Dernières modifications :

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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 "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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-#| "avec parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003."
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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"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -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."
+#| "fr.html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été "
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+#| "que b) j'avais moi-même proposé quelque chose de similaire lors des "
+#| "[élections en 2010|https://www.debian.org/vote/2010/platforms/plessy]..."
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 "While the vote on init systems was being prepared, I thought about proposing "
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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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+#, no-wrap
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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
+#, fuzzy
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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 "
+#| "avec parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003."
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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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-#, fuzzy
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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"
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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+"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."]]

Avion
diff --git a/biblio/16586749.mdwn b/biblio/16586749.mdwn
new file mode 100644
index 00000000..db424b23
--- /dev/null
+++ b/biblio/16586749.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genetic Factors Affecting the Strength of Linkage in Drosophila."]]
+[[!tag Drosophila chromosome variants]]
+
+Proc Natl Acad Sci U S A. 1917 Sep;3(9):555-8 doi:10.1073/pnas.3.9.555
+
+Sturtevant AH
+
+Genetic Factors Affecting the Strength of Linkage in Drosophila.
+
+[[!pmid 16586749 desc="Chromosomal inversions (not recognised as such at the time) strongly reduce crossing overs in their vicinity."]]

LAVA elements.
diff --git a/biblio/25209798.mdwn b/biblio/25209798.mdwn
index 0c95e810..487e4faf 100644
--- a/biblio/25209798.mdwn
+++ b/biblio/25209798.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Gibbon genome and the fast karyotype evolution of small apes."]]
-[[!tag chromosome synteny evolution]]
+[[!tag chromosome synteny evolution repeat]]
 
 Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J,
 Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C,
@@ -20,4 +20,4 @@ Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679
 
 Gibbon genome and the fast karyotype evolution of small apes.
 
-[[!pmid 25209798 desc="“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”"]]
+[[!pmid 25209798 desc="“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”  Insertion of LAVA (3'-L1-AluS-VNTR-Alu-like-5') elements in genes related to cell division might have caused the accelerated evolution of the karyotype in gibbons."]]

OIST
diff --git a/biblio/31386470.mdwn b/biblio/31386470.mdwn
new file mode 100644
index 00000000..c90f5ec4
--- /dev/null
+++ b/biblio/31386470.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Error-Speed Correlations in Biopolymer Synthesis."]]
+[[!tag enzyme]]
+
+Chiuchiú D, Tu Y, Pigolotti S.
+
+Phys Rev Lett. 2019 Jul 19;123(3):038101. doi:10.1103/PhysRevLett.123.038101
+
+Error-Speed Correlations in Biopolymer Synthesis.
+
+[[!pmid 31386470 desc="The sign of the correlation can provide insight in the mechanism of the polymerisation.  Proofreading suppresses the speed-error correlation."]]

U12 not found in F. borealis either.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 16286552..dd41624c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -214,7 +214,8 @@ Genes and pathways
  - In line with the above, “There is no H2AX homolog in O. dioica.” (H2AX is
    implicated in DNA repair).  [[Moosmann and coll., 2011|biblio/21756361]]
  - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Marz
-   et al., 2008|biblio/19030770]]), [[Denoeud et al., 2010|biblio/21097902]]).
+   et al., 2008|biblio/19030770]]), [[Denoeud et al., 2010|biblio/21097902]]),
+   nor in _F. borealis_ ([[Henriet and coll., 2019|biblio/31543449]]).
    It is found in _Ciona_ but not in _C. elegans_ ([[Marz et al.,
    2008|biblio/19030770]]).
  - More than 50 % of the Rab family is lost ([[Coppola and coll., 2019|biblio/31028425]]):

Typo
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index 606174ae..f02c8785 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -5,7 +5,7 @@ _bibliography in progress..._
  - `last-postmask` ([[Frith, 2011|biblio/22205972]]): discards alignments that
    contain a significant amount of lower-case-masked sequences.
 
