Dernières modifications :

Café
diff --git a/biblio/34107272.mdwn b/biblio/34107272.mdwn
new file mode 100644
index 00000000..f5ea2a1e
--- /dev/null
+++ b/biblio/34107272.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nkx2-1 and FoxE regionalize glandular (mucus-producing) and thyroid-equivalent traits in the endostyle of the chordate Oikopleura dioica."]]
+[[!tag Oikopleura]]
+
+Onuma TA, Nakanishi R, Sasakura Y, Ogasawara M.
+
+Dev Biol. 2021 Jun 6:S0012-1606(21)00142-1. doi: 10.1016/j.ydbio.2021.05.021.
+
+Nkx2-1 and FoxE regionalize glandular (mucus-producing) and thyroid-equivalent traits in the endostyle of the chordate Oikopleura dioica.
+
+[[!pmid 34107272 desc="Found vWFL (von Willebrand factor-like, a single gene, whereas Ciona has two), and the thyroid-related peroxidases, TPO and Duox, and the thyroid-related TFs Nkx2-1 and FoxE.  Also reported a SCO spondin in the supplemental material.  “Nkx2-1 knockdown suppressed vWFL expression in 8 hpf larvae. In contrast, FoxE knockdown had no effect on vWFL expression.”  “Nkx2-1 knockdown decreased TPO expression in the endostyle of over 90% of larvae.”  “FoxE knockdown did not affect Duox expression.”  “Nkx2-1 knockdown caused malformation of the endostyle in 80% of the larvae. In contrast, FoxE knockdown did not affect endostyle morphology.”  “Nkx2-1 expression was decreased by Nkx2-1 knockdown, but not by FoxE knockdown. On the other hand, FoxE expression was decreased in two-thirds of the Nkx2-1 knockdown larvae as well as in FoxE knockdown larvae.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c62f3ace..86c71c2c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -236,6 +236,8 @@ Genes and pathways
  - Metallothioneins _OdMT1_ and _OdMT2_ [[Calatayud and coll., 2018|biblio/30284576]].
  - 2 NUMB genes were found; both are closer to Vertebrate NUMB than to Vertebrate NUMB-Like
    ([[Confalonieri and coll., 2019|biblio/31451549]]).
+ - Genes related to thyroid functions (_vWFL_, _Nkx2-1_, _FoxE_, _TPO_ and _Duox_)
+   were studied by [[Onuma and coll., 2020|biblio/34107272]].
 
 ### Lost
 

Café
diff --git a/biblio/24493737.mdwn b/biblio/24493737.mdwn
new file mode 100644
index 00000000..89cc27cf
--- /dev/null
+++ b/biblio/24493737.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Improved search heuristics find 20,000 new alignments between human and mouse genomes."]]
+[[!tag LAST alignment]]
+
+Frith MC, Noé L.
+
+Nucleic Acids Res. 2014 Apr;42(7):e59. doi:10.1093/nar/gku104
+
+Improved search heuristics find 20,000 new alignments between human and mouse genomes.
+
+[[!pmid 24493737 desc="“using more codesigned seed patterns makes the alignment more sensitive but slower. The interesting point, though, is that using more seeds beats increasing the rareness threshold. For example, using four seeds with m 1⁄4 10 is both faster and more sensitive than one seed with m 1⁄4 100. The downside is that more seeds require more memory.”  “We also tried aligning 10 000 random 1-kb chunks of the _melanogaster_ genome to the _pseudoobscura_ genome. In this case, the 1:1 [transitions:transversions] seeds perform better than the 3:2 seeds, as expected.”  “Mammals have a greater excess than _Drosophila_, presumably because they have more methylcytosine, which mutates rapidly to thymine. Less-similar genomes have a lower excess of transitions: this is as expected because the transitions cannot keep increasing linearly but instead tend to an asymptote.”"]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index fc0a0dfa..49e93fcd 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -2,6 +2,9 @@
 
 _bibliography in progress..._
 
+ - `lastdb` can use various seeding schemes to build its index.
+    [[Frith and Noé (2014)|biblio/24493737]] discuss some of them.
+
  - `last-postmask` ([[Frith, 2011|biblio/22205972]]): discards alignments that
    contain a significant amount of lower-case-masked sequences.
 

Café
diff --git a/biblio/32808665.mdwn b/biblio/32808665.mdwn
new file mode 100644
index 00000000..56c72045
--- /dev/null
+++ b/biblio/32808665.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning."]]
+[[!tag genome population haplotype]]
+
+Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD.
+
+Gigascience. 2020 Aug 1;9(8):giaa088. doi:10.1093/gigascience/giaa088
+
+A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning.
+
+[[!pmid 32808665 desc="“Heterozygosity of the F1 offspring was estimated to be ∼1.9%”  “the 2 scaffolded assemblies [were concatenated], mapped the 10X Illumina data [...], called variants [...], then applied homozygous non-reference edits to the assembly using bcftools consensus.”  “Assemblytics detected 32,203 SVs between the haplotype assemblies, affecting 51.6 Mb of the genome”"]]

Café
diff --git a/biblio/34041785.mdwn b/biblio/34041785.mdwn
new file mode 100644
index 00000000..a069d783
--- /dev/null
+++ b/biblio/34041785.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The filter-house of the larvacean Oikopleura dioica. A complex extracellular architecture: from fiber production to rudimentary state to inflated house."]]
+[[!tag Oikopleura]]
+
+The filter-house of the larvacean Oikopleura dioica. A complex extracellular architecture: from fiber production to rudimentary state to inflated house.
+
+J Morphol. 2021 May 26. doi:10.1002/jmor.21382
+
+Razghandi K, Janßen NF, Le Mai-Lee V, Stach T.
+
+[[!pmid 34041785 desc="Developmental origin of the escape slot and the outlet valve."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 202f99be..c62f3ace 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -497,7 +497,8 @@ House
  - A 8th cell was seen in the Fol area at 10 hpf in the 3D tomography analysis
    of [[Nishida and coll., 2021|biblio/33649401]].  It is possible that this cell
    is lost during later development.
-
+ - Study of the _O. dioica_ house and the origin of its components on the oikoblastic
+   epithelium, using multiple microscopy techniques [[Razghandi and coll., 2020|biblio/34041785]].
 
