by the widespread family of AbiEi antitoxins and transcriptional regulators can contribute to negative autoregulation
-::
-
-<br/>
-
-::card{icon="ooui:article-ltr"}
-#title
-Beck IN, Usher B, Hampton HG, Fineran PC, Blower TR. Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences. Biochem J. 2020 Jun 26;477(12):2401-2419. doi: 10.1042/BCJ20200368. PMID: 32519742; PMCID: PMC7319586.
-
-#description
-Toxin-antitoxin systems play key roles in bacterial adaptation, including protection from antibiotic assault and infection by bacteriophages. The type IV toxin-antitoxin system AbiE encodes a DUF1814 nucleotidyltransferase-like toxin, and a two-domain antitoxin. In Streptococcus agalactiae, the antitoxin AbiEi negatively autoregulates abiE expression through positively co-operative binding to inverted repeats within the promoter. The human pathogen Mycobacterium tuberculosis encodes four DUF1814 putative toxins, two of which have antitoxins homologous to AbiEi. One such M. tuberculosis antitoxin, named Rv2827c, is required for growth and whilst the structure has previously been solved, the mode of regulation is unknown. To complete the gaps in our understanding, we first solved the structure of S. agalactiae AbiEi to 1.83 Å resolution for comparison with M. tuberculosis Rv2827c. AbiEi contains an N-terminal DNA binding domain and C-terminal antitoxicity domain, with bilateral faces of opposing charge. The overall AbiEi fold is similar to Rv2827c, though smaller, and with a 65° difference in C-terminal domain orientation. We further demonstrate that, like AbiEi, Rv2827c can autoregulate toxin-antitoxin operon expression. In contrast with AbiEi, the Prv2827c promoter contains two sets of inverted repeats, which bind Rv2827c with differing affinities depending on the sequence consensus. Surprisingly, Rv2827c bound with negative co-operativity to the full Prv2827c promoter, demonstrating an unexpectedly complex form of transcriptional regulation.
-::
-
-<br/>
-
-::card{icon="ooui:article-ltr"}
-#title
-Hampton HG, Smith LM, Ferguson S, Meaden S, Jackson SA, Fineran PC. Functional genomics reveals the toxin-antitoxin repertoire and AbiE activity in Serratia. Microb Genom. 2020 Nov;6(11):mgen000458. doi: 10.1099/mgen.0.000458. PMID: 33074086; PMCID: PMC7725324.\*\*
-
-#description
-Bacteriophage defences are divided into innate and adaptive systems. Serratia sp. ATCC 39006 has three CRISPR-Cas adaptive immune systems, but its innate immune repertoire is unknown. Here, we re-sequenced and annotated the Serratia genome and predicted its toxin-antitoxin (TA) systems. TA systems can provide innate phage defence through abortive infection by causing infected cells to 'shut down', limiting phage propagation. To assess TA system function on a genome-wide scale, we utilized transposon insertion and RNA sequencing. Of the 32 TA systems predicted bioinformatically, 4 resembled pseudogenes and 11 were demonstrated to be functional based on transposon mutagenesis. Three functional systems belonged to the poorly characterized but widespread, AbiE, abortive infection/TA family. AbiE is a type IV TA system with a predicted nucleotidyltransferase toxin. To investigate the mode of action of this toxin, we measured the transcriptional response to AbiEii expression. We observed dysregulated levels of tRNAs and propose that the toxin targets tRNAs resulting in bacteriostasis. A recent report on a related toxin shows this occurs through addition of nucleotides to tRNA(s). This study has demonstrated the utility of functional genomics for probing TA function in a high-throughput manner, defined the TA repertoire in Serratia and shown the consequences of AbiE induction.
-::
-
-## Sources
-
-1. Garvey P, Fitzgerald GF, Hill C. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl Environ Microbiol. 1995 Dec;61(12):4321-8. doi: 10.1128/aem.61.12.4321-4328.1995. PMID: 8534099; PMCID: PMC167743.