- - `last-split` ([[Frith and Kawaguchi, 2017|biblio/25994148]]): heuristic
+ - `last-split` ([[Frith and Kawaguchi, 2015|biblio/25994148]]): heuristic
    algorithm inspired by the “repeated matches algorithm” of Durbin and coll.
    (1998).  It searchs for an optimal set of local alignments (as opposed to a set
    of optimal local alignments).   Its output is also used by third-party tool

Caf∂e
diff --git a/biblio/10.1101_831495.mdwn b/biblio/10.1101_831495.mdwn
new file mode 100644
index 00000000..b21a6829
--- /dev/null
+++ b/biblio/10.1101_831495.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High throughput, error corrected Nanopore single cell transcriptome sequencing"]]
+[[!tag bioRxiv Nanopore single_cell]]
+
+Kevin Lebrigand, Virginie Magnone, Pascal Barbry and Rainer Waldmann
+
+Posted November 05, 2019
+
+High throughput, error corrected Nanopore single cell transcriptome sequencing
+
+[[!doi 10.1101/831495 desc="Sequences libraries with Illumina first, to find UMI and cell barcode sequences, and then sequences again with Nanopore."]]

scaffolders...
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 450bf877..9f9bd5b6 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -21,13 +21,13 @@ Nagarajan and Šikić, 2017|biblio/28100585]]).
 When coverage is too low for efficient reference-free assembly, related
 references can be used as a guide.  The Ragout software ([[Kolmogorov and
 coll., 2014|biblio/24931998]], [[Kolmogorov and coll., 2018|biblio/30341161]])
-can take multiple reference genomes to guide the assembly of one target.
-Polymorphisms unique to the target genome can be recovered, but chromosome
-fusions are typically hard to detect.  Compared to version 1, version 2 infers
-phylogenetic relationships between the reference genomes automatically.  An
-alterative reference-guided assembler, RagOO ([[Alonge and coll.,
-2019|biblio/31661016]]) is reported to be faster, but can only take a single
-reference.
+can take multiple reference genomes to guide the scaffolding of a target
+assembly.  Polymorphisms unique to the target genome can be recovered, but
+chromosome fusions are typically hard to detect.  Compared to version 1,
+version 2 infers phylogenetic relationships between the reference genomes
+automatically.  An alterative reference-guided scaffolder, RagOO ([[Alonge and
+coll., 2019|biblio/31661016]]) is reported to be faster, but can only take a
+single reference.
 
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for

Café
diff --git a/biblio/31661016.mdwn b/biblio/31661016.mdwn
new file mode 100644
index 00000000..b5641dba
--- /dev/null
+++ b/biblio/31661016.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RaGOO: fast and accurate reference-guided scaffolding of draft genomes."]]
+[[!tag assembly software]]
+
+Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC.
+
+Genome Biol. 2019 Oct 28;20(1):224. doi:10.1186/s13059-019-1829-6
+
+RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
+
+[[!pmid 31661016 desc="Aligns contigs to a reference genome with minimap2, and resolves structural variants with a modified version of Assemblytics that uses minimap2."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index d58f2667..450bf877 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -24,7 +24,10 @@ coll., 2014|biblio/24931998]], [[Kolmogorov and coll., 2018|biblio/30341161]])
 can take multiple reference genomes to guide the assembly of one target.
 Polymorphisms unique to the target genome can be recovered, but chromosome
 fusions are typically hard to detect.  Compared to version 1, version 2 infers
-phylogenetic relationships between the reference genomes automatically.
+phylogenetic relationships between the reference genomes automatically.  An
+alterative reference-guided assembler, RagOO ([[Alonge and coll.,
+2019|biblio/31661016]]) is reported to be faster, but can only take a single
+reference.
 
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for

Café
diff --git a/biblio/22265598.mdwn b/biblio/22265598.mdwn
new file mode 100644
index 00000000..313c6e8d
--- /dev/null
+++ b/biblio/22265598.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Three-dimensional folding and functional organization principles of the Drosophila genome."]]
+[[!tag Drosophila chromosome structure]]
+
+Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G.
+
+Cell. 2012 Feb 3;148(3):458-72. doi:10.1016/j.cell.2012.01.010
+
+Three-dimensional folding and functional organization principles of the Drosophila genome.
+
+[[!pmid 22265598 desc="Co-clustering of the centromeres."]]

Café
diff --git a/biblio/29148971.mdwn b/biblio/29148971.mdwn
new file mode 100644
index 00000000..eedf8dbb
--- /dev/null
+++ b/biblio/29148971.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo."]]
+[[!tag Drosophila chromosome structure]]
+
+Stadler MR, Haines JE, Eisen MB.
+
+Elife. 2017 Nov 17;6. pii: e29550. doi:10.7554/eLife.29550
+
+Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo.
+
+[[!pmid 29148971 desc="High-resolution Hi-C analysis of Drosophila chromosomes in Rabl conformation during embryogenesis.  “We propose a model in which insulators achieve domain separation by lowering the compaction ratio of bound chromatin, thereby converting the short lengths of insulator DNA (measured in base pairs) into large relative physical distances.”"]]

