Dernières modifications :

updated PO files
diff --git "a/Debian/debi\303\242neries/open.en.po" "b/Debian/debi\303\242neries/open.en.po"
index eb5c1f2f..db191c5f 100644
--- "a/Debian/debi\303\242neries/open.en.po"
+++ "b/Debian/debi\303\242neries/open.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2021-04-10 22:31+0000\n"
+"POT-Creation-Date: 2021-04-10 22:38+0000\n"
 "PO-Revision-Date: 2021-04-11 07:36+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
-"Language-Team: \n"
 "X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text

Open Debian
diff --git "a/Debian/debi\303\242neries/open.en.po" "b/Debian/debi\303\242neries/open.en.po"
index 9e1f2cec..eb5c1f2f 100644
--- "a/Debian/debi\303\242neries/open.en.po"
+++ "b/Debian/debi\303\242neries/open.en.po"
@@ -3,38 +3,38 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2021-04-10 22:31+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2021-04-11 07:36+0900\n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Sun, 11 Apr 2021 07:21:40 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Sun, 11 Apr 2021 07:21:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Sun, 11 Apr 2021 07:21:40 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Sun, 11 Apr 2021 07:21:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Debian Bullseye: plus d'ouverture\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Debian Bullseye: more open\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -43,12 +43,19 @@ msgid ""
 "elle devrait avoir un résultat similaire à l'ouverture en cliquant avec la "
 "souris depuis un gestionnaire de fichiers."
 msgstr ""
+"Debian Bullseye will provide the command `/usr/bin/open` for your greatest "
+"comfort at the command line. On a system with a graphical desktop "
+"environment, the command should have a similar result as when opening a "
+"document from a mouse-and-click file browser."
 
 #. type: Plain text
 msgid ""
-"Techniquement, `/usr/bin/open` est un lien symbolique géré par "
-"[`update-alternatives`](https://manpages.debian.org/update-alternatives)  de "
-"façon à pointer vers [`xdg-open`](https://manpages.debian.org/xdg-open) si "
-"disponible et sinon "
-"[`run-mailcap`](https://manpages.debian.org/run-mailcap)."
+"Techniquement, `/usr/bin/open` est un lien symbolique géré par [`update-"
+"alternatives`](https://manpages.debian.org/update-alternatives)  de façon à "
+"pointer vers [`xdg-open`](https://manpages.debian.org/xdg-open) si "
+"disponible et sinon [`run-mailcap`](https://manpages.debian.org/run-mailcap)."
 msgstr ""
+"Technically, `/usr/bin/open` is a symbolic link managed by [`update-"
+"alternatives`](https://manpages.debian.org/update-alternatives) to point "
+"towards [`xdg-open`](https://manpages.debian.org/xdg-open) if available and "
+"otherwise [`run-mailcap`](https://manpages.debian.org/run-mailcap)."

updated PO files
diff --git "a/Debian/debi\303\242neries/open.en.po" "b/Debian/debi\303\242neries/open.en.po"
new file mode 100644
index 00000000..9e1f2cec
--- /dev/null
+++ "b/Debian/debi\303\242neries/open.en.po"
@@ -0,0 +1,54 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2021-04-10 22:31+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sun, 11 Apr 2021 07:21:40 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sun, 11 Apr 2021 07:21:40 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Debian Bullseye: plus d'ouverture\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Debian Bullseye contiendra la commande `/usr/bin/open` pour votre plus grand "
+"confort en ligne de commande.  Sur un système ayant une interface graphique, "
+"elle devrait avoir un résultat similaire à l'ouverture en cliquant avec la "
+"souris depuis un gestionnaire de fichiers."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Techniquement, `/usr/bin/open` est un lien symbolique géré par "
+"[`update-alternatives`](https://manpages.debian.org/update-alternatives)  de "
+"façon à pointer vers [`xdg-open`](https://manpages.debian.org/xdg-open) si "
+"disponible et sinon "
+"[`run-mailcap`](https://manpages.debian.org/run-mailcap)."
+msgstr ""

Open Debian
diff --git "a/Debian/debi\303\242neries/open.mdwn" "b/Debian/debi\303\242neries/open.mdwn"
new file mode 100644
index 00000000..9c4d9e20
--- /dev/null
+++ "b/Debian/debi\303\242neries/open.mdwn"
@@ -0,0 +1,16 @@
+[[!meta date="Sun, 11 Apr 2021 07:21:40 +0900"]]
+[[!meta updated="Sun, 11 Apr 2021 07:21:40 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Debian Bullseye: plus d'ouverture"]]
+
+Debian Bullseye contiendra la commande `/usr/bin/open` pour votre plus grand
+confort en ligne de commande.  Sur un système ayant une interface graphique,
+elle devrait avoir un résultat similaire à l'ouverture en cliquant avec la
+souris depuis un gestionnaire de fichiers.
+
+Techniquement, `/usr/bin/open` est un lien symbolique géré par
+[`update-alternatives`](https://manpages.debian.org/update-alternatives)
+de façon à pointer vers
+[`xdg-open`](https://manpages.debian.org/xdg-open) si disponible et sinon
+[`run-mailcap`](https://manpages.debian.org/run-mailcap).

IkIwIkI
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.en.po" "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
index 46674a8d..7551f634 100644
--- "a/Debian/debi\303\242neries/DebianAnalytica.en.po"
+++ "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2021-04-05 14:05+0000\n"
-"PO-Revision-Date: 2021-04-05 22:55+0900\n"
+"PO-Revision-Date: 2021-04-05 23:06+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -61,10 +61,9 @@ msgstr ""
 "until 2010."
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "![Visualisation t-SNE de la matrice des votes](DebianAnalytica.png)"
+#, no-wrap
 msgid "[[!img DebianAnalytica.png alt=\"Visualisation t-SNE de la matrice des votes\"]]\n"
-msgstr "![t-SNE visualisation of the vote matrix](DebianAnalytica.png)"
+msgstr "[[!img DebianAnalytica.png \"t-SNE visualisation of the vote matrix\"]]\n"
 
 #. type: Plain text
 msgid ""

updated PO files
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.en.po" "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
index 398e9a8c..46674a8d 100644
--- "a/Debian/debi\303\242neries/DebianAnalytica.en.po"
+++ "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2021-04-05 14:00+0000\n"
+"POT-Creation-Date: 2021-04-05 14:05+0000\n"
 "PO-Revision-Date: 2021-04-05 22:55+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -61,7 +61,9 @@ msgstr ""
 "until 2010."
 
 #. type: Plain text
-msgid "![Visualisation t-SNE de la matrice des votes](DebianAnalytica.png)"
+#, fuzzy, no-wrap
+#| msgid "![Visualisation t-SNE de la matrice des votes](DebianAnalytica.png)"
+msgid "[[!img DebianAnalytica.png alt=\"Visualisation t-SNE de la matrice des votes\"]]\n"
 msgstr "![t-SNE visualisation of the vote matrix](DebianAnalytica.png)"
 
 #. type: Plain text

iKiWiKi
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.mdwn" "b/Debian/debi\303\242neries/DebianAnalytica.mdwn"
index ade629d8..df5afa33 100644
--- "a/Debian/debi\303\242neries/DebianAnalytica.mdwn"
+++ "b/Debian/debi\303\242neries/DebianAnalytica.mdwn"
@@ -14,7 +14,7 @@ par votant et ma position avec un point rouge.  Les ronds sont espacés en
 fonction de la similarité des profils de votes après avoir concaténé les
 résultats de toutes les GRs jusqu'à 2010.
 
-![Visualisation t-SNE de la matrice des votes](DebianAnalytica.png)
+[[!img DebianAnalytica.png alt="Visualisation t-SNE de la matrice des votes"]]
 
 Donc si tant est qu'il y ait moyen de tirer quelque chose de ces données, il
 faudrait au moins un analyste plus chevronné…  Cela ne m'empêche pas de penser

updated PO files
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.en.po" "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
index 2127f929..398e9a8c 100644
--- "a/Debian/debi\303\242neries/DebianAnalytica.en.po"
+++ "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2021-04-05 13:44+0000\n"
+"POT-Creation-Date: 2021-04-05 14:00+0000\n"
 "PO-Revision-Date: 2021-04-05 22:55+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
-"Language-Team: \n"
 "X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text

Image et traduction.
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.en.po" "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
index 25696d40..2127f929 100644
--- "a/Debian/debi\303\242neries/DebianAnalytica.en.po"
+++ "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
@@ -3,38 +3,38 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2021-04-05 13:44+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2021-04-05 22:55+0900\n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Mon, 05 Apr 2021 22:33:55 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Mon, 05 Apr 2021 22:33:55 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Mon, 05 Apr 2021 22:33:55 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Mon, 05 Apr 2021 22:33:55 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Debian Analytica\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Debian Analytica\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -42,6 +42,9 @@ msgid ""
 "pourrait étudier les résultats publics de nos votes passés et exposer les "
 "fractures de notre communauté."
 msgstr ""
+"A couple of days ago I wrote on _debian-vote@_ that a junior analyst could "
+"study the tally sheets of our general resolutions and find the cracks in our "
+"community."
 
 #. type: Plain text
 msgid ""
@@ -51,10 +54,15 @@ msgid ""
 "en fonction de la similarité des profils de votes après avoir concaténé les "
 "résultats de toutes les GRs jusqu'à 2010."
 msgstr ""
+"In the end, with a quite naïve approach and a time budget of a few hours, I "
+"did not manage anything of interest. The figure below shows one circle per "
+"voter and my position as a red dot. The circles are spaces according to the "
+"similarity of the vote profiles after I concatenated the results of all GRs "
+"until 2010."
 
 #. type: Plain text
 msgid "![Visualisation t-SNE de la matrice des votes](DebianAnalytica.png)"
-msgstr ""
+msgstr "![t-SNE visualisation of the vote matrix](DebianAnalytica.png)"
 
 #. type: Plain text
 msgid ""
@@ -63,3 +71,6 @@ msgid ""
 "penser que nous devrions voter anonymement pour tous nos scrutins, et cesser "
 "de diffuser ce genre de données."
 msgstr ""
+"So if there is something to extract from these data, it will need a more "
+"expert analyst… This said, I think that our future votes should all be "
+"anonymous, and that we should stop distributing that kind of data."
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.png" "b/Debian/debi\303\242neries/DebianAnalytica.png"
new file mode 100644
index 00000000..14a8c2cb
Binary files /dev/null and "b/Debian/debi\303\242neries/DebianAnalytica.png" differ

updated PO files
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.en.po" "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
new file mode 100644
index 00000000..25696d40
--- /dev/null
+++ "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
@@ -0,0 +1,65 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2021-04-05 13:44+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Mon, 05 Apr 2021 22:33:55 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Mon, 05 Apr 2021 22:33:55 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Debian Analytica\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Il y a quelques jours j'écrivais sur _debian-vote@_ qu'un analyste junior "
+"pourrait étudier les résultats publics de nos votes passés et exposer les "
+"fractures de notre communauté."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Finalement, avec une approche assez naïve et un budget temps de quelques "
+"heures, je n'ai rien réussi d'intéressant.  L'image ci-dessous montre un "
+"rond par votant et ma position avec un point rouge.  Les ronds sont espacés "
+"en fonction de la similarité des profils de votes après avoir concaténé les "
+"résultats de toutes les GRs jusqu'à 2010."
+msgstr ""
+
+#. type: Plain text
+msgid "![Visualisation t-SNE de la matrice des votes](DebianAnalytica.png)"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Donc si tant est qu'il y ait moyen de tirer quelque chose de ces données, il "
+"faudrait au moins un analyste plus chevronné… Cela ne m'empêche pas de "
+"penser que nous devrions voter anonymement pour tous nos scrutins, et cesser "
+"de diffuser ce genre de données."
+msgstr ""

Debian Analytica.
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.mdwn" "b/Debian/debi\303\242neries/DebianAnalytica.mdwn"
new file mode 100644
index 00000000..ade629d8
--- /dev/null
+++ "b/Debian/debi\303\242neries/DebianAnalytica.mdwn"
@@ -0,0 +1,22 @@
+[[!meta date="Mon, 05 Apr 2021 22:33:55 +0900"]]
+[[!meta updated="Mon, 05 Apr 2021 22:33:55 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Debian Analytica"]]
+
+Il y a quelques jours j'écrivais sur _debian-vote@_ qu'un analyste junior
+pourrait étudier les résultats publics de nos votes passés et exposer
+les fractures de notre communauté.
+
+Finalement, avec une approche assez naïve et un budget temps de quelques
+heures, je n'ai rien réussi d'intéressant.  L'image ci-dessous montre un rond
+par votant et ma position avec un point rouge.  Les ronds sont espacés en
+fonction de la similarité des profils de votes après avoir concaténé les
+résultats de toutes les GRs jusqu'à 2010.
+
+![Visualisation t-SNE de la matrice des votes](DebianAnalytica.png)
+
+Donc si tant est qu'il y ait moyen de tirer quelque chose de ces données, il
+faudrait au moins un analyste plus chevronné…  Cela ne m'empêche pas de penser
+que nous devrions voter anonymement pour tous nos scrutins, et cesser de
+diffuser ce genre de données.

En voiture
diff --git a/biblio/21906039.mdwn b/biblio/21906039.mdwn
new file mode 100644
index 00000000..fa244ad7
--- /dev/null
+++ b/biblio/21906039.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The use of melting curves as a novel approach for validation of real-time PCR instruments."]]
+[[!tag method qPCR]]
+
+Von Keyserling H, Bergmann T, Wiesel M, Kaufmann AM.
+
+Biotechniques. 2011 Sep;51(3):179-84. doi:10.2144/000113735
+
+The use of melting curves as a novel approach for validation of real-time PCR instruments.
+
+[[!pmid 21906039 desc="Variations between technical replicates in melting temperature evaluated with melting curve analysis may identify heating biases of the instrument."]]

Updated.
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
index 0e50d260..7fb82e40 100644
--- "a/Debian/debi\303\242neries/grToxique.en.po"
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2021-03-27 01:38+0000\n"
-"PO-Revision-Date: 2021-03-27 10:37+0900\n"
+"PO-Revision-Date: 2021-03-27 10:39+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -22,10 +22,9 @@ msgid "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 msgstr "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:37:36 +0900\"]]\n"
-msgstr "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
+msgstr "[[!meta updated=\"Sat, 27 Mar 2021 10:37:36 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap

updated PO files
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
index b0c5add5..0e50d260 100644
--- "a/Debian/debi\303\242neries/grToxique.en.po"
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -6,8 +6,8 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2021-03-27 01:35+0000\n"
-"PO-Revision-Date: 2021-03-27 10:14+0900\n"
+"POT-Creation-Date: 2021-03-27 01:38+0000\n"
+"PO-Revision-Date: 2021-03-27 10:37+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -22,8 +22,9 @@ msgid "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 msgstr "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
+msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:37:36 +0900\"]]\n"
 msgstr "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 
 #. type: Plain text
@@ -66,12 +67,6 @@ msgstr ""
 "go."
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "Et si nos deux candidats au poste de DPL annoncaient que si élus, ils "
-#| "refuseraient de financer des activités liées à la FSF jusqu'à que rms "
-#| "démissionne à nouveau.  Ça permettrait à Debian de rester dans le temps "
-#| "de l'action, et peut-être d'annuler cette GR ?"
 msgid ""
 "Et si nos deux candidats au poste de DPL annoncaient que si élus, ils "
 "refuseraient de financer des activités liées à la FSF jusqu'à que rms "
@@ -80,6 +75,7 @@ msgid ""
 "peut-être d'annuler cette GR ?"
 msgstr ""
 "What if our two DPL candidates would issue a statement that, if elected, "
-"they would refuse to fund events linked to the FSF until rms quits again? "
-"This would let Debian be part of the wave of reaction on time, and maybe "
-"allow us to cancel this GR?"
+"they would refuse to fund events linked to the FSF until rms quits again "
+"(and also the directors, if that is what the DPL candidate wishes to "
+"propose). This would let Debian be part of the wave of reaction on time, and "
+"maybe allow us to cancel this GR?"