-2. Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res. 2014;42(7):4590-4605. doi:10.1093/nar/gkt1419
-
-
-::references-list
----
-items:
- - 10.1093/nar/gkt1419
- - 10.1128/aem.61.12.4321-4328.1995
----
-::
-
-
diff --git a/content/2.defense-systems/3.AVAST.md b/content/2.defense-systems/3.AVAST.md
deleted file mode 100644
index fa0097b73dd96c8f3239ae3e3a52ffc816e62b5e..0000000000000000000000000000000000000000
--- a/content/2.defense-systems/3.AVAST.md
+++ /dev/null
@@ -1,18 +0,0 @@
-# AVAST
-
-AVAST (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
-
-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)
-
-## Relevant abstracts
-
-**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**
-
-Bacteria and archaea are frequently attacked by viruses and other mobile genetic elements and rely on dedicated antiviral defense systems, such as restriction endonucleases and CRISPR, to survive. The enormous diversity of viruses suggests that more types of defense systems exist than are currently known. By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. These systems incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis. In addition, we computationally predict a diverse set of other putative defense genes that remain to be characterized. These results highlight an immense array of molecular functions that microbes use against viruses.
-
-## References
-
-**1\.** 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
-
diff --git a/content/2.defense-systems/_dir.yml b/content/2.defense-systems/_dir.yml
deleted file mode 100644
index 24957f0b2727272d7728c3a498f4d5a594db970f..0000000000000000000000000000000000000000
--- 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.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
new file mode 100644
index 0000000000000000000000000000000000000000..351668ba0d0859d8cafc802204b3a636c43e579d
--- /dev/null
+++ b/content/2.defense-systems/abi2.md
@@ -0,0 +1,27 @@
+---
+title: Abi2
+---
+
+## Example of genomic structure
+
+The Abi2 system is composed of one protein: Abi_2.
+
+Here is an example found in the RefSeq database:
+
+
+
+Abi2 system in the genome of *Clostridium butyricum* (GCF_014131795.1) is composed of 1 protein: Abi_2 (WP_035763709.1).
+
+## Distribution of the system among prokaryotes
+
+The Abi2 system is present in a total of 176 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes (5.3 %).
+
+
+
+
+*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+
+## Relevant abstracts
+
diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md
new file mode 100644
index 0000000000000000000000000000000000000000..b10dd9da9f592022bb535ab24559e99e5b95fc6d
--- /dev/null
+++ b/content/2.defense-systems/abia.md
@@ -0,0 +1,55 @@
+# AbiA
+
+## Example of genomic structure
+
+The AbiA system have been describe in a total of 2 subsystems.
+
+Here is some example found in the RefSeq database:
+
+
+
+AbiA_large subsystem in the genome of *Lactobacillus amylovorus* (GCF_002706375.1) is composed of 1 protein: AbiA_large (WP_056940268.1).
+
+
+
+AbiA_small subsystem in the genome of *Mesobacillus foraminis* (GCF\_003667765.1) is composed of 2 proteins: AbiA\_small (WP\_121614402.1)and, AbiA\_SLATT (WP\_121614403.1).
+
+## Distribution of the system among prokaryotes
+
+The AbiA system is present in a total of 35 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (0.2 %).
+
+
+
+*Proportion of genome encoding the AbiA 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.*
+
+## Experimental validation
+
+AbiA systems were experimentally validated using:
+
+A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
+
+## Relevant abstracts
+
+
+::references-list
+---
+items:
+ - 10.1016/j.mib.2005.06.006
+ - 10.1023/A:1002027321171
+ - 10.1093/nar/gkac467
+---
+::
+
+<!-- 10.1016/j.mib.2005.06.006 -->
+
+**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
+Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
+
+**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
+The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
+
+**Mestre, M. R. et al. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Research 50, 6084-6101 (2022).**
+Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
+
diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md
new file mode 100644
index 0000000000000000000000000000000000000000..7d9fb3716887ed135d9ac499bc6f2fb3b4f00e63
--- /dev/null
+++ b/content/2.defense-systems/abie.md
@@ -0,0 +1,54 @@
+---
+title: AbiE
+---
+
+## Description
+
+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.Â
+
+It is classified as an Abortive infection system.
+
+## Molecular mechanism
+
+AbiE systems are encoded by two mandatory genes, abiEi and abiEii (1,2).  The latter encodes for AbiEii, a GTP-binding nucleotidyltransferase (NTase) which expression induce a reversible growth arrest.  On the other hand, abiEi encodes for a AbiEi a transcriptional autorepressor that  binds to the promoter of the abiE operon.
+
+Based on this mechanisms, AbiE systems are classified as Type IV Toxin-Antitoxin system, where the antitoxin and toxin are both proteins that do not directly interact with each other.