Simplification
diff --git a/biblio/16600568.mdwn b/biblio/16600568.mdwn
index 66893fe2..64e74f53 100644
--- a/biblio/16600568.mdwn
+++ b/biblio/16600568.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Differentially expressed transcripts from phenotypically identified olfactory sensory neurons."]]
-[[!tag olfaction promoter gene-structure]]
+[[!tag olfaction promoter]]
 [[!pmid 15682396 desc="Related OR genes can have a different intron-exon structure and even share promoters."]]
diff --git a/tags/gene-structure.mdwn b/tags/gene-structure.mdwn
deleted file mode 100644
index 54b2b35f..00000000
--- a/tags/gene-structure.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged gene-structure"]]
-
-[[!inline pages="tagged(gene-structure)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/29776991.mdwn b/biblio/29776991.mdwn
new file mode 100644
index 00000000..19643891
--- /dev/null
+++ b/biblio/29776991.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Inversion variants in human and primate genomes."]]
+[[!tag chromosome variants]]
+
+Catacchio CR, Maggiolini FAM, D'Addabbo P, Bitonto M, Capozzi O, Lepore Signorile M, Miroballo M, Archidiacono N, Eichler EE, Ventura M, Antonacci F.
+
+Genome Res. 2018 Jun;28(6):910-920. doi:10.1101/gr.234831.118
+
+Inversion variants in human and primate genomes.
+
+[[!pmid 29776991 desc="105 validation inversions between human and either chimpanzee, gorilla, orangutan, or macaque genomes, that range in size from 103 kb to 91 Mb."]]

Dans l'avion
diff --git a/biblio/30497373.mdwn b/biblio/30497373.mdwn
new file mode 100644
index 00000000..ed899729
--- /dev/null
+++ b/biblio/30497373.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies."]]
+[[!tag assembly software]]
+
+Roach MJ, Schmidt SA, Borneman AR.
+
+BMC Bioinformatics. 2018 Nov 29;19(1):460. doi:10.1186/s12859-018-2485-7
+
+Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.
+
+[[!pmid 30497373 desc="Aligns the reads to the draft genome in order to estimate coverage.  A bimodal distribution is expected: the 0.5× peak represents areas where both alleles are present in the assembly."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 9d5a0012..d58f2667 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -38,6 +38,10 @@ Relase notes of HM2 version 20180603 suggest to use “_HapCUT2 or other phasing
 tools to get the high-quality haplotype assembly based on the reference haploid
 assembly_”.
 
+Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an
+alternative to HaploMerger that takes read coverage into account when detecting
+potential haplotigs.
+
 SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis
 that most contact points are due to local (same-chromosome) proximity.  Version

normalisation
diff --git a/biblio/19624849.mdwn b/biblio/19624849.mdwn
index ad1cce3e..e539fa92 100644
--- a/biblio/19624849.mdwn
+++ b/biblio/19624849.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data."]]
-[[!tag tags CAGE power_law normalisation]]
+[[!tag sequence_tags CAGE power_law normalisation]]
 
 Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.
 
diff --git a/biblio/21543516.mdwn b/biblio/21543516.mdwn
index 15b323b6..fb31aac7 100644
--- a/biblio/21543516.mdwn
+++ b/biblio/21543516.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq."]]
-[[!tag STRT template_switching single_cell method transcriptome tags]]
+[[!tag STRT template_switching single_cell method transcriptome sequence_tags]]
 
 Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.
 
diff --git a/tags/tags.mdwn b/tags/tags.mdwn
deleted file mode 100644
index 1b8430b8..00000000
--- a/tags/tags.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged tags"]]
-
-[[!inline pages="tagged(tags)" actions="no" archive="yes"
-feedshow=10]]

More tags.
diff --git a/biblio/31649060.mdwn b/biblio/31649060.mdwn
index a38b3e53..bdaf0105 100644
--- a/biblio/31649060.mdwn
+++ b/biblio/31649060.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection."]]
-[[!tag variants]]
+[[!tag chromosome assembly variants]]
 
 Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L.
 

