Dernières modifications :

Mdwn
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0c9fa4e..92f0d02 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -138,7 +138,6 @@ Genes and pathways
 
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]).
-
  - Histones: “Densitometric analyses of Southern blots yielded estimates of
    9–11 H4 genes, 11–14 H3 genes, 15–19 H2A genes, 18–20 H2B genes, and 4–7 H1
    genes” ([[Chioda, Eskeland and Thompson, 2002|biblio/12446815]]).  “47 histone

Histones
diff --git a/biblio/21756361.mdwn b/biblio/21756361.mdwn
new file mode 100644
index 0000000..4b8bc5b
--- /dev/null
+++ b/biblio/21756361.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Histone variant innovation in a rapidly evolving chordate lineage."]]
+[[!tag Oikopleura histone]]
+
+Histone variant innovation in a rapidly evolving chordate lineage.
+
+BMC Evol Biol. 2011 Jul 15;11:208. doi: 10.1186/1471-2148-11-208.
+
+Moosmann A, Campsteijn C, Jansen PW, Nasrallah C, Raasholm M, Stunnenberg HG, Thompson EM.
+
+[[!pmid 21756361 desc="“47 histone genes (6 H4, 10 H3, 15 H2A, 11 H2B and 5 H1 genes) encoding 31 different histone proteins (2 H4, 6 H3, 11 H2A, 7 H2B and 5 H1) were identified.” “There is no H2AX homolog in O. dioica.” (H2AX is implicated in DNA repair)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 17acb7e..0c9fa4e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -138,9 +138,13 @@ Genes and pathways
 
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]).
- - “Densitometric analyses of Southern blots yielded estimates of 9–11 H4
-   genes, 11–14 H3 genes, 15–19 H2A genes, 18–20 H2B genes, and 4–7 H1 genes.”
-   [[Chioda, Eskeland and Thompson, 2002|biblio/12446815]]
+
+ - Histones: “Densitometric analyses of Southern blots yielded estimates of
+   9–11 H4 genes, 11–14 H3 genes, 15–19 H2A genes, 18–20 H2B genes, and 4–7 H1
+   genes” ([[Chioda, Eskeland and Thompson, 2002|biblio/12446815]]).  “47 histone
+   genes (6 H4, 10 H3, 15 H2A, 11 H2B and 5 H1 genes) encoding 31 different
+   histone proteins (2 H4, 6 H3, 11 H2A, 7 H2B and 5 H1) were identified”
+   ([[Moosmann and coll., 2011|biblio/21756361]]).
  - 2 cellulose synthase genes, possibly acquired by horizontal gene transfer
    from an actinobacteria ([[Nakashima and coll., 2004|biblio/14740209]]), were
    found by [[Sagane et al. (2010)|biblio/20335363]] and [[Nakashima et al.
@@ -186,6 +190,8 @@ Genes and pathways
    conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
    An alternative or microhomology (MH)-driven end joining pathway is active
    and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
+ - In line with the above, “There is no H2AX homolog in O. dioica.” (H2AX is
+   implicated in DNA repair).  [[Moosmann and coll., 2011|biblio/21756361]]
  - 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.,

creating tag page tags/species
diff --git a/tags/species.mdwn b/tags/species.mdwn
new file mode 100644
index 0000000..99f657b
--- /dev/null
+++ b/tags/species.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged species"]]
+
+[[!inline pages="tagged(species)" actions="no" archive="yes"
+feedshow=10]]

Ciona
diff --git a/biblio/10.1111_jzs.12101.mdwn b/biblio/10.1111_jzs.12101.mdwn
new file mode 100644
index 0000000..5151874
--- /dev/null
+++ b/biblio/10.1111_jzs.12101.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis."]]
+[[!tag Ciona species]]
+
+Brunetti, R. , Gissi, C. , Pennati, R. , Caicci, F. , Gasparini, F. and Manni, L. 
+
+J Zoolog Syst Evol Res, 2015, 53: 186-193. doi:10.1111/jzs.12101
+
+Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: _Ciona robusta_ and _Ciona intestinalis_.
+
+[[!doi 10.1111_jzs.12101 desc="Discriminates C. robusta from C. intestinalis by the presence of tubercular prominences in the tunic."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 77551c2..23058f7 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -25,13 +25,18 @@ were F1 and of _C. int_ maternal origin.
 Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A
 and B (now renamed _robusta_ and _intestinalis sensu_) are as distant as
 distinct species ([[Nydam and Harrison,
-2007|biblio/10.1007_s00227-007-0617-0]]).  Mitochondrial gene order differ
-between the two species ([[Ianelli and coll., 2007|biblio/17640763]]).
-Sequencing of nuclear genes showed intragenic recombination in _C. robusta_ and
-_C. intestinalis_, buy supported monophyly of these two species.  Both data
-also supported paraphyly of _C. intestinalis_ with respcet to _C. roulei_
-([[Nydam and Harrison, 2010|biblio/20403444]]).  Speciation is estimated to
-have happened during the Pliocene (≈ 3.8 Ma); a recent introgression then
-happened 15,000 years ago ([[Roux and coll., 2013|biblio/23564941]]).
+2007|biblio/10.1007_s00227-007-0617-0]]).  [[Caputi and coll.,
+2007|biblio/17517633]] and others proposed to use some pigmentation differences
+as a morphological marker.  In 2015, [[Brunetti and
+coll|biblio/10.1111_jzs.12101]] proposed the presence of “tubercular
+prominences” in the tunic as a more accurate morphological marker.
+Mitochondrial gene order differ between the two species ([[Ianelli and coll.,
+2007|biblio/17640763]]).  Sequencing of nuclear genes showed intragenic
+recombination in _C. robusta_ and _C. intestinalis_, buy supported monophyly of
+these two species.  Both data also supported paraphyly of _C. intestinalis_
+with respcet to _C. roulei_ ([[Nydam and Harrison, 2010|biblio/20403444]]).
+Speciation is estimated to have happened during the Pliocene (≈ 3.8 Ma); a
+recent introgression then happened 15,000 years ago ([[Roux and coll.,
+2013|biblio/23564941]]).
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Now in PubMed.
diff --git a/biblio/10.2307_1934145.mdwn b/biblio/28973811.mdwn
similarity index 73%
rename from biblio/10.2307_1934145.mdwn
rename to biblio/28973811.mdwn
index 580e475..fcce507 100644
--- a/biblio/10.2307_1934145.mdwn
+++ b/biblio/28973811.mdwn
@@ -7,4 +7,4 @@ Ecology 52:577–586 (1971)
 
 The Nonconcept of Species Diversity: A Critique and Alternative Parameters
 
-[[!doi 10.2307/1934145 desc="Base of the “rarefy” function in R's “vegan” package."]]
+[[!pmid 28973811 desc="Base of the “rarefy” function in R's “vegan” package."]]

Cellulose in O. rufescens
diff --git a/biblio/11732199.mdwn b/biblio/11732199.mdwn
new file mode 100644
index 0000000..90ac70f
--- /dev/null
+++ b/biblio/11732199.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cellulose in the house of the appendicularian Oikopleura rufescens."]]
+[[!tag Oikopleura cellulose]]
+
+Kimura S, Ohshima C, Hirose E, Nishikawa J, Itoh T.
+
+Protoplasma. 2001;216(1-2):71-4.
+
+Cellulose in the house of the appendicularian Oikopleura rufescens.
+
+[[!pmid 11732199 desc="Electron diffraction analysis found highly crystalline cellulose I."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5a67836..17acb7e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -145,9 +145,10 @@ Genes and pathways
    from an actinobacteria ([[Nakashima and coll., 2004|biblio/14740209]]), were
    found by [[Sagane et al. (2010)|biblio/20335363]] and [[Nakashima et al.
    (2011)|biblio/20972815]].  They are used to produce different crystalline forms
-   of cellulose ([[Nakashima et al., 2011|biblio/20972815]]).  The CesA gene
-   is trans-spliced in the ascidian _Ciona intestinalis_ ([[Matthysse and coll.,
-   2004|biblio/14722352]]).
+   of cellulose ([[Nakashima et al., 2011|biblio/20972815]]).  Crystalline
+   cellulose I was also found in _O. rufescens by_ [[Kimura and coll
+   (2001)|biblio/11732199]]. The CesA gene is trans-spliced in the ascidian _Ciona
+   intestinalis_ ([[Matthysse and coll., 2004|biblio/14722352]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).

mmmhhhh
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index 106e5ea..1aa7a80 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-05-22 22:31+0000\n"
-"PO-Revision-Date: 2019-05-23 07:32+0900\n"
+"PO-Revision-Date: 2019-05-23 08:30+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"

typo
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index c6a123d..106e5ea 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-05-22 22:31+0000\n"
-"PO-Revision-Date: 2019-05-23 07:30+0900\n"
+"PO-Revision-Date: 2019-05-23 07:32+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -39,14 +39,6 @@ msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
 msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "En qualité de mainteneur du paquet (mime-support)[https://packages.debian."
-#| "org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
-#| "Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media "
-#| "[text/vnd.sosi](http://people.skolelinux.org/pere/blog/"
-#| "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
-#| "suivi !"
 msgid ""
 "En qualité de mainteneur du paquet [`mime-support`](https://packages.debian."
 "org/mime-support]) dans Debian, je voudrais dire « kudos » à Petter "
@@ -55,8 +47,8 @@ msgid ""
 "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
 "suivi !"
 msgstr ""
-"As the maintainer of the (mime-support)[https://packages.debian.org/mime-"
-"support] in Debian, I would like to give Kudos to  Petter Reinholdtsen, who "
+"As the maintainer of the [`mime-support`](https://packages.debian.org/mime-"
+"support) in Debian, I would like to give Kudos to  Petter Reinholdtsen, who "
 "just opened a ticket at the IANA to create a [text/vnd.sosi](http://people."
 "skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html) "
 "media type. May  his example be followed by others!"

updated PO files
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index 65cccc7..c6a123d 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-05-22 22:30+0000\n"
+"POT-Creation-Date: 2019-05-22 22:31+0000\n"
 "PO-Revision-Date: 2019-05-23 07:30+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -39,9 +39,17 @@ msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
 msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "En qualité de mainteneur du paquet (mime-support)[https://packages.debian."
+#| "org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
+#| "Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media "
+#| "[text/vnd.sosi](http://people.skolelinux.org/pere/blog/"
+#| "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
+#| "suivi !"
 msgid ""
-"En qualité de mainteneur du paquet (mime-support)[https://packages.debian."
-"org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
+"En qualité de mainteneur du paquet [`mime-support`](https://packages.debian."
+"org/mime-support]) dans Debian, je voudrais dire « kudos » à Petter "
 "Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media [text/"
 "vnd.sosi](http://people.skolelinux.org/pere/blog/"
 "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "

typo
diff --git "a/Debian/debi\303\242neries/mime-iana.mdwn" "b/Debian/debi\303\242neries/mime-iana.mdwn"
index 5bb7a36..c1ae25d 100644
--- "a/Debian/debi\303\242neries/mime-iana.mdwn"
+++ "b/Debian/debi\303\242neries/mime-iana.mdwn"
@@ -5,7 +5,7 @@
 [[!meta title="Enregistrez vos types media auprès de l'IANA !"]]
 
 En qualité de mainteneur du paquet
-(mime-support)[https://packages.debian.org/mime-support] dans Debian, je
+[`mime-support`](https://packages.debian.org/mime-support]) dans Debian, je
 voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à l'IANA
 pour créer le type media
 [text/vnd.sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html).

typo
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index 06483c7..65cccc7 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-05-22 22:30+0000\n"
-"PO-Revision-Date: 2019-05-23 07:29+0900\n"
+"PO-Revision-Date: 2019-05-23 07:30+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -39,14 +39,6 @@ msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
 msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "En qualité de mainteneur du paquet `(mime-support)[https://packages."
-#| "debian.org/mime-support]` dans Debian, je voudrais dire « kudos » à "
-#| "Petter Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type "
-#| "media [text/vnd.sosi](http://people.skolelinux.org/pere/blog/"
-#| "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
-#| "suivi !"
 msgid ""
 "En qualité de mainteneur du paquet (mime-support)[https://packages.debian."
 "org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
@@ -55,7 +47,7 @@ msgid ""
 "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
 "suivi !"
 msgstr ""
-"As the maintainer of the `(mime-support)`[https://packages.debian.org/mime-"
+"As the maintainer of the (mime-support)[https://packages.debian.org/mime-"
 "support] in Debian, I would like to give Kudos to  Petter Reinholdtsen, who "
 "just opened a ticket at the IANA to create a [text/vnd.sosi](http://people."
 "skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html) "

updated PO files
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index 0e1eeae..06483c7 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-05-22 22:29+0000\n"
+"POT-Creation-Date: 2019-05-22 22:30+0000\n"
 "PO-Revision-Date: 2019-05-23 07:29+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -39,9 +39,17 @@ msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
 msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "En qualité de mainteneur du paquet `(mime-support)[https://packages."
+#| "debian.org/mime-support]` dans Debian, je voudrais dire « kudos » à "
+#| "Petter Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type "
+#| "media [text/vnd.sosi](http://people.skolelinux.org/pere/blog/"
+#| "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
+#| "suivi !"
 msgid ""
-"En qualité de mainteneur du paquet `(mime-support)[https://packages.debian."
-"org/mime-support]` dans Debian, je voudrais dire « kudos » à Petter "
+"En qualité de mainteneur du paquet (mime-support)[https://packages.debian."
+"org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
 "Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media [text/"
 "vnd.sosi](http://people.skolelinux.org/pere/blog/"
 "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "

typo
diff --git "a/Debian/debi\303\242neries/mime-iana.mdwn" "b/Debian/debi\303\242neries/mime-iana.mdwn"
index fdc1552..5bb7a36 100644
--- "a/Debian/debi\303\242neries/mime-iana.mdwn"
+++ "b/Debian/debi\303\242neries/mime-iana.mdwn"
@@ -5,7 +5,7 @@
 [[!meta title="Enregistrez vos types media auprès de l'IANA !"]]
 