 Phenotypes
 ----------

Café
diff --git a/biblio/20052388.mdwn b/biblio/20052388.mdwn
new file mode 100644
index 00000000..7d66f3d8
--- /dev/null
+++ b/biblio/20052388.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="How fast is the sessile ciona?"]]
+[[!tag Ciona speciation]]
+
+Berná L, Alvarez-Valin F, D'Onofrio G.
+
+Comp Funct Genomics. 2009;2009:875901. doi:10.1155/2009/875901
+
+How fast is the sessile ciona?
+
+[[!pmid 20052388 desc="“Tajima’s test results [...] for the great majority of the alignments, _Ciona_ genes evolve faster than those of all vertebrate groups[...].”  “On the average, _Ciona_ evolves 50% faster than all vertebrates, with the exception of _O. anatinus_ and _M. domestica_.”  “The divergence between _C. intestinalis_ and _C. savignyi_ was reestimated and found to took place ~184 (±15) My ago.”"]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index aa1838e7..55873314 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -9,8 +9,11 @@
 
 _C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
 vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).  They are
-estimated to have diverged 122 ± 33 million years ago ([[Delsuc and coll.,
-2018|biblio/29653534]]).
+estimated to have diverged ~184 (±15) My ago based on protein sequence
+comparisons and estimation of the acceleration of the molecular clock in
+tunicates [[Berná, Alvarez-Valin and D'Onofrio, 2009|biblio/20052388]] or
+122 ± 33 million years ago based on sequence analysis of 258 proteins from 63
+species ([[Delsuc and coll., 2018|biblio/29653534]]).
 
 _Ciona robusta_'s sperm can efficiently fertilise _C. intestinalis_ eggs, but
 the fertilisation rates are much lower in the reciprocal crosses ([[Suzuki,
diff --git a/tags/speciation.mdwn b/tags/speciation.mdwn
index 240b8e82..8c73eea3 100644
--- a/tags/speciation.mdwn
+++ b/tags/speciation.mdwn
@@ -1,4 +1,3 @@
 [[!meta title="pages tagged speciation"]]
 
-[[!inline pages="tagged(speciation)" actions="no" archive="yes"
-feedshow=10]]
+[[!inline pages="tagged(speciation)" limit=0]]

Café
diff --git a/biblio/33927397.mdwn b/biblio/33927397.mdwn
new file mode 100644
index 00000000..64f7b09f
--- /dev/null
+++ b/biblio/33927397.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum."]]
+[[!tag chromosome epigenetic genome transcription]]
+
+Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum.
+
+Marinov GK, Trevino AE, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ.
+
+Nat Genet. 2021 May;53(5):613-617. doi: 10.1038/s41588-021-00848-5.
+
+[[!pmid 33927397 desc="“each dinoTAD corresponded to a pair of divergent gene arrays”  “α-amanitin treatment resulted in a dose-dependent, progressive dinoTAD decompaction”"]]

Add missing piece
diff --git "a/Debian/debi\303\242neries/r-4.1.en.po" "b/Debian/debi\303\242neries/r-4.1.en.po"
index 726ef3f0..441cd445 100644
--- "a/Debian/debi\303\242neries/r-4.1.en.po"
+++ "b/Debian/debi\303\242neries/r-4.1.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2021-05-24 02:21+0000\n"
-"PO-Revision-Date: 2021-05-24 11:24+0900\n"
+"PO-Revision-Date: 2021-05-24 11:26+0900\n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
@@ -83,6 +83,13 @@ msgstr ""
 "        users=  # Here put your username\n"
 "        root-groups=root\n"
 "        profile=desktop\n"
+"        personality=linux\n"
+"        preserve-environment=true\n"
+"    sudo schroot -c r-4.1\n"
+"    vi /etc/apt/sources.list # To add the experimental distribution\n"
+"    apt update\n"
+"    apt install sudo vim wget\n"
+"    exit\n"
 
 #. type: Plain text
 msgid "Installation de R:"

R 4.1
diff --git "a/Debian/debi\303\242neries/r-4.1.en.po" "b/Debian/debi\303\242neries/r-4.1.en.po"
index 7f6c9160..726ef3f0 100644
--- "a/Debian/debi\303\242neries/r-4.1.en.po"
+++ "b/Debian/debi\303\242neries/r-4.1.en.po"
@@ -3,51 +3,54 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2021-05-24 02:21+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2021-05-24 11:24+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: \n"
+"Language-Team: \n"
+"X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Mon, 24 May 2021 10:22:43 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Mon, 24 May 2021 10:22:43 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Mon, 24 May 2021 10:22:43 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Mon, 24 May 2021 10:22:43 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"J'essaye R 4.1\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Trying R 4.1\"]]\n"
 