Normalise
diff --git a/biblio/16136133.mdwn b/biblio/16136133.mdwn
index aa16959c..85ee4448 100644
--- a/biblio/16136133.mdwn
+++ b/biblio/16136133.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication."]]
-[[!tag chromosome variations]]
+[[!tag chromosome variants]]
 
 Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ.
 
diff --git a/tags/variations.mdwn b/tags/variations.mdwn
deleted file mode 100644
index 47fe6435..00000000
--- a/tags/variations.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged variations"]]
-
-[[!inline pages="tagged(variations)" actions="no" archive="yes"
-feedshow=10]]

In the bus.
diff --git a/biblio/31649060.mdwn b/biblio/31649060.mdwn
new file mode 100644
index 00000000..a38b3e53
--- /dev/null
+++ b/biblio/31649060.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection."]]
+[[!tag variants]]
+
+Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L.
+
+Genome Res. 2019 Nov;29(11):1919-1928. doi:10.1101/gr.253435.119
+
+A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.
+
+[[!pmid 31649060 desc="Linkage analysis of 45,000 markers from 2 crosses with ~50 offsprings each confirmed that there are 26 linkage groups, and suggests ~1 recombination per chromosome pair at meiosis.  Recombination rate is lower towards centromeres.  This is in line with the known fact that 3 chromosomes are metacentric and the other are acrocentric.  When comparing with other fish species, genes tend to stay on the same chromosomes, but move within (like birds and invertebrates, but unlike mammals).  A 7.8-Mb region on chr12 with strange linkage desequilibrium pattern was shown to be an inversion between southern and northern individuals.  It may act as a supergene.  Genetic exchanges between both haplotypes is reduced by the inversion."]]

last-split
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index b0cb4e60..606174ae 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -7,8 +7,9 @@ _bibliography in progress..._
 
  - `last-split` ([[Frith and Kawaguchi, 2017|biblio/25994148]]): heuristic
    algorithm inspired by the “repeated matches algorithm” of Durbin and coll.
-   (1998).  Its output is also used by third-party tool NanoSV ([[Cretu and
-   coll., 2017|biblio/29109544]].
+   (1998).  It searchs for an optimal set of local alignments (as opposed to a set
+   of optimal local alignments).   Its output is also used by third-party tool
+   NanoSV ([[Cretu and coll., 2017|biblio/29109544]]).
 
  - `last-train` ([[Hamada, Ono, Asai and Frith, 2017|biblio/28039163]]):
    estimation of alignment parameters.

To read
diff --git a/biblio/31504804.mdwn b/biblio/31504804.mdwn
new file mode 100644
index 00000000..1a6c464e
--- /dev/null
+++ b/biblio/31504804.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA."]]
+[[!tag cap to_read]]
+
+Nucleic Acids Res. 2019 Nov 18;47(20):e130. doi:10.1093/nar/gkz751
+
+Wang J, Alvin Chew BL, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu
+CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC.
+
+Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA.
+
+[[!pmid 31504804 desc="CapQuant, to read"]]

One more phylogeny.
diff --git a/biblio/12116483.mdwn b/biblio/12116483.mdwn
new file mode 100644
index 00000000..c1c7457f
--- /dev/null
+++ b/biblio/12116483.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Urochordates are monophyletic within the deuterostomes."]]
+[[!tag Oikopleura tunicate]]
+
+Syst Biol. 2000 Mar;49(1):52-64 doi:10.1080/10635150050207384
+
+Swalla BJ, Cameron CB, Corley LS, Garey JR.
+
+Urochordates are monophyletic within the deuterostomes.
+
+[[!pmid 12116483 desc="Places appendicularians as sister to all other tunicates, but notes that long branches raise uncertaincies."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c717b238..16286552 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -39,13 +39,15 @@ Parasites: _Oodinium pouchetii_ and others.
 Phylogeny
 ---------
 
+ - 18S rDNA phylogeny of [[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
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
  - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]])
    and then 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
-   show that Oikopleuridae is basal to all other tunicates.
+   show that Oikopleuridae is sister to all other tunicates.
  - “The difference between coding sequences was considerably higher in
    comparisons between strains of different oceans than within the Bergen gene
    pool.  We ignore whether and how Oikopleura dioica is subdivided into multiple

Typo.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 9103cbcd..c717b238 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -21,7 +21,7 @@ Some links:
  - Études sur les Appendiculaires du Détroit de Messine, Hermann Fol, 1872
    ([[ark:/13960/t7fr0vj77|https://archive.org/details/cbarchive_100233_etudessurlesappendiculairesdud1821]]).
  - [A day in the life of an Oikopleura lab](http://thenode.biologists.com/day-life-oikopleura-lab/).
- - OSA2016 genome on aniseed: <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
+ - OSAKA2016 genome on aniseed: <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
 
 Food tested in laboratory (totally incomplete list): _Isochrysis galbana_ (5.5
 µm in size), _Tetraselmis suecica_ (9.5 µm), and the chlorophyte _Chlorella

creating tag page tags/experiment_design
diff --git a/tags/experiment_design.mdwn b/tags/experiment_design.mdwn
new file mode 100644
index 00000000..ae7a5322
--- /dev/null
+++ b/tags/experiment_design.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged experiment design"]]
+
+[[!inline pages="tagged(experiment_design)" actions="no" archive="yes"
+feedshow=10]]

