Dernières modifications :

SmartAmp
diff --git a/biblio/22295077.mdwn b/biblio/22295077.mdwn
new file mode 100644
index 00000000..1ad735e8
--- /dev/null
+++ b/biblio/22295077.mdwn
@@ -0,0 +1,14 @@
+[[!meta title="One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation."]]
+[[!tag amplification detection diagnostic]]
+
+Kawai Y, Kimura Y, Lezhava A, Kanamori H, Usui K, Hanami T, Soma T, Morlighem 
+JÉ, Saga S, Ishizu Y, Aoki S, Endo R, Oguchi-Katayama A, Kogo Y, Mitani Y,
+Ishidao T, Kawakami C, Kurata H, Furuya Y, Saito T, Okazaki N, Chikahira M,
+Hayashi E, Tsuruoka S, Toguchi T, Saito Y, Ban T, Izumi S, Uryu H, Kudo K,
+Sakai-Tagawa Y, Kawaoka Y, Hirai A, Hayashizaki Y, Ishikawa T.
+
+PLoS One. 2012;7(1):e30236. doi: 10.1371/journal.pone.0030236 doi: 10.1371/journal.pone.0030236
+
+One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation.
+
+[[!pmid 22295077 desc="Inactivation in 5% SDS, gel filtration on Sephacryl S-400 HR in Micro-Bio-Spin colum, and RT-SmartAmp AMV RTase, Aac DNA pol."]]

Codon capture hypothesis
diff --git a/biblio/2515289.mdwn b/biblio/2515289.mdwn
new file mode 100644
index 00000000..7c9a7830
--- /dev/null
+++ b/biblio/2515289.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution of the mitochondrial genetic code. II. Reassignment of codon AUA from isoleucine to methionine."]]
+[[!tag mitochondrion]]
+
+J Mol Evol. 1989 Nov;29(5):373-80 doi:10.1007/bf02602907
+
+Osawa S, Ohama T, Jukes TH, Watanabe K, Yokoyama S.
+
+Evolution of the mitochondrial genetic code. II. Reassignment of codon AUA from isoleucine to methionine.
+
+[[!pmid 2515289 desc="Codon capture hypothesis.  Cites the Crick preprint."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 0c9fd506..641ab4c1 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -45,6 +45,7 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ use different code(s).
  - Another hemichordate code, in cephalodiscidae: TAA → Y, TGA → W, AGA → Ser
    AGG → Lys ([[Li and coll., 2019|biblio/30476024]]).
+ - The codon capture hypothesis: [[Osawa and coll., 1989|biblio/2515289]].
 
 ```
                      AGA   AGG   ATA   AAA   TGA

eDNA
diff --git a/biblio/31937756.mdwn b/biblio/31937756.mdwn
new file mode 100644
index 00000000..6fe6ecc4
--- /dev/null
+++ b/biblio/31937756.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Environmental DNA reveals seasonal shifts and potential interactions in a marine community."]]
+[[!tag Oikopleura eDNA]]
+
+Djurhuus A, Closek CJ, Kelly RP, Pitz KJ, Michisaki RP, Starks HA, Walz KR,
+Andruszkiewicz EA, Olesin E, Hubbard K, Montes E, Otis D, Muller-Karger FE,
+Chavez FP, Boehm AB, Breitbart M.
+
+Nat Commun. 2020 Jan 14;11(1):254. doi: 10.1038/s41467-019-14105-1.
+
+Environmental DNA reveals seasonal shifts and potential interactions in a marine community.
+
+[[!pmid desc="Found Oikopleura 18S sequences in MiSeq run SRR8473276."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7a05fba5..20406bdb 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -557,7 +557,8 @@ Ecology
 
  - California  ([[C. Essenbergm, 1922|biblio/1929090]]); rare in summer's warm
    (> 20ºC) waters and more abundant in winter's cool (13~16 ºC) waters.
- -  Throurought the North Pacific ([[Tokioka, 1960|biblio/10.5134_174644]]).
+ - Also found in eDNA form Monterey bay ([[Djurhuus and coll., 2020|biblio/31937756]]).
+ - Throurought the North Pacific ([[Tokioka, 1960|biblio/10.5134_174644]]).
  - Alaska, where it is more abundant in summer and near the coast ([[Doubleday
    and Hopcroft, 2015|biblio/10.1093_plankt_fbu092]]).
  - Giant appendicularians could be observed in high abundance from deep submersibles
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
index 0d5ce17e..8187c113 100644
--- a/tags/eDNA.mdwn
+++ b/tags/eDNA.mdwn
@@ -2,5 +2,7 @@
 
  - Oikopleura detected in 18S rRNA amplified with universal primers:
    [[Berry and coll., 2019|biblio/30735490]].
+ - Oikopleura 18S detected in at least one MiSeq run from
+   [[Djurhuus and coll. 2020|biblio/31937756]]
 
 [[!inline pages="tagged(eDNA)" limit=0]]

Café
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6acf359b..7a05fba5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -588,6 +588,6 @@ Ecology
    valdiviae_, _O. drygalskii_, and _O. weddelli_ are actually a single species
    (with oral gland cells and ~8 to 14 subchordal cells).
  - Indian ocean near Australia: detected in eDNA sequencing of 18S rRNA
-   ([[Berry and coll., 2019|biblio/30735490.mdwn]])
+   ([[Berry and coll., 2019|biblio/30735490]])
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
index 8de2bd36..0d5ce17e 100644
--- a/tags/eDNA.mdwn
+++ b/tags/eDNA.mdwn
@@ -1,4 +1,6 @@
 [[!meta title="pages tagged eDNA"]]
 
-[[!inline pages="tagged(eDNA)" actions="no" archive="yes"
-feedshow=10]]
+ - Oikopleura detected in 18S rRNA amplified with universal primers:
+   [[Berry and coll., 2019|biblio/30735490]].
+
+[[!inline pages="tagged(eDNA)" limit=0]]

creating tag page tags/eDNA
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
new file mode 100644
index 00000000..8de2bd36
--- /dev/null
+++ b/tags/eDNA.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged eDNA"]]
+
+[[!inline pages="tagged(eDNA)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/30735490.mdwn b/biblio/30735490.mdwn
new file mode 100644
index 00000000..a4ad451a
--- /dev/null
+++ b/biblio/30735490.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events."]]
+[[!tag Oikopleura eDNA]]
+
+PLoS Genet. 2019 Feb 8;15(2):e1007943. doi:10.1371/journal.pgen.1007943
+
+Berry TE, Saunders BJ, Coghlan ML, Stat M, Jarman S, Richardson AJ, Davies CH, Berry O, Harvey ES, Bunce M.
+
+Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events.
+
+[[!pmid desc="Oikopleura detected in the 18S data."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index a8b4a569..6acf359b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -587,5 +587,7 @@ Ecology
    (2003)|biblio/10.1017_S0954102003001585]] proposed that _O. gaussica_, _O.
    valdiviae_, _O. drygalskii_, and _O. weddelli_ are actually a single species
    (with oral gland cells and ~8 to 14 subchordal cells).
+ - Indian ocean near Australia: detected in eDNA sequencing of 18S rRNA
+   ([[Berry and coll., 2019|biblio/30735490.mdwn]])
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Correct tags
diff --git a/biblio/31363093.mdwn b/biblio/31363093.mdwn
index 38d14a04..26504000 100644
--- a/biblio/31363093.mdwn
+++ b/biblio/31363093.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="MAPCap allows high-resolution detection and differential expression analysis of transcription start sites."]]
-[[!tag method library reverse-transcription]]
+[[!tag method library reverse_transcription]]
 
 Bhardwaj V, Semplicio G, Erdogdu NU, Manke T, Akhtar A.
 
diff --git a/biblio/Chenchick_1998.mdwn b/biblio/Chenchick_1998.mdwn
index 91dd84ea..fa51b3bc 100644
--- a/biblio/Chenchick_1998.mdwn
+++ b/biblio/Chenchick_1998.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Generation and use of high-quality cDNA from small amounts of total RNA by SMART PCR."]]
-[[!tag reverse_transcriptase template_switching]]
+[[!tag reverse_transcription template_switching]]
 
 Alex Chenchick, York Y. Shu, Luda Diatchenko, Roger Li, Jason Hill and Paul D. Siebert.
 (Gene Cloning and Analysis Group, CLONETECH Laboratories, Pao Alto, CA, USA).

Café
diff --git a/biblio/10.1101_2020.03.14.992248v3.mdwn b/biblio/10.1101_2020.03.14.992248v3.mdwn
new file mode 100644
index 00000000..5dc046eb
--- /dev/null
+++ b/biblio/10.1101_2020.03.14.992248v3.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads"]]
+[[!tag bioRxiv genome assembly chromosome]]
+
+Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren
+
+bioRxiv 2020.03.14.992248; doi: https://doi.org/10.1101/2020.03.14.992248 
+
+HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
+
+[[!doi 10.1101/2020.03.14.992248v3 desc="“HiCanu modifies the input reads by
+compressing every homopolymer to a single nucleotide.”  “Outputs contigs as
+“pseudo-haplotypes” that preserve local allelic phasing but may switch between
+haplotypes”"]]

Café
diff --git a/biblio/29145518.mdwn b/biblio/29145518.mdwn
new file mode 100644
index 00000000..38ea5c74
--- /dev/null
+++ b/biblio/29145518.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The prehistory of biology preprints: A forgotten experiment from the 1960s."]]
+[[!tag bioRxiv]]
+
+Cobb M.
+
+PLoS Biol. 2017 Nov 16;15(11):e2003995. doi:10.1371/journal.pbio.2003995
+
+The prehistory of biology preprints: A forgotten experiment from the 1960s.
+
+[[!pmid 29145518 desc="Preprints in the 60s!"]]
diff --git a/biblio/b19979307.mdwn b/biblio/b19979307.mdwn
new file mode 100644
index 00000000..39c2bf97
--- /dev/null
+++ b/biblio/b19979307.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="Codon - Anticodon Pairing The Wobble Hypothesis"]]
+[[!tag Crick]]
+
+F. H. C. Crick
+
+1966 ?
+
+Codon - Anticodon Pairing The Wobble Hypothesis
+
+A paper for the Informational Exchange Group No. 7,
+"Nucleic acids and the genetic code". 
+
+https://wellcomelibrary.org/item/b19979307
+
+Discusses a possible mechanism for exchanging ATA and ATG 
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index bd9ccec8..a8b4a569 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -147,9 +147,11 @@ Genome
 Repeat elements
 ---------------
 
- - The main groups of retrotransposons present in _O. dioica_ are  Odin (Oikopleura dioicanon-LTR),
-   Tor (Ty3/gypsy Oikopleura retrotransposon), DIRS1-like and Penelope-like
-   [[Volff and coll., 2004|biblio/15254255]].
+ - The main groups of retrotransposons present in _O. dioica_ are  Odin
+   (Oikopleura dioicanon-LTR), Tor (Ty3/gypsy Oikopleura retrotransposon),
+   DIRS1-like and Penelope-like [[Volff and coll., 2004|biblio/15254255]]. “F.
+   borealis has no Odin elements but has members of other LINE families.”
+   ([[Naville and coll., 2019|biblio/30880010]])
  - “LTR retrotransposons account for a significant part of the indel polymorphism
    in the _Oikopleura_ genome.”
    “Tor-3G elements are frequently inserted into exons and can be transcribed
@@ -162,6 +164,8 @@ Repeat elements
    ([[Denoeud et al., 2010|biblio/21097902]]).
  - SINE and MITE account for a large part of genome expansion in larger oikopleurid
    species ([[Naville and coll., 2019|biblio/30880010]]).
+ - _O. dioica's_ Y chroomosome contains 43% of the TOR insertions ([[Naville
+   and coll., 2019|biblio/30880010]]).
 
 
 Genes and pathways

Reorganise
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 4cc9f38c..bd9ccec8 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -110,9 +110,6 @@ Genome
    in human.  In other tunicates, all mitochondrial genes are on the same DNA strand
    and 24 tRNAs are present, instead of 22 in other chordates (reviewed by [[Gissi and coll.,
    2008|biblio/18612321]]).
- - The main groups of retrotransposons present in _O. dioica_ are  Odin (Oikopleura dioicanon-LTR),
-   Tor (Ty3/gypsy Oikopleura retrotransposon), DIRS1-like and Penelope-like
-   [[Volff and coll., 2004|biblio/15254255]].
  - The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014
    in Genbank are probably a contamination and a misidentification, respectively
    ([[Sakaguchi and coll., 2017|biblio/10.1007_s12562-017-1106-0]]).
@@ -131,18 +128,6 @@ Genome
    ([[Frey and Pucker, 2020|biblio/32085510]]).
  - Operons are enriched for houskeeping genes and depleted for developmental genes
    ([[Denoeud et al., 2010|biblio/21097902]]).
- - “LTR retrotransposons account for a significant part of the indel polymorphism
-   in the _Oikopleura_ genome.”
-   “Tor-3G elements are frequently inserted into exons and can be transcribed
-   together with their host gene, although transcripts initiated in the LTR
-   are also detected (Figure S11).”
-   “The low allelic frequency of Tor-3G insertions is correlated with the
-   almost exclusive occurrence of heterozygous genotypes in the populations.
-   Moreover, experimental crosses between selected heterozygous parents for
-   the same insertion have thus far not resulted in homozygous offsprings.”
-   ([[Denoeud et al., 2010|biblio/21097902]]).
- - SINE and MITE account for a large part of genome expansion in larger oikopleurid
-   species ([[Naville and coll., 2019|biblio/30880010]]).
  - “Highly conserved elements (HCEs) lie around these developmental genes.”
    “Spots of sequence ultraconservation are almost systematically located
    in non coding regions, including introns that are larger than average
@@ -159,6 +144,26 @@ Genome
    from other chrodates ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]).
 
 
+Repeat elements
+---------------
+
+ - The main groups of retrotransposons present in _O. dioica_ are  Odin (Oikopleura dioicanon-LTR),
+   Tor (Ty3/gypsy Oikopleura retrotransposon), DIRS1-like and Penelope-like
+   [[Volff and coll., 2004|biblio/15254255]].
+ - “LTR retrotransposons account for a significant part of the indel polymorphism
+   in the _Oikopleura_ genome.”
+   “Tor-3G elements are frequently inserted into exons and can be transcribed
+   together with their host gene, although transcripts initiated in the LTR
+   are also detected (Figure S11).”
+   “The low allelic frequency of Tor-3G insertions is correlated with the
+   almost exclusive occurrence of heterozygous genotypes in the populations.
+   Moreover, experimental crosses between selected heterozygous parents for
+   the same insertion have thus far not resulted in homozygous offsprings.”
+   ([[Denoeud et al., 2010|biblio/21097902]]).
+ - SINE and MITE account for a large part of genome expansion in larger oikopleurid
+   species ([[Naville and coll., 2019|biblio/30880010]]).
+
+
 Genes and pathways
 ------------------
 

Café
diff --git a/biblio/15254255.mdwn b/biblio/15254255.mdwn
new file mode 100644
index 00000000..4970d59e
--- /dev/null
+++ b/biblio/15254255.mdwn
@@ -0,0 +1,18 @@
+[[!meta title="Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica."]]
+[[!tag repeat transposon Oikopleura]]
+
+Mol Biol Evol. 2004 Nov;21(11):2022-33 doi:10.1093/molbev/msh207
+
+Volff JN, Lehrach H, Reinhardt R, Chourrout D.
+
+Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica.
+
+[[!pmid 15254255 desc="Primary paper for Odin (Oikopleura dioicanon-LTR) and Tor (Ty3/gypsy Oikopleura retrotransposon) elements.
+
+TBlastN search for reverse-transcriptases suggests “extinction, or at least strong copy number reduction, of major clades of non-LTR retrotransposons”.  “About 80 Odin reverse transcriptase sequences were detected by TBlastN analysis in the 41 Mb genome assembly of O. dioica using a 335 amino acid reverse transcriptase sequence as a query (we can not exclude that some nonoverlapping short hits might belong to a same partially sequenced element). About 30% of Odin endonuclease and reverse transcriptase-encoding sequences were corrupted by stop or frameshift mutations, suggesting that an important proportion of Odin elements is not functional. The degree of nucleotide sequence identity between Odin elements ranged from less than 60% up to 90%.”
+
+“About 180 Tor reverse transcriptase sequences were detected in the 41 Mb genome assembly (about 50 sequences for Tor2, Tor3, and Tor4, but only two for Tor1; the remaining sequences were too short to be classified unambiguously). The degree of nucleotide identity inside of the Tor2, Tor3, and Tor4 families ranged from less than 60% up to 98–99% (the two Tor1 elements showed 70% nucleotide identity). On average, open reading frame–corrupting mutations were observed each 7.5 kb, 2.8 kb, and 16 kb for Tor2, Tor3, and Tor4, respectively.” “The Tor4b family might have acquired its env-like gene from a paramyxovirus.”
+
+“Among other groups of LTR retrotransposons, only DIRS1-like elements were found in Oikopleura.”   “About 70 reverse transcriptase sequences from DIRS1-related elements were detected in the 41 Mb genome assembly, with degrees of nucleotide identity ranging from less than 60% up to 90%. DIRS1-related elements were apparently absent from the sea squirt genome and would therefore represent the only type of autonomous retroelement lost in C. intestinalis but present in O. dioica.”
+
+“Penelope-like retroelements were detected in the genome of both O. dioica and C. intestinalis. [...] Complete elements with an apparently intact unique open reading frame encoding a reverse transcriptase and a C-terminal YIG endonuclease were identified, suggesting recent activity. This was confirmed by the presence of very similar elements presenting 98–99% nucleotide identity. However, the high divergence between some copies (less than 60% nucleotide identity) showed the diversity and ancient origin of the group [...]. About 60 reverse transcriptase sequences were detected in the 41 Mb genome assembly.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ed44af89..4cc9f38c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -110,6 +110,9 @@ Genome
    in human.  In other tunicates, all mitochondrial genes are on the same DNA strand
    and 24 tRNAs are present, instead of 22 in other chordates (reviewed by [[Gissi and coll.,
    2008|biblio/18612321]]).
+ - The main groups of retrotransposons present in _O. dioica_ are  Odin (Oikopleura dioicanon-LTR),
+   Tor (Ty3/gypsy Oikopleura retrotransposon), DIRS1-like and Penelope-like
+   [[Volff and coll., 2004|biblio/15254255]].
  - The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014
    in Genbank are probably a contamination and a misidentification, respectively
    ([[Sakaguchi and coll., 2017|biblio/10.1007_s12562-017-1106-0]]).

Correct unit.
diff --git a/biblio/31363093.mdwn b/biblio/31363093.mdwn
index 0f92090a..38d14a04 100644
--- a/biblio/31363093.mdwn
+++ b/biblio/31363093.mdwn
@@ -9,4 +9,4 @@ MAPCap allows high-resolution detection and differential expression analysis of
 
 [[!pmid 31363093 desc="Reports that in their reverse-transcription reaction, G-addition is very low."]]
 
-RT reaction in 20 µL: 10x Buffer 2 μL; dNTP (10 mM) 1 μL → 500 nM final; MgCl2 (25 mM) 4 μL → 5 mM final; DTT (0.1 M) 2 μL → 10 mM final; RNaseOUT (40 U/μl) 1 μL; SSIII (200 U/μL) 1 μL
+RT reaction in 20 µL: 10x Buffer 2 μL; dNTP (10 mM) 1 μL → 500 µM final; MgCl2 (25 mM) 4 μL → 5 mM final; DTT (0.1 M) 2 μL → 10 mM final; RNaseOUT (40 U/μl) 1 μL; SSIII (200 U/μL) 1 μL

RT with low G-addition.
diff --git a/biblio/31363093.mdwn b/biblio/31363093.mdwn
new file mode 100644
index 00000000..0f92090a
--- /dev/null
+++ b/biblio/31363093.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="MAPCap allows high-resolution detection and differential expression analysis of transcription start sites."]]
+[[!tag method library reverse-transcription]]
+
+Bhardwaj V, Semplicio G, Erdogdu NU, Manke T, Akhtar A.
+
+Nat Commun. 2019 Jul 30;10(1):3219. doi:10.1038/s41467-019-11115-x
+
+MAPCap allows high-resolution detection and differential expression analysis of transcription start sites.
+
+[[!pmid 31363093 desc="Reports that in their reverse-transcription reaction, G-addition is very low."]]
+
+RT reaction in 20 µL: 10x Buffer 2 μL; dNTP (10 mM) 1 μL → 500 nM final; MgCl2 (25 mM) 4 μL → 5 mM final; DTT (0.1 M) 2 μL → 10 mM final; RNaseOUT (40 U/μl) 1 μL; SSIII (200 U/μL) 1 μL
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 3555b57d..618d0eca 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -65,6 +65,8 @@ to mismatches can be the explanation.
  - [[Mohr and coll, 2013|biblio/23697550]] showed that the Thermostable group
    II intron reverse transcriptase also adds non-templated As.
 
+ - [[Bhardwaj and coll, 2020|biblio/31363093]] report a reverse-transcription
+   with very low G-addition.
 
 ### Templated TdT activity
 

Hemichordates
diff --git a/biblio/30476024.mdwn b/biblio/30476024.mdwn
new file mode 100644
index 00000000..6e4489a4
--- /dev/null
+++ b/biblio/30476024.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Mitogenomics Reveals a Novel Genetic Code in Hemichordata."]]
+[[!tag mitochondrion]]
+
+Li Y, Kocot KM, Tassia MG, Cannon JT, Bernt M, Halanych KM.
+
+Genome Biol Evol. 2019 Jan 1;11(1):29-40. doi:10.1093/gbe/evy254
+
+Mitogenomics Reveals a Novel Genetic Code in Hemichordata.
+
+[[!pmid 30476024 desc="UAA → Tyr, AAA → Lys,  UGA → W, AGA → Ser"]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 3609bc61..0c9fd506 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -43,6 +43,8 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
  - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s
    mitochondrial sequences can be translated with the ascidian genetic code, and
    suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ use different code(s).
+ - Another hemichordate code, in cephalodiscidae: TAA → Y, TGA → W, AGA → Ser
+   AGG → Lys ([[Li and coll., 2019|biblio/30476024]]).
 
