Dernières modifications :

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]]

Merge tags
diff --git a/biblio/22820316.mdwn b/biblio/22820316.mdwn
index fe9c4b08..091e390d 100644
--- a/biblio/22820316.mdwn
+++ b/biblio/22820316.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A tissue-engineered jellyfish with biomimetic propulsion."]]
-[[!tag synthethic_biology]]
+[[!tag synthethic]]
 
 Nawroth JC, Lee H, Feinberg AW, Ripplinger CM, McCain ML, Grosberg A, Dabiri JO, Parker KK.
 
diff --git a/biblio/25417166.mdwn b/biblio/25417166.mdwn
index 3fba3365..cfb8e0f9 100644
--- a/biblio/25417166.mdwn
+++ b/biblio/25417166.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Toehold switches: de-novo-designed regulators of gene expression."]]
-[[!tag not_read synthethic_biology]]
+[[!tag not_read synthethic]]
 
 Cell. 2014 Nov 6;159(4):925-39. doi:10.1016/j.cell.2014.10.002
 
diff --git a/biblio/30069045.mdwn b/biblio/30069045.mdwn
index 749021c3..0e604bc9 100644
--- a/biblio/30069045.mdwn
+++ b/biblio/30069045.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Creating a functional single-chromosome yeast."]]
-[[!tag yeast genome synthethic_biology]]
+[[!tag yeast genome synthethic]]
 
 Nature. 2018 Aug 1. doi:10.1038/s41586-018-0382-x
 
diff --git a/biblio/31932426.mdwn b/biblio/31932426.mdwn
index f77fa660..21a308d9 100644
--- a/biblio/31932426.mdwn
+++ b/biblio/31932426.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A scalable pipeline for designing reconfigurable organisms."]]
-[[!tag synthethic_biology]]
+[[!tag synthethic]]
 
 Kriegman S, Blackiston D, Levin M, Bongard J
 
diff --git a/tags/synthethic_biology.mdwn b/tags/synthethic_biology.mdwn
deleted file mode 100644
index 8b576474..00000000
--- a/tags/synthethic_biology.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged synthethic biology"]]
-
-[[!inline pages="tagged(synthethic_biology)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/31932426.mdwn b/biblio/31932426.mdwn
new file mode 100644
index 00000000..f77fa660
--- /dev/null
+++ b/biblio/31932426.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A scalable pipeline for designing reconfigurable organisms."]]
+[[!tag synthethic_biology]]
+
+Kriegman S, Blackiston D, Levin M, Bongard J
+
+Proc Natl Acad Sci U S A. 2020 Jan 13. pii: 201910837. doi:10.1073/pnas.1910837117
+
+A scalable pipeline for designing reconfigurable organisms.
+
+[[!pmid 31932426 desc="Uses an “evolutionary search method that, unlike learning methods, enables the design of the machine’s physical structure along with its behavior”. “Pluripotent stem cells are first harvested from blastula stage Xenopus laevis embryos, dissociated, and pooled to achieve the desired number of cells. Following an incubation period, the aggregated tissue is then manually shaped by subtraction using a combination of microsurgery forceps and a 13-μm wire tip cautery electrode, producing a biological approximation of the simulated design. Further, contractile tissue can be layered into the organism through the harvesting and embedding of Xenopus cardiac progenitor cells, an embryonically derived cell type which naturally develops into cardiomyocytes (heart muscle) and produces contractile waves at specific locations in the resultant shaped form.”"]]

Café
diff --git a/biblio/4976834.mdwn b/biblio/4976834.mdwn
new file mode 100644
index 00000000..23c9d7ae
--- /dev/null
+++ b/biblio/4976834.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Isolement, en culture in vivo, de lignées cellulaires diploïdes de Drosophila melanogaster."]]
+[[!tag Drosophila cell_line]]
+
+Echalier G, Ohanessian A.
+
+C R Acad Hebd Seances Acad Sci D. 1969 Mar 31;268(13):1771-3.
+
+https://gallica.bnf.fr/ark:/12148/bpt6k62969219/f623.image
+
+[[!pmid 4976834 desc="Spontaneous transformation after multiple months of culture."]]

Café
diff --git a/biblio/31249862.mdwn b/biblio/31249862.mdwn
new file mode 100644
index 00000000..edd153ed
--- /dev/null
+++ b/biblio/31249862.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication."]]
+[[!tag chromosome evolution]]
+
+Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM; NISC Comparative Sequencing Program, Mullikin JC, Burgess SM.
+
+Sci Adv. 2019 Jun 26;5(6):eaav0547. doi:10.1126/sciadv.aav0547
+
+De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.
+
+[[!pmid 31249862 desc="Genomes and transcriptomes from the goldfish.  Because of whole-genome duplication (WGD), “fifty-eight percent of the BUSCO genes could be found in two complete copies”.  Speciation time ~11 Ma ago and WGD time ~14.4 Ma ago.  Subgenomes were well conserved: “No large interchromosomal translocations were found between the 25 zebrafish chromosomes and the 50 goldfish LGs”.  However, some large intrachromosomal variations were found.  Cross-study with the common carp (which last common ancestor with goldfish was after the WGD, and the grass carp (pre-WGD) showed that gene “expression distance increased as the sequence identity decreased” and that “the loss of CNEs reduced the expression variance among different tissues (dynamic range) rather than affected the expression divergence between ohnolog gene pairs, i.e., CNE loss reduced tissue-specific expression variation”."]]

2018...
diff --git a/biblio/30275530.mdwn b/biblio/30275530.mdwn
new file mode 100644
index 00000000..7699ecdf
--- /dev/null
+++ b/biblio/30275530.mdwn
@@ -0,0 +1,18 @@
+[[!meta title="Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci."]]
+[[!tag olfaction]]
+
+Nat Genet. 2018 Nov;50(11):1574-1583. doi:10.1038/s41588-018-0223-8
+
+Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W,
+Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M,
+Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein
+M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M,
+Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S,
+Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L,
+Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold
+G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B,
+Keane TM.
+
+Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
+
+[[!pmid 30275530 desc="Loss and gain of OR genes in various mouse lineages."]]

Café
diff --git a/biblio/11126119.mdwn b/biblio/11126119.mdwn
new file mode 100644
index 00000000..736089f5
--- /dev/null
+++ b/biblio/11126119.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="5' RACE by tailing a general template-switching oligonucleotide."]]
+[[!tag template_switching method library]]
+
+Shi X, Kaminskyj SG.
+
+Biotechniques. 2000 Dec;29(6):1192-5 doi:10.2144/00296bm07
+
+5' RACE by tailing a general template-switching oligonucleotide.
+
+[[!pmid 11126119 desc="Generate a collection of TSOs by TdT tailing DNA oligos with GTP.  As the lengh of the G tail is variable, it is thought to be more suited to the template switching on cDNAs where the C tail is also variable in length."]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index d3bef696..0d388dce 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -11,8 +11,12 @@
    cDNAs with dA, and add 5′ linkers with T4 DNA ligase and duplex adapters
    ending with a (T)TTTGGG overhang.
 
+ - Noticing that the length of the dC tail on the first-strand cDNA is varialbe,
+   [[Shi and Kaminskyj (2000)|biblio/11126119]] prepared collections of TSOs
+   with variable rG tail length, using TdT.
+
  - In SMART (switching mechanism at the 5′ end of the RNA transcript), [[Zhu,
-   Machleder, Chenchik, Li and Siebert (2001)]] , first-strand cDNAs are
+   Machleder, Chenchik, Li and Siebert (2001)|biblio/11314272]] , first-strand cDNAs are
    prepared with rGrGrG TSOs containing a SfiIB site and oligo-dT RT primers
    containing a SfiIA site.  Second-strand synthesis with low-cycle PCR, followed
    with standard cloning methods.

CapFinder.
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 24ba14f9..d3bef696 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -2,6 +2,10 @@
 
 (work in progress.  For alternative cap enrichement methods see the [[cap]] tag page)
 
+ - 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.
+
  - 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

SMART
diff --git a/biblio/11314272.mdwn b/biblio/11314272.mdwn
new file mode 100644
index 00000000..c65659a6
--- /dev/null
+++ b/biblio/11314272.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction."]]
+[[!tag template_switching library method]]
+
+Biotechniques. 2001 Apr;30(4):892-7.
+
+Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD.
+
+Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction.
+
+[[!pmid 11314272 desc="SMART: “switching mechanism at the 5′ end of the RNA transcript”.  Template-swiching with a rGrGrG oligo containing SfiIB, reverse transcription with an oligo-dT primer containing a SfiIA site. Second-strand cDNA synthesis with low-cycle PCR.  Cloning with standard methods."]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 351d4908..24ba14f9 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -7,6 +7,12 @@
    cDNAs with dA, and add 5′ linkers with T4 DNA ligase and duplex adapters
    ending with a (T)TTTGGG overhang.
 