Heard of at the ICSB2019
diff --git a/biblio/27180805.mdwn b/biblio/27180805.mdwn
new file mode 100644
index 00000000..f54dc076
--- /dev/null
+++ b/biblio/27180805.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Fast machine-learning online optimization of ultra-cold-atom experiments."]]
+[[!tag machine_learning experiment_design]]
+
+Sci Rep. 2016 May 16;6:25890. doi:10.1038/srep25890
+
+Wigley PB, Everitt PJ, van den Hengel A, Bastian JW, Sooriyabandara MA,
+McDonald GD, Hardman KS, Quinlivan CD, Manju P, Kuhn CC, Petersen IR, Luiten AN, 
+Hope JJ, Robins NP, Hush MR.
+
+Fast machine-learning online optimization of ultra-cold-atom experiments.
+
+[[!pmid desc="Primary paper for https://github.com/michaelhush/M-LOOP (Machine-learning online optimization package)"]]

Café
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1259ee44..9103cbcd 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -211,9 +211,9 @@ Genes and pathways
    and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
  - In line with the above, “There is no H2AX homolog in O. dioica.” (H2AX is
    implicated in DNA repair).  [[Moosmann and coll., 2011|biblio/21756361]]
- - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Martz
+ - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Marz
    et al., 2008|biblio/19030770]]), [[Denoeud et al., 2010|biblio/21097902]]).
-   It is found in _Ciona_ but not in _C. elegans_ ([[Martz et al.,
+   It is found in _Ciona_ but not in _C. elegans_ ([[Marz et al.,
    2008|biblio/19030770]]).
  - More than 50 % of the Rab family is lost ([[Coppola and coll., 2019|biblio/31028425]]):
    Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, RabX1 and the

Tyop
diff --git a/biblio/19030770.mdwn b/biblio/19030770.mdwn
index 0d62fc19..bb0f49be 100644
--- a/biblio/19030770.mdwn
+++ b/biblio/19030770.mdwn
@@ -1,4 +1,4 @@
-[[!meta title=""Evolution of spliceosomal snRNA genes in metazoan animals.]]
+[[!meta title="Evolution of spliceosomal snRNA genes in metazoan animals."]]
 [[!tag Oikopleura splicing]]
 
 J Mol Evol. 2008 Dec;67(6):594-607. doi:10.1007/s00239-008-9149-6

Café
diff --git a/biblio/19030770.mdwn b/biblio/19030770.mdwn
new file mode 100644
index 00000000..0d62fc19
--- /dev/null
+++ b/biblio/19030770.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=""Evolution of spliceosomal snRNA genes in metazoan animals.]]
+[[!tag Oikopleura splicing]]
+
+J Mol Evol. 2008 Dec;67(6):594-607. doi:10.1007/s00239-008-9149-6
+
+Marz M, Kirsten T, Stadler PF.
+
+Evolution of spliceosomal snRNA genes in metazoan animals.
+
+[[!pmid 19030770 desc="”The snRNAs of the minor spliceosome were in most cases single-copy genes.”  The minor spliceosome was not found in Oikopleura dioica, but it was found in Ciona. “SnRNA locations are not syntenically conserved, i.e., snRNA behave like mobile elements in their genomic context.” "]]

