Dernières modifications :

Minor.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 31050f3..7a33481 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -139,7 +139,7 @@ Physiology
  - Most members of retinoic acid pathway gene network (biosynthesis, signalling
    and degradation) are lost in _O. dioica_.  Some of the remaining ones show
    signs of neofunctionalisation or specialisation in their ancestral activity in
-   digestion or chemical defence. ([[Martí-Solans et al., 2016|biblio/27406791]]) 
+   digestion or chemical defence ([[Martí-Solans et al., 2016|biblio/27406791]]).
 
 
 Phenotypes
@@ -157,7 +157,7 @@ Ecology
 
  - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans
    ([[Bouquet et al., 2018|biblio/29298334]]).
- - _O. Dioica_ has “a very large mutation rate, and/or a very large effective
+ - _O. dioica_ has “a very large mutation rate, and/or a very large effective
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).
 

Syntax.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index affc1fb..31050f3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -139,7 +139,7 @@ Physiology
  - Most members of retinoic acid pathway gene network (biosynthesis, signalling
    and degradation) are lost in _O. dioica_.  Some of the remaining ones show
    signs of neofunctionalisation or specialisation in their ancestral activity in
-   digestion or chemical defence. ([Martí-Solans et al., 2016|biblio/27406791]) 
+   digestion or chemical defence. ([[Martí-Solans et al., 2016|biblio/27406791]]) 
 
 
 Phenotypes

RA
diff --git a/biblio/27406791.mdwn b/biblio/27406791.mdwn
new file mode 100644
index 0000000..1ac5037
--- /dev/null
+++ b/biblio/27406791.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate."]]
+[[!tag Oikopleura]]
+
+Martí-Solans J, Belyaeva OV, Torres-Aguila NP, Kedishvili NY, Albalat R, Cañestro C. 
+
+Mol Biol Evol. 2016 Sep;33(9):2401-16. doi:10.1093/molbev/msw118 
+
+Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate. 
+
+[[!pmid 27406791 desc="Some genes are lost (_Aldh1a_, _Cyp26_, _Rdh10_, _Rdh16_, and _Bco1_) and others show signs of neofunctionalisation (_RdhE2_, _Aldh8a1_). “_O. dioica_ did not contain atRA at concentrations that were likely to play any role in developmental or physiological processes.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b9deb05..affc1fb 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -136,6 +136,11 @@ Physiology
  - Adh3 is the only medium-chain alcohol dehydrogenase (MDR-Adh) in _Oikopleura_
    (like in other non-vertebrates).  Conservation of critical residues and similarity
    in expression pattern suggest that its metabolic targets are the same as in other species.
+ - Most members of retinoic acid pathway gene network (biosynthesis, signalling
+   and degradation) are lost in _O. dioica_.  Some of the remaining ones show
+   signs of neofunctionalisation or specialisation in their ancestral activity in
+   digestion or chemical defence. ([Martí-Solans et al., 2016|biblio/27406791]) 
+
 
 Phenotypes
 ----------

creating tag page tags/Helicos
diff --git a/tags/Helicos.mdwn b/tags/Helicos.mdwn
new file mode 100644
index 0000000..1244247
--- /dev/null
+++ b/tags/Helicos.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Helicos"]]
+
+[[!inline pages="tagged(Helicos)" actions="no" archive="yes"
+feedshow=10]]

Tag.
diff --git a/biblio/18388294.mdwn b/biblio/18388294.mdwn
index 4c1f680..34e1bb6 100644
--- a/biblio/18388294.mdwn
+++ b/biblio/18388294.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Single-molecule DNA sequencing of a viral genome."]]
-[[!tag sequencing]]
+[[!tag sequencing Helicos]]
 [[!pmid 18388294 desc="Primary paper for Helicos sequencing."]]

HeliScopeCAGE.
diff --git a/biblio/21596820.mdwn b/biblio/21596820.mdwn
new file mode 100644
index 0000000..340bdb9
--- /dev/null
+++ b/biblio/21596820.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Unamplified cap analysis of gene expression on a single-molecule sequencer."]]
+[[!tag CAGE Helicos sequence_tag method]]
+
+Genome Res. 2011 Jul;21(7):1150-9. doi:10.1101/gr.115469.110
+
+Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y.
+
+Unamplified cap analysis of gene expression on a single-molecule sequencer.
+
+[[!pmid 21596820 desc="HeliScopeCAGE, a CAGE method for the Helicos sequencers.  Actinomycin D was added to the reverse-transcription to prevent antisense artefacts."]]

Ahmad 2018.
diff --git a/tags/EcoP15I.mdwn b/tags/EcoP15I.mdwn
index 7b3104f..a6f23cb 100644
--- a/tags/EcoP15I.mdwn
+++ b/tags/EcoP15I.mdwn
@@ -6,6 +6,7 @@ A few facts about EcoP15I
  - Cleavage is impaired by proteins bound between the sites [[Meisel et al., 1995|biblio/7796821]].
  - Positive bias for adenine stretches on the 5′ or 3′ side of CAGCAG [[Möncke-Buchner et al., 2009|biblio/19250940]].
  - Stimulated by AdoMet and sinefungin [[Raghavendra & Rao, 2005|biblio/16026759]].
+ - Single-site cleavage is possible with higher concentration of enzyme ([[Ahmad and co., 2018|biblio/29846668]]).
 
 Used in [[SuperSAGE|biblio/14676315]], [[HELP-tagging|biblio/20359321]], [[nanoCAGE|biblio/20543846]], [[CAGE|biblio/22362160]].  (non-exhaustive list)
 

Au bureau.
diff --git a/biblio/29846668.mdwn b/biblio/29846668.mdwn
new file mode 100644
index 0000000..5fbc74d
--- /dev/null
+++ b/biblio/29846668.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated."]]
+[[!tag EcoP15I]]
+
+Ahmad I, Kulkarni M, Gopinath A, Saikrishnan K.
+
+Nucleic Acids Res. 2018 Jul 6;46(12):6229-6237. doi:10.1093/nar/gky344
+
+Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated.
+
+[[!pmid 29846668 desc="Single-site cleavage happens by cooperation between activated enzymes contacting each other by 3D diffusion, and therefore requires higher concentrations of enzyme than two-site cleavage, where contacts happen through 1D diffusion or looping."]]

In English.
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.en.po" "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
index 8ef8f5d..c139ef1 100644
--- "a/Debian/debi\303\242neries/no-debconf-2018.en.po"
+++ "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2018-07-09 21:07+0000\n"
-"PO-Revision-Date: 2018-07-10 05:51+0900\n"
+"PO-Revision-Date: 2018-07-10 06:08+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -32,11 +32,10 @@ msgid "[[!tag Debian]]\n"
 msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+#, no-wrap
 msgid "[[!meta title=\"Debconf cette année, c'est râpé.\"]]\n"
 msgstr ""
-"[[!meta title=\"Debconf cette année, c'est râpé.\n"
+"[[!meta title=\"Still not going to Debconf....\n"
 "\"]]\n"
 
 #. type: Plain text
@@ -48,6 +47,10 @@ msgid ""
 "décalage horaire, mais voilà, je vais déménager au même moment, à Okinawa, le\n"
 "premier août.\n"
 msgstr ""
+"I was looking forward to this year's [Debconf in\n"
+"Taiwan](https://debconf18.debconf.org/), the first in Asia, and the perspective\n"
+"of attending it with no jet lag, but I happen to be moving to Okinawa and\n"
+"changing jobs on August 1<sup>st</sup>, right at the middle of it...\n"
 
 #. type: Plain text
 msgid ""
@@ -55,6 +58,10 @@ msgid ""
 "de la mélancolie pour ce et ceux que nous allons quitter.  Mais il y a des "
 "vols très bon marché pour Tôkyô et Yokohama..."
 msgstr ""
+"Moving is a mixed feeling of happiness and excitation for what I am about\n"
+"to find, and melancholy about what and whom I am about to leave.  But "
+"flights\n"
+"to Tôkyô and Yokohama are very affordable."
 
 #. type: Plain text
 msgid ""
@@ -62,3 +69,6 @@ msgid ""
 "tokyodebian-team.pages.debian.net/), où ma première clé GPG a été signée par "
 "des développeurs Debian il y a fort longtemps."
 msgstr ""
+"Special thanks to the [Tôkyô Debian study\n"
+"group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key\n"
+"signed by Debian developers a long time ago :)"

updated PO files
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.en.po" "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
index ca61ee0..8ef8f5d 100644
--- "a/Debian/debi\303\242neries/no-debconf-2018.en.po"
+++ "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
@@ -3,59 +3,62 @@
 # 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: 2018-07-09 20:46+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"
+"Project-Id-Version: \n"
+"POT-Creation-Date: 2018-07-09 21:07+0000\n"
+"PO-Revision-Date: 2018-07-10 05:51+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"
+"X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+msgid "[[!meta title=\"Debconf cette année, c'est râpé.\"]]\n"
 msgstr ""
+"[[!meta title=\"Debconf cette année, c'est râpé.\n"
+"\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid ""
-"I was looking forward to this year's [Debconf in\n"
-"Taiwan](https://debconf18.debconf.org/), the first in Asia, and the "
-"perspective\n"
-"of attending it with no jet lag, but I happen to be moving to Okinawa and\n"
-"changing jobs on August 1<sup>st</sup>, right at the middle of it...\n"
+"Je me réjouissais de la tenue de la [18<sup>ème</sup> conférence Debian à\n"
+"Taiwan](https://debconf18.debconf.org/), pour la première fois en Asie, en\n"
+"espérant y participer pour la première fois aussi et profiter de l'absence de\n"
+"décalage horaire, mais voilà, je vais déménager au même moment, à Okinawa, le\n"
+"premier août.\n"
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"Moving is a mixed feeling of happiness and excitation for what I am about to "
-"find, and melancholy about what and whom I am about to leave.  But flights "
-"to Tôkyô and Yokohama are very affordable."
+"Ce déménagement me donne de la joie pour ce que je vais rejoindre mais aussi "
+"de la mélancolie pour ce et ceux que nous allons quitter.  Mais il y a des "
+"vols très bon marché pour Tôkyô et Yokohama..."
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"Special thanks to the [Tôkyô Debian study "
-"group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key "
-"signed by Debian developers a long time ago :)"
+"Spéciale dédicace pour le [cercle d'étude Debian de Tôkyô](https://"
+"tokyodebian-team.pages.debian.net/), où ma première clé GPG a été signée par "
+"des développeurs Debian il y a fort longtemps."
 msgstr ""

En français, nom de Dieu !
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.mdwn" "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
index b8d9a60..f47a826 100644
--- "a/Debian/debi\303\242neries/no-debconf-2018.mdwn"
+++ "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
@@ -2,17 +2,19 @@
 [[!meta updated="Tue, 10 Jul 2018 05:35:20 +0900"]]
 [[!tag Debian]]
 
-[[!meta title="Not going to Debconf this year."]]
+[[!meta title="Debconf cette année, c'est râpé."]]
 
-I was looking forward to this year's [Debconf in
-Taiwan](https://debconf18.debconf.org/), the first in Asia, and the perspective
-of attending it with no jet lag, but I happen to be moving to Okinawa and
-changing jobs on August 1<sup>st</sup>, right at the middle of it...
+Je me réjouissais de la tenue de la [18<sup>ème</sup> conférence Debian à
+Taiwan](https://debconf18.debconf.org/), pour la première fois en Asie, en
+espérant y participer pour la première fois aussi et profiter de l'absence de
+décalage horaire, mais voilà, je vais déménager au même moment, à Okinawa, le
+premier août.
 