+
+## Example of genomic structure
+
+The AbiE system is composed of 2 proteins: AbiEi_1 and, AbiEii.
+
+Here is an example found in the RefSeq database:
+
+
+
+
+AbiE system in the genome of *Desulfuromonas versatilis* (GCF\_019704135.1) is composed of 2 proteins: AbiEi\_1 (WP\_221251730.1)and, AbiEii (WP\_221251731.1).
+
+## Distribution of the system among prokaryotes
+
+The AbiE system is present in a total of 962 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 3742 genomes (16.4 %).
+
+
+
+*Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+
+## Experimental validation
+
+AbiE systems were experimentally validated using:
+
+A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
+
+## Relevant abstracts
+
+**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
+Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
+
+**Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C. & Fineran, P. C. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res 42, 4590-4605 (2014).**
+Bacterial abortive infection (Abi) systems are 'altruistic' cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin-antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase ? family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins.
+
+**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
+The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
+
diff --git a/content/2.defense-systems/avast.md b/content/2.defense-systems/avast.md
new file mode 100644
index 0000000000000000000000000000000000000000..e3f5aca25ea1f2feb7d1f75ce4cf8dd758a40ee0
--- /dev/null
+++ b/content/2.defense-systems/avast.md
@@ -0,0 +1,111 @@
+---
+title: AVAST
+---
+
+## Description
+AVAST (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
+
+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.
+
+## Example of genomic structure
+
+The AVAST system have been describe in a total of 5 subsystems.
+
+Here is some example found in the RefSeq database:
+
+
+
+
+AVAST_I subsystem in the genome of *Vibrio sp.* (GCF\_905175355.1) is composed of 3 proteins: Avs1A (WP\_208445041.1), Avs1B (WP\_208445042.1)and, Avs1C (WP_108173272.1).
+
+
+
+
+AVAST_II subsystem in the genome of *Escherichia coli* (GCF_018884505.1) is composed of 1 protein: Avs2A (WP_032199984.1).
+
+
+
+
+AVAST_III subsystem in the genome of *Enterobacter cancerogenus* (GCF_002850575.1) is composed of 2 proteins: Avs3B (WP_199559884.1)and, Avs3A (WP_101737373.1).
+
+
+
+
+AVAST_IV subsystem in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: Avs4A (WP_000240574.1).
+
+
+
+
+AVAST_V subsystem in the genome of *Leclercia adecarboxylata* (GCF_006171285.1) is composed of 1 protein: Avs5A (WP_139565349.1).
+
+## Distribution of the system among prokaryotes
+
+The AVAST system is present in a total of 363 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 1046 genomes (4.6 %).
+
+
+
+*Proportion of genome encoding the AVAST 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.*
+
+## Experimental validation
+
+AVAST systems were experimentally validated using:
+
+Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Escherichia coli* has an anti-phage effect against T4, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
+
+Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Salmonella enterica * has an anti-phage effect against P22, BTP1, ES18, det7 (Fillol-Salom et al., 2022)
+
+Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Klebsiella pneumoniae * has an anti-phage effect against Pokey (Fillol-Salom et al., 2022)
+
+Subsystem Metallo beta-lactamase + protease + STAND (Type 1) with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2020)
+
+Subsystem STAND (Type 2) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1 (Gao et al., 2020)
+
+Subsystem DUF4297-STAND (Type 3) with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T3, T7, PhiV-1 (Gao et al., 2020)
+
+Subsystem Mrr-STAND (Type 4) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020)
+
+Subsystem SIR2-STAND (Type 5) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2 (Gao et al., 2020)
+
+Subsystem SeAvs1 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
+
+Subsystem EcAcs1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
+
+Subsystem EpAvs1 with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1, Lambda, , ZL-19 (Gao et al., 2022)
+
+Subsystem SeAvs3 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
+
+Subsystem KvAvs3 with a system from *Klebsiella variicola* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
+
+Subsystem EcAvs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, P1, T4, T5, ZL-19 (Gao et al., 2022)
+
+Subsystem Ec2Avs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2022)
+
+Subsystem EcAvs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
+
+Subsystem Ec2Avs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
+
+Subsystem KpAvs4 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
+
+Subsystem CcAvs4 with a system from *Corallococcus coralloides* in *Escherichia coli* has an anti-phage effect against T7 (Gao et al., 2022)
+
+## Relevant abstracts
+
+
+::references-list
+---
+items:
+ - 10.1126/science.abm4096
+ - 10.1126/science.aba0372
+---
+::
+
+**Gao, L. A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).**
+Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
+
+**Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077-1084 (2020).**
+Bacteria and archaea are frequently attacked by viruses and other mobile genetic elements and rely on dedicated antiviral defense systems, such as restriction endonucleases and CRISPR, to survive. The enormous diversity of viruses suggests that more types of defense systems exist than are currently known. By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. These systems incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis. In addition, we computationally predict a diverse set of other putative defense genes that remain to be characterized. These results highlight an immense array of molecular functions that microbes use against viruses.