Café
diff --git a/biblio/31543449.mdwn b/biblio/31543449.mdwn
new file mode 100644
index 00000000..396eb71a
--- /dev/null
+++ b/biblio/31543449.mdwn
@@ -0,0 +1,17 @@
+[[!meta title="Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis."]]
+[[!tag Oikopleura intron]]
+
+Curr Biol. 2019 Oct 7;29(19):3193-3199.e4. doi:10.1016/j.cub.2019.07.092
+
+Henriet S, Colom Sanmartí B, Sumic S, Chourrout D.
+
+Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis.
+
+[[!pmid 31543449 desc="In Fritillaria borealis, most ancestral canonical
+introns were lost.  New introns with non-canonical splice sites were created by
+the insertion of MITEs (miniature inverted-repeat transposable elements) after
+TA sites.  Splicing of non-canonical introns can be inhibited with Pladienolide
+B.  Non-canonical introns of F. bor and O. dioica genes can not be spliced in
+HEK293T cells, but canonical introns can.  In ~90% of lariats from F. bor or O.
+dio, the branchpoint is an A.  Distance to 3′ splice site is similar in both
+species.  A single U2 spliceosome was found in F. bor."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 752a59d6..1259ee44 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -255,12 +255,17 @@ Transcriptome
  - “Maternal promoters in O. dioica were located on the X-chromosome more
    frequently than expected” ([[Danks et al, 2018|biblio/29482522]]).
  - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb, [[Denoeud et
-   al., 2010|biblio/21097902]]) and subjected to a large turnover: many ancestral
-   introns are lost, and many new species-specific introns found ([[Edvarsen et
-   al., 2004|biblio/15638456]]).  Introns are gained by insertion of transposon-like elements and
-   by reverse splicing, ([[Denoeud et al., 2010|biblio/21097902]]).  Larger introns tend
-   to be older, and among the large introns, the older contain repeat elements less frequently
-   than the newer ([[Denoeud et al., 2010|biblio/21097902]]). 
+   al., 2010|biblio/21097902]]) and subjected to a large turnover: many
+   ancestral introns are lost, and many new species-specific introns found
+   ([[Edvarsen et al., 2004|biblio/15638456]]).  Introns are gained by insertion
+   of transposon-like elements and by reverse splicing, ([[Denoeud et al.,
+   2010|biblio/21097902]]).  Larger introns tend to be older, and among the large
+   introns, the older contain repeat elements less frequently than the newer
+   ([[Denoeud et al., 2010|biblio/21097902]]).  In _Fritilaria borealis_, most
+   introns are derived from the insertion of MITE elements and are non-canonical
+   ([[Henriet and coll., 2019|biblio/31543449]]).
+ - HEK293T cells can only splice canonical _O. dioica_ (and _F. borealis_) introns,
+   but not the non-canonical ones ([[Henriet and coll., 2019|biblio/31543449]]).
  - 12 developmental stages were studied with tiling arrays by [[Danks et al., 2013|biblio/23185044]].
  - On the histone mRNAs, no purine-rich histone downstream element (HDE) was found
    by [[Chioda, Eskeland and Thompson in 2002|biblio/12446815]].

Typo
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index 7c171678..b94dae10 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -1,7 +1,7 @@
 [[!meta title="pages tagged microplastic"]]
 
 [[Oikopleura]] can ingest microplastics and participate to their sedimentation
-([[Katija and coll., 2017|28835922]], [[Choy and coll., 2019|biblio/31171833]]).
+([[Katija and coll., 2017|biblio/28835922]], [[Choy and coll., 2019|biblio/31171833]]).
 
 To do: read Furukawa M, Kawakami N, Oda K, Miyamoto K (2018) Acceleration of
 enzymatic degradation of poly(ethylene terephthalate) by surface coating with

Café sans café
diff --git a/biblio/31646721.mdwn b/biblio/31646721.mdwn
new file mode 100644
index 00000000..417a63bc
--- /dev/null
+++ b/biblio/31646721.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution."]]
+[[!tag microplastic enzyme]]
+
+EMBO Rep. 2019 Nov 5;20(11):e49365. doi:10.15252/embr.201949365
+
+Hiraga K, Taniguchi I, Yoshida S, Kimura Y, Oda K
+
+Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution.
+
+[[!pmid 31646721 desc="Cites that “the use of surfactants can enhance PET
+degradation at least by a factor of 120”.  Points that “isolation and analysis
+of other PET‐degrading organisms and enzymes from high‐salt environment are
+also important for the biodegradation of waste PET directly in the ocean”."]]
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index e43c1695..7c171678 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -1,4 +1,15 @@
 [[!meta title="pages tagged microplastic"]]
 
-[[!inline pages="tagged(microplastic)" actions="no" archive="yes"
-feedshow=10]]
+[[Oikopleura]] can ingest microplastics and participate to their sedimentation
+([[Katija and coll., 2017|28835922]], [[Choy and coll., 2019|biblio/31171833]]).
+
+To do: read Furukawa M, Kawakami N, Oda K, Miyamoto K (2018) Acceleration of
+enzymatic degradation of poly(ethylene terephthalate) by surface coating with
+anionic surfactants. Chem Sus Chem 11: 4018–4025
+
+Hiraga, Taniguchi, Yoshida, Kimura and Oda K proposed in
+[[2019|biblio/31646721]] that PET-degrading organisms can be the foundation for
+a biological recycling of plastic.  They also underlined that salt-tolerating
+enzymes would be needed for bioremediation of oceans.
+
+[[!inline pages="tagged(microplastic)" limit=0]]