 En qualité de mainteneur du paquet
-`(mime-support)[https://packages.debian.org/mime-support]` dans Debian, je
+(mime-support)[https://packages.debian.org/mime-support] dans Debian, je
 voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à l'IANA
 pour créer le type media
 [text/vnd.sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html).

typo
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index 4fc19c2..0e1eeae 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-05-22 22:29+0000\n"
-"PO-Revision-Date: 2019-05-23 07:21+0900\n"
+"PO-Revision-Date: 2019-05-23 07:29+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -39,14 +39,6 @@ msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
 msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "En qualité de mainteneur du paquet (`mime-support`)[https://packages."
-#| "debian.org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
-#| "Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media "
-#| "[text/vnd.sosi](http://people.skolelinux.org/pere/blog/"
-#| "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
-#| "suivi !"
 msgid ""
 "En qualité de mainteneur du paquet `(mime-support)[https://packages.debian."
 "org/mime-support]` dans Debian, je voudrais dire « kudos » à Petter "
@@ -55,7 +47,7 @@ msgid ""
 "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
 "suivi !"
 msgstr ""
-"As the maintainer of the (`mime-support`)[https://packages.debian.org/mime-"
+"As the maintainer of the `(mime-support)`[https://packages.debian.org/mime-"
 "support] in Debian, I would like to give Kudos to  Petter Reinholdtsen, who "
 "just opened a ticket at the IANA to create a [text/vnd.sosi](http://people."
 "skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html) "

updated PO files
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index d93bca9..4fc19c2 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-05-22 22:20+0000\n"
+"POT-Creation-Date: 2019-05-22 22:29+0000\n"
 "PO-Revision-Date: 2019-05-23 07:21+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -39,9 +39,17 @@ msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
 msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "En qualité de mainteneur du paquet (`mime-support`)[https://packages."
+#| "debian.org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
+#| "Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media "
+#| "[text/vnd.sosi](http://people.skolelinux.org/pere/blog/"
+#| "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
+#| "suivi !"
 msgid ""
-"En qualité de mainteneur du paquet (`mime-support`)[https://packages.debian."
-"org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
+"En qualité de mainteneur du paquet `(mime-support)[https://packages.debian."
+"org/mime-support]` dans Debian, je voudrais dire « kudos » à Petter "
 "Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media [text/"
 "vnd.sosi](http://people.skolelinux.org/pere/blog/"
 "MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
diff --git a/index.en.po b/index.en.po
index 61f4f61..d819167 100644
--- a/index.en.po
+++ b/index.en.po
@@ -2,7 +2,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2016-07-25 12:44+0000\n"
+"POT-Creation-Date: 2019-05-22 22:29+0000\n"
 "PO-Revision-Date: 2013-09-29 10:45+0900\n"
 "Last-Translator: Charles Plessy <>\n"
 "Language-Team: Hopla\n"
@@ -42,12 +42,21 @@ msgstr ""
 "[développeur Debian]:\thttp://qa.debian.org/developer.php?login=plessy"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "Je travaille au [RIKEN][] depuis quelques années, et j'y développe des "
+#| "technologies pour mesurer l'activité des cellules en séquençant leurs ARN "
+#| "messagers.  Je publie mes [résultats en anglais][].  Avant de déménager "
+#| "au Japon, j'étudiais le [poisson-zèbre][zfin] à Illkirch.  J'ai encore "
+#| "quelques images de mes [poissons transgéniques][gfp] sur ce site."
 msgid ""
-"Je travaille au [RIKEN][] depuis quelques années, et j'y développe des "
-"technologies pour mesurer l'activité des cellules en séquençant leurs ARN "
-"messagers.  Je publie mes [résultats en anglais][].  Avant de déménager au "
-"Japon, j'étudiais le [poisson-zèbre][zfin] à Illkirch.  J'ai encore quelques "
-"images de mes [poissons transgéniques][gfp] sur ce site."
+"Je travaille à OIST [OIST][], où nous étudions un petit zooplankton appelé "
+"_Oikopleura dioica_ en séquençant le génome d'individus isolés.  Je publie "
+"mes [résultats en anglais][].  Avant déménager à Okinawa, je développais au "
+"RIKEN[] (Yokohama) des technologies pour mesurer l'activité des cellules en "
+"séquençant leurs ARN messagers.  et avant de déménager au Japon, j'étudiais "
+"le [poisson-zèbre][zfin] à Illkirch.  J'ai encore quelques images de mes "
+"[poissons transgéniques][gfp] sur ce site."
 msgstr ""
 "I am working at [RIKEN](http://population-transcriptomics.org/ \"RIKEN "
 "CLST's Genomics Miniaturisation Technology Unit\") since some years, and "
@@ -59,12 +68,19 @@ msgstr ""
 "picture_gallery) on this website."
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "[RIKEN]: http://population-transcriptomics.org/ \"RIKEN CLST's Genomics "
+#| "Miniaturisation Technology Unit\" [zfin]: http://zfin.org/ZDB-"
+#| "PERS-010827-9 [gfp]: http://photo.charles.plessy.org/picture_gallery "
+#| "\"Gros plans sur des poissons transgéniques\" [résultats en anglais]: "
+#| "http://www.ncbi.nlm.nih.gov/pubmed?term=plessy%20c"
 msgid ""
-"[RIKEN]: http://population-transcriptomics.org/ \"RIKEN CLST's Genomics "
-"Miniaturisation Technology Unit\" [zfin]: http://zfin.org/ZDB-PERS-010827-9 "
-"[gfp]: http://photo.charles.plessy.org/picture_gallery \"Gros plans sur des "
-"poissons transgéniques\" [résultats en anglais]: http://www.ncbi.nlm.nih.gov/"
-"pubmed?term=plessy%20c"
+"[OIST]: https://www.oist.jp/ [RIKEN]: http://population-transcriptomics.org/ "
+"\"RIKEN CLST's Genomics Miniaturisation Technology Unit\" [zfin]: http://"
+"zfin.org/ZDB-PERS-010827-9 [gfp]: http://photo.charles.plessy.org/"
+"picture_gallery \"Gros plans sur des poissons transgéniques\" [résultats en "
+"anglais]: http://www.ncbi.nlm.nih.gov/pubmed?term=plessy%20c"
 msgstr "<!-- Liens Markdown intégrés au paragraphe précédent. -->"
 
 #. type: Plain text

typo
diff --git "a/Debian/debi\303\242neries/mime-iana.mdwn" "b/Debian/debi\303\242neries/mime-iana.mdwn"
index 16b27ef..fdc1552 100644
--- "a/Debian/debi\303\242neries/mime-iana.mdwn"
+++ "b/Debian/debi\303\242neries/mime-iana.mdwn"
@@ -5,7 +5,7 @@
 [[!meta title="Enregistrez vos types media auprès de l'IANA !"]]
 
 En qualité de mainteneur du paquet
-(`mime-support`)[https://packages.debian.org/mime-support] dans Debian, je
+`(mime-support)[https://packages.debian.org/mime-support]` dans Debian, je
 voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à l'IANA
 pour créer le type media
 [text/vnd.sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html).

Today.
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index 7817491..d93bca9 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-05-22 22:20+0000\n"
-"PO-Revision-Date: 2019-05-23 07:19+0900\n"
+"PO-Revision-Date: 2019-05-23 07:21+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -17,16 +17,16 @@ msgstr ""
 "X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta date=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta date=\"Thu, 23 May 2019 07:19:35 +0900\"]]\n"
-msgstr "[[!meta date=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+msgstr ""
+"[[!meta date=\"Thu, 23 May 2019 07:19:35 +0900\"]]\n"
+"\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta updated=\"Thu, 23 May 2019 07:19:35 +0900\"]]\n"
-msgstr "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+msgstr "[[!meta updated=\"Thu, 23 May 2019 07:19:35 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap

updated PO files
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index a493582..7817491 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -6,24 +6,26 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-05-22 14:25+0000\n"
+"POT-Creation-Date: 2019-05-22 22:20+0000\n"
 "PO-Revision-Date: 2019-05-23 07:19+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
-"Language-Team: \n"
 "X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta date=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta date=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+msgid "[[!meta date=\"Thu, 23 May 2019 07:19:35 +0900\"]]\n"
 msgstr "[[!meta date=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+msgid "[[!meta updated=\"Thu, 23 May 2019 07:19:35 +0900\"]]\n"
 msgstr "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
 
 #. type: Plain text
@@ -38,12 +40,15 @@ msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
 msgid ""
-"En qualité de mainteneur du paquet (`mime-support`)[https://packages.debian.org/mime-support] dans Debian, "
-"je voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media "
-"[text/vnd.sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  "
-"Que son example soit suivi !"
+"En qualité de mainteneur du paquet (`mime-support`)[https://packages.debian."
+"org/mime-support] dans Debian, je voudrais dire « kudos » à Petter "
+"Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media [text/"
+"vnd.sosi](http://people.skolelinux.org/pere/blog/"
+"MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  Que son example soit "
+"suivi !"
 msgstr ""
-"As the maintainer of the (`mime-support`)[https://packages.debian.org/mime-support] in Debian, I would "
-"like to give Kudos to  Petter Reinholdtsen, who just opened a ticket at the IANA to create a [text/vnd."
-"sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html) media type. "
-"May  his example be followed by others!"
+"As the maintainer of the (`mime-support`)[https://packages.debian.org/mime-"
+"support] in Debian, I would like to give Kudos to  Petter Reinholdtsen, who "
+"just opened a ticket at the IANA to create a [text/vnd.sosi](http://people."
+"skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html) "
+"media type. May  his example be followed by others!"

Aujourd'hui.
diff --git "a/Debian/debi\303\242neries/mime-iana.mdwn" "b/Debian/debi\303\242neries/mime-iana.mdwn"
index e964b41..16b27ef 100644
--- "a/Debian/debi\303\242neries/mime-iana.mdwn"
+++ "b/Debian/debi\303\242neries/mime-iana.mdwn"
@@ -1,5 +1,5 @@
-[[!meta date="Wed, 22 May 2019 22:29:09 +0900"]]
-[[!meta updated="Wed, 22 May 2019 22:29:09 +0900"]]
+[[!meta date="Thu, 23 May 2019 07:19:35 +0900"]]
+[[!meta updated="Thu, 23 May 2019 07:19:35 +0900"]]
 [[!tag Debian]]
 
 [[!meta title="Enregistrez vos types media auprès de l'IANA !"]]

Kudos.
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
index befec6e..a493582 100644
--- "a/Debian/debi\303\242neries/mime-iana.en.po"
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -3,45 +3,47 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2019-05-22 14:25+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2019-05-23 07:19+0900\n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Register your media types to the IANA !\"]]\n"
 
 #. type: Plain text
 msgid ""
-"En qualité de mainteneur du paquet "
-"(`mime-support`)[https://packages.debian.org/mime-support] dans Debian, je "
-"voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à "
-"l'IANA pour créer le type media "
+"En qualité de mainteneur du paquet (`mime-support`)[https://packages.debian.org/mime-support] dans Debian, "
+"je voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à l'IANA pour créer le type media "
 "[text/vnd.sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  "
 "Que son example soit suivi !"
 msgstr ""
+"As the maintainer of the (`mime-support`)[https://packages.debian.org/mime-support] in Debian, I would "
+"like to give Kudos to  Petter Reinholdtsen, who just opened a ticket at the IANA to create a [text/vnd."
+"sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html) media type. "
+"May  his example be followed by others!"