MaJ
diff --git "a/Debian/debi\303\242neries/grToxique.mdwn" "b/Debian/debi\303\242neries/grToxique.mdwn"
index 250f4d6e..4422ef27 100644
--- "a/Debian/debi\303\242neries/grToxique.mdwn"
+++ "b/Debian/debi\303\242neries/grToxique.mdwn"
@@ -1,5 +1,5 @@
 [[!meta date="Sat, 27 Mar 2021 10:06:40 +0900"]]
-[[!meta updated="Sat, 27 Mar 2021 10:06:40 +0900"]]
+[[!meta updated="Sat, 27 Mar 2021 10:37:36 +0900"]]
 [[!tag Debian]]
 
 [[!meta title="GR toxique"]]

updated PO files
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
index 6577bba8..b0c5add5 100644
--- "a/Debian/debi\303\242neries/grToxique.en.po"
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2021-03-27 01:14+0000\n"
+"POT-Creation-Date: 2021-03-27 01:35+0000\n"
 "PO-Revision-Date: 2021-03-27 10:14+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -66,11 +66,18 @@ msgstr ""
 "go."
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "Et si nos deux candidats au poste de DPL annoncaient que si élus, ils "
+#| "refuseraient de financer des activités liées à la FSF jusqu'à que rms "
+#| "démissionne à nouveau.  Ça permettrait à Debian de rester dans le temps "
+#| "de l'action, et peut-être d'annuler cette GR ?"
 msgid ""
 "Et si nos deux candidats au poste de DPL annoncaient que si élus, ils "
 "refuseraient de financer des activités liées à la FSF jusqu'à que rms "
-"démissionne à nouveau.  Ça permettrait à Debian de rester dans le temps de "
-"l'action, et peut-être d'annuler cette GR ?"
+"démissionne à nouveau (et les directeurs aussi si c'est ce que le candidat "
+"propose).  Ça permettrait à Debian de rester dans le temps de l'action, et "
+"peut-être d'annuler cette GR ?"
 msgstr ""
 "What if our two DPL candidates would issue a statement that, if elected, "
 "they would refuse to fund events linked to the FSF until rms quits again? "

Correction
diff --git "a/Debian/debi\303\242neries/grToxique.mdwn" "b/Debian/debi\303\242neries/grToxique.mdwn"
index 5e326a01..250f4d6e 100644
--- "a/Debian/debi\303\242neries/grToxique.mdwn"
+++ "b/Debian/debi\303\242neries/grToxique.mdwn"
@@ -18,5 +18,6 @@ de leur voie à suivre.
 
 Et si nos deux candidats au poste de DPL annoncaient que si élus, ils
 refuseraient de financer des activités liées à la FSF jusqu'à que rms
-démissionne à nouveau.  Ça permettrait à Debian de rester dans le temps de
-l'action, et peut-être d'annuler cette GR ?
+démissionne à nouveau (et les directeurs aussi si c'est ce que le candidat
+propose).  Ça permettrait à Debian de rester dans le temps de l'action, et
+peut-être d'annuler cette GR ?

RM
diff --git "a/Debian/debi\303\242neries/mailcap-optionnel.en.po" "b/Debian/debi\303\242neries/mailcap-optionnel.en.po"
deleted file mode 100644
index 0f165c47..00000000
--- "a/Debian/debi\303\242neries/mailcap-optionnel.en.po"
+++ /dev/null
@@ -1,71 +0,0 @@
-# SOME DESCRIPTIVE TITLE
-# Copyright (C) YEAR Free Software Foundation, Inc.
-# This file is distributed under the same license as the PACKAGE package.
-# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
-#
-#, fuzzy
-msgid ""
-msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2021-03-27 00:58+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
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-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta date=\"\"Fri, 13 Nov 2020 05:24:10 +0900]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Fri, 13 Nov 2020 05:24:10 +0900\"]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!tag Debian]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta title=\"Mailcap devient optionel\"]]\n"
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Mailcap, un système pour associer des types de fichiers à des applications "
-"pour les ouvrir, est présent sur les systèmes Debian standard via le paquet "
-"`mime-support` depuis plus de 20 ans.  C'est lui qui fournit la commande "
-"`run-mailcap`."
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Pour mieux permettre à Mailcap d'évoluer, j'ai décidé de le rendre "
-"optionnel.  Cela permettra à ceux qui le souhaitent de déveloper des "
-"versions alternatives,"
-msgstr ""
-
-#. type: Plain text
-msgid "et aux utilisat"
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Le changement ne sera pas immédiat car pour le moment un certain nombre de "
-"paquets dépendent encore de l'ancien paquet `mime-support` pour installer le "
-"fichier `/etc/mime-types` et vont donc causer l'installation de `mailcap`"
-msgstr ""
-
-#. type: Plain text
-msgid "(mais y en-a-t-il des standard ?)"
-msgstr ""
-
-#. type: Plain text
-msgid "Mettre liens vers anciens articles."
-msgstr ""

updated PO files
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
index ccebbcfa..6577bba8 100644
--- "a/Debian/debi\303\242neries/grToxique.en.po"
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2021-03-27 01:07+0000\n"
+"POT-Creation-Date: 2021-03-27 01:14+0000\n"
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+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
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Traduction.
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
index e46cc098..ccebbcfa 100644
--- "a/Debian/debi\303\242neries/grToxique.en.po"
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -3,38 +3,38 @@
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-#, fuzzy
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+"Project-Id-Version: \n"
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 #. type: Plain text
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 msgid "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"GR toxique\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"GR toxique\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -47,6 +47,13 @@ msgid ""
 "Debian et laissera des trace, au moins sous la forme d'une liste publique de "
 "votes de qui a voté pour quoi et comme qui."
 msgstr ""
+"Many quickly reacted to the return of rms to the FSF and asked that he "
+"leaves again; some also asked for the whole board of directors to resign and "
+"some not. Meanwhile, Debian discusses a general resolution on that matter. "
+"Maybe it was not the original intent, but in practice the object of the GR "
+"is about FSF's board of directors. Perhaps we will have the result after rms "
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@@ -54,6 +61,9 @@ msgid ""
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@@ -62,3 +72,7 @@ msgid ""
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 msgstr ""
+"What if our two DPL candidates would issue a statement that, if elected, "
+"they would refuse to fund events linked to the FSF until rms quits again? "
+"This would let Debian be part of the wave of reaction on time, and maybe "
+"allow us to cancel this GR?"

updated PO files
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
new file mode 100644
index 00000000..e46cc098
--- /dev/null
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -0,0 +1,64 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2021-03-27 01:07+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"GR toxique\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Beaucoup ont réagi rapidement au retour de rms à la FSF et demandé son "
+"départ, certains demandant aussi la démission de ses directeurs, d'autres "
+"non.  Pendant ce temps Debian discute une résolution générale à ce sujet.  "
+"Ce n'était peut-être pas l'intention originale, mais dans les faits l'objet "
+"de la GR est sur la démission des directeurs.  Peut-être aura-t-on le "
+"résultat après la démission de rms ? Comme beaucoup de GRs, elle va diviser "
+"Debian et laissera des trace, au moins sous la forme d'une liste publique de "
+"votes de qui a voté pour quoi et comme qui."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Je ne pense pas que la plupart des autres organisations soient passées par "
+"un processus aussi plénier et collégial, mais aussi lourd et clivant, pour "
+"décider de leur voie à suivre."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Et si nos deux candidats au poste de DPL annoncaient que si élus, ils "
+"refuseraient de financer des activités liées à la FSF jusqu'à que rms "
+"démissionne à nouveau.  Ça permettrait à Debian de rester dans le temps de "
+"l'action, et peut-être d'annuler cette GR ?"
+msgstr ""

GR toxique
diff --git "a/Debian/debi\303\242neries/grToxique.mdwn" "b/Debian/debi\303\242neries/grToxique.mdwn"
new file mode 100644
index 00000000..5e326a01
--- /dev/null
+++ "b/Debian/debi\303\242neries/grToxique.mdwn"
@@ -0,0 +1,22 @@
+[[!meta date="Sat, 27 Mar 2021 10:06:40 +0900"]]
+[[!meta updated="Sat, 27 Mar 2021 10:06:40 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="GR toxique"]]
+
+Beaucoup ont réagi rapidement au retour de rms à la FSF et demandé son départ, certains
+demandant aussi la démission de ses directeurs, d'autres non.  Pendant ce temps Debian
+discute une résolution générale à ce sujet.  Ce n'était peut-être pas l'intention originale,
+mais dans les faits l'objet de la GR est sur la démission des directeurs.  Peut-être
+aura-t-on le résultat après la démission de rms ?  Comme beaucoup de GRs, elle va diviser
+Debian et laissera des trace, au moins sous la forme d'une liste publique de votes de qui
+a voté pour quoi et comme qui.
+
+Je ne pense pas que la plupart des autres organisations soient passées par un
+processus aussi plénier et collégial, mais aussi lourd et clivant, pour décider
+de leur voie à suivre.
+
+Et si nos deux candidats au poste de DPL annoncaient que si élus, ils
+refuseraient de financer des activités liées à la FSF jusqu'à que rms
+démissionne à nouveau.  Ça permettrait à Debian de rester dans le temps de
+l'action, et peut-être d'annuler cette GR ?

updated PO files
diff --git "a/Debian/debi\303\242neries/mailcap-optionnel.en.po" "b/Debian/debi\303\242neries/mailcap-optionnel.en.po"
new file mode 100644
index 00000000..0f165c47
--- /dev/null
+++ "b/Debian/debi\303\242neries/mailcap-optionnel.en.po"
@@ -0,0 +1,71 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2021-03-27 00:58+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"\"Fri, 13 Nov 2020 05:24:10 +0900]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Fri, 13 Nov 2020 05:24:10 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Mailcap devient optionel\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Mailcap, un système pour associer des types de fichiers à des applications "
+"pour les ouvrir, est présent sur les systèmes Debian standard via le paquet "
+"`mime-support` depuis plus de 20 ans.  C'est lui qui fournit la commande "
+"`run-mailcap`."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Pour mieux permettre à Mailcap d'évoluer, j'ai décidé de le rendre "
+"optionnel.  Cela permettra à ceux qui le souhaitent de déveloper des "
+"versions alternatives,"
+msgstr ""
+
+#. type: Plain text
+msgid "et aux utilisat"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Le changement ne sera pas immédiat car pour le moment un certain nombre de "
+"paquets dépendent encore de l'ancien paquet `mime-support` pour installer le "
+"fichier `/etc/mime-types` et vont donc causer l'installation de `mailcap`"
+msgstr ""
+
+#. type: Plain text
+msgid "(mais y en-a-t-il des standard ?)"
+msgstr ""
+
+#. type: Plain text
+msgid "Mettre liens vers anciens articles."
+msgstr ""

creating tag page tags/phylogeny
diff --git a/tags/phylogeny.mdwn b/tags/phylogeny.mdwn
new file mode 100644
index 00000000..e0377dac
--- /dev/null
+++ b/tags/phylogeny.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged phylogeny"]]
+
+[[!inline pages="tagged(phylogeny)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/33649401.mdwn b/biblio/33649401.mdwn
new file mode 100644
index 00000000..85ee5cc8
--- /dev/null
+++ b/biblio/33649401.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM."]]
+[[!tag Oikopleura]]
+
+3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM.
+
+Nishida H, Ohno N, Caicci F, Manni L.
+
+Sci Rep. 2021 Mar 1;11(1):4833. doi:10.1038/s41598-021-83706-y
+
+[[!pmid 33649401 desc="“The bilateral arrangement of precursor cells of the oikoplastic epidermis was already attained by the hatching stage.”  “Upon 3D construction, additional single cells, which showed similar features to giant Fol cells, albeit slightly smaller, were present in the lateral part. It is possible that this cell will be lost after larval development.”  “The gonad syncytium formation already starts as early as in 10 hpf juveniles by the cell fusion of germ cells, although it is not possible to discern males or females at this stage.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c29ff625..2c1b15c3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -332,6 +332,7 @@ Development
  - The oocytes originate from a specialised syncitium, the coenocyst, in which
    nurse cells and oocytes are connected by cytoplasmic bridges, the ring channels
    ([[Ganot and coll., 2007|biblio/17126826]]).
+ - The gonad syncytium forms as early at 10 hpf ([[Nishida and coll., 2021|biblio/33649401]]).
  - Oocytes lacking odCDK1d can not resume from meiosis from prophase I arrest,
    and therefore are non-viable after spawning ([[Øvrebø and coll., 2015|biblio/25714331]]).
  - Oocytes are in metaphase I stage at the time of spawning ([[Ganot, Kallesøe
@@ -392,7 +393,8 @@ Development
  - The oral gland precursor is a syncytium with 4 nuclei that migrates
    anteriorly.  The two differentiated oral gland cells have two nuclei each,
    as demonstrated by a co-staining of nuclei (H2B-mCherry) and cell membrane
-   (PH-YF) by [[Kishi and coll, 2014|biblio/25224225]].
+   (PH-YF) by [[Kishi and coll, 2014|biblio/25224225]], as well as SEM tomography
+   ([[Nishida and coll., 2021|biblio/33649401]]).
  - Oral gland and subchordal cells, which were thought to be related, do not originate
    from the same blastomere ([[Onuma and coll., 2020|biblio/32029598]]).
  - The subchordal cell precursors migrate along the right side of the notochord
@@ -431,6 +433,8 @@ Anatomy
    in the central canal ([[Holmberg and Olsson, 1984|biblio/reissner_oik]]).
  - In contrary to Kowalevskiidae, ([[Brena, Cima and Burighel, 2003|biblio/10.1002_jmor.10145]]),
    _Oikopleura_ do have a heart.
+ - A 3D reconstitution of hatchlings and jufeniles was done by SEM tomography by
+   [[Nishida and coll., 2021|biblio/33649401]].
 
 Physiology
 ----------
@@ -486,6 +490,9 @@ House
    1985|biblio/10.2307_1541178]]).  In these species, light is produced by
    granular inclusions in the house.  In species without oral glands,
    bioluminescence might be caused by dinoflagellates.
+ - A 8th cell was seen in the Fol area at 10 hpf in the 3D tomography analysis
+   of [[Nishida and coll., 2021|biblio/33649401]].  It is possible that this cell
+   is lost during later development.
 
 
 Phenotypes

Café
diff --git a/biblio/33563718.mdwn b/biblio/33563718.mdwn
new file mode 100644
index 00000000..43d83ff5
--- /dev/null
+++ b/biblio/33563718.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution of genome structure in the Drosophila simulans species complex."]]
+[[!tag Drosophila synteny]]
+
+Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ.
+
+Genome Res. 2021 Feb 9. doi:10.1101/gr.263442.120
+
+Evolution of genome structure in the Drosophila simulans species complex.
+
+[[!pmid 33563718 desc="“de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago.”  “Genome-wide, ∼15% of sim-complex genome content fails to align uniquely to D. melanogaster.”  “Within aligned sequence blocks, the sim-complex species show ∼7% divergence from D. melanogaster”  “535–542 rearrangements between D. melanogaster and the sim-complex (approximately 90 mutations per million years), and 113–177 rearrangements within the sim-complex (226–354 mutations per million years)”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 1a531eab..0a15e461 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -15,7 +15,10 @@ compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparis
 are highly significant”
 
 [[Ranz and coll., 2001|biblio/11157786]] estimate an evolution rate of 0.9–1.4
-chromosomal inversions fixed per million years in _Drosophila_.
+chromosomal inversions fixed per million years in _Drosophila_.  A comparison
+between _D. mel_ and members of the _simulans_ species complex led to an estimation
+of 90 rearrangements per MY (_mel_ / _simulans_) and 226–354 per MY (_sim_ / _sim_)
+([[Chakraborty and coll., 2021|biblio/33563718]]).
 