 #. type: Plain text
 msgid ""
-"J'essaye [R "
-"4.1](https://stat.ethz.ch/pipermail/r-devel/2021-May/080724.html)  dans un "
-"conteneur [schroot](https://manpages.debian.org/schroot) _experimental_ en "
-"attendant la publication de _Bullseye_ qui permettra la migration dans _Sid_ "
-"et la recompilation des paquets R que nous fournissions."
+"J'essaye [R 4.1](https://stat.ethz.ch/pipermail/r-devel/2021-May/080724."
+"html)  dans un conteneur [schroot](https://manpages.debian.org/schroot) "
+"_experimental_ en attendant la publication de _Bullseye_ qui permettra la "
+"migration dans _Sid_ et la recompilation des paquets R que nous fournissions."
 msgstr ""
+"I am trying [R 4.1](https://stat.ethz.ch/pipermail/r-devel/2021-May/080724."
+"html) in a [schroot](https://manpages.debian.org/schroot) _experimental_ "
+"container, while waiting that _Bullseye_'s release will allow the package to "
+"be uploaded to _Sid_ and the needed dependencies to be recompiled."
 
 #. type: Plain text
 msgid "Le _schroot_:"
-msgstr ""
+msgstr "The _schroot_:"
 
 #. type: Plain text
 #, no-wrap
@@ -70,30 +73,45 @@ msgid ""
 "    apt install sudo vim wget\n"
 "    exit\n"
 msgstr ""
+"    sudo debootstrap sid /srv/chroot/r-4.1 http://deb.debian.org/debian\n"
+"    sudo vi /etc/schroot/chroot.d/r-4.1\n"
+"    # Edit it to have something like\n"
+"        [r-4.1]\n"
+"        description=R 4.1 (experimental)\n"
+"        type=directory\n"
+"        directory=/srv/chroot/r-4.1\n"
+"        users=  # Here put your username\n"
+"        root-groups=root\n"
+"        profile=desktop\n"
 
 #. type: Plain text
 msgid "Installation de R:"
-msgstr ""
+msgstr "Installation of R:"
 
 #. type: Plain text
 #, no-wrap
 msgid ""
 "    schroot -c r-4.1\n"
 "    sudo apt install r-base/experimental -texperimental\n"
-"    sudo apt install -texperimental pandoc libxml2-dev libcurl4-openssl-dev "
-"git libssl-dev texlive\n"
+"    sudo apt install -texperimental pandoc libxml2-dev libcurl4-openssl-dev git libssl-dev texlive\n"
 msgstr ""
+"    schroot -c r-4.1\n"
+"    sudo apt install r-base/experimental -texperimental\n"
+"    sudo apt install -texperimental pandoc libxml2-dev libcurl4-openssl-dev git libssl-dev texlive\n"
 
 #. type: Plain text
 msgid "Et de Rstudio (il faut la version _preview_)"
-msgstr ""
+msgstr "And RStudio (_preview_ version needed)"
 
 #. type: Plain text
 #, no-wrap
 msgid ""
-"    wget "
-"https://s3.amazonaws.com/rstudio-ide-build/desktop/bionic/amd64/rstudio-1.4.1714-amd64.deb\n"
+"    wget https://s3.amazonaws.com/rstudio-ide-build/desktop/bionic/amd64/rstudio-1.4.1714-amd64.deb\n"
 "    sudo apt install libnss3 libasound2\n"
 "    sudo dpkg -i rstudio-1.4.1714-amd64.deb \n"
 "    sudo apt -f install -texperimental\n"
 msgstr ""
+"    wget https://s3.amazonaws.com/rstudio-ide-build/desktop/bionic/amd64/rstudio-1.4.1714-amd64.deb\n"
+"    sudo apt install libnss3 libasound2\n"
+"    sudo dpkg -i rstudio-1.4.1714-amd64.deb \n"
+"    sudo apt -f install -texperimental\n"

updated PO files
diff --git "a/Debian/debi\303\242neries/r-4.1.en.po" "b/Debian/debi\303\242neries/r-4.1.en.po"
new file mode 100644
index 00000000..7f6c9160
--- /dev/null
+++ "b/Debian/debi\303\242neries/r-4.1.en.po"
@@ -0,0 +1,99 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2021-05-24 02:21+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Mon, 24 May 2021 10:22:43 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Mon, 24 May 2021 10:22:43 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"J'essaye R 4.1\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'essaye [R "
+"4.1](https://stat.ethz.ch/pipermail/r-devel/2021-May/080724.html)  dans un "
+"conteneur [schroot](https://manpages.debian.org/schroot) _experimental_ en "
+"attendant la publication de _Bullseye_ qui permettra la migration dans _Sid_ "
+"et la recompilation des paquets R que nous fournissions."
+msgstr ""
+
+#. type: Plain text
+msgid "Le _schroot_:"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"    sudo debootstrap sid /srv/chroot/r-4.1 http://deb.debian.org/debian\n"
+"    sudo vi /etc/schroot/chroot.d/r-4.1\n"
+"    # Edit it to have something like\n"
+"        [r-4.1]\n"
+"        description=R 4.1 (experimental)\n"
+"        type=directory\n"
+"        directory=/srv/chroot/r-4.1\n"
+"        users=  # Here put your username\n"
+"        root-groups=root\n"
+"        profile=desktop\n"
+"        personality=linux\n"
+"        preserve-environment=true\n"
+"    sudo schroot -c r-4.1\n"
+"    vi /etc/apt/sources.list # To add the experimental distribution\n"
+"    apt update\n"
+"    apt install sudo vim wget\n"
+"    exit\n"
+msgstr ""
+
+#. type: Plain text
+msgid "Installation de R:"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"    schroot -c r-4.1\n"
+"    sudo apt install r-base/experimental -texperimental\n"
+"    sudo apt install -texperimental pandoc libxml2-dev libcurl4-openssl-dev "
+"git libssl-dev texlive\n"
+msgstr ""
+
+#. type: Plain text
+msgid "Et de Rstudio (il faut la version _preview_)"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"    wget "
+"https://s3.amazonaws.com/rstudio-ide-build/desktop/bionic/amd64/rstudio-1.4.1714-amd64.deb\n"
+"    sudo apt install libnss3 libasound2\n"
+"    sudo dpkg -i rstudio-1.4.1714-amd64.deb \n"
+"    sudo apt -f install -texperimental\n"
+msgstr ""