Lu il y a longtemps.
diff --git a/biblio/25079858.mdwn b/biblio/25079858.mdwn
new file mode 100644
index 00000000..3f8da97d
--- /dev/null
+++ b/biblio/25079858.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tn5 transposase and tagmentation procedures for massively scaled sequencing projects."]]
+[[!tag transposase enzyme method]]
+
+Picelli S, Björklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R.
+
+Genome Res. 2014 Dec;24(12):2033-40. doi:10.1101/gr.177881.114
+
+Tn5 transposase and tagmentation procedures for massively scaled sequencing projects.
+
+[[!pmid 25079858 desc="Production and purification of the Tn5 transposase."]]

syntaxerror
diff --git a/biblio/29914971.mdwn b/biblio/29914971.mdwn
index 0405ef44..4d085a8e 100644
--- a/biblio/29914971.mdwn
+++ b/biblio/29914971.mdwn
@@ -1,4 +1,4 @@
-[[!meta title=""Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.]]
+[[!meta title="Epigenetic maintenance of topological domains in the highly rearranged gibbon genome."]]
 [[!tag to_read synteny]]
 
 Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L.

syntaxerror
diff --git a/biblio/25209798.mdwn b/biblio/25209798.mdwn
index f95f9b7a..0c95e810 100644
--- a/biblio/25209798.mdwn
+++ b/biblio/25209798.mdwn
@@ -20,4 +20,4 @@ Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679
 
 Gibbon genome and the fast karyotype evolution of small apes.
 
-[[!pmid 25209798 desc=""“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”]]
+[[!pmid 25209798 desc="“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”"]]

FFPE-seq
diff --git a/biblio/31649055.mdwn b/biblio/31649055.mdwn
new file mode 100644
index 00000000..23854b46
--- /dev/null
+++ b/biblio/31649055.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples."]]
+[[!tag nanoCAGE method template_switching manganese]]
+
+Genome Res. 2019 Oct 24. doi:10.1101/gr.249656.119
+
+Vahrenkamp JM, Szczotka K, Dodson MK, Jarboe EA, Soisson AP, Gertz J.
+
+FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
+
+[[!pmid 31649055 desc="Terminator, concatenation blocker, no manganese, indexes. Fails to cite our latest protocol."]]
diff --git a/tags/manganese.mdwn b/tags/manganese.mdwn
index 5aec4360..7b7ff5a9 100644
--- a/tags/manganese.mdwn
+++ b/tags/manganese.mdwn
@@ -1,4 +1,6 @@
 [[!meta title="pages tagged manganese"]]
 
-[[!inline pages="tagged(manganese)" actions="no" archive="yes"
-feedshow=10]]
+See [[template_switching]] for the effect of manganese addition on cap
+specificity of transcriptome methods.
+
+[[!inline pages="tagged(manganese)" limit=0]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index ece27413..351d4908 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -57,7 +57,8 @@ as a replacement for RNA.
 
  - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
    of the TSO, and therefore blocks concatenation
-   ([[Kapteyn et al., 2010|biblio/20598146]]).
+   ([[Kapteyn et al., 2010|biblio/20598146]]).  This was also used in
+   FFPEcap-seq ([[Vahrenkamp and coll., 2019|biblio/31649055]]).
 
 ### Effect of TSO concentration
 
@@ -73,9 +74,12 @@ as a replacement for RNA.
    concentration: 1 mM each.  [[Pinto & Lindblad (2010)|biblio/19837043]] also
    used manganese.
 
- - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
+ - [[Lee and coll. (2017)|biblio/28327113]] increased the efficiency of template
    switching non-capped molecules by increasing dNTPs to 2 mM and
    Mg<sup>2+</sup> to 9 mM.
 
+ - [[Vahrenkamp and coll. (2019)|biblio/31649055]] reported that addition of
+   1 mM manganese increases the formation of TSO concatenates and the fraction
+   of reads aliging to ribosomal sequences.
 
 [[!inline pages="tagged(template_switching)" limit=0]]

Café
diff --git a/biblio/25209798.mdwn b/biblio/25209798.mdwn
new file mode 100644
index 00000000..f95f9b7a
--- /dev/null
+++ b/biblio/25209798.mdwn
@@ -0,0 +1,23 @@
+[[!meta title="Gibbon genome and the fast karyotype evolution of small apes."]]
+[[!tag chromosome synteny evolution]]
+
+Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J,
+Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C,
+Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS,
+Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L,
+Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW,
+Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG,
+Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, 
+Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA,
+O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann 
+GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E,
+Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan
+SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF,
+Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC,
+Rogers J, Wilson RK, Gibbs RA.
+
+Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679
+
+Gibbon genome and the fast karyotype evolution of small apes.
+
+[[!pmid 25209798 desc=""“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 6dd88e5b..4ece1256 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -1,6 +1,11 @@
 [[!meta title="pages tagged synteny"]]
 