 In insects, the Osiris gene family shows conservation of synteny over ~400
 million years ([[Sah and coll., 2012|biblio/22384409]]).

Café
diff --git a/biblio/10.1111_1755-0998.13356.mdwn b/biblio/10.1111_1755-0998.13356.mdwn
new file mode 100644
index 00000000..307206fa
--- /dev/null
+++ b/biblio/10.1111_1755-0998.13356.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity"]]
+[[!tag eDNA]]
+
+Mahsa Mousavi‐Derazmahalleh, Audrey Stott, Rose Lines, Georgia Peverley, Georgia Nester, Tiffany Simpson, Michal Zawierta, Marco De La Pierre, Michael Bunce, Claus T. Christophersen
+
+Molecular Ecology Resources. 2021
+
+eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity
+
+[[!doi 10.1111/1755-0998.13356 desc="DSL1"]]
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
index 55342d8d..d17cbe9b 100644
--- a/tags/eDNA.mdwn
+++ b/tags/eDNA.mdwn
@@ -9,4 +9,6 @@
  - Primer design “considering the unconventional base pairing in the T/G bond”
    instead of using degenerate bases: [[Miya and coll (2015)|biblio/26587265]].
 
+ - A Nextflow pipeline: eDNAFlow [[Mousavi‐Derazmahalleh and coll., 2021|biblio/10.1111_1755-0998.13356]].
+
 [[!inline pages="tagged(eDNA)" limit=0]]

Café
diff --git a/biblio/29182778.mdwn b/biblio/29182778.mdwn
new file mode 100644
index 00000000..56d7294b
--- /dev/null
+++ b/biblio/29182778.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Jointly aligning a group of DNA reads improves accuracy of identifying large deletions."]]
+[[!tag LAST]]
+
+Shrestha AMS, Frith MC, Asai K, Richard H.
+
+Nucleic Acids Res. 2018 Feb 16;46(3):e18. doi:10.1093/nar/gkx1175
+
+Jointly aligning a group of DNA reads improves accuracy of identifying large deletions.
+
+[[!pmid 29182778 desc="For short reads."]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index c6fbd8f4..fc0a0dfa 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -24,4 +24,6 @@ _bibliography in progress..._
  - LAST can align DNA sequences to protein databases using a 64 x 21 substitution
    matrix [[Yao and Frith, 2020|biblio/10.1101_2021.01.25.428050]].
 
+ - JRA (Joint Read Alignment) uses LAST [[Shrestha and coll., 2018|biblio/29182778]].
+
 [[!inline pages="tagged(LAST)" actions="no" limit=0]]

Bandage
diff --git a/biblio/26099265.mdwn b/biblio/26099265.mdwn
new file mode 100644
index 00000000..97f3042e
--- /dev/null
+++ b/biblio/26099265.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Bandage: interactive visualization of de novo genome assemblies."]]
+[[!tag assembly]]
+
+Wick RR, Schultz MB, Zobel J, Holt KE.
+
+Bioinformatics. 2015 Oct 15;31(20):3350-2. doi:10.1093/bioinformatics/btv383
+
+Bandage: interactive visualization of de novo genome assemblies.
+
+[[!pmid 26099265 desc="Interactive visualisation and command-line generation of reports."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 8d4962e3..79f5f2d7 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -23,6 +23,9 @@ fast. Shasta assemblies tend to be more fragmented, but have less disagreement
 with the reference.  Shasta also comes with polishing modules similar to Racon
 and Medaka, but also  to be faster. 
 
+Some genome assemblers produce a graph file that can be visualised
+with tools such as Bandage [[Wick and coll., 2015|biblio/26099265]].
+
 After assembly, the contigs can be further polished with Racon ([[Vaser, Sović,
 Nagarajan and Šikić, 2017|biblio/28100585]]).
 

Traduction
diff --git "a/Debian/debi\303\242neries/conteneurs.en.po" "b/Debian/debi\303\242neries/conteneurs.en.po"
index d966a0a1..94736d07 100644
--- "a/Debian/debi\303\242neries/conteneurs.en.po"
+++ "b/Debian/debi\303\242neries/conteneurs.en.po"
@@ -19,22 +19,22 @@ msgstr ""
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Tue, 23 Feb 2021 01:11:52 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Tue, 23 Feb 2021 01:11:52 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Tue, 23 Feb 2021 01:11:52 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Tue, 23 Feb 2021 01:11:52 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Conteneurs\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Containers\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -48,3 +48,14 @@ msgid ""
 "miracle ! Je finis par trouver l'image Docker de Ubuntu contient à la fois "
 "_coreutils_, _sed_ et _ps_ !"
 msgstr ""
+"I was using a container for a bioinformatics tool released two weeks ago, "
+"but my shell script wrapping the tools could not run because the container "
+"was built around an old version of Debian (_Jessie_) that was released "
+"in 2015.  I was asked to use a container for bioinformatics, based on conda, "
+"and found one that distributes _coreutils_, but it did not include a real version "
+"of _sed_.  I try Debian's docker image.  No luck; it does not contain "
+"_ps_, which my workflow manager needs.  But fortunately I eventually "
+"figured out that Ubuntu's Docker image contains _coreutils_, _sed_ "
+"and _ps_ together!  In the world of containers, this sounds like "
+"a little miracle."
+

updated PO files
diff --git "a/Debian/debi\303\242neries/conteneurs.en.po" "b/Debian/debi\303\242neries/conteneurs.en.po"
new file mode 100644
index 00000000..d966a0a1
--- /dev/null
+++ "b/Debian/debi\303\242neries/conteneurs.en.po"
@@ -0,0 +1,50 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2021-02-22 16:20+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Tue, 23 Feb 2021 01:11:52 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Tue, 23 Feb 2021 01:11:52 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Conteneurs\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'utilisais un conteneur pour un outil bioinformatique mis à jour il y a "
+"deux semaines, mais mon script shell autour de l'outil plantait parce que "
+"son conteneur était bâti sur une version de Debian (_Jessie_) datant de "
+"2015.  On me demande d'utiliser un conteneur de bioinformatique pour "
+"_coreutils_ basé sur conda.  Pas de chance, il ne contient pas une véritable "
+"version de _sed_.  Je me rabat sur l'image Docker de Debian.  Pas de bol, "
+"elle ne contient pas _ps_, dont a besoin mon gestionnaire de flux.  Mais "
+"miracle ! Je finis par trouver l'image Docker de Ubuntu contient à la fois "
+"_coreutils_, _sed_ et _ps_ !"
+msgstr ""

Oh p... ce qu'il est blaire, mon conténaire, ...
diff --git "a/Debian/debi\303\242neries/conteneurs.mdwn" "b/Debian/debi\303\242neries/conteneurs.mdwn"
new file mode 100644
index 00000000..18150945
--- /dev/null
+++ "b/Debian/debi\303\242neries/conteneurs.mdwn"
@@ -0,0 +1,14 @@
+[[!meta date="Tue, 23 Feb 2021 01:11:52 +0900"]]
+[[!meta updated="Tue, 23 Feb 2021 01:11:52 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Conteneurs"]]
+
+J'utilisais un conteneur pour un outil bioinformatique mis à jour il y a deux
+semaines, mais mon script shell autour de l'outil plantait parce que son
+conteneur était bâti sur une version de Debian (_Jessie_) datant de 2015.  On
+me demande d'utiliser un conteneur de bioinformatique pour _coreutils_ basé sur
+conda.  Pas de chance, il ne contient pas une véritable version de _sed_.  Je
+me rabat sur l'image Docker de Debian.  Pas de bol, elle ne contient pas _ps_,
+dont a besoin mon gestionnaire de flux.  Mais miracle ! Je finis par trouver
+l'image Docker de Ubuntu contient à la fois _coreutils_, _sed_ et _ps_ !

Café
diff --git a/biblio/33468658.mdwn b/biblio/33468658.mdwn
new file mode 100644
index 00000000..f3f9d544
--- /dev/null
+++ b/biblio/33468658.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A short ORF-encoded transcriptional regulator."]]
+[[!tag synthetic]]
+
+Koh M, Ahmad I, Ko Y, Zhang Y, Martinez TF, Diedrich JK, Chu Q, Moresco JJ, Erb MA, Saghatelian A, Schultz PG, Bollong MJ.
+
+Proc Natl Acad Sci U S A. 2021 Jan 26;118(4):e2021943118. doi:10.1073/pnas.2021943118
+
+A short ORF-encoded transcriptional regulator.
+
+[[!pmid 33468658 desc=""“To introduce a photo-crosslinker into [short ORF-encoded peptides (SEPs)] in mammalian cells, we used an evolved mutant of the Methanosarcina barkeri pyrrolysyl aminoacyl transfer RNA (tRNA) synthetase/tRNA pair (expressed from the vector pCMV-AbK) to genetically encode the diazirine functionalized ncAA N6-[[2-(3-Methyl-3H-diazirin-3-yl)ethoxy]carbonyl]-l-lysine (AbK).”]]

Café
diff --git a/biblio/10.1134_S1063074019020111.mdwn b/biblio/10.1134_S1063074019020111.mdwn
new file mode 100644
index 00000000..78994384
--- /dev/null
+++ b/biblio/10.1134_S1063074019020111.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The First Ultrastructural Description of Appendicularians (Chordata: Tunicata) Infected by Microsporidia-Like Protists"]]
+[[!tag Oikopleura]]
+
+Savelieva, A.V.
+
+Russ J Mar Biol 45, 145–151 (2019). doi:10.1134/S1063074019020111
+
+The First Ultrastructural Description of Appendicularians (Chordata: Tunicata) Infected by Microsporidia-Like Protists
+
+[[!doi 10.1134/S1063074019020111 desc="Parasites ressembling to microsporidia and their spores found in _O. gracilis_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 91428e0a..c29ff625 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -27,7 +27,8 @@ Some links:
    <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
 
 
-Parasites: _Oodinium pouchetii_ and others.
+Parasites: _Oodinium pouchetii_, microsporidia (on _O. gracilis_ ([[Savelieva
+2019|biblio/10.1134_S1063074019020111]])) and others.
 
 
 Phylogeny

Café
diff --git a/biblio/10.1002_jmor.10145.mdwn b/biblio/10.1002_jmor.10145.mdwn
new file mode 100644
index 00000000..c579845c
--- /dev/null
+++ b/biblio/10.1002_jmor.10145.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Alimentary tract of kowalevskiidae (appendicularia, tunicata) and evolutionary implications"]]
+[[!tag Oikopleura]]
+
+Carlo Brena, Francesca Cima, Paolo Burighel
+
+Volume 258, Issue 2, November 2003, Pages 225-238, doi:10.1002/jmor.10145
+
+Alimentary tract of kowalevskiidae (appendicularia, tunicata) and evolutionary implications
+
+[[!doi 10.1002/jmor.10145 desc="No heart was found."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b812e9e0..91428e0a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -428,7 +428,8 @@ Anatomy
    secreting the Reissner's fiber (reviewed in [[Olsson, 1993|biblio/10.1007_978-3-642-78013-4_5]]).
    Electron microscopy shows a large perikaryon, cisternas and a cilium which is inserted
    in the central canal ([[Holmberg and Olsson, 1984|biblio/reissner_oik]]).
-
+ - In contrary to Kowalevskiidae, ([[Brena, Cima and Burighel, 2003|biblio/10.1002_jmor.10145]]),
+   _Oikopleura_ do have a heart.
 
 Physiology
 ----------

pubmed
diff --git a/biblio/10.1101_2020.01.16.905182.mdwn b/biblio/10.1101_2020.01.16.905182.mdwn
deleted file mode 100644
index a19df767..00000000
--- a/biblio/10.1101_2020.01.16.905182.mdwn
+++ /dev/null
@@ -1,10 +0,0 @@
-[[!meta title="Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq"]]
-[[!tag bioRxiv promoter method]]
-
-bioRxiv Posted January 16, 2020 doi:10.1101/2020.01.16.905182 
-
-Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner
-
-Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
-
-[[!doi 10.1101/2020.01.16.905182 desc="Terminator-treated RNA reverse-transcribed with random N5 primers.  The (biotinylated) TSO is added in the last 5 min of the RT (~40 µM final).  The TSO carries a P5 linker and the RTP a P7 (indexed) linker.  Follows a standard PCR and sequencing.  The YR motif is detected in yeast and K562 cells.  High amounts of rRNA remains in yeast"]]
diff --git a/biblio/32660958.mdwn b/biblio/32660958.mdwn
new file mode 100644
index 00000000..188300cf
--- /dev/null
+++ b/biblio/32660958.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq"]]
+[[!tag promoter method]]
+
+Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner
+
+Genome Res. 2020 Jun;30(6):910-923. doi:10.1101/gr.261545.120
+
+Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
+
+[[!pmid 32660958 desc="Terminator-treated RNA reverse-transcribed with random N5 primers.  The (biotinylated) TSO is added in the last 5 min of the RT (~40 µM final).  The TSO carries a P5 linker and the RTP a P7 (indexed) linker.  Follows a standard PCR and sequencing.  The YR motif is detected in yeast and K562 cells.  High amounts of rRNA remains in yeast"]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 1d0d7a0b..35a15b58 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -55,6 +55,10 @@
    ~15% of the 5′ end alignments have extra Gs, but the genomic distribution is
    bimodal.  Peaks with significant amounts of "extra G" nucleotides are marked as TSS.
 
+ - [[Policastro and coll, 2020|bilbio/32660958]] and others before them add the
+   template-switching oligonucleotide after the reverse-transription has been
+   incubated for some time.
+
 ### Effect of chemical composition of the TS oligonucleotide
 
 Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,

Café
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index c6d23e90..b519f32b 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -6,6 +6,8 @@ Automated synthesis laboratory (ASL): [[Godfrey, Masquelin and Hemmerle (2013)|b
 
 “A mobile robotic chemist” ([[Burger and coll., 2020|biblio/32641813]]).
 
+Screening parameter space with Maholo LabDroid and Bayesian optimisation: [[Kanda and coll., 2020|biblio/10.1101_2020.11.25.392936]].
+
 Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).
 
 Computational control of an organic chemistry system.  Position of the

Café
diff --git a/biblio/10.1101_2020.11.25.392936.mdwn b/biblio/10.1101_2020.11.25.392936.mdwn
new file mode 100644
index 00000000..5d33692b
--- /dev/null
+++ b/biblio/10.1101_2020.11.25.392936.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Robotic Search for Optimal Cell Culture in Regenerative Medicine"]]
+[[!tag bioRxiv automation]]
+
+Genki N. Kanda, Taku Tsuzuki, Motoki Terada, Noriko Sakai, Naohiro Motozawa, Tomohiro Masuda, Mitsuhiro Nishida, Chihaya T. Watanabe, Tatsuki Higashi, Shuhei A. Horiguchi, Taku Kudo, Motohisa Kamei, Genshiro A. Sunagawa, Kenji Matsukuma, Takeshi Sakurada, Yosuke Ozawa, Masayo Takahashi, Koichi Takahashi, Tohru Natsume
+
+bioRxiv 2020.11.25.392936; doi: https://doi.org/10.1101/2020.11.25.392936
+
+Robotic Search for Optimal Cell Culture in Regenerative Medicine
+
+[[!doi 10.1101/2020.11.25.392936  desc="Uses the Maholo LabDroid and Batch Bayesian optimization (BBO) to screen a 7-dimensions parameter space."]]

Vanadium
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5ef447a9..b812e9e0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -615,6 +615,11 @@ Ecology
    ([[Berry and coll., 2019|biblio/30735490]])
  - TARA Oceans ([[Vorobev and coll., 2020|biblio/32205368]]).
 