+ - In SMART (switching mechanism at the 5′ end of the RNA transcript), [[Zhu,
+   Machleder, Chenchik, Li and Siebert (2001)]] , first-strand cDNAs are
+   prepared with rGrGrG TSOs containing a SfiIB site and oligo-dT RT primers
+   containing a SfiIA site.  Second-strand synthesis with low-cycle PCR, followed
+   with standard cloning methods.
+
  - The "_terminal continuation_" method ([[Ginsberg et al.,
    2002|biblio/12462399]], [[Che et al., 2004|biblio/14647400]]) is essentially
    a template switching with DNA oligonucleotides ending in `CCC` or `GGG`.  `AAA`

Café
diff --git a/biblio/10.1101_2020.01.16.905182.mdwn b/biblio/10.1101_2020.01.16.905182.mdwn
new file mode 100644
index 00000000..a19df767
--- /dev/null
+++ b/biblio/10.1101_2020.01.16.905182.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq"]]
+[[!tag bioRxiv promoter method]]
+
+bioRxiv Posted January 16, 2020 doi:10.1101/2020.01.16.905182 
+
+Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner
+
+Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
+
+[[!doi 10.1101/2020.01.16.905182 desc="Terminator-treated RNA reverse-transcribed with random N5 primers.  The (biotinylated) TSO is added in the last 5 min of the RT (~40 µM final).  The TSO carries a P5 linker and the RTP a P7 (indexed) linker.  Follows a standard PCR and sequencing.  The YR motif is detected in yeast and K562 cells.  High amounts of rRNA remains in yeast"]]

Café
diff --git a/biblio/25714331.mdwn b/biblio/25714331.mdwn
new file mode 100644
index 00000000..c95b2876
--- /dev/null
+++ b/biblio/25714331.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Functional specialization of chordate CDK1 paralogs during oogenic meiosis."]]
+[[!tag Oikopleura H3S28p]]
+
+Øvrebø JI, Campsteijn C, Kourtesis I, Hausen H, Raasholm M, Thompson EM.
+
+Cell Cycle. 2015;14(6):880-93. doi:10.1080/15384101.2015.1006000
+
+Functional specialization of chordate CDK1 paralogs during oogenic meiosis.
+
+[[!pmid 25714331 desc="”Differential spatiotemporal dynamics of the odCDK1a, d and e paralogs and the meiotic polo-like kinase 1 (Plk1) and aurora kinase determine the subset of meiotic nuclei in prophase I arrest that will seed growing oocytes and complete meiosis. Whereas we find odCDK1e to be non-essential, knockdown of the odCDK1a paralog resulted in the spawning of non-viable oocytes of reduced size. Knockdown of odCDK1d also resulted in the spawning of non-viable oocytes. In this case, the oocytes were of normal size, but were unable to extrude polar bodies upon exposure to sperm, because they were unable to resume meiosis from prophase I arrest, a classical function of the sole CDK1 during meiosis in other organisms.“"]]

Café
diff --git a/tags/H3S28p.mdwn b/tags/H3S28p.mdwn
index b202a048..12de3826 100644
--- a/tags/H3S28p.mdwn
+++ b/tags/H3S28p.mdwn
@@ -28,6 +28,8 @@ at telophase.  Table S1, listing the antibodies used, is missing.
 In [[Campsteijn and coll, 2012|biblio/21734012]], the H3S28p antibody is reported to
 be from Abcam, with no catalog number.  Figure 1 shows centromere staining in some cells,
 broader staining in other cells and no staining in most cells in tadpoles (6 h p.f.).
+[[Øvrebø and coll., 2015|biblio/25714331]] refers to Campsteijn and coll, 2012
+for its antibody stainings.
 
 In [[Subramaniam and coll., 2014|biblio/24695788]], the H3S28p antibody is
 reported to be from Abcam; no catalog number.  Figure 4 shows mitotic and meiotic
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b0f68a9b..fbf49d9a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -169,7 +169,8 @@ Genes and pathways
    (2001)|biblio/11732199]]. The CesA gene is trans-spliced in the ascidian _Ciona
    intestinalis_ ([[Matthysse and coll., 2004|biblio/14722352]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
-   implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
+   implicated in oogenesis ([[Øvrebø and coll., 2015|biblio/25714331]],
+   [[Feng & Thompson, 2018|biblio/29969934]]).
  - _O. dioica_ CDK1a and b locate on LG2; CDK1c and is CDK1e on LG1.
    CDK1d is on the X chromosome near CycBa.  In _O. albicans_, CDK1a,b and c are
    on the same chromosome ([[Ma, Øvrebø and Thompson, 2019|biblio/10.1101_817783]]).
@@ -288,6 +289,8 @@ Development
  - The oocytes originate from a specialised syncitium, the coenocyst, in which
    nurse cells and oocytes are connected by cytoplasmic bridges, the ring channels
    ([[Ganot and coll., 2007|biblio/17126826]]).
+ - Oocytes lacking odCDK1d can not resume from meiosis from prophase I arrest,
+   and therefore are non-viable after spawning ([[Øvrebø and coll., 2015|biblio/25714331]]).
  - Oocytes are in metaphase I stage at the time of spawning ([[Ganot, Kallesøe
    and Thompson (2007)|biblio/17123503]]).
  - Inhibition of the MAPK pathway cause some nurse cell nuclei to enter the

Café
diff --git a/biblio/18845138.mdwn b/biblio/18845138.mdwn
new file mode 100644
index 00000000..23770378
--- /dev/null
+++ b/biblio/18845138.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oocyte selection is concurrent with meiosis resumption in the coenocystic oogenesis of Oikopleura."]]
+[[!tag H3S10p H3S28p Oikopleura]]
+
+Ganot P, Moosmann-Schulmeister A, Thompson EM.
+
+Dev Biol. 2008 Dec 15;324(2):266-76. doi:10.1016/j.ydbio.2008.09.016
+
+Oocyte selection is concurrent with meiosis resumption in the coenocystic oogenesis of Oikopleura.
+
+[[!pmid 18845138 desc="H3S28p signal grows becomes highest only in the subset of H2S10p-labeled oocytes that become selected for maturation.  MAPK inhibition has a similar effect to microtubule destabilisation."]]
diff --git a/tags/H3S28p.mdwn b/tags/H3S28p.mdwn
index 4764bf06..b202a048 100644
--- a/tags/H3S28p.mdwn
+++ b/tags/H3S28p.mdwn
@@ -10,6 +10,11 @@ In [[Schulmeister and coll., 2007|biblio/17333540]], H3S28p (Abcam ab10543
 staining is more familiar to the ones described as centromeric in other
 publications.
 
+In [[Ganot, Moosmann-Schulmeister and Thompson (2008), |biblio/18845138]]:
+rabbit polyclonal anti-histone H3 phospho-serine 10 (H3S10P, 06-570) and
+anti-histone H3 phospho-serine 28 (H3S28P, 07-145) from Upstate; secondary
+antibodies from chemicon.  H3S28P stronger in selected oocytes.
+
 In [[Olsen and coll., 2018|biblio/29486709]], Figure 5e shows H3S28p staining
 (Abcam ab10543  1:100) of whole chromosomes in most cells, and a more punctate
 staining in other cells.  Figure 5f also shows extrachromosomal staining.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index e3a500c2..b0f68a9b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -290,6 +290,9 @@ Development
    ([[Ganot and coll., 2007|biblio/17126826]]).
  - Oocytes are in metaphase I stage at the time of spawning ([[Ganot, Kallesøe
    and Thompson (2007)|biblio/17123503]]).
+ - Inhibition of the MAPK pathway cause some nurse cell nuclei to enter the
+   oocyte through the ring channels ([[Ganot, Moosmann-Schulmeister and Thompson,
+   2008|biblio/18845138]]).
  - The first and second polar bodies are visible 5 and 15 min after fertilisation,
    respectively ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
  - First embryonic cleavages are deterministic and “Clonal organization of the