-Moving is a mixed feeling of happiness and excitation for what I am about
-to find, and melancholy about what and whom I am about to leave.  But flights
-to Tôkyô and Yokohama are very affordable.
+Ce déménagement me donne de la joie pour ce que je vais rejoindre mais aussi de
+la mélancolie pour ce et ceux que nous allons quitter.  Mais il y a des vols
+très bon marché pour Tôkyô et Yokohama...
+
+Spéciale dédicace pour le [cercle d'étude Debian de
+Tôkyô](https://tokyodebian-team.pages.debian.net/), où ma première clé GPG a
+été signée par des développeurs Debian il y a fort longtemps.
 
-Special thanks to the [Tôkyô Debian study
-group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key
-signed by Debian developers a long time ago :)

updated PO files
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.en.po" "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
new file mode 100644
index 0000000..ca61ee0
--- /dev/null
+++ "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
@@ -0,0 +1,61 @@
+# 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: 2018-07-09 20:46+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, 10 Jul 2018 05:35:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"I was looking forward to this year's [Debconf in\n"
+"Taiwan](https://debconf18.debconf.org/), the first in Asia, and the "
+"perspective\n"
+"of attending it with no jet lag, but I happen to be moving to Okinawa and\n"
+"changing jobs on August 1<sup>st</sup>, right at the middle of it...\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Moving is a mixed feeling of happiness and excitation for what I am about to "
+"find, and melancholy about what and whom I am about to leave.  But flights "
+"to Tôkyô and Yokohama are very affordable."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Special thanks to the [Tôkyô Debian study "
+"group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key "
+"signed by Debian developers a long time ago :)"
+msgstr ""

Je n'irai pas à Debconf.
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.mdwn" "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
new file mode 100644
index 0000000..b8d9a60
--- /dev/null
+++ "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
@@ -0,0 +1,18 @@
+[[!meta date="Tue, 10 Jul 2018 05:35:20 +0900"]]
+[[!meta updated="Tue, 10 Jul 2018 05:35:20 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Not going to Debconf this year."]]
+
+I was looking forward to this year's [Debconf in
+Taiwan](https://debconf18.debconf.org/), the first in Asia, and the perspective
+of attending it with no jet lag, but I happen to be moving to Okinawa and
+changing jobs on August 1<sup>st</sup>, right at the middle of it...
+
+Moving is a mixed feeling of happiness and excitation for what I am about
+to find, and melancholy about what and whom I am about to leave.  But flights
+to Tôkyô and Yokohama are very affordable.
+
+Special thanks to the [Tôkyô Debian study
+group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key
+signed by Debian developers a long time ago :)

Ein prosit.
diff --git a/biblio/20141418.mdwn b/biblio/20141418.mdwn
new file mode 100644
index 0000000..c2f2dba
--- /dev/null
+++ b/biblio/20141418.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oikopleura dioica alcohol dehydrogenase class 3 provides new insights into the evolution of retinoic acid synthesis in chordates."]]
+[[!tag Oikopleura metabolism]]
+
+Zoolog Sci. 2010 Feb;27(2):128-33. doi:10.2108/zsj.27.128.
+
+Oikopleura dioica alcohol dehydrogenase class 3 provides new insights into the evolution of retinoic acid synthesis in chordates. 
+
+Cañestro C, Albalat R, Postlethwait JH.
+
+[[!pmid 20141418 desc="Adh3 is the only MDR-Adh in the _Oikopleura_ genome. It strictly conserves the eight residues that constitute the signature of all Adh3 and other residues as well, therefore probably metabolising the same types of substrates as in other species.  (Adh3 is the ancestral MDR-Adh genes in vertebrates; Adh1, 2 and 4 show signs of neofunctionalisation)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1466f8a..b9deb05 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -133,7 +133,9 @@ Physiology
 
  - Searching for an immune system, [[Denoeud et al., 2010|biblio/21097902]] excluded
    LRR proteins, as none of the 74 models found had a transmembrane domain.
-
+ - Adh3 is the only medium-chain alcohol dehydrogenase (MDR-Adh) in _Oikopleura_
+   (like in other non-vertebrates).  Conservation of critical residues and similarity
+   in expression pattern suggest that its metabolic targets are the same as in other species.
 
 Phenotypes
 ----------

Train et café
diff --git a/biblio/28115992.mdwn b/biblio/28115992.mdwn
new file mode 100644
index 0000000..3a7c736
--- /dev/null
+++ b/biblio/28115992.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Sex-specific chromatin landscapes in an ultra-compact chordate genome."]]
+[[!tag Oikopleura epigenetic]]
+
+Navratilova P, Danks GB, Long A, Butcher S, Manak JR, Thompson EM.
+
+Epigenetics Chromatin. 2017 Jan 17;10:3. doi:10.1186/s13072-016-0110-4
+
+Sex-specific chromatin landscapes in an ultra-compact chordate genome.
+
+[[!pmid 28115992 desc="Chromatin domains usually smaller than 7 nucleosomes."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c2fd16c..1466f8a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -49,6 +49,7 @@ Genome
    indistinguishable from random for distances smaller than 30 genes and a modest
    level of conserved synteny at larger distances.” ([[Denoeud et al.,
    2010|biblio/21097902]])
+ - Chromatin domains are rarely longer than 7 nucleosomes ([Navratilova et al., 2017|biblio/28115992]).
  - The entire machinery required for performing NHEJ repair of DSB (which is
    conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).

creating tag page tags/vaccine
diff --git a/tags/vaccine.mdwn b/tags/vaccine.mdwn
new file mode 100644
index 0000000..097a68e
--- /dev/null
+++ b/tags/vaccine.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged vaccine"]]
+
+[[!inline pages="tagged(vaccine)" actions="no" archive="yes"
+feedshow=10]]

Ce matin.
diff --git a/biblio/29720524.mdwn b/biblio/29720524.mdwn
new file mode 100644
index 0000000..9dcb634
--- /dev/null
+++ b/biblio/29720524.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High Rate of Infection by Only Oncogenic Human Papillomavirus in Amerindians."]]
+[[!tag HPV vaccine]]
+
+mSphere. 2018 May 2;3(3). pii: e00176-18 doi:10.1128/mSphere.00176-18
+
+Vargas-Robles D, Magris M, Morales N, de Koning MNC, Rodríguez I, Nieves T, Godoy-Vitorino F, Sánchez GI, Alcaraz LD, Forney LJ, Pérez ME, García-Briceño L, van Doorn LJ, Domínguez-Bello MG.
+
+High Rate of Infection by Only Oncogenic Human Papillomavirus in Amerindians.
+
+[[!pmid 29720524 desc="HPV 39 is highly prevalent in Amerindians from the Amazonas state of Venezuela, but is not included in contemporary vaccines."]]
diff --git a/tags/FACS.mdwn b/tags/FACS.mdwn
deleted file mode 100644
index 1fa1cf2..0000000
--- a/tags/FACS.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged FACS"]]
-
-[[!inline pages="tagged(FACS)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/cytometry
diff --git a/tags/cytometry.mdwn b/tags/cytometry.mdwn
new file mode 100644
index 0000000..132707d
--- /dev/null
+++ b/tags/cytometry.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged cytometry"]]
+
+[[!inline pages="tagged(cytometry)" actions="no" archive="yes"
+feedshow=10]]

Correct tags.
diff --git a/biblio/22668417.mdwn b/biblio/22668417.mdwn
index 1b4665a..aa2b50a 100644
--- a/biblio/22668417.mdwn
+++ b/biblio/22668417.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain."]]
-[[!tag trehalose FACS]]
+[[!tag trehalose cytometry]]
 
 Saxena A, Wagatsuma A, Noro Y, Kuji T, Asaka-Oba A, Watahiki A, Gurnot C, Fagiolini M, Hensch TK, Carninci P.
 
diff --git a/biblio/29903975.mdwn b/biblio/29903975.mdwn
index a7e5d2e..083ac1f 100644
--- a/biblio/29903975.mdwn
+++ b/biblio/29903975.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Ghost cytometry."]]
-[[!tag imaging method FACS]]
+[[!tag single_cell imaging cytometry]]
 
 Ota S, Horisaki R, Kawamura Y, Ugawa M, Sato I, Hashimoto K, Kamesawa R, Setoyama K, Yamaguchi S, Fujiu K, Waki K, Noji H.
 

Café
diff --git a/biblio/29903975.mdwn b/biblio/29903975.mdwn
new file mode 100644
index 0000000..a7e5d2e
--- /dev/null
+++ b/biblio/29903975.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ghost cytometry."]]
+[[!tag imaging method FACS]]
+
+Ota S, Horisaki R, Kawamura Y, Ugawa M, Sato I, Hashimoto K, Kamesawa R, Setoyama K, Yamaguchi S, Fujiu K, Waki K, Noji H.
+
+Science. 2018 Jun 15;360(6394):1246-1251. doi:10.1126/science.aan0096
+
+Ghost cytometry.
+
+[[!pmid 29903975 desc="Single-pixel imaging."]]

creating tag page tags/proteomics
diff --git a/tags/proteomics.mdwn b/tags/proteomics.mdwn
new file mode 100644
index 0000000..46d762e
--- /dev/null
+++ b/tags/proteomics.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged proteomics"]]
+
+[[!inline pages="tagged(proteomics)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/peroxydase
diff --git a/tags/peroxydase.mdwn b/tags/peroxydase.mdwn
new file mode 100644
index 0000000..77be76b
--- /dev/null
+++ b/tags/peroxydase.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged peroxydase"]]
+
+[[!inline pages="tagged(peroxydase)" actions="no" archive="yes"
+feedshow=10]]

Proteomics
diff --git a/biblio/21483721.mdwn b/biblio/21483721.mdwn
index 40571a4..3cc66b2 100644
--- a/biblio/21483721.mdwn
+++ b/biblio/21483721.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms."]]
-[[!tag method microscopy]]
+[[!tag method peroxydase microscopy]]
 
 PLoS Biol. 2011 Apr;9(4):e1001041. doi:10.1371/journal.pbio.1001041.
 
diff --git a/biblio/23086203.mdwn b/biblio/23086203.mdwn
new file mode 100644
index 0000000..92d5ebb
--- /dev/null
+++ b/biblio/23086203.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy."]]
+[[!tag microscopy peroxydase method]]
+
+Nat Biotechnol. 2012 Nov;30(11):1143-8. doi:10.1038/nbt.2375
+
+Martell JD, Deerinck TJ, Sancak Y, Poulos TL, Mootha VK, Sosinsky GE, Ellisman MH, Ting AY.
+
+Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy.
+
+[[!pmid 23086203 desc="APEX: a “genetically encodable EM tag that is active in all cellular compartments and does not require light APEX is a monomeric 28-kDa peroxidase that withstands strong EM fixation to give excellent ultrastructural preservation”."]]
diff --git a/biblio/23371551.mdwn b/biblio/23371551.mdwn
new file mode 100644
index 0000000..4c76810
--- /dev/null
+++ b/biblio/23371551.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging."]]
+[[!tag peroxydase method proteomics]]
+
+Science. 2013 Mar 15;339(6125):1328-1331. doi:10.1126/science.1230593
+
+Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY.
+
+Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.
+
+[[!pmid 23371551 desc="Uses APEX to bind biotin-phenol tags to proteins."]]
diff --git a/biblio/28751582.mdwn b/biblio/28751582.mdwn
index 58a2e12..61a2a4d 100644
--- a/biblio/28751582.mdwn
+++ b/biblio/28751582.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells."]]
-[[!tag method chromatin microscopy]]
+[[!tag method peroxydase chromatin microscopy]]
 