+### In the past:
+
+ - Fossils in China: [[Zhang Aiyun, 1987|biblio/10.1360_yb1987-30-8-888]].
+   Body rich in vanadium but not the house.
+
 Laboratory culture
 ------------------
 

Fix file name.
diff --git a/biblio/10.1360_yb1987-30-8-888 b/biblio/10.1360_yb1987-30-8-888.mdwn
similarity index 100%
rename from biblio/10.1360_yb1987-30-8-888
rename to biblio/10.1360_yb1987-30-8-888.mdwn

Café
diff --git a/biblio/10.1360_yb1987-30-8-888 b/biblio/10.1360_yb1987-30-8-888
new file mode 100644
index 00000000..1f2ae6f8
--- /dev/null
+++ b/biblio/10.1360_yb1987-30-8-888
@@ -0,0 +1,10 @@
+[[!meta title="Fossil appendicularians in the early cambrian"]]
+[[!tag Oikopleura]]
+
+Zhang Aiyun (张爱云)
+
+Citation: Science in China Series B-Chemistry, Biological, Agricultural, Medical & Earth Sciences 30, 888 (1987); doi: 10.1360/yb1987-30-8-888
+
+Fossil appendicularians in the early cambrian
+
+[[!doi 10.1360/yb1987-30-8-888 desc="“The content of fossil animal's coats increases with the quantity of algae.”  “The coat of fossil animals does not contain vanadium.”  “There is also a highly concentrated vanadium compount in the body of fossil animals.”"]]

purge_dups
diff --git a/biblio/31971576.mdwn b/biblio/31971576.mdwn
new file mode 100644
index 00000000..f284f5f3
--- /dev/null
+++ b/biblio/31971576.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Identifying and removing haplotypic duplication in primary genome assemblies."]]
+[[!tag assembly software]]
+
+Guan D, McCarthy SA, Wood J, Howe K, Wang Y, Durbin R.
+
+Bioinformatics. 2020 May 1;36(9):2896-2898. doi: 10.1093/bioinformatics/btaa025.
+
+Identifying and removing haplotypic duplication in primary genome assemblies.
+
+[[!pmid 31971576 desc="Used by the Vertebrate Genomes Project assembly pipeline.  Remaps the reads onto the assembly to evaluate heterozygocity of regions where the genome self-maps to itself, and removes the regions where necessary."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index a396000b..8d4962e3 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -53,8 +53,11 @@ Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an
 alternative to HaploMerger that takes read coverage into account when detecting
 potential haplotigs.  However, it does not merge haplotypes.
 
-`purge_dups`, another alternative tp HaploMerger and Purge Haplotivs, performed
-well on Flye 2.5 assemblies ([[Guiglielmoni and coll.,2020|biblio/10.1101_2020.03.16.993428]]).
+[`purge_dups`](https://github.com/dfguan/purge_dups) [[Guan and coll.,
+2020|biblio/31971576]], is another alternative to HaploMerger2.  Like Purge
+Haplotigs, it does not attempt to merge contigs.  `purge_dups` performed well
+on Flye 2.5 assemblies ([[Guiglielmoni and
+coll.,2020|biblio/10.1101_2020.03.16.993428]]).
 
 SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis

Café
diff --git a/biblio/10.1101_2021.01.25.428050.mdwn b/biblio/10.1101_2021.01.25.428050.mdwn
new file mode 100644
index 00000000..b9592bb0
--- /dev/null
+++ b/biblio/10.1101_2021.01.25.428050.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Improved DNA-versus-Protein Homology Search for Protein Fossils"]]
+[[!tag bioRxiv LAST repeat]]
+
+Yin Yao, Martin C. Frith
+
+bioRxiv 2021.01.25.428050; doi: https://doi.org/10.1101/2021.01.25.428050
+
+Improved DNA-versus-Protein Homology Search for Protein Fossils
+
+[[!doi 10.1101/2021.01.25.428050 desc="Uses a 64 x 21 substitution matrix and automatically learns the genetic code.  Detected fossils of the polinton and DIRS/Ngaro repeat elements in the human genome.  10 times faster than blastx."]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index f02c8785..c6fbd8f4 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -21,4 +21,7 @@ _bibliography in progress..._
  - `tandem-genotypes` ([[Mitsuhashi and coll., 2019|biblio/30890163]]): detection
    of expansion of tandem repeats, after alignment with `last-split`.
 
+ - LAST can align DNA sequences to protein databases using a 64 x 21 substitution
+   matrix [[Yao and Frith, 2020|biblio/10.1101_2021.01.25.428050]].
+
 [[!inline pages="tagged(LAST)" actions="no" limit=0]]

syntax
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index a07df442..a396000b 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -54,8 +54,7 @@ alternative to HaploMerger that takes read coverage into account when detecting
 potential haplotigs.  However, it does not merge haplotypes.
 
 `purge_dups`, another alternative tp HaploMerger and Purge Haplotivs, performed
-well on Flye 2.5 assemblies ([[Guiglielmoni and coll.,2020 |
-biblio/10.1101_2020.03.16.993428]]).
+well on Flye 2.5 assemblies ([[Guiglielmoni and coll.,2020|biblio/10.1101_2020.03.16.993428]]).
 
 SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis

Café
diff --git a/biblio/10.1101_2020.03.16.993428.mdwn b/biblio/10.1101_2020.03.16.993428.mdwn
new file mode 100644
index 00000000..f14b9cc5
--- /dev/null
+++ b/biblio/10.1101_2020.03.16.993428.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms"]]
+[[!tag bioRxiv assembly benchmark]]
+
+Nadège Guiglielmoni, Antoine Houtain, Alessandro Derzelle, Karine van Doninck, Jean-François Flot
+
+bioRxiv 2020.03.16.993428; doi: https://doi.org/10.1101/2020.03.16.993428 
+
+Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms
+
+[[!pmid 10.1101/2020.03.16.993428 desc="Benchark using a bdelloid rotifer.  Performance of most software plateaus over 50× depth. purge_dups performed well on Flye assemblies.  Filtering our shorter reads did not dramatically change the N50 of Flye 2.5 assemblies"]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 6ff69435..a07df442 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -53,6 +53,10 @@ Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an
 alternative to HaploMerger that takes read coverage into account when detecting
 potential haplotigs.  However, it does not merge haplotypes.
 
+`purge_dups`, another alternative tp HaploMerger and Purge Haplotivs, performed
+well on Flye 2.5 assemblies ([[Guiglielmoni and coll.,2020 |
+biblio/10.1101_2020.03.16.993428]]).
+
 SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis
 that most contact points are due to local (same-chromosome) proximity.  Version

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
Café
diff --git a/biblio/30535005.mdwn b/biblio/30535005.mdwn
new file mode 100644
index 00000000..b87ef5c5
--- /dev/null
+++ b/biblio/30535005.mdwn
@@ -0,0 +1,21 @@
+[[!meta title="A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates."]]
+[[!tag Oikopleura enhancer]]
+
+Nash AJ, Lenhard B.
+
+Bioinformatics. 2019 Jul 15;35(14):2354-2361. doi: 10.1093/bioinformatics/bty1014.
+
+A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates.
+
+[[!pmid 30535005 desc="“our method may have utility in the analysis of GRB developmental gene regulation in species that have undergone extreme genome compaction such as the puffer fish, Tetraodon nigroviridis, and the sea squirt, Oikopleura dioica”"]]
+
+“The kurtosis of the distribution of the lengths of all identical sequences was calculated in [30 kbp] bins across the genome.”
+
+“Runs of 100% sequence identity were [...] filtered for annotated repeats and exonic sequences.”
+
+“The kurtosis of the distribution of lengths in each bin was then calculated as [...] R(F) = q0.99(F) − q0.01(F) / G50
+where F is the distribution of the lengths of runs of perfect sequence identity in a bin, and G50 is the range of the middle 50% of the distribution of lengths of all runs of identity, from all bins (background distribution); calculated as [...] q0.75(J) − q0.25(J) where J is the distribution of the lengths of runs of perfect sequence identity across the whole genome.”
+
+“This is an adaptation of the robust kurtosis measure proposed in Ruppert (1987).”
+
+“There is a strong correlation between kurtosis and CNE density, and this correlation is greater within GRBs than outside GRBs”
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 765e0202..c5d156e9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -140,7 +140,9 @@ Genome
    ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]).
  - Proteins of O. dioica are shorter and contain less disordored domains than proteins
    from other chrodates ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]).
-
+ - [[Nash and Lenhard (2019)|biblio/30535005]] proposed a kurtosis-based measure of
+   pairwise non-coding conservation that “may have utility in the analysis of”
+   conserved non-coding elements in _Oikopleura_.
 
 Repeat elements
 ---------------

Wikipedia link to the microbial food.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 765e0202..0d5e622c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -629,21 +629,31 @@ Culture protocols (incomplete list):
 
 Food tested in laboratory (totally incomplete list):
 
- - Flagellates _Isochrysis galbana_ (4 µm width) and _Monochrysis lutheri_ (4 µm
+ - Flagellates [_Isochrysis galbana_][] (4 µm width) and _Monochrysis lutheri_ (4 µm
    width), and the diatom _Cyclotella nana_ (Thalassiosira pseudonana) which had
    a width of 5 µm ([[G.-A. Paffenhöfer, 1973|biblio/10.1007_BF00391782]]).
 
- - _Isochrysis galbana_ (5.5 µm in size), _Tetraselmis suecica_ (9.5 µm), and
+ - _Isochrysis galbana_ (5.5 µm in size), [_Tetraselmis suecica_][] (9.5 µm), and
    the chlorophyte _Chlorella sp._ (3.5 µm) [[Acuña and Kiefer,
    2000|biblio/10.4319_lo.2000.45.3.0608]].
 
- - The diatom _Chaetoceros calcitrans_, often used as a food, can be toxic at
+ - The diatom [_Chaetoceros calcitrans_][], often used as a food, can be toxic at
    high concentrations, probably because of the production of biotoxins
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
 
  - The Postlethwait lab has been feeding their animals with (_Dunaliella
-   tertiolecta_, _Isochrysis galbana_, _Rhodomonas lens_, _Nanochloropsis sp._,
+   tertiolecta_, [_Isochrysis galbana_][], _Rhodomonas lens_, _Nanochloropsis sp._,
    and _Micromonas sp._ (strain Dw-8)) [[Bassham and Postlethwait
    (2000)|biblio/10753519]]).
 
+ - The Luscombe lab ([[Masunaga and coll., 2020|biblio/32628172]]) uses
+   [_Chaetoceros calcitrans_][], [_Isochrysis galbana_],
+   [_Rhinomonas reticulata_][], and [_Synechococcus sp._][].
+
+[_Chaetoceros calcitrans_]: https://en.wikipedia.org/wiki/Chaetoceros
+[_Isochrysis galbana_]:     https://en.wikipedia.org/wiki/Isochrysis_galbana
+[_Rhinomonas reticulata_]:  https://en.wikipedia.org/wiki/Rhinomonas
+[_Synechococcus sp._]:      https://en.wikipedia.org/wiki/Synechococcus
+[_Tetraselmis suecica_]:    https://en.wikipedia.org/wiki/Tetraselmis_suecica
+
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Dnmt2
diff --git a/biblio/22140515.mdwn b/biblio/22140515.mdwn
new file mode 100644
index 00000000..c45576eb
--- /dev/null
+++ b/biblio/22140515.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2."]]
+[[!tag Oikopleura]]
+
+Jurkowski TP, Jeltsch A.
+
+On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2.
+
+PLoS One. 2011;6(11):e28104. doi:10.1371/journal.pone.0028104
+
+[[!pmid 22140515 desc="Did not find Dnmt2 in O. dioica."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3dd6b38b..765e0202 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -236,6 +236,7 @@ Genes and pathways
  - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]],
    [[Albalat, Martí-Solans and Cañestro, 2012|biblio/22389042]]).
    It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
+   [[Jurkowski and Jeltsch (2011)|bilbio/22140515]] did not find Dnmt2 in O. dioica.
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).
  - No olfactory receptors have been found in _Oikopleura_ nor in _Ciona_

Only Dnmt2 (Trdmt1) is found in Oikopleura.
diff --git a/biblio/22389042.mdwn b/biblio/22389042.mdwn
new file mode 100644
index 00000000..dcc43f93
--- /dev/null
+++ b/biblio/22389042.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates."]]
+[[!tag Oikopleura epigenetic methylation]]
+
+Albalat R, Martí-Solans J, Cañestro C
+
+Brief Funct Genomics. 2012 Mar;11(2):142-55. doi:10.1093/bfgp/els009
+
+DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates.
+
+[[!pmid 22389042 desc="Only Dnmt2 (Trdmt1) is found in Oikopleura."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cfe791d9..3dd6b38b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -233,7 +233,8 @@ Genes and pathways
 
 ### Lost
 
- - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+ - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]],
+   [[Albalat, Martí-Solans and Cañestro, 2012|biblio/22389042]]).
    It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).

Café
diff --git a/biblio/33408411.mdwn b/biblio/33408411.mdwn
new file mode 100644
index 00000000..a6dc671b
--- /dev/null
+++ b/biblio/33408411.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Platypus and echidna genomes reveal mammalian biology and evolution."]]
+[[!tag genome synteny]]
+
+Zhou Y, Shearwin-Whyatt L, Li J, Song Z, Hayakawa T, Stevens D, Fenelon JC, Peel E, Cheng Y, Pajpach F, Bradley N, Suzuki H, Nikaido M, Damas J, Daish T, Perry T, Zhu Z, Geng Y, Rhie A, Sims Y, Wood J, Haase B, Mountcastle J, Fedrigo O, Li Q, Yang H, Wang J, Johnston SD, Phillippy AM, Howe K, Jarvis ED, Ryder OA, Kaessmann H, Donnelly P, Korlach J, Lewin HA, Graves J, Belov K, Renfree MB, Grutzner F, Zhou Q, Zhang G.
+
+Nature. 2021 Jan 6. doi:10.1038/s41586-020-03039-0
+
+Platypus and echidna genomes reveal mammalian biology and evolution. 
+
+[[!pmid 33408411 desc="The ancestral mammalian genome had 30 pairs of chromosomes."]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 5899c801..1a531eab 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -9,17 +9,6 @@ were enriched near CTCF-binding events.
 distribution follows a power law and explain it with a model that requires
 breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
 
-The ancestral chordate has 17 chromosomes according to amphioxus assemblies of
-[[Putnam and coll, 2008|biblio/18563158]] and [[Simakov and coll., 2020|biblio/32313176]].
-
-The scallop genome has 19 chromosomes, which are syntenic to the 17 ancestral
-chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
-elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].  The annelid
-worm _Dimorphilus gyrociliatus_ also has
-([[Martín-Durán and coll., 2020|biblio/10.1101_2020.05.07.078311]]).
-
-The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
-
 [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints
 (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
@@ -31,4 +20,19 @@ chromosomal inversions fixed per million years in _Drosophila_.
 In insects, the Osiris gene family shows conservation of synteny over ~400
 million years ([[Sah and coll., 2012|biblio/22384409]]).
 
+### Ancestral karyotpyes
+
+ - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll., 2021|biblio/33408411]]).
+
+ - The ancestral chordate has 17 chromosomes according to amphioxus assemblies
+  ([[Putnam and coll, 2008|biblio/18563158]], [[Simakov and coll., 2020|biblio/32313176]]).
+
+ - The scallop genome has 19 chromosomes, which are syntenic to the 17 ancestral
+   chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
+   elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].  The annelid
+   worm _Dimorphilus gyrociliatus_ also has
+   ([[Martín-Durán and coll., 2020|biblio/10.1101_2020.05.07.078311]]).
+
+ - The ancestral amniote has 49 chromosomes ([[Sacerdot and coll., 2018|biblio/30333059]]).
+
 [[!inline pages="tagged(synteny)" limit=0]]

To read
diff --git a/biblio/10.1111_cla.12405.mdwn b/biblio/10.1111_cla.12405.mdwn
new file mode 100644
index 00000000..fec5609f
--- /dev/null
+++ b/biblio/10.1111_cla.12405.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea"]]
+[[!tag to_read Oikopleura]]
+
+Katrin Braun, Fanny Leubner, Thomas Stach
+
+Cladistics Volume36, Issue3, June 2020, Pages 259–300 doi:10.1111/cla.12405
+
+Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea
+
+[[!doi 10.1111/cla.12405 desc="Places appendicularians basal in tunicates."]]