Café
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8ea9b3c8..e3a500c2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -288,6 +288,8 @@ Development
  - The oocytes originate from a specialised syncitium, the coenocyst, in which
    nurse cells and oocytes are connected by cytoplasmic bridges, the ring channels
    ([[Ganot and coll., 2007|biblio/17126826]]).
+ - Oocytes are in metaphase I stage at the time of spawning ([[Ganot, Kallesøe
+   and Thompson (2007)|biblio/17123503]]).
  - The first and second polar bodies are visible 5 and 15 min after fertilisation,
    respectively ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
  - First embryonic cleavages are deterministic and “Clonal organization of the

café
diff --git a/biblio/12917355.mdwn b/biblio/12917355.mdwn
new file mode 100644
index 00000000..408bb115
--- /dev/null
+++ b/biblio/12917355.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Phosphorylation of serine 10 in histone H3, what for?"]]
+[[!tag review H3S10p]]
+
+Prigent C, Dimitrov S.
+
+J Cell Sci. 2003 Sep 15;116(Pt 18):3677-85 doi:10.1242/jcs.00735
+
+Phosphorylation of serine 10 in histone H3, what for?
+
+[[!pmid 12917355 desc="H3 serine 10 is phosphorylated in mitosis and meiosis."]]
diff --git a/biblio/17123503.mdwn b/biblio/17123503.mdwn
index cd086dd7..2d720487 100644
--- a/biblio/17123503.mdwn
+++ b/biblio/17123503.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura."]]
-[[!tag Oikopleura telomere]]
+[[!tag Oikopleura telomere H3S10p]]
 
 Ganot P, Kallesøe T, Thompson EM.
 
@@ -7,4 +7,4 @@ Dev Biol. 2007 Feb 15;302(2):577-90 doi:10.1016/j.ydbio.2006.10.022
 
 The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura.
 
-[[!pmid 17123503 desc="In early meiotic nuclei, telomeres and nuclear pore complexes ”cluster in non-overlapping regions of the nuclear envelope”.  During some stages of oocyte maturation, the telomeres of the endocycling nurse cells “clustered at the nuclear periphery, in a compartment with no detectable elongating RNA polymerase II”.  Colchicine treatment induced early oocyte differenciation."]]
+[[!pmid 17123503 desc="In early meiotic nuclei, telomeres and nuclear pore complexes ”cluster in non-overlapping regions of the nuclear envelope”.  During some stages of oocyte maturation, the telomeres of the endocycling nurse cells “clustered at the nuclear periphery, in a compartment with no detectable elongating RNA polymerase II”.  Colchicine treatment induced early oocyte differenciation.  Used rabbit polyclonal anti-histone H3 phospho-serine 10 (H3S10P) from Upstate, cat. num. 06-570."]]
diff --git a/tags/H3S10p.mdwn b/tags/H3S10p.mdwn
index 15d9e1e5..267b4cbd 100644
--- a/tags/H3S10p.mdwn
+++ b/tags/H3S10p.mdwn
@@ -1,4 +1,9 @@
 [[!meta title="pages tagged H3S10p"]]
 
-[[!inline pages="tagged(H3S10p)" actions="no" archive="yes"
-feedshow=10]]
+Histone 3 serine 10 is phosphorylated in mitosis and meiosis, see [[Prigent and
+Dmitrov (2003)|biblio/12917355]] for review.
+
+Figure 1j of [[Ganot P1, Kallesøe T, Thompson EM (2007)|biblio/17123503]] shows
+H3S10p staining of meiotic chromosomes in π-conformation in mature oocytes.
+
+[[!inline pages="tagged(H3S10p)" limit=0]]

creating tag page tags/recombination
diff --git a/tags/recombination.mdwn b/tags/recombination.mdwn
new file mode 100644
index 00000000..e9a51b06
--- /dev/null
+++ b/tags/recombination.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged recombination"]]
+
+[[!inline pages="tagged(recombination)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/repair
diff --git a/tags/repair.mdwn b/tags/repair.mdwn
new file mode 100644
index 00000000..97194c04
--- /dev/null
+++ b/tags/repair.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged repair"]]
+
+[[!inline pages="tagged(repair)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/31740957.mdwn b/biblio/31740957.mdwn
new file mode 100644
index 00000000..53198ec2
--- /dev/null
+++ b/biblio/31740957.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote."]]
+[[!tag recombination repair]]
+
+Smirnov A, Fishman V, Yunusova A, Korablev A, Serova I, Skryabin BV, Rozhdestvensky TS, Battulin N.
+
+Nucleic Acids Res. 2020 Jan 24;48(2):719-735. doi:10.1093/nar/gkz1085
+
+DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote.
+
+[[!pmid 31740957 desc="A library of constructs bearing a different barcode at each end was injected in mouse pronuclei and the resulting transgenes were sequenced from 10 embryos.  New combinations of barcodes were observed in the majority of the copies inside concatemers.  The data does not support the hypothesis of a rolling circle replication of individual constructs.  The model is: first, some linear constructs are concatemerised by NHEJ (non-homologous end joining), then HR (homologous recombination) incorporates extra copies, causing exchange of barcodes as side effect."]]

Syntax
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8ef453fd..8ea9b3c8 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -287,7 +287,7 @@ Development
 
  - The oocytes originate from a specialised syncitium, the coenocyst, in which
    nurse cells and oocytes are connected by cytoplasmic bridges, the ring channels
-   ([[Ganot and coll., 2007|17126826]]).
+   ([[Ganot and coll., 2007|biblio/17126826]]).
  - The first and second polar bodies are visible 5 and 15 min after fertilisation,
    respectively ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
  - First embryonic cleavages are deterministic and “Clonal organization of the

coenocyst
diff --git a/biblio/17126826.mdwn b/biblio/17126826.mdwn
new file mode 100644
index 00000000..946d8620
--- /dev/null
+++ b/biblio/17126826.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The Oikopleura coenocyst, a unique chordate germ cell permitting rapid, extensive modulation of oocyte production."]]
+[[!tag Oikopleura]]
+
+Ganot P, Bouquet JM, Kallesøe T, Thompson EM.
+
+Dev Biol. 2007 Feb 15;302(2):591-600 doi:10.1016/j.ydbio.2006.10.021
+
+The Oikopleura coenocyst, a unique chordate germ cell permitting rapid, extensive modulation of oocyte production.
+
+[[!pmid 17126826 desc="The coenocyst is a syncytium containing nurse nuclei and meiotic nuclei surrounded by their cytoplasms and connected by ring channels.  Figure 1p of spawned oocytes in cortical metaphase I shows 3 DNA masses.  Germline-specific expression of Vasa."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6b418a3c..8ef453fd 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -285,11 +285,16 @@ Tools
 Development
 -----------
 
+ - The oocytes originate from a specialised syncitium, the coenocyst, in which
+   nurse cells and oocytes are connected by cytoplasmic bridges, the ring channels
+   ([[Ganot and coll., 2007|17126826]]).
  - The first and second polar bodies are visible 5 and 15 min after fertilisation,
    respectively ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
  - First embryonic cleavages are deterministic and “Clonal organization of the
    tissues is essentially invariant among individuals” ([[Stach and coll.,
    2008|biblio/18490654]]).
+ - Colchicine treatment induced early differenciation of the oocytes
+   ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
  - Generation times shortens when temperature rises.  First spawnings are seen
    on day 6 at 14.2 °C, and on day 8 at 17.2 °C ([[Bouquet and coll.,
    2018|biblio/29298334]]).  Reported generation times in the litterature: 149 ± 2
@@ -303,8 +308,6 @@ Development
    eventually pause.  Animals in GA can survive ~18 days at 15°C.  GA can also be
    induced by inhibiting the TOR pathway ([[Subramaniam, Campsteijn and Thompson,
    2014|biblio/24695788]]).
- - Colchicine treatment induced early differenciation of the oocytes
-   ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
  - Telomeres are localised at the nuclear envelope and do not overlap with nuclear
    pore complexes in early meiotic oocytes before H3S10 phosphorylation.  In nurse
    cells at a later stage of oocyte development, the telomeres localise in silent