Oups.
diff --git "a/Debian/debi\303\242neries/2019.en.po" "b/Debian/debi\303\242neries/2019.en.po"
deleted file mode 100644
index c2fae18..0000000
--- "a/Debian/debi\303\242neries/2019.en.po"
+++ /dev/null
@@ -1,70 +0,0 @@
-# SOME DESCRIPTIVE TITLE
-# Copyright (C) YEAR Free Software Foundation, Inc.
-# This file is distributed under the same license as the PACKAGE package.
-# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
-#
-#, fuzzy
-msgid ""
-msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2019-05-22 14:25+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta date=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!tag Debian]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta title=\"Debian en 2019: plus fort que jamais\"]]\n"
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Comme Norbert, j'ai été interloqué par une opinion récemment publiée sur "
-"Planet Debian par un long compagnon de route de Debian disant « C'était bon "
-"en 1990.  Ça ne l'est plus maintenant » à propos des frictions "
-"technologiques empêchant Debian d'évoluer, prenant comme example le fait que "
-"la plupart de nos infrastructures ne permettent pas d'avoir un appercu de "
-"Debian en temps réel: des changements mettent plusieurs minutes, heures, "
-"voire plus, pour être visibles."
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid ""
-"Debian a ses deux pieds fermement dans le XXIème siècle.  Parmis les\n"
-"innovations majeurs depuis 2010: nos paquets sont testés régulièrement "
-"après\n"
-"leur publication (<https://ci.debian.net/>).  Les paquets cassés sont "
-"retirés\n"
-"automatiquement de la future distribution stable en preparation.  De plus en "
-"plus\n"
-"de nos paquets peuvent être reconstruits à l'identique (<>)\n"
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"(Le blog parle aussi des frictions sociales; je pense qu'on est tous "
-"d'accord que c'était mauvais dans les années 90 et que ça l'est toujours "
-"autant mainteant.  Je pense que ça ne changera pas tant que le principal "
-"lieu de recherche de consensus restera nos listes de diffusion "
-"électronique.)"
-msgstr ""

updated PO files
diff --git "a/Debian/debi\303\242neries/2019.en.po" "b/Debian/debi\303\242neries/2019.en.po"
new file mode 100644
index 0000000..c2fae18
--- /dev/null
+++ "b/Debian/debi\303\242neries/2019.en.po"
@@ -0,0 +1,70 @@
+# 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: 2019-05-22 14:25+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Debian en 2019: plus fort que jamais\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Comme Norbert, j'ai été interloqué par une opinion récemment publiée sur "
+"Planet Debian par un long compagnon de route de Debian disant « C'était bon "
+"en 1990.  Ça ne l'est plus maintenant » à propos des frictions "
+"technologiques empêchant Debian d'évoluer, prenant comme example le fait que "
+"la plupart de nos infrastructures ne permettent pas d'avoir un appercu de "
+"Debian en temps réel: des changements mettent plusieurs minutes, heures, "
+"voire plus, pour être visibles."
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"Debian a ses deux pieds fermement dans le XXIème siècle.  Parmis les\n"
+"innovations majeurs depuis 2010: nos paquets sont testés régulièrement "
+"après\n"
+"leur publication (<https://ci.debian.net/>).  Les paquets cassés sont "
+"retirés\n"
+"automatiquement de la future distribution stable en preparation.  De plus en "
+"plus\n"
+"de nos paquets peuvent être reconstruits à l'identique (<>)\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"(Le blog parle aussi des frictions sociales; je pense qu'on est tous "
+"d'accord que c'était mauvais dans les années 90 et que ça l'est toujours "
+"autant mainteant.  Je pense que ça ne changera pas tant que le principal "
+"lieu de recherche de consensus restera nos listes de diffusion "
+"électronique.)"
+msgstr ""
diff --git "a/Debian/debi\303\242neries/mime-iana.en.po" "b/Debian/debi\303\242neries/mime-iana.en.po"
new file mode 100644
index 0000000..befec6e
--- /dev/null
+++ "b/Debian/debi\303\242neries/mime-iana.en.po"
@@ -0,0 +1,47 @@
+# 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: 2019-05-22 14:25+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=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Wed, 22 May 2019 22:29:09 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Enregistrez vos types media auprès de l'IANA !\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"En qualité de mainteneur du paquet "
+"(`mime-support`)[https://packages.debian.org/mime-support] dans Debian, je "
+"voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à "
+"l'IANA pour créer le type media "
+"[text/vnd.sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html).  "
+"Que son example soit suivi !"
+msgstr ""

Kudos
diff --git "a/Debian/debi\303\242neries/mime-iana.mdwn" "b/Debian/debi\303\242neries/mime-iana.mdwn"
new file mode 100644
index 0000000..e964b41
--- /dev/null
+++ "b/Debian/debi\303\242neries/mime-iana.mdwn"
@@ -0,0 +1,12 @@
+[[!meta date="Wed, 22 May 2019 22:29:09 +0900"]]
+[[!meta updated="Wed, 22 May 2019 22:29:09 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Enregistrez vos types media auprès de l'IANA !"]]
+
+En qualité de mainteneur du paquet
+(`mime-support`)[https://packages.debian.org/mime-support] dans Debian, je
+voudrais dire « kudos » à Petter Reinholdtsen, qui a ouvert un ticket à l'IANA
+pour créer le type media
+[text/vnd.sosi](http://people.skolelinux.org/pere/blog/MIME_type__text_vnd_sosi__for_SOSI_map_data.html).
+Que son example soit suivi !

typo
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index e8bf6b6..5a67836 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -195,7 +195,7 @@ Genes and pathways
 
 
 Epigenome
----------`
+---------
 
  - “Knobs” of heterochromatin strongly marked by H3K9me3 and enriched in H3K4me3 are prominent in
    endocycling cells ([[Spada, Vincent and Thompson (2005)|biblio/15791412]]).  H4K20me2 also

creating tag page tags/H3S10p
diff --git a/tags/H3S10p.mdwn b/tags/H3S10p.mdwn
new file mode 100644
index 0000000..15d9e1e
--- /dev/null
+++ b/tags/H3S10p.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H3S10p"]]
+
+[[!inline pages="tagged(H3S10p)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/H4K16Ac
diff --git a/tags/H4K16Ac.mdwn b/tags/H4K16Ac.mdwn
new file mode 100644
index 0000000..2de1cea
--- /dev/null
+++ b/tags/H4K16Ac.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H4K16Ac"]]
+
+[[!inline pages="tagged(H4K16Ac)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/H3S28p
diff --git a/tags/H3S28p.mdwn b/tags/H3S28p.mdwn
new file mode 100644
index 0000000..53ccd42
--- /dev/null
+++ b/tags/H3S28p.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H3S28p"]]
+
+[[!inline pages="tagged(H3S28p)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/H4K20me2
diff --git a/tags/H4K20me2.mdwn b/tags/H4K20me2.mdwn
new file mode 100644
index 0000000..62ec723
--- /dev/null
+++ b/tags/H4K20me2.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H4K20me2"]]
+
+[[!inline pages="tagged(H4K20me2)" actions="no" archive="yes"
+feedshow=10]]

H4K20me2
diff --git a/biblio/15937898.mdwn b/biblio/15937898.mdwn
new file mode 100644
index 0000000..14a88d9
--- /dev/null
+++ b/biblio/15937898.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Histone H4 post-translational modifications in chordate mitotic and endoreduplicative cell cycles."]]
+[[!tag Oikopleura H4K20me2 H3S28p H3S10p H4K16Ac]]
+
+Spada F, Chioda M, Thompson EM.
+
+J Cell Biochem. 2005 Aug 1;95(5):885-901. doi:10.1002/jcb.20416
+
+Histone H4 post-translational modifications in chordate mitotic and endoreduplicative cell cycles.
+
+[[!pmid 15937898 desc="Knobs are also seem to be in H4K20me2.  In endocycling cells, H4K20me2 tends to be stronger in BrdU-negative (short pulse) cells.  CldU/IdU staining confirms that H4K20me2 decreases during the S phase of endocycling cells.  In mitotically cycling cells, BrdU-low cells tended to be H4K20me2-weak.  Strong H3S28p and H3S10p staining (M phase markers) correlated with strong H4K20me2 staining.  In NIH3T3 cells, H4K20me2 peaks at M phase and then decreases from G1 to G2.  H4K16Ac stainings were not reproducible across antibodies."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 52ea178..e8bf6b6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -198,12 +198,15 @@ Epigenome
 ---------`
 
  - “Knobs” of heterochromatin strongly marked by H3K9me3 and enriched in H3K4me3 are prominent in
-   endocycling cells ([[Spada, Vincent and Thompson (2005)|biblio/15791412]]).
+   endocycling cells ([[Spada, Vincent and Thompson (2005)|biblio/15791412]]).  H4K20me2 also
+   seems to be enriched ([[Spada, Chioda and Thompson (2006)|biblio/15937898]]).
  - Histone 3.3 phosphorylation is seen in mitotic and meiotic cells, but not in
    endocycling ones ([[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]]).
  - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
  - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
-
+ - H4K20me2 decreases during S phase.  In mitotic cells, it then increases at M
+   phase, while in endocycling cells, it increases directly after the end of
+   the S phase ([[Spada, Chioda and Thompson (2006)|biblio/15937898]]).
 
 Transcriptome
 -------------

creating tag page tags/H42K20me2
diff --git a/tags/H42K20me2.mdwn b/tags/H42K20me2.mdwn
new file mode 100644
index 0000000..892e12b
--- /dev/null
+++ b/tags/H42K20me2.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H42K20me2"]]
+
+[[!inline pages="tagged(H42K20me2)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/H4K8Ac
diff --git a/tags/H4K8Ac.mdwn b/tags/H4K8Ac.mdwn
new file mode 100644
index 0000000..8f5e2b3
--- /dev/null
+++ b/tags/H4K8Ac.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H4K8Ac"]]
+
+[[!inline pages="tagged(H4K8Ac)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/H3K4me2
diff --git a/tags/H3K4me2.mdwn b/tags/H3K4me2.mdwn
new file mode 100644
index 0000000..7b1003c
--- /dev/null
+++ b/tags/H3K4me2.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H3K4me2"]]
+
+[[!inline pages="tagged(H3K4me2)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/H3K4me4
diff --git a/tags/H3K4me4.mdwn b/tags/H3K4me4.mdwn
new file mode 100644
index 0000000..c383d66
--- /dev/null
+++ b/tags/H3K4me4.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H3K4me4"]]
+
+[[!inline pages="tagged(H3K4me4)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/5mC
diff --git a/tags/5mC.mdwn b/tags/5mC.mdwn
new file mode 100644
index 0000000..117328a
--- /dev/null
+++ b/tags/5mC.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged 5mC"]]
+
+[[!inline pages="tagged(5mC)" actions="no" archive="yes"
+feedshow=10]]

Café hier
diff --git a/biblio/17288541.mdwn b/biblio/17288541.mdwn
new file mode 100644
index 0000000..f2f61b0
--- /dev/null
+++ b/biblio/17288541.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura."]]
+[[!tag Oikopleura]]
+
+Biol Cell. 2007 May;99(5):273-87 doi:10.1042/BC20060124
+
+Spada F, Koch J, Sadoni N, Mitchell N, Ganot P, De Boni U, Zink D, Thompson EM.
+
+Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura.
+
+[[!pmid 17288541 desc="“[In endocycling cells,] simultaneous staining of DNA, RNA and membranes showed [...] deep invaginations of the nuclear envelope.”  “O. dioica endocycling nuclei showed no polytenization or in loco gene amplification.”  “An oikosin 6 probe [indicated] a family of related genes at multiple loci.  Oikosin 4 and 6 were physically linked in a number of BAC clones.”  “[Antibodies against splicing factors] failed to detect speckles in O. dioica endocycling nuclei and no interchromatin cluster granules were observed in the TEM images, suggesting these nuclei lack prominent splicing-factor domains.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 30b8f0b..52ea178 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -199,6 +199,8 @@ Epigenome
 
  - “Knobs” of heterochromatin strongly marked by H3K9me3 and enriched in H3K4me3 are prominent in
    endocycling cells ([[Spada, Vincent and Thompson (2005)|biblio/15791412]]).
+ - Histone 3.3 phosphorylation is seen in mitotic and meiotic cells, but not in
+   endocycling ones ([[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]]).
  - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
  - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
 
@@ -287,8 +289,9 @@ Development
    Postlethwait (2000)|biblio/10753519]]).
  - Expression of development genes is retarded by polyunsaturated aldehydes produced
    by diatoms ([[Torres-Águila and coll., 2018|biblio/30272001]]).
- - Histone 3.3 phosphorylation is seen in mitotic and meiotic cells, but not in
-   endocycling ones ([[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]]).
+ - Endocycling cells show no polytenisation nor _in loco_ amplifications.  Deep invaginations
+   of the nuclear envelopper are shown by simultaneous staining of DNA, RNA and membranes
+   ([[Spada and coll., 2007|biblio/17288541]]).
 
 
 Anatomy

Café
diff --git a/biblio/15791412.mdwn b/biblio/15791412.mdwn
new file mode 100644
index 0000000..06da2d0
--- /dev/null
+++ b/biblio/15791412.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin."]]
+[[!tag Oikopleura histone H3K9me2 H42K20me2 5mC H3K4me4 H3K9me3 H4K8Ac H3K4me2]]
+
+Chromosome Res. 2005;13(1):57-72 doi:10.1007/s10577-005-6845-6
+
+Spada F, Vincent M, Thompson EM.
+
+Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin.
+
+[[!pmid 15791412 desc="“Knobs” of heterochromatin, prominently visible in endocycling nuclei, are mildly enriched for H3K9me2 and H42K20me2 and 5mC, enriched for H3K4me4, highly enriched for H3K9me3 and depleted in H4K8Ac and H3K4me2 and elongating RNA Polymerase II.  “Inhibition of polII transcription in NIH3T3 cells does not diminish global levels of H3 Me3K4 and results in increased H3 Me3K4 labelling in pericentromeric chromatin.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5df283d..30b8f0b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -83,8 +83,6 @@ Genome
    [[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]].
  - Genome compaction in _Oikopleura_ and _Ciona_ have been reviewed in parallel
    by [[Berná and Alvarez-Valin (2014)|biblio/25008364]].
- - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
- - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
  - 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
@@ -196,6 +194,15 @@ Genes and pathways
    the EF-rab chimera Rasef and EFcab4/Rab44.
 
 
+Epigenome
+---------`
+
+ - “Knobs” of heterochromatin strongly marked by H3K9me3 and enriched in H3K4me3 are prominent in
+   endocycling cells ([[Spada, Vincent and Thompson (2005)|biblio/15791412]]).
+ - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
+ - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
+
+
 Transcriptome
 -------------
 

Expand.
diff --git a/biblio/16448564.mdwn b/biblio/16448564.mdwn
index c916d41..037ef84 100644
--- a/biblio/16448564.mdwn
+++ b/biblio/16448564.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="The RIN: an RNA integrity number for assigning integrity values to RNA measurements."]]
 [[!tag method product RNA]]
+
+BMC Mol Biol. 2006 Jan 31;7:3 doi:10.1186/1471-2199-7-3
+
+Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T.
+
+The RIN: an RNA integrity number for assigning integrity values to RNA measurements.
+
 [[!pmid 16448564 desc="Primary reference for RINs"]]

Café
diff --git a/biblio/31053062.mdwn b/biblio/31053062.mdwn
new file mode 100644
index 0000000..11ca99c
--- /dev/null
+++ b/biblio/31053062.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication."]]
+[[!tag Nanopore mitochondrion]]
+
+Gan HM, Grandjean F, Jenkins TL, Austin CM.
+
+BMC Genomics. 2019 May 3;20(1):335. doi: 10.1186/s12864-019-5704-3.
+
+Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication.
+
+[[!pmid 31053062 desc="Canu assembly after collecting reads matching an illumina-assembled draft genome."]]