 Science. 2017 Jul 28;357(6349). pii: eaag0025. doi:10.1126/science.aag0025.
 
diff --git a/biblio/29735996.mdwn b/biblio/29735996.mdwn
new file mode 100644
index 0000000..a4de362
--- /dev/null
+++ b/biblio/29735996.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2."]]
+[[!tag peroxydase method proteomics]]
+
+Nat Methods. 2018 May 7. doi:10.1038/s41592-018-0006-2
+
+Gao XD, Tu LC, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu
+LJ, Wolfe SA, Sontheimer EJ.
+
+C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.
+
+[[!pmid 29735996 desc="Links APEX2 to Cas9 in order to label protein near target loci.  dCas9-APEX2 biotinylation at genomic elements by restricted spatial tagging (C-BERST)"]]
diff --git a/biblio/29735997.mdwn b/biblio/29735997.mdwn
new file mode 100644
index 0000000..68a28af
--- /dev/null
+++ b/biblio/29735997.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling."]]
+[[!tag proteomics peroxydase method]]
+
+Myers SA, Wright J, Peckner R, Kalish BT, Zhang F, Carr SA
+
+Nat Methods. 2018 May 7. doi:10.1038/s41592-018-0007-1
+
+Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling.
+
+[[!pmid 29735997 desc="Genomic locus proteomics (GLoPro) uses dCas9 to localise APEX to specific loci, where it will biotinylate the proteins in proximity."]]

Quotes from the genome paper.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1923e9b..c2fd16c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -64,9 +64,25 @@ Genome
    et al., 2008|biblio/19030770]], [[Denoeud et al., 2010|biblio/21097902]]).
    It is found in _Ciona_ but not in _C. elegans_ ()[[Martz et al.,
    2008|biblio/19030770]]. The major spliceosome is hypothethised to have evolved
-   to become more permissive in order to splice G*-AG sites ([[Denoeud et al., 2010|biblio/21097902]]).
+   to become more permissive in order to splice G*-AG sites.  ”A large fraction
+   (more than 10%) of the (...) introns displayed non-canonical (non GT-AG)
+   splice sites, whereas the usual proportion is around 1%-1.5% in other genomes”
+   ([[Denoeud et al., 2010|biblio/21097902]]).
  - Operons are enriched for houskeeping genes and depleted for developmental genes
    ([[Denoeud et al., 2010|biblio/21097902]]).
+ - “LTR retrotransposons account for a significant part of the indel polymorphism in the Oikopleura genome.”
+   “Tor-3G elements are frequently inserted into exons and can be transcribed
+    together with their host gene, although transcripts initiated in the LTR
+    are also detected (Figure S11).”
+   “The low allelic frequency of Tor-3G insertions is correlated with the
+    almost exclusive occurrence of heterozygous genotypes in the populations.
+    Moreover, experimental crosses between selected heterozygous parents for
+    the same insertion have thus far not resulted in homozygous offsprings.”
+    ([[Denoeud et al., 2010|biblio/21097902]]).
+ - ”Highly conserved elements (HCEs) lie around these developmental genes.”
+   “Spots of sequence ultraconservation are almost systematically located
+    in non coding regions, including introns that are larger than average
+    in such genes than in others.” ([[Denoeud et al., 2010|biblio/21097902]]).
 
 
 Transcriptome

Café
diff --git a/biblio/29734294.mdwn b/biblio/29734294.mdwn
new file mode 100644
index 0000000..0f0a869
--- /dev/null
+++ b/biblio/29734294.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Multiplexed precision genome editing with trackable genomic barcodes in yeast."]]
+[[!tag CRISPR yeast screen method]]
+
+Nat Biotechnol. 2018 Jul;36(6):512-520. doi:10.1038/nbt.4137
+
+Roy KR, Smith JD, Vonesch SC, Lin G, Tu CS, Lederer AR, Chu A, Suresh S, Nguyen M, Horecka J, Tripathi A, Burnett WT, Morgan MA, Schulz J, Orsley KM, Wei W, Aiyar RS, Davis RW, Bankaitis VA, Haber JE, Salit ML, St Onge RP, Steinmetz LM,
+
+Multiplexed precision genome editing with trackable genomic barcodes in yeast.
+
+[[!pmid 29734294 desc="Multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) uses plasmids providing homologous recombination arms and expressing CRISPR-Cas9 guides.  Recombination rates are further enhanced by LexA sites on the plasmid recruiting a LexA-Fkh1p fusion protein."]]

Avant le café
diff --git a/biblio/29734295.mdwn b/biblio/29734295.mdwn
new file mode 100644
index 0000000..9ce057a
--- /dev/null
+++ b/biblio/29734295.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision."]]
+[[!tag CRISPR method screen yeast]]
+
+Nat Biotechnol. 2018 Jul;36(6):505-508. doi:10.1038/nbt.4132
+
+Bao Z, HamediRad M, Xue P, Xiao H, Tasan I, Chao R, Liang J, Zhao H.
+
+Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision.
+
+[[!pmid 29734295 desc="CRISPR–Cas9- and homology-directed-repair (HDR)-assisted genome-scale engineering (CHAnGE) uses plasmids containing HR arms to frameshift or point-mutate precise locations, which are cleaved by Cas9 using a guide RNA expressed by the same plasmid.  Plasmid libraries are made by cloning libraries of long oligonucleotides synthesised on microarrays."]]

Long introns.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cb71b32..1923e9b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -81,11 +81,13 @@ Transcriptome
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
- - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb) [[Denoeud et
-   al., 2010|biblio/21097902]] and subjected to a large turnover: many ancestral
+ - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb, [[Denoeud et
+   al., 2010|biblio/21097902]]) and subjected to a large turnover: many ancestral
    introns are lost, and many new species-specific introns found ([[Edvarsen et
    al., 2004|biblio/15638456]]).  Introns are gained by insertion of transposon-like elements and
-   by reverse splicing, ([[Denoeud et al., 2010|biblio/21097902]]).  
+   by reverse splicing, ([[Denoeud et al., 2010|biblio/21097902]]).  Larger introns tend
+   to be older, and among the large introns, the older contain repeat elements less frequently
+   than the newer ([[Denoeud et al., 2010|biblio/21097902]]). 
 
 
 Tools

Operons.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0aa8394..cb71b32 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -65,6 +65,8 @@ Genome
    It is found in _Ciona_ but not in _C. elegans_ ()[[Martz et al.,
    2008|biblio/19030770]]. The major spliceosome is hypothethised to have evolved
    to become more permissive in order to splice G*-AG sites ([[Denoeud et al., 2010|biblio/21097902]]).
+ - Operons are enriched for houskeeping genes and depleted for developmental genes
+   ([[Denoeud et al., 2010|biblio/21097902]]).
 
 
 Transcriptome

Developmental genes.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6fe6f38..0aa8394 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -66,6 +66,7 @@ Genome
    2008|biblio/19030770]]. The major spliceosome is hypothethised to have evolved
    to become more permissive in order to splice G*-AG sites ([[Denoeud et al., 2010|biblio/21097902]]).
 
+
 Transcriptome
 -------------
 
@@ -90,15 +91,20 @@ Tools
 
  - DNAi was used to screen for maternal genes ([[Omotezako et al., 2017|biblio/28281645]]).
 
+
 Development
 -----------
 
- - The Oikopleura CNS possesses homologs of the vertebrate forebrain,
+ - The _Oikopleura_ CNS possesses homologs of the vertebrate forebrain,
    hindbrain, and spinal cord, but not the midbrain.  No expression of
    _pax2/5/8_ is detected between the _otxa_ + _otxb_ and the _hox1_ territories.
    ([[Cañestro et al., 2005|biblio/16111672]]).
  - The _pum1_ and _vas4_ RNAs show localised expression during development. Prior
    hatching, _pum1_ is found outside the embryo ([[Olsen et al., 2018|biblio/29486709]]).
+ - Duplicated developmental genes were found by [[Denoeud et al., 2010|biblio/21097902]],
+   who noted that it is exceptional in invertebrates, and hypothethise that it may
+   be caused by neofunctionalisation (house production, ...) or by the small size of
+   the genome (doubling the genes would then double the amount of regulatory sequences).
 
 
 Physiology

Immunity.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 78bfbb3..6fe6f38 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -101,6 +101,13 @@ Development
    hatching, _pum1_ is found outside the embryo ([[Olsen et al., 2018|biblio/29486709]]).
 
 
+Physiology
+----------
+
+ - Searching for an immune system, [[Denoeud et al., 2010|biblio/21097902]] excluded
+   LRR proteins, as none of the 74 models found had a transmembrane domain.
+
+
 Phenotypes
 ----------
 

Population size.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index dace30b..78bfbb3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -114,7 +114,11 @@ Phenotypes
 Ecology
 -------
 
- - O. dioica populations may have a higher fitness in warmer and more acid oceans
+ - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans
    ([[Bouquet et al., 2018|biblio/29298334]]).
+ - _O. Dioica_ has “a very large mutation rate, and/or a very large effective
+   population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
+   of silent and non-silent substitution rates in coding sequences).
+
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

How many species ?
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0260969..dace30b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -19,7 +19,7 @@ Some links:
  - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/>
 
 
-Evolution
+Phylogeny
 ---------
 
  - Based on 18S rRNA sequences from 110 species including 4 Oikopleuridae, this
@@ -29,6 +29,10 @@ Evolution
  - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]])
    and then 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
    show that Oikopleuridae is basal to all other tunicates.
+ - “The difference between coding sequences was considerably higher in
+   comparisons between strains of different oceans than within the Bergen gene
+   pool.  We ignore whether and how Oikopleura dioica is subdivided into multiple
+   species” ([[Denoeud et al., 2010|biblio/21097902]]).
 
 
 Genome

No minor spliceosome.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index fea0925..0260969 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -56,7 +56,11 @@ Genome
    in human.
  - Analysis of sex-linked markers supports genetic sex determination with male heterogamety –
    that is: X chromosomes for females and Y for males.  ([[Denoeud et al., 2010|biblio/21097902]])
-
+ - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Martz
+   et al., 2008|biblio/19030770]], [[Denoeud et al., 2010|biblio/21097902]]).
+   It is found in _Ciona_ but not in _C. elegans_ ()[[Martz et al.,
+   2008|biblio/19030770]]. The major spliceosome is hypothethised to have evolved
+   to become more permissive in order to splice G*-AG sites ([[Denoeud et al., 2010|biblio/21097902]]).
 