Café
diff --git a/biblio/10.2108_zsj.15.723.mdwn b/biblio/10.2108_zsj.15.723.mdwn
new file mode 100644
index 00000000..49c44f50
--- /dev/null
+++ b/biblio/10.2108_zsj.15.723.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid Oocyte Growth and Artificial Fertilization of the Larvaceans Oikopleura dioica and Oikopleura longicauda"]]
+[[!tag Oikopleura]]
+
+Atsuo Nishino, and Masaaki Morisawa
+
+ZOOLOGICAL SCIENCE 15: 723–727 (1998) doi:10.2108/zsj.15.723
+
+Rapid Oocyte Growth and Artificial Fertilization of the Larvaceans Oikopleura dioica and Oikopleura longicauda
+
+[[!doi 10.2108/zsj.15.723 desc="Oikopleura (dioica and longicauda) sampled from Moroiso bay, Misaki, Miura peninsula and cultivated at 18 °C.  In O. dioica, the first polar body is visible 5 min after fertilisation and the second polar body 15 min after fertilisation.  O. longicauda individuals can self-fertilise.  F. pellucida could not be in vitro fertilised with the same method."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5e887a52..6b418a3c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -285,6 +285,8 @@ Tools
 Development
 -----------
 
+ - The first and second polar bodies are visible 5 and 15 min after fertilisation,
+   respectively ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
  - First embryonic cleavages are deterministic and “Clonal organization of the
    tissues is essentially invariant among individuals” ([[Stach and coll.,
    2008|biblio/18490654]]).
@@ -471,6 +473,8 @@ Ecology
    (1980)|biblio/10069_30542]].
  - It was already reported to be frequent in Japanese waters [[in 1907 by T.
    Aida|biblio/AA0069577]].
+ - _O. dioica_, _longicauda_ and _cophocerca_ April 1997 in Moroiso Bay,
+   Misaki, Miura-peninsula, Kanagawa ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
  - Oikopleuridae can be found in the deep see.  For instance, [[Lindsay and
    coll., 2014|biblio/10.1007_978-4-431-54865-2_51]] reported _Oikopleura_, _Mesochordaeus_
    and _Bathochordaeus_ individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.

Café
diff --git a/biblio/31924754.mdwn b/biblio/31924754.mdwn
new file mode 100644
index 00000000..1d602302
--- /dev/null
+++ b/biblio/31924754.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing."]]
+[[!tag CAGE promoter motif]]
+
+Nepal C, Hadzhiev Y, Balwierz P, Tarifeño-Saldivia E, Cardenas R, Wragg JW, Suzuki AM, Carninci P, Peers B, Lenhard B, Andersen JB, Müller F.
+
+Nat Commun. 2020 Jan 10;11(1):168. doi:10.1038/s41467-019-13687-0
+
+Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing.
+
+[[!pmid 31924754 desc="In zebrafish, human and drosophila, the majority promoters containing a YC (5′-TOP) TSS motif also carry a YR (PyPu) TSS motif.  In dual YC/YR promoters expression of the two TSS types can be coordinated, but profiling at the zebrafish maternal-zygotic transition also shows cases where they are regulated independently.  The expression of snoRNAs was better correlated with YC-initiation than with YR-initiation."]]

Café
diff --git a/biblio/26586757.mdwn b/biblio/26586757.mdwn
new file mode 100644
index 00000000..6c988fd3
--- /dev/null
+++ b/biblio/26586757.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Stable recombination hotspots in birds."]]
+[[!tag H3K4me3 meiosis]]
+
+Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M.
+
+Science. 2015 Nov 20;350(6263):928-32. doi:10.1126/science.aad0843
+
+Stable recombination hotspots in birds.
+
+[[!pmid 26586757 desc="Recombination maps obtained from genome sequences of 24 zebra finches and 20 long-tail finches, in which SNP Haplotypes were inferred from phase-informative reads and family phasing.  Recombination rates estimated as ρ = 26.2/kb and 14.0/kb, respectively (0.14 cM/Mb in both species).  3—4000 Hotspots “operationally defined them as regions that are at least 2 kb in length; have at least five times the background recombination rate as estimated across the 80 kb of sequence surrounding the region; and are statistically supported as hotspots by a likelihood ratio test” (18).  “73% of zebra finch hotspots (...) were detected as shared between the two species.”  “Hotspots in the zebra finch and long-tailed finch genomes are enriched near transcription start sites (TSSs), transcription stop sites (TESs), and CpG islands (CGIs), with close to half of all hotspots occurring within 3 kb of one of these features.” “Median recombination rates across and within chromosomes vary over nearly six orders of magnitude (...) with regions of elevated recombination near telomeres and large intervening deserts."]]

Café
diff --git a/biblio/31727682.mdwn b/biblio/31727682.mdwn
new file mode 100644
index 00000000..586aa54e
--- /dev/null
+++ b/biblio/31727682.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Copolymerization of single-cell nucleic acids into balls of acrylamide gel."]]
+[[!tag single_cell emulsion method]
+
+Li S, Kendall J, Park S, Wang Z, Alexander J, Moffitt A, Ranade N, Danyko C,
+Gegenhuber B, Fischer S, Robinson BD, Lepor H, Tollkuhn J, Gillis J, Brouzes E,
+Krasnitz A, Levy D, Wigler M.
+
+Genome Res. 2019 Nov 14. doi:10.1101/gr.253047.119
+
+Copolymerization of single-cell nucleic acids into balls of acrylamide gel.
+
+[[!pmid 31727682 desc="In a droplet, DNA or RNA from a single cell is annealed to a acrydite primer.  An acrylamide gel is then polymerised before emulsion is broken.  DNA strands are then polymerised.  Barcoding is then done by split-and-pool method."]]

cleanup
diff --git a/biblio/24752080.mdwn b/biblio/24752080.mdwn
index a560fa07..98f54760 100644
--- a/biblio/24752080.mdwn
+++ b/biblio/24752080.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms."]]
-[[!tag sequence alignment]]
+[[!tag sequence RNA-seq software]]
 
 Patro R, Mount SM, Kingsford C.
 
diff --git a/tags/sequence.mdwn b/tags/sequence.mdwn
deleted file mode 100644
index 6a90b3fd..00000000
--- a/tags/sequence.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged sequence"]]
-
-[[!inline pages="tagged(sequence)" actions="no" archive="yes"
-feedshow=10]]

cleanup
diff --git a/biblio/6117828.mdwn b/biblio/6117828.mdwn
index 721e42c2..28c8ee09 100644
--- a/biblio/6117828.mdwn
+++ b/biblio/6117828.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Polypeptides encoded by polyadenylated and non-polyadenylated messenger RNAs from normal and heat shocked HeLa cells."]]
-[[!tag mRNA non-polyadenylated protein-coding]]
+[[!tag mRNA non-polyadenylated protein]]
 [[!pmid 6117828 desc="Evidence from translation of non-polyA RNA from control and heat shocked cells in rabbit reticulocyte cell-free system. Lists additional genes (actin, histons, myosin heavy chain, albumin) in the discussion."]]
diff --git a/tags/protein-coding.mdwn b/tags/protein-coding.mdwn
deleted file mode 100644
index ce0e9be0..00000000
--- a/tags/protein-coding.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged protein-coding"]]
-
-[[!inline pages="tagged(protein-coding)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/20133332.mdwn b/biblio/20133332.mdwn
index f1ca25ce..2ff2bfe4 100644
--- a/biblio/20133332.mdwn
+++ b/biblio/20133332.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Digital transcriptome profiling from attomole-level RNA samples."]]
-[[!tag HeliScope RNA-seq transcriptome]]
+[[!tag Helicos RNA-seq transcriptome]]
 
 Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM.
 
diff --git a/biblio/20671709.mdwn b/biblio/20671709.mdwn
index 3663b558..642b5e2d 100644
--- a/biblio/20671709.mdwn
+++ b/biblio/20671709.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism."]]
-[[!tag small_RNA HeliScope antisense]]
+[[!tag small_RNA Helicos antisense]]
 [[!pmid 20671709 desc="5′-polyuridylated RNAs."]]
diff --git a/biblio/21176148.mdwn b/biblio/21176148.mdwn
index 75403e5e..46b71d13 100644
--- a/biblio/21176148.mdwn
+++ b/biblio/21176148.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘dark matter’ un-annotated RNA"]]
-[[!tag HeliScope RNA-seq intron]]
+[[!tag Helicos RNA-seq intron]]
 [[!pmid 21176148 desc="RNA-seq analysis finds up to 47 % of intronic transcripts in human total RNA."]]
diff --git a/tags/HeliScope.mdwn b/tags/HeliScope.mdwn
deleted file mode 100644
index 9e6653ed..00000000
--- a/tags/HeliScope.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged HeliScope"]]
-
-[[!inline pages="tagged(HeliScope)" actions="no" archive="yes"
-feedshow=10]]