Café
diff --git a/biblio/30424578.mdwn b/biblio/30424578.mdwn
new file mode 100644
index 0000000..b74fa20
--- /dev/null
+++ b/biblio/30424578.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes."]]
+[[!tag Nanopore mitochondrion]]
+
+Wang S, Song Q, Li S, Hu Z, Dong G, Song C, Huang H, Liu Y.
+
+Genes (Basel). 2018 Nov 12;9(11). pii: E547. doi:10.3390/genes9110547
+
+Assembly of a Complete Mitogenome of _Chrysanthemum nankingense_ Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes.
+
+[[!pmid 30424578 desc="“For the assembly using the ONT-only assembly method, the mitochondrial long reads were firstly filtered from the total ONT sequencing data using BWA v0.7.16 and SAMtools v1.9 using the contig of hybrid assembly as the reference. Then, an ONT-only assembly was generated using Canu v1.7.”"]]

Café
diff --git a/biblio/30928201.mdwn b/biblio/30928201.mdwn
new file mode 100644
index 0000000..980078e
--- /dev/null
+++ b/biblio/30928201.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes."]]
+[[!tag Nanopore mitochondrion]]
+
+Gan HM, Linton SM, Austin CM.
+
+Mar Genomics. 2019 Mar 27. pii: S1874-7787(18)30218-6. doi:10.1016/j.margen.2019.02.002
+
+Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes.
+
+[[!pmid 30928201 desc="9 Nanopore reads were identified by alignment to reference mitochondrial sequences with mimimap2, and then used for hybrid assembly."]]

Café télomères.
diff --git a/biblio/17123503.mdwn b/biblio/17123503.mdwn
new file mode 100644
index 0000000..cd086dd
--- /dev/null
+++ b/biblio/17123503.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura."]]
+[[!tag Oikopleura telomere]]
+
+Ganot P, Kallesøe T, Thompson EM.
+
+Dev Biol. 2007 Feb 15;302(2):577-90 doi:10.1016/j.ydbio.2006.10.022
+
+The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura.
+
+[[!pmid 17123503 desc="In early meiotic nuclei, telomeres and nuclear pore complexes ”cluster in non-overlapping regions of the nuclear envelope”.  During some stages of oocyte maturation, the telomeres of the endocycling nurse cells “clustered at the nuclear periphery, in a compartment with no detectable elongating RNA polymerase II”.  Colchicine treatment induced early oocyte differenciation."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 567c8c5..5df283d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -242,6 +242,12 @@ Development
    culture conditions might differ.
  - Increased food abundance increases egg number but does not change diameter nor
    generation time ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).
+ - Colchicine treatment induced early differenciation of the oocytes
+   ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
+ - Telomeres are localised at the nuclear envelope and do not overlap with nuclear
+   pore complexes in early meiotic oocytes before H3S10 phosphorylation.  In nurse
+   cells at a later stage of oocyte development, the telomeres localise in silent
+   chromatin at the nuclear periphery ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
  - 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.

MthRnl
diff --git a/biblio/18829718.mdwn b/biblio/18829718.mdwn
new file mode 100644
index 0000000..13248de
--- /dev/null
+++ b/biblio/18829718.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA."]]
+[[!tag enzyme ligase adenylylation]]
+
+Torchia C, Takagi Y, Ho CK.
+
+Nucleic Acids Res. 2008 Nov;36(19):6218-27. doi:10.1093/nar/gkn602
+
+Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA.
+
+[[!pmid 18829718 desc="Used in the NEB's 5´ DNA Adenylation Kit.  Lacks specificity for RNA and DNA."]]
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index baa0d3c..2ba035e 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -13,7 +13,7 @@ On T4 RNL1:
    Adenylation efficiency after 6h: C >> U ~ A > G ([[McLaughlin et al., 1985|biblio/3978074]]).
  - Also used for single-strand DNA ligation ([[Tessier, Brousserau & Vernet, 1986|biblio/3799962]])
    with PEG and hexamine cobalt chloride (HCC) as additives.
- - Can dephoshporylate RNA 3′ ends ([[Krug & Uhlenbeck, 1982|biblio/7082652]]).  
+ - Can dephoshporylate RNA 3′ ends ([[Krug & Uhlenbeck, 1982|biblio/7082652]]).
 
 On T4 RNL2:
 
@@ -37,12 +37,19 @@ DNA and RNA ligases can be used to adenylylate a substrate.
  - [[Hoffmann and McLaughlin (1987)|biblio/3299268]] used T4 RNL 1 to
    adenylylate RNA, and noted that ssNpR(A) are good acceptors, and pCpN
    are good donors.
+ - [[Wang and Unrau (2002)|biblio/12503310]] noted that purified
+   recombinant ligase can be partly adenylylated, which blocks the
+   reaction on pre-adenylylated substrates.  Pre-incubation with
+   pyrophosphate can displace AMP moiety.  Commercial ligases
+   are reported to contain mostly non-adenylylated proteins.
  - [[Ho, Wang, Lima and Shuman (2004)|biblio/14962393]] reported the
    use of RNL(1-249) on pre-adenylylated RNA in absence of ATP for
    avoiding concatemerisation.
  - [[Silverman (2004)|biblio/15037782]] reported the use a complementary
    DNA oligonucleotide (leaving 3-4 protruding 5'ribonucleotides) when
    adenylylating with T4 RNL 1.
+ - [[Torchia, Takagi and Ho (2008)|biblio/18829718]] reported the use
+   of the Methanobacterium RNA ligase (MthRnl) to adenylylate RNA.
 
 [[!inline pages="tagged(ligase)" limit=0]]
 [[!meta title="pages tagged adenylylation"]]

adenylylation
diff --git a/tags/adenylylation.mdwn b/tags/adenylylation.mdwn
index a33771e..3a77ffa 100644
--- a/tags/adenylylation.mdwn
+++ b/tags/adenylylation.mdwn
@@ -3,7 +3,7 @@
 Adenylylation
 =============
 
-Adenylylation is the addition of an AMP moiety to a phosphorylated end.  In vitro,
-it is performed by [[ligases|ligases]].
+Adenylylation is the addition of an AMP moiety to a phosphorylated end.  In
+vitro, it is performed by ligases.  See the [[ligase]] tag for details.
 
 [[!inline pages="tagged(adenylylation)" limit=0]]
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 0fd14bf..baa0d3c 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -2,9 +2,6 @@
 
 Work in progress.
 
-DNA and RNA ligases can be used to adenylylate a substrate; seee the
-[[adenylylation]] tag for details.
-
 Ligases are inhibited by high concentrations of ATP ([[Tessier, Brousserau &
 Vernet, 1986|biblio/3799962]] and many others).
 
@@ -32,4 +29,23 @@ On T4 RNL2:
    linker to RNA ends, thus prevents unwanted ligation products
    ([[Viollet et al., 2011|biblio/21722378]]).
 
+DNA and RNA ligases can be used to adenylylate a substrate.
+
+ - [[McLaughlin, Piel and Graeser (1985)|biblio/3978074]] noted that
+   adenylylated RNA is a better substrate for T4 RNA ligase, and that
+   adenylylation efficiency after 6h was C » U ~ A > G. 
+ - [[Hoffmann and McLaughlin (1987)|biblio/3299268]] used T4 RNL 1 to
+   adenylylate RNA, and noted that ssNpR(A) are good acceptors, and pCpN
+   are good donors.
+ - [[Ho, Wang, Lima and Shuman (2004)|biblio/14962393]] reported the
+   use of RNL(1-249) on pre-adenylylated RNA in absence of ATP for
+   avoiding concatemerisation.
+ - [[Silverman (2004)|biblio/15037782]] reported the use a complementary
+   DNA oligonucleotide (leaving 3-4 protruding 5'ribonucleotides) when
+   adenylylating with T4 RNL 1.
+
 [[!inline pages="tagged(ligase)" limit=0]]
+[[!meta title="pages tagged adenylylation"]]
+
+
+[[!inline pages="tagged(adenylylation)" limit=0]]

Adenylylation.
diff --git a/tags/adenylylation.mdwn b/tags/adenylylation.mdwn
index 0c0fe76..a33771e 100644
--- a/tags/adenylylation.mdwn
+++ b/tags/adenylylation.mdwn
@@ -1,4 +1,9 @@
 [[!meta title="pages tagged adenylylation"]]
 
-[[!inline pages="tagged(adenylylation)" actions="no" archive="yes"
-feedshow=10]]
+Adenylylation
+=============
+
+Adenylylation is the addition of an AMP moiety to a phosphorylated end.  In vitro,
+it is performed by [[ligases|ligases]].
+
+[[!inline pages="tagged(adenylylation)" limit=0]]

Link to adenylylation tag.
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 015ca74..0fd14bf 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -2,6 +2,9 @@
 
 Work in progress.
 
+DNA and RNA ligases can be used to adenylylate a substrate; seee the
+[[adenylylation]] tag for details.
+
 Ligases are inhibited by high concentrations of ATP ([[Tessier, Brousserau &
 Vernet, 1986|biblio/3799962]] and many others).
 

simplify
diff --git a/biblio/22770214.mdwn b/biblio/22770214.mdwn
index 9c862cb..f4e9a08 100644
--- a/biblio/22770214.mdwn
+++ b/biblio/22770214.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="U1 snRNP determines mRNA length and regulates isoform expression."]]
-[[!tag not_read method polyadenylation splicing]]
+[[!tag not_read method splicing]]
 
 Berg MG, Singh LN, Younis I, Liu Q, Pinto AM, Kaida D, Zhang Z, Cho S, Sherrill-Mix S, Wan L, Dreyfuss G.
 
diff --git a/tags/polyadenylation.mdwn b/tags/polyadenylation.mdwn
deleted file mode 100644
index 81e4e3f..0000000
--- a/tags/polyadenylation.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged polyadenylation"]]
-
-[[!inline pages="tagged(polyadenylation)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/telomere
diff --git a/tags/telomere.mdwn b/tags/telomere.mdwn
new file mode 100644
index 0000000..3d39944
--- /dev/null
+++ b/tags/telomere.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged telomere"]]
+
+[[!inline pages="tagged(telomere)" actions="no" archive="yes"
+feedshow=10]]

Telomeres and PH3.
diff --git a/biblio/17333540.mdwn b/biblio/17333540.mdwn
new file mode 100644
index 0000000..a403704
--- /dev/null
+++ b/biblio/17333540.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica."]]
+[[!tag Oikopleura histone telomere]]
+
+Chromosome Res. 2007;15(2):189-201. doi:10.1007/s10577-006-1112-z
+
+Schulmeister A, Schmid M, Thompson EM.
+
+Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica.
+
+[[!pmid 17333540 desc="Telomeric FISH stainings with a (TTAGGG)n probe. H3.3S31
+is phosphorylated during mitosis and meiosis, and not in endocycling cells.
+“On prometaphase chromosomes [...] H3S28P was restricted to distal chromosomal
+regions adjacent to telomeres whereas H3.3S31P spread throughout entire
+chromosomes.” “[The histone 3.3 genes] contain introns, are found outside
+histone clusters and their transcripts are polyadenylated.” "]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5c2ac56..567c8c5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -79,6 +79,8 @@ 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]])
+ - Telomere sequence is (TTAGGG)n, as evidenced by successful FISH stainings by
+   [[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]].
  - Genome compaction in _Oikopleura_ and _Ciona_ have been reviewed in parallel
    by [[Berná and Alvarez-Valin (2014)|biblio/25008364]].
  - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
@@ -272,6 +274,9 @@ Development
    Postlethwait (2000)|biblio/10753519]]).
  - Expression of development genes is retarded by polyunsaturated aldehydes produced
    by diatoms ([[Torres-Águila and coll., 2018|biblio/30272001]]).
+ - Histone 3.3 phosphorylation is seen in mitotic and meiotic cells, but not in
+   endocycling ones ([[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]]).
+
 
 Anatomy
 -------
@@ -289,6 +294,7 @@ Anatomy
    Electron microscopy shows a large perikaryon, cisternas and a cilium which is inserted
    in the central canal ([[Holmberg and Olsson, 1984|biblio/reissner_oik]]).
 