 ```
                      AGA   AGG   ATA   AAA   TGA
@@ -56,6 +58,7 @@ Tunicates             G     G     M     K     W   (O. di, salps, ascidians)
  B. stygius           G     G     I     K     R
 Cephalochordates      S    S,ø?   M     K     W   (standard invertebrate)
 Hemichordates         S     ø     I     ø     W
+Hemichordates (alt)   S     K     I     K     W   And also TAA → Y
 Echinoderms           S     S     I     N     W
 ```
 

Added more codes.
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 37342a54..3609bc61 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -46,6 +46,9 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
 
 ```
                      AGA   AGG   ATA   AAA   TGA
+Standard (non-mito)   R     R     I     K     *
+Yeast                 R     R     M     K     W   (plus other yeast-specific changes)
+Invertebrates         S     S     M     K     W
 Vertebrates           *     *     M     K     W
 Tunicates             G     G     M     K     W   (O. di, salps, ascidians)
  O. longicauda        G     G     I     K     ø?

echinoderms
diff --git a/biblio/3678836.mdwn b/biblio/3678836.mdwn
new file mode 100644
index 00000000..c498e255
--- /dev/null
+++ b/biblio/3678836.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA."]]
+[[!tag mitochondrion]]
+
+Himeno H, Masaki H, Kawai T, Ohta T, Kumagai I, Miura K, Watanabe K.
+
+Gene. 1987;56(2-3):219-30 doi:10.1016/0378-1119(87)90139-9
+
+Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA.
+
+[[!pmid 3678836 desc="AGA and AGG code for serine as in the main invertebrate mitochondrial code, but AUA codes for isoleucine and AAA for asparagine."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 85c979fa..37342a54 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -36,6 +36,8 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
  - In the hemichordate _Balanoglossus carnosus_ ([[Castresana and coll.,
    1998|biblio/9799263]]): ATA → Ile, AGA → Ser, AGG → ø and AAA → ø.
+ - In echinoderms ([[Himeno and coll., 1987|biblio/3678836]]):
+   AGA, AGG → Ser, ATA → Ile, AAA → Asn. 
  - _Ciona savignyi_ uses the same mitochodrial genetic code as of other ascidians
     studied before ([[Yokobori, Watanabe and Oshima, 2003|biblio/14738316]]).
  - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s

Café
diff --git a/biblio/32076268.mdwn b/biblio/32076268.mdwn
new file mode 100644
index 00000000..c7993d65
--- /dev/null
+++ b/biblio/32076268.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gene expression and cell identity controlled by anaphase-promoting complex."]]
+[[!tag promoter differentiation epigenetic]]
+
+Nature. 2020 Mar;579(7797):136-140. doi:10.1038/s41586-020-2034-1
+
+Oh E, Mark KG, Mocciaro A, Watson ER, Prabu JR, Cha DD, Kampmann M, Gamarra N, Zhou CY, Rape M.
+
+Gene expression and cell identity controlled by anaphase-promoting complex.
+
+[[!pmid 32076268 desc="TBP and WDR5 bind transcription start sites at interphase and recruit APC/C during mitosis.  APC/C then ubiquitinylates the histones, which get degraded after mitosis, leaving chromatin open and ready for transcription."]]

Syntax.
diff --git a/biblio/32148763.mdwn b/biblio/32148763.mdwn
index e38c794a..cc377503 100644
--- a/biblio/32148763.mdwn
+++ b/biblio/32148763.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="Widespread use of the "ascidian" mitochondrial genetic code in tunicates."]]
+[[!meta title="Widespread use of the “ascidian” mitochondrial genetic code in tunicates."]]
 [[!tag Oikopleura mitochondrion OIST]]
 
 Pichon J, Luscombe NM, Plessy C.

Café il y a quelques jours
diff --git a/biblio/32133395.mdwn b/biblio/32133395.mdwn
new file mode 100644
index 00000000..418d0659
--- /dev/null
+++ b/biblio/32133395.mdwn
@@ -0,0 +1,14 @@
+[[!meta title="Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas."]]
+[[!tag speciation]]
+
+Hu Y, Thapa A, Fan H, Ma T, Wu Q, Ma S, Zhang D, Wang B, Li M, Yan L, Wei F.
+
+Sci Adv. 2020 Feb 26;6(9):eaax5751. doi:10.1126/sciadv.aax5751
+
+Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas.
+
+[[!pmid 32133395 desc="“Data from 65 whole genomes, 49 Y-chromosomes, and 49
+mitochondrial genomes provide the first comprehensive genetic evidence for
+species divergence in red pandas, demonstrating substantial inter-species
+genetic divergence for all three markers and correcting species-distribution
+boundaries.”"]]