 Transcriptome
 -------------

Merge to items.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 19af857..fea0925 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -35,9 +35,10 @@ Genome
 ------
 
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
- - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
- - A genome was assembled from the shotgun sequencing of sperm DNA from ~200 partially
-   inbred males (11 successive sib-matings).  Two distinct haplotypes were found
+ - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al,
+   2001|biblio/11752568]].  A 70.4 Mb genome "reference assembly" was later
+   produced from the shotgun sequencing of sperm DNA from ~200 partially inbred
+   males (11 successive sib-matings).  Two distinct haplotypes were found
    ([[Denoeud et al., 2010|biblio/21097902]]).
  - “No signal of synteny conservation is detected between _Oikopleura_ and _Ciona
    intestinalis_. (...) _Oikopleura_ showed a local gene order that is

Haplotypes.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 9769a7a..19af857 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -34,8 +34,11 @@ Evolution
 Genome
 ------
 
- - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
+ - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
+ - A genome was assembled from the shotgun sequencing of sperm DNA from ~200 partially
+   inbred males (11 successive sib-matings).  Two distinct haplotypes were found
+   ([[Denoeud et al., 2010|biblio/21097902]]).
  - “No signal of synteny conservation is detected between _Oikopleura_ and _Ciona
    intestinalis_. (...) _Oikopleura_ showed a local gene order that is
    indistinguishable from random for distances smaller than 30 genes and a modest

Note on conservation of NHEJ.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6d1911b..9769a7a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -41,8 +41,8 @@ Genome
    indistinguishable from random for distances smaller than 30 genes and a modest
    level of conserved synteny at larger distances.” ([[Denoeud et al.,
    2010|biblio/21097902]])
- - The entire machinery required for performing NHEJ repair of DSB is undetectable.
-   [[Denoeud et al., 2010|biblio/21097902]]
+ - The entire machinery required for performing NHEJ repair of DSB (which is
+   conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 

Au bureau.
diff --git a/biblio/29760081.mdwn b/biblio/29760081.mdwn
new file mode 100644
index 0000000..12e6ea3
--- /dev/null
+++ b/biblio/29760081.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast."]]
+[[!tag yeast genetics evolution]]
+
+Proc Natl Acad Sci U S A. 2018 May 14. pii: 201801040. doi:10.1073/pnas.1801040115
+
+Sharp NP, Sandell L, James CG, Otto SP.
+
+The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast.
+
+[[!pmid 29760081 desc="16 generations per day for 100 days in 220 cell lines yielded 2,000 mutations, with more single-nuceotide mutations in haploids and more copy number variations in diploids."]]

X-linked markers.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f8b7363..6d1911b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -41,6 +41,8 @@ Genome
    indistinguishable from random for distances smaller than 30 genes and a modest
    level of conserved synteny at larger distances.” ([[Denoeud et al.,
    2010|biblio/21097902]])
+ - The entire machinery required for performing NHEJ repair of DSB is undetectable.
+   [[Denoeud et al., 2010|biblio/21097902]]
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
@@ -48,6 +50,8 @@ Genome
    2010|biblio/21097902]], due to cloning and sequencing difficulties that may
    have been caused by oligo-dT stretches.  A/T-rich codons are more frequent than
    in human.
+ - Analysis of sex-linked markers supports genetic sex determination with male heterogamety –
+   that is: X chromosomes for females and Y for males.  ([[Denoeud et al., 2010|biblio/21097902]])
 
 
 Transcriptome
@@ -85,6 +89,16 @@ Development
    hatching, _pum1_ is found outside the embryo ([[Olsen et al., 2018|biblio/29486709]]).
 
 
+Phenotypes
+----------
+
+ - A low-frequency variant providing natural tail fluorescence late stages
+   shortly before sexual maturation was found to have X-like inheritance
+   ([[Denoeud et al., 2010|biblio/21097902]], Fig. S20).  It deviates from
+   mendelian inheritance (Table S10), but is is recovered after sperm
+   cryopreservation of male carriers.
+
+
 Ecology
 -------
 

Genome paper.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0a7822e..f8b7363 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -36,9 +36,18 @@ Genome
 
  - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
+ - “No signal of synteny conservation is detected between _Oikopleura_ and _Ciona
+   intestinalis_. (...) _Oikopleura_ showed a local gene order that is
+   indistinguishable from random for distances smaller than 30 genes and a modest
+   level of conserved synteny at larger distances.” ([[Denoeud et al.,
+   2010|biblio/21097902]])
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
+ - Only a partial mitochondrial genome was reconstituted in [[Denoeud et al.,
+   2010|biblio/21097902]], due to cloning and sequencing difficulties that may
+   have been caused by oligo-dT stretches.  A/T-rich codons are more frequent than
+   in human.
 
 
 Transcriptome
@@ -53,8 +62,11 @@ Transcriptome
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
- - Introns are subjected to a large turnover: many ancestral introns are lost, and many
-   new species-specific introns found ([[Edvarsen et al., 2004|biblio/15638456]]).
+ - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb) [[Denoeud et
+   al., 2010|biblio/21097902]] and subjected to a large turnover: many ancestral
+   introns are lost, and many new species-specific introns found ([[Edvarsen et
+   al., 2004|biblio/15638456]]).  Introns are gained by insertion of transposon-like elements and
+   by reverse splicing, ([[Denoeud et al., 2010|biblio/21097902]]).  
 
 
 Tools

Café
diff --git a/biblio/25752748.mdwn b/biblio/25752748.mdwn
new file mode 100644
index 0000000..9983e85
--- /dev/null
+++ b/biblio/25752748.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements."]]
+[[!tag promoter enhancer chromatin mouse ES]]
+
+Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.
+
+Genome Res. 2015 Apr;25(4):582-97. doi:10.1101/gr.185272.114
+
+The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.
+
+[[!pmid 25752748 desc="Uses 39,021 bioninylated RNA baits targetting 22,225 promoters."]]

Old
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 5ccf4b1..a8ba77b 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -39,6 +39,7 @@ transcriptases have a TdT activity.
    transcriptase of the long terminal repeat retrotransposon Tf1, like other
    DNA polymerases, also adds non-templated As to blunt DNA duplexes.
 
+
 ### Templated TdT activity
 
 Surprisingly, reverse transcriptases can also extend cDNAs using a single
@@ -55,6 +56,12 @@ nucleotide as a template.
    2017b|biblio/28747695]]).
 
 
+### The 5′ cap enhances C-tailing
+
+ - [[Schmidt & Mueller, 1999|biblio/10518626]] showed that extra cytosine are
+   more frequently added in presence of the 5′ cap.
+
+
 ### The 5′ cap is reverse-transcribed
 
  - [[Hirzmann et al., 1993|biblio/8346046]] observed the presence of an extra G

Old
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 5c3a109..b78625d 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -45,7 +45,9 @@ as a replacement for RNA.
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
  - 3′ phosphate or biotin blocking groups abolish template-switching
-   ([[Turchinovich et al (2014)|biblio/24922482]] and others).
+   ([[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).
 
  - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
    of the TSO, and therefore blocks concatenation
@@ -62,10 +64,12 @@ as a replacement for RNA.
    magnesium concentration (to 6 mM) or adding manganese at the end of the
    reaction (1 or 2 mM) increased the frequency of dC addition (moderately
    for Mg<sup>2+</sup> and strongly for Mn<sup>2+</sup>).  Enzyme: SSII; dNTP
-   concentration: 1 mM each.
+   concentration: 1 mM each.  [[Pinto & Lindblad (2010)|biblio/19837043]] also
+   used manganese.
 
  - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
    switching non-capped molecules by increasing dNTPs to 2 mM and
    Mg<sup>2+</sup> to 9 mM.
 
+
 [[!inline pages="tagged(template_switching)" limit=0]]

Old.
diff --git a/biblio/19837043.mdwn b/biblio/19837043.mdwn
index 32875d4..045a852 100644
--- a/biblio/19837043.mdwn
+++ b/biblio/19837043.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="A guide for in-house design of template-switch-based 5′ rapid amplification of cDNA ends systems."]]
-[[!tag method template_switching]]
+[[!tag method template_switching manganese]]
+
+Anal Biochem. 2010 Feb 15;397(2):227-32. doi:10.1016/j.ab.2009.10.022
+
+Pinto FL, Lindblad P.
+
+A guide for in-house design of template-switch-based 5' rapid amplification of cDNA ends systems.
+
 [[!pmid 19837043 desc="Uses desoxyriboguanosine tails for template switching (but the last one is blocked by a propyl group (C3 spacer)."]]

Old.
diff --git a/biblio/21131977.mdwn b/biblio/21131977.mdwn
new file mode 100644
index 0000000..584c3e8
--- /dev/null
+++ b/biblio/21131977.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcription of functionally related constitutive genes is not coordinated."]]
+[[!tag yeast single_cell transcription]]
+
+Nat Struct Mol Biol. 2011 Jan;18(1):27-34. doi:10.1038/nsmb.1934
+
+Gandhi SJ, Zenklusen D, Lionnet T, Singer RH.
+
+Transcription of functionally related constitutive genes is not coordinated.
+
+[[!pmid 21131977 desc="Even two constitutively expressed alleles (MDN1) are not correlated.  Stoechoimetry is postulated to be acheived post-transcriptionally and post-traductionally."]]

strt
diff --git a/biblio/29180631.mdwn b/biblio/29180631.mdwn
new file mode 100644
index 0000000..85d3199
--- /dev/null
+++ b/biblio/29180631.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array."]]
+[[!tag tag library method template_switching]]
+
+Sci Rep. 2017 Nov 27;7(1):16327. doi:10.1038/s41598-017-16546-4
+
+Hochgerner H, Lönnerberg P, Hodge R, Mikes J, Heskol A, Hubschle H, Lin P, Picelli S, La Manno G, Ratz M, Dunne J, Husain S, Lein E, Srinivasan M, Zeisel A, Linnarsson S.
+
+STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.
+
+[[!pmid 29180631 desc="STRT for the icell8 platform.  SSIII better than SSIII with RNA TSO.  Optimum: ~2 μM."]]

sRNA.
diff --git a/biblio/28327113.mdwn b/biblio/28327113.mdwn
index a3dfc9d..ed6b575 100644
--- a/biblio/28327113.mdwn
+++ b/biblio/28327113.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium."]]
-[[!tag template_switching reverse_transcription]]
+[[!tag template_switching reverse_transcription sRNA]]
 
 Lee YH, Hsueh YW, Peng YH, Chang KC, Tsai KJ, Sun HS, Su IJ, Chiang PM.
 

Café
diff --git a/biblio/20598146.mdwn b/biblio/20598146.mdwn
new file mode 100644
index 0000000..9aa458f
--- /dev/null
+++ b/biblio/20598146.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples."]]
+[[!tag template_switching reverse_transcription]]
+
+BMC Genomics. 2010 Jul 2;11:413. doi:10.1186/1471-2164-11-413
+
+Kapteyn J, He R, McDowell ET, Gang DR.
+
+Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples.
+
+[[!pmid 20598146 desc="TSO starting with iCiGiC (iso-dC / iso-dG) does not form concatenates because the RTase is inhibited by these nucleotides, therefore it does not reach the end and no extra template switching occurs."]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index e7f8577..5c3a109 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -47,6 +47,10 @@ as a replacement for RNA.
  - 3′ phosphate or biotin blocking groups abolish template-switching
    ([[Turchinovich et al (2014)|biblio/24922482]] and others).
 
+ - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
+   of the TSO, and therefore blocks concatenation
+   ([[Kapteyn et al., 2010|biblio/20598146]]).
+
 ### Effect of TSO concentration
 
  - For the STRT method, [[Zajac et al (2013)|biblio/24392002]] concluded that

Corrections, simplifications.
diff --git a/biblio/15500255.mdwn b/biblio/15500255.mdwn
index abe68a2..28d781e 100644
--- a/biblio/15500255.mdwn
+++ b/biblio/15500255.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method."]]
-[[!tag cap enzyme]]
+[[!tag cap reverse_transcription]]
+
+DNA Res. 2004 Aug 31;11(4):305-9
+
+Ohtake H, Ohtoko K, Ishimaru Y, Kato S.
+
+Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method.
+
 [[!pmid 15500255 desc="ADP cap templates extra T in the first strand cDNA."]]
diff --git a/biblio/15520289.mdwn b/biblio/15520289.mdwn
index 42fcc47..6a087f0 100644
--- a/biblio/15520289.mdwn
+++ b/biblio/15520289.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity."]]
-[[!tag cap enzyme]]
+[[!tag cap reverse_transcription]]
 
 Lavie L, Maldener E, Brouha B, Meese EU, Mayer J.
 
diff --git a/biblio/22035236.mdwn b/biblio/22035236.mdwn
index cc97666..0825b78 100644
--- a/biblio/22035236.mdwn
+++ b/biblio/22035236.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Template-independent DNA synthesis activity associated with the reverse transcriptase of the long terminal repeat retrotransposon Tf1."]]
-[[!tag enzyme reverse_transcription terminal_transferase]]
+[[!tag reverse_transcription]]
 
 Oz-Gleenberg I, Herzig E, Hizi A.
 
diff --git a/biblio/8346046.mdwn b/biblio/8346046.mdwn
index a4c8180..c350725 100644
--- a/biblio/8346046.mdwn
+++ b/biblio/8346046.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Determination of messenger RNA 5'-ends by reverse transcription of the cap structure."]]
-[[!tag cap enzyme]]
+[[!tag cap reverse_transcription]]
+
+Nucleic Acids Res. 1993 Jul 25;21(15):3597-8
+
+Hirzmann J, Luo D, Hahnen J, Hobom G.
+
+Determination of messenger RNA 5'-ends by reverse transcription of the cap structure.
+
 [[!pmid 8346046 desc="The mRNA cap can template an extra C in the first strand cDNA."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index b8914e0..5ccf4b1 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -71,7 +71,7 @@ nucleotide as a template.
    sequences of retrotransposons, showing that endogenous reverse-transcriptases
    also reverse-transcribe the cap.
 
- - [[Zhang et al, 2017|biblio/28673998] published a structure of an RNA-GpppG
+ - [[Zhang et al, 2017|biblio/28673998]] published a structure of an RNA-GpppG
    complex that suggests that a m7GpppNm / DNA duplex could form during the
    reverse-transcription of the cap
 
diff --git a/tags/terminal_transferase.mdwn b/tags/terminal_transferase.mdwn
deleted file mode 100644
index 23f3c37..0000000
--- a/tags/terminal_transferase.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged terminal transferase"]]
-
-[[!inline pages="tagged(terminal_transferase)" actions="no" archive="yes"
-feedshow=10]]

The cap is reverse-transcribed.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 8719370..b8914e0 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -35,6 +35,15 @@ transcriptases have a TdT activity.
    Activity increased with concentration for MMLV.  (High-concentration AMV was
    not available.)
 
+ - [[Oz-Gleenberg et al, 2011|biblio/22035236]] showed that the the reverse
+   transcriptase of the long terminal repeat retrotransposon Tf1, like other
+   DNA polymerases, also adds non-templated As to blunt DNA duplexes.
+
+### Templated TdT activity
+
+Surprisingly, reverse transcriptases can also extend cDNAs using a single
+nucleotide as a template.
+
  - Following an initial observation of [[Clark et al (1987)|biblio/3323527]] on
    the Klenow fragment, [[Ohtsubo et al, 2017a|biblio/28150748]] showed that
    specific tailing is enhanced by the complementary dNMP (C enhanced by dGMP,
@@ -45,6 +54,28 @@ transcriptases have a TdT activity.
    tailing when longer reaction times are allowed ([[Ohtsubo et al.,
    2017b|biblio/28747695]]).
 
+
+### The 5′ cap is reverse-transcribed
+
+ - [[Hirzmann et al., 1993|biblio/8346046]] observed the presence of an extra G
+   at the 5′ end of cDNA clones, and concluded that the cap can be
+   reverse-transcribed.  They supported their conclusion with molecular modelling.
+
+ - [[Volloch et al, 1995|biblio/8534373]] studied cap transcription (but I could
+   not access the article).
+
+ - [[Ohtake et al, 2004|biblio/15500255]] synthethised RNAs with A-caps and
+   showed that they are reverse-transcribed as Ts.
+
+ - [[Lavie et al, 2004|biblio/15520289]] found extra Gs at the ends of genomic
+   sequences of retrotransposons, showing that endogenous reverse-transcriptases
+   also reverse-transcribe the cap.
+
+ - [[Zhang et al, 2017|biblio/28673998] published a structure of an RNA-GpppG
+   complex that suggests that a m7GpppNm / DNA duplex could form during the
+   reverse-transcription of the cap
+
+
 ### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].

Onigiri.
diff --git a/biblio/28747695.mdwn b/biblio/28747695.mdwn
new file mode 100644
index 0000000..816248e
--- /dev/null
+++ b/biblio/28747695.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase."]]
+[[!tag reverse_transcription]]
+
+Sci Rep. 2017 Jul 26;7(1):6520. doi:10.1038/s41598-017-04765-8
+
+Ohtsubo Y, Nagata Y, Tsuda M.
+
+Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase.
+
+[[!pmid 28747695 desc="rA, r/dG, r/dC are potent enhancers of tailing.  In longer reactions, GMP, GDP or CDP promote continuous extension of the tail.  Reactions performed with 100 fmols of substrate DNA, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 6 mM MgCl2, 2 mM DTT, 4 mM dATP, dCTP, dGTP, or dTTP, 4 mM MnCl2, and 50 U MMLV-RT, at 30 °C."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 6866b55..8719370 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -36,10 +36,15 @@ transcriptases have a TdT activity.
    not available.)
 
  - Following an initial observation of [[Clark et al (1987)|biblio/3323527]] on
-   the Klenow fragment, [[Ohtsubo et al, 2017|biblio/28150748]] showed that
+   the Klenow fragment, [[Ohtsubo et al, 2017a|biblio/28150748]] showed that
    specific tailing is enhanced by the complementary dNMP (C enhanced by dGMP,
    etc.), except for A-tailing, which is already the strongest.
 
+ - Other nucleotides than dNMPs can enhance tailing.  In particular, rA, dA, dG
+   and dC potently induce tailing, and GMP, GDP and CDP induce continuous
+   tailing when longer reaction times are allowed ([[Ohtsubo et al.,
+   2017b|biblio/28747695]]).
+
 ### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].

Normalisation.
diff --git a/biblio/28150748.mdwn b/biblio/28150748.mdwn
index 5023be5..38b0b49 100644
--- a/biblio/28150748.mdwn
+++ b/biblio/28150748.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase."]]
-[[!tag reverse-transcription]]
+[[!tag reverse_transcription]]
 
 Sci Rep. 2017 Feb 2;7:41769. doi:10.1038/srep41769
 

NMP
diff --git a/biblio/28150748.mdwn b/biblio/28150748.mdwn
new file mode 100644
index 0000000..5023be5
--- /dev/null
+++ b/biblio/28150748.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase."]]
+[[!tag reverse-transcription]]
+
+Sci Rep. 2017 Feb 2;7:41769. doi:10.1038/srep41769
+
+Ohtsubo Y, Nagata Y, Tsuda M.
+
+Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase.
+
+[[!pmid 28150748 desc="Specific tailing of first-strand cDNAs is robustly enhanced by the complementary dNMP (C enhanced by dGMP, etc.).  A-tailing is not enhanced, perhaps because it is already very strong.  Reactions made in presence of manganese; not tested with only magnesium."]]
diff --git a/biblio/3323527.mdwn b/biblio/3323527.mdwn
new file mode 100644
index 0000000..6570f75
--- /dev/null
+++ b/biblio/3323527.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli."]]
+[[!tag enzyme]]
+
+J Mol Biol. 1987 Nov 5;198(1):123-7.
+
+Clark JM, Joyce CM, Beardsley GP.
+
+Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli.
+
+[[!pmid 3323527 desc="Reports enhancement of +1 tailing by Klenow fragment with dNMPs."]]
diff --git a/biblio/7507249.mdwn b/biblio/7507249.mdwn
new file mode 100644
index 0000000..75611fe
--- /dev/null
+++ b/biblio/7507249.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Marked infidelity of human immunodeficiency virus type 1 reverse transcriptase at RNA and DNA template ends."]]
+[[!tag reverse_transcription]]
+
+Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):549-53 doi:10.1073/pnas.91.2.549
+
+Patel PH & Preston BD.
+
+Marked infidelity of human immunodeficiency virus type 1 reverse transcriptase at RNA and DNA template ends.
+
+[[!pmid 7507249 desc="On DNA/DNA blunt ends, adds a single nucleotide (A > G >> C|T).  On RNA/DNA blund ends, adds more nucleotides.  Addition is favoured by increased dNTP levels."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 696155c..6866b55 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -24,12 +24,22 @@ _(redaction in progress)_
 Like other DNA polymerases ([[Clark, 1988|biblio/2460825]]), reverse
 transcriptases have a TdT activity.
 
+ - [[Patel & Preston, 1994|biblio/7507249]] showed that HIV RT adds one
+   nucleotide (A > G >> T|C) on DNA/DNA duplexes, and more on DNA/RNA duplexes.
+   Addition is favoured by increased dNTP levels.  MMLV and AMV were also
+   reported (data not shown) to add multiple nucleotides.
+
  - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
    AMV, with a preference for adding As.  For MMLV, activity reduced abruptly
    between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.
    Activity increased with concentration for MMLV.  (High-concentration AMV was
    not available.)
 
+ - Following an initial observation of [[Clark et al (1987)|biblio/3323527]] on
+   the Klenow fragment, [[Ohtsubo et al, 2017|biblio/28150748]] showed that
+   specific tailing is enhanced by the complementary dNMP (C enhanced by dGMP,
+   etc.), except for A-tailing, which is already the strongest.
+
 ### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].

Café
diff --git a/biblio/28408603.mdwn b/biblio/28408603.mdwn
new file mode 100644
index 0000000..6de6c99
--- /dev/null
+++ b/biblio/28408603.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)."]]
+[[!tag single_cell amplification transposase genome method]]
+
+Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS.
+
+Science. 2017 Apr 14;356(6334):189-194. doi:10.1126/science.aak9787
+
+Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI).
+
+[[!pmid 28408603 desc="Tn5 tagmentation with custom adapters ending with T7 promoters, followed by linear amplification by transcription, followed by cDNA synthesis and sequencing."]]

slack
diff --git a/biblio/26152304.mdwn b/biblio/26152304.mdwn
new file mode 100644
index 0000000..41a1fb8
--- /dev/null
+++ b/biblio/26152304.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A new method to prevent carry-over contaminations in two-step PCR NGS library preparations."]]
+[[!tag library amplification method]]
+
+Seitz V, Schaper S, Dröge A, Lenze D, Hummel M, Hennig S.
+
+Nucleic Acids Res. 2015 Nov 16;43(20):e135. doi:10.1093/nar/gkv694
+
+A new method to prevent carry-over contaminations in two-step PCR NGS library preparations.
+
+[[!pmid 26152304 desc="Proposes to introduce indexes during the cDNA PCR, and to partially match them during Library PCR, so that 1) the PCR is more stringent and 2) contaminations can be detected by sequence analysis."]]