+
diff --git a/content/2.defense-systems/1.PARIS.md b/content/2.defense-systems/paris.md
similarity index 68%
rename from content/2.defense-systems/1.PARIS.md
rename to content/2.defense-systems/paris.md
index 449053c8cebb3411674e40281f69faf1b1f0e690..fc6d7898f19abd749c0c02e6f7d60317060efbb5 100644
--- a/content/2.defense-systems/1.PARIS.md
+++ b/content/2.defense-systems/paris.md
@@ -1,13 +1,14 @@
---
title: Paris
toc: true
+layout: article
---
# PARIS system
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
@@ -21,30 +22,19 @@ There is 2 types of PARIS systems:
### Paris type I
-::card
-#title
Paris type I : AriA*I Â (AAA*15) + AriB (DUF4435) or AriAB (fused AAA_15 + DUF4435)
-#description
-::
<br/>
-::card
-#title
Paris type I system in _Salmonella enterica_ (GCF\__000006945.2). AriA_I:_ NP_461673.1; AriB: NP_461674.1
-#description
-::
<br/>
-::card
-#title
Paris type I merge system in _Sideroxydans lithotrophicus_ (GCF\__000025705.1). AriAB_I:_ WP_013030315.1
-::
### Paris type II
@@ -60,12 +50,6 @@ Paris type II merge system in _Desulfovibrio desulfuricans_ (GCF\__000025705.1).
## ReferencesÂ
-1. François Rousset, Julien Dowding, Aude Bernheim, Eduardo P.C. Rocha, David Bikard, Prophage-encoded hotspots of bacterial immune systems, bioRxiv 2021.01.21.427644; doi: https://doi.org/10.1101/2021.01.21.427644
-
-2. Isaev A, Drobiazko A, Sierro N, et al. Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence \[published correction appears in Nucleic Acids Res. 2020 Jul 27;48(13):7601-7602\]. _Nucleic Acids Res_. 2020;48(10):5397-5406. doi:10.1093/nar/gkaa290
-
-3. Studier FW. Gene 0.3 of bacteriophage T7 acts to overcome the DNA restriction system of the host. J Mol Biol. 1975 May 15;94(2):283-95. doi: 10.1016/0022-2836(75)90083-2. PMID: 1095770.
-
::references-list
---
items:
@@ -73,4 +57,4 @@ items:
- 10.1093/nar/gkaa290
- 10.1016/0022-2836(75)90083-2
---
-::
\ No newline at end of file
+::
diff --git a/content/2.defense-systems/rm.md b/content/2.defense-systems/rm.md
new file mode 100644
index 0000000000000000000000000000000000000000..98337030a22fa6307283fb37d3e9f19a6ae9926d
--- /dev/null
+++ b/content/2.defense-systems/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/2.defense-systems/viperin.md b/content/2.defense-systems/viperin.md
new file mode 100644
index 0000000000000000000000000000000000000000..3e8196ab143c7a55de35572580e72897b5a4162c
--- /dev/null
+++ b/content/2.defense-systems/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/docker-compose.yml b/docker-compose.yml
index 45cfae8ca9dee5687ac5ebabe6821cec91ac866b..8744a0047384421a569ae4e7125c963c4b62e3ca 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -4,15 +4,45 @@ services:
build:
context: .