Dans PubMed !
diff --git a/biblio/32148763.mdwn b/biblio/32148763.mdwn
new file mode 100644
index 00000000..e38c794a
--- /dev/null
+++ b/biblio/32148763.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Widespread use of the "ascidian" mitochondrial genetic code in tunicates."]]
+[[!tag Oikopleura mitochondrion OIST]]
+
+Pichon J, Luscombe NM, Plessy C.
+
+F1000Res. 2019 Dec 10;8:2072. doi:10.12688/f1000research.21551.1
+
+Widespread use of the "ascidian" mitochondrial genetic code in tunicates.
+
+[[!pmid 32148763 desc="NCBI's table 13 is to be used for O. dioica.  However, for longicauda and *chordaeus, the code might differ."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6c68f951..ed44af89 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -113,6 +113,10 @@ Genome
  - The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014
    in Genbank are probably a contamination and a misidentification, respectively
    ([[Sakaguchi and coll., 2017|biblio/10.1007_s12562-017-1106-0]]).
+ - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s
+   mitochondrial sequences can be translated with the ascidian genetic code, and
+   suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ (all in the _Coecaria_ genus)
+   use different code(s).
  - Analysis of sex-linked markers supports genetic sex determination with male heterogamety –
    that is: X chromosomes for females and Y for males.  ([[Denoeud et al., 2010|biblio/21097902]])
  - The major spliceosome is hypothethised to have evolved
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 20e369db..85c979fa 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -38,15 +38,17 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    1998|biblio/9799263]]): ATA → Ile, AGA → Ser, AGG → ø and AAA → ø.
  - _Ciona savignyi_ uses the same mitochodrial genetic code as of other ascidians
     studied before ([[Yokobori, Watanabe and Oshima, 2003|biblio/14738316]]).
-
+ - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s
+   mitochondrial sequences can be translated with the ascidian genetic code, and
+   suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ use different code(s).
 
 ```
                      AGA   AGG   ATA   AAA   TGA
 Vertebrates           *     *     M     K     W
 Tunicates             G     G     M     K     W   (O. di, salps, ascidians)
- O. lon ?             G     G     I     K     ø?
- M. ery ?             G     G     ø?    K     ?
- B. sty ?             G     G     I     K     R
+ O. longicauda        G     G     I     K     ø?
+ M. erythrocephalus   G     G     ø?    K     ?
+ B. stygius           G     G     I     K     R
 Cephalochordates      S    S,ø?   M     K     W   (standard invertebrate)
 Hemichordates         S     ø     I     ø     W
 Echinoderms           S     S     I     N     W

Tag concentration.
diff --git a/biblio/26083756.mdwn b/biblio/26083756.mdwn
index 0dcfbde0..dc571810 100644
--- a/biblio/26083756.mdwn
+++ b/biblio/26083756.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Single-cell chromatin accessibility reveals principles of regulatory variation."]]
-[[!tag single_cell ATAC-seq tag]]
+[[!tag single_cell epigenetic tag]]
 
 Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590
 
diff --git a/tags/ATAC-seq.mdwn b/tags/ATAC-seq.mdwn
deleted file mode 100644
index dcd7b186..00000000
--- a/tags/ATAC-seq.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged ATAC-seq"]]
-
-[[!inline pages="tagged(ATAC-seq)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/32042188.mdwn b/biblio/32042188.mdwn
new file mode 100644
index 00000000..21f7204d
--- /dev/null
+++ b/biblio/32042188.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Long-range single-molecule mapping of chromatin accessibility in eukaryotes."]]
+[[!tag method methylation Nanopore epigenetic]]
+
+Nat Methods. 2020 Mar;17(3):319-327. doi:10.1038/s41592-019-0730-2
+
+Shipony Z, Marinov GK, Swaffer MP, Sinnott-Armstrong NA, Skotheim JM, Kundaje A, Greenleaf WJ.
+
+Long-range single-molecule mapping of chromatin accessibility in eukaryotes.
+
+[[!pmid 32042188 desc="Single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq). Methylation of accessible chromatin with the EcoGII N6-methyladenosine (m6A) methyltransferase, followed by Nanopore sequencing.  Specific improvements compared to other methods: single-strand resolution (on DNA wrapped to nucleosomes for instance), and chromatin coaccessibility patterns."]]

Café
diff --git a/biblio/32001511.mdwn b/biblio/32001511.mdwn
new file mode 100644
index 00000000..316b02d4
--- /dev/null
+++ b/biblio/32001511.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="HELLS and PRDM9 form a pioneer complex to open chromatin at meiotic recombination hot spots."]]
+[[!tag meiosis H3K4me3 H3K4me1 H3K36me3 H3K9ac]]
+
+HELLS and PRDM9 form a pioneer complex to open chromatin at meiotic recombination hot spots.
+
+Spruce C, Dlamini S, Ananda G, Bronkema N, Tian H, Paigen K, Carter GW, Baker CL.
+
+Genes Dev. 2020 Mar 1;34(5-6):398-412. doi:10.1101/gad.333542.119
+
+[[!pmid 32001511 desc="“[One] chromatin states [...] was enriched for PRDM9-binding sites.”  (H3K4me3 > H3K4me1 > H3K36me3 > H3K9ac)  “The majority [of the] locations overlap with previously reported locations of B6 meiosis-specific DSBs and PRDM9-dependent H3K4me3 modification.”  “Interestingly, compared with other phyla, we did not detect H2A.Z at hot spots in mice.”  “At PRDM9-dependent H3K4me3 sites, we detected increased DNA accessibility [ATAC-seq] overlapping with PRDM9 motif locations.”  Changing the DNA binding specificity of PRDM9 moved the whole epigenetic mark to new locations.  Testis-conditional KO of Hells relocates meiotic DSBs (identified by DMC1 binding) to promoter regions (determined as such by annotation and by chromatin state).  The hotspot chromatin state is reduced in Hells mutants, although PRDM9 is still present.  “These data show that HELLS is required for establishment of the epigenomic state and chromatin accessibility at hot spots.”  Hells interacts with a “PRDM9 variant that lacks the DNA-binding domain (PRDM9ΔZF) [...], suggesting that this interaction is independent of PRDM9-directed DNA binding.”  “Critically, upon loss of HELLS, PRDM9C binding at hot spots was reduced to background levels (Fig. 6H). Together, these data show that PRDM9 and HELLS form a complex in vivo and, by extension, suggests that active chromatin remodeling is required for robust PRDM9 binding at hot spots.”"]]

creating tag page tags/muller_element
diff --git a/tags/muller_element.mdwn b/tags/muller_element.mdwn
new file mode 100644
index 00000000..99eb6d49
--- /dev/null
+++ b/tags/muller_element.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged muller element"]]
+
+[[!inline pages="tagged(muller_element)" actions="no" archive="yes"
+feedshow=10]]

Crevettes à l'ail.
diff --git a/biblio/31806031.mdwn b/biblio/31806031.mdwn
new file mode 100644
index 00000000..364ac337
--- /dev/null
+++ b/biblio/31806031.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence."]]
+[[!tag muller_element chromosome synteny]]
+
+Meisel RP, Delclos PJ, Wexler JR.
+
+BMC Biol. 2019 Dec 5;17(1):100. doi:10.1186/s12915-019-0721-x
+
+The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence.
+
+[[!pmid 31806031 desc="“We provide two lines of evidence that the X chromosome of the German cockroach, B. germanica, is homologous to Muller element F, which is X-linked in most flies. First, there is a reduced sequencing coverage of nearly half of the Muller element F homologs in male cockroach, consistent with a haploid dose of the X chromosome in males (Fig. 2). Second, there is a decreased heterozygosity of element F homologs in male cockroach, including those with reduced male sequencing coverage (Fig. 3). We therefore hypothesize that element F is an ancient X chromosome that was present in the most recent common ancestor (MRCA) of flies and cockroaches, and it has been conserved as an X chromosome in the German cockroach and many fly species.”"]]

Caps
diff --git a/biblio/32103016.mdwn b/biblio/32103016.mdwn
new file mode 100644
index 00000000..4aa7f3da
--- /dev/null
+++ b/biblio/32103016.mdwn
@@ -0,0 +1,17 @@
+[[!meta title="Dinucleoside polyphosphates act as 5'-RNA caps in bacteria."]]
+[[!tag cap]]
+
+Hudeček O, Benoni R, Reyes-Gutierrez PE, Culka M, Šanderová H, Hubálek M, Rulíšek L, Cvačka J, Krásný L, Cahová H. 
+
+Nat Commun. 2020 Feb 26;11(1):1052. doi:10.1038/s41467-020-14896-8
+
+Dinucleoside polyphosphates act as 5'-RNA caps in bacteria.
+
+[[!pmid 32103016 desc="T7 RNAP and E. coli RNAP efficiently initiate
+transcription with N(p)nN cap analogs at mM concentrations.  LC-MS analysis of
+sRNAs digested with Nuclease P1 detects N(p)nN caps.  Existence of the internal
+polyphosphate chain demonstrated by the fact that the N(p)nN caps are not
+fragmented by ionization, like GppppG and unlike pppGpG.  m7Gp4Gm and m6Ap3A
+were further identified using synthethic standards.  The RppH and ApaH enzymes
+cleaved caps, leaving 5′-p or 5′-ppp ends respectively.  Cap methylation
+protects from RppH cleavage but not from ApaH."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 8e2ae7f3..2b911981 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -69,4 +69,7 @@ Atypical caps (work in progress)
  - 5′-phospho-ADP-ribosylated RNA/DNA cap, synthethysed by RNA
    2′-phosphotransferase Tpt1 ([[Munir, Banerjee and Shuman, 2018|biblio/30202863]]).
 
+ - Mass spectroscopy and molecular biology detected dinucleoside polyphosphate caps
+   in bacteria ([[Hudeček and coll., 2020|biblio/32103016]]).
+
 [[!inline pages="tagged(cap)" limit=0]]

Café
diff --git a/tags/cellulose.mdwn b/tags/cellulose.mdwn
index 5bf15a48..273e6c35 100644
--- a/tags/cellulose.mdwn
+++ b/tags/cellulose.mdwn
@@ -14,4 +14,8 @@ expression in the epidermis.
 A cellulose synthase and several endoglycanase genes were observed in the _C.
 intestinalis_ genome by [[Dehal and coll., 2002|biblio/12481130]].
 
+_CesA_ is not found in other animals outside Tunicates.  The GH6 (cellulose hydrolase)
+gene is found as an independent copy an as a domain of _CesA_ in Tunicates
+([[Inoue, Nakashima and Satoh, 2019|biblio/30974905]]).
+
 [[!inline pages="tagged(cellulose)" limit=0]]

Café
diff --git a/biblio/30974905.mdwn b/biblio/30974905.mdwn
new file mode 100644
index 00000000..176412f6
--- /dev/null
+++ b/biblio/30974905.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but Not in Other Animal Genomes."]]
+[[!tag Oikopleura cellulose]]
+
+Inoue J, Nakashima K, Satoh N.
+
+Genes (Basel). 2019 Apr 10;10(4). pii: E294. doi:10.3390/genes10040294
+
+ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but Not in Other Animal Genomes.
+
+[[!pmid 30974905 desc="A second GH6 gene (with no CesA domain) was found in Tunicates."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7f0bd9a3..6c68f951 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -175,6 +175,9 @@ Genes and pathways
    cellulose I was also found in _O. rufescens by_ [[Kimura and coll
    (2001)|biblio/11732199]]. The CesA gene is trans-spliced in the ascidian _Ciona
    intestinalis_ ([[Matthysse and coll., 2004|biblio/14722352]]).
+ - A GH6 (glycosyl hydrolase family 6) domain is found in the CesA genes,
+   as well as an independent genes, in Tunicates
+   ([[Inoue, Nakashima and Satoh, 2019|biblio/30974905]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Øvrebø and coll., 2015|biblio/25714331]],
    [[Feng & Thompson, 2018|biblio/29969934]]).
@@ -234,6 +237,8 @@ Genes and pathways
  - Components of the constitutive centromere-associated network (CCAN) of the
    inner kinetochore cound not be found in the genome by ([[Feng and coll.,
    2019|biblio/31306061]]).
+ - _Nodal_ is not found in _O. dioica_'s genome ([[Onuma and coll., 2020|biblio/32029598]]).
+
 
 Epigenome
 ---------
@@ -249,6 +254,7 @@ Epigenome
    phase, while in endocycling cells, it increases directly after the end of
    the S phase ([[Spada, Chioda and Thompson (2006)|biblio/15937898]]).
 
+
 Transcriptome
 -------------
 
@@ -283,6 +289,7 @@ Transcriptome
  - On the histone mRNAs, no purine-rich histone downstream element (HDE) was found
    by [[Chioda, Eskeland and Thompson in 2002|biblio/12446815]].
 
+
 Tools
 -----
 
@@ -339,7 +346,9 @@ Development
    the genome (doubling the genes would then double the amount of regulatory sequences).
  - Regular calcium waves are pulsing during embyogenesis.  Their propagation and
    synchronicity is severly disrupted by the knockdown of the connexins CxA and CxB
-   ([[Mikhaleva, Tolstenkov and Glover 2019|biblio/30905687]]).
+   ([[Mikhaleva, Tolstenkov and Glover 2019|biblio/30905687]]).  The calcium waves
+   are required for Bmp.a expression in descendants of the R (Right) blastomere
+   ([[Onuma and coll., 2020|biblio/32029598]]).
  - The tandem _propA_ and _propB_ genes control directly or indirectly _oik41a_
    and proper development of the house-secreting epithelium ([[Mikhaleva et
    al., 2018|biblio/30217597]]).

Typo
diff --git a/biblio/7511410.mdwn b/biblio/7511410.mdwn
index df2599b9..9ce07cb8 100644
--- a/biblio/7511410.mdwn
+++ b/biblio/7511410.mdwn
@@ -7,4 +7,4 @@ Biochemistry. 1994 Apr 5;33(13):3890-5 doi:10.1021/bi00179a014
 
 Fidelity of in vitro DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase.
 
-[[!pmid 7511410 desc="When the extra base added by the RTase in a template-switching reaction is determined by sequencing, the result does not reflect previous results obrained by primer extension assay (where A >> C on non-capped blunt DNA/RNA ends).  This may be because of the differential efficiency of the RTase to extend a template over various single-base mismatches.  In this assay, T to C and G to C were more frequent than T to A and G to A.  Nevertheless, the experiments support previous evidence that addition is mostly limited to a single nucleotide.  RT reaction: 50 mM Tris-HCl, pH 8.0; 75 mM KCl;, 0.1 mM EDTA; 1 mM DTT; 0.1% Triton X-100; 100 µM each dNTP; 7 mM MgCl2; 200 nM 24-base DNA-40-base RNA primer-template; 700 nM 41-base RNA template 2; 700 nM 42-base RNA template 3; and 100 nM HIV-1 RT in a final volume of 10 µL. When reaction products were to be sequenced, mixtures were incubated at 37 °C for 2 h."]]
+[[!pmid 7511410 desc="When the extra base added by the RTase in a template-switching reaction is determined by sequencing, the result does not reflect previous results obtained by primer extension assay (where A >> C on non-capped blunt DNA/RNA ends).  This may be because of the differential efficiency of the RTase to extend a template over various single-base mismatches.  In this assay, T to C and G to C were more frequent than T to A and G to A.  Nevertheless, the experiments support previous evidence that addition is mostly limited to a single nucleotide.  RT reaction: 50 mM Tris-HCl, pH 8.0; 75 mM KCl;, 0.1 mM EDTA; 1 mM DTT; 0.1% Triton X-100; 100 µM each dNTP; 7 mM MgCl2; 200 nM 24-base DNA-40-base RNA primer-template; 700 nM 41-base RNA template 2; 700 nM 42-base RNA template 3; and 100 nM HIV-1 RT in a final volume of 10 µL. When reaction products were to be sequenced, mixtures were incubated at 37 °C for 2 h."]]

Reaction conditions.
diff --git a/biblio/8346046.mdwn b/biblio/8346046.mdwn
index c3507254..4c42ad74 100644
--- a/biblio/8346046.mdwn
+++ b/biblio/8346046.mdwn
@@ -7,4 +7,8 @@ Hirzmann J, Luo D, Hahnen J, Hobom G.
 
 Determination of messenger RNA 5'-ends by reverse transcription of the cap structure.
 
-[[!pmid 8346046 desc="The mRNA cap can template an extra C in the first strand cDNA."]]
+[[!pmid 8346046 desc="The mRNA cap can template an extra C in the first strand cDNA. “50% of the cDNAs of capped mRNA molecules had an extra G”"]]
+
+“poly(A)+ RNA was obtained using Hybond-mAP paper (Amersham). 1 µg of poly(A)+ -RNA in 9.65 µL of water was heated to 60°C for 3 min, cooled on ice, added to 4 µL of 5 × RT buffer (1 × RT buffer is 40 mM Tris-HCl, pH 8.3, 5 mM MgCl2, 40 mM KCl, 2 mM DTE), 3 µL dNTPs (10 mM each), 0.25 µL (10 units) of RNasin (Promega), 2.5 µL of XhoI-(dT)17 oligonucleotide primer (300 pmol, 0.5 µg/µL). and 0.6 µL (16 units) of avian
+myeloblastosis virus (AMV) reverse transcriptase (Boehringer).  The reaction was continued at 42 °C for 2 hours, and excess XhoI-(dT)17 primer and substrates were removed by glass powder purification followed by ethanol precipitation.”
+

Café
diff --git a/biblio/32029598.mdwn b/biblio/32029598.mdwn
new file mode 100644
index 00000000..ad6de061
--- /dev/null
+++ b/biblio/32029598.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A chordate species lacking Nodal utilizes calcium oscillation and Bmp for left-right patterning."]]
+[[!tag Oikopleura]]
+
+Onuma TA, Hayashi M, Gyoja F, Kishi K, Wang K, Nishida H.
+
+Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4188-4198. doi:10.1073/pnas.1916858117
+
+A chordate species lacking Nodal utilizes calcium oscillation and Bmp for left-right patterning.
+
+[[!pmid 32029598 desc="“Descendant cells of the L- and R-cells were distributed asymmetrically throughout the organism, even in most morphologically symmetric organs.”  “L- and R-cells in the two-cell embryo show stereotyped asymmetries in their cell fates; this is in contrast to ascidian and vertebrate embryos.”  “Both oral glands [...] were L-descendants. In contrast, the subchordal cells, [...] were R-descendants.  The oral gland and subchordal cells have been proposed to share an ontogenic origin, because only larvacean species with an oral gland have subchordal cells. However, our results suggest that these two cells had a different origin.”  “Bmp.a expression was detected in 40% of the R-cells, but none of the L-cells.”  “Ca2+ oscillation is required for Bmp.a expression.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 06d0a29b..7f0bd9a3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -343,23 +343,25 @@ Development
  - The tandem _propA_ and _propB_ genes control directly or indirectly _oik41a_
    and proper development of the house-secreting epithelium ([[Mikhaleva et
    al., 2018|biblio/30217597]]).
- - 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]].
  - The endodermal strand is the strand of 16 cells that lie in a single line.
    The endodermal cells strand migrate from the tail to the trunk and give
    rise to the posterior part of the digestive tract (rectum), but not the anus.
    Removal of the trunk suggests that it is not necessary for initiation of the
    migration ([[Kishi and coll, 2014|biblio/25224225]]).
- - Notochord cell precursors express _Brachyury_ like in other chordates
-   ([[Bassham and Postlethwait (2000)|biblio/10753519]]).
+ - The 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]].
+ - 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
    in the space that has been filled with endodermal strand cells.  Amputation
    experiments indicate that the posterior portion of the tail is required for
    posterior migration of subchordal cell precursors ([[Kishi and coll,
    2014|biblio/25224225]]).  They express _Brachyury_ ([[Bassham and
    Postlethwait (2000)|biblio/10753519]]).
+ - Notochord cell precursors express _Brachyury_ like in other chordates
+   ([[Bassham and Postlethwait (2000)|biblio/10753519]]).
  - Expression of development genes is retarded by polyunsaturated aldehydes produced
    by diatoms ([[Torres-Águila and coll., 2018|biblio/30272001]]).
  - Endocycling cells show no polytenisation nor _in loco_ amplifications.  Deep invaginations

ANISEED
diff --git a/biblio/31680137.mdwn b/biblio/31680137.mdwn
new file mode 100644
index 00000000..1f25a000
--- /dev/null
+++ b/biblio/31680137.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates."]]
+[[!tag Oikopleura genome database]]
+
+Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse MB, Louis A, Nitta KR, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult-Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan JF, Davidson B, Nishida H, Dantec C, Lemaire P.
+
+Nucleic Acids Res. 2020 Jan 8;48(D1):D668-D675. doi:10.1093/nar/gkz955
+
+ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates.
+
+[[!pmid 31680137 desc="First release of ANISEED with O. dioica in."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 96e607bd..06d0a29b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -22,7 +22,8 @@ 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: <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
+ - OSAKA2016 genome on aniseed ([[Dardaillon and coll., 2020|biblio/31680137]]):
+   <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
 
 Food tested in laboratory (totally incomplete list): _Isochrysis galbana_ (5.5
 µm in size), _Tetraselmis suecica_ (9.5 µm), and the chlorophyte _Chlorella

Engrish
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index dd551db2..102b2f80 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2020-02-27 22:00+0000\n"
-"PO-Revision-Date: 2020-02-28 06:59+0900\n"
+"PO-Revision-Date: 2020-02-28 07:01+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -22,10 +22,11 @@ msgid "[[!meta date=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 msgstr "[[!meta date=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta updated=\"Fri, 28 Feb 2020 07:00:04 +0900\"]]\n"
-msgstr "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
+msgstr ""
+"[[!meta updated=\"Fri, 28 Feb 2020 07:00:04 +0900\"]]\n"
+"\n"
 
 #. type: Plain text
 #, no-wrap
@@ -112,7 +113,5 @@ msgid ""
 msgstr "grep evince /etc/mailcap >> $HOME/.mailcap\n"
 
 #. type: Plain text
-#, fuzzy
-#| msgid "_édité le 28 février pour ajouter `$HOME` à l'exemple."
 msgid "_édité le 28 février pour ajouter `$HOME` à l'exemple._"
 msgstr "_edited on feb. 28th to add `$HOME` to the example._"

updated PO files
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index 9f1a02a2..dd551db2 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -6,8 +6,8 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2020-02-27 21:58+0000\n"
-"PO-Revision-Date: 2020-02-27 22:40+0900\n"
+"POT-Creation-Date: 2020-02-27 22:00+0000\n"
+"PO-Revision-Date: 2020-02-28 06:59+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -22,8 +22,9 @@ msgid "[[!meta date=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 msgstr "[[!meta date=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
+msgid "[[!meta updated=\"Fri, 28 Feb 2020 07:00:04 +0900\"]]\n"
 msgstr "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 
 #. type: Plain text
@@ -104,15 +105,14 @@ msgstr ""
 "instance (but beware, it is simplistic):"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid ""
-#| "grep evince /etc/mailcap >> .mailcap\n"
-#| "\n"
+#, no-wrap
 msgid ""
 "grep evince /etc/mailcap >> $HOME/.mailcap\n"
 "\n"
-msgstr "grep evince /etc/mailcap >> .mailcap\n"
+msgstr "grep evince /etc/mailcap >> $HOME/.mailcap\n"
 
 #. type: Plain text
-msgid "_édité le 28 février pour ajouter `$HOME` à l'exemple."
-msgstr ""
+#, fuzzy
+#| msgid "_édité le 28 février pour ajouter `$HOME` à l'exemple."
+msgid "_édité le 28 février pour ajouter `$HOME` à l'exemple._"
+msgstr "_edited on feb. 28th to add `$HOME` to the example._"

Syntaxe et màj
diff --git "a/Debian/debi\303\242neries/pdf.mdwn" "b/Debian/debi\303\242neries/pdf.mdwn"
index 93d5c988..6815fabe 100644
--- "a/Debian/debi\303\242neries/pdf.mdwn"
+++ "b/Debian/debi\303\242neries/pdf.mdwn"
@@ -1,5 +1,5 @@
 [[!meta date="Thu, 27 Feb 2020 22:33:17 +0900"]]
-[[!meta updated="Thu, 27 Feb 2020 22:33:17 +0900"]]
+[[!meta updated="Fri, 28 Feb 2020 07:00:04 +0900"]]
 [[!tag Debian]]
 
 [[!meta title="Comment ne pas ouvrir un PDF avec GIMP"]]
@@ -38,4 +38,4 @@ exemple (pour faire simple):
 grep evince /etc/mailcap >> $HOME/.mailcap
 ```
 