R 4.1
diff --git "a/Debian/debi\303\242neries/r-4.1.mdwn" "b/Debian/debi\303\242neries/r-4.1.mdwn"
new file mode 100644
index 00000000..8c06e251
--- /dev/null
+++ "b/Debian/debi\303\242neries/r-4.1.mdwn"
@@ -0,0 +1,43 @@
+[[!meta date="Mon, 24 May 2021 10:22:43 +0900"]]
+[[!meta updated="Mon, 24 May 2021 10:22:43 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="J'essaye R 4.1"]]
+
+J'essaye [R 4.1](https://stat.ethz.ch/pipermail/r-devel/2021-May/080724.html)
+dans un conteneur [schroot](https://manpages.debian.org/schroot) _experimental_
+en attendant la publication de _Bullseye_ qui permettra la migration dans _Sid_
+et la recompilation des paquets R que nous fournissions.
+
+Le _schroot_:
+
+    sudo debootstrap sid /srv/chroot/r-4.1 http://deb.debian.org/debian
+    sudo vi /etc/schroot/chroot.d/r-4.1
+    # Edit it to have something like
+        [r-4.1]
+        description=R 4.1 (experimental)
+        type=directory
+        directory=/srv/chroot/r-4.1
+        users=  # Here put your username
+        root-groups=root
+        profile=desktop
+        personality=linux
+        preserve-environment=true
+    sudo schroot -c r-4.1
+    vi /etc/apt/sources.list # To add the experimental distribution
+    apt update
+    apt install sudo vim wget
+    exit
+
+Installation de R:
+
+    schroot -c r-4.1
+    sudo apt install r-base/experimental -texperimental
+    sudo apt install -texperimental pandoc libxml2-dev libcurl4-openssl-dev git libssl-dev texlive
+ 
+Et de Rstudio (il faut la version _preview_)
+
+    wget https://s3.amazonaws.com/rstudio-ide-build/desktop/bionic/amd64/rstudio-1.4.1714-amd64.deb
+    sudo apt install libnss3 libasound2
+    sudo dpkg -i rstudio-1.4.1714-amd64.deb 
+    sudo apt -f install -texperimental

Café
diff --git a/biblio/33927399.mdwn b/biblio/33927399.mdwn
new file mode 100644
index 00000000..d22f582e
--- /dev/null
+++ b/biblio/33927399.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum."]]
+[[!tag chromosome transcription epigenetic genome]]
+
+Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.
+
+Nand A, Zhan Y, Salazar OR, Aranda M, Voolstra CR, Dekker J.
+
+Nat Genet. 2021 May;53(5):618-629. doi: 10.1038/s41588-021-00841-y
+
+[[!pmid 33927399 desc="“We find two chromosome-scale patterns of GC content fluctuations: (1) GC content increases towards the ends of the chromosomes and (2) GC content dips to form small local minima at Hi-C domain boundaries.”  “most domain boundaries observed by Hi-C are located at positions where transcription of blocks of unidirectional genes converges.”  “chromatin conformation is sensitive to treatment of cells with triptolide and DRB.”"]]

Café
diff --git a/biblio/32873878.mdwn b/biblio/32873878.mdwn
new file mode 100644
index 00000000..7f8c0a0e
--- /dev/null
+++ b/biblio/32873878.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution."]]
+[[!tag genome synteny chromosome epigenetic evolution]]
+
+Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS
+
+Commun Biol. 2020 Sep 1;3(1):480. doi:10.1038/s42003-020-1096-9
+
+Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution.
+
+[[!pmid 32873878 desc="“Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites.”"]]
+
+“During the ~4.9 million years since the divergence of M. muntjak and M. reevesi, the M. muntjak lineage experienced 26 fusions for a rate of ~5.3 changes per million years.”  “M. muntjak and M. reevesi [...] genomes are locally very similar, with 98.5% identity in aligned regions and a nucleotide divergence of 0.0130 substitutions per site, based on fourfold degenerate positions.”  “The pairwise alignment of the muntjac genomes contains 2.45 Gb of contig sequence [...] average sequence identity of 98.5%, excluding indels [...] In comparison, alignments of red deer, reindeer, and muntjacs to B. taurus contain 1.80–2.21 Gb of contig sequences with 92.7–93.2% average identity.”  “The nucleotide and temporal divergence between the two muntjac species is comparable to the divergence between humans and chimpanzees. The observed chromosome dynamism in muntjacs, however, far exceeds the rate in the chimpanzee and human lineages”  “we noted the maintenance of distinct Hi-C boundaries in several examples, such as the junction between the X and autosomal segments on MMU3_X circa 133 Mb. Other fusion sites, however, show no notable difference compared with the rest of the genome in M. muntjak. As expected, M. reevesi shows a clear distinction between intra- and inter-chromosome contacts, including across fusion sites in M. muntjak.”
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index ead25ecd..f915e414 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -27,6 +27,11 @@ of 90 rearrangements per MY (_mel_ / _simulans_) and 226–354 per MY (_sim_ / _
 In insects, the Osiris gene family shows conservation of synteny over ~400
 million years ([[Sah and coll., 2012|biblio/22384409]]).
 