+
 Physiology
 ----------
 

Café
diff --git a/biblio/12446815.mdwn b/biblio/12446815.mdwn
new file mode 100644
index 0000000..8bfcd80
--- /dev/null
+++ b/biblio/12446815.mdwn
@@ -0,0 +1,20 @@
+[[!meta title="Histone gene complement, variant expression, and mRNA processing in a urochordate Oikopleura dioica that undergoes extensive polyploidization."]]
+[[!tag Oikopleura histone]]
+
+Chioda M, Eskeland R, Thompson EM.
+
+Mol Biol Evol. 2002 Dec;19(12):2247-60 doi:10.1093/oxfordjournals.molbev.a004048
+
+Histone gene complement, variant expression, and mRNA processing in a urochordate Oikopleura dioica that undergoes extensive polyploidization.
+
+ - [Oikopleura dioica H3.1 gene, H4.1 gene, H1.1 gene, and H2A.1 gene](https://www.ncbi.nlm.nih.gov/nuccore/AJ494848)
+ - [Oikopleura dioica H2A.3 gene for histone h2A.3](https://www.ncbi.nlm.nih.gov/nuccore/AJ494849)
+ - [Oikopleura dioica H3.2 gene for histone h3.2](https://www.ncbi.nlm.nih.gov/nuccore/AJ494850)
+ - [Oikopleura dioica partial H2A.2 gene for histone h2A.2](https://www.ncbi.nlm.nih.gov/nuccore/AJ494851)
+ - [Oikopleura dioica partial H2A.4 gene for histone H2A.4](https://www.ncbi.nlm.nih.gov/nuccore/AJ494852)
+ - [Oikopleura dioica mRNA for histone H2A.1a (H2A.1a gene)](https://www.ncbi.nlm.nih.gov/nuccore/AJ494853)
+ - [Oikopleura dioica partial mRNA for histone h2A.1b (H2a.1b gene)](https://www.ncbi.nlm.nih.gov/nuccore/AJ494854)
+ - [Oikopleura dioica partial mRNA for histone h4 (H4 gene)](https://www.ncbi.nlm.nih.gov/nuccore/AJ494855)
+ - [Oikopleura dioica partial mRNA for histone h1.2 (H1.2 gene)](https://www.ncbi.nlm.nih.gov/nuccore/AJ494856)
+
+[[!pmid 12446815 desc="“Densitometric analyses of Southern blots yielded estimates of 9–11 H4 genes, 11–14 H3 genes, 15–19 H2A genes, 18–20 H2B genes, and 4–7 H1 genes.” “The quintet cluster consisted of a central H1 gene flanked by divergently transcribed H3-H4 and H2A-H2B pairs, an organization found in other organisms such as humans. The quintet cluster is extremely compact, covering only 3.5 kb.” “Both visual inspection and PRATT analysis (Jonassen 1997 ) of the sequences 3′ to the conserved stem-loop revealed no consensus 3′ purine-rich histone downstream element (HDE) that interacts with U7 snRNA in the processing of histone mRNAs. In fact, no consensus sequence or pattern motif of any kind was discovered 3′ of the stem-loop in O. dioica histone gene sequences.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7bd4a26..5c2ac56 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -138,6 +138,9 @@ Genes and pathways
 
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]).
+ - “Densitometric analyses of Southern blots yielded estimates of 9–11 H4
+   genes, 11–14 H3 genes, 15–19 H2A genes, 18–20 H2B genes, and 4–7 H1 genes.”
+   [[Chioda, Eskeland and Thompson, 2002|biblio/12446815]]
  - 2 cellulose synthase genes, possibly acquired by horizontal gene transfer
    from an actinobacteria ([[Nakashima and coll., 2004|biblio/14740209]]), were
    found by [[Sagane et al. (2010)|biblio/20335363]] and [[Nakashima et al.
@@ -215,7 +218,8 @@ Transcriptome
    to be older, and among the large introns, the older contain repeat elements less frequently
    than the newer ([[Denoeud et al., 2010|biblio/21097902]]). 
  - 12 developmental stages were studied with tiling arrays by [[Danks et al., 2013|biblio/23185044]].
-
+ - On the histone mRNAs, no purine-rich histone downstream element (HDE) was found
+   by [[Chioda, Eskeland and Thompson in 2002|biblio/12446815]].
 
 Tools
 -----

More minor corrections
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 2d3c63a..b9f8620 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -20,7 +20,7 @@ Nagarajan and Šikić, 2017|biblio/28100585]]).
 
 When coverage is too low for efficient reference-free assembly, related
 references can be used as a guide.  The Ragout software ([[Kolmogorov and
-coll., 2014|biblio/24931998]]), [[Kolmogorov and coll., 2018|biblio/30341161]])
+coll., 2014|biblio/24931998]], [[Kolmogorov and coll., 2018|biblio/30341161]])
 can take multiple reference genomes to guide the assembly of one target.
 Polymorphisms unique to the target genome can be recovered, but chromosome
 fusions are typically hard to detect.  Compared to version 1, version 2 infers

More minor corrections
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index f244ca8..2d3c63a 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -8,11 +8,11 @@ Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows
 for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
-The Flye assembler ([[Kolmogorov and coll. (2018)|biblio/30936562]]) creates an
+The Flye assembler ([[Kolmogorov and coll., 2018|biblio/30936562]]) creates an
 A-Bruijn (assembly) graph from draft contigs using long error-prone reads,
 untangles the graph by resolving repeats, and then uses it to refine the
 contings and increase their accuracy.  (The predecessor of Flye, ABruijn, was
-reported by [[Istace and coll.  (2017)|biblio/28369459]] to be able to assemble
+reported by [[Istace and coll. (2017)|biblio/28369459]] to be able to assemble
 mitochondrial genomes, unlike Canu and other assemblers.)
 
 After assembly, the contigs can be further polished with Racon ([[Vaser, Sović,
@@ -20,7 +20,7 @@ Nagarajan and Šikić, 2017|biblio/28100585]]).
 
 When coverage is too low for efficient reference-free assembly, related
 references can be used as a guide.  The Ragout software ([[Kolmogorov and
-coll., 2014|biblio/24931998), [[Kolmogorov and coll., 2018|biblio/30341161]])
+coll., 2014|biblio/24931998]]), [[Kolmogorov and coll., 2018|biblio/30341161]])
 can take multiple reference genomes to guide the assembly of one target.
 Polymorphisms unique to the target genome can be recovered, but chromosome
 fusions are typically hard to detect.  Compared to version 1, version 2 infers
@@ -38,7 +38,7 @@ Relase notes of HM2 version 20180603 suggest to use “_HapCUT2 or other phasing
 tools to get the high-quality haplotype assembly based on the reference haploid
 assembly_”.
 
-SALSA (Simple AssembLy ScAffolder, [Ghurye and coll., 2017|biblio/28701198]])
+SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis
 that most contact points are due to local (same-chromosome) proximity.  Version
 2 of SALSA uses unitigs and the assembly graph as input ([[Ghurye and coll.,

correction
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index db55c0f..f244ca8 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -8,13 +8,12 @@ Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows
 for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
-The Flye assembler ([[Kolmogorov and coll, bioRxiv
-2018|biblio/30936562]]) creates an A-Bruijn (assembly) graph from draft
-contigs using long error-prone reads, untangles the graph by resolving repeats,
-and then uses it to refine the contings and increase their accuracy.  (The
-predecessor of Flye, ABruijn, was reported by [[Istace and coll.
-(2017)|biblio/28369459]] to be able to assemble mitochondrial genomes, unlike
-Canu and other assemblers.)
+The Flye assembler ([[Kolmogorov and coll. (2018)|biblio/30936562]]) creates an
+A-Bruijn (assembly) graph from draft contigs using long error-prone reads,
+untangles the graph by resolving repeats, and then uses it to refine the
+contings and increase their accuracy.  (The predecessor of Flye, ABruijn, was
+reported by [[Istace and coll.  (2017)|biblio/28369459]] to be able to assemble
+mitochondrial genomes, unlike Canu and other assemblers.)
 
 After assembly, the contigs can be further polished with Racon ([[Vaser, Sović,
 Nagarajan and Šikić, 2017|biblio/28100585]]).

Flye published in Nat. Biotechnol.
diff --git a/biblio/10.1101_247148.mdwn b/biblio/10.1101_247148.mdwn
deleted file mode 100644
index 3b80d26..0000000
--- a/biblio/10.1101_247148.mdwn
+++ /dev/null
@@ -1,10 +0,0 @@
-[[!meta title="Assembly of Long Error-Prone Reads Using Repeat Graphs"]]
-[[!tag genome assembly method]]
-
-Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner
-
-bioRxiv, Posted January 12, 2018.
-
-Assembly of Long Error-Prone Reads Using Repeat Graphs
-
-[[!doi 10.1101/247148 desc="“Flye constructs (overlapping) contigs with possible assembly errors at the initial stage, combines them into an accurate assembly graph, resolves repeats in the assembly graph using small variations between various repeat instances that were left unresolved during the initial assembly stage, constructs a new, less tangled assembly graph based on resolved repeats, and finally outputs accurate contigs as paths in this graph.”"]]
diff --git a/biblio/30936562.mdwn b/biblio/30936562.mdwn
new file mode 100644
index 0000000..77f9c76
--- /dev/null
+++ b/biblio/30936562.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Assembly of Long Error-Prone Reads Using Repeat Graphs"]]
+[[!tag genome assembly method]]
+
+Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner
+
+Nat Biotechnol. 2019 May;37(5):540-546. doi:10.1038/s41587-019-0072-8
+
+Assembly of Long Error-Prone Reads Using Repeat Graphs
+
+[[!pmid 30936562 desc="“Flye constructs (overlapping) contigs with possible assembly errors at the initial stage, combines them into an accurate assembly graph, resolves repeats in the assembly graph using small variations between various repeat instances that were left unresolved during the initial assembly stage, constructs a new, less tangled assembly graph based on resolved repeats, and finally outputs accurate contigs as paths in this graph.”"]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index e5d120f..db55c0f 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -9,7 +9,7 @@ for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
 The Flye assembler ([[Kolmogorov and coll, bioRxiv
-2018|biblio/10.1101_247148]]) creates an A-Bruijn (assembly) graph from draft
+2018|biblio/30936562]]) creates an A-Bruijn (assembly) graph from draft
 contigs using long error-prone reads, untangles the graph by resolving repeats,
 and then uses it to refine the contings and increase their accuracy.  (The
 predecessor of Flye, ABruijn, was reported by [[Istace and coll.

Café
diff --git a/biblio/21297618.mdwn b/biblio/21297618.mdwn
new file mode 100644
index 0000000..fb75f64
--- /dev/null
+++ b/biblio/21297618.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High-throughput single-molecule optofluidic analysis."]]
+[[!tag microfluidic]]
+
+Kim S, Streets AM, Lin RR, Quake SR, Weiss S, Majumdar DS.
+
+Nat Methods. 2011 Mar;8(3):242-5. doi:10.1038/nmeth.1569
+
+High-throughput single-molecule optofluidic analysis.
+
+[[!pmid 21297618 desc="A microfluidics device sequentially generates various combinations of reagent concentrations exploring the parameter space of a reaction or a phenomenon, for instance: iunfluence of salts and strand molarity on DNA hybridisation, or influence of glutamate concentration on RNA polymerase activity.  In both cases, the readout was a FRET measurement of two fluorophores bound at two extremities of a DNA probe."]]

Typos.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f7b9186..7bd4a26 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -183,9 +183,9 @@ Genes and pathways
    An alternative or microhomology (MH)-driven end joining pathway is active
    and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
  - 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]].
+   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]]).
  - More than 50 % of the Rab family is lost ([[Coppola and coll., 2019|biblio/31028425]]):
    Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, RabX1 and the
    the EF-rab chimera Rasef and EFcab4/Rab44.

Café
diff --git a/biblio/31028425.mdwn b/biblio/31028425.mdwn
new file mode 100644
index 0000000..83983ba
--- /dev/null
+++ b/biblio/31028425.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The evolutionary landscape of the Rab family in chordates."]]
+[[!tag Oikopleura]]
+
+Coppola U, Ristoratore F, Albalat R, D'Aniello S.
+
+Cell Mol Life Sci. 2019 Apr 26. doi:10.1007/s00018-019-03103-7
+
+The evolutionary landscape of the Rab family in chordates.
+
+[[!pmid 31028425 desc="“O. dioica lineage showed 11 additional losses, Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, Rasef, EFcab4/Rab44 and RabX1. This species has, therefore, lost almost the 50% of the Rab toolkit, being the metazoan species with the smallest number of Rab subfamilies described so far.” “We detected [...] 5 independent duplications in O. dioica (Rab5/17, Rab6, Rab7, Rab10, Rab35).”  O. dioica lost the Rab-EF chimeras Rasef and EFcab4/44, but kept Rab46."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cfaa2fe..f7b9186 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -165,6 +165,8 @@ Genes and pathways
    muscular arouse after the separation of the appendicularian and ascidian lineages,
    and 3 are cytoplasmic, one of them being intronless and possibly originated by
    retrotransposition.
+ - Duplications in the Rab family: Rab5/17, Rab6, Rab7, Rab10, Rab35.  The EF-Rab chimera
+   Rab46 is kept ([[Coppola and coll., 2019|biblio/31028425]]).  See below for the losses. 
 
 ### Lost
 
@@ -184,7 +186,9 @@ Genes and pathways
    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]].
-
+ - More than 50 % of the Rab family is lost ([[Coppola and coll., 2019|biblio/31028425]]):
+   Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, RabX1 and the
+   the EF-rab chimera Rasef and EFcab4/Rab44.
 
 
 Transcriptome

Café
diff --git a/biblio/30217598.mdwn b/biblio/30217598.mdwn
new file mode 100644
index 0000000..1983a69
--- /dev/null
+++ b/biblio/30217598.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Developmental atlas of appendicularian Oikopleura dioica actins provides new insights into the evolution of the notochord and the cardio-paraxial muscle in chordates."]]
+[[!tag Oikopleura]]
+
+Dev Biol. 2018 Sep 11. pii: S0012-1606(17)30888-6. doi:10.1016/j.ydbio.2018.09.003
+
+Almazán A, Ferrández-Roldán A, Albalat R, Cañestro C.
+
+Developmental atlas of appendicularian Oikopleura dioica actins provides new insights into the evolution of the notochord and the cardio-paraxial muscle in chordates.
+
+[[!pmid 30217598 desc="7 actins: 4 muscular that have the same common ancestor with all muscular actins from other species, and 3 cytoplasmic ones."]]
+
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b7b9f7b..cfaa2fe 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -161,6 +161,10 @@ Genes and pathways
  - A single ortholog of _Brachyury_ (_TBXT_, or _T_) was cloned by [[Bassham
    and Postlethwait (2000)|biblio/10753519]].  Accession number:
    [[AF204208|https://www.ncbi.nlm.nih.gov/nuccore/AF204208]].
+ - 7 actin genes were found by [[Almazán and coll. (2018)|biblio/30217598]].  4 of them are
+   muscular arouse after the separation of the appendicularian and ascidian lineages,
+   and 3 are cytoplasmic, one of them being intronless and possibly originated by
+   retrotransposition.
 