-_édité le 28 février pour ajouter `$HOME` à l'exemple.
+_édité le 28 février pour ajouter `$HOME` à l'exemple._

updated PO files
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index 8599c5fa..9f1a02a2 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2020-02-27 13:38+0000\n"
+"POT-Creation-Date: 2020-02-27 21:58+0000\n"
 "PO-Revision-Date: 2020-02-27 22:40+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -104,8 +104,15 @@ msgstr ""
 "instance (but beware, it is simplistic):"
 
 #. type: Plain text
-#, no-wrap
+#, fuzzy, no-wrap
+#| msgid ""
+#| "grep evince /etc/mailcap >> .mailcap\n"
+#| "\n"
 msgid ""
-"grep evince /etc/mailcap >> .mailcap\n"
+"grep evince /etc/mailcap >> $HOME/.mailcap\n"
 "\n"
 msgstr "grep evince /etc/mailcap >> .mailcap\n"
+
+#. type: Plain text
+msgid "_édité le 28 février pour ajouter `$HOME` à l'exemple."
+msgstr ""

HOME
diff --git "a/Debian/debi\303\242neries/pdf.mdwn" "b/Debian/debi\303\242neries/pdf.mdwn"
index 0b38d511..93d5c988 100644
--- "a/Debian/debi\303\242neries/pdf.mdwn"
+++ "b/Debian/debi\303\242neries/pdf.mdwn"
@@ -35,5 +35,7 @@ qui se trouve dans `/etc/mailcap` et la mettre dans `$HOME/.mailcap`. Par
 exemple (pour faire simple):
 
 ```
-grep evince /etc/mailcap >> .mailcap
+grep evince /etc/mailcap >> $HOME/.mailcap
 ```
+
+_édité le 28 février pour ajouter `$HOME` à l'exemple.

Bisrepetitat
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index 50e2af03..8599c5fa 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2020-02-27 13:38+0000\n"
-"PO-Revision-Date: 2020-02-27 22:39+0900\n"
+"PO-Revision-Date: 2020-02-27 22:40+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -66,7 +66,7 @@ msgstr ""
 "usr/share/applications` in [FreeDesktop format](https://specifications."
 "freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest.html). The "
 "_Debian Policy_ specifies that the packages that provide informations in the "
-"FreeDesktop format refrain from repeat them in mailcap format  ([9.7.2]]"
+"FreeDesktop format refrain from repeat them in mailcap format  ([9.7.2]"
 "(https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-"
 "media-type-handlers-with-mailcap-entries))."
 

Syntax
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index 43ecce3c..50e2af03 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2020-02-27 13:38+0000\n"
-"PO-Revision-Date: 2020-02-27 22:36+0900\n"
+"PO-Revision-Date: 2020-02-27 22:39+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -37,12 +37,6 @@ msgid "[[!meta title=\"Comment ne pas ouvrir un PDF avec GIMP\"]]\n"
 msgstr "[[!meta title=\"How to not open a PDF with GIMP\"]]\n"
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "Des outils comme le client courriel en ligne de commande [`neomutt`]"
-#| "(https://neomutt.org) peuvent lancer des applications graphiques.  Pour "
-#| "sélectionner quelle application pour quel type de fichier, `mutt` utilise "
-#| "le système `mailcap`, fourni par le paquet [[!debpkg `mime-support`]]."
 msgid ""
 "Des outils comme le client courriel en ligne de commande [`neomutt`](https://"
 "neomutt.org) peuvent lancer des applications graphiques.  Pour sélectionner "
@@ -52,20 +46,9 @@ msgstr ""
 "Some tools such as the command-line email client [`neomutt`](https://neomutt."
 "org) can launch graphical applications. In order to select which application "
 "for which file, `mutt` uses the `mailcap` system, provided by the [[!debpkg "
-"`mime-support`]] package."
+"mime-support]] package."
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "`mailcap` tire ses informations par défaut de deux sources: des fichiers "
-#| "installés dans `/usr/lib/mime/packages` au [format mailcap](https://"
-#| "manpages.debian.org/mailcap) ou dans `/usr/share/applications` au format "
-#| "[FreeDesktop](https://specifications.freedesktop.org/desktop-entry-spec/"
-#| "desktop-entry-spec-latest.html)  par les paquets distribuant les "
-#| "applications.  La _charte Debian_ demande que les paquets fournissant des "
-#| "informations au format FreeDesktop évitent de les répéter au format "
-#| "mailcap [[9.7.2]](https://www.debian.org/doc/debian-policy/ch-opersys."
-#| "html#registration-of-media-type-handlers-with-mailcap-entries)."
 msgid ""
 "`mailcap` tire ses informations par défaut de deux sources: des fichiers "
 "installés dans `/usr/lib/mime/packages` au [format mailcap](https://manpages."
@@ -83,9 +66,9 @@ msgstr ""
 "usr/share/applications` in [FreeDesktop format](https://specifications."
 "freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest.html). The "
 "_Debian Policy_ specifies that the packages that provide informations in the "
-"FreeDesktop format refrain from repeat them in mailcap format  [[9.7.2]]"
+"FreeDesktop format refrain from repeat them in mailcap format  ([9.7.2]]"
 "(https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-"
-"media-type-handlers-with-mailcap-entries)."
+"media-type-handlers-with-mailcap-entries))."
 
 #. type: Plain text
 msgid ""
@@ -125,7 +108,4 @@ msgstr ""
 msgid ""
 "grep evince /etc/mailcap >> .mailcap\n"
 "\n"
-msgstr ""
-"<pre>\n"
-"grep evince /etc/mailcap >> .mailcap\n"
-"</pre>\n"
+msgstr "grep evince /etc/mailcap >> .mailcap\n"

updated PO files
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index a003c051..43ecce3c 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2020-02-27 13:35+0000\n"
+"POT-Creation-Date: 2020-02-27 13:38+0000\n"
 "PO-Revision-Date: 2020-02-27 22:36+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -37,11 +37,17 @@ msgid "[[!meta title=\"Comment ne pas ouvrir un PDF avec GIMP\"]]\n"
 msgstr "[[!meta title=\"How to not open a PDF with GIMP\"]]\n"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "Des outils comme le client courriel en ligne de commande [`neomutt`]"
+#| "(https://neomutt.org) peuvent lancer des applications graphiques.  Pour "
+#| "sélectionner quelle application pour quel type de fichier, `mutt` utilise "
+#| "le système `mailcap`, fourni par le paquet [[!debpkg `mime-support`]]."
 msgid ""
 "Des outils comme le client courriel en ligne de commande [`neomutt`](https://"
 "neomutt.org) peuvent lancer des applications graphiques.  Pour sélectionner "
 "quelle application pour quel type de fichier, `mutt` utilise le système "
-"`mailcap`, fourni par le paquet [[!debpkg `mime-support`]]."
+"`mailcap`, fourni par le paquet [[!debpkg mime-support]]."
 msgstr ""
 "Some tools such as the command-line email client [`neomutt`](https://neomutt."
 "org) can launch graphical applications. In order to select which application "
@@ -49,6 +55,17 @@ msgstr ""
 "`mime-support`]] package."
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "`mailcap` tire ses informations par défaut de deux sources: des fichiers "
+#| "installés dans `/usr/lib/mime/packages` au [format mailcap](https://"
+#| "manpages.debian.org/mailcap) ou dans `/usr/share/applications` au format "
+#| "[FreeDesktop](https://specifications.freedesktop.org/desktop-entry-spec/"
+#| "desktop-entry-spec-latest.html)  par les paquets distribuant les "
+#| "applications.  La _charte Debian_ demande que les paquets fournissant des "
+#| "informations au format FreeDesktop évitent de les répéter au format "
+#| "mailcap [[9.7.2]](https://www.debian.org/doc/debian-policy/ch-opersys."
+#| "html#registration-of-media-type-handlers-with-mailcap-entries)."
 msgid ""
 "`mailcap` tire ses informations par défaut de deux sources: des fichiers "
 "installés dans `/usr/lib/mime/packages` au [format mailcap](https://manpages."
@@ -56,9 +73,9 @@ msgid ""
 "(https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-"
 "spec-latest.html)  par les paquets distribuant les applications.  La _charte "
 "Debian_ demande que les paquets fournissant des informations au format "
-"FreeDesktop évitent de les répéter au format mailcap [[9.7.2]](https://www."
+"FreeDesktop évitent de les répéter au format mailcap ([9.7.2](https://www."
 "debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-"
-"handlers-with-mailcap-entries)."
+"handlers-with-mailcap-entries))."
 msgstr ""
 "`mailcap` gets its default informations from two sources: some files "
 "installed by packages distributing the applications in either `/usr/lib/mime/"

Syntaxe
diff --git "a/Debian/debi\303\242neries/pdf.mdwn" "b/Debian/debi\303\242neries/pdf.mdwn"
index f748289a..0b38d511 100644
--- "a/Debian/debi\303\242neries/pdf.mdwn"
+++ "b/Debian/debi\303\242neries/pdf.mdwn"
@@ -7,7 +7,7 @@
 Des outils comme le client courriel en ligne de commande
 [`neomutt`](https://neomutt.org) peuvent lancer des applications graphiques.
 Pour sélectionner quelle application pour quel type de fichier, `mutt` utilise
-le système `mailcap`, fourni par le paquet [[!debpkg `mime-support`]].
+le système `mailcap`, fourni par le paquet [[!debpkg mime-support]].
 
 `mailcap` tire ses informations par défaut de deux sources: des fichiers
 installés dans `/usr/lib/mime/packages` au [format
@@ -17,7 +17,7 @@ au format
 par les paquets distribuant les applications.  La _charte Debian_ demande que
 les paquets fournissant des informations au format FreeDesktop évitent de les
 répéter au format mailcap
-[[9.7.2]](https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-mailcap-entries).
+([9.7.2](https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-mailcap-entries)).
 
 L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des
 fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF par

Send!
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index d9df8bba..a003c051 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2020-02-27 13:35+0000\n"
-"PO-Revision-Date: 2020-02-27 22:35+0900\n"
+"PO-Revision-Date: 2020-02-27 22:36+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -71,17 +71,6 @@ msgstr ""
 "media-type-handlers-with-mailcap-entries)."
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir "
-#| "des fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur "
-#| "de PDF par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) "
-#| "le déclare dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les "
-#| "environnements de bureau suivant la norme FreeDesktop ont accès à des "
-#| "informations complémentaires donnant la priorité à Evince.  Le système "
-#| "`mailcap` ne les consulte pas, et donne la priorité à l'ordre "
-#| "alphabétique.  Donc quand on ouvre un fichier PDF avec `mutt`, on l'ouvre "
-#| "avec GIMP, ce qui n'est vraiment pas pratique."
 msgid ""
 "L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des "
 "fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF "

updated PO files
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index 83d75947..d9df8bba 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -6,8 +6,8 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2020-02-27 13:34+0000\n"
-"PO-Revision-Date: 2020-02-27 22:32+0900\n"
+"POT-Creation-Date: 2020-02-27 13:35+0000\n"
+"PO-Revision-Date: 2020-02-27 22:35+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -17,16 +17,14 @@ msgstr ""
 "X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta date=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta date=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
-msgstr "[[!meta date=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+msgstr "[[!meta date=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
-msgstr "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+msgstr "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
@@ -80,20 +78,20 @@ msgstr ""
 #| "de PDF par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) "
 #| "le déclare dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les "
 #| "environnements de bureau suivant la norme FreeDesktop ont accès à des "
-#| "informations complémentaires donnant la priorité à GIMP.  Le système "
+#| "informations complémentaires donnant la priorité à Evince.  Le système "
 #| "`mailcap` ne les consulte pas, et donne la priorité à l'ordre "
 #| "alphabétique.  Donc quand on ouvre un fichier PDF avec `mutt`, on l'ouvre "
 #| "avec GIMP, ce qui n'est vraiment pas pratique."
 msgid ""
 "L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des "
 "fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF "
-"par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) le déclare "
-"dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements "
-"de bureau suivant la norme FreeDesktop ont accès à des informations "
-"complémentaires donnant la priorité à Evince.  Le système `mailcap` ne les "
-"consulte pas, et donne la priorité à l'ordre alphabétique.  Donc quand on "
-"ouvre un fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est "
-"vraiment pas pratique."
+"par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince), le "
+"déclare dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les "
+"environnements de bureau suivant la norme FreeDesktop ont accès à des "
+"informations complémentaires donnant la priorité à Evince.  Le système "
+"`mailcap` ne les consulte pas, et donne la priorité à l'ordre alphabétique.  "
+"Donc quand on ouvre un fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui "
+"n'est vraiment pas pratique."
 msgstr ""
 "The [GIMP](https://www.gimp.org/) image editor declares its capacity to open "
 "PDF files in the file `/usr/share/applications/gimp.desktop`. GNOME's "

Virgule
diff --git "a/Debian/debi\303\242neries/pdf.mdwn" "b/Debian/debi\303\242neries/pdf.mdwn"
index 94a09310..f748289a 100644
--- "a/Debian/debi\303\242neries/pdf.mdwn"
+++ "b/Debian/debi\303\242neries/pdf.mdwn"
@@ -21,7 +21,7 @@ répéter au format mailcap
 
 L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des
 fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF par
-défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) le déclare dans
+défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince), le déclare dans
 `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements de
 bureau suivant la norme FreeDesktop ont accès à des informations
 complémentaires donnant la priorité à Evince.  Le système `mailcap` ne les consulte

updated PO files
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index a444b8c0..83d75947 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -6,24 +6,26 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2020-02-27 13:20+0000\n"
+"POT-Creation-Date: 2020-02-27 13:34+0000\n"
 "PO-Revision-Date: 2020-02-27 22:32+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
-#, no-wrap
-msgid "[[!meta date=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta date=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+msgid "[[!meta date=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 msgstr "[[!meta date=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+msgid "[[!meta updated=\"Thu, 27 Feb 2020 22:33:17 +0900\"]]\n"
 msgstr "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
 
 #. type: Plain text
@@ -38,57 +40,81 @@ msgstr "[[!meta title=\"How to not open a PDF with GIMP\"]]\n"
 
 #. type: Plain text
 msgid ""
-"Des outils comme le client courriel en ligne de commande [`neomutt`](https://neomutt.org) peuvent lancer "
-"des applications graphiques.  Pour sélectionner quelle application pour quel type de fichier, `mutt` "
-"utilise le système `mailcap`, fourni par le paquet [[!debpkg `mime-support`]]."
+"Des outils comme le client courriel en ligne de commande [`neomutt`](https://"
+"neomutt.org) peuvent lancer des applications graphiques.  Pour sélectionner "
+"quelle application pour quel type de fichier, `mutt` utilise le système "
+"`mailcap`, fourni par le paquet [[!debpkg `mime-support`]]."
 msgstr ""
-"Some tools such as the command-line email client [`neomutt`](https://neomutt.org) can launch graphical "
-"applications. In order to select which application for which file, `mutt` uses the `mailcap` system, "
-"provided by the [[!debpkg `mime-support`]] package."
+"Some tools such as the command-line email client [`neomutt`](https://neomutt."
+"org) can launch graphical applications. In order to select which application "
+"for which file, `mutt` uses the `mailcap` system, provided by the [[!debpkg "
+"`mime-support`]] package."
 