+The indian munjac has only 3 chromosomes, which are the result of fusions in
+the past ~5 My.  The chinese munjak has undergone much less fusions.  In most
+cases, long-range chromosome structure (Hi-C) is not conserved between theses
+two species [[Mudd and coll, 2020|biblio/32873878]].
+
 ### Ancestral karyotpyes
 
  - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll., 2021|biblio/33408411]]).

Café
diff --git a/biblio/10.1007_s00227-021-03887-y.mdwn b/biblio/10.1007_s00227-021-03887-y.mdwn
new file mode 100644
index 00000000..6fbcb49e
--- /dev/null
+++ b/biblio/10.1007_s00227-021-03887-y.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Toward a global reference database of COI barcodes for marine zooplankton."]]
+[[!tag review eDNA]]
+
+Ann Bucklin, Katja T. C. A. Peijnenburg, Ksenia N. Kosobokova, Todd D. O’Brien, Leocadio Blanco-Bercial, Astrid Cornils, Tone Falkenhaug, Russell R. Hopcroft, Aino Hosia, Silke Laakmann, Chaolun Li, Luis Martell, Jennifer M. Questel, Deborah Wall-Palmer, Minxiao Wang, Peter H. Wiebe & Agata Weydmann-Zwolicka
+
+Mar Biol 168, 78 (2021). doi:10.1007/s00227-021-03887-y
+
+Toward a global reference database of COI barcodes for marine zooplankton.
+
+[[!doi 10.1007/s00227-021-03887-y desc="MetaZooGene Barcode Atlas and Database (MZGdb).  Database built on top of BOLD and GenBank.  It includes species from which COI data is not yet available."]]

Café
diff --git a/biblio/33899125.mdwn b/biblio/33899125.mdwn
new file mode 100644
index 00000000..d235c3c5
--- /dev/null
+++ b/biblio/33899125.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Establishing Sustainable Cell Lines of a Coral, Acropora tenuis."]]
+[[!tag coral cell_culture cell_line]]
+
+Kawamura K, Nishitsuji K, Shoguchi E, Fujiwara S, Satoh N.
+
+Mar Biotechnol (NY). 2021 Apr 26. doi:10.1007/s10126-021-10031-w
+
+Establishing Sustainable Cell Lines of a Coral, Acropora tenuis.
+
+[[!pmid  33899125 desc="Dissociation with “a mixture of trypsin, EDTA, and collagenase”.  “Treatment for 1–2 h at 25–28 °C did not complete cell dissociation, but after 3–4 h, only single cells without debris were found in the culture dish.”  “[The modular protease] plasmin (2 μg/mL) was effective in maintaining dissociated cells in culture for more than 2 weeks, during which a large number of a new type of cell appeared in the culture dish.”  “Aliquots of polyclonal cell population were harvested from the primary 24-well culture plate, diluted fivefold with growth medium containing plasmin, and dispensed into 96-well plates (100 μL/well). Cells in clumps proliferated with a doubling time of 2–3 days.”"]]
diff --git a/tags/cell_line.mdwn b/tags/cell_line.mdwn
index 72dcb22b..b3df749e 100644
--- a/tags/cell_line.mdwn
+++ b/tags/cell_line.mdwn
@@ -4,5 +4,6 @@ A few notes that just scratch the surface of a vast field…
 
  - [[Echalier and Ohanessian (1969)|biblio/4976834]] reported a culture of _Drosophila_ cells that spontaneously transformed.
  - [[Schneider's (1972)|biblio/4625067]] report of the establishment of the S2 cell line.
+ - [[Kawamura and coll (2021)|biblio/33899125]] reported the use of plasmin to establish coral cell lines.
 
 [[!inline pages="tagged(cell_line)" limit=0]]

Typos
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index c4eb67c8..b48f6760 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -15,8 +15,8 @@ D. silvestris diverged 5.1 My ago.
 The ITS2 sequence of Drosophila species diverged at the speed of 1.2 % per million
 year ([[Schlötterer and coll., 1994|biblio/8015444]]).
 
-12 Drosophila genomes were sequenced and compared by the [[(Drosophila 12
-Genomes Consortium (2007)|biblio/17994087)]].
+12 Drosophila genomes were sequenced and compared by the [[Drosophila 12
+Genomes Consortium (2007)|biblio/17994087]].
 
 See also [[Muller elements|muller_element]].
 
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 116648a6..ead25ecd 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -1,6 +1,6 @@
 [[!meta title="pages tagged synteny"]]
 
-[[(Drosophila 12 Genomes Consortium (2007)|biblio/17994087)]] sequenced
+[[Drosophila 12 Genomes Consortium (2007)|biblio/17994087]] sequenced
 across the _Drosophila_ genus and showed synteny conservation ranging
 between few large blocks with many genes to many small blocks with few genes.
 

Café
diff --git a/biblio/17994087.mdwn b/biblio/17994087.mdwn
new file mode 100644
index 00000000..d7dfe06e
--- /dev/null
+++ b/biblio/17994087.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution of genes and genomes on the Drosophila phylogeny."]]
+[[!tag Drosophila synteny]]
+
+Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.
+
+Nature. 2007 Nov 8;450(7167):203-18. doi:10.1038/nature06341
+
+Evolution of genes and genomes on the Drosophila phylogeny.
+
+[[!pmid 17994087 desc="The result of pairwise comparisons between the species ranges between a few tens or hundreds of synteny blocks of up to ~1000 genes, to ~1000 synteny blocks with a few (tens of) genes."]]
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index 68c6d5e5..c4eb67c8 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -15,6 +15,9 @@ D. silvestris diverged 5.1 My ago.
 The ITS2 sequence of Drosophila species diverged at the speed of 1.2 % per million
 year ([[Schlötterer and coll., 1994|biblio/8015444]]).
 