Dans le train.
diff --git a/biblio/29615780.mdwn b/biblio/29615780.mdwn
new file mode 100644
index 0000000..c0092c7
--- /dev/null
+++ b/biblio/29615780.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution."]]
+[[!tag evolution genome]]
+
+Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ.
+
+Sci Rep. 2018 Apr 3;8(1):5518. doi:10.1038/s41598-018-23749-w
+
+De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution.
+
+[[!pmid 29615780 desc="159 Mb assembly (82% of the predicted 194 Mb genome).  Comparison with other tunicates confirms extensive breakage of gene clusters."]]

Old
diff --git a/biblio/18426769.mdwn b/biblio/18426769.mdwn
new file mode 100644
index 0000000..4a9caef
--- /dev/null
+++ b/biblio/18426769.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Current techniques for single-cell lysis."]]
+[[!tag single_cell method lysis]]
+
+Brown RB, Audet J.
+
+J R Soc Interface. 2008 Oct 6;5 Suppl 2:S131-8. doi:10.1098/rsif.2008.0009.focus
+
+Current techniques for single-cell lysis.
+
+[[!pmid 18426769 desc="Does not cover lysis by heating."]]

Monophyletic chordates.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 5066380..2cd6d2d 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -7,4 +7,4 @@ Nature. 2006 Feb 23;439(7079):965-8.
 
 Tunicates and not cephalochordates are the closest living relatives of vertebrates.
 
-[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates."]]
+[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  This was refuted by Bourlat et al. in 2006.  Oikopleura is basal to other tunicates (and was not included in Bourlat et al)."]]
diff --git a/biblio/17051155.mdwn b/biblio/17051155.mdwn
new file mode 100644
index 0000000..8a0ced0
--- /dev/null
+++ b/biblio/17051155.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida."]]
+[[!tag evolution]]
+
+Bourlat SJ1, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES, Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ.
+
+Nature. 2006 Nov 2;444(7115):85-8 doi:10.1038/nature05241
+
+Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.
+
+[[!pmid 17051155 desc="Incorporation of a newly sequenced hemichordate produces a phylogenetic tree supporting the monophyly of chordates."]]

Encore.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 35f17ba..5066380 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -7,4 +7,4 @@ Nature. 2006 Feb 23;439(7079):965-8.
 
 Tunicates and not cephalochordates are the closest living relatives of vertebrates.
 
-[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]
+[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates."]]

Réparation.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 114bf48..35f17ba 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -7,4 +7,4 @@ Nature. 2006 Feb 23;439(7079):965-8.
 
 Tunicates and not cephalochordates are the closest living relatives of vertebrates.
 
-[[!pmid 16495997 desc='Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the "Olfactores" clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]
+[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]

Standardisation.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index ecaf314..114bf48 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Tunicates and not cephalochordates are the closest living relatives of vertebrates."]]
-[[!tag phylogeny Oikopleura]]
+[[!tag evolution Oikopleura]]
 
 Delsuc F, Brinkmann H, Chourrout D, Philippe H.
 
diff --git a/tags/phylogeny.mdwn b/tags/phylogeny.mdwn
deleted file mode 100644
index e0377da..0000000
--- a/tags/phylogeny.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged phylogeny"]]
-
-[[!inline pages="tagged(phylogeny)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/phylogeny
diff --git a/tags/phylogeny.mdwn b/tags/phylogeny.mdwn
new file mode 100644
index 0000000..e0377da
--- /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]]

Banane
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f132027..0a7822e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -26,8 +26,9 @@ Evolution
    clade is sister of Stolidobranchia (that is, not basal in Tunicates).
    Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
- - Based on 258 orthologous proteins from 63 species, Oikopleuridae is basal to
-   all other tunicates ([[Delsuc et al., 2018|biblio/29653534]]).
+ - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]])
+   and then 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
+   show that Oikopleuridae is basal to all other tunicates.
 
 
 Genome

Onigiri.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
new file mode 100644
index 0000000..ecaf314
--- /dev/null
+++ b/biblio/16495997.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tunicates and not cephalochordates are the closest living relatives of vertebrates."]]
+[[!tag phylogeny Oikopleura]]
+
+Delsuc F, Brinkmann H, Chourrout D, Philippe H.
+
+Nature. 2006 Feb 23;439(7079):965-8.
+
+Tunicates and not cephalochordates are the closest living relatives of vertebrates.
+
+[[!pmid 16495997 desc='Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the "Olfactores" clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]

Phylogénie.
diff --git a/biblio/19656395.mdwn b/biblio/19656395.mdwn
new file mode 100644
index 0000000..2fe9e0e
--- /dev/null
+++ b/biblio/19656395.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models."]]
+[[!tag Oikopleura evolution]]
+
+Tsagkogeorga G, Turon X, Hopcroft RR, Tilak MK, Feldstein T, Shenkar N, Loya Y, Huchon D, Douzery EJ, Delsuc F.
+
+BMC Evol Biol. 2009 Aug 5;9:187. doi:10.1186/1471-2148-9-187
+
+An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.
+
+[[!pmid 19656395 desc="Phylogenetic tree built with 18S rRNA sequences from 110 species including 4 Oikopleuridae places Oikopleuridae as sister group of Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or long-branch attraction.  Many other articles on the topic are cited in this paper."]]
diff --git a/biblio/29653534.mdwn b/biblio/29653534.mdwn
new file mode 100644
index 0000000..331833b
--- /dev/null
+++ b/biblio/29653534.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A phylogenomic framework and timescale for comparative studies of tunicates."]]
+[[!tag Oikopleura evolution]]
+
+Delsuc F, Philippe H, Tsagkogeorga G, Simion P, Tilak MK, Turon X, López-Legentil S, Piette J, Lemaire P, Douzery EJP.
+
+BMC Biol. 2018 Apr 13;16(1):39. doi:10.1186/s12915-018-0499-2
+
+A phylogenomic framework and timescale for comparative studies of tunicates.
+
+[[!pmid 29653534 desc="Phylogenetic tree based on 258 orthologous proteins from 63 species shows Oikopleura as a sister group of all other tunicates, with a split 447 ± 20 Mya ago.  A long-branch attraction artefact can nevertheless not be excluded."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index becb9e5..f132027 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -18,6 +18,18 @@ Some links:
  - Genoscope's genome browser: <http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/>
  - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/>
 
+
+Evolution
+---------
+
+ - 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
+   long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
+ - Based on 258 orthologous proteins from 63 species, Oikopleuridae is basal to
+   all other tunicates ([[Delsuc et al., 2018|biblio/29653534]]).
+
+
 Genome
 ------
 
@@ -27,6 +39,7 @@ Genome
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
 
+
 Transcriptome
 -------------
 

Intron turnover.
diff --git a/biblio/15638456.mdwn b/biblio/15638456.mdwn
new file mode 100644
index 0000000..39190f5
--- /dev/null
+++ b/biblio/15638456.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica."]]
+[[!tag Oikopleura intron]]
+
+J Mol Evol. 2004 Oct;59(4):448-57 doi:10.1007/s00239-004-2636-5
+
+Edvardsen RB, Lerat E, Maeland AD, Flåt M, Tewari R, Jensen MF, Lehrach H, Reinhardt R, Seo HC, Chourrout D.
+
+Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica.
+
+[[!pmid 15638456 desc="Study on housekeeping genes suggests that “Most Oikopleura introns occupy nonconserved positions and probably originate from numerous late intron gains or sliding of ancient introns”.  Conservation within paralogs suggest possible gene conversion events."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 51f691d..becb9e5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -39,6 +39,9 @@ Transcriptome
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
+ - Introns are subjected to a large turnover: many ancestral introns are lost, and many
+   new species-specific introns found ([[Edvarsen et al., 2004|biblio/15638456]]).
+
 
 Tools
 -----

Length of O. dioica's SL.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8342708..51f691d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -31,7 +31,7 @@ Transcriptome
 -------------
 
  - O. dioica is the first chordate where gene operons have been described.  A
-   5′ splice leader (SL) bearing a trimethylated cap is found in some RNAs.
+   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
    ([[Ganot et al., 2004|biblio/15314184]]).

Normalise
diff --git a/biblio/26668163.mdwn b/biblio/26668163.mdwn
index a5f945d..873c1b0 100644
--- a/biblio/26668163.mdwn
+++ b/biblio/26668163.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis."]]
-[[!tag Ciona_intestinalis oligo_capping trans-splicing]]
+[[!tag Ciona_intestinalis oligo-capping trans-splicing]]
 
 Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K.
 
diff --git a/tags/oligo_capping.mdwn b/tags/oligo_capping.mdwn
deleted file mode 100644
index c314d3a..0000000
--- a/tags/oligo_capping.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged oligo capping"]]
-
-[[!inline pages="tagged(oligo_capping)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/oligo_capping
diff --git a/tags/oligo_capping.mdwn b/tags/oligo_capping.mdwn
new file mode 100644
index 0000000..c314d3a
--- /dev/null
+++ b/tags/oligo_capping.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged oligo capping"]]
+
+[[!inline pages="tagged(oligo_capping)" actions="no" archive="yes"
+feedshow=10]]

Trans-splicing again.
diff --git a/biblio/26668163.mdwn b/biblio/26668163.mdwn
new file mode 100644
index 0000000..a5f945d
--- /dev/null
+++ b/biblio/26668163.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis."]]
+[[!tag Ciona_intestinalis oligo_capping trans-splicing]]
+
+Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K.
+
+Genome Res. 2016 Jan;26(1):140-50. doi:10.1101/gr.184648.114
+
+Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.
+
+[[!pmid 26668163 desc="TSS-Seq libraries made of 200 µg of total RNA, sequenced on Illumina GA with a read length of 36, which is sufficient to go through the 16-nt splice leader."]]

creating tag page tags/Ciona_intestinalis
diff --git a/tags/Ciona_intestinalis.mdwn b/tags/Ciona_intestinalis.mdwn
new file mode 100644
index 0000000..84c7dee
--- /dev/null
+++ b/tags/Ciona_intestinalis.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Ciona intestinalis"]]
+
+[[!inline pages="tagged(Ciona_intestinalis)" actions="no" archive="yes"
+feedshow=10]]

Trans-splicing in C. intestinalis; size of splice leader.
diff --git a/biblio/16822859.mdwn b/biblio/16822859.mdwn
new file mode 100644
index 0000000..651deb5
--- /dev/null
+++ b/biblio/16822859.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis."]]
+[[!tag trans-splicing Ciona_intestinalis]]
+
+Nucleic Acids Res. 2006 Jul 5;34(11):3378-88 doi:10.1093/nar/gkl418
+
+Satou Y, Hamaguchi M, Takeuchi K, Hastings KE, Satoh N.
+
+Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis.
+
+[[!pmid 16822859 desc="Analysis of oligo-capped cDNAs reports a single splice leader (16 nt-long) in 27% of the cDNAs."]]
diff --git a/tags/trans-splicing.mdwn b/tags/trans-splicing.mdwn
index 22bf646..31411ab 100644
--- a/tags/trans-splicing.mdwn
+++ b/tags/trans-splicing.mdwn
@@ -1,4 +1,5 @@
 [[!meta title="pages tagged trans-splicing"]]
 
-[[!inline pages="tagged(trans-splicing)" actions="no" archive="yes"
-feedshow=10]]
+The splice leader is 16-nt in C. intestinalis ([[Satou et al, 2006|biblio/16822859]]) and 40-nt in O. dioica ([[Ganot et al., 2004|biblio/15314184]]).
+
+[[!inline pages="tagged(trans-splicing)" actions="no" limit=0]]

au bureau.
diff --git a/biblio/29449511.mdwn b/biblio/29449511.mdwn
new file mode 100644
index 0000000..343d94c
--- /dev/null
+++ b/biblio/29449511.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity."]]
+[[!tag CRISPR HPV method]]
+
+Science. 2018 Feb 15. pii: eaar6245. doi:10.1126/science.aar6245
+
+Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA.
+
+CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity.
+
+[[!pmid 29449511 desc="DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR).  Cas12a activates a single-strand nuclease after matching its target double-strand DNA.  A single-strand probe terminated by a fluorophore and a quencher signals the activation."]]