 #. type: Plain text
 msgid ""
-"`mailcap` tire ses informations par défaut de deux sources: des fichiers installés dans `/usr/lib/mime/"
-"packages` au [format mailcap](https://manpages.debian.org/mailcap) ou dans `/usr/share/applications` au "
-"format [FreeDesktop](https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest."
-"html)  par les paquets distribuant les applications.  La _charte Debian_ demande que les paquets "
-"fournissant des informations au format FreeDesktop évitent de les répéter au format mailcap [[9.7.2]]"
-"(https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-"
-"mailcap-entries)."
+"`mailcap` tire ses informations par défaut de deux sources: des fichiers "
+"installés dans `/usr/lib/mime/packages` au [format mailcap](https://manpages."
+"debian.org/mailcap) ou dans `/usr/share/applications` au format [FreeDesktop]"
+"(https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-"
+"spec-latest.html)  par les paquets distribuant les applications.  La _charte "
+"Debian_ demande que les paquets fournissant des informations au format "
+"FreeDesktop évitent de les répéter au format mailcap [[9.7.2]](https://www."
+"debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-"
+"handlers-with-mailcap-entries)."
 msgstr ""
-"`mailcap` gets its default informations from two sources: some files installed by packages distributing "
-"the applications in either `/usr/lib/mime/packages` in [mailcap format](https://manpages.debian.org/"
-"mailcap) or in `/usr/share/applications` in [FreeDesktop format](https://specifications.freedesktop.org/"
-"desktop-entry-spec/desktop-entry-spec-latest.html). The _Debian Policy_ specifies that the packages that "
-"provide informations in the FreeDesktop format refrain from repeat them in mailcap format  [[9.7.2]]"
-"(https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-"
-"mailcap-entries)."
+"`mailcap` gets its default informations from two sources: some files "
+"installed by packages distributing the applications in either `/usr/lib/mime/"
+"packages` in [mailcap format](https://manpages.debian.org/mailcap) or in `/"
+"usr/share/applications` in [FreeDesktop format](https://specifications."
+"freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest.html). The "
+"_Debian Policy_ specifies that the packages that provide informations in the "
+"FreeDesktop format refrain from repeat them in mailcap format  [[9.7.2]]"
+"(https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-"
+"media-type-handlers-with-mailcap-entries)."
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir "
+#| "des fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur "
+#| "de PDF par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) "
+#| "le déclare dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les "
+#| "environnements de bureau suivant la norme FreeDesktop ont accès à des "
+#| "informations complémentaires donnant la priorité à GIMP.  Le système "
+#| "`mailcap` ne les consulte pas, et donne la priorité à l'ordre "
+#| "alphabétique.  Donc quand on ouvre un fichier PDF avec `mutt`, on l'ouvre "
+#| "avec GIMP, ce qui n'est vraiment pas pratique."
 msgid ""
-"L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des fichiers PDF dans `/usr/share/"
-"applications/gimp.desktop`.  Le lecteur de PDF par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/"
-"Evince) le déclare dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements de "
-"bureau suivant la norme FreeDesktop ont accès à des informations complémentaires donnant la priorité à "
-"GIMP.  Le système `mailcap` ne les consulte pas, et donne la priorité à l'ordre alphabétique.  Donc "
-"quand on ouvre un fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est vraiment pas pratique."
+"L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des "
+"fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF "
+"par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) le déclare "
+"dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements "
+"de bureau suivant la norme FreeDesktop ont accès à des informations "
+"complémentaires donnant la priorité à Evince.  Le système `mailcap` ne les "
+"consulte pas, et donne la priorité à l'ordre alphabétique.  Donc quand on "
+"ouvre un fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est "
+"vraiment pas pratique."
 msgstr ""
-"The [GIMP](https://www.gimp.org/) image editor declares its capacity to open PDF files in the file `/usr/"
-"share/applications/gimp.desktop`. GNOME's default PDF reader, [Evince](https://wiki.gnome.org/Apps/"
-"Evince), declares this in `/usr/share/applications/org.gnome.Evince.desktop`. Desktop environments that "
-"follow the FreeDesktop standard have access to extra informations that give the priority to Evince. The "
-"`mailcap` system does not access them and gives the priority to alphabetic order. Therefore when one "
+"The [GIMP](https://www.gimp.org/) image editor declares its capacity to open "
+"PDF files in the file `/usr/share/applications/gimp.desktop`. GNOME's "
+"default PDF reader, [Evince](https://wiki.gnome.org/Apps/Evince), declares "
+"this in `/usr/share/applications/org.gnome.Evince.desktop`. Desktop "
+"environments that follow the FreeDesktop standard have access to extra "
+"informations that give the priority to Evince. The `mailcap` system does not "
+"access them and gives the priority to alphabetic order. Therefore when one "
 "opens a PDF with `mutt`, it opens with GIMP, which is not convenient."
 
 #. type: Plain text
 msgid ""
-"Heureusement, `mailcap` est facilement configurable.  Pour changer la priorité pour son compte "
-"personnel, on peut simplement copier l'entrée correspondante qui se trouve dans `/etc/mailcap` et la "
-"mettre dans `$HOME/.mailcap`. Par exemple (pour faire simple):"
+"Heureusement, `mailcap` est facilement configurable.  Pour changer la "
+"priorité pour son compte personnel, on peut simplement copier l'entrée "
+"correspondante qui se trouve dans `/etc/mailcap` et la mettre dans `$HOME/."
+"mailcap`. Par exemple (pour faire simple):"
 msgstr ""
-"Fortunately, `mailcap` is easy to configure.  In order to change the priority for one's personal "
-"account, one just has to copy the `evince` entry that is found in `/etc/mailcap` and place it into `"
-"$HOME/.mailcap`. For instance (but beware, it is simplistic):"
+"Fortunately, `mailcap` is easy to configure.  In order to change the "
+"priority for one's personal account, one just has to copy the `evince` entry "
+"that is found in `/etc/mailcap` and place it into `$HOME/.mailcap`. For "
+"instance (but beware, it is simplistic):"
 
 #. type: Plain text
 #, no-wrap

On envoye.
diff --git "a/Debian/debi\303\242neries/pdf.mdwn" "b/Debian/debi\303\242neries/pdf.mdwn"
index 92ff9627..94a09310 100644
--- "a/Debian/debi\303\242neries/pdf.mdwn"
+++ "b/Debian/debi\303\242neries/pdf.mdwn"
@@ -1,5 +1,5 @@
-[[!meta date="Thu, 27 Feb 2020 21:53:40 +0900"]]
-[[!meta updated="Thu, 27 Feb 2020 21:53:40 +0900"]]
+[[!meta date="Thu, 27 Feb 2020 22:33:17 +0900"]]
+[[!meta updated="Thu, 27 Feb 2020 22:33:17 +0900"]]
 [[!tag Debian]]
 
 [[!meta title="Comment ne pas ouvrir un PDF avec GIMP"]]
@@ -24,7 +24,7 @@ fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF par
 défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) le déclare dans
 `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements de
 bureau suivant la norme FreeDesktop ont accès à des informations
-complémentaires donnant la priorité à GIMP.  Le système `mailcap` ne les consulte
+complémentaires donnant la priorité à Evince.  Le système `mailcap` ne les consulte
 pas, et donne la priorité à l'ordre alphabétique.  Donc quand on ouvre un
 fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est vraiment pas
 pratique.

English
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
index e1d4b8f3..a444b8c0 100644
--- "a/Debian/debi\303\242neries/pdf.en.po"
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -3,81 +3,92 @@
 # 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: 2020-02-27 13:20+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"
+"PO-Revision-Date: 2020-02-27 22:32+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=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Comment ne pas ouvrir un PDF avec GIMP\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"How to not open a PDF with GIMP\"]]\n"
 
 #. type: Plain text
 msgid ""
-"Des outils comme le client courriel en ligne de commande "
-"[`neomutt`](https://neomutt.org) peuvent lancer des applications "
-"graphiques.  Pour sélectionner quelle application pour quel type de fichier, "
-"`mutt` utilise le système `mailcap`, fourni par le paquet [[!debpkg "
-"`mime-support`]]."
+"Des outils comme le client courriel en ligne de commande [`neomutt`](https://neomutt.org) peuvent lancer "
+"des applications graphiques.  Pour sélectionner quelle application pour quel type de fichier, `mutt` "
+"utilise le système `mailcap`, fourni par le paquet [[!debpkg `mime-support`]]."
 msgstr ""
+"Some tools such as the command-line email client [`neomutt`](https://neomutt.org) can launch graphical "
+"applications. In order to select which application for which file, `mutt` uses the `mailcap` system, "
+"provided by the [[!debpkg `mime-support`]] package."
 
 #. type: Plain text
 msgid ""
-"`mailcap` tire ses informations par défaut de deux sources: des fichiers "
-"installés dans `/usr/lib/mime/packages` au [format "
-"mailcap](https://manpages.debian.org/mailcap) ou dans "
-"`/usr/share/applications` au format "
-"[FreeDesktop](https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest.html)  "
-"par les paquets distribuant les applications.  La _charte Debian_ demande "
-"que les paquets fournissant des informations au format FreeDesktop évitent "
-"de les répéter au format mailcap "
-"[[9.7.2]](https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-mailcap-entries)."
+"`mailcap` tire ses informations par défaut de deux sources: des fichiers installés dans `/usr/lib/mime/"
+"packages` au [format mailcap](https://manpages.debian.org/mailcap) ou dans `/usr/share/applications` au "
+"format [FreeDesktop](https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest."
+"html)  par les paquets distribuant les applications.  La _charte Debian_ demande que les paquets "
+"fournissant des informations au format FreeDesktop évitent de les répéter au format mailcap [[9.7.2]]"
+"(https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-"
+"mailcap-entries)."
 msgstr ""
+"`mailcap` gets its default informations from two sources: some files installed by packages distributing "
+"the applications in either `/usr/lib/mime/packages` in [mailcap format](https://manpages.debian.org/"
+"mailcap) or in `/usr/share/applications` in [FreeDesktop format](https://specifications.freedesktop.org/"
+"desktop-entry-spec/desktop-entry-spec-latest.html). The _Debian Policy_ specifies that the packages that "
+"provide informations in the FreeDesktop format refrain from repeat them in mailcap format  [[9.7.2]]"
+"(https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-"
+"mailcap-entries)."
 
 #. type: Plain text
 msgid ""
-"L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des "
-"fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF "
-"par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) le déclare "
-"dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements "
-"de bureau suivant la norme FreeDesktop ont accès à des informations "
-"complémentaires donnant la priorité à GIMP.  Le système `mailcap` ne les "
-"consulte pas, et donne la priorité à l'ordre alphabétique.  Donc quand on "
-"ouvre un fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est "
-"vraiment pas pratique."
+"L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des fichiers PDF dans `/usr/share/"
+"applications/gimp.desktop`.  Le lecteur de PDF par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/"
+"Evince) le déclare dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements de "
+"bureau suivant la norme FreeDesktop ont accès à des informations complémentaires donnant la priorité à "
+"GIMP.  Le système `mailcap` ne les consulte pas, et donne la priorité à l'ordre alphabétique.  Donc "
+"quand on ouvre un fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est vraiment pas pratique."
 msgstr ""
+"The [GIMP](https://www.gimp.org/) image editor declares its capacity to open PDF files in the file `/usr/"
+"share/applications/gimp.desktop`. GNOME's default PDF reader, [Evince](https://wiki.gnome.org/Apps/"
+"Evince), declares this in `/usr/share/applications/org.gnome.Evince.desktop`. Desktop environments that "
+"follow the FreeDesktop standard have access to extra informations that give the priority to Evince. The "
+"`mailcap` system does not access them and gives the priority to alphabetic order. Therefore when one "
+"opens a PDF with `mutt`, it opens with GIMP, which is not convenient."
 
 #. type: Plain text
 msgid ""
-"Heureusement, `mailcap` est facilement configurable.  Pour changer la "
-"priorité pour son compte personnel, on peut simplement copier l'entrée "
-"correspondante qui se trouve dans `/etc/mailcap` et la mettre dans "
-"`$HOME/.mailcap`. Par exemple (pour faire simple):"
+"Heureusement, `mailcap` est facilement configurable.  Pour changer la priorité pour son compte "
+"personnel, on peut simplement copier l'entrée correspondante qui se trouve dans `/etc/mailcap` et la "
+"mettre dans `$HOME/.mailcap`. Par exemple (pour faire simple):"
 msgstr ""
+"Fortunately, `mailcap` is easy to configure.  In order to change the priority for one's personal "
+"account, one just has to copy the `evince` entry that is found in `/etc/mailcap` and place it into `"
+"$HOME/.mailcap`. For instance (but beware, it is simplistic):"
 
 #. type: Plain text
 #, no-wrap
@@ -85,3 +96,6 @@ msgid ""
 "grep evince /etc/mailcap >> .mailcap\n"
 "\n"
 msgstr ""
+"<pre>\n"
+"grep evince /etc/mailcap >> .mailcap\n"
+"</pre>\n"

updated PO files
diff --git "a/Debian/debi\303\242neries/pdf.en.po" "b/Debian/debi\303\242neries/pdf.en.po"
new file mode 100644
index 00000000..e1d4b8f3
--- /dev/null
+++ "b/Debian/debi\303\242neries/pdf.en.po"
@@ -0,0 +1,87 @@
+# 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: 2020-02-27 13:20+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=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Thu, 27 Feb 2020 21:53:40 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Comment ne pas ouvrir un PDF avec GIMP\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Des outils comme le client courriel en ligne de commande "
+"[`neomutt`](https://neomutt.org) peuvent lancer des applications "
+"graphiques.  Pour sélectionner quelle application pour quel type de fichier, "
+"`mutt` utilise le système `mailcap`, fourni par le paquet [[!debpkg "
+"`mime-support`]]."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"`mailcap` tire ses informations par défaut de deux sources: des fichiers "
+"installés dans `/usr/lib/mime/packages` au [format "
+"mailcap](https://manpages.debian.org/mailcap) ou dans "
+"`/usr/share/applications` au format "
+"[FreeDesktop](https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest.html)  "
+"par les paquets distribuant les applications.  La _charte Debian_ demande "
+"que les paquets fournissant des informations au format FreeDesktop évitent "
+"de les répéter au format mailcap "
+"[[9.7.2]](https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-mailcap-entries)."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des "
+"fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF "
+"par défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) le déclare "
+"dans `/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements "
+"de bureau suivant la norme FreeDesktop ont accès à des informations "
+"complémentaires donnant la priorité à GIMP.  Le système `mailcap` ne les "
+"consulte pas, et donne la priorité à l'ordre alphabétique.  Donc quand on "
+"ouvre un fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est "
+"vraiment pas pratique."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Heureusement, `mailcap` est facilement configurable.  Pour changer la "
+"priorité pour son compte personnel, on peut simplement copier l'entrée "
+"correspondante qui se trouve dans `/etc/mailcap` et la mettre dans "
+"`$HOME/.mailcap`. Par exemple (pour faire simple):"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"grep evince /etc/mailcap >> .mailcap\n"
+"\n"
+msgstr ""

PDF et GIMP
diff --git "a/Debian/debi\303\242neries/pdf.mdwn" "b/Debian/debi\303\242neries/pdf.mdwn"
new file mode 100644
index 00000000..92ff9627
--- /dev/null
+++ "b/Debian/debi\303\242neries/pdf.mdwn"
@@ -0,0 +1,39 @@
+[[!meta date="Thu, 27 Feb 2020 21:53:40 +0900"]]
+[[!meta updated="Thu, 27 Feb 2020 21:53:40 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Comment ne pas ouvrir un PDF avec GIMP"]]
+
+Des outils comme le client courriel en ligne de commande
+[`neomutt`](https://neomutt.org) peuvent lancer des applications graphiques.
+Pour sélectionner quelle application pour quel type de fichier, `mutt` utilise
+le système `mailcap`, fourni par le paquet [[!debpkg `mime-support`]].
+
+`mailcap` tire ses informations par défaut de deux sources: des fichiers
+installés dans `/usr/lib/mime/packages` au [format
+mailcap](https://manpages.debian.org/mailcap) ou dans `/usr/share/applications`
+au format
+[FreeDesktop](https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest.html)
+par les paquets distribuant les applications.  La _charte Debian_ demande que
+les paquets fournissant des informations au format FreeDesktop évitent de les
+répéter au format mailcap
+[[9.7.2]](https://www.debian.org/doc/debian-policy/ch-opersys.html#registration-of-media-type-handlers-with-mailcap-entries).
+
+L'éditeur d'image [GIMP](https://www.gimp.org/) déclare pouvoir ouvrir des
+fichiers PDF dans `/usr/share/applications/gimp.desktop`.  Le lecteur de PDF par
+défaut de GNOME, [Evince](https://wiki.gnome.org/Apps/Evince) le déclare dans
+`/usr/share/applications/org.gnome.Evince.desktop`.  Les environnements de
+bureau suivant la norme FreeDesktop ont accès à des informations
+complémentaires donnant la priorité à GIMP.  Le système `mailcap` ne les consulte
+pas, et donne la priorité à l'ordre alphabétique.  Donc quand on ouvre un
+fichier PDF avec `mutt`, on l'ouvre avec GIMP, ce qui n'est vraiment pas
+pratique.
+
+Heureusement, `mailcap` est facilement configurable.  Pour changer la priorité
+pour son compte personnel, on peut simplement copier l'entrée correspondante
+qui se trouve dans `/etc/mailcap` et la mettre dans `$HOME/.mailcap`. Par
+exemple (pour faire simple):
+
+```
+grep evince /etc/mailcap >> .mailcap
+```

correct date
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 2b15d5db..96e607bd 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -483,7 +483,7 @@ Ecology
    to 17 microplastic particles were found in sinking houses in the Monterey Bay
    [[Choy and coll., 2019|biblio/31171833]].
  - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus
-   ([[Lawrence and coll., 2017|biblio/10.1002_lno.10734]]).  This study does not assess
+   ([[Lawrence and coll., 2018|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.
 