+12 Drosophila genomes were sequenced and compared by the [[(Drosophila 12
+Genomes Consortium (2007)|biblio/17994087)]].
+
 See also [[Muller elements|muller_element]].
 
 [[!inline pages="tagged(Drosophila)" limit=0]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 0a15e461..116648a6 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -1,5 +1,9 @@
 [[!meta title="pages tagged synteny"]]
 
+[[(Drosophila 12 Genomes Consortium (2007)|biblio/17994087)]] sequenced
+across the _Drosophila_ genus and showed synteny conservation ranging
+between few large blocks with many genes to many small blocks with few genes.
+
 [[Carbone and coll. (2014)|biblio/25209798]] found 96 gibbon–human synteny
 breakpoints (~30 per Gb), associated with segmental duplication or Alu element
 enrichment.  They often bore signatures of non-homology based mechanisms, and

Parasites.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7d43fee1..202f99be 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -30,7 +30,8 @@ Some links:
    <https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=0tPT7vwSO1Vm5QV9iKqfAC>.
 
 Parasites: _Oodinium pouchetii_, microsporidia (on _O. gracilis_ ([[Savelieva
-2019|biblio/10.1134_S1063074019020111]])) and others.
+2019|biblio/10.1134_S1063074019020111]])), bacteria ([[Flood,
+1991|biblio/24817302]]), and others.
 
 
 Phylogeny

Café
diff --git a/biblio/31244882.mdwn b/biblio/31244882.mdwn
new file mode 100644
index 00000000..10cbb01a
--- /dev/null
+++ b/biblio/31244882.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A Nuclear mtDNA Concatemer (Mega-NUMT) Could Mimic Paternal Inheritance of Mitochondrial Genome."]]
+[[!tag mitochondrion]]
+
+Balciuniene J, Balciunas D.
+
+Front Genet. 2019 Jun 6;10:518. doi:10.3389/fgene.2019.00518
+
+A Nuclear mtDNA Concatemer (Mega-NUMT) Could Mimic Paternal Inheritance of Mitochondrial Genome.
+
+[[!pmid 31244882 desc="Postulates the existence of concatemerised mtDNA copies in nuclear genomes."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 318a642c..c31a6fd1 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -90,4 +90,6 @@ coll., 2019|biblio/31387118]]), or multicellular ([[Yahalomi and coll.,
 Mitochondrial DNA has a few rNTP misincorporated, but they do not seem to be
 detrimental ([[Wanrooij and coll., 2020|biblio/32513727]]).
 
+The presence of mtDNA concatemers in nuclear genomes was postulated by [[Balciuniene and Balciunas (2019)|biblio/31244882]].
+
 [[!inline pages="tagged(mitochondrion)" limit=0]]

Café
diff --git a/biblio/33423048.mdwn b/biblio/33423048.mdwn
new file mode 100644
index 00000000..270356b3
--- /dev/null
+++ b/biblio/33423048.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae."]]
+[[!tag synthetic yeast chromosome]]
+
+Postma ED, Dashko S, van Breemen L, Taylor Parkins SK, van den Broek M, Daran JM, Daran-Lapujade P.
+
+Nucleic Acids Res. 2021 Feb 22;49(3):1769-1783. doi:10.1093/nar/gkaa1167
+
+A supernumerary designer chromosome for modular in vivo pathway assembly in _Saccharomyces cerevisiae_.
+
+[[!pmid 33423048 desc="Circular neochromosome assembled in vivo by homologous recombination of fragments containing short homology regions (60 bp).  Includes “a centromere and autonomously replicating sequences (ARS) spaced every 30–40 kb, and markers to facilitate [...] selection”.  Used as “landing pads” for integration of ~30kb-scale fragments, using CRISPR/Cas9 to cleave the integration site.  The neochromosomes can contain entire metabolic pathways, either endogenous (after knocking-out the endogenous copies) or exogenous."]]
diff --git a/tags/synthetic.mdwn b/tags/synthetic.mdwn
index c1548515..06d8d9a3 100644
--- a/tags/synthetic.mdwn
+++ b/tags/synthetic.mdwn
@@ -6,4 +6,6 @@ Sc3.0 roadmap: [[Dai and coll., 2020|biblio/32791980]].
 
 “Biosynthesis of medicinal tropane alkaloids in yeast”: [[Srinivasan and Smolke and coll., 2020|biblio/32879484]]
 
+Example of neochromosome synthesis in yeast: [[Postma and coll., 2021|biblio/33423048]].
+
 [[!inline pages="tagged(synthethic)" limit=0]]

Café
diff --git a/biblio/8015444.mdwn b/biblio/8015444.mdwn
new file mode 100644
index 00000000..2ebfa537
--- /dev/null
+++ b/biblio/8015444.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative evolutionary analysis of rDNA ITS regions in Drosophila."]]
+[[!tag Drosophila ribosome]]
+
+Schlötterer C, Hauser MT, von Haeseler A, Tautz D.
+
+Mol Biol Evol. 1994 May;11(3):513-22. doi:10.1093/oxfordjournals.molbev.a040131
+
+Comparative evolutionary analysis of rDNA ITS regions in Drosophila.
+
+[[!pmid 8015444 desc="Average substitution rate of 1.2% per million year."]]
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index 78a4581f..68c6d5e5 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -12,6 +12,9 @@ and Nei  (1995)|biblio/7739381]]) suggests that D. mel and D. pseudoobscura
 diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and
 D. silvestris diverged 5.1 My ago.
 