target: dev
- container_name: docus_dev
+ container_name: nuxt
volumes:
- .:/usr/src/app
- defense-finder-wiki-node-modules:/usr/src/app/node_modules
- - defense-finder-wiki-dotnuxt:/usr/src/app/.nuxt
+ - /usr/src/app/.nuxt
ports:
- "3000:3000"
- "24678:24678"
- "4000:4000"
+ labels:
+ - "traefik.enable=true"
+ - "traefik.docker.network=main"
+ - "traefik.http.routers.nuxt.service=nuxt-service"
+ - "traefik.http.routers.nuxt.rule=Host(`localhost`)"
+ - "traefik.http.routers.nuxt.entrypoints=web"
+ - "traefik.http.services.nuxt-service.loadbalancer.server.port=3000"
+ networks:
+ - main
+
+ traefik:
+ image: traefik:v2.9
+ command:
+ - "--log.level=DEBUG"
+ - "--api.insecure=true"
+ - "--providers.docker=true"
+ - "--providers.docker.exposedbydefault=true"
+ - "--entrypoints.web.address=:80"
+
+ ports:
+ - "8082:80"
+ - "8080:8080"
+ volumes:
+ - "/var/run/docker.sock:/var/run/docker.sock:ro"
+ networks:
+ - main
+
volumes:
defense-finder-wiki-node-modules:
- defense-finder-wiki-dotnuxt:
+
+networks:
+ main:
+ driver: bridge
diff --git a/layouts/article.vue b/layouts/article.vue
new file mode 100644
index 0000000000000000000000000000000000000000..46805b472cd8a1c1b6a294279710b8abac8be3ec
--- /dev/null
+++ b/layouts/article.vue
@@ -0,0 +1,39 @@
+<script setup lang="ts">
+const { page, surround } = useContent();
+import { useCustomTheme } from '~/composables/useCustomTheme'
+
+const { isDark } = useCustomTheme()
+
+</script>
+<template>
+ <VApp :theme="isDark ? 'dark' : 'light'">
+ <v-main style="min-height: 300px">
+ <!-- <v-container class="fill-height w-auto" > -->
+ <!-- <v-card flat max-width="1000" min-height="300" color="transparent">
+ <v-card-text> -->
+ <v-container>
+ <slot />
+ <!-- </v-card-text>
+ </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-row>
+ </v-container>
+ <v-footer id="app-footer" app>footer</v-footer>
+ <!-- </v-container> -->
+ </v-main>
+ <NavNavbar />
+ <NavTableOfContent :links="page.body.toc.links" />
+ </VApp>
+</template>
+
+<style scoped>
+#app-footer {
+ border-top: 1px solid rgba(var(--v-border-color), var(--v-border-opacity));
+}
+</style>
diff --git a/layouts/custom.vue b/layouts/custom.vue
new file mode 100644
index 0000000000000000000000000000000000000000..d608a56fc267b2a7fa56b132363da7da8422df61
--- /dev/null
+++ b/layouts/custom.vue
@@ -0,0 +1,21 @@
+<template>
+ <v-card>
+ <VApp :theme="isDark ? 'dark' : 'light'">
+ <NavNavbar />
+
+ <v-main style="min-height: 300px">
+ <v-container>
+ <slot />
+ <v-footer app>footer</v-footer>
+ </v-container></v-main>
+ </VApp>
+ </v-card>
+</template>
+<script setup lang="ts">
+import { useCustomTheme } from '~/composables/useCustomTheme'
+
+const { isDark } = useCustomTheme()
+const { navigation } = useContent();
+
+const drawer = ref(true);
+</script>
diff --git a/nuxt.config.ts b/nuxt.config.ts
old mode 100755
new mode 100644
index a41081b0d1f20091a468d653616002719e10fadc..04c36373a8d957ae6b54ade61a5151997c1cd29f
--- a/nuxt.config.ts
+++ b/nuxt.config.ts
@@ -1,11 +1,21 @@
+// https://v3.nuxtjs.org/api/configuration/nuxt.config
export default defineNuxtConfig({
- extends: '@nuxt-themes/docus',
+ modules: ['@nuxt/content', 'vuetify-nuxt-module', '@vueuse/nuxt'],
content: {
- // issue with docker compose to open ws on port 4000
- watch: false
+ documentDriven: {
+ injectPage: false,
+ }
},
- modules: [
- '@vueuse/nuxt',
- ],
+ vuetify: {
+ vuetifyOptions: {
+ labComponents: true
+ }
+ },
+ devtools: {
+ enabled: false
+ },
+ // app: {
+ // baseURL: '/defense-finder-wiki-test/',
+ // }
})
diff --git a/package-lock.json b/package-lock.json
index c4f39ae470df5ac4f67cdd463821ef15ad348fcc..9795b41daa1810f43f98229779837cff0829a9cb 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,71 +1,134 @@
{
- "name": "docus-starter",
- "version": "0.1.0",
+ "name": "wiki",
"lockfileVersion": 3,
"requires": true,
"packages": {
"": {
- "name": "docus-starter",
- "version": "0.1.0",
- "dependencies": {
- "@vueuse/nuxt": "^9.12.0"
- },
"devDependencies": {
- "@nuxt-themes/docus": "^1.8.2",
- "nuxt": "^3.2.0"
+ "@nuxt/content": "^2.7.2",
+ "@types/node": "^18.15.12",
+ "@vueuse/core": "^10.4.1",
+ "@vueuse/nuxt": "^10.4.1",
+ "nuxt": "^3.7.0",
+ "vuetify-nuxt-module": "^0.5.7"
}
},
"node_modules/@ampproject/remapping": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.0.tgz",
- "integrity": "sha512-qRmjj8nj9qmLTQXXmaR1cck3UXSRMPrbsLJAasZpF+t3riI71BXed5ebIOYwQntykeZuhjsdweEc9BxH5Jc26w==",
+ "version": "2.2.1",
+ "dev": true,
+ "license": "Apache-2.0",
"dependencies": {
- "@jridgewell/gen-mapping": "^0.1.0",
+ "@jridgewell/gen-mapping": "^0.3.0",
"@jridgewell/trace-mapping": "^0.3.9"
},
"engines": {
"node": ">=6.0.0"
}
},
+ "node_modules/@antfu/utils": {
+ "version": "0.7.6",
+ "dev": true,
+ "license": "MIT",
+ "funding": {
+ "url": "https://github.com/sponsors/antfu"
+ }
+ },
"node_modules/@babel/code-frame": {
- "version": "7.18.6",
- "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz",
- "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==",