 ### Lost
 

RT clamping.
diff --git a/biblio/20876692.mdwn b/biblio/20876692.mdwn
index a22c239..5fae50b 100644
--- a/biblio/20876692.mdwn
+++ b/biblio/20876692.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Reverse transcriptases can clamp together nucleic acids strands with two complementary bases at their 3'-termini for initiating DNA synthesis."]]
-[[!tag template_switching enzyme manganese]]
+[[!tag reverse_transcription template_switching enzyme manganese]]
 
 Oz-Gleenberg I, Herschhorn A, Hizi A.
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 22f5603..8b290f1 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -11,6 +11,7 @@ _(redaction in progress)_
  - [[T4 bacteriophage gene 32 protein|ssbp]] (T4gp32, [[Kenzelmann _et al._, 2004|biblio/15028277]],
    [[Piché _et al._, 2005|biblio/16461948]]).
 
+
 ### DNA-dependent DNA polymerase activity
 
  - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.
@@ -20,6 +21,16 @@ _(redaction in progress)_
    artefacts ([[Perocchi et al., 2007|biblio/17897965]], [[Kanamori-Katayama et al., 2011|biblio/21596820]]).
  - Its error profile is different from other DNA polymerases ([[de Paz et al., 2018|biblio/29718339]]).
 
+
+### Clamping activity
+
+ - Reverse transcriptases can bind duplexes that are only annealed through a
+   2-nt homology.  A single nucleotide is not enough and GC-rich sequences are
+   strongly favoured.  This binding is enhanced by dGTP.  The assays demonstrating
+   this used an ELISA approach ([[Oz-Gleenberg, Herschhorn and Hizi,
+   2011|biblio/20876692]]).
+
+
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 
 Like other DNA polymerases ([[Clark, 1988|biblio/2460825]]), reverse

A-addition by RTase.
diff --git a/biblio/23697550.mdwn b/biblio/23697550.mdwn
index ce3450e..5bd2b28 100644
--- a/biblio/23697550.mdwn
+++ b/biblio/23697550.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing."]]
-[[!tag enzyme method small_RNA template_switching]]
+[[!tag reverse_transcription enzyme method small_RNA template_switching]]
 
 Mohr S, Ghanem E, Smith W, Sheeter D, Qin Y, King O, Polioudakis D, Iyer VR, Hunicke-Smith S, Swamy S, Kuersten S, Lambowitz AM.
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index c73e930..22f5603 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -40,6 +40,9 @@ 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.
 
+ - [[Mohr and coll, 2013|biblio/23697550]] showed that the Thermostable group
+   II intron reverse transcriptase also adds non-templated As.
+
 
 ### Templated TdT activity
 

Café
diff --git a/biblio/30872679.mdwn b/biblio/30872679.mdwn
new file mode 100644
index 0000000..d7c662a
--- /dev/null
+++ b/biblio/30872679.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway."]]
+[[!tag OIST genome]]
+
+Sci Rep. 2019 Mar 14;9(1):4607. doi:10.1038/s41598-019-40955-2
+
+Nishitsuji K, Arimoto A, Higa Y, Mekaru M, Kawamitsu M, Satoh N, Shoguchi E.
+
+Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway.
+
+[[!pmid 30872679 desc="Ito-mozuku.  The L-fucokinase and GDP-fucose pyrophosphorylase proteins are fused, like in C. okamuranus."]]

Café
diff --git a/biblio/21097902.mdwn b/biblio/21097902.mdwn
index 1b40479..3be4886 100644
--- a/biblio/21097902.mdwn
+++ b/biblio/21097902.mdwn
@@ -15,4 +15,6 @@ Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D.
 
 Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.
 
+Link to [[Supplementary Material|https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/bin/NIHMS352565-supplement.pdf]].
+
 [[!pmid 21097902 desc="1,260 scaffolds (70.4 Mb), 395 Kb N50, 15,152 ESTs clusters in the reference assembly, excluding 4,196 the allelic scaffolds (45 Mb, 21.8 Kb N50)."]]

Café
diff --git a/biblio/10753519.mdwn b/biblio/10753519.mdwn
new file mode 100644
index 0000000..f6aab4a
--- /dev/null
+++ b/biblio/10753519.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Brachyury (T) expression in embryos of a larvacean urochordate, Oikopleura dioica, and the ancestral role of T."]]
+[[!tag Oikopleura]]
+
+Bassham S and Postlethwait J.
+
+Dev Biol. 2000 Apr 15;220(2):322-32 DOI:10.1006/dbio.2000.9647
+
+Brachyury (T) expression in embryos of a larvacean urochordate, Oikopleura dioica, and the ancestral role of T.
+
+[[!pmid 10753519 desc="O. dioica contains a single ortholog of Brachyury (T, TBXT).  Early expression appears restricted to notochord precursors.  Later, subchordal cells, and even later, hindgut cells also express TBXT.  Translated cDNA sequence was deposited under accession number AAG22592. "]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0671a7c..b7b9f7b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -27,7 +27,10 @@ Food tested in laboratory (totally incomplete list): _Isochrysis galbana_ (5.5
 sp._ (3.5 µm) [[Acuña and Kiefer, 2000|biblio/10.4319_lo.2000.45.3.0608]].
 The diatom _Chaetoceros calcitrans_, often used as a food, can be toxic at high
 concentrations, probably because of the production of biotoxins
-([[Torres-Águila and coll., 2018|biblio/30272001]]).
+([[Torres-Águila and coll., 2018|biblio/30272001]]).  The Postlethwait lab
+has been feeding their animals with (_Dunaliella tertiolecta_, _Isochrysis
+galbana_, _Rhodomonas lens_, _Nanochloropsis sp._, and _Micromonas sp._ (strain Dw-8))
+[[Bassham and Postlethwait (2000)|biblio/10753519]]).
 
 Parasites: _Oodinium pouchetii_ and others.
 
@@ -155,6 +158,9 @@ Genes and pathways
  - _O. dioica_ has 83 homeobox genes, according to [[Edvardsen and coll., 2005|biblio/15649342]].
  - Southern blot analysis suggest the presence of a SCO-spondin gene in _O.
    dioica_ ([[Gobron and coll., 1999|biblio/10197783]]).
+ - A single ortholog of _Brachyury_ (_TBXT_, or _T_) was cloned by [[Bassham
+   and Postlethwait (2000)|biblio/10753519]].  Accession number:
+   [[AF204208|https://www.ncbi.nlm.nih.gov/nuccore/AF204208]].
 
 ### Lost
 
@@ -244,11 +250,14 @@ Development
    rise to the posterior part of the digestive tract (rectum), but not the anus.
    Removal of the trunk suggests that it is not necessary for initiation of the
    migration ([[Kishi and coll, 2014|biblio/25224225]]).
+ - Notochord cell precursors express _Brachyury_ like in other chordates
+   ([[Bassham and Postlethwait (2000)|biblio/10753519]]).
  - The subchordal cell precursors migrate along the right side of the notochord
    in the space that has been filled with endodermal strand cells.  Amputation
    experiments indicate that the posterior portion of the tail is required for
    posterior migration of subchordal cell precursors ([[Kishi and coll,
-   2014|biblio/25224225]]).
+   2014|biblio/25224225]]).  They express _Brachyury_ ([[Bassham and
+   Postlethwait (2000)|biblio/10753519]]).
  - Expression of development genes is retarded by polyunsaturated aldehydes produced
    by diatoms ([[Torres-Águila and coll., 2018|biblio/30272001]]).
 

ワカレオタマボヤ
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7ee55bc..0671a7c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -11,7 +11,7 @@ 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_").
+("_Appendicularia_").  The japanese name of _O. dioica_ is ワカレオタマボヤ.
 
 Some links:
 

typo
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index cd060d2..e5d120f 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -50,6 +50,6 @@ BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 genes in the assemblies.
 
 A reference assembly can be used to search for structural variants in a different
-individual, for instance with NanoSV ([[Cretu and coll., 2017|biblio/29109544]].
+individual, for instance with NanoSV ([[Cretu and coll., 2017|biblio/29109544]]).
 
 [[!inline pages="tagged(assembly)" actions="no" limit=0]]

Racon
diff --git a/biblio/28100585.mdwn b/biblio/28100585.mdwn
new file mode 100644
index 0000000..1b49fca
--- /dev/null
+++ b/biblio/28100585.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Fast and accurate de novo genome assembly from long uncorrected reads."]]
+[[!tag genome assembly software]]
+
+Vaser R, Sović I, Nagarajan N, Šikić M.
+
+Genome Res. 2017 May;27(5):737-746. doi:10.1101/gr.214270.116
+
+Fast and accurate de novo genome assembly from long uncorrected reads.
+
+[[!pmid 28100585 desc="Racon can be used to correct contigs or to correct raw reads."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 7c2b19b..cd060d2 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -11,11 +11,13 @@ read length is satisfactory.
 The Flye assembler ([[Kolmogorov and coll, bioRxiv
 2018|biblio/10.1101_247148]]) creates an A-Bruijn (assembly) graph from draft
 contigs using long error-prone reads, untangles the graph by resolving repeats,
-and then uses it to refine the contings and increase their accuracy.
+and then uses it to refine the contings and increase their accuracy.  (The
+predecessor of Flye, ABruijn, was reported by [[Istace and coll.
+(2017)|biblio/28369459]] to be able to assemble mitochondrial genomes, unlike
+Canu and other assemblers.)
 
-The predecessor of Flye, ABruijn, was reported by [[Istace and coll.
-(2017)|biblio/28369459]] to be able to assemble mitochondrial genomes (unlike
-Canu and other assemblers).
+After assembly, the contigs can be further polished with Racon ([[Vaser, Sović,
+Nagarajan and Šikić, 2017|biblio/28100585]]).
 
 When coverage is too low for efficient reference-free assembly, related
 references can be used as a guide.  The Ragout software ([[Kolmogorov and

emph
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 71fb420..7ee55bc 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -25,7 +25,7 @@ Some links:
 Food tested in laboratory (totally incomplete list): _Isochrysis galbana_ (5.5
 µm in size), _Tetraselmis suecica_ (9.5 µm), and the chlorophyte _Chlorella
 sp._ (3.5 µm) [[Acuña and Kiefer, 2000|biblio/10.4319_lo.2000.45.3.0608]].
-The diatom Chaetoceros calcitrans, often used as a food, can be toxic at high
+The diatom _Chaetoceros calcitrans_, often used as a food, can be toxic at high
 concentrations, probably because of the production of biotoxins
 ([[Torres-Águila and coll., 2018|biblio/30272001]]).
 

Café
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index b36d5f8..7c2b19b 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -47,4 +47,7 @@ BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy
 genes in the assemblies.
 
+A reference assembly can be used to search for structural variants in a different
+individual, for instance with NanoSV ([[Cretu and coll., 2017|biblio/29109544]].
+
 [[!inline pages="tagged(assembly)" actions="no" limit=0]]

creating tag page tags/variants
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
new file mode 100644
index 0000000..86f3ec8
--- /dev/null
+++ b/tags/variants.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged variants"]]
+
+[[!inline pages="tagged(variants)" actions="no" archive="yes"
+feedshow=10]]

NanoSV
diff --git a/biblio/29109544.mdwn b/biblio/29109544.mdwn
new file mode 100644
index 0000000..3b05e14
--- /dev/null
+++ b/biblio/29109544.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Mapping and phasing of structural variation in patient genomes using nanopore sequencing."]]
+[[!tag LAST software variants]]
+
+Cretu Stancu M, van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, de Ligt
+J, Pregno G, Giachino D, Mandrile G, Espejo Valle-Inclan J, Korzelius J, de
+Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP.
+
+Nat Commun. 2017 Nov 6;8(1):1326. doi:10.1038/s41467-017-01343-4
+
+Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
+
+[[!pmid 29109544 desc="Primary paper for NanoSV.  Fed with last-split alignments."]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index 064373b..b0cb4e6 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -7,7 +7,8 @@ _bibliography in progress..._
 
  - `last-split` ([[Frith and Kawaguchi, 2017|biblio/25994148]]): heuristic
    algorithm inspired by the “repeated matches algorithm” of Durbin and coll.
-   (1998).
+   (1998).  Its output is also used by third-party tool NanoSV ([[Cretu and
+   coll., 2017|biblio/29109544]].
 