+The ITS2 sequence of Drosophila species diverged at the speed of 1.2 % per million
+year ([[Schlötterer and coll., 1994|biblio/8015444]]).
+
 See also [[Muller elements|muller_element]].
 
 [[!inline pages="tagged(Drosophila)" limit=0]]

OKI2018_I69
diff --git a/biblio/33781200.mdwn b/biblio/33781200.mdwn
new file mode 100644
index 00000000..cec762c1
--- /dev/null
+++ b/biblio/33781200.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing."]]
+[[!tag Oikopleura OIST]]
+
+Bliznina A, Masunaga A, Mansfield MJ, Tan Y, Liu AW, West C, Rustagi T, Chien HC, Kumar S, Pichon J, Plessy C, Luscombe NM.
+
+BMC Genomics. 2021 Mar 29;22(1):222. doi: 10.1186/s12864-021-07512-6.
+
+Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing.
+
+[[!pmid 33781200 desc="The OKI2018_I69 assembly."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7222e21e..7d43fee1 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -23,9 +23,11 @@ Some links:
  - Études sur les Appendiculaires du Détroit de Messine, Hermann Fol, 1872
    ([[ark:/13960/t7fr0vj77|https://archive.org/details/cbarchive_100233_etudessurlesappendiculairesdud1821]]).
  - [A day in the life of an Oikopleura lab](http://thenode.biologists.com/day-life-oikopleura-lab/).
- - OSAKA2016 genome on aniseed ([[Dardaillon and coll., 2020|biblio/31680137]]):
+ - OSAKA2016 genome ([[Wang and coll., 2020|biblio/32677034]]) on aniseed
+   ([[Dardaillon and coll., 2020|biblio/31680137]]):
    <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
-
+ - OKI2018_I69 genome [[Bliznina and coll., 2021|biblio/33781200]] on ZENBU:
+   <https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=0tPT7vwSO1Vm5QV9iKqfAC>.
 
 Parasites: _Oodinium pouchetii_, microsporidia (on _O. gracilis_ ([[Savelieva
 2019|biblio/10.1134_S1063074019020111]])) and others.

Café
diff --git a/biblio/23826120.mdwn b/biblio/23826120.mdwn
new file mode 100644
index 00000000..12b3ef1e
--- /dev/null
+++ b/biblio/23826120.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences–a proof of concept."]]
+[[!tag phylogeny ribosome speciation]]
+
+Wolf M, Chen S, Song J, Ankenbrand M, Müller T.
+
+PLoS One. 2013 Jun 24;8(6):e66726. doi:10.1371/journal.pone.0066726
+
+Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept.
+
+[[!pmid 23826120 desc="The CBC Species Concept"]]
diff --git a/biblio/23990606.mdwn b/biblio/23990606.mdwn
index 5a4944b4..5df48186 100644
--- a/biblio/23990606.mdwn
+++ b/biblio/23990606.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The shared genomic architecture of human nucleolar organizer regions."]]
-[[!tag human rDNA nucleolus]]
+[[!tag human ribosome nucleolus]]
 
 Floutsakou I, Agrawal S, Nguyen TT, Seoighe C, Ganley AR, McStay B.
 
diff --git a/tags/rDNA.mdwn b/tags/rDNA.mdwn
deleted file mode 100644
index a9ee3d55..00000000
--- a/tags/rDNA.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged rDNA"]]
-
-[[!inline pages="tagged(rDNA)" actions="no" archive="yes"
-feedshow=10]]

Cultivation of O. lon.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 71b543de..7222e21e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -637,6 +637,7 @@ Culture protocols (incomplete list):
 
  - [[Fenaux and Gorsky (1985)|biblio/art0358]] published a method using a
    helicoidal paddle to stir the culture.
+ - Rotating vessels: [[Sato and coll, 1999|biblio/10005415955].
  - Tested once in Ctenophore tubes ([[Patry, Bubel, Hansen and Knowles,
    2020|biblio/32292660]]).
  - Nishida lab protocol: [[Nishida 2008|biblio/18494706]].
@@ -654,6 +655,10 @@ Food tested in laboratory (totally incomplete list):
    the chlorophyte _Chlorella sp._ (3.5 µm) [[Acuña and Kiefer,
    2000|biblio/10.4319_lo.2000.45.3.0608]].
 
+ - _I. gal_, _Tetraselmis sp_ for _O. dioica_ and the same plus an
+   “unidentified flagellate of 2 µm cell diameter” for _O. longicauda_ ([[Sato
+   and coll, 1999|biblio/10005415955]).
+
  - 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]]).

Culture of O. lon
diff --git a/biblio/10005415955.mdwn b/biblio/10005415955.mdwn
new file mode 100644
index 00000000..0059e176
--- /dev/null
+++ b/biblio/10005415955.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="New apparatuses for cultivation of appendicularians."]]
+[[!tag Oikopleura]]
+
+Sato Riki, Yu Jingshan, Tanaka Yuji, Ishimaru Takashi
+
+Plankton Biology and Ecology 46(2), 162-164, 1999-08-01
+
+New apparatuses for cultivation of appendicularians
+
+[Culture of O. dioica and O. longicauda in rotating vessels.  O. lon required an “unidentified flagellate of 2µm cell diameter”.](https://ci.nii.ac.jp/naid/10005415955)