Caƒƒé
diff --git a/biblio/31862872.mdwn b/biblio/31862872.mdwn
new file mode 100644
index 00000000..b3e71f95
--- /dev/null
+++ b/biblio/31862872.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells."]]
+[[!tag Helicos method]]
+
+Cao H, Salazar-García L, Gao F, Wahlestedt T, Wu CL, Han X, Cai Y, Xu D, Wang 
+F, Tang L, Ricciardi N, Cai D, Wang H, Chin MPS, Timmons JA, Wahlestedt C,
+Kapranov P.
+
+Nat Commun. 2019 Dec 20;10(1):5799. doi:10.1038/s41467-019-13602-7
+
+Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells.
+
+[[!pmid 31862872 desc="SSiNGLe: “single-strand break mapping at nucleotide genome level”. In the simplest form of this method, 3′-OH breaks are poly-A tailed and sequenced on a SeqLL (ex-Helicos) platform. A more complicated Illumina version exists. The authors found more breaks in gene regions (promoters, exons, introns), an also in mitochondrial DNA of aged patients and in regions displaying more sequence variants in the human population."]]

cleanup
diff --git a/biblio/18656947.mdwn b/biblio/18656947.mdwn
index a6aa4cc0..c95e6614 100644
--- a/biblio/18656947.mdwn
+++ b/biblio/18656947.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Triazole-linked analogue of deoxyribonucleic acid ((TL)DNA): design, synthesis, and double-strand formation with natural DNA."]]
-[[!tag (TL)DNA not_read]]
+[[!tag not_read]]
 
 Org Lett. 2008 Sep 4;10(17):3729-32. doi: 10.1021/ol801230k. Epub 2008 Jul 26.
 
diff --git a/biblio/24048476.mdwn b/biblio/24048476.mdwn
index 7fd7dca4..68185d97 100644
--- a/biblio/24048476.mdwn
+++ b/biblio/24048476.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Genomic organization of human transcription initiation complexes."]]
-[[!tag promoter TATA-box [retracted]]]
+[[!tag promoter TATA-box]]
 
 Venters BJ, Pugh BF
 
diff --git a/tags/__40__TL__41__DNA.mdwn b/tags/__40__TL__41__DNA.mdwn
deleted file mode 100644
index 819a0a66..00000000
--- a/tags/__40__TL__41__DNA.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged (TL)DNA"]]
-
-[[!inline pages="tagged(__40__TL__41__DNA)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/__91__retracted.mdwn b/tags/__91__retracted.mdwn
deleted file mode 100644
index 6d63ec5f..00000000
--- a/tags/__91__retracted.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged [retracted"]]
-
-[[!inline pages="tagged(__91__retracted)" actions="no" archive="yes"
-feedshow=10]]

Typo
diff --git a/biblio/17735049.mdwn b/biblio/17735049.mdwn
index a3b0803e..e0c091f9 100644
--- a/biblio/17735049.mdwn
+++ b/biblio/17735049.mdwn
@@ -1,4 +1,4 @@
-[[!meta title=""Giant larvacean houses: observations from deep submersibles.]]
+[[!meta title="Giant larvacean houses: observations from deep submersibles."]]
 [[!tag Oikopleura]]
 
 Barham EG.

Café
diff --git a/biblio/31840110.mdwn b/biblio/31840110.mdwn
new file mode 100644
index 00000000..feb116ea
--- /dev/null
+++ b/biblio/31840110.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis."]]
+[[!tag OIST]]
+
+Commun Biol. 2019 Dec 11;2:465. doi:10.1038/s42003-019-0661-6
+
+Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marlétaz F, Simakov O, Rokhsar DS.
+
+New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis.
+
+[[!pmid 31840110 desc="Euprymna brenneri.  Molecular phylogeny of Cox1 and orthogroups from transcriptome data."]]

Café
diff --git a/biblio/22495300.mdwn b/biblio/22495300.mdwn
index 3bb3d473..e35d0c13 100644
--- a/biblio/22495300.mdwn
+++ b/biblio/22495300.mdwn
@@ -7,4 +7,4 @@ Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.
 
 Topological domains in mammalian genomes identified by analysis of chromatin interactions.
 
-[[!pmid 22495300 desc="Topolgically associated domains."]]
+[[!pmid 22495300 desc="A directionality index (DI), to detect topolgically associated domains, is described in the supplemental material.  Bin size: 40 kbp, max distance: 2 Mbp."]]

Café
diff --git a/biblio/22495300.mdwn b/biblio/22495300.mdwn
new file mode 100644
index 00000000..3bb3d473
--- /dev/null
+++ b/biblio/22495300.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Topological domains in mammalian genomes identified by analysis of chromatin interactions."]]
+[[!tag chromosome]]
+
+Nature. 2012 Apr 11;485(7398):376-80. doi:10.1038/nature11082
+
+Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.
+
+Topological domains in mammalian genomes identified by analysis of chromatin interactions.
+
+[[!pmid 22495300 desc="Topolgically associated domains."]]

Bathochordaeus
diff --git a/biblio/17735049.mdwn b/biblio/17735049.mdwn
new file mode 100644
index 00000000..a3b0803e
--- /dev/null
+++ b/biblio/17735049.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=""Giant larvacean houses: observations from deep submersibles.]]
+[[!tag Oikopleura]]
+
+Barham EG.
+
+Science. 1979 Sep 14;205(4411):1129-31 doi:10.1126/science.205.4411.1129
+
+Giant larvacean houses: observations from deep submersibles.
+
+[[!pmid 17735049 desc="Abundances as high as one per cubic meter reported at depth of 25 to 50 m in pelagic waters near the western middle American coast."]]
diff --git a/biblio/Fishery_Bulletin_77_2_514.mdwn b/biblio/Fishery_Bulletin_77_2_514.mdwn
new file mode 100644
index 00000000..289ef921
--- /dev/null
+++ b/biblio/Fishery_Bulletin_77_2_514.mdwn
@@ -0,0 +1,14 @@
+[[!meta title="First records of a giant pelagic tunicate, Bathochordaeus charon (Urochordata, Larvacea), from the eastern Pacific Ocean, with notes on its biology"]]
+[[!tag Oikopleura]]
+
+Galt, Charles P.
+
+Fishery Bulletin 1979, 77(2), pp514–9
+
+First records of a giant pelagic tunicate, Bathochordaeus charon (Urochordata, Larvacea), from the eastern Pacific Ocean, with notes on its biology
+
+https://www.st.nmfs.noaa.gov/spo/FishBull/77-2/772toc.html
+
+https://www.st.nmfs.noaa.gov/spo/FishBull/77-2/galt.pdf
+
+Specimens collected at 500 m depth in Isaacs-Kidd midwater trawls (California).
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 293c0f7a..5e887a52 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -509,6 +509,9 @@ Ecology
  -  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
+   near Californian and middle American coasts ([[Barham, 1979|biblio/17735049]],
+   [[Galt, 1979|bilbio/Fishery_Bulletin_77_2_514]]).
 
 ### Elsewhere in the World
 

Café
diff --git a/biblio/27708388.mdwn b/biblio/27708388.mdwn
new file mode 100644
index 00000000..c564feef
--- /dev/null
+++ b/biblio/27708388.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family."]]
+[[!tag chromosome genetics]]
+
+Kuang YY, Zheng XH, Li CY, Li XM, Cao DC, Tong GX, Lv WH, Xu W, Zhou Y, Zhang 
+XF, Sun ZP, Mahboob S, Al-Ghanim KA, Li JT, Sun XW.
+
+Sci Rep. 2016 Oct 6;6:34849. doi:10.1038/srep34849
+
+The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family.
+
+[[!pmid 27708388 desc="Linkage groups infered from RNA-seq data of 2 parents and > 70 offsprings."]]