  - `last-train` ([[Hamada, Ono, Asai and Frith, 2017|biblio/28039163]]):
    estimation of alignment parameters.

avant café
diff --git a/biblio/10.1007_BF00390593.mdwn b/biblio/10.1007_BF00390593.mdwn
new file mode 100644
index 0000000..36d10a7
--- /dev/null
+++ b/biblio/10.1007_BF00390593.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Predator-prey interactions between the larvacean Oikopleura dioica and bacterioplankton in enclosed water columns"]]
+[[!tag Oikopleura]]
+
+King, K.R., Hollibaugh, J.T. & Azam, F.
+
+Mar. Biol. (1980) 56: 49–57. doi:10.1007/BF00390593
+
+Predator-prey interactions between the larvacean Oikopleura dioica and bacterioplankton in enclosed water columns
+
+[[!doi 10.1007/BF00390593 desc="“Apparently, O. dioica has minimal influence on the population dynamics of the free-living bacteria, although bacteria may form a substantial portion of the larvacean's diet.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8b98a84..71fb420 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -319,6 +319,10 @@ Phenotypes
 Ecology
 -------
 
+ - _O. dioica_ grazes on bacterioplankton, which can be a significant share
+    of its own diet, but the grazing has only “minimal influence on the
+    population dynamics of the free-living bacteria” ([[King, Hollibaugh and
+    Azam, 1980|biblio/10.1007_BF00390593]])
  - In a rRNA metabarcoding study [[López-Escardó and coll, 2018|biblio/29904074]] report that 28 %
    of the RNA reads in oxic micro/mesoplanktonic samples originate from tunicates, mostly appendicularian.
  - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans

Parenthèses manquantes.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c96454e..8b98a84 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -48,7 +48,7 @@ Phylogeny
    species” ([[Denoeud et al., 2010|biblio/21097902]]).
  - Giant Oikopleurid species, such as  exist in deeper waters. _Bathochordaeus charon_'s 18S
    RNA is 97% identical to the one of _O. dioica_ ([[Sherlock and coll, 2016|biblio/10.1186_s41200-016-0075-9]]).
- - CO1 DNA of _B. mcnutti_ and _B. strygius_ are ~12% different[[Sherlock and coll., 2017|biblio/28042175]].
+ - CO1 DNA of _B. mcnutti_ and _B. strygius_ are ~12% different ([[Sherlock and coll., 2017|biblio/28042175]]).
 
 
 Genome

tag
diff --git a/biblio/22205972.mdwn b/biblio/22205972.mdwn
index cc4d364..7a6168a 100644
--- a/biblio/22205972.mdwn
+++ b/biblio/22205972.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Gentle masking of low-complexity sequences improves homology search."]]
-[[!tag alignment]]
+[[!tag LAST alignment]]
 
 Frith MC
 
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index 463ab23..064373b 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -2,6 +2,9 @@
 
 _bibliography in progress..._
 
+ - `last-postmask` ([[Frith, 2011|biblio/22205972]]): discards alignments that
+   contain a significant amount of lower-case-masked sequences.
+
  - `last-split` ([[Frith and Kawaguchi, 2017|biblio/25994148]]): heuristic
    algorithm inspired by the “repeated matches algorithm” of Durbin and coll.
    (1998).

normalisation
diff --git a/tags/repeats.mdwn b/tags/repeats.mdwn
deleted file mode 100644
index 4fe8b27..0000000
--- a/tags/repeats.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged repeats"]]
-
-[[!inline pages="tagged(repeats)" actions="no" archive="yes"
-feedshow=10]]

Normalisation.
diff --git a/biblio/30880010.mdwn b/biblio/30880010.mdwn
index 4c8d4a7..5878465 100644
--- a/biblio/30880010.mdwn
+++ b/biblio/30880010.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements."]]
-[[!tag Oikopleura repeats]]
+[[!tag Oikopleura repeat]]
 
 Naville M, Henriet S, Warren I, Sumic S, Reeve M, Volff JN, Chourrout D.
 

Café
diff --git a/biblio/30890163.mdwn b/biblio/30890163.mdwn
new file mode 100644
index 0000000..c24f060
--- /dev/null
+++ b/biblio/30890163.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads."]]
+[[!tag LAST alignment repeat]]
+
+Mitsuhashi S, Frith MC, Mizuguchi T, Miyatake S, Toyota T, Adachi H, Oma Y, Kino Y, Mitsuhashi H, Matsumoto N.
+
+Genome Biol. 2019 Mar 19;20(1):58. doi:10.1186/s13059-019-1667-6
+
+Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.
+
+[[!pmid 30890163 desc="Primary paper for the `tandem-genotypes` tool.  Be sure to compar both strands to prevent confusion between alleles and sequencer-specific biases."]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index bbe708a..463ab23 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -13,4 +13,7 @@ _bibliography in progress..._
    and display of rearrangements supported by multiple long reads and by the
    ancestrality of the reference sequence.
 
+ - `tandem-genotypes` ([[Mitsuhashi and coll., 2019|biblio/30890163]]): detection
+   of expansion of tandem repeats, after alignment with `last-split`.
+
 [[!inline pages="tagged(LAST)" actions="no" limit=0]]

OMG
diff --git a/biblio/10.1007_s12562-017-1106-0.mdwn b/biblio/10.1007_s12562-017-1106-0.mdwn
new file mode 100644
index 0000000..2cce9cd
--- /dev/null
+++ b/biblio/10.1007_s12562-017-1106-0.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Morphological identity of a taxonomically unassigned cytochrome c oxidase subunit I sequence from stomach contents of juvenile chum salmon determined using polymerase chain reaction"]]
+[[!tag Oikopleura]]
+
+Sakiko Orui Sakaguchi, Tetsuro Ikuta, Gen Ogawa, Kodai Yamane, Naonobu Shiga, Hiroshi Kitazato, Katsunori Fujikura, Kiyotaka Takishita.
+
+Fish Sci (2017) 83: 757. https://doi.org/10.1007/s12562-017-1106-0 
+
+Morphological identity of a taxonomically unassigned cytochrome c oxidase subunit I sequence from stomach contents of juvenile chum salmon determined using polymerase chain reaction
+
+[[!doi 10.1007/s12562-017-1106-0 desc="Finds that the COI sequence AY116609 and the 18S sequence AB013014 are probably mis-labled."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c2c7ef9..c96454e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -86,6 +86,9 @@ Genome
    in human.  In other tunicates, all mitochondrial genes are on the same DNA strand
    and 24 tRNAs are present, instead of 22 in other chordates (reviewed by [[Gissi and coll.,
    2008|biblio/18612321]]).
+ - The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014
+   in Genbank are probably a contamination and a misidentification, respectively
+   ([[Sakaguchi and coll., 2017|biblio/10.1007_s12562-017-1106-0]]).
  - 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 major spliceosome is hypothethised to have evolved

LAST
diff --git a/biblio/29272440.mdwn b/biblio/29272440.mdwn
new file mode 100644
index 0000000..358d3d9
--- /dev/null
+++ b/biblio/29272440.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A survey of localized sequence rearrangements in human DNA."]]
+[[!tag LAST alignment]]
+
+Nucleic Acids Res. 2018 Feb 28;46(4):1661-1673. doi:10.1093/nar/gkx1266
+
+Frith MC and Khan S.
+
+A survey of localized sequence rearrangements in human DNA.
+
+[[!pmid 29272440 desc="Detection and display of rearrangements supported by multiple reads and ancestrality of the reference sequence."]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index b89cfba..bbe708a 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -9,4 +9,8 @@ _bibliography in progress..._
  - `last-train` ([[Hamada, Ono, Asai and Frith, 2017|biblio/28039163]]):
    estimation of alignment parameters.
 
+ - `local-rearrangements` ([[Frith and Khan, 2018|biblio/29272440]]): detection
+   and display of rearrangements supported by multiple long reads and by the
+   ancestrality of the reference sequence.
+
 [[!inline pages="tagged(LAST)" actions="no" limit=0]]

LAST
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index b2682b5..b89cfba 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -2,10 +2,11 @@
 
 _bibliography in progress..._
 
- - `last-split` [[Frith and Kawaguchi, 2017|biblio/25994148]]: heuristic
-   algorithm inspired by the “repeated matches algorithm” of Durbin and coll
+ - `last-split` ([[Frith and Kawaguchi, 2017|biblio/25994148]]): heuristic
+   algorithm inspired by the “repeated matches algorithm” of Durbin and coll.
    (1998).
 
- - `last-train` [[|Hamada, Ono, Asai and Frith, 2017biblio/28039163]]: estimation of alignment parameters.
+ - `last-train` ([[Hamada, Ono, Asai and Frith, 2017|biblio/28039163]]):
+   estimation of alignment parameters.
 
 [[!inline pages="tagged(LAST)" actions="no" limit=0]]

LAST
diff --git a/biblio/25994148.mdwn b/biblio/25994148.mdwn
index 0f8185f..d353c2b 100644
--- a/biblio/25994148.mdwn
+++ b/biblio/25994148.mdwn
@@ -7,4 +7,4 @@ Genome Biol. 2015 May 21;16:106. doi:10.1186/s13059-015-0670-9
 
 Split-alignment of genomes finds orthologies more accurately.
 
-[[!pmid 25994148 desc="Optimal set of local alignments.  Striking example of intra-chromosomal loss of synteny between D. melanogaster and D. pseudoobscura."]]
+[[!pmid 25994148 desc="Optimal set of local alignments.  Striking example of intra-chromosomal loss of synteny between D. melanogaster and D. pseudoobscura.  Heuristic approach inspired by the “repeated matches algorithm” of Durbin and coll., 1998."]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index 12a6a69..b2682b5 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -1,4 +1,11 @@
 [[!meta title="pages tagged LAST"]]
 
-[[!inline pages="tagged(LAST)" actions="no" archive="yes"
-feedshow=10]]
+_bibliography in progress..._
+
+ - `last-split` [[Frith and Kawaguchi, 2017|biblio/25994148]]: heuristic
+   algorithm inspired by the “repeated matches algorithm” of Durbin and coll
+   (1998).
+
+ - `last-train` [[|Hamada, Ono, Asai and Frith, 2017biblio/28039163]]: estimation of alignment parameters.
+
+[[!inline pages="tagged(LAST)" actions="no" limit=0]]

creating tag page tags/ocean_acidification
diff --git a/tags/ocean_acidification.mdwn b/tags/ocean_acidification.mdwn
new file mode 100644
index 0000000..35fb1c4
--- /dev/null
+++ b/tags/ocean_acidification.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged ocean acidification"]]
+
+[[!inline pages="tagged(ocean_acidification)" actions="no" archive="yes"
+feedshow=10]]

Mesocosm.
diff --git a/biblio/28410436.mdwn b/biblio/28410436.mdwn
new file mode 100644
index 0000000..96f3ad1
--- /dev/null
+++ b/biblio/28410436.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ocean acidification effects on mesozooplankton community development: Results from a long-term mesocosm experiment."]]
+[[!tag Oikopleura ocean_acidification]]
+
+PLoS One. 2017 Apr 14;12(4):e0175851. doi:10.1371/journal.pone.0175851
+
+Algueró-Muñiz M, Alvarez-Fernandez S, Thor P, Bach LT, Esposito M, Horn HG, Ecker U, Langer JAF, Taucher J, Malzahn AM, Riebesell U, Boersma M.
+
+Ocean acidification effects on mesozooplankton community development: Results from a long-term mesocosm experiment.
+
+[[!pmid 28410436 desc="Concludes that “the Gullmar Fjord mesozooplankton community structure is not expected to change much under realistic end-of-century OA [ocean acidification] scenarios as used here”. Data submitted to PANGEA includes Oikopleura abundance. https://doi.pangaea.de/10.1594/PANGAEA.871233"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0590620..c2c7ef9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -319,7 +319,10 @@ Ecology
  - In a rRNA metabarcoding study [[López-Escardó and coll, 2018|biblio/29904074]] report that 28 %
    of the RNA reads in oxic micro/mesoplanktonic samples originate from tunicates, mostly appendicularian.
  - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans
-   ([[Bouquet et al., 2018|biblio/29298334]]).
+   ([[Bouquet et al., 2018|biblio/29298334]]).  Another mesocosm study that took place
+   in the Gullmar Fjord ([[Algueró-Muñiz M and coll., 2017|biblio/28410436]])
+   did not predict major changes in mesozooplankton community structure and provides raw data
+   including _O. dioica_, for which no significant changes are visible.
  - In California, _O. dioica_ was reported by C. Essenberg
    ([[1922|biblio/1929090]]) to be rare in summer's warm (> 20ºC) waters and
    more abundant in winter's cool (13~16 ºC) waters.

doi
diff --git a/biblio/10.3800_pbr.3.152.mdwn b/biblio/10.3800_pbr.3.152.mdwn
index 4038201..2ce1dd1 100644
--- a/biblio/10.3800_pbr.3.152.mdwn
+++ b/biblio/10.3800_pbr.3.152.mdwn
@@ -7,4 +7,4 @@ Plankton and Benthos Research 2008 Volume 3 Issue 3 Pages 152-164
 
 Species composition and horizontal distribution of the appendicularian community in waters adjacent to the Kuroshio in winter–early spring
 
-[[!pmid 10.3800/pbr.3.152 desc="In 1972, 1976, 1977, 1978, 1982 or 1986, O. dioica was rare but relatively more abuntant in slope waters, which are colder (~15—17°C) as opposed to oceanic area Kuroshio (18.5–20.0°C) or subtropical waters (similar temperatures as Kuroshio)."]]
+[[!doi 10.3800/pbr.3.152 desc="In 1972, 1976, 1977, 1978, 1982 or 1986, O. dioica was rare but relatively more abuntant in slope waters, which are colder (~15—17°C) as opposed to oceanic area Kuroshio (18.5–20.0°C) or subtropical waters (similar temperatures as Kuroshio)."]]