Café
diff --git a/biblio/19-505187.mdwn b/biblio/19-505187.mdwn
new file mode 100644
index 00000000..ff0fabb8
--- /dev/null
+++ b/biblio/19-505187.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A new appendicularian, Oikopleura gorskyi n. sp. (Tunicata), from norwegian fjords"]]
+[[!tag Oikopleura]]
+
+Beaufortia, 2000, Volume 50 - Issue 2 p. 69-77 urn:nbn:nl:ui:19-505187
+
+Flood (Per R.)
+
+A new appendicularian, _Oikopleura gorskyi_ n. sp. (Tunicata), from norwegian fjords
+
+[2 oral gland cells with 2 nuclei each.  5–7 Eisen oikoblasts surrounded by an unusually low number of neben cells.  Luminosomes (inclusion bodies) found on the house.  ~8 + ~13 subchordal cells lie ventrally in the tail.  Found in Sognefjorden at 400 to 1200 m depth and in Herdlefjorden below 270 m.  Tempeature: ~7.1°C.  Might be found at shallower depth as well.](https://www.persistent-identifier.nl/urn:nbn:nl:ui:19-505187)
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 2c1b15c3..71b543de 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -394,7 +394,8 @@ Development
    anteriorly.  The two differentiated oral gland cells have two nuclei each,
    as demonstrated by a co-staining of nuclei (H2B-mCherry) and cell membrane
    (PH-YF) by [[Kishi and coll, 2014|biblio/25224225]], as well as SEM tomography
-   ([[Nishida and coll., 2021|biblio/33649401]]).
+   ([[Nishida and coll., 2021|biblio/33649401]]).  _O. Gorskyi_ also has two cells
+   with 2 nuclei each ([[Flood 2000|biblio/19-505187]]).
  - Oral gland and subchordal cells, which were thought to be related, do not originate
    from the same blastomere ([[Onuma and coll., 2020|biblio/32029598]]).
  - The subchordal cell precursors migrate along the right side of the notochord

Café
diff --git a/biblio/33828295.mdwn b/biblio/33828295.mdwn
new file mode 100644
index 00000000..7353abfb
--- /dev/null
+++ b/biblio/33828295.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The structure, function and evolution of a complete human chromosome 8."]]
+[[!tag centromere]]
+
+Nature. 2021 Apr 7. doi:10.1038/s41586-021-03420-7
+
+Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, Bzikadze AV, Kremitzki M, Graves-Lindsay TA, Jain C, Hoekzema K, Murali SC, Munson KM, Baker C, Sorensen M, Lewis AM, Surti U, Gerton JL, Larionov V, Ventura M, Miga KH, Phillippy AM, Eichler EE.
+
+The structure, function and evolution of a complete human chromosome 8.
+
+[[!pmid 33828295 desc="Nanopore ultra-long reads barcoded with singly unique nucleotide k-mers (SUNKs) of length 20 and assembled.  Sequence was then corrected with HiFi PacBio reads bearing the same k-mer barcodes.  The centromere was assembled with 11 ultra-long reads.  5 different evolutionary strates were found."]]
diff --git a/tags/centromere.mdwn b/tags/centromere.mdwn
index 6a3d6ca9..d3c212c0 100644
--- a/tags/centromere.mdwn
+++ b/tags/centromere.mdwn
@@ -24,5 +24,7 @@ _Work in progress_
    2020|biblio/31958060]].
  - Centromere relocation to a transcribed region in yeast, detected by ChIP of
    centromeric H3 [[Ola and coll., 2020|biblio/32424070]].
+ - 5 evolutionary strates were found in human chr8 centromere ([[Logdson and
+   coll, 2021|biblio/33828295]]).
 
 [[!inline pages="tagged(centromere)" limit="0"]]

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

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

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

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

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

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

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

updated PO files
diff --git "a/Debian/debi\303\242neries/DebianAnalytica.en.po" "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
index 2127f929..398e9a8c 100644
--- "a/Debian/debi\303\242neries/DebianAnalytica.en.po"
+++ "b/Debian/debi\303\242neries/DebianAnalytica.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2021-04-05 13:44+0000\n"
+"POT-Creation-Date: 2021-04-05 14:00+0000\n"
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+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
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 #. type: Plain text

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

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

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

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

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

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

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

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

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

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

updated PO files
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
index ccebbcfa..6577bba8 100644
--- "a/Debian/debi\303\242neries/grToxique.en.po"
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -6,14 +6,14 @@
 msgid ""
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-"POT-Creation-Date: 2021-03-27 01:07+0000\n"
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Traduction.
diff --git "a/Debian/debi\303\242neries/grToxique.en.po" "b/Debian/debi\303\242neries/grToxique.en.po"
index e46cc098..ccebbcfa 100644
--- "a/Debian/debi\303\242neries/grToxique.en.po"
+++ "b/Debian/debi\303\242neries/grToxique.en.po"
@@ -3,38 +3,38 @@
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-#, fuzzy
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 #. type: Plain text
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-msgstr ""
+msgstr "[[!meta date=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Sat, 27 Mar 2021 10:06:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"GR toxique\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"GR toxique\"]]\n"
 
 #. type: Plain text
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@@ -47,6 +47,13 @@ msgid ""
 "Debian et laissera des trace, au moins sous la forme d'une liste publique de "
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 msgstr ""
+"Many quickly reacted to the return of rms to the FSF and asked that he "
+"leaves again; some also asked for the whole board of directors to resign and "
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+"Maybe it was not the original intent, but in practice the object of the GR "
+"is about FSF's board of directors. Perhaps we will have the result after rms "
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+"What if our two DPL candidates would issue a statement that, if elected, "
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+"allow us to cancel this GR?"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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