More background.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 18545b2..8342708 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -3,12 +3,14 @@
 Oikopleura
 ==========
 
-_Oikopleura dioica_ is a tunicate plankton.  Thus, it belongs to the same
-"chordate" phylum as us.  Its genome is very small, as each cell only contains
-70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
-Each animal secretes a mucus "house" that is used for feeding (and perhaps
-defending).  The main house proteins are called _oikosins_ and half or them
-are unique to Oikopleura and related animals ("_Appendicularia_").
+_Oikopleura dioica_ is a tunicate larvacean (synonym: urochordate
+appendicularian) plankton.  Thus, it belongs to the same "chordate" phylum as
+us.  As the name indicates, it is the only _dioecious_ species of _Oikopleura_
+(that is: male and female organisms are distinct).  Its reproduction is
+_semelparous_: the animals die afer releasing its gametes.  Each animal
+secretes a mucus "house" that is used for feeding (and perhaps defending).  The
+main house proteins are called _oikosins_ and half or them are unique to
+Oikopleura and related animals ("_Appendicularia_").
 
 Some links:
 
@@ -20,6 +22,7 @@ Genome
 ------
 
  - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
+ - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 

Expand.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cd23cbc..18545b2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -27,9 +27,11 @@ Genome
 Transcriptome
 -------------
 
- - Some genes are organised in operons.  A 5′ splice leader (SL) is found in some RNAs.
+ - O. dioica is the first chordate where gene operons have been described.  A
+   5′ splice leader (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 ([[Ganot et al., 2004|biblio/15314184]]).
+   times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus
+   ([[Ganot et al., 2004|biblio/15314184]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with

Correction.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 43de0f4..cd23cbc 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -48,7 +48,7 @@ Development
    _pax2/5/8_ is detected between the _otxa_ + _otxb_ and the _hox1_ territories.
    ([[Cañestro et al., 2005|biblio/16111672]]).
  - The _pum1_ and _vas4_ RNAs show localised expression during development. Prior
-   hatching, _pum1_ is found outside the embryo ([[|biblio/29486709]]).
+   hatching, _pum1_ is found outside the embryo ([[Olsen et al., 2018|biblio/29486709]]).
 
 
 Ecology

Extracellular RNA localisation !?
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c5e5eb0..43de0f4 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -47,6 +47,9 @@ Development
    hindbrain, and spinal cord, but not the midbrain.  No expression of
    _pax2/5/8_ is detected between the _otxa_ + _otxb_ and the _hox1_ territories.
    ([[Cañestro et al., 2005|biblio/16111672]]).
+ - The _pum1_ and _vas4_ RNAs show localised expression during development. Prior
+   hatching, _pum1_ is found outside the embryo ([[|biblio/29486709]]).
+
 
 Ecology
 -------

In the train
diff --git a/biblio/29486709.mdwn b/biblio/29486709.mdwn
new file mode 100644
index 0000000..1f0a06f
--- /dev/null
+++ b/biblio/29486709.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evidence for a centrosome-attracting body like structure in germ-soma segregation during early development, in the urochordate Oikopleura dioica."]]
+[[!tag Oikopleura localisation germ_line]]
+
+Olsen LC, Kourtesis I, Busengdal H, Jensen MF, Hausen H, Chourrout D.
+
+BMC Dev Biol. 2018 Feb 27;18(1):4. doi:10.1186/s12861-018-0165-5
+
+Evidence for a centrosome-attracting body like structure in germ-soma segregation during early development, in the urochordate Oikopleura dioica.
+
+[[!pmid 29486709 desc="Localised pumilio (pum1) and vasa (vas4) RNAs.  Prior hatching, pum1 is found outside the embryo!"]]

Old
diff --git a/biblio/14757812.mdwn b/biblio/14757812.mdwn
new file mode 100644
index 0000000..0000c97
--- /dev/null
+++ b/biblio/14757812.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome annotation by high-throughput 5' RNA end determination."]]
+[[!tag sequence_tags trans-splicing]]
+
+Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1650-5. doi:10.1073/pnas.0308384100
+
+Hwang BJ, Müller HM, Sternberg PW.
+
+Genome annotation by high-throughput 5' RNA end determination.
+
+[[!pmid 14757812 desc="TC-RED: primes with oligo-dT, amplifies primers complementary to the splice leader, cleaves tags with BpmI and sequences concatemers"]]

Au parc
diff --git a/biblio/29440632.mdwn b/biblio/29440632.mdwn
new file mode 100644
index 0000000..894a325
--- /dev/null
+++ b/biblio/29440632.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Detecting RNA base methylations in single cells by in situ hybridization"]]
+[[!tag methylation hybridisation]]
+
+Ranasinghe RT, Challand MR, Ganzinger KA, Lewis BW, Softley C, Schmied WH, Horrocks MH, Shivji N, Chin JW, Spencer J, Klenerman D
+
+Nat Commun. 2018 Feb 13;9(1):655. doi:10.1038/s41467-017-02714-7
+
+Detecting RNA base methylations in single cells by in situ hybridization
+
+[[!pmid 29440632 desc="“MR-FISH”: Molecular beacons designed against known bases known to be
+methylated on their Watson-Crick interface have reduced affinity or fail to
+hybridise."]]

creating tag page tags/DNAi
diff --git a/tags/DNAi.mdwn b/tags/DNAi.mdwn
new file mode 100644
index 0000000..a4b2096
--- /dev/null
+++ b/tags/DNAi.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged DNAi"]]
+
+[[!inline pages="tagged(DNAi)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/maternal
diff --git a/tags/maternal.mdwn b/tags/maternal.mdwn
new file mode 100644
index 0000000..567b6b5
--- /dev/null
+++ b/tags/maternal.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged maternal"]]
+
+[[!inline pages="tagged(maternal)" actions="no" archive="yes"
+feedshow=10]]

DNAi
diff --git a/biblio/28281645.mdwn b/biblio/28281645.mdwn
new file mode 100644
index 0000000..f9f25ba
--- /dev/null
+++ b/biblio/28281645.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica."]]
+[[!tag Oikopleura screen DNAi maternal]]
+
+Omotezako T, Matsuo M, Onuma TA, Nishida H
+
+Sci Rep. 2017 Mar 10;7:44226. doi:10.1038/srep44226
+
+DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica.
+
+[[!pmid 28281645 desc="A clone library was prepared by subtracting male to female cDNAs.  Clones were screened by pools of 5 and then resolved individually.  Identifies genes related to cell structure and adhesion."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 930c9e7..c5e5eb0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -35,6 +35,10 @@ Transcriptome
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
 
+Tools
+-----
+
+ - DNAi was used to screen for maternal genes ([[Omotezako et al., 2017|biblio/28281645]]).
 
 Development
 -----------

mraw
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index e10cf4a..e7f8577 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -21,6 +21,12 @@
    can extend a linker with the sequence of a small RNA via a template switching
    reaction.  (That is: a sRNA can play the same role as a TS oligonucleotide.)
 
+ - in _Capture and Amplification by Tailing and Switching_ (CATS,
+   [[Turchinovich et al (2014)|biblio/24922482]]), short and long RNAs are A-tailed,
+   oligo-dT-primed, and template swiched.  A PNK treatement is needed on
+   circulating RNAs, to remove phosphates or cyclophosphates that would
+   prevent the A-tailing.
+
 ### Effect of chemical composition of the TS oligonucleotide
 
 Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,
@@ -38,6 +44,9 @@ as a replacement for RNA.
  - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
+ - 3′ phosphate or biotin blocking groups abolish template-switching
+   ([[Turchinovich et al (2014)|biblio/24922482]] and others).
+
 ### Effect of TSO concentration
 
  - For the STRT method, [[Zajac et al (2013)|biblio/24392002]] concluded that

Tag.
diff --git a/biblio/24922482.mdwn b/biblio/24922482.mdwn
index 1e10e5c..c7cc9ad 100644
--- a/biblio/24922482.mdwn
+++ b/biblio/24922482.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA."]]
-[[!tag template_switching amplification method]]
+[[!tag sRNA template_switching amplification method]]
 
 RNA Biol. 2014;11(7):817-28. doi:10.4161/rna.29304
 

XbaI
diff --git a/biblio/29482522.mdwn b/biblio/29482522.mdwn
new file mode 100644
index 0000000..1b0cdc8
--- /dev/null
+++ b/biblio/29482522.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate."]]
+[[!tag Oikopleura CAGE promoter motif]]
+
+Danks GB, Navratilova P, Lenhard B, Thompson EM 
+
+BMC Genomics. 2018 Feb 26;19(1):164. doi:10.1186/s12864-018-4504-5
+
+Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.
+
+[[!pmid 29482522 desc="“369/502 (73.5%) of genes that are specifically expressed in the testis are associated with a TCTAGA promoter element, compared to 100/906 (11.0%) that are specific to the ovary and 7/275 (2.5%) that are specific to the trunk.” “Strong association of gene body DNA methylation with TATA-dependent promoters in O. dioica.” "]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ed52be9..930c9e7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -32,6 +32,9 @@ Transcriptome
    times in the genome ([[Ganot et al., 2004|biblio/15314184]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
+ - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
+   CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
+
 
 Development
 -----------

Minor
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index edae7db..e10cf4a 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -14,7 +14,7 @@
    [[Ginsberg, 2005|biblio/16308152]].
 
  - In the  single-cell tagged reverse transcription (STRT) method,
-   [[Islam et al, 2011|biblio/21543516]]) use template switching and unique
+   [[Islam et al, (2011)|biblio/21543516]] use template switching and unique
    molecular identifiers to sequence 5′ ends.  The method is oligo-dT-primed.
 
  - [[Mohr et al (2013)|biblio/23697550]] have shown (Fig 6) that retroviral RTs

tag
diff --git a/biblio/21543516.mdwn b/biblio/21543516.mdwn
index 8ead64b..15b323b 100644
--- a/biblio/21543516.mdwn
+++ b/biblio/21543516.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq."]]
-[[!tag template_switching single_cell method transcriptome tags]]
+[[!tag STRT template_switching single_cell method transcriptome tags]]
 
 Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.
 