 ### Distribution near Japan

Parenthèse
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 750919a6..2b15d5db 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -120,7 +120,7 @@ Genome
    splice sites, whereas the usual proportion is around 1%-1.5% in other genomes”
    ([[Denoeud et al., 2010|biblio/21097902]]).
  - The consensus sequence around GA/AG splice sites is AG|GAA/AG
-   ([[Frey and Pucker, 2020|biblio/32085510]].
+   ([[Frey and Pucker, 2020|biblio/32085510]]).
  - Operons are enriched for houskeeping genes and depleted for developmental genes
    ([[Denoeud et al., 2010|biblio/21097902]]).
  - “LTR retrotransposons account for a significant part of the indel polymorphism

Consensus splice site.
diff --git a/biblio/32085510.mdwn b/biblio/32085510.mdwn
new file mode 100644
index 00000000..7fb36d0b
--- /dev/null
+++ b/biblio/32085510.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites."]]
+[[!tag Oikopleura]]
+
+Frey K, Pucker B.
+
+Cells. 2020 Feb 18;9(2). pii: E458. doi:10.3390/cells9020458
+
+Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites.
+
+[[!pmid 32085510 desc="A bioinformatics screen confirms the increased use of GA/AG splicing in _Oikopleura dioica_ and the copepod _Eurytemora affinis_, out of 489 animal species.  In both cases, an extended consensus was found: AG|GAA/AG (vertical bar is end of exon)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ce1d0d6d..750919a6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -119,6 +119,8 @@ Genome
    (more than 10%) of the (...) introns displayed non-canonical (non GT-AG)
    splice sites, whereas the usual proportion is around 1%-1.5% in other genomes”
    ([[Denoeud et al., 2010|biblio/21097902]]).
+ - The consensus sequence around GA/AG splice sites is AG|GAA/AG
+   ([[Frey and Pucker, 2020|biblio/32085510]].
  - Operons are enriched for houskeeping genes and depleted for developmental genes
    ([[Denoeud et al., 2010|biblio/21097902]]).
  - “LTR retrotransposons account for a significant part of the indel polymorphism

Write down splice site motifs.
diff --git a/biblio/31543449.mdwn b/biblio/31543449.mdwn
index 396eb71a..7c5363bb 100644
--- a/biblio/31543449.mdwn
+++ b/biblio/31543449.mdwn
@@ -7,8 +7,8 @@ Henriet S, Colom Sanmartí B, Sumic S, Chourrout D.
 
 Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis.
 
-[[!pmid 31543449 desc="In Fritillaria borealis, most ancestral canonical
-introns were lost.  New introns with non-canonical splice sites were created by
+[[!pmid 31543449 desc="In Fritillaria borealis, most ancestral GT/AG canonical
+introns were lost.  New AG/AR introns with non-canonical splice sites were created by
 the insertion of MITEs (miniature inverted-repeat transposable elements) after
 TA sites.  Splicing of non-canonical introns can be inhibited with Pladienolide
 B.  Non-canonical introns of F. bor and O. dioica genes can not be spliced in
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1eca8ec1..ce1d0d6d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -115,7 +115,7 @@ Genome
  - Analysis of sex-linked markers supports genetic sex determination with male heterogamety –
    that is: X chromosomes for females and Y for males.  ([[Denoeud et al., 2010|biblio/21097902]])
  - The major spliceosome is hypothethised to have evolved
-   to become more permissive in order to splice G*-AG sites.  ”A large fraction
+   to become more permissive in order to splice G*/AG sites.  ”A large fraction
    (more than 10%) of the (...) introns displayed non-canonical (non GT-AG)
    splice sites, whereas the usual proportion is around 1%-1.5% in other genomes”
    ([[Denoeud et al., 2010|biblio/21097902]]).
@@ -272,10 +272,10 @@ Transcriptome
    2010|biblio/21097902]]).  Larger introns tend to be older, and among the large
    introns, the older contain repeat elements less frequently than the newer
    ([[Denoeud et al., 2010|biblio/21097902]]).  In _Fritilaria borealis_, most
-   introns are derived from the insertion of MITE elements and are non-canonical
+   introns are derived from the insertion of MITE elements and are AG/AR non-canonical
    ([[Henriet and coll., 2019|biblio/31543449]]).
- - HEK293T cells can only splice canonical _O. dioica_ (and _F. borealis_) introns,
-   but not the non-canonical ones ([[Henriet and coll., 2019|biblio/31543449]]).
+ - HEK293T cells can only splice canonical GT/AG _O. dioica_ (and _F. borealis_) introns,
+   but not the non-canonical AG/AR ones ([[Henriet and coll., 2019|biblio/31543449]]).
  - 12 developmental stages were studied with tiling arrays by [[Danks et al., 2013|biblio/23185044]].
  - On the histone mRNAs, no purine-rich histone downstream element (HDE) was found
    by [[Chioda, Eskeland and Thompson in 2002|biblio/12446815]].

Café
diff --git a/biblio/2479023.mdwn b/biblio/2479023.mdwn
new file mode 100644
index 00000000..0291af1b
--- /dev/null
+++ b/biblio/2479023.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Extension of mismatched 3' termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase."]]
+[[!tag reverse-transcription]]
+
+Proc Natl Acad Sci U S A. 1989 Nov;86(21):8343-7 doi:10.1073/pnas.86.21.8343
+
+Perrino FW, Preston BD, Sandell LL, Loeb LA.
+
+Extension of mismatched 3' termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase.
+
+[[!pmid 2479023 desc="HIV-1 RT can extend A-mismatches with various efficiencies: A:C >> A:A > A:G."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index f9dea9a2..3555b57d 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -127,7 +127,9 @@ nucleotide as a template.
 
 ### Reverse-transcriptases tolerate terminal mismatches
 
- - Reported by [[Mizuno et al., 1999|biblio/9973624]].
+ - HIV-1 RT can extend A-mismatches with various efficiencies: A:C >> A:A > A:G
+   ([[Perrino and coll., 1898|biblio/2479023]]). 
+ - Reported by [[Mizuno et al., 1999|biblio/9973624]] for double-mismatches and MMLV.
  - Utilised in [[Arnaud et al., 2016|biblio/27071605]] to reduce priming or
    ribosomal or hemoglobin RNA.
  - Specificity of RT nevertheless increases with reaction temperature.  For

Correct tag.
diff --git a/biblio/1279806.mdwn b/biblio/1279806.mdwn
index 6e954f17..a3e5891f 100644
--- a/biblio/1279806.mdwn
+++ b/biblio/1279806.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase."]]
-[[!tag reverse_transcriptase]]
+[[!tag reverse_transcription]]
 
 Science. 1992 Nov 13;258(5085):1112-8 doi:10.1126/science.1279806
 

Café
diff --git a/biblio/7511410.mdwn b/biblio/7511410.mdwn
new file mode 100644
index 00000000..df2599b9
--- /dev/null
+++ b/biblio/7511410.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Fidelity of in vitro DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase."]]
+[[!tag reverse_transcription template_switching]]
+
+Peliska JA, Benkovic SJ.
+
+Biochemistry. 1994 Apr 5;33(13):3890-5 doi:10.1021/bi00179a014
+
+Fidelity of in vitro DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase.
+
+[[!pmid 7511410 desc="When the extra base added by the RTase in a template-switching reaction is determined by sequencing, the result does not reflect previous results obrained by primer extension assay (where A >> C on non-capped blunt DNA/RNA ends).  This may be because of the differential efficiency of the RTase to extend a template over various single-base mismatches.  In this assay, T to C and G to C were more frequent than T to A and G to A.  Nevertheless, the experiments support previous evidence that addition is mostly limited to a single nucleotide.  RT reaction: 50 mM Tris-HCl, pH 8.0; 75 mM KCl;, 0.1 mM EDTA; 1 mM DTT; 0.1% Triton X-100; 100 µM each dNTP; 7 mM MgCl2; 200 nM 24-base DNA-40-base RNA primer-template; 700 nM 41-base RNA template 2; 700 nM 42-base RNA template 3; and 100 nM HIV-1 RT in a final volume of 10 µL. When reaction products were to be sequenced, mixtures were incubated at 37 °C for 2 h."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index d57c0a65..f9dea9a2 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -36,9 +36,11 @@ _(redaction in progress)_
 Like other DNA polymerases ([[Clark, 1988|biblio/2460825]]), reverse
 transcriptases have a TdT activity.
 
-Peliska JA, Benkovic SJ.
-
-Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase.
+Choice of the assay for studying TdT activity can strongly influence the results.
+For instance, [[Pelisca and Benkovic, 1994|biblio/7511410]] showed strong
+discrepancy between radiolabelled primer extension assay and sequencing cDNAs
+that have been further extended.  They suppose that differential tolerance of RT
+to mismatches can be the explanation.
 
  - [[Peliska and Benkovic, 1992|biblio/1279806]] showed that HIV-1 RT adds one
    nucleotide on non-capped oligonucleotide duplexes.   A > G > T > C ratio:

To read
diff --git a/biblio/31712313.mdwn b/biblio/31712313.mdwn
new file mode 100644
index 00000000..33efefa8
--- /dev/null
+++ b/biblio/31712313.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-Seq."]]
+[[!tag to_read]]
+
+J Biol Chem. 2019 Dec 20;294(51):19764-19784. doi:10.1074/jbc.RA119.011337
+
+Lentzsch AM, Yao J, Russell R, Lambowitz AM.
+
+Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-Seq.
+
+[[!pmid 31712313 desc="À lire"]]

Café
diff --git a/biblio/1279806.mdwn b/biblio/1279806.mdwn
new file mode 100644
index 00000000..6e954f17
--- /dev/null
+++ b/biblio/1279806.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase."]]
+[[!tag reverse_transcriptase]]
+
+Science. 1992 Nov 13;258(5085):1112-8 doi:10.1126/science.1279806
+
+Peliska JA, Benkovic SJ.
+
+Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase.
+
+[[!pmid 1279806 desc="Addition of 1 extra nucleotide happens at an apparent rate of 0.1 / min.  Addition of subsequent bases is visible (Fig 3) but much slower.  This addition does not requrie RNAseH activity.  A > G > T > C ratio on a non-capped oligonucleotide duplex: 1 : 0.5 : 0.2 : 0.07, determined by incubating the reaction with each individual dNTP.  50 mM Tris-HCl pH 8, 75 mM KCl, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton X-100, 200 nM DNA/RNA duplex, each dNTP at 100 µM, 7 mM MgCl2, 800 nM TSO and 200 nM HIV-1 RT, at 37 °C."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 3e3d5b97..d57c0a65 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -36,6 +36,15 @@ _(redaction in progress)_
 Like other DNA polymerases ([[Clark, 1988|biblio/2460825]]), reverse
 transcriptases have a TdT activity.
 
+Peliska JA, Benkovic SJ.
+
+Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase.
+
+ - [[Peliska and Benkovic, 1992|biblio/1279806]] showed that HIV-1 RT adds one
+   nucleotide on non-capped oligonucleotide duplexes.   A > G > T > C ratio:
+   1 : 0.5 : 0.2 : 0.07.  Addition of subsequent bases is visible but much
+   slower.
+
  - [[Patel & Preston, 1994|biblio/7507249]] showed that HIV RT adds one
    nucleotide (A > G >> T|C) on DNA/DNA duplexes, and more on DNA/RNA duplexes.
    Addition is favoured by increased dNTP levels.  MMLV and AMV were also

Café
diff --git a/biblio/31958060.mdwn b/biblio/31958060.mdwn
new file mode 100644
index 00000000..75b20142
--- /dev/null
+++ b/biblio/31958060.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Loss of centromere function drives karyotype evolution in closely related Malassezia species."]]
+[[!tag chromosome centromere yeast]]
+
+Sankaranarayanan SR, Ianiri G, Coelho MA, Reza MH, Thimmappa BC, Ganguly P, Vadnala RN, Sun S, Siddharthan R, Tellgren-Roth C, Dawson TL Jnr, Heitman J, Sanyal K.
+
+Elife. 2020 Jan 20;9. pii: e53944. doi: 10.7554/eLife.53944 doi:10.7554/eLife.53944
+
+Loss of centromere function drives karyotype evolution in closely related Malassezia species.
+
+[[!pmid 31958060 desc="Hypothetises that AT-richness at centromeres can trigger breaks, and structural changes.  Centromeres detected by ChIP-seq on GFP-Mtw1 in M. sympodialis.  ”PhyloGibbs-MP predicted a 12 bp long AT-rich 239 motif common to all of the centromere sequences.”  “In each chromosome, the centromere region shows between 7 and 13 motif matches, while no other 500 bp window shows more than 3 matches.”  “In the absence of any centromere exclusive DNA sequence, the unique and distinguishing features of centromere regions in M. sympodialis are an AT-rich core region of <1 kb [...] enriched with the 12 bp motif in a kinetochore protein-bound region of 3 to 5 kb [containing] a reduced level of histone H3.”  “Syntenic regions of all 8 M. sympodialis centromeres are present in the genomes of M. globosa and M. slooffiae [(each carries 9 chromosomes)].”  “In the case of M. restricta, 7 putative centromeres are completely syntenic with M. sympodialis centromeres and one centromere retained partial gene synteny.”  “No gene synteny conservation was observed at the centromeres of Chr2 in M. globosa, Chr5 in M. slooffiae, or Chr8 in M. restricta, indicative of loss of a centromere during the transition from the 9-chromosome state to the 8-302 chromosome state.”"]]
diff --git a/tags/centromere.mdwn b/tags/centromere.mdwn
index f3ba3420..8b7d5d35 100644
--- a/tags/centromere.mdwn
+++ b/tags/centromere.mdwn
@@ -1,4 +1,14 @@
 [[!meta title="pages tagged centromere"]]
 
-[[!inline pages="tagged(centromere)" actions="no" archive="yes"
-feedshow=10]]
+_Work in progress_
+
+ - Brute-force analysis to find the most abundant large tandem repeat can find
+   centromeres ([[Melters and coll., 2013|biblio/23363705]]).
+ - In medaka, study of homologous pairs of centromeres suggest that the
+   acrocentric ones evolve slower ([[Ichikawa and coll., 2017|biblio/29184138]]).
+ - In Oikopleura (and many others) H3S28p marks mitotic centromeres [[Fent and
+   coll., 2019|biblio/31306061]].
+ - Centromere breakage and inactivation in yeast: [[Sankaranarayanan and coll.,
+   2020|biblio/31958060]].
+
+[[!inline pages="tagged(centromere)" limit="0"]]

18S
diff --git a/biblio/8127885.mdwn b/biblio/8127885.mdwn
index ce711cbe..909ff968 100644
--- a/biblio/8127885.mdwn
+++ b/biblio/8127885.mdwn
@@ -7,4 +7,4 @@ Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1801-4 doi:10.1073/pnas.91.5.1801
 
 Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA.
 
-[[!pmid 8127885 desc="to read"]]
+[[!pmid 8127885 desc="Source for the 18S sequence D14360"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 90162efe..1eca8ec1 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -40,8 +40,8 @@ Parasites: _Oodinium pouchetii_ and others.
 Phylogeny
 ---------
 
- - 18S rDNA phylogeny of [[Swalla and coll., 2000|biblio/12116483]] places
-   larvaceans sister to all tunicates.
+ - 18S rDNA phylogeny of [[Wada and Satoh, 1994|biblio/8127885]] and [[Swalla
+   and coll., 2000|biblio/12116483]] places 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

À lire
diff --git a/biblio/8127885.mdwn b/biblio/8127885.mdwn
new file mode 100644
index 00000000..ce711cbe
--- /dev/null
+++ b/biblio/8127885.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA."]]
+[[!tag Oikopleura]]
+
+Wada H, Satoh N.
+
+Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1801-4 doi:10.1073/pnas.91.5.1801
+
+Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA.
+
+[[!pmid 8127885 desc="to read"]]

correction
diff --git a/biblio/8534373.mdwn b/biblio/8534373.mdwn
index dcc8c296..c4b86348 100644
--- a/biblio/8534373.mdwn
+++ b/biblio/8534373.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Transcription of the 5'-terminal cap nucleotide by RNA-dependent DNA polymerase: possible involvement in retroviral reverse transcription."]]
-[[!tag reverse_transcriptase cap]]
+[[!tag reverse_transcription cap]]
 
 Volloch VZ, Schweitzer B, Rits S.
 