Mention one more phylogeny.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7a6f9891..cfe791d9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -33,8 +33,9 @@ Parasites: _Oodinium pouchetii_ and others.
 Phylogeny
 ---------
 
- - 18S rDNA phylogeny of [[Wada and Satoh, 1994|biblio/8127885]] and [[Swalla
-   and coll., 2000|biblio/12116483]] places larvaceans sister to all tunicates.
+ - 18S rDNA phylogenies of [[Wada and Satoh, 1994|biblio/8127885]],
+   [[Wada 1998|biblio/9729883]] and [[Swalla and coll., 2000|biblio/12116483]]
+   place larvaceans sister to all tunicates.
  - Based on 18S rRNA sequences from 110 species including 4 Oikopleuridae, this
    clade is sister of Stolidobranchia (that is, not basal in Tunicates).
    Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or

Café
diff --git a/biblio/31451549.mdwn b/biblio/31451549.mdwn
new file mode 100644
index 00000000..8b60d2d9
--- /dev/null
+++ b/biblio/31451549.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2."]]
+[[!tag Ciona Oikopleura]]
+
+Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2.
+
+Confalonieri S, Colaluca IN, Basile A, Pece S, Di Fiore PP.
+
+G3 (Bethesda). 2019 Oct 7;9(10):3359-3367. doi: 10.1534/g3.119.400494.
+
+[[!pmid 31451549 desc="Ciona NUMB can inhibit ubiquitination of P53 by MDM2.  This and a phylogenetic analysis demonstrates that PTB-long isoform encoded by Exon3 is a Chordate invention. O. dioica has 2 NUMB genes, more similar to NUMB than to vertebrate-specific NUMBL.  Their intron/exon structures are different from any other organism."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7821f2c2..7a6f9891 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -227,6 +227,8 @@ Genes and pathways
    Tolstenkov and Glover 2019|biblio/30905687]]).
  - Piwi ([[Henriet and coll., 2015|biblio/25779047]]).
  - Metallothioneins _OdMT1_ and _OdMT2_ [[Calatayud and coll., 2018|biblio/30284576]].
+ - 2 NUMB genes were found; both are closer to Vertebrate NUMB than to Vertebrate NUMB-Like
+   ([[Confalonieri and coll., 2019|biblio/31451549]]).
 
 ### Lost
 

Café
diff --git a/biblio/33380456.mdwn b/biblio/33380456.mdwn
new file mode 100644
index 00000000..d1a1e904
--- /dev/null
+++ b/biblio/33380456.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="True scale-free networks hidden by finite size effects."]]
+[[!tag network power_law]]
+
+Serafino M, Cimini G, Maritan A, Rinaldo A, Suweis S, Banavar JR, Caldarelli G.
+
+Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):e2013825118. doi:10.1073/pnas.2013825118
+
+True scale-free networks hidden by finite size effects.
+
+[[!pmid 33380456 desc="Sub-sampling of 185 different networks shows that in half of them the degree distribution is scale-invariant."]]
diff --git a/tags/power_law.mdwn b/tags/power_law.mdwn
index 5d385263..a4df2b11 100644
--- a/tags/power_law.mdwn
+++ b/tags/power_law.mdwn
@@ -11,6 +11,7 @@ Bonner (2002)|biblio/12136033]] to follow a power law.  [[Balwierz et al.,
 normalisation method fitting the data to the power law.
 
 Power laws are also seen in other areas, for instance in parameters describing
-network topologies ([[Barabási & Albert, 1999|biblio/10521342]]).
+network topologies ([[Barabási & Albert, 1999|biblio/10521342]], [[Serafino and
+coll., 2021|biblio/33380456]]).
 
 [[!inline pages="tagged(power_law)" limit=0]]

Café
diff --git a/biblio/26587265.mdwn b/biblio/26587265.mdwn
new file mode 100644
index 00000000..e8b1a23c
--- /dev/null
+++ b/biblio/26587265.mdwn
@@ -0,0 +1,24 @@
+[[!meta title="MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species."]]
+[[!tag eDNA]]
+
+Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W.
+
+MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.
+
+R Soc Open Sci. 2015 Jul 22;2(7):150088. doi:10.1098/rsos.150088
+
+[[!pmid 26587265 desc="“Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera.”"]]
+
+“considering the unconventional base pairing in the T/G bond, the designed primers use G rather than A when the template is variably C or T, and T rather than C when the template is A or G;”
+
+“2 l lots of seawater from the 10 l samples were vacuum-filtered onto 47 mm diameter glass-fibre filters [and then] stored in −20°C before eDNA extraction.”  “Two litres of Milli-Q water was used as the negative control.”  ”Lysis using proteinase K [at] 56°C [...] for 30 min.”  “Six random hexamers (N) are used to enhance cluster separation on the flowcells during [basecall]”
+
+“35 cycles of a 12 μl reaction volume containing 6.0 μl 2× KAPA HiFi HotStart ReadyMix (including DNA polymerase, reaction buffer, dNTPs and MgCl2 (at a final concentration of 2.5 mM)) (KAPA Biosystems, Wilmington, MA, USA), 0.7 μl of each primer (5 μM), 2.6 μl sterile distilled H2O and 2.0 μl template. [...] The thermal cycle profile after an initial 3 min denaturation at 95°C was as follows: denaturation at 98°C for 20 s; annealing at 65°C for 15 s; and extension at 72°C for 15 s with the final extension at the same temperature for 5 min.”  “The first PCR product was diluted 10 times using Milli-Q water and used as a template for the second PCR.”
+
+“The pre-processed reads from the above custom pipeline were dereplicated using a ‘derep_fulllength’ command in UCLUST”
+
+“Optimal experimental conditions for the first PCR with these primers were achieved through trial and error, and we found that choice of a PCR kit (KAPA HiFi HotStart ReadyMix) and associated high-annealing temperatures (65–67°C) in the first PCR are the two most important factors contributing to successful amplifications showing distinct single PCR bands on the agarose gel.”
+
+“MiFish-U/E primers also amplified eDNA from a [...] spotted dolphin”
+
+“The occasional detection of [non-tank species] in the negative controls strongly suggests cross contamination in the laboratory, which seems unavoidable in eDNA studies using PCR amplifications.”
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
index 289530cb..55342d8d 100644
--- a/tags/eDNA.mdwn
+++ b/tags/eDNA.mdwn
@@ -6,4 +6,7 @@
    [[Djurhuus and coll. 2020|biblio/31937756]]
  - Oikopleuridae detected in TARA Oceans ([[Vorobev and coll., 2020|biblio/32205368]]).
 
+ - Primer design “considering the unconventional base pairing in the T/G bond”
+   instead of using degenerate bases: [[Miya and coll (2015)|biblio/26587265]].
+
 [[!inline pages="tagged(eDNA)" limit=0]]

Syntax
diff --git a/biblio/10.1101_2020.12.23.423594.mdwn b/biblio/10.1101_2020.12.23.423594.mdwn
index 3c2f8fbf..77093509 100644
--- a/biblio/10.1101_2020.12.23.423594.mdwn
+++ b/biblio/10.1101_2020.12.23.423594.mdwn
@@ -7,4 +7,4 @@ bioRxiv 2020.12.23.423594; doi:10.1101/2020.12.23.423594
 
 SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
 
-[[!doi 10.1101/2020.12.23.423594 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two "gene" annotations."]]
+[[!doi 10.1101/2020.12.23.423594 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two “gene” annotations."]]

Café
diff --git a/biblio/10.1101_2020.12.23.423594.mdwn b/biblio/10.1101_2020.12.23.423594.mdwn
new file mode 100644
index 00000000..3c2f8fbf
--- /dev/null
+++ b/biblio/10.1101_2020.12.23.423594.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data"]]
+[[!tag Oikopleura bioRxiv]]
+
+Marius Wenzel, Berndt Mueller, Jonathan Pettitt
+
+bioRxiv 2020.12.23.423594; doi:10.1101/2020.12.23.423594
+
+SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
+
+[[!doi 10.1101/2020.12.23.423594 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two "gene" annotations."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ab0d6eb5..7821f2c2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -282,7 +282,8 @@ Transcriptome
    40-nt 5′ [[splice leader|tags/trans-splicing]] (SL) bearing a trimethylated cap is found in some RNAs.
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
    times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus.
-   Reported intercistronic regions are short (<30 nt) ([[Ganot et al., 2004|biblio/15314184]]).
+   Reported intercistronic regions are short: <30 nt ([[Ganot et al., 2004|biblio/15314184]])
+   or ~33 nt ([[Wenzel, Mueller and Pettitt, 2020|biblio/10.1101_2020.12.23.423594]]).
  - The splice leader found in the Norwegian strain by ([[Ganot et al., 2004|biblio/15314184]])
    was found indentical in a Japanese strain by ([[Wang and coll., 2015|biblio/26032664]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the

Kaffe
diff --git a/biblio/23523957.mdwn b/biblio/23523957.mdwn
new file mode 100644
index 00000000..dd732bea
--- /dev/null
+++ b/biblio/23523957.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A remote-controlled adaptive medchem lab: an innovative approach to enable drug discovery in the 21st Century."]]
+[[!tag automation]]
+
+Godfrey AG, Masquelin T, Hemmerle H.
+
+Drug Discov Today. 2013 Sep;18(17-18):795-802. doi:10.1016/j.drudis.2013.03.001
+
+A remote-controlled adaptive medchem lab: an innovative approach to enable drug discovery in the 21st Century.
+
+[[!pmid 23523957 desc="Automated Synthesis Laboratory (ASL)"]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 44c50ffc..c6d23e90 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -2,6 +2,8 @@
 
 “Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery” ([[Kitano 2016|biblio/AI_37_2642]]).
 
+Automated synthesis laboratory (ASL): [[Godfrey, Masquelin and Hemmerle (2013)|biblio/23523957]]
+
 “A mobile robotic chemist” ([[Burger and coll., 2020|biblio/32641813]]).
 
 Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).

Café
diff --git a/biblio/30498165.mdwn b/biblio/30498165.mdwn
new file mode 100644
index 00000000..30ed5a92
--- /dev/null
+++ b/biblio/30498165.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Organic synthesis in a modular robotic system driven by a chemical programming language."]]
+[[!tag automation]]
+
+Steiner S, Wolf J, Glatzel S, Andreou A, Granda JM, Keenan G, Hinkley T, Aragon-Camarasa G, Kitson PJ, Angelone D, Cronin L.
+
+Science. 2019 Jan 11;363(6423):eaav2211. doi: 10.1126/science.aav2211.
+
+Organic synthesis in a modular robotic system driven by a chemical programming language.
+
+[[!pmid 30498165 desc="“The physical routing that links the connected modules is described in [GraphML]”.  Hardware-unknowing domain-specific language (DSL) is compiled in robot commands, so that the same DSL instructions can be executed on robots with different layouts but same equipment.  The commands are first simulated to check for potential issues such as overfilling, etc.  Valves etc. are connected to and commanded by the computer."]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 3851ef67..44c50ffc 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -6,6 +6,10 @@
 
 Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).
 
+Computational control of an organic chemistry system.  Position of the
+instruments are stored relative to each other in a graph.
+([[Steiner and coll., 2019|biblio/30498165]])
+
 Computational planning of compounts for a robotic platform that can assemble an run flow chemistry modules: [[Coley and coll., 2019|biblio/31395756]].
 
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].

Café
diff --git a/biblio/31395756.mdwn b/biblio/31395756.mdwn
new file mode 100644
index 00000000..f7fe14f3
--- /dev/null
+++ b/biblio/31395756.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A robotic platform for flow synthesis of organic compounds informed by AI planning."]]
+[[!tag automation]]
+
+Coley CW, Thomas DA 3rd, Lummiss JAM, Jaworski JN, Breen CP, Schultz V, Hart T, Fishman JS, Rogers L, Gao H, Hicklin RW, Plehiers PP, Byington J, Piotti JS, Green WH, Hart AJ, Jamison TF, Jensen KF.
+
+Science. 2019 Aug 9;365(6453):eaax1566. doi:10.1126/science.aax1566
+
+A robotic platform for flow synthesis of organic compounds informed by AI planning.
+
+[[!pmid  31395756 desc="An algorithm proposes a synthetic route for a robotic flow chemistry platform, an expect makes practical amendments for safety or efficiency, and the robot assembles the flow platform and runs the synthesis.  Practical challenges remain, such as predicting solubility of the products to avoid clogging the pipes with precipitates."]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index fd4fcf0b..3851ef67 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -6,6 +6,8 @@
 
 Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).
 
+Computational planning of compounts for a robotic platform that can assemble an run flow chemistry modules: [[Coley and coll., 2019|biblio/31395756]].
+
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
 
 Synthetic sequences that have the same function in a genome need to differ from each other, to prevent from spurious homologous recombinations.  Hossain and coll ([[2020|biblio/32661437]]) optimised an algorithm for producing libraries of "nonrepetitive" elements such as promoters.

Café
diff --git a/biblio/32661437.mdwn b/biblio/32661437.mdwn
new file mode 100644
index 00000000..1f0a37b6
--- /dev/null
+++ b/biblio/32661437.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Automated design of thousands of nonrepetitive parts for engineering stable genetic systems."]]
+[[!tag synthetic]]
+
+Hossain A, Lopez E, Halper SM, Cetnar DP, Reis AC, Strickland D, Klavins E, Salis HM.
+
+Nat Biotechnol. 2020 Dec;38(12):1466-1475. doi: 10.1038/s41587-020-0584-2
+
+Automated design of thousands of nonrepetitive parts for engineering stable genetic systems.
+
+[[!pmid 32661437 desc="To avoid homologous recombinations, synthetic parts of a genome that have the same function (promoter, ...) need to have a different sequence.  Constructing a set of functional synthetic sequences that never share k-mers of a given length (10 to 20) is difficult because the graph of related sequences is very dense.  Therefore, the authors have optimised an algorithm for very dense graph."]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 082ef04b..fd4fcf0b 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -8,4 +8,6 @@ Computational planning of the synthesis of complex natural products. ([[Mikulak-
 
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
 
+Synthetic sequences that have the same function in a genome need to differ from each other, to prevent from spurious homologous recombinations.  Hossain and coll ([[2020|biblio/32661437]]) optimised an algorithm for producing libraries of "nonrepetitive" elements such as promoters.
+
 [[!inline pages="tagged(automation)" limit=0]]

Café
diff --git a/biblio/33049755.mdwn b/biblio/33049755.mdwn
new file mode 100644
index 00000000..598e30d8
--- /dev/null
+++ b/biblio/33049755.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Computational planning of the synthesis of complex natural products."]]
+[[!tag automation]]
+
+Mikulak-Klucznik B, Gołębiowska P, Bayly AA, Popik O, Klucznik T, Szymkuć S, Gajewska EP, Dittwald P, Staszewska-Krajewska O, Beker W, Badowski T, Scheidt KA, Molga K, Mlynarski J, Mrksich M, Grzybowski BA.
+
+Nature. 2020 Dec;588(7836):83-88. doi:10.1038/s41586-020-2855-y
+
+Computational planning of the synthesis of complex natural products.
+
+[[!pmid 33049755 desc="Searches for the shortest path in a graph of compounds.  “computational synthesis planning”.  “the program has been taught [100,000] mechanism-based reaction rules”  “inclusion of [...] heuristics that prescribe how to strategize over multiple steps, taking into account how certain reaction choices imply succession (or elimination) of other transformations.”  “allowing [...] to overcome local maxima”  In a “Turing test“, evaluators could not distinguish plannings made by human and those made by the program.  “When needed, organic chemists performing the syntheses were allowed to adjust reaction conditions [...] for the sake of optimization.”"]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 6dc18731..082ef04b 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -4,6 +4,8 @@
 
 “A mobile robotic chemist” ([[Burger and coll., 2020|biblio/32641813]]).
 
+Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).
+
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
 
 [[!inline pages="tagged(automation)" limit=0]]

Café
diff --git a/biblio/32810209.mdwn b/biblio/32810209.mdwn
new file mode 100644
index 00000000..113da47d
--- /dev/null
+++ b/biblio/32810209.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform."]]
+[[!tag sequencing]]
+
+Hirose Y, Shiozaki T, Hamano I, Yoshihara S, Tokumoto H, Eki T, Harada N.
+
+DNA Res. 2020 Aug 1;27(4):dsaa017. doi:10.1093/dnares/dsaa017
+
+A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform.
+
+[[!pmid 32810209 desc="N704/S507 index pair considered harmful on MiSeq."]]

creating tag page tags/karyotype
diff --git a/tags/karyotype.mdwn b/tags/karyotype.mdwn
new file mode 100644
index 00000000..a81787cf
--- /dev/null
+++ b/tags/karyotype.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged karyotype"]]
+
+[[!inline pages="tagged(karyotype)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/10.1101_2020.09.08.286724.mdwn b/biblio/10.1101_2020.09.08.286724.mdwn
new file mode 100644
index 00000000..9cea5b64
--- /dev/null
+++ b/biblio/10.1101_2020.09.08.286724.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cell culture-based shark karyotyping as a resource for chromosome-scale genome analysis"]]
+[[!tag bioRxiv cell_culture karyotype]]
+
+Yoshinobu Uno, Ryo Nozu, Itsuki Kiyatake, Nobuyuki Higashiguchi, Shuji Sodeyama, Kiyomi Murakumo, Keiichi Sato, Shigehiro Kuraku
+
+bioRxiv 2020.09.08.286724; doi: https://doi.org/10.1101/2020.09.08.286724
+
+Cell culture-based shark karyotyping as a resource for chromosome-scale genome analysis
+
+[[!doi 10.1101/2020.09.08.286724 desc="Primary cell culture of fibroblasts and lymphocytes.  Mitogens were used to stimulate lymphocyte growth. “2n = 102 for the whale shark (Rhincodon typus) and zebra shark (Stegostoma fasciatum), and 2n = 106 for the brownbanded bamboo shark (Chiloscyllium punctatum) and whitespotted bamboo shark (C. plagiosum)”.  In comparison with teleost cell culture medium, shark cells needed a higher osmolarity and the medium was supplemented with 333 mM urea, 188 mM NaCl and 54 mM trimethylamine N-oxide."]]

re-read
diff --git a/biblio/10471753.mdwn b/biblio/10471753.mdwn
index 495da5a4..fc24caa9 100644
--- a/biblio/10471753.mdwn
+++ b/biblio/10471753.mdwn
@@ -7,6 +7,7 @@ Shagin DA, Lukyanov KA, Vagner LL, Matz MV.
 
 Regulation of average length of complex PCR product.
 
-[[!pmid 10471753 desc="Amplify preferentially long PCR product with a single
-primer. Shorter molecules have a higher probability of undergoing
-inhibitory intramolecular interactions. (suppressive PCR)"]]
+[[!pmid 10471753 desc="Suppression PCR amplification of a phage lambda digested
+by HindII on which inverted terminal repeats were ligated.  Suppression effect
+is stronger when the PCR primer is shorter than the terminal repeats, and
+when the PCR primer molarity is lower (tested in a 750–0 nM range)."]]
diff --git a/tags/amplification.mdwn b/tags/amplification.mdwn
index 531fee71..798fcbaf 100644
--- a/tags/amplification.mdwn
+++ b/tags/amplification.mdwn
@@ -5,6 +5,10 @@ _work in progress..._
 ‘Suppression PCR’ was first published in English in [[Siebert and coll.,
 1995|biblio/7731798]].  Figure 1B shows a ‘panhandle’ structure.
 
+Primer concentration (lower -> stronger suppression) and length ratio between
+inverted tandem repeats and PCR primer (shorter PCR primer -> stronger
+suppression) were investigated by Shagin and coll ([[1999|biblio/10471753]]).
+
 Suppression PCR usually does not affect long (6~8 kbp) DNA molecules
 (mentionned in [[Lukyanov and coll., 2007|biblio/10.1007_978-1-4020-6040-3_2]]).
 

Café
diff --git a/biblio/17194496.mdwn b/biblio/17194496.mdwn
index 0b068de4..495ae4f4 100644
--- a/biblio/17194496.mdwn
+++ b/biblio/17194496.mdwn
@@ -1,3 +1,19 @@
 [[!meta title="PCR-suppression effect: kinetic analysis and application to representative or long-molecule biased PCR-based amplification of complex samples."]]
-[[!tag template_switching]]
-[[!pmid 17194496 desc="Uses a 3′ phosphate to prevent the template switching oligonucleotide to prime a first strand cDNA."]]
+[[!tag amplification template_switching]]
+
+Dai ZM, Zhu XJ, Chen Q, Yang WJ.
+
+J Biotechnol. 2007 Feb 20;128(3):435-43. doi:10.1016/j.jbiotec.2006.10.018
+
+PCR-suppression effect: kinetic analysis and application to representative or long-molecule biased PCR-based amplification of complex samples.
+
+[[!pmid 17194496 desc="PCR amplification of a GeneRuler 1kb DNA Ladder (Fermentas) on which adatpers were ligated.  Investigates “parameters which affect ITR self-annealing: (i) the length  of PCR  products [...] (ii) Primer concentration [...] (iii)  The  ratio of ITR  length to  primer length [and] (iv) [annealing temperature]”.  Uses a 3′ phosphate to prevent the template switching oligonucleotide to prime a first strand cDNA."]]
+
+“The 10 µl final [RT] reaction mixture contained 50 mM Tris–Cl (pH 8.3 at 25°C), 75 mM KCl,6 mM MgCl2, 2 mM MnCl2, 0.2 mg/ml BSA, 10 mM DTT, 1 mM dNTPs, 1µM TS-oligo, 1µM oligo(dT) adaptor (, 10 U RNase Inhibitor, and 150 U SuperScript II [and] was incubated at 42 °C for 1 h, followed by 45 °C for 30 min, and 50 °C for 10 min.”
+
+
+“Using [...] the shortest adaptor, whose length is equal to [the PCR primer], short fragments corresponding to 0.25 kb were efficiently amplified, while longer fragments (>3.5 kb) could not be distinguished from the background.  Using [...] the longest adaptor, whose length is more than twice [the PCR primer], fragments shorter than 1.5 kb were suppressed, while fragments up to 10 kb were efficiently amplified.” [My comment: this analysis does not take into account the overall reduction of PCR efficiency with increasing and the fact that mass of shortest fragments were also lower in the GeneRuler ladder.  This also contributes to the disappearance of these bands on the electrophoresis pictures.  This might explain why the high-length fragments could not resolve in the amplifications with highest yields.]
+
+“Lower [annealing temperature] enhanced the PS-effect under any condition.  [Annealing temperature] greatly affected the PS-effect when the primer concentration was low (P2 = 0.04M).  [The] average length  of  the products was longer at lower [annealing temperature].  [...] From 50 to 61.2°C), longer products (up to 10 kb) wer eefficiently amplified. When [annealing temperature] was higher (>65.9°C), much shorter products (<4 kb) were efficiently amplified and longer products disappeared. [Annealing temperature] also affected the PS-effect when primer concentration was 15-fold higher [...]  The average product length between higher (70◦C) and lower (60◦C) [annealing temperature] was significantly different, regardless of adaptors used.”
+
+“[Only] with the longest adaptor [...] we were able to amplify products in a wide range (from 0.25 to 10 kb) simultaneously with a slight over-representation of longer molecules.  [To] representatively amplify a complex sample, relatively long ITR (compared to primer length), high [annealing temperature], and high concentratio nof primer should be used.”
diff --git a/tags/amplification.mdwn b/tags/amplification.mdwn
index 995b611f..531fee71 100644
--- a/tags/amplification.mdwn
+++ b/tags/amplification.mdwn
@@ -8,4 +8,10 @@ _work in progress..._
 Suppression PCR usually does not affect long (6~8 kbp) DNA molecules
 (mentionned in [[Lukyanov and coll., 2007|biblio/10.1007_978-1-4020-6040-3_2]]).
 
+4 parameters (template length, inverted repeat length vs primer length, primer
+concentration and annealing temperature) were investigated by [[Dai and coll.,
+2020|biblio/17194496]], who concluded that to “representatively amplify a
+complex sample, relatively long ITR (compared to primer length), high
+[annealing temperature], and high concentration of primer should be used.”.
+
 [[!inline pages="tagged(amplification)" limit=0]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index a0f28cf8..1d0d7a0b 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -78,7 +78,8 @@ as a replacement for RNA.
  - 3′ phosphate or biotin blocking groups abolish template-switching
    ([[Turchinovich et al (2014)|biblio/24922482]] and others).  However,
    [[Pinto & Lindblad (2010)|biblio/19837043]] report the use of a
-   3′ C3 spacer (on all-DNA TSOs).
+   3′ C3 spacer (on all-DNA TSOs) and [[Dai and coll. 2020|biblio/17194496]].
+   report successful use of a phosphorylated TSO.
 
  - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
    of the TSO, and therefore blocks concatenation

Café
diff --git a/biblio/29712911.mdwn b/biblio/29712911.mdwn
new file mode 100644
index 00000000..cadf5c3b
--- /dev/null
+++ b/biblio/29712911.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty."]]
+[[!tag evolution]]
+
+Paps J, Holland PWH.
+
+Nat Commun. 2018 Apr 30;9(1):1730. doi:10.1038/s41467-018-04136-5
+
+Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty
+
+[[!pmid 29712911 desc="“[Homology groups] derived from the first animal genome were abundant in protein classes implicated in gene regulation [...] and catalytic activities [...]. The most abundant GO pathways include many signalling pathways.”"]]

Café
diff --git a/biblio/33057197.mdwn b/biblio/33057197.mdwn
new file mode 100644
index 00000000..ee8112f1
--- /dev/null
+++ b/biblio/33057197.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Dense and pleiotropic regulatory information in a developmental enhancer."]]
+[[!tag Drosophila enhancer automation]]
+
+Fuqua T, Jordan J, van Breugel ME, Halavatyi A, Tischer C, Polidoro P, Abe N, Tsai A, Mann RS, Stern DL, Crocker J.
+
+Nature. 2020 Nov;587(7833):235-239. doi:10.1038/s41586-020-2816-5
+
+Dense and pleiotropic regulatory information in a developmental enhancer
+
+[[!pmid 33057197 desc="Study of the E3N enhancer of the shavenbaby (svb) gene.  Immunohistochemistry automated with liquid handling robots.  “sequence conservation is not an accurate predictor of the quantitative roles of individual sites in the E3N enhancer”  “most mutations in E3N led to changes in transcriptional outputs, suggesting that regulatory information is distributed densely within this enhancer”"]]

Bière et tchidjimi.
diff --git a/biblio/10.1073_pnas.1003250107.mdwn b/biblio/10.1073_pnas.1003250107.mdwn
new file mode 100644
index 00000000..4b756aea
--- /dev/null
+++ b/biblio/10.1073_pnas.1003250107.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Universal robotic gripper based on the jamming of granular material"]]
+[[!tag robot]]
+
+Eric Brown, Nicholas Rodenberg, John Amend, Annan Mozeika, Erik Steltz, Mitchell R. Zakin, Hod Lipson, and Heinrich M. Jaeger
+
+Proc Natl Acad Sci U S A. 2010 Nov 2; 107(44): 18809–18814. doi:10.1073/pnas.1003250107
+
+Universal robotic gripper based on the jamming of granular material
+
+[[!doi 10.1073/pnas.1003250107 desc="Doraemon !"]]
diff --git a/tags/robot.mdwn b/tags/robot.mdwn
index e671a3a9..01b6c733 100644
--- a/tags/robot.mdwn
+++ b/tags/robot.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged robot"]]
 
-[[!inline pages="tagged(robot)" actions="no" archive="yes"
-feedshow=10]]
+(work in progress)
+
+ - A ball gripper that reminds me Doraemon's hand: [[Brown and coll.,
+   2010|biblio/10.1073_pnas.1003250107]].
+
+[[!inline pages="tagged(robot)" limit=0]]

Café
diff --git a/biblio/10.1007_978-1-4020-6040-3_2.mdwn b/biblio/10.1007_978-1-4020-6040-3_2.mdwn
new file mode 100644
index 00000000..db71efa6
--- /dev/null
+++ b/biblio/10.1007_978-1-4020-6040-3_2.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Selective Suppression of Polymerase Chain Reaction and Its Most Popular Applications."]]
+[[!tag amplification]]
+
+Lukyanov S.A., Lukyanov K.A., Gurskaya N.G., Bogdanova E.A., Buzdin A.A.
+
+(2007)
+
+Selective Suppression of Polymerase Chain Reaction and Its Most Popular Applications.
+
+In: Buzdin A.A., Lukyanov S.A. (eds) Nucleic Acids Hybridization Modern Applications. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6040-3_2
+
+[[!doi 10.1007/978-1-4020-6040-3_2 desc="Mentions that the “SSP [selective suppression PCR] effect does not inhibit, or inhibits sparingly, amplification of very long DNA ([...] usually 6–8 kbp).” "]]
diff --git a/tags/amplification.mdwn b/tags/amplification.mdwn
index f5162ec2..995b611f 100644
--- a/tags/amplification.mdwn
+++ b/tags/amplification.mdwn
@@ -5,4 +5,7 @@ _work in progress..._
 ‘Suppression PCR’ was first published in English in [[Siebert and coll.,
 1995|biblio/7731798]].  Figure 1B shows a ‘panhandle’ structure.
 
+Suppression PCR usually does not affect long (6~8 kbp) DNA molecules
+(mentionned in [[Lukyanov and coll., 2007|biblio/10.1007_978-1-4020-6040-3_2]]).
+
 [[!inline pages="tagged(amplification)" limit=0]]

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index ee50f858..78892dd7 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-11-02 03:50+0000\n"
+"POT-Creation-Date: 2020-11-02 06:36+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -71,17 +71,18 @@ msgstr ""
 #. type: Plain text
 msgid ""
 "I have complemented my work on CAGE with the development of a gene-centred "
-"technique for detecting promoters, termed Deep-RACE ([Olivarius and coll., "
-"2009](https://pubmed.gov/19317658), [Plessy and coll., 2012](http://dx.doi."
-"org/10.1002/9783527644582.ch4)), which we used to validate our discovery of "
-"the pervasive expression of retrotransposons detected by CAGE ([Faulkner and "
-"coll., 2009](https://pubmed.gov/19377475)). To study transcription start "
-"activity at nucleotide resolution in zebrafish transfected with chimeric "
-"transgenes containing a copy of an endogenous promoter, I combined Deep-"
-"RACE, CAGE and paired-end sequencing in a technology that we called “Single-"
-"Locus CAGE” ([Haberle and coll., 2014](https://pubmed.gov/24531765)). With "
-"my contributions related to CAGE development and analysis, I have been a "
-"**member of the FANTOM consortium** since FANTOM3."
+"technique for detecting promoters, termed **Deep-RACE** ([Olivarius and "
+"coll., 2009](https://pubmed.gov/19317658), [Plessy and coll., 2012](http://"
+"dx.doi.org/10.1002/9783527644582.ch4)), which we used to validate our "
+"discovery of the pervasive expression of retrotransposons detected by CAGE "
+"([Faulkner and coll., 2009](https://pubmed.gov/19377475)). To study "
+"transcription start activity at nucleotide resolution in zebrafish "
+"transfected with chimeric transgenes containing a copy of an endogenous "
+"promoter, I combined Deep-RACE, CAGE and paired-end sequencing in a "
+"technology that we called “Single-Locus CAGE” ([Haberle and coll., 2014]"
+"(https://pubmed.gov/24531765)). With my contributions related to CAGE "
+"development and analysis, I have been a **member of the FANTOM consortium** "
+"since FANTOM3."
 msgstr ""
 
 #. type: Plain text
@@ -96,17 +97,23 @@ msgid ""
 "(https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory "
 "epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with "
 "this promoter-centric work, I have also explored the huge repertoire of the "
-"T cell antigen receptors.  I also applied the nanoCAGE technology to patient "
-"samples infected with the human papillomavirus (HPV) ([Taguchi and coll., "
-"2020](https://pubmed.gov/33093512))."
+"**T cell antigen receptors**.  I also applied the nanoCAGE technology to "
+"patient samples infected with the **human papillomavirus** (HPV) ([Taguchi "
+"and coll., 2020](https://pubmed.gov/33093512))."
 msgstr ""
 
 #. type: Plain text
 msgid ""
 "I joined OIST in 2018, to study **the genetic structure and population "
-"variations** of an animal plankton, _Oikopleura dioica_, that has a genome "
-"50 time more compact than the human one, which empowers us to sequence at "
-"chromosomal resolution many individual sampled from all over the World."
+"variations** of an animal plankton, **_Oikopleura dioica_**, that has a "
+"genome 50 time more compact than the human one, which empowers us to "
+"sequence at chromosomal resolution many individual sampled from all over the "
+"World.  Its mitochondria use a different genetic code than ours ([Pichon and "
+"coll., 2019](https://pubmed.gov/32148763)).  We assembled whole-chromosome "
+"sequences for the Okinawan _O. dioica_ population ([Bliznina and coll., 2020]"
+"(https://doi.org/10.1101/2020.09.11.292656)), which has 3 pairs of "
+"chromosomes ([Liu and coll, 2020](https://f1000research.com/articles/9-780/"
+"v1))  like the other dioceous species."
 msgstr ""
 
 #. type: Plain text

Emphasis and papers.
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index a7cabb82..dc03f0ad 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -41,7 +41,7 @@ for FACS-isolated cells, and one for the Fluidigm C1 platform ([Kouno and coll.,
 2019](https://pubmed.gov/30664627)).
 