STRT.
diff --git a/biblio/21543516.mdwn b/biblio/21543516.mdwn
new file mode 100644
index 0000000..8ead64b
--- /dev/null
+++ b/biblio/21543516.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq."]]
+[[!tag template_switching single_cell method transcriptome tags]]
+
+Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.
+
+Genome Res. 2011 Jul;21(7):1160-7. doi:10.1101/gr.110882.110
+
+Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.
+
+[[!pmid 21543516 desc="Single-cell Tagged Reverse Transcription (STRT)"]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 4619e75..edae7db 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -13,6 +13,10 @@
    and `TTT` were also tested.  An extensive protocol was published in
    [[Ginsberg, 2005|biblio/16308152]].
 
+ - In the  single-cell tagged reverse transcription (STRT) method,
+   [[Islam et al, 2011|biblio/21543516]]) use template switching and unique
+   molecular identifiers to sequence 5′ ends.  The method is oligo-dT-primed.
+
  - [[Mohr et al (2013)|biblio/23697550]] have shown (Fig 6) that retroviral RTs
    can extend a linker with the sequence of a small RNA via a template switching
    reaction.  (That is: a sRNA can play the same role as a TS oligonucleotide.)
@@ -34,6 +38,11 @@ as a replacement for RNA.
  - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
+### Effect of TSO concentration
+
+ - For the STRT method, [[Zajac et al (2013)|biblio/24392002]] concluded that
+   1 μM of TSO gave the highest yield.
+
 ### Effect of magnesium, manganese and dNTP concentrations
 
  - [[Schmidt and Mueller, 1999|biblio/10518626]] showed that increasing

CapSelect.
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index f24e517..4619e75 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -2,6 +2,11 @@
 
 (work in progress)
 
+ - In the "_CapSelect_" method, [[Schmidt and Mueller, 1999|biblio/10518626]]
+   stimulate template switching with manganese (see below), tail the first-strand
+   cDNAs with dA, and add 5′ linkers with T4 DNA ligase and duplex adapters
+   ending with a (T)TTTGGG overhang.
+
  - The "_terminal continuation_" method ([[Ginsberg et al.,
    2002|biblio/12462399]], [[Che et al., 2004|biblio/14647400]]) is essentially
    a template switching with DNA oligonucleotides ending in `CCC` or `GGG`.  `AAA`

More details on Mg / Mn addition.
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 7af520c..f24e517 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -12,10 +12,6 @@
    can extend a linker with the sequence of a small RNA via a template switching
    reaction.  (That is: a sRNA can play the same role as a TS oligonucleotide.)
 
- - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
-   switching non-capped molecules by increasing dNTPs to 2 mM and
-   Mg<sup>2+</sup> to 9 mM.
-
 ### Effect of chemical composition of the TS oligonucleotide
 
 Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,
@@ -33,4 +29,16 @@ as a replacement for RNA.
  - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
+### Effect of magnesium, manganese and dNTP concentrations
+
+ - [[Schmidt and Mueller, 1999|biblio/10518626]] showed that increasing
+   magnesium concentration (to 6 mM) or adding manganese at the end of the
+   reaction (1 or 2 mM) increased the frequency of dC addition (moderately
+   for Mg<sup>2+</sup> and strongly for Mn<sup>2+</sup>).  Enzyme: SSII; dNTP
+   concentration: 1 mM each.
+
+ - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
+   switching non-capped molecules by increasing dNTPs to 2 mM and
+   Mg<sup>2+</sup> to 9 mM.
+
 [[!inline pages="tagged(template_switching)" limit=0]]

More details.
diff --git a/biblio/10518626.mdwn b/biblio/10518626.mdwn
index f69b0d8..7c7c1f6 100644
--- a/biblio/10518626.mdwn
+++ b/biblio/10518626.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs."]]
-[[!tag cap method enzyme manganese]]
+[[!tag cap method reverse_transcription manganese template_switching]]
 
 Nucleic Acids Res. 1999 Nov 1;27(21):e31.
 
@@ -7,4 +7,4 @@ Schmidt WM, Mueller MW.
 
 CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs.
 
-[[!pmid 10518626 desc="In presence of the 5' cap and Mn2+, the SuperScriptII enzyme adds 3-4 extra dC residues to the first strand cDNA."]]
+[[!pmid 10518626 desc="Extra cytosine are more frequently added in presence of the 5′ cap.  Increasing Mg2+ to 6 mM increases the frequency of addition of more than 1 C, but only moderately.  Instead, when adding BSA in the reaction, supplementing it with 1 or 2 mM Mn2+ after 1h, 3-4 extra dC residues are added to most of the first strand cDNAs.  Standard reaction: 0.75 μM oligo dT (or 0.25 μM gene-specific RT primer); 50 mM Tris-HCl (pH 8.3); 75 mM KCl; 3 mM MgCl2; 5 mM DTT; dNTPs 1mM each; 0.1 mg BSA; 20 U RNAse inhibitor (Roche), 200 U SuperScript II; 1h at 42 °C."]]

Oops, already had it.
diff --git a/biblio/2460825.mdwn b/biblio/2460825.mdwn
index 997b5cd..dfa2bcf 100644
--- a/biblio/2460825.mdwn
+++ b/biblio/2460825.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases."]]
-[[!tag reverse_transcription enzyme polymerase]]
+[[!tag reverse_transcription template_switching enzyme polymerase]]
 
 Nucleic Acids Res. 1988 Oct 25;16(20):9677-86
 
@@ -7,4 +7,7 @@ Clark JM
 
 Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases.
 
-[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Perference for adding As."]]
+[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Perference for adding As.  ‘We cannot exclude the formal possibility that some of these latter
++events, particularly the addition of dCMP by AMV reverse transcriptase, involve the use of coding
++information made available as a result of a transient misalignment of the primer/template
++substrate.’"]]

Earlier report.
diff --git a/biblio/2460825.mdwn b/biblio/2460825.mdwn
index 1e7faae..997b5cd 100644
--- a/biblio/2460825.mdwn
+++ b/biblio/2460825.mdwn
@@ -1,6 +1,10 @@
 [[!meta title="Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases."]]
-[[!tag template_switching enzyme]]
-[[!pmid 2460825 desc="‘we cannot exclude the formal possibility that some of these latter
-events, particularly the addition of dCMP by AMV reverse transcriptase, involve the use of coding
-information made available as a result of a transient misalignment of the primer/template
-substrate.’"]]
+[[!tag reverse_transcription enzyme polymerase]]
+
+Nucleic Acids Res. 1988 Oct 25;16(20):9677-86
+
+Clark JM
+
+Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases.
+
+[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Perference for adding As."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 2f7c195..696155c 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -21,6 +21,9 @@ _(redaction in progress)_
 
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 
+Like other DNA polymerases ([[Clark, 1988|biblio/2460825]]), reverse
+transcriptases have a TdT activity.
+
  - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
    AMV, with a preference for adding As.  For MMLV, activity reduced abruptly
    between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.

more
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 14fe42d..2f7c195 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -22,7 +22,10 @@ _(redaction in progress)_
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 
  - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
-   AMV, with a preference for adding As.
+   AMV, with a preference for adding As.  For MMLV, activity reduced abruptly
+   between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.
+   Activity increased with concentration for MMLV.  (High-concentration AMV was
+   not available.)
 
 ### Reverse-transcriptases tolerate terminal mismatches
 

More on TdT.
diff --git a/biblio/11252793.mdwn b/biblio/11252793.mdwn
index d2c2f1e..ab611b9 100644
--- a/biblio/11252793.mdwn
+++ b/biblio/11252793.mdwn
@@ -7,4 +7,4 @@ Chen D, Patton JT.
 
 Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5'-RACE and primer extension.
 
-[[!pmid 11252793 desc="Terminal desoxynucleotidyl transferase activity of reverse transcriptases MMLV and AMV: preference for adding As."]]
+[[!pmid 11252793 desc="Terminal desoxynucleotidyl transferase activity on double-stranded substrates of reverse transcriptases MMLV and AMV: preference for adding As.  For MMLV, activity reduced abruptly between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.  Activity increased with concentration for MMLV.  (High-concentration AMV was not available.)"]]

Only two authors...
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 3c53de4..14fe42d 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -21,7 +21,7 @@ _(redaction in progress)_
 
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 
- - [[Chen et al., 2001|biblio/11252793]] reported a TdT activity for MMLV and
+ - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
    AMV, with a preference for adding As.
 
 ### Reverse-transcriptases tolerate terminal mismatches

TdT.
diff --git a/biblio/11252793.mdwn b/biblio/11252793.mdwn
new file mode 100644
index 0000000..d2c2f1e
--- /dev/null
+++ b/biblio/11252793.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5'-RACE and primer extension."]]
+[[!tag reverse_transcription]]
+
+Biotechniques. 2001 Mar;30(3):574-80, 582
+
+Chen D, Patton JT.
+
+Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5'-RACE and primer extension.
+
+[[!pmid 11252793 desc="Terminal desoxynucleotidyl transferase activity of reverse transcriptases MMLV and AMV: preference for adding As."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index fcc0363..3c53de4 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -5,13 +5,13 @@ The reverse transcriptase
 
 _(redaction in progress)_
 
-## Additives that increase reaction performance:
+### Additives that increase reaction performance
 
  - Actinomycin D ([[Perocchi et al., 2007|biblio/17897965]]).
  - [[T4 bacteriophage gene 32 protein|ssbp]] (T4gp32, [[Kenzelmann _et al._, 2004|biblio/15028277]],
    [[Piché _et al._, 2005|biblio/16461948]]).
 
-## DNA-dependent DNA polymerase activity.
+### DNA-dependent DNA polymerase activity
 
  - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.
  - It is also a source of antisense artefacts when the RT makes a second-strand cDNA
@@ -19,17 +19,22 @@ _(redaction in progress)_
    but not RNA-dependent polymerase activity and is used to suppress these
    artefacts ([[Perocchi et al., 2007|biblio/17897965]], [[Kanamori-Katayama et al., 2011|biblio/21596820]]).
 
-## Reverse-transcriptases tolerate terminal mismatches:
+### Terminal desoxynucleotidyl transferase (TdT) activity
+
+ - [[Chen et al., 2001|biblio/11252793]] reported a TdT activity for MMLV and
+   AMV, with a preference for adding As.
+
+### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].
- - Utilised in [[Arnaud et al., 2015|biblio/27071605]] to reduce priming or
+ - Utilised in [[Arnaud et al., 2016|biblio/27071605]] to reduce priming or
    ribosomal or hemoglobin RNA.
 
-## Reverse-transcription primers:
+### Reverse-transcription primers
 
  - "N15" random pentadecamers: [[Stangegaard et al., 2006|biblio/16708763]].
  - Multi-targeted primers (MTP): [[Adomas et al., 2010|biblio/20716356]].
  - "Not-so random" (NSR) primers: [[Armour et al., 2009|biblio/19668204]].
- - "Pseudo-random" primers: [[Arnaud et al., 2015|biblio/27071605]].
+ - "Pseudo-random" primers: [[Arnaud et al., 2016|biblio/27071605]].
 
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]