+ "version": "7.22.13",
+ "dev": true,
+ "license": "MIT",
"dependencies": {
- "@babel/highlight": "^7.18.6"
+ "@babel/highlight": "^7.22.13",
+ "chalk": "^2.4.2"
},
"engines": {
"node": ">=6.9.0"
}
},
+ "node_modules/@babel/code-frame/node_modules/ansi-styles": {
+ "version": "3.2.1",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "color-convert": "^1.9.0"
+ },
+ "engines": {
+ "node": ">=4"
+ }
+ },
+ "node_modules/@babel/code-frame/node_modules/chalk": {
+ "version": "2.4.2",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "ansi-styles": "^3.2.1",
+ "escape-string-regexp": "^1.0.5",
+ "supports-color": "^5.3.0"
+ },
+ "engines": {
+ "node": ">=4"
+ }
+ },
+ "node_modules/@babel/code-frame/node_modules/color-convert": {
+ "version": "1.9.3",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "color-name": "1.1.3"
+ }
+ },
+ "node_modules/@babel/code-frame/node_modules/color-name": {
+ "version": "1.1.3",
+ "dev": true,
+ "license": "MIT"
+ },
+ "node_modules/@babel/code-frame/node_modules/escape-string-regexp": {
+ "version": "1.0.5",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": ">=0.8.0"
+ }
+ },
+ "node_modules/@babel/code-frame/node_modules/supports-color": {
+ "version": "5.5.0",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "has-flag": "^3.0.0"
+ },
+ "engines": {
+ "node": ">=4"
+ }
+ },
"node_modules/@babel/compat-data": {
- "version": "7.20.14",
- "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.20.14.tgz",
- "integrity": "sha512-0YpKHD6ImkWMEINCyDAD0HLLUH/lPCefG8ld9it8DJB2wnApraKuhgYTvTY1z7UFIfBTGy5LwncZ+5HWWGbhFw==",
+ "version": "7.22.9",
+ "dev": true,
+ "license": "MIT",
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/core": {
- "version": "7.20.12",
- "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.20.12.tgz",
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+ "json5": "^2.2.3",
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+ "dev": true,
+ "license": "ISC",
"bin": {
"semver": "bin/semver.js"
}
},
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+ "license": "MIT",
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+ "@babel/types": "^7.22.5"
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}
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"dependencies": {
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}
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+ "dev": true,
+ "license": "ISC",
"bin": {
"semver": "bin/semver.js"
}
},
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+ "version": "7.22.15",
+ "dev": true,
+ "license": "MIT",
"dependencies": {
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+ "@babel/helper-split-export-declaration": "^7.22.6",
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},
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@@ -167,189 +216,197 @@
"@babel/core": "^7.0.0"
}
},
+ "node_modules/@babel/helper-create-class-features-plugin/node_modules/semver": {
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+ "dev": true,
+ "license": "ISC",
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+ "dev": true,
+ "license": "MIT",
"engines": {
"node": ">=6.9.0"
}
},
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- "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.19.0.tgz",
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+ "dev": true,
+ "license": "MIT",
"dependencies": {
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- "@babel/types": "^7.19.0"
+ "@babel/template": "^7.22.5",
+ "@babel/types": "^7.22.5"
},
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}
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+ "dev": true,
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+ "@babel/types": "^7.22.5"
},
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}
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+ "license": "MIT",
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+ "dev": true,
+ "license": "MIT",
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}
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+ "version": "7.22.15",
+ "dev": true,
+ "license": "MIT",
"dependencies": {
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+ "license": "MIT",
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- "chalk": "^2.0.0",
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},
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@@ -358,8 +415,8 @@
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+ "dev": true,
+ "license": "MIT",
"dependencies": {
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},
@@ -369,8 +426,8 @@
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+ "dev": true,
+ "license": "MIT",
"dependencies": {
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@@ -380,18 +437,42 @@
"node": ">=4"
}
},
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+ "dev": true,
+ "license": "MIT",
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+ "dev": true,