-[[Renschler and coll, (2019)|biblio/31601616]] found 20 synteny breakpoints
+[[Carbone and coll. (2014)|biblio/25209798]] found 96 gibbon–human synteny
+breakpoints (~30 per Gb), associated with segmental duplication or Alu element
+enrichment.  They often bore signatures of non-homology based mechanisms, and
+were enriched near CTCF-binding events.
+
+[[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints
 (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
 are highly significant”

To read
diff --git a/biblio/29914971.mdwn b/biblio/29914971.mdwn
new file mode 100644
index 00000000..0405ef44
--- /dev/null
+++ b/biblio/29914971.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=""Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.]]
+[[!tag to_read synteny]]
+
+Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L.
+
+Genome Res. 2018 Jul;28(7):983-997. doi:10.1101/gr.233874.117
+
+Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.
+
+[[!pmid desc="to read"]]

Café
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index ce49564f..6dd88e5b 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged synteny"]]
 
-[[!inline pages="tagged(synteny)" actions="no" archive="yes"
-feedshow=10]]
+[[Renschler and coll, (2019)|biblio/31601616]] found 20 synteny breakpoints
+(SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
+compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
+are highly significant”
+
+[[!inline pages="tagged(synteny)" limit=0]]

creating tag page tags/synteny
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
new file mode 100644
index 00000000..ce49564f
--- /dev/null
+++ b/tags/synteny.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged synteny"]]
+
+[[!inline pages="tagged(synteny)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/31601616.mdwn b/biblio/31601616.mdwn
new file mode 100644
index 00000000..a96cc4fe
--- /dev/null
+++ b/biblio/31601616.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling."]]
+[[!tag chromosome evolution synteny]]
+
+Renschler G, Richard G, Valsecchi CIK, Toscano S, Arrigoni L, Ramírez F, Akhtar A.
+
+Genes Dev. 2019 Oct 10. doi: 10.1101/gad.328971.119
+
+Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling.
+
+[[!pmid 31601616 desc="Found 20 synteny breakpoints (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons are highly significant”"]]

Encore au café
diff --git a/biblio/7739381.mdwn b/biblio/7739381.mdwn
new file mode 100644
index 00000000..e203d9b0
--- /dev/null
+++ b/biblio/7739381.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Molecular phylogeny and divergence times of drosophilid species."]]
+[[!tag Drosophila speciation]]
+
+Russo CA, Takezaki N, Nei M.
+
+Mol Biol Evol. 1995 May;12(3):391-404 doi:10.1093/oxfordjournals.molbev.a040214
+
+Molecular phylogeny and divergence times of drosophilid species.
+
+[[!pmid 7739381 desc="Study of Adh genes, nuclear 18S rRNA and mitochondrial
+DNA suggests that D. mel and D. pseudoobscura diverged 24.9 +/- 2.88 My ago,
+based on the assumption that D. picticornis and D. silvestris diverged 5.1 My
+ago."]]
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index 5ff9700f..5d7fe7f3 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -7,5 +7,9 @@ Analysis of Cox2 sequences of _Drosophila_ species by [[Beckenbach, Wei and Liu
 melanogaster_ and _D. pseudoobscura_ ~35 My ago.  Sequence divergence between
 _D. mel._ and members of the _D. obscura_ species group is in average of 11.4 %.
 
-[[!inline pages="tagged(Drosophila)" actions="no" archive="yes"
-feedshow=10]]
+A study of Adh genes, nuclear 18S rRNA and mitochondrial DNA ([[Russo, Takezaki
+and Nei  (1995)|biblio/7739381]]) suggests that D. mel and D. pseudoobscura
+diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and
+D. silvestris diverged 5.1 My ago.
+
+[[!inline pages="tagged(Drosophila)" limit=0]]

Normalise tags.
diff --git a/biblio/10.1111_jzs.12101.mdwn b/biblio/10.1111_jzs.12101.mdwn
index 51518745..22419adf 100644
--- a/biblio/10.1111_jzs.12101.mdwn
+++ b/biblio/10.1111_jzs.12101.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis."]]
-[[!tag Ciona species]]
+[[!tag Ciona speciation]]
 
 Brunetti, R. , Gissi, C. , Pennati, R. , Caicci, F. , Gasparini, F. and Manni, L. 
 
diff --git a/tags/species.mdwn b/tags/species.mdwn
deleted file mode 100644
index 99f657ba..00000000
--- a/tags/species.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged species"]]
-
-[[!inline pages="tagged(species)" actions="no" archive="yes"
-feedshow=10]]