AUGUSTUS
diff --git a/biblio/30466165.mdwn b/biblio/30466165.mdwn
new file mode 100644
index 00000000..d4ca13ce
--- /dev/null
+++ b/biblio/30466165.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Predicting Genes in Single Genomes with AUGUSTUS."]]
+[[!tag genome annotation software]]
+
+Hoff KJ, Stanke M.
+
+Curr Protoc Bioinformatics. 2019 Mar;65(1):e57. doi:10.1002/cpbi.57
+
+Predicting Genes in Single Genomes with AUGUSTUS.
+
+[[!pmid 30466165 desc="Explain how to train AUGUSTUS for new species using transcriptome data."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 9f9bd5b6..0dbe7275 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -53,7 +53,11 @@ that most contact points are due to local (same-chromosome) proximity.  Version
 
 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.
+genes in the assemblies.  Seppey, Manni and Zdobnov EM ([[2019|biblio/31020564]])
+wrote a good introduction in _Methods Mol Biol_.
+
+BUSCO uses AUGUSTUS, and AUGUSTUS can be trained for a new species with
+transcriptome data, as explained by [[Hoff and Stanke, 2018|biblio/30466165]].
 
 A reference assembly can be used to search for structural variants in a different
 individual, for instance with NanoSV ([[Cretu and coll., 2017|biblio/29109544]]).

Not happy
diff --git "a/Debian/debi\303\242neries/bts.en.po" "b/Debian/debi\303\242neries/bts.en.po"
index 8732f639..a64e2f0f 100644
--- "a/Debian/debi\303\242neries/bts.en.po"
+++ "b/Debian/debi\303\242neries/bts.en.po"
@@ -3,38 +3,38 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2019-12-17 14:33+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2019-12-17 23:36+0900\n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Tue, 17 Dec 2019 23:32:24 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Tue, 17 Dec 2019 23:32:24 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Tue, 17 Dec 2019 23:32:24 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Tue, 17 Dec 2019 23:32:24 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"... et pendant ce temps, dans le BTS\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"... meanwhile, in the BTS\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -42,3 +42,5 @@ msgid ""
 "listes de diffusion, on continue à nous balancer des rapports de bug "
 "malpolis via le BTS..."
 msgstr ""
+"An while people still debate about legitimate aggression in our mailing "
+"lists, we still get offensive bug reports via the BTS..."

updated PO files
diff --git "a/Debian/debi\303\242neries/bts.en.po" "b/Debian/debi\303\242neries/bts.en.po"
new file mode 100644
index 00000000..8732f639
--- /dev/null
+++ "b/Debian/debi\303\242neries/bts.en.po"
@@ -0,0 +1,44 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2019-12-17 14:33+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Tue, 17 Dec 2019 23:32:24 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Tue, 17 Dec 2019 23:32:24 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"... et pendant ce temps, dans le BTS\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Et pendant que l'on discute des circonstances de légitime aggression sur nos "
+"listes de diffusion, on continue à nous balancer des rapports de bug "
+"malpolis via le BTS..."
+msgstr ""

pas content
diff --git "a/Debian/debi\303\242neries/bts.mdwn" "b/Debian/debi\303\242neries/bts.mdwn"
new file mode 100644
index 00000000..af89eb54
--- /dev/null
+++ "b/Debian/debi\303\242neries/bts.mdwn"
@@ -0,0 +1,9 @@
+[[!meta date="Tue, 17 Dec 2019 23:32:24 +0900"]]
+[[!meta updated="Tue, 17 Dec 2019 23:32:24 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="... et pendant ce temps, dans le BTS"]]
+
+Et pendant que l'on discute des circonstances de légitime aggression sur nos
+listes de diffusion, on continue à nous balancer des rapports de bug malpolis
+via le BTS...

inopinata
diff --git a/biblio/30866802.mdwn b/biblio/30866802.mdwn
new file mode 100644
index 00000000..c2f32431
--- /dev/null
+++ b/biblio/30866802.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="A large close relative of C. elegans is slow-developing but not long-lived."]]
+[[!tag nematode]]
+
+Woodruff GC, Johnson E, Phillips PC.
+
+BMC Evol Biol. 2019 Mar 11;19(1):74. doi:10.1186/s12862-019-1388-1
+
+A large close relative of C. elegans is slow-developing but not long-lived.
+
+[[!pmid 30866802 desc="“C. inopinata females were longer-lived than wild-type
+C. elegans hermaphrodites at 25°C, with a median total lifespan that was four
+days higher [...]  However, C. inopinata females were only marginally longer
+lived than C. elegans (fog-2) pseudo-females.”"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index ff6352d9..38b124d9 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -17,6 +17,11 @@
    explained by a different chromosome number or a higher number of cells
    ([[Woodruff, Willis and Phillips, 2018|biblio/30283693]]).
 
+ - _C. inopinata_ appears to have a longer life span that _C. elegans_, but
+   this can be explained by the cost of reproduction, as virgin pseudo-female
+   _C. elegans_ also have a longer life span ([[Woodruff, Johnson and Phillips PC,
+   2019|biblio/30866802]]).
+
  - The _C. inopinata_ genome is ~123 Mb and contains active transposons that
    may explain the increased genome size compared with _C. elegans_.
    Structural changes between both species are mainly intra-chromosomal ([[Kanzaki

BUSCO
diff --git a/biblio/31020564.mdwn b/biblio/31020564.mdwn
new file mode 100644
index 00000000..cfbe2231
--- /dev/null
+++ b/biblio/31020564.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="BUSCO: Assessing Genome Assembly and Annotation Completeness."]]
+[[!tag annotation software]]
+
+Methods Mol Biol. 2019;1962:227-245. doi:10.1007/978-1-4939-9173-0_14
+
+Seppey M, Manni M, Zdobnov EM.
+
+BUSCO: Assessing Genome Assembly and Annotation Completeness.
+
+[[!pmid 31020564 desc="A guide on how to use BUSCO"]]

inopinata
diff --git a/biblio/30283693.mdwn b/biblio/30283693.mdwn
new file mode 100644
index 00000000..8f944f99
--- /dev/null
+++ b/biblio/30283693.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Dramatic evolution of body length due to postembryonic changes in cell size in a newly discovered close relative of Caenorhabditis elegans"]]
+[[!tag nematode]]
+
+Evol Lett. 2018 Jul 16;2(4):427-441. doi:10.1002/evl3.67
+
+Woodruff GC, Willis JH, Phillips PC.
+
+Dramatic evolution of body length due to postembryonic changes in cell size in a newly discovered close relative of Caenorhabditis elegans
+
+[[!pmid 30283693 desc="“This difference in size is not attributable to differences in germ line chromosome number or the number of somatic cells.”"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index 24014fa7..ff6352d9 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -13,6 +13,10 @@
    and is specialised on both its prefered fig and wasp [[(Woodruff and
    Phillips, 2018)|biblio/30129423]].
 
+ - _C. inopinata_ is larger than _C. elegans_ but this difference is not 
+   explained by a different chromosome number or a higher number of cells
+   ([[Woodruff, Willis and Phillips, 2018|biblio/30283693]]).
+
  - The _C. inopinata_ genome is ~123 Mb and contains active transposons that
    may explain the increased genome size compared with _C. elegans_.
    Structural changes between both species are mainly intra-chromosomal ([[Kanzaki

nematode.
diff --git a/biblio/24929830.mdwn b/biblio/24929830.mdwn
index 301feb8d..076789f6 100644
--- a/biblio/24929830.mdwn
+++ b/biblio/24929830.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction."]]
-[[!tag genome chromosome]]
+[[!tag nematode genome chromosome]]
 
 Nat Genet. 2014 Jul;46(7):693-700. doi:10.1038/ng.3010
 
diff --git a/biblio/28943090.mdwn b/biblio/28943090.mdwn
index 5298cf05..5ac0af5f 100644
--- a/biblio/28943090.mdwn
+++ b/biblio/28943090.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Genome Architecture and Evolution of a Unichromosomal Asexual Nematode."]]
-[[!tag genome chromosome]]
+[[!tag nematode genome chromosome]]
 
 Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC.
 
diff --git a/biblio/31754114.mdwn b/biblio/31754114.mdwn
index e421c3cb..7cc5e569 100644
--- a/biblio/31754114.mdwn
+++ b/biblio/31754114.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The genome of a subterrestrial nematode reveals adaptations to heat"]]
-[[!tag genome]]
+[[!tag nematode genome]]
 
 Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K,
 Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR.