Bathochordaeus
diff --git a/biblio/28042175.mdwn b/biblio/28042175.mdwn
new file mode 100644
index 0000000..1d1dc52
--- /dev/null
+++ b/biblio/28042175.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Morphology, ecology, and molecular biology of a new species of giant larvacean in the eastern North Pacific: Bathochordaeus mcnutti sp. nov."]]
+[[!tag Oikopleura]]
+
+Sherlock RE, Walz KR, Schlining KL, Robison BH.
+
+Mar Biol. 2017;164(1):20. doi:10.1007/s00227-016-3046-0
+
+Morphology, ecology, and molecular biology of a new species of giant larvacean in the eastern North Pacific: Bathochordaeus mcnutti sp. nov.
+
+[[!pmid 28042175 desc="_B. mcnutti_ are 3–10 cm long.  Their tails have a blue outline.  Gravid individuals descend as low as 800 m, but spawning is thought to happen above 100 m.  The CO1 gene is ~12% different between _B. mcnutti_ and _B. strygius_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8279291..0590620 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -48,6 +48,8 @@ Phylogeny
    species” ([[Denoeud et al., 2010|biblio/21097902]]).
  - Giant Oikopleurid species, such as  exist in deeper waters. _Bathochordaeus charon_'s 18S
    RNA is 97% identical to the one of _O. dioica_ ([[Sherlock and coll, 2016|biblio/10.1186_s41200-016-0075-9]]).
+ - CO1 DNA of _B. mcnutti_ and _B. strygius_ are ~12% different[[Sherlock and coll., 2017|biblio/28042175]].
+
 
 Genome
 ------
@@ -293,7 +295,7 @@ House
    its expansion and contraction at high spatial and temporal resolution.
  - In _O. labradorensis_, [[Flood (1991)|biblio/10.1007_BF01986351]] estimated
    that 35 ml of water were filtered per hour.  In comparison, the giant
-   species Bathochordaeus mcnutti was reported to filter as much as 76 L/h
+   species _Bathochordaeus mcnutti_ was reported to filter as much as 76 L/h
    ([[Katija and coll., 2018|biblio/28508058]]).
  - Filter-feeding in marine animals has been reviewed by [[Conley, Lombard and
    Sutherland (2018)|biblio/29720410]].
@@ -342,6 +344,8 @@ Ecology
  - Oikopleuridae can be found in the deep see.  For instance, [[Lindsay and
    coll., 2014|biblio/10.1007_978-4-431-54865-2_51]] reported _Oikopleura_, _Mesochordaeus_
    and _Bathochordaeus_ individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.
+ - Gravid _B mcnutti_ individuals are found at down to 800 m, but spawning is supposed to
+   happen closer to the surface ([[Sherlock and coll., 2017|biblio/28042175]]).
  - Oikopleuridae have been reported to be able to ingest microplastics.  Example(s):
    _B. stygius_ ([[Katija and coll., 2017b|biblio/28835922]]).
  - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus

Café
diff --git a/biblio/1956_17226.mdwn b/biblio/1956_17226.mdwn
new file mode 100644
index 0000000..adcf888
--- /dev/null
+++ b/biblio/1956_17226.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Studies on the house building epithelium of Oikopleurid appendicularia (Tunicata): Early differentiation and description of the adult pattern of oikoplast cells"]]
+[[!tag Oikopleura]]
+
+Endy Spriet
+
+1997, Master thesis, the University of Bergen.
+
+Studies on the house building epithelium of Oikopleurid appendicularia (Tunicata): Early differentiation and description of the adult pattern of oikoplast cells
+
+[[!hdl 1956/17226 desc="High-resolution pictures of nuclear stains of _O.labradoriensis_,
+   _O. vanhoeffeni_, _O. dioica_, _O. villafrancae_ and _O. albicans_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index e969569..8279291 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -283,6 +283,11 @@ House
    1986|biblio/10.1007_BF00312043]].  He also observed that, when in the house,
    “the tails beat slowly when the suspended particles were numerous and rapidly
    when they were few”.
+ - The master thesis of [[E. Spriet (1997)|biblio/1956_17226]] provides high-resolution
+   pictures of nuclar stains of the oikoblastic epithelium for _O.labradoriensis_,
+   _O. vanhoeffeni_, _O. dioica_, _O. villafrancae_ and _O. albicans_.  The complexity
+   of nuclear ramifications varies between species.  (Interstingly, it might correlate
+   with genome size).
  - The food collecting filter in the house was described as a “self-cleaning
    filter” by [[Conley and coll., 2017|biblio/10.1002_lno.10680]], who observed
    its expansion and contraction at high spatial and temporal resolution.

HTTPS DOI ; handle.net
diff --git a/shortcuts.mdwn b/shortcuts.mdwn
index d9bfad7..c188136 100644
--- a/shortcuts.mdwn
+++ b/shortcuts.mdwn
@@ -69,7 +69,8 @@ This page controls what shortcut links the wiki supports.
 * [[!shortcut name=pmid url="http://pubmed.gov/%s"]]
 * [[!shortcut name=unihan url="http://www.unicode.org/cgi-bin/GetUnihanData.pl?codepoint=%S"]]
 * [[!shortcut name=arxiv url="http://arxiv.org/abs/%s"]]
-* [[!shortcut name=doi url="http://dx.doi.org/%s"]]
+* [[!shortcut name=doi url="https://doi.org/%s"]]
+* [[!shortcut name=hdl url="https://hdl.handle.net//%s"]]
 
 To add a new shortcut, use the `shortcut`
 [[ikiwiki/directive]]. In the url, "%s" is replaced with the

Biger oiks
diff --git a/biblio/30880010.mdwn b/biblio/30880010.mdwn
new file mode 100644
index 0000000..4c8d4a7
--- /dev/null
+++ b/biblio/30880010.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements."]]
+[[!tag Oikopleura repeats]]
+
+Naville M, Henriet S, Warren I, Sumic S, Reeve M, Volff JN, Chourrout D.
+
+Curr Biol. 2019 Mar 2. pii: S0960-9822(19)30139-3. doi:10.1016/j.cub.2019.01.080
+
+Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements.
+
+[[!pmid 30880010 desc="Larger genomes found in larger species.  No evidence for genome duplication.  Transposable element density correlated with genome size.  SINEs (short interspersed nuclear elements) and MITEs (miniature inverted transposable elements) account for most of the TE expansion.  Ancestor is likely to have had a small genome."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 56090f7..e969569 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -103,6 +103,8 @@ Genome
    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]]).
+ - SINE and MITE account for a large part of genome expansion in larger oikopleurid
+   species ([[Naville and coll., 2019|biblio/30880010]]).
  - “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

Oik size.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 420e327..56090f7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -64,6 +64,11 @@ Genome
    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]]).
+ - Other oikopleuid genomes have been sequenced by [[Naville and coll. (2019)|biblio/30880010]]:
+   small genomes are also found in _O. longicauda_ (131 Mbp) and _F. borealis_ (91 Mbp).
+   There is an apparent correlation between organism size and genome size:
+   _O. albicans_ (356 Mbp), _Bathochordaeus sp._ (396 Mbp), _O. vanhoeffeni_ (632 Mbp)
+   and _M. erythrocephalus_ (874 Mbp) all have larger body sizes than _O. dio._, _O. lon._ and _F. bor_.
  - “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

Lost genes.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 04e24f6..420e327 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -73,10 +73,6 @@ Genome
    by [[Berná and Alvarez-Valin (2014)|biblio/25008364]].
  - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
  - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
- - The entire machinery required for performing classical NHEJ repair of DSB (which is
-   conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
- - An alternative or microhomology (MH)-driven end joining pathway is active
-   and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
  - 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
@@ -85,10 +81,7 @@ Genome
    2008|biblio/18612321]]).
  - 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
+ - The major spliceosome is hypothethised to have evolved
    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”
@@ -161,6 +154,15 @@ Genes and pathways
    ([[Niimura, 2009|biblio/20333175]]).
  - Most members of retinoic acid pathway gene network (biosynthesis, signalling
    and degradation) are lost in _O. dioica_ ([[Martí-Solans et al., 2016|biblio/27406791]]).
+ - The entire machinery required for performing classical NHEJ repair of DSB (which is
+   conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
+   An alternative or microhomology (MH)-driven end joining pathway is active
+   and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
+ - 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]].
+
 
 
 Transcriptome

Lost genes and pathways.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b639ee0..04e24f6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -124,6 +124,8 @@ Genome
 Genes and pathways
 ------------------
 
+### Present or gained
+
 (See also other sections)
 
  - ~80 "house proteins" have been identified and more than half lack similarity
@@ -137,17 +139,11 @@ Genes and pathways
    2004|biblio/14722352]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
- - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
-   It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
- - CYP1 family genes and their regulator AhR are not detectable
-   ([[Yadetie et al, 2012|biblio/22300585]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).
    They are expressed in the nervous system ([[Lynagh et al., 2018|biblio/30061402]]).
  - Some muscle genes were duplicated in the _Oikopleura_ stem lineage
    ([[Inoue & Satoh|biblio/29319812]]), prehaps reflecting the importance of
    tail movements at larval and adult stages.
- - No olfactory receptors have been found in _Oikopleura_ nor in _Ciona_
-   ([[Niimura, 2009|biblio/20333175]]).
  - Defensome genes such as dehydrogenases and  (Glutamate-cysteine ligase modifier subunit; Gclm)
    are activated by polyunsaturated aldehydes produced by diatoms
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
@@ -155,6 +151,18 @@ Genes and pathways
  - Southern blot analysis suggest the presence of a SCO-spondin gene in _O.
    dioica_ ([[Gobron and coll., 1999|biblio/10197783]]).
 
+### Lost
+
+ - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+   It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
+ - CYP1 family genes and their regulator AhR are not detectable
+   ([[Yadetie et al, 2012|biblio/22300585]]).
+ - No olfactory receptors have been found in _Oikopleura_ nor in _Ciona_
+   ([[Niimura, 2009|biblio/20333175]]).
+ - Most members of retinoic acid pathway gene network (biosynthesis, signalling
+   and degradation) are lost in _O. dioica_ ([[Martí-Solans et al., 2016|biblio/27406791]]).
+
+
 Transcriptome
 -------------
 
@@ -254,8 +262,7 @@ 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
+ - Some members of retinoic acid pathway gene network that were not lost in _O. dioica_ show
    signs of neofunctionalisation or specialisation in their ancestral activity in
    digestion or chemical defence ([[Martí-Solans et al., 2016|biblio/27406791]]).
 

Dnmt2 renamed Trdmt1.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 885d8d7..b639ee0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -137,7 +137,8 @@ Genes and pathways
    2004|biblio/14722352]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
- - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+ - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+   It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).

Add reference
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8a07b6a..885d8d7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -137,7 +137,7 @@ Genes and pathways
    2004|biblio/14722352]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
- - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.
+ - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).

CAPsmart
diff --git a/biblio/25003736.mdwn b/biblio/25003736.mdwn
index 878bb0f..6f72640 100644
--- a/biblio/25003736.mdwn
+++ b/biblio/25003736.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Four methods of preparing mRNA 5' end libraries using the illumina sequencing platform."]]
-[[!tag template_switching method oligo-capping benchmark]]
+[[!tag cap template_switching method oligo-capping benchmark]]
 
 Machida RJ, Lin YY.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 34d054e..8e2ae7f 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -56,6 +56,13 @@ in the [[template_switching]] tag page.
  - [[Kwak et al., 2013|biblio/23430654]] modified oligo-capping to create Pro-cap, a method for nuclear
    run-on analysis at single-nucleotide resulution.
 
+ - CapSMART ([[Machida and Lin, 2014|biblio/25003736]]): non-capped RNAs are
+   dephosphorylated, rephoshporylated and a blocking linker containing
+   isoguanosines and isocytidines (so that it can not be reverse-transcribed) is
+   ligated to them.  A classical SMART protocol follows.  cDNAs are amplified with
+   biotinylated forward primers, so that the 5′ end can be recovered after
+   mechanical fragmentation.
+
 Atypical caps (work in progress)
 --------------------------------
 

crosslink
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 351bb60..34d054e 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -21,6 +21,9 @@ Methods for enriching capped RNAs
    uncover functional phosphate with decapping enzyme, and ligate RNA adaptor
    with T4 RNA ligase.
 
+(wip: template-switching: find original publication. Described in deeper details
+in the [[template_switching]] tag page.
+
 (wip: Fromont-racine et al.)
 
  - CAPture ([[Edery, Chu, Sonenberg and Pelletier, 1995|biblio/7760832]]):
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 5226ece..ece2741 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -1,6 +1,6 @@
 [[!meta title="pages tagged template_switching"]]
 
-(work in progress)
+(work in progress.  For alternative cap enrichement methods see the [[cap]] tag page)
 
  - In the "_CapSelect_" method, [[Schmidt and Mueller, 1999|biblio/10518626]]
    stimulate template switching with manganese (see below), tail the first-strand

Café
diff --git a/biblio/3028775.mdwn b/biblio/3028775.mdwn
new file mode 100644
index 0000000..2962fcd
--- /dev/null
+++ b/biblio/3028775.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cloning of the human cDNA for the U1 RNA-associated 70K protein."]]
+[[!tag cap method library]]
+
+Theissen H, Etzerodt M, Reuter R, Schneider C, Lottspeich F, Argos P, Lührmann R, Philipson L.
+
+EMBO J. 1986 Dec 1;5(12):3209-17.
+
+Cloning of the human cDNA for the U1 RNA-associated 70K protein.
+
+[[!pmid 3028775 desc="Clones the full-length cDNA by affinity purification with m7G antibodies, and RNAse A digestion of the incomplete cDNA/RNA duplexes.  Cites Schneider 1986 for the method, but could not find this reference."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index afc78ea..351bb60 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -10,6 +10,11 @@ Methods for enriching capped RNAs
 
  - See the Wikipedia for [[CAGE methods|https://en.wikipedia.org/wiki/Cap_analysis_gene_expression]] (Cap Analysis Gene Expression).
 
+ - [[Thiessen and coll., 1986|biblio/3028775]] cloned the full-length cDNA by
+   affinity purification with m7G antibodies, and RNAse A digestion of the
+   incomplete cDNA/RNA duplexes.  They cite Schneider 1986 for the method, but
+   I could not find this reference.
+
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
  - Oligo-capping ([[Maruyama et al., 1994|biblio/8125298]]): dephosphorylate,