Café
diff --git a/biblio/8534373.mdwn b/biblio/8534373.mdwn
new file mode 100644
index 00000000..dcc8c296
--- /dev/null
+++ b/biblio/8534373.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcription of the 5'-terminal cap nucleotide by RNA-dependent DNA polymerase: possible involvement in retroviral reverse transcription."]]
+[[!tag reverse_transcriptase cap]]
+
+Volloch VZ, Schweitzer B, Rits S.
+
+DNA Cell Biol. 1995 Dec;14(12):991-6 doi:10.1089/dna.1995.14.991
+
+Transcription of the 5'-terminal cap nucleotide by RNA-dependent DNA polymerase: possible involvement in retroviral reverse transcription.
+
+[[!pmid 8534373 desc="Utilises a 5′ hairpin in the beta-globin mRNA to design a cDNA extension assay where the reverse-transcribed cap creates a terminal mismatch that inhibits extension.  De-capping the RNA removes the inhibition.  40 mM Tris 8.3, 40 mM KCl, 5 mM MgCl2, 2 mM DTT.  AMV, 45°C"]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 51efdcd8..3e3d5b97 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -79,8 +79,9 @@ nucleotide as a template.
    at the 5′ end of cDNA clones, and concluded that the cap can be
    reverse-transcribed.  They supported their conclusion with molecular modelling.
 
- - [[Volloch et al, 1995|biblio/8534373]] studied cap transcription (but I could
-   not access the article).
+ - [[Volloch, Schweitzer and Rits, 1995|biblio/8534373]] showed that the AMV
+   reverse-transcribes the cap, using an assay where the extension of a natural
+   hairpin in the beta-globin cDNA can be enabled by decapping.
 
  - [[Kulpa, Topping and Telesnitsky, 1997|biblio/9049314]] noted the addition
    of one G at the position where the 5′ end of the MMLV RNA was

Bientôt café
diff --git a/biblio/10.1590_S1516-89132010000100020.mdwn b/biblio/10.1590_S1516-89132010000100020.mdwn
new file mode 100644
index 00000000..e73fcdf3
--- /dev/null
+++ b/biblio/10.1590_S1516-89132010000100020.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Seasonal and spatial variability of appendicularian density and taxonomic composition in the Caravelas Estuary (Northeastern Brazil) and adjacent coastal area"]]
+[[!tag Oikopleura]]
+
+Pedro Freitas de Carvalho; Sérgio Luiz Costa Bonecker
+
+Braz. arch. biol. technol. vol.53 no.1 Curitiba Jan./Feb. 2010
+
+Seasonal and spatial variability of appendicularian density and taxonomic composition in the Caravelas Estuary (Northeastern Brazil) and adjacent coastal area
+
+[[!doi 10.1590/S1516-89132010000100020 desc="“O. dioica was the most frequent and abundant species in all the samples.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 996fda64..90162efe 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -545,7 +545,8 @@ Ecology
    Roff, 1998|biblio/10.1093_plankt_20.3.557]]).
  - South Atlantic: found all year near Mar del Plata in 2000—1, where it was
    most abundant in summer ([[Viñas and coll.,
-   2013|biblio/10.1080_17451000.2012.745003]]).
+   2013|biblio/10.1080_17451000.2012.745003]]), Caravelas river estuary and
+   adjascent costal areas ([[Carvalho and Bonecker, 2010|biblio/10.1590_S1516-89132010000100020]]).
  - Southen sea of Cortez (Mexico), near Isla El Paradito (water temperature =
    30 °C; night dives), _O. dioica_ was found but not as abundant as other
    larvaceans ([[Galt, Grober and Sykes, 1985|biblio/10.2307_1541178]]).

Bientôt café
diff --git a/biblio/10.4067_S0716-078X2002000200005.mdwn b/biblio/10.4067_S0716-078X2002000200005.mdwn
index a377b27f..10522f06 100644
--- a/biblio/10.4067_S0716-078X2002000200005.mdwn
+++ b/biblio/10.4067_S0716-078X2002000200005.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Taxonomic identification of appendicularians collected in the epipelagic waters off northern Chile (Tunicata, Appendicularia)"]]
-[[!tag to_read]]
+[[!tag Oikopleura]]
 
 Guillermo Aravena & Sergio Palma
 
@@ -7,4 +7,4 @@ Rev. chil. hist. nat. v.75 n.2 Santiago jun. 2002
 
 Taxonomic identification of appendicularians collected in the epipelagic waters off northern Chile (Tunicata, Appendicularia)
 
-[[!doi 10.4067/S0716-078X2002000200005 desc="to_read"]]
+[[!doi 10.4067/S0716-078X2002000200005 desc="O. dioica and many other appendicularians found near northern Chile.  Detailed taxonomical descriptions."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 18e4974d..996fda64 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -533,6 +533,7 @@ Ecology
  - Giant appendicularians could be observed in high abundance from deep submersibles
    near Californian and middle American coasts ([[Barham, 1979|biblio/17735049]],
    [[Galt, 1979|bilbio/Fishery_Bulletin_77_2_514]]).
+ - Northern Chile: [[Aravena and Palma, 2002|biblio/10.4067_S0716-078X2002000200005]].
 
 ### Elsewhere in the World
 

Bioluminescence.
diff --git a/biblio/10.1007_BF00396313.mdwn b/biblio/10.1007_BF00396313.mdwn
new file mode 100644
index 00000000..db6373cc
--- /dev/null
+++ b/biblio/10.1007_BF00396313.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Sites of bioluminescence in the appendicularians Oikopleura dioica and O. labradoriensis (Urochordata: Larvacea)."]]
+[[!tag Oikopleura]]
+
+Galt, C.P., Sykes, P.F.
+
+Mar. Biol. 77, 155–159 (1983). doi:10.1007/BF00396313
+
+Sites of bioluminescence in the appendicularians _Oikopleura dioica_ and _O. labradoriensis_ (Urochordata: Larvacea). 
+
+[[!doi 10.1007/BF00396313 desc="Light is produced by the granular inclusions."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1611bea0..18e4974d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -428,9 +428,11 @@ House
    1999)|biblio/10.1093_plankt_21.10.1923]]: mesopelagic species with a large
    (~30 cm) house.
  - Houses of _O. dioica_ and related species that have oral glands have
-   granular inclusions that are bioluminescent ([[Galt, Grober and Sykes,
-   1985|biblio/10.2307_1541178]]).  In species without oral glands, bioluminescence
-   might be caused by dinoflagellates.
+   granular inclusions that are bioluminescent ([[Galt and Sykes
+   (1983)|biblio/10.1007_BF00396313]], [[Galt, Grober and Sykes,
+   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.
 
 
 Phenotypes

Bioluminescence of Vexillaria subgenus. Japanese name.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index fbf49d9a..1611bea0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -11,7 +11,8 @@ organisms are distinct).  Its reproduction is _semelparous_: the animals die
 afer releasing its gametes.  Each animal secretes a mucus "house" that is used
 for feeding (and perhaps defending).  The main house proteins are called
 _oikosins_ and half or them are unique to Oikopleura and related animals
-("_Appendicularia_").  The japanese name of _O. dioica_ is ワカレオタマボヤ.
+("_Appendicularia_").  The japanese name of _O. dioica_ is
+[ワカレオタマボヤ](https://www.godac.jamstec.go.jp/bismal/j/view/9018229).
 
 Some links:
 
@@ -55,6 +56,9 @@ Phylogeny
  - Giant Oikopleurid species, such as  exist in deeper waters. _Bathochordaeus charon_'s 18S
    RNA is 97% identical to the one of _O. dioica_ ([[Sherlock and coll, 2016|biblio/10.1186_s41200-016-0075-9]]).
  - CO1 DNA of _B. mcnutti_ and _B. strygius_ are ~12% different ([[Sherlock and coll., 2017|biblio/28042175]]).
+ - There are two subgenus of _Oikopleura_: _Vexillaria_ and _Coecaria_.  _Vexillaria_,
+   to which _dioica_ and _rufescens_ belong, have oral glands and bioluminescence
+   ([[Galt, Grober and Sykes, 1985|biblio/10.2307_1541178]]).
 
 
 Karyotype

Lu encore.
diff --git a/biblio/7507249.mdwn b/biblio/7507249.mdwn
index 75611fef..0f69fda8 100644
--- a/biblio/7507249.mdwn
+++ b/biblio/7507249.mdwn
@@ -7,4 +7,4 @@ Patel PH & Preston BD.
 
 Marked infidelity of human immunodeficiency virus type 1 reverse transcriptase at RNA and DNA template ends.
 
-[[!pmid 7507249 desc="On DNA/DNA blunt ends, adds a single nucleotide (A > G >> C|T).  On RNA/DNA blund ends, adds more nucleotides.  Addition is favoured by increased dNTP levels."]]
+[[!pmid 7507249 desc="On DNA/DNA blunt ends, adds a single nucleotide (A > G >> C|T).  On RNA/DNA blund ends, adds more nucleotides (A >> G > C|T).  Addition is favoured by increased dNTP levels."]]

café
diff --git a/biblio/Chenchick_1998.mdwn b/biblio/Chenchick_1998.mdwn
index 50f0ed52..91dd84ea 100644
--- a/biblio/Chenchick_1998.mdwn
+++ b/biblio/Chenchick_1998.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Generation and use of high-quality cDNA from small amounts of total RNA by SMART PCR."]]
-[[!tag template_switching]]
+[[!tag reverse_transcriptase template_switching]]
 
 Alex Chenchick, York Y. Shu, Luda Diatchenko, Roger Li, Jason Hill and Paul D. Siebert.
 (Gene Cloning and Analysis Group, CLONETECH Laboratories, Pao Alto, CA, USA).

café
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index adb34865..51efdcd8 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -71,13 +71,9 @@ nucleotide as a template.
    2017b|biblio/28747695]]).
 
 
-### The 5′ cap enhances C-tailing
-
- - [[Schmidt & Mueller, 1999|biblio/10518626]] showed that extra cytosine are
-   more frequently added in presence of the 5′ cap.
+### Reverse-transcription of the 5′ cap.
 
-
-### The 5′ cap is reverse-transcribed
+#### Pro:
 
  - [[Hirzmann et al., 1993|biblio/8346046]] observed the presence of an extra G
    at the 5′ end of cDNA clones, and concluded that the cap can be
@@ -91,6 +87,9 @@ nucleotide as a template.
    reverse-transcribed, with a frequency of 10 %.  They also discussed if it
    could be that the cap was reverse-transcribed.
 
+ - [[Schmidt & Mueller, 1999|biblio/10518626]] showed that extra cytosine are
+   more frequently added in presence of the 5′ cap.
+
  - [[Ohtake et al, 2004|biblio/15500255]] synthethised RNAs with A-caps and
    showed that they are reverse-transcribed as Ts.
 
@@ -100,13 +99,20 @@ nucleotide as a template.
 
  - [[Zhang et al, 2017|biblio/28673998]] published a structure of an RNA-GpppG
    complex that suggests that a m7GpppNm / DNA duplex could form during the
-   reverse-transcription of the cap
+   reverse-transcription of the cap.
+
+#### Con:
 
- - Nevertheless, in [[Dallmeier and Neyts, 2013|biblio/23123427]], where
+ - [[Chenchick and coll., 1998|biblio/Chenchick_1998]] reported that non-capped
+   oligonucleotides were extended with long (1~5) cytosine tails, and that the
+   presene of a cap did not have a “significant influence”.
+
+ - In [[Dallmeier and Neyts, 2013|biblio/23123427]], where
    first-strand cDNAs prepared with a phosphorylated reverse-transcription
    primer were circularised, amplified and sequenced, there is not visible
    evidence for G addition.
 
+
 ### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].

café
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 3945efb2..a0f28cf8 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -2,6 +2,8 @@
 
 (work in progress.  For alternative cap enrichement methods see the [[cap]] tag page)
 
+### Methods papers.
+
  - 1996: ”Synthesis of high-quality cDNA from nanograms of total or polyA+ RNA
    with the CapFinder PCR cDNA library construction kit.”  Zhu, Y., A. Chenchik
    and P.D. Siebert.  CLONTECHniques 1 1:12-13.  Could not find the PDF.
@@ -59,6 +61,9 @@ Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,
 TSOs where only the last 3 bases are RNA became popular.   LNA was also tested
 as a replacement for RNA.
 
+ - [[Chenchick and coll., 1998|biblio/Chenchick_1998]] reported (rG)n >> rG >
+   dGdGdG >> rUrUrU.
+
  - [[Picelli et al (2013)|biblio/24056875]] reported a higher performance for
    RRL compared to RRR, when preparing Smart-seq2 libraries.
 

Café
diff --git a/biblio/Chenchick_1998.mdwn b/biblio/Chenchick_1998.mdwn
new file mode 100644
index 00000000..50f0ed52
--- /dev/null
+++ b/biblio/Chenchick_1998.mdwn
@@ -0,0 +1,28 @@
+[[!meta title="Generation and use of high-quality cDNA from small amounts of total RNA by SMART PCR."]]
+[[!tag template_switching]]
+
+Alex Chenchick, York Y. Shu, Luda Diatchenko, Roger Li, Jason Hill and Paul D. Siebert.
+(Gene Cloning and Analysis Group, CLONETECH Laboratories, Pao Alto, CA, USA).
+
+In: Gene Cloning and Analysis by RT-PCR.  Edited by Paul Siebert and James Larrick. 1998
+
+Generation and use of high-quality cDNA from small amounts of total RNA by SMART PCR.
+
+Reaction mixture: 1 µM RTP; 1 µM TSO; 50–1000 ng total RNA; 2 mM DTT, 1 mM dNTP, 200 U SSII in 10 µL.
+
+
+DNA/RNA ends tested: HO-G, Cap-G, HO-A, Cap-A, HO-C, Cap-C, HO-T
+
+TSOs tested: rG, rGrG, rGrGrG, rGrGrGrGrG, rUrUrU, GGG, rGrGrG in all-r oligo.
+
+With the wild-type MMLVm the HO-G DNA/RNA duplex is tailed with 1~5 extra
+nucleotides (Fig 2).  Using radiolabelled nucleotides suggests that they are
+mostly Cs.  "Not shown" experiments suggest that the presence of a cap "does
+not significantly influence the preference of addition of these non-templated
+nucleotides".  The consensus tail is AACCC.  SSII (RNAseH-) has a lower
+efficiency for adding nucleotides, compared with wild-type MMLV.
+
+Template-switching is more efficient with at least 2 rG.  dG is notably less
+efficient and rU has no visible efficiency (Figure 2).
+
+In 2 % of the cDNAs, RT was primed by the TSO.
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index c4165c23..3945efb2 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -6,6 +6,12 @@
    with the CapFinder PCR cDNA library construction kit.”  Zhu, Y., A. Chenchik
    and P.D. Siebert.  CLONTECHniques 1 1:12-13.  Could not find the PDF.
 
+ - 1998: “Generation and use of high-quality cDNA from small amounts of total
+   RNA by SMART PCR” [[Chenchick and coll., 1998|biblio/Chenchick_1998]].
+   Oligo-dT-primed total RNA is template-switched with rGrGrG DNA/RNA hybrids.
+   SMART means “Switch Mechanism At the 5′ end of RNA Templates”.  Is that
+   the primary paper for SMART ?
+
  - In the "_CapSelect_" method, [[Schmidt and Mueller, 1999|biblio/10518626]]
    stimulate template switching with manganese (see below), tail the first-strand
    cDNAs with dA, and add 5′ linkers with T4 DNA ligase and duplex adapters

PNAS
diff --git a/biblio/31988135.mdwn b/biblio/31988135.mdwn
new file mode 100644
index 00000000..962a94a6
--- /dev/null
+++ b/biblio/31988135.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA sequencing by direct tagmentation of RNA/DNA hybrids."]]
+[[!tag transposase RNA-seq method]]
+
+Di L, Fu Y, Sun Y, Li J, Liu L, Yao J, Wang G, Wu Y, Lao K, Lee RW, Zheng G, Xu J, Oh J, Wang D, Xie XS, Huang Y, Wang J.
+
+Proc Natl Acad Sci U S A. 2020 Jan 27. pii: 201919800. doi:10.1073/pnas.1919800117
+
+RNA sequencing by direct tagmentation of RNA/DNA hybrids.
+
+[[!pmid 31988135 desc="Impact on size profile is much harder to notice compared with DNA/DNA tagmentation (Figs S9 and S10)."]]