inopinata
diff --git a/biblio/30097582.mdwn b/biblio/30097582.mdwn
new file mode 100644
index 00000000..6ccada09
--- /dev/null
+++ b/biblio/30097582.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Biology and genome of a newly discovered sibling species of Caenorhabditis elegans"]]
+[[!tag nematode genome]]
+
+Nat Commun. 2018 Aug 10;9(1):3216. doi:10.1038/s41467-018-05712-5
+
+Kanzaki N, Tsai IJ, Tanaka R, Hunt VL, Liu D, Tsuyama K, Maeda Y, Namai S,
+Kumagai R, Tracey A, Holroyd N, Doyle SR, Woodruff GC, Murase K, Kitazume H, Chai
+C, Akagi A, Panda O, Ke HM, Schroeder FC, Wang J, Berriman M, Sternberg PW,
+Sugimoto A, Kikuchi T.
+
+Biology and genome of a newly discovered sibling species of Caenorhabditis elegans
+
+[[!pmid 30097582 desc="123-Mb genome assembled into six chromosomes.  Divergence time between C. elegans and C. inopinata estimated to about 10.5 Mya (142.73 million generations ago, assuming a generation time of 30 days).  Proliferation of transposons and other repetitive elements (LTR, LINE, and Tc1/mariner).  “The C. inopinata genome contains 641 LTR retrotransposon elements, 104 of which contain full protein domains (intact LTRs) In comparison, C. elegans and C. briggsae have 62 and 128 LTR retrotransposon elements, respectively, with 10 intact LTRs found in each.”  “The most common type of repetitive sequence in the C. inopinata genome is the TcMar transposase Tc1 family [...] comprising 8.85% of the genome, compared with 1.31% and 3.04% of the C. elegans and C. briggsae genomes, respectively”.  “Gene collinearity is largely conserved despite frequent intra chromosomal rearrangements.”  “Higher synonymous substitution rates (dS) in autosomal arm regions than in the centre regions for C. elegans and C. inopinata one-to-one orthologues.”  “Notably, C. inopinata has highly conserved gene synteny and orthology of essential genes with C. elegans and C. briggsae, but differs substantially in morphology and ecology. We hypothesise that activation of transposable elements possibly due to de-silencing through an altered small RNA pathway could be a driving force of rapid diversification of C. inopinata from other Caenorhabditis species.”"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index fb04f59e..24014fa7 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -1,8 +1,24 @@
 [[!meta title="pages tagged nematode"]]
 
- - _C. inopinata_ travels from fig to fig on Ceratosolen pollinating wasps and
-   is specialised on both its prefered fig and wasp [[(Woodruff and Phillips,
-   2018)|biblio/30129423]].
+... in progress ...
+
+### _C. inopinata_
+
+ - _C. inopinata_ was discovered in 2018 to be the closest species to _C.
+   elegans_ despite stronger differences (compared with more distant species)
+   in morphology and ecological niche ([[Kanzaki and coll.,
+   2018|biblio/30097582]]).
+
+ - _C. inopinata_ travels from fig to fig on _Ceratosolen_ pollinating wasps
+   and is specialised on both its prefered fig and wasp [[(Woodruff and
+   Phillips, 2018)|biblio/30129423]].
+
+ - The _C. inopinata_ genome is ~123 Mb and contains active transposons that
+   may explain the increased genome size compared with _C. elegans_.
+   Structural changes between both species are mainly intra-chromosomal ([[Kanzaki
+   and coll., 2018|biblio/30097582]]).
+
+### Other nematodes
 
  - _Diploscapter pachys_ has a single chromosome, that is still organised in
    ancestral domains homologous to the ones of other nematodes ([[Fradin and

Mdwn
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index b511c8ca..6dc5e6bb 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-12-08 01:04+0000\n"
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 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -37,16 +37,6 @@ msgid "[[!meta title=\"A voté\"]]\n"
 msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
-#, fuzzy
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 msgid ""
 "Lors de la préparation du vote sur les systèmes d'initialisation dans "
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@@ -58,12 +48,12 @@ msgid ""
 "2010](https://www.debian.org/vote/2010/platforms/plessy)..."
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+"b) I proposed something similar in the [elections in 2010](https://www."
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updated PO files
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index a11e9f57..b511c8ca 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
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@@ -6,7 +6,7 @@
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@@ -37,15 +37,25 @@ msgid "[[!meta title=\"A voté\"]]\n"
 msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "Lors de la préparation du vote sur les systèmes d'initialisation dans "
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+#| "nécessaire et rappelant qu'il faut utiliser les résolutions générales "
+#| "avec parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003."
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Mdwn
diff --git "a/Debian/debi\303\242neries/initgr.mdwn" "b/Debian/debi\303\242neries/initgr.mdwn"
index de6aba98..5770703f 100644
--- "a/Debian/debi\303\242neries/initgr.mdwn"
+++ "b/Debian/debi\303\242neries/initgr.mdwn"
@@ -7,11 +7,11 @@
 Lors de la préparation du vote sur les systèmes d'initialisation dans Debian,
 j'ai pensé proposer une option disant que ce vote n'est pas nécessaire et
 rappelant qu'il faut utiliser les résolutions générales avec parcimonie [comme
-en 2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].
+en 2014](https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc).
 Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme
 proposant de lancer des votes plus souvent et que b) j'avais moi-même proposé
 quelque chose de similaire lors des [élections en
-2010|https://www.debian.org/vote/2010/platforms/plessy]...
+2010](https://www.debian.org/vote/2010/platforms/plessy)...
 
 Néanmoins je suis écrasé sous le nombre d'options.  Leurs textes sont longs,
 parfois très similaires, et ne séparent pas clairement le normatif du

Spelling and date
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index 4c042e3b..a11e9f57 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
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updated PO files
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index a0676d6c..4c042e3b 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -6,24 +6,26 @@
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 #. type: Plain text
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 msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
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+#| "Lors de la préparation du vote sur les systèmes d'initialisation dans "
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+#| "nécessaire et rappellant qu'il faut utiliser les résolutions générales "
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date et orthographe
diff --git "a/Debian/debi\303\242neries/initgr.mdwn" "b/Debian/debi\303\242neries/initgr.mdwn"
index ea4d3ddc..de6aba98 100644
--- "a/Debian/debi\303\242neries/initgr.mdwn"
+++ "b/Debian/debi\303\242neries/initgr.mdwn"
@@ -1,12 +1,12 @@
-[[!meta date="Sun, 08 Dec 2019 08:09:02 +0900"]]
-[[!meta updated="Sun, 08 Dec 2019 08:09:02 +0900"]]
+[[!meta date="Sun, 08 Dec 2019 08:57:43 +0900"]]
+[[!meta updated="Sun, 08 Dec 2019 08:57:43 +0900"]]
 [[!tag Debian]]
 
 [[!meta title="A voté"]]
 
 Lors de la préparation du vote sur les systèmes d'initialisation dans Debian,
 j'ai pensé proposer une option disant que ce vote n'est pas nécessaire et
-rappellant qu'il faut utiliser les résolutions générales avec parcimonie [comme
+rappelant qu'il faut utiliser les résolutions générales avec parcimonie [comme
 en 2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].
 Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme
 proposant de lancer des votes plus souvent et que b) j'avais moi-même proposé

I voted
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index dc8ba203..a0676d6c 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -3,51 +3,57 @@
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+"whom I feel in phase. I have not voted for the others, which ranks them "
+"equally under « further discussion »."

updated PO files
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
new file mode 100644
index 00000000..dc8ba203
--- /dev/null
+++ "b/Debian/debi\303\242neries/initgr.en.po"
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+msgstr ""
+
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+"modernes, j'en suis réduit à ne prendre en considération que les "
+"propositions écrites ou parrainées par des personnes avec qui je me sens en "
+"phase.  Je n'ai pas voté pour les autres, ce qui les place indistinctement "
+"sous le niveau « discussion supplémentaire »."
+msgstr ""

A voté
diff --git "a/Debian/debi\303\242neries/initgr.mdwn" "b/Debian/debi\303\242neries/initgr.mdwn"
new file mode 100644
index 00000000..ea4d3ddc
--- /dev/null
+++ "b/Debian/debi\303\242neries/initgr.mdwn"
@@ -0,0 +1,22 @@
+[[!meta date="Sun, 08 Dec 2019 08:09:02 +0900"]]
+[[!meta updated="Sun, 08 Dec 2019 08:09:02 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="A voté"]]
+
+Lors de la préparation du vote sur les systèmes d'initialisation dans Debian,
+j'ai pensé proposer une option disant que ce vote n'est pas nécessaire et
+rappellant qu'il faut utiliser les résolutions générales avec parcimonie [comme
+en 2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].
+Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme
+proposant de lancer des votes plus souvent et que b) j'avais moi-même proposé
+quelque chose de similaire lors des [élections en
+2010|https://www.debian.org/vote/2010/platforms/plessy]...
+
+Néanmoins je suis écrasé sous le nombre d'options.  Leurs textes sont longs,
+parfois très similaires, et ne séparent pas clairement le normatif du
+préambule.  Comme dans une parodie des dysfonctionnements des démocraties
+modernes, j'en suis réduit à ne prendre en considération que les propositions
+écrites ou parrainées par des personnes avec qui je me sens en phase.  Je n'ai
+pas voté pour les autres, ce qui les place indistinctement sous le niveau
+« discussion supplémentaire ».

nematode
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index ad53c985..fb04f59e 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -12,4 +12,8 @@
    according to BUSCO and CEGMA) ([[Weinstein and coll.,
    2019|biblio/31754114]]).
 