+ "license": "MIT"
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+ "dev": true,
+ "license": "MIT",
"engines": {
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}
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+ "node_modules/@babel/highlight/node_modules/supports-color": {
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"dev": true,
+ "license": "MIT",
"funding": {
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"url": "https://github.com/sponsors/wooorm"
}
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"dev": true,
+ "license": "BSD-3-Clause",
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+ "dev": true,
"funding": [
{
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"url": "https://github.com/sponsors/fb55"
}
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- "domelementtype": "^2.2.0",
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},
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+ "type-fest": "^3.8.0"
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}
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"dev": true,
+ "license": "MIT",
"funding": {
"type": "github",
"url": "https://github.com/sponsors/wooorm"
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+ "dev": true,
+ "license": "MIT",
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+ "version": "6.5.2",
"dev": true,
+ "license": "MIT",
"dependencies": {
"@socket.io/component-emitter": "~3.1.0",
"debug": "~4.3.1",
- "engine.io-parser": "~5.0.3",
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"dev": true,
+ "license": "MIT",
"engines": {
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@@ -3774,18 +3092,17 @@
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+ "version": "5.2.1",
"dev": true,
+ "license": "MIT",
"engines": {
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}
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+ "version": "5.15.0",
+ "dev": true,
+ "license": "MIT",
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@@ -3795,17 +3112,20 @@
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+ "version": "4.5.0",
+ "dev": true,
+ "license": "BSD-2-Clause",
+ "engines": {
+ "node": ">=0.12"
+ },
"funding": {
"url": "https://github.com/fb55/entities?sponsor=1"
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+ "dev": true,
+ "license": "MIT",
"dependencies": {
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},
@@ -3813,17 +3133,11 @@
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+ "version": "0.19.2",
+ "dev": true,
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+ "license": "MIT",
"bin": {
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@@ -3831,47 +3145,47 @@
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+ "dev": true,
+ "license": "MIT",
"engines": {
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+ "dev": true,
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+ "dev": true,
+ "license": "MIT",
"engines": {
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@@ -3879,44 +3193,23 @@
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+ "dev": true,
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+ "license": "MIT",
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+ "dev": true,
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- "fast-glob": "^3.2.11",
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+ "license": "MIT",
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@@ -4512,11 +3661,23 @@
"url": "https://opencollective.com/unified"
}
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"dev": true,
+ "license": "MIT",
"funding": {
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"url": "https://opencollective.com/unified"
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"dev": true,
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},
@@ -4535,11 +3695,23 @@
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}
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+ "dev": true,
+ "license": "MIT"
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"dev": true,
+ "license": "MIT",
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@@ -4549,11 +3721,23 @@
"url": "https://opencollective.com/unified"
}
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+ "license": "MIT",
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+ "dev": true,
+ "license": "MIT"
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"dev": true,
+ "license": "MIT",
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},
@@ -4562,11 +3746,23 @@
"url": "https://opencollective.com/unified"
}
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+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
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+ "version": "2.0.8",
+ "dev": true,
+ "license": "MIT"
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"dev": true,
+ "license": "MIT",
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@@ -4585,82 +3781,150 @@