 I have complemented my work on CAGE with the development of a gene-centred
-technique for detecting promoters, termed Deep-RACE ([Olivarius and coll.,
+technique for detecting promoters, termed **Deep-RACE** ([Olivarius and coll.,
 2009](https://pubmed.gov/19317658), [Plessy and coll.,
 2012](http://dx.doi.org/10.1002/9783527644582.ch4)), which we used to validate
 our discovery of the pervasive expression of retrotransposons detected by CAGE
@@ -63,16 +63,21 @@ demonstrate the expression of haemoglobin in the midbrain ([Biagioli and coll.,
 localisation of RNA in **Purkinje neurons** ([Kratz and coll.,
 2014](https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory
 epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with
-this promoter-centric work, I have also explored the huge repertoire of the T
-cell antigen receptors.  I also applied the nanoCAGE technology to patient
-samples infected with the human papillomavirus (HPV) ([Taguchi and coll.,
+this promoter-centric work, I have also explored the huge repertoire of the **T
+cell antigen receptors**.  I also applied the nanoCAGE technology to patient
+samples infected with the **human papillomavirus** (HPV) ([Taguchi and coll.,
 2020](https://pubmed.gov/33093512)).
 
 I joined OIST in 2018, to study **the genetic structure and population
-variations** of an animal plankton, _Oikopleura dioica_, that has a genome
-50 time more compact than the human one, which empowers us to sequence
-at chromosomal resolution many individual sampled from all over the
-World.
+variations** of an animal plankton, **_Oikopleura dioica_**, that has a genome
+50 time more compact than the human one, which empowers us to sequence at
+chromosomal resolution many individual sampled from all over the World.  Its
+mitochondria use a different genetic code than ours ([Pichon and coll.,
+2019](https://pubmed.gov/32148763)).  We assembled whole-chromosome sequences
+for the Okinawan _O. dioica_ population ([Bliznina and coll.,
+2020](https://doi.org/10.1101/2020.09.11.292656)), which has 3 pairs of
+chromosomes ([Liu and coll, 2020](https://f1000research.com/articles/9-780/v1))
+like the other dioceous species.
 
 I am also a **Free Software** enthusiast, and contribute to the Debian Med
 project, by **packaging bioinformatics tools**, which are redistributed in

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 1788c12c..ee50f858 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-16 01:18+0000\n"
+"POT-Creation-Date: 2020-11-02 03:50+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -28,10 +28,9 @@ msgid ""
 "enhancers ([Blader and coll., 2003](https://pubmed.gov/12559493)) and their "
 "evolutionary conservation ([Plessy and coll., 2005](https://pubmed."
 "gov/15797614)). This gave me a strong interest for whole-transcriptome "
-"analysis and technology. For that purpose, I have joined RIKEN in 2004, "
-"where have worked on high-throughput methods for **profiling promoters and "
-"inferring gene networks**, and in particular on CAGE (Cap Analysis Gene "
-"Expression)."
+"analysis and technology. For that purpose, I have worked at RIKEN in 2004–18 "
+"on high-throughput methods for **profiling promoters and inferring gene "
+"networks**, and in particular on CAGE (Cap Analysis Gene Expression)."
 msgstr ""
 
 #. type: Plain text
@@ -47,25 +46,26 @@ msgid ""
 "gov/23180801)), combining multiple cap-enrichment steps ([Batut and coll., "
 "2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic "
 "acids for template switching ([Harbers and coll., 2013](https://pubmed."
-"gov/24079827)), and reducing the number of primer artefacts and unwanted "
+"gov/24079827)), reducing the number of primer artefacts and unwanted "
 "sequences generated by ribosomal RNAs using low-complexity “pseudo-random” "
 "reverse-transcription primers ([Arnaud and coll., 2016](https://pubmed."
-"gov/27071605))."
+"gov/27071605)), and screening for optimal parameters of the template-"
+"switching reaction ([Poulain and coll., 2020](https://pubmed.gov/32025730))."
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"On April 2013, I started a new development cycle as the leader of the "
-"Genomics Miniaturization Technology Unit at RIKEN Center for Life Sciences, "
-"Division of Genomics Technology, to expand this work on single cells "
-"following a **population transcriptomics** approach ([Plessy and coll., 2013]"
-"(https://pubmed.gov/23281054)) focused on sampling the largest possible "
-"number of cells. In our ongoing developments, we have reached **single-cell "
-"and single molecule resolution** through the introduction of transposase "
-"fragmentation and unique molecular identifiers ([Poulain and coll., 2017]"
-"(https://pubmed.gov/28349422)). The protocol exists in two versions, one for "
-"FACS-isolated cells, and one for the Fluidigm C1 platform ([Kouno and coll., "
-"2019](https://pubmed.gov/30664627))."
+"In 2013–8, I lead a new development cycle at the Genomics Miniaturization "
+"Technology Unit in RIKEN's Center for Life Sciences, Division of Genomics "
+"Technology, to expand this work on single cells following a **population "
+"transcriptomics** approach ([Plessy and coll., 2013](https://pubmed."
+"gov/23281054)) focused on sampling the largest possible number of cells. In "
+"our ongoing developments, we have reached **single-cell and single molecule "
+"resolution** through the introduction of transposase fragmentation and "
+"unique molecular identifiers ([Poulain and coll., 2017](https://pubmed."
+"gov/28349422)). The protocol exists in two versions, one for FACS-isolated "
+"cells, and one for the Fluidigm C1 platform ([Kouno and coll., 2019](https://"
+"pubmed.gov/30664627))."
 msgstr ""
 
 #. type: Plain text
@@ -96,7 +96,9 @@ msgid ""
 "(https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory "
 "epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with "
 "this promoter-centric work, I have also explored the huge repertoire of the "
-"**T cell antigen receptors**."
+"T cell antigen receptors.  I also applied the nanoCAGE technology to patient "
+"samples infected with the human papillomavirus (HPV) ([Taguchi and coll., "
+"2020](https://pubmed.gov/33093512))."
 msgstr ""
 
 #. type: Plain text

creating tag page tags/RIKEN
diff --git a/tags/RIKEN.mdwn b/tags/RIKEN.mdwn
new file mode 100644
index 00000000..b77112a6
--- /dev/null
+++ b/tags/RIKEN.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged RIKEN"]]
+
+[[!inline pages="tagged(RIKEN)" actions="no" archive="yes"
+feedshow=10]]

More papers !
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index 41a4ad95..a7cabb82 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -6,9 +6,9 @@ and zebrafish**, where I studied the activity of transcription enhancers
 ([Blader and coll., 2003](https://pubmed.gov/12559493)) and their evolutionary
 conservation ([Plessy and coll., 2005](https://pubmed.gov/15797614)). This gave
 me a strong interest for whole-transcriptome analysis and technology. For that
-purpose, I have joined RIKEN in 2004, where have worked on high-throughput
-methods for **profiling promoters and inferring gene networks**, and in
-particular on CAGE (Cap Analysis Gene Expression).
+purpose, I have worked at RIKEN in 2004–18  on high-throughput methods for
+**profiling promoters and inferring gene networks**, and in particular on CAGE
+(Cap Analysis Gene Expression).
 
 I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to
 analyse small samples yielding only nanograms of RNA ([Plessy and coll.,
@@ -21,13 +21,15 @@ the molecular barcodes ([Tang and coll., 2013](https://pubmed.gov/23180801)),
 combining multiple cap-enrichment steps ([Batut and coll.,
 2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic
 acids for template switching ([Harbers and coll.,
-2013](https://pubmed.gov/24079827)), and reducing the number of primer
-artefacts and unwanted sequences generated by ribosomal RNAs using
-low-complexity “pseudo-random” reverse-transcription primers ([Arnaud and
-coll., 2016](https://pubmed.gov/27071605)).
+2013](https://pubmed.gov/24079827)), reducing the number of primer artefacts
+and unwanted sequences generated by ribosomal RNAs using low-complexity
+“pseudo-random” reverse-transcription primers ([Arnaud and coll.,
+2016](https://pubmed.gov/27071605)), and screening for optimal parameters of
+the template-switching reaction ([Poulain and coll.,
+2020](https://pubmed.gov/32025730)).
 
-On April 2013, I started a new development cycle as the leader of the Genomics
-Miniaturization Technology Unit at RIKEN Center for Life Sciences, Division of
+In 2013–8, I lead a new development cycle at the Genomics
+Miniaturization Technology Unit in RIKEN's Center for Life Sciences, Division of
 Genomics Technology, to expand this work on single cells following a
 **population transcriptomics** approach ([Plessy and coll.,
 2013](https://pubmed.gov/23281054)) focused on sampling the largest possible
@@ -61,8 +63,10 @@ demonstrate the expression of haemoglobin in the midbrain ([Biagioli and coll.,
 localisation of RNA in **Purkinje neurons** ([Kratz and coll.,
 2014](https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory
 epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with
-this promoter-centric work, I have also explored the huge repertoire of the **T
-cell antigen receptors**.
+this promoter-centric work, I have also explored the huge repertoire of the T
+cell antigen receptors.  I also applied the nanoCAGE technology to patient
+samples infected with the human papillomavirus (HPV) ([Taguchi and coll.,
+2020](https://pubmed.gov/33093512)).
 
 I joined OIST in 2018, to study **the genetic structure and population
 variations** of an animal plankton, _Oikopleura dioica_, that has a genome

nanoCAGE on HPV patient samples.
diff --git a/biblio/33093512.mdwn b/biblio/33093512.mdwn
new file mode 100644
index 00000000..9e32a576
--- /dev/null
+++ b/biblio/33093512.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages."]]
+[[!tag RIKEN OIST nanoCAGE HPV]]
+
+Taguchi A, Nagasaka K, Plessy C, Nakamura H, Kawata Y, Kato S, Hashimoto K, Nagamatsu T, Oda K, Kukimoto I, Kawana K, Carninci P, Osuga Y, Fujii T.
+
+Sci Rep. 2020 Oct 22;10(1):17991. doi:10.1038/s41598-020-75133-2
+
+Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages.
+
+[[!pmid 33093512 desc="nanoCAGE in HPV patient samples."]]
diff --git a/tags/nanoCAGE.mdwn b/tags/nanoCAGE.mdwn
index fd96652b..031609dd 100644
--- a/tags/nanoCAGE.mdwn
+++ b/tags/nanoCAGE.mdwn
@@ -1,4 +1,3 @@
 [[!meta title="pages tagged nanoCAGE"]]
 
-[[!inline pages="tagged(nanoCAGE)" actions="no" archive="yes"
-feedshow=10]]
+[[!inline pages="tagged(nanoCAGE)" limit=0]]

Syntax
diff --git a/biblio/US5759822.mdwn b/biblio/US5759822.mdwn
index 749d6074..c6a2b499 100644
--- a/biblio/US5759822.mdwn
+++ b/biblio/US5759822.mdwn
@@ -1,4 +1,6 @@
 [[!meta title="Method for suppressing DNA fragment amplification during PCR."]]
 [[!tag patent amplification]]
-[[https://patents.google.com/patent/US5759822A|Suppressive PCR]]
-See also patent [[https://patents.google.com/patent/US5565340|US5565340]].
+
+[Suppressive PCR](https://patents.google.com/patent/US5759822A).
+
+See also patent [US5565340](https://patents.google.com/patent/US5565340).

Syntax
diff --git a/biblio/US5759822.mdwn b/biblio/US5759822.mdwn
index 72b60138..749d6074 100644
--- a/biblio/US5759822.mdwn
+++ b/biblio/US5759822.mdwn
@@ -1,4 +1,4 @@
 [[!meta title="Method for suppressing DNA fragment amplification during PCR."]]
 [[!tag patent amplification]]
-[[https://patents.google.com/patent/US5759822A desc="Suppressive PCR."]]
-See also patent [[https://patents.google.com/patent/US5565340 desc="US5565340"]].
+[[https://patents.google.com/patent/US5759822A|Suppressive PCR]]
+See also patent [[https://patents.google.com/patent/US5565340|US5565340]].
diff --git a/tags/patent.mdwn b/tags/patent.mdwn
index fd30c0a2..f3e265bc 100644
--- a/tags/patent.mdwn
+++ b/tags/patent.mdwn
@@ -2,7 +2,7 @@
 
 Expired:
 
- - [[Method for suppressing DNA fragment amplification during PCR (1996)|bilbio/US5565340]]
+ - [[Method for suppressing DNA fragment amplification during PCR (1996)|bilbio/US5759822]]
  - [[Method for suppressing DNA fragment amplification during PCR (1998)|biblio/US5759822]]
 
 [[!inline pages="tagged(patent)" limit=0]]

Expired
diff --git a/biblio/US5759822.mdwn b/biblio/US5759822.mdwn
index eff3b18f..72b60138 100644
--- a/biblio/US5759822.mdwn
+++ b/biblio/US5759822.mdwn
@@ -1,4 +1,4 @@
 [[!meta title="Method for suppressing DNA fragment amplification during PCR."]]
 [[!tag patent amplification]]
-[[!gpatent Ak0jAAAAEBAJ desc="Suppressive PCR."]]
-See also patent [[!gpatent L-ccAAAAEBAJ desc="5565340"]].
+[[https://patents.google.com/patent/US5759822A desc="Suppressive PCR."]]
+See also patent [[https://patents.google.com/patent/US5565340 desc="US5565340"]].
diff --git a/tags/patent.mdwn b/tags/patent.mdwn
index 3ad87a82..fd30c0a2 100644
--- a/tags/patent.mdwn
+++ b/tags/patent.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged patent"]]
 
-[[!inline pages="tagged(patent)" actions="no" archive="yes"
-feedshow=10]]
+Expired:
+
+ - [[Method for suppressing DNA fragment amplification during PCR (1996)|bilbio/US5565340]]
+ - [[Method for suppressing DNA fragment amplification during PCR (1998)|biblio/US5759822]]
+
+[[!inline pages="tagged(patent)" limit=0]]

Café
diff --git a/biblio/33055213.mdwn b/biblio/33055213.mdwn
new file mode 100644
index 00000000..c7c6ba4d
--- /dev/null
+++ b/biblio/33055213.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts."]]
+[[!tag cap method]]
+
+Culjkovic-Kraljacic B, Skrabanek L, Revuelta MV, Gasiorek J, Cowling VH, Cerchietti L, Borden KLB.
+
+Proc Natl Acad Sci U S A. 2020 Oct 27;117(43):26773-26783. doi:10.1073/pnas.2002360117
+
+The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts.
+
+[[!pmid 33055213 desc="Some RNAs have more than half of their molecules non-capped.  Increasing expression of eIF4E increases their capped proportion to similar levels as other genes.  Enzymatic (cap quantification; CapQ) and quantitative cap immunoprecipitation (CapIP) methods.  Uses the mouse IgG2aκ anti-7-methylguanosine (m7G)-Cap antibody of MBL (RN016M). The maker's site notes that “This antibody (Clone 150-15) reacts with 5′-terminal 7-methylguanosine (m7G) cap structure of RNA and partially cross-reacts with m7G within RNA”.  Overexpression of eIF4E-Flag in  RNA immunoprecipitation experiments increased enrichment of RNA export targets such as RNMT or RNGTT, but export-deficient S53A-eIF4E-Flag mutants did not.  Overexpression also shifted RNA translation to heavier polysomal fractions and elevated m7G levels in the nuclear and cytoplasmic compartments. This elevation is reduced by RNMT knockdown and stronger on specific target, for instance from the capping machinery and the Myc pathway.  A CapQ assay (sequencing an oligo-capping library and a control PNK library) confirmed the observations made by immunoprecipitation.  In control conditions, the capping rate of the targets of eIF4E capping are lower than those of the non-targets."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 2b911981..552aa76d 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -72,4 +72,11 @@ Atypical caps (work in progress)
  - Mass spectroscopy and molecular biology detected dinucleoside polyphosphate caps
    in bacteria ([[Hudeček and coll., 2020|biblio/32103016]]).
 