+ - The whipworms _Trichuris trichiura_ and _Trichuris muris_ have 3
+   chromosomes, as determined by a synteny comparison between two related
+   species ([[Foth and coll., 2014|biblio/24929830]]).
+
 [[!inline pages="tagged(nematode)" limit=0]]

nematode
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index d7606f40..ad53c985 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -4,5 +4,12 @@
    is specialised on both its prefered fig and wasp [[(Woodruff and Phillips,
    2018)|biblio/30129423]].
 
-[[!inline pages="tagged(nematode)" actions="no" archive="yes"
-feedshow=10]]
+ - _Diploscapter pachys_ has a single chromosome, that is still organised in
+   ancestral domains homologous to the ones of other nematodes ([[Fradin and
+   coll., 2019|biblio/28943090]]).
+
+ - The genome of _Halicephalobus mephisto_ is only 61.4 Mb (95% complete
+   according to BUSCO and CEGMA) ([[Weinstein and coll.,
+   2019|biblio/31754114]]).
+
+[[!inline pages="tagged(nematode)" limit=0]]

nematode
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index dd41624c..293c0f7a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -82,7 +82,9 @@ Genome
    2001|biblio/11752568]].  A 70.4 Mb genome "reference assembly" was later
    produced from the shotgun sequencing of sperm DNA from ~200 partially inbred
    males (11 successive sib-matings).  Two distinct haplotypes were found
-   ([[Denoeud et al., 2010|biblio/21097902]]).
+   ([[Denoeud et al., 2010|biblio/21097902]]).  In 2019, it is the smallest
+   sequenced chordate genome, but some [[nematodes|nematode]] have been found
+   with smaller genomes.
  - Other oikopleuid genomes have been sequenced by [[Naville and coll. (2019)|biblio/30880010]]:
    small genomes are also found in _O. longicauda_ (131 Mbp) and _F. borealis_ (91 Mbp).
    There is an apparent correlation between organism size and genome size:

inopinata
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index 1e99f97b..d7606f40 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged nematode"]]
 
+ - _C. inopinata_ travels from fig to fig on Ceratosolen pollinating wasps and
+   is specialised on both its prefered fig and wasp [[(Woodruff and Phillips,
+   2018)|biblio/30129423]].
+
 [[!inline pages="tagged(nematode)" actions="no" archive="yes"
 feedshow=10]]

creating tag page tags/nematode
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
new file mode 100644
index 00000000..1e99f97b
--- /dev/null
+++ b/tags/nematode.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged nematode"]]
+
+[[!inline pages="tagged(nematode)" actions="no" archive="yes"
+feedshow=10]]

nematode
diff --git a/biblio/30129423.mdwn b/biblio/30129423.mdwn
new file mode 100644
index 00000000..69f3fea7
--- /dev/null
+++ b/biblio/30129423.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps."]]
+[[!tag nematode]]
+
+Woodruff GC, Phillips PC.
+
+BMC Ecol. 2018 Aug 21;18(1):26. doi: 10.1186/s12898-018-0182-z.
+
+Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps.
+
+[[!pmid 30129423 desc="C. inopinata is travelling from fig to fig on Ceratosolen pollinating fig wasps.  It appears to be very specialised in both the fig species and the wasp species."]]

Formatting.
diff --git a/biblio/30166445.mdwn b/biblio/30166445.mdwn
index 320f0bb1..e7ecad1d 100644
--- a/biblio/30166445.mdwn
+++ b/biblio/30166445.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics."]]
+[[!meta title="Muller “Elements” in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics."]]
 [[!tag Drosophila chromosome variants review]]
 
 Schaeffer SW

Dans l'avion et le bus
diff --git a/biblio/30166445.mdwn b/biblio/30166445.mdwn
new file mode 100644
index 00000000..320f0bb1
--- /dev/null
+++ b/biblio/30166445.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics."]]
+[[!tag Drosophila chromosome variants review]]
+
+Schaeffer SW
+
+Genetics. 2018 Sep;210(1):3-13. doi:10.1534/genetics.118.301084
+
+Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics.
+
+[[!pmid 30166445 desc="Review"]]

Dans l'avion
diff --git a/biblio/28943090.mdwn b/biblio/28943090.mdwn
new file mode 100644
index 00000000..5298cf05
--- /dev/null
+++ b/biblio/28943090.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome Architecture and Evolution of a Unichromosomal Asexual Nematode."]]
+[[!tag genome chromosome]]
+
+Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC.
+
+Curr Biol. 2017 Oct 9;27(19):2928-2939.e6. doi:10.1016/j.cub.2017.08.038
+
+Genome Architecture and Evolution of a Unichromosomal Asexual Nematode.
+
+[[!pmid 28943090 desc="“By comparing divergence rates with those of Caenorhabditis, we estimate that the asexual clade originated ca. 18 mya”.  “We obtained a genome assembly of 158 Mb with an N50 of 124 kb”.  “the haploid size [...] is ~88 Mb”.  “~4% average difference between [heterozygous] alleles.”  “Genomic regions in D. pachys have generally maintained the same chro- mosomal identity since diverging from Caenorhabditis”.  “ we used macro- synteny with C. elegans to infer an ancestral chromosome iden- tity (ACD) for each D. pachys scaffold.”  “We identified specific patterns of rearrangements consistent with an order of ACD fusions.”  “The data [of reciprocal reaggangements between ACDs] thus allow us to propose that four ancestral chromosomes became fused in the order I-X-III-II”  “Telomeres are either absent from the D. pachys genome or are highly divergent from the ancestral telomeric sequence.”  “The combined absence of telomere sequences and mainte- nance proteins suggests a connection between chromosome fusion and loss of telomeres”.  “84% of homozygous regions localize to ACDs I and X, which are neighbors in the inferred chromosomal fusion”.  ”The reductional division during meiosis I is skipped; the two chromosomes condense but do not pair or synapse.”  “The phenotype of C. elegans rec-8 mutants is reminiscent of the modified meiosis in D. pachys. [...] rec-8 is one of the conserved meiosis genes that was not detected in the D. pachys and D. coronatus genomes”"]]

dessert
diff --git a/biblio/31754114.mdwn b/biblio/31754114.mdwn
new file mode 100644
index 00000000..e421c3cb
--- /dev/null
+++ b/biblio/31754114.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="The genome of a subterrestrial nematode reveals adaptations to heat"]]
+[[!tag genome]]
+
+Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K,
+Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR.
+
+Nat Commun. 2019 Nov 21;10(1):5268. doi:10.1038/s41467-019-13245-8
+
+The genome of a subterrestrial nematode reveals adaptations to heat
+
+[[!pmid 31754114 desc="“61.4 Mb comprising 880 scaffolds with N50 of 313 kb, though 90% of the sequence is encoded on just 193 scaffolds. ~95% complete according to BUSCO and CEGMA.”"]]

Café
diff --git a/biblio/24929830.mdwn b/biblio/24929830.mdwn
new file mode 100644
index 00000000..301feb8d
--- /dev/null
+++ b/biblio/24929830.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction."]]
+[[!tag genome chromosome]]
+
+Nat Genet. 2014 Jul;46(7):693-700. doi:10.1038/ng.3010
+
+Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton 
+JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman
+M.
+
+Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.
+
+[[!pmid 24929830 desc="Clustering scaffolds on the number of shared orthologs they have with scaffolds of a related species' genome identifies three chromosomes."]]