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+ "node_modules/hast-util-raw/node_modules/@types/hast": {
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+ "license": "MIT",
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+ "dev": true,
+ "license": "MIT"
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+ "license": "MIT",
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}
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+ "node_modules/hast-util-raw/node_modules/unist-util-position": {
+ "version": "4.0.4",
"dev": true,
+ "license": "MIT",
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},
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+ "license": "MIT",
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+ "license": "MIT"
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+ "node_modules/hast-util-to-string": {
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+ "dev": true,
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+ "dev": true,
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+ "dev": true,
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+ "version": "5.5.3",
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"dev": true,
+ "license": "MIT",
"funding": {
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"url": "https://feross.org/support"
}
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"funding": {
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"dev": true,
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"url": "https://opencollective.com/unified"
}
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"url": "https://opencollective.com/unified"
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}
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}
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+ "version": "2.0.10",
+ "dev": true,
+ "license": "MIT",
"funding": {
"url": "https://github.com/sponsors/harlan-zw"
}
},
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old mode 100755
new mode 100644
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--- a/package.json
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{
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"private": true,
"scripts": {
- "dev": "nuxi dev",
- "build": "nuxi build",
- "generate": "nuxi generate",
- "preview": "nuxi preview"
+ "build": "nuxt build",
+ "dev": "nuxt dev",
+ "generate": "nuxt generate",
+ "preview": "nuxt preview"
},
"devDependencies": {
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- "nuxt": "^3.2.0"
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+ "@vueuse/core": "^10.4.1",
+ "@vueuse/nuxt": "^10.4.1",
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}
}
diff --git a/pages/[...slug].vue b/pages/[...slug].vue
new file mode 100644
index 0000000000000000000000000000000000000000..e0c2b132aae1a4bc07b1ad7291c2eee020d2dd61
--- /dev/null
+++ b/pages/[...slug].vue
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+<template>
+ <v-row justify="center">
+ <v-col cols="auto">
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+ <v-card-text>
+ <ContentDoc />
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+ </v-row>
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diff --git a/public/preview.png b/public/preview.png
deleted file mode 100644
index e28a3f3339b76cc008cbb49b5cfd19a7a8f9d991..0000000000000000000000000000000000000000
Binary files a/public/preview.png and /dev/null differ
diff --git a/public/site.webmanifest b/public/site.webmanifest
deleted file mode 100644
index fa99de77db6ead952ba6fef2e42f1525cc0a2968..0000000000000000000000000000000000000000
--- a/public/site.webmanifest
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "name": "",
- "short_name": "",
- "icons": [
- {
- "src": "/android-chrome-192x192.png",
- "sizes": "192x192",
- "type": "image/png"
- },
- {
- "src": "/android-chrome-512x512.png",
- "sizes": "512x512",
- "type": "image/png"
- }
- ],
- "theme_color": "#ffffff",
- "background_color": "#ffffff",
- "display": "standalone"
-}
diff --git a/renovate.json b/renovate.json
deleted file mode 100755
index 75ac0dd39ddeafe587776a5a651d53a77f5312d6..0000000000000000000000000000000000000000
--- a/renovate.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "extends": [
- "@nuxtjs"
- ],
- "lockFileMaintenance": {
- "enabled": true
- }
-}
diff --git a/tokens.config.ts b/tokens.config.ts
deleted file mode 100644
index 451b9b53e8766f35657755c19fca2c42907ee766..0000000000000000000000000000000000000000
--- a/tokens.config.ts
+++ /dev/null
@@ -1,7 +0,0 @@
-import { defineTheme, palette } from 'pinceau'
-
-export default defineTheme({
- color: {
- primary: palette('orange')
- }
-})
diff --git a/tsconfig.json b/tsconfig.json
index 4b34df1571f7bfb636c02bbb718603cc2d9d1382..a7bfa186c3fdc5f5f410168bdbad2291177ff9bc 100755
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -1,3 +1,4 @@
{
+ // https://v3.nuxtjs.org/concepts/typescript
"extends": "./.nuxt/tsconfig.json"
}