+Cap physiology (work in progress)
+---------------------------------
+
+Some RNAs have more than half of their molecules non-capped.  Increasing
+expression of eIF4E increases their capped proportion to similar levels as
+other genes.  [[Culjkovic-Kraljacic and coll, 2020|biblio/33055213]]
+
 [[!inline pages="tagged(cap)" limit=0]]

Café
diff --git a/biblio/33020265.mdwn b/biblio/33020265.mdwn
new file mode 100644
index 00000000..59138c90
--- /dev/null
+++ b/biblio/33020265.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Dynamic evolution of great ape Y chromosomes."]]
+[[!tag chromosome]]
+
+Cechova M, Vegesna R, Tomaszkiewicz M, Harris RS, Chen D, Rangavittal S, Medvedev P, Makova KD.
+
+Proc Natl Acad Sci U S A. 2020 Oct 20;117(42):26273-26280. doi:10.1073/pnas.2001749117
+
+Dynamic evolution of great ape Y chromosomes.
+
+[[!pmid 33020265 desc="“Unexpectedly, the rates of gene death were similar between ampliconic and X-degenerate genes.”"]]

Café
diff --git a/biblio/10.1101_2020.05.07.078311.mdwn b/biblio/10.1101_2020.05.07.078311.mdwn
new file mode 100644
index 00000000..be6a0ea9
--- /dev/null
+++ b/biblio/10.1101_2020.05.07.078311.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conservative route to genome compaction in a miniature annelid"]]
+[[!tag genome synteny]]
+
+José M. Martín-Durán, Bruno C. Vellutini, Ferdinand Marlétaz, Viviana Cetrangolo, Nevena Cvetesic, Daniel Thiel, Simon Henriet, Xavier Grau-Bové, Allan M. Carrillo-Baltodano, Wenjia Gu, Alexandra Kerbl, Yamile Marquez, Nicolas Bekkouche, Daniel Chourrout, Jose Luis Gómez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol
+
+bioRxiv 2020.05.07.078311; doi:10.1101/2020.05.07.078311 
+
+Conservative route to genome compaction in a miniature annelid
+
+[[!doi 10.1101/2020.05.07.078311 desc="Genome assembly (PacBio, 73.8 Mb, 95.8% BUSCO genes, 2.24 Mb N50, 4.87% transposable elements, 14,203 protein-coding genes) for the annelid Dimorphilus gyrociliatus, a meiobenthic segmented worm.  Synteny with the scallop genome is visible.  The Hox cluster is present and lacks only one gene, post1.  However, in situ hybridisation suggests lack of temporal colinearity.  The Myc pathway  “lacks the regulators mad (in D. gyrociliatus) and mnt (in all Dinophilidae), a condition also shared with the appendicularian O. dioica”.  “Open chromatin regions [ATAC-seq peaks] are short and mostly found in promoters.”  “Promoters [CAGE] are narrow (<150 bp) and use pyrimidine-purine dinucleotides as preferred initiators.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 9b27c1df..5899c801 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -14,7 +14,9 @@ The ancestral chordate has 17 chromosomes according to amphioxus assemblies of
 
 The scallop genome has 19 chromosomes, which are syntenic to the 17 ancestral
 chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
-elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].
+elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].  The annelid
+worm _Dimorphilus gyrociliatus_ also has
+([[Martín-Durán and coll., 2020|biblio/10.1101_2020.05.07.078311]]).
 
 The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
 

Endosymbiosis.
diff --git a/biblio/33080189.mdwn b/biblio/33080189.mdwn
index 2fe0e343..742c2210 100644
--- a/biblio/33080189.mdwn
+++ b/biblio/33080189.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Oikopleura."]]
-[[!tag Oikopleura review]]
+[[!tag Oikopleura review endosymbiosis]]
 
 Glover JC.
 
@@ -7,4 +7,4 @@ Curr Biol. 2020 Oct 19;30(20):R1243-R1245. doi:10.1016/j.cub.2020.07.075
 
 Oikopleura.
 
-[[!pmid 33080189 desc="Introduction for non-specialists."]]
+[[!pmid 33080189 desc="Introduction for non-specialists.  Mentions the ideas that the CesA gene could have been transferred from an endosymbion."]]

PETase.
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index 0b513673..e59edbf2 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -1,8 +1,12 @@
 [[!meta title="pages tagged microplastic"]]
 
+# Microplastics
+
 [[Oikopleura]] can ingest microplastics and participate to their sedimentation
 ([[Katija and coll., 2017|biblio/28835922]], [[Choy and coll., 2019|biblio/31171833]]).
 
+# [[PETase|https://en.wikipedia.org/wiki/PETase]]
+
 To read: A bacterium that degrades and assimilates poly(ethylene terephthalate)
 Shosuke Yoshida1,2,*, Kazumi Hiraga1, Toshihiko Takehana3, Ikuo Taniguchi4, Hironao Yamaji1, Yasuhito Maeda5, Kiyotsuna Toyohara5, Kenji Miyamoto2,†, Yoshiharu Kimura4, Kohei Oda1,† Science  11 Mar 2016: Vol. 351, Issue 6278, pp. 1196-1199 DOI: 10.1126/science.aad6359 
 

Café
diff --git a/biblio/33080189.mdwn b/biblio/33080189.mdwn
new file mode 100644
index 00000000..2fe0e343
--- /dev/null
+++ b/biblio/33080189.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oikopleura."]]
+[[!tag Oikopleura review]]
+
+Glover JC.
+
+Curr Biol. 2020 Oct 19;30(20):R1243-R1245. doi:10.1016/j.cub.2020.07.075
+
+Oikopleura.
+
+[[!pmid 33080189 desc="Introduction for non-specialists."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7770a977..ab0d6eb5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -13,6 +13,7 @@ for feeding (and perhaps defending).  The main house proteins are called
 _oikosins_ and half or them are unique to Oikopleura and related animals
 ("_Appendicularia_").  The japanese name of _O. dioica_ is
 [ワカレオタマボヤ](https://www.godac.jamstec.go.jp/bismal/j/view/9018229).
+Review for non-specialists: [[Glover, 2020|biblio/33080189]].
 
 Some links:
 

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
Paper to read.
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index b94dae10..a97370dc 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -3,6 +3,9 @@
 [[Oikopleura]] can ingest microplastics and participate to their sedimentation
 ([[Katija and coll., 2017|biblio/28835922]], [[Choy and coll., 2019|biblio/31171833]]).
 
+To read: A bacterium that degrades and assimilates poly(ethylene terephthalate)
+Shosuke Yoshida1,2,*, Kazumi Hiraga1, Toshihiko Takehana3, Ikuo Taniguchi4, Hironao Yamaji1, Yasuhito Maeda5, Kiyotsuna Toyohara5, Kenji Miyamoto2,†, Yoshiharu Kimura4, Kohei Oda1,† Science  11 Mar 2016: Vol. 351, Issue 6278, pp. 1196-1199 DOI: 10.1126/science.aad6359 
+
 To do: read Furukawa M, Kawakami N, Oda K, Miyamoto K (2018) Acceleration of
 enzymatic degradation of poly(ethylene terephthalate) by surface coating with
 anionic surfactants. Chem Sus Chem 11: 4018–4025

Café hier.
diff --git a/biblio/33087570.mdwn b/biblio/33087570.mdwn
new file mode 100644
index 00000000..fb62d375
--- /dev/null
+++ b/biblio/33087570.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Liquid drop of DNA libraries reveals total genome information."]]
+[[!tag emulsion PCR]]
+
+Terekhov SS, Eliseev IE, Ovchinnikova LA, Kabilov MR, Prjibelski AD, Tupikin AE, Smirnov IV, Belogurov AA Jr, Severinov KV, Lomakin YA, Altman S, Gabibov AG.
+
+Proc Natl Acad Sci U S A. 2020 Oct 21:202017138. doi:10.1073/pnas.2017138117.
+
+Liquid drop of DNA libraries reveals total genome information.
+
+[[!pmid 33087570 desc="“[...] either 3% of Abil EM 180 (A-oil) or a mixture of 4.5% Span 80/0.4% Tween 80/0.05% Triton X-100 (T-oil) was used [...] The homogeneity of the amplified DNA was much better in the case of A-oil, whereas ePCR in T-oil resulted in the formation of high-molecular-weight by-products [...] Thirty-five cycles of ePCR in A-oil were sufficient to reach saturation in the majority of the droplets. T-oil was less stable, displaying droplet coalescence after 25 cycles [...].”  “Appearance of clear amplicon bands on electropherograms does not correlate with the uniformity of amplification during ePCR.”  “ePCR clearly outperformed bulk PCR, reducing the number of reads with gross errors by twofold [and] resulted in a more uniform distribution of amplified sequences”"]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 55eb466a..577847f6 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -21,6 +21,7 @@ Different kinds of surfactants:
  - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])
  - DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]]
  - 3% fluorosurfactant (RAN Biotechnologies) in Novec HFE-7500 / 0.015% Tween 80 for double emulsions in [[Masted and coll., 2018|biblio/10.1101_409086]].
+ - 3% of Abil EM 180 or 4.5% Span 80/0.4% Tween 80/0.05% Triton X-100 were compared for ePCR by [[Terekhov and coll., 2020|biblio/33087570]]. “T-oil was less stable, displaying droplet coalescence after 25 cycles.”  “ePCR clearly outperformed bulk PCR, reducing the number of reads with gross errors by twofold [and] resulted in a more uniform distribution of amplified sequences”
 
 Reactive droplets:
 

PETase et Hi-C
diff --git a/biblio/32968280.mdwn b/biblio/32968280.mdwn
new file mode 100644
index 00000000..a9106713
--- /dev/null
+++ b/biblio/32968280.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conformation of sister chromatids in the replicated human genome."]]
+[[!tag H3K27me3 method tags chromosome structure]]
+
+Mitter M, Gasser C, Takacs Z, Langer CCH, Tang W, Jessberger G, Beales CT, Neuner E, Ameres SL, Peters JM, Goloborodko A, Micura R, Gerlich DW.
+
+Nature. 2020 Oct;586(7827):139-144. doi:10.1038/s41586-020-2744-4
+
+Conformation of sister chromatids in the replicated human genome.
+
+[[!pmid 32968280 desc="Sister-chromatid-sensitive Hi-C (scsHi-C) “4-thio-thymidine (4sT) converted into 5mC by OsO4/NH4Cl”  “A read was assigned to the Watson strand if it contained two or more A-to-G mutations and no T-to-C mutations. Similarly, if a read contained two or more T-to-C mutations, but no A-to-G mutations it was assigned to the Crick strand. Then, contacts were classified as cis sister contacts if (after correcting for the opposite read-strandedness of Illumina sequencing of the two mates) both mates mapped to the same strand. Conversely, contacts were classified as trans sister contacts if the two mates mapped to opposing strands.”“Highly paired TADs were markedly enriched in trimethylation of lysine 27 of histone 3 (H3K27me3).”  “Trans sister contacts were particularly enriched at many TAD boundaries.“  The cohesin loading factor NIPBL was homozygously tagged with auxin-inducible degrons to deplete loop-forming cohesin.  “Loop-forming cohesin is necessary to separate sister chromatids within TADs, resulting in locally enriched sister-chromatid contacts at TAD boundaries.”   Sororin was homozygously tagged with AID to deplete the pool of cohesin that mediates sister-chromatid cohesion.  “The sororin-stabilized pool of cohesin is [...] not required to form intra-chromatid loops or TADs in G2, but it is required to prevent the separation of sister chromatids and to maintain their global alignment during the G2 phase.”"]]
diff --git a/biblio/32989159.mdwn b/biblio/32989159.mdwn
new file mode 100644
index 00000000..0ae5dbff
--- /dev/null
+++ b/biblio/32989159.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Characterization and engineering of a two-enzyme system for plastics depolymerization."]]
+[[!tag microplastic structure]]
+
+Knott BC, Erickson E, Allen MD, Gado JE, Graham R, Kearns FL, Pardo I, Topuzlu E, Anderson JJ, Austin HP, Dominick G, Johnson CW, Rorrer NA, Szostkiewicz CJ, Copié V, Payne CM, Woodcock HL, Donohoe BS, Beckham GT, McGeehan JE.
+
+Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25476-25485. doi:10.1073/pnas.2006753117
+
+Characterization and engineering of a two-enzyme system for plastics depolymerization.
+
+[[!pmid 32989159 desc="“No MHETase activity was detected for [mono(2-hydroxyethyl)-isophthalate (MHEI) and mono(2-hydroxyethyl)-furanoate (MHEF)].”  “Degradation scales with PETase loading and the presence of MHETase, even at low concentrations relative to PETase, improves total degradation.”  “Chimeric proteins covalently linking the C terminus of MHETase to the N terminus of PETase, using flexible glycine-serine linkers of 8, 12, and 20 total glycine and serine residues, were generated.”  “When comparing the extent of degradation achieved by PETase alone, MHETase alone, and an equimolar mix of PETase and MHETase, the chimeric proteins outperform PETase, as well as the mixed reaction containing both PETase and MHETase unlinked in solution.”"]]
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index b94dae10..a788a748 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -12,4 +12,7 @@ Hiraga, Taniguchi, Yoshida, Kimura and Oda K proposed in
 a biological recycling of plastic.  They also underlined that salt-tolerating
 enzymes would be needed for bioremediation of oceans.
 
+[[Knott and coll, 2020|biblio/32989159]] showed that a chimeric MHETase:PETase
+protein is more efficient than the two free enzymes.
+
 [[!inline pages="tagged(microplastic)" limit=0]]

creating tag page tags/PETM
diff --git a/tags/PETM.mdwn b/tags/PETM.mdwn
new file mode 100644
index 00000000..83645ecb
--- /dev/null
+++ b/tags/PETM.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged PETM"]]
+
+[[!inline pages="tagged(PETM)" actions="no" archive="yes"
+feedshow=10]]