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
café
diff --git a/biblio/23123427.mdwn b/biblio/23123427.mdwn
new file mode 100644
index 00000000..a71b0591
--- /dev/null
+++ b/biblio/23123427.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Simple and inexpensive three-step rapid amplification of cDNA 5' ends using 5' phosphorylated primers."]]
+[[!tag reverse_transcription cap]]
+
+Dallmeier K, Neyts J.
+
+Anal Biochem. 2013 Mar 1;434(1):1-3. doi:10.1016/j.ab.2012.10.031
+
+Simple and inexpensive three-step rapid amplification of cDNA 5' ends using 5' phosphorylated primers.
+
+[[!pmid 23123427 desc="No G-addition observed on mRNAs expressed from a SV40 promoter in Vero-B (African green monkey kidney) cells."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 8880db01..3b304dcd 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -102,6 +102,10 @@ nucleotide as a template.
    complex that suggests that a m7GpppNm / DNA duplex could form during the
    reverse-transcription of the cap
 
+ - Nevertheless, in [[Dallmeier and Neyts, 2013|biblio/23123427]], where
+   first-strand cDNAs prepared with a phosphorylated reverse-transcription
+   primer were circularised, amplified and sequenced, there is not visible
+   evidence for G addition.
 
 ### Reverse-transcriptases tolerate terminal mismatches
 

Café
diff --git a/biblio/9049314.mdwn b/biblio/9049314.mdwn
new file mode 100644
index 00000000..66dad947
--- /dev/null
+++ b/biblio/9049314.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Determination of the site of first strand transfer during Moloney murine leukemia virus reverse transcription and identification of strand transfer-associated reverse transcriptase errors."]]
+[[!tag reverse_transcription cap]]
+
+EMBO J. 1997 Feb 17;16(4):856-65 doi:10.1093/emboj/16.4.856
+
+Kulpa D, Topping R, Telesnitsky A.
+
+Determination of the site of first strand transfer during Moloney murine leukemia virus reverse transcription and identification of strand transfer-associated reverse transcriptase errors.
+
+[[!pmid 9049314 desc="“The results presented here support the model that +1 substitutions arise during reverse transcription via non‐templated addition followed by mismatch extension upon strand transfer. Another possibility we considered was that +1G could potentially be templated by the 7‐methyl‐G cap present on mRNAs and viral genomic RNAs (Coffin, 1996). Avian myeloblastosis virus reverse transcriptase can add a cap‐complementary C residue during cDNA synthesis on mRNA in vitro, but not when the RNA has been de‐capped (Volloch et al., 1995). However, studies with purified enzymes and model primer–templates have demonstrated that +1G can arise at template switch junctions in the absence of a 7‐methyl‐G cap (Peliska and Benkovic, 1994), and our detection of +1C mutants demonstrates that not all additions to −ssDNA could be cap‐templated.”"]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index fe9f0ec2..8880db01 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -86,6 +86,11 @@ nucleotide as a template.
  - [[Volloch et al, 1995|biblio/8534373]] studied cap transcription (but I could
    not access the article).
 
+ - [[Kulpa, Topping and Telesnitsky, 1997|biblio/9049314]] noted the addition
+   of one G at the position where the 5′ end of the MMLV RNA was
+   reverse-transcribed, with a frequency of 10 %.  They also discussed if it
+   could be that the cap was reverse-transcribed.
+
  - [[Ohtake et al, 2004|biblio/15500255]] synthethised RNAs with A-caps and
    showed that they are reverse-transcribed as Ts.
 

Reformat
diff --git a/biblio/2460825.mdwn b/biblio/2460825.mdwn
index dfa2bcfe..20b41926 100644
--- a/biblio/2460825.mdwn
+++ b/biblio/2460825.mdwn
@@ -7,7 +7,4 @@ Clark JM
 
 Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases.
 
-[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Perference for adding As.  ‘We cannot exclude the formal possibility that some of these latter
-+events, particularly the addition of dCMP by AMV reverse transcriptase, involve the use of coding
-+information made available as a result of a transient misalignment of the primer/template
-+substrate.’"]]
+[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Preference for adding As.  ‘We cannot exclude the formal possibility that some of these latter events, particularly the addition of dCMP by AMV reverse transcriptase, involve the use of coding information made available as a result of a transient misalignment of the primer/template substrate.’"]]

Pas lu
diff --git a/biblio/22691702.mdwn b/biblio/22691702.mdwn
new file mode 100644
index 00000000..fc3d70cb
--- /dev/null
+++ b/biblio/22691702.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants."]]
+[[!tag reverse_transcription not_read]]
+
+Baranauskas A, Paliksa S, Alzbutas G, Vaitkevicius M, Lubiene J, Letukiene V, Burinskas S, Sasnauskas G, Skirgaila R.
+
+Protein Eng Des Sel. 2012 Oct;25(10):657-68 doi:10.1093/protein/gzs034
+
+Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants.
+
+[[!pmid 22691702 desc="not read"]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index fe9f0ec2..cdef0de7 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -118,5 +118,7 @@ nucleotide as a template.
 
  - E69K, E302R, W313F, L435G and N454K collectively increase the half-life of
    MMLV RT at 55 °C ([[Arezi and Hogrefe, 2009|biblio/19056821]]).
+ - D200N, L603W, T330P, L139P and E607K (not read, [[Baranauskas and coll.,
+   2012|biblio/22691702]]).
 
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

Publié !
diff --git a/biblio/32025730.mdwn b/biblio/32025730.mdwn
new file mode 100644
index 00000000..d3a08301
--- /dev/null
+++ b/biblio/32025730.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Machine-driven parameter screen of biochemical reactions."]]
+[[!tag nanoCAGE enzyme template_switching]]
+
+Poulain S, Arnaud O, Kato S, Chen I, Ishida H, Carninci P, Plessy C.
+
+Nucleic Acids Res. 2020 Feb 6. pii: gkaa079. doi:10.1093/nar/gkaa079
+
+Machine-driven parameter screen of biochemical reactions.
+
+[[!pmid 32025730 desc="Our work using a Labcyte Echo machine to assemble thousands of nanoCAGE reactions."]]

Contacts between paired chromosome arms in Ciona.
diff --git a/biblio/15930823.mdwn b/biblio/15930823.mdwn
new file mode 100644
index 00000000..6f236327
--- /dev/null
+++ b/biblio/15930823.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Molecular cytogenetic characterization of Ciona intestinalis chromosomes."]]
+[[!tag ciona chromosome]]
+
+Zoolog Sci. 2005 May;22(5):511-6 doi:10.2108/zsj.22.511
+
+Shoguchi E, Kawashima T, Nishida-Umehara C, Matsuda Y, Satoh N.
+
+Molecular cytogenetic characterization of Ciona intestinalis chromosomes.
+
+[[!pmid 15930823 desc="Ciona intestinalis has 10 metacentric pairs and 8 submetacentric or subtelomeric pairs of chromosomes."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 5b05baee..aa1838e7 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -42,7 +42,10 @@ recent introgression then happened 15,000 years ago ([[Roux and coll.,
 Latest _Ciona robusta_ genome: version HT ([[Satou and coll.,
 2019|biblio/31621849]]) is a reassembly of the KS genome using Hi-C and PacBio
 additional data, in which over 95 % of the dequences is included in
-chromosomes.
+chromosomes.  Out of 14 pairs of chromosomes, 10 are metacentric ([[Shoguchi
+and coll., 2005|biblio/15930823]]); the Hi-C contact map suggests that their
+arms interact with each other almost as much as with themselves.
+Inter-chromosomal contacts are much more rare in comparison.
 
 Mitochondrial gene order differs even within the _Ciona_ genus ([[Gissi,
 Iannelli and Pesole 2004|biblio/15114417]]).

dotplot
diff --git a/biblio/29888139.mdwn b/biblio/29888139.mdwn
new file mode 100644
index 00000000..eb597467
--- /dev/null
+++ b/biblio/29888139.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="D-GENIES: dot plot large genomes in an interactive, efficient and simple way."]]
+[[!tag software assembly]]
+
+Cabanettes F, Klopp C.
+
+PeerJ. 2018 Jun 4;6:e4958. doi:10.7717/peerj.4958
+
+D-GENIES: dot plot large genomes in an interactive, efficient and simple way.
+
+[[!pmid 29888139 desc="Can export to SVG format as well."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 268d2911..b999bbb0 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -51,6 +51,10 @@ that most contact points are due to local (same-chromosome) proximity.  Version
 2 of SALSA uses unitigs and the assembly graph as input ([[Ghurye and coll.,
 2019|biblio/31433799]]).
 
+Assemblies can be aligned with [[last-dotplot|LAST]] or, for SVG export and
+interactive browsing with D-GENIES ([[Cabanettes and Klopp
+2018|biblio/29888139]]).
+
 BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy
 genes in the assemblies.  Seppey, Manni and Zdobnov EM ([[2019|biblio/31020564]])

Published
diff --git a/biblio/10.1101_499954.mdwn b/biblio/10.1101_499954.mdwn
deleted file mode 100644
index 438c86f3..00000000
--- a/biblio/10.1101_499954.mdwn
+++ /dev/null
@@ -1,10 +0,0 @@
-[[!meta title="A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing"]]
-[[!tag genome assembly mosquito method extraction]]
-
-Sarah Kingan, Haynes Heaton, Juliana Cudini, Christine Lambert, Primo Baybayan, Brendan Galvin, Richard Durbin, Jonas Korlach, Mara Lawniczak
-
-bioRxiv preprint
-
-A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing
-
-[[!doi 10.1101/499954 desc="Single individual ground with no twisting (only up-down movements).  DNA extracted with Qiagen MagAttract HMW kit, gentle flipping and wide-bore tips.  One contig was a bacterial genome, probably from gut flora.  Two contigs contained multiple copies of the mitochondrial chromosome.  Comparison with Sanger assembly corrected repeat compression."]]
diff --git a/biblio/30669388.mdwn b/biblio/30669388.mdwn
new file mode 100644
index 00000000..74c3c509
--- /dev/null
+++ b/biblio/30669388.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing"]]
+[[!tag genome assembly mosquito method extraction]]
+
+Sarah Kingan, Haynes Heaton, Juliana Cudini, Christine Lambert, Primo Baybayan, Brendan Galvin, Richard Durbin, Jonas Korlach, Mara Lawniczak
+
+Genes (Basel). 2019 Jan 18;10(1). pii: E62. doi:10.3390/genes10010062
+
+A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing
+
+[[!pmid 30669388 10.1101/499954 desc="Single individual ground with no twisting (only up-down movements).  DNA extracted with Qiagen MagAttract HMW kit, gentle flipping and wide-bore tips.  One contig was a bacterial genome, probably from gut flora.  Two contigs contained multiple copies of the mitochondrial chromosome.  Comparison with Sanger assembly corrected repeat compression."]]

Café
diff --git a/biblio/31719208.mdwn b/biblio/31719208.mdwn
new file mode 100644
index 00000000..00673cc8
--- /dev/null
+++ b/biblio/31719208.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Definitive demonstration by synthesis of genome annotation completeness."]]
+[[!tag synthethic]]
+
+Jaschke PR, Dotson GA, Hung KS, Liu D, Endy D.
+
+Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):24206-24213. doi:10.1073/pnas.1905990116
+
+Definitive demonstration by synthesis of genome annotation completeness.
+
+[[!pmid 31719208 desc="A øX174 genome where most cryptic ORFs were erased is still viable.  In its initial version, its growth was slower than the wild type, but an in vitro selection isolated a point mutant that recovered the growth phenotype.  Additional experiments suggest that the point mutation affected the translation levels of one of the major ORFs.  A øX174 genome where the major ORFs are mutated is not viable, and only a single cryptic ORF shows detectable levels of expression."]]

Café; thx MH !
diff --git a/biblio/10.1101_837542.mdwn b/biblio/10.1101_837542.mdwn
new file mode 100644
index 00000000..df5c2c40
--- /dev/null
+++ b/biblio/10.1101_837542.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Multiplexed direct detection of barcoded protein reporters on a nanopore array"]]
+[[!tag bioRxiv nanopore]]
+
+Posted November 11, 2019.
+
+Nicolas Cardozo, Karen Zhang, Katie Doroschak, Aerilynn Nguyen, Zoheb Siddiqui, Karin Strauss, Luis Ceze and Jeff Nivala.
+
+Multiplexed direct detection of barcoded protein reporters on a nanopore array
+
+[[!doi 10.1101/837542 desc="Detection of peptide barcodes in Nanopore flow cells."]]

Template switching to a plasmid.
diff --git a/biblio/1279521.mdwn b/biblio/1279521.mdwn
new file mode 100644
index 00000000..ef568ca9
--- /dev/null
+++ b/biblio/1279521.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Temperature-dependent template switching during in vitro cDNA synthesis by the AMV-reverse transcriptase."]]
+[[!tag template_switching]]
+
+Nucleic Acids Res. 1992 Oct 25;20(20):5443-50 doi:10.1093/nar/20.20.5443
+
+Ouhammouch M, Brody EN.
+
+Temperature-dependent template switching during in vitro cDNA synthesis by the AMV-reverse transcriptase.
+
+[[!pmid 1279521 desc="Template switching from a cDNA to a plasmid with the AMV RT."]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 0d388dce..c4165c23 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -96,4 +96,9 @@ as a replacement for RNA.
    1 mM manganese increases the formation of TSO concatenates and the fraction
    of reads aliging to ribosomal sequences.
 
+### Related works
+
+ - The AMV RT was reported by Ouhammouch and Brody ([[1992|biblio/1279521]]) to
+   template-switch from a mRNA to a plasmid.
+
 [[!inline pages="tagged(template_switching)" limit=0]]

Point mutants
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 8b290f13..fe9f0ec2 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -114,4 +114,9 @@ nucleotide as a template.
  - "Not-so random" (NSR) primers: [[Armour et al., 2009|biblio/19668204]].
  - "Pseudo-random" primers: [[Arnaud et al., 2016|biblio/27071605]].
 
+### Reverse-transcriptase point mutations
+
+ - E69K, E302R, W313F, L435G and N454K collectively increase the half-life of
+   MMLV RT at 55 °C ([[Arezi and Hogrefe, 2009|biblio/19056821]]).
+
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

Details.
diff --git a/biblio/19056821.mdwn b/biblio/19056821.mdwn
index c2451f86..f58f6330 100644
--- a/biblio/19056821.mdwn
+++ b/biblio/19056821.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer."]]
-[[!tag enzyme]]
+[[!tag enzyme reverse_transcription]]
+
+Nucleic Acids Res. 2009 Feb;37(2):473-81. doi:10.1093/nar/gkn952
+
+Arezi B, Hogrefe H.
+
+Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer.
+
 [[!pmid 19056821 desc="From Agilent/Stratagene."]]

Purge Haplotigs does not merge contigs.
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 0dbe7275..268d2911 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -43,7 +43,7 @@ assembly_”.
 
 Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an
 alternative to HaploMerger that takes read coverage into account when detecting
-potential haplotigs.
+potential haplotigs.  However, it does not merge haplotypes.
 
 SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis

creating tag page tags/database
diff --git a/tags/database.mdwn b/tags/database.mdwn
new file mode 100644
index 00000000..277f1ca9
--- /dev/null
+++ b/tags/database.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged database"]]
+
+[[!inline pages="tagged(database)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/30395283.mdwn b/biblio/30395283.mdwn
new file mode 100644
index 00000000..7860383f
--- /dev/null
+++ b/biblio/30395283.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs."]]
+[[!tag database]]
+
+Kriventseva EV, Kuznetsov D, Tegenfeldt F, Manni M, Dias R, Simão FA, Zdobnov EM.
+
+Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811. doi:10.1093/nar/gky1053
+
+OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.
+
+[[!pmid 30395283 desc="“When there are multiple genomes available with greater than about 96% identity using MASH estimates, we sample the best annotated representatives with the most complete gene sets according to BUSCO metrics.”"]]

backlog
diff --git a/biblio/17488851.mdwn b/biblio/17488851.mdwn
new file mode 100644
index 00000000..77f3fc82
--- /dev/null
+++ b/biblio/17488851.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Characterization of Agrobacterium tumefaciens DNA ligases C and D."]]
+[[!tag enzyme ligase]]
+
+Zhu H and Shuman S.
+
+Nucleic Acids Res. 2007;35(11):3631-45 doi:10.1093/nar/gkm145
+
+Characterization of Agrobacterium tumefaciens DNA ligases C and D.
+
+[[!pmid 17488851 desc="In presence of Co²⁺, can extend an oligonucleotide on a template using rNTPs."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 7f3abe58..eedb614f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -662,9 +662,6 @@ No correlation between in situ expression pattern and gene ontology in the brain
 17405768 [microfluidics]
 Cycling 100 times (94°C for 30 s, 55°C for 30 s, and 72°C for 60 s) in 0.1% DDM, x1 Pfu Buffer before use improves product yield.
 
-17488851 [enzymes]
-In presence of Co²⁺, can extend an oligonucleotide on a template using rNTPs.
-
 17488852 [enzymes]
 Useful to prepare 2' phosphate ends, which are substrate for the yeast tRNA ligase.
 

creating tag page tags/cell_line
diff --git a/tags/cell_line.mdwn b/tags/cell_line.mdwn
new file mode 100644
index 00000000..6e03a931
--- /dev/null
+++ b/tags/cell_line.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged cell line"]]
+
+[[!inline pages="tagged(cell_line)" actions="no" archive="yes"
+feedshow=10]]