Dernières modifications :

Merian elements
diff --git a/biblio/38383850.mdwn b/biblio/38383850.mdwn
new file mode 100644
index 00000000..7887a912
--- /dev/null
+++ b/biblio/38383850.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera."]]
+[[!tag synteny]]
+
+Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M.
+
+Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera.
+
+Nat Ecol Evol. 2024 Feb 21. doi:10.1038/s41559-024-02329-4
+
+[[!pmid  38383850 desc="“We assigned 4,112 orthologues (78%) to 32 ALGs: 31 autosomes and Z, the sex chromosome. Hereafter, we refer to these ALGs as Merian elements, named after the seventeenth-century lepidopterist and botanical artist, Maria Sibylla Merian”  ”Merian elements have remained intact in most species”  “Lepidopteran chromosomes arising from fusions retain syntenic domains that reflect the original elements. Remarkably, this includes the M17 + M20 fusion, which occurred ~200 million years ago”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 6672f561..70cb6be3 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -92,6 +92,10 @@ can be observed in fungi even when ITS sequences are 100% identical.
    bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/10.1101_2023.10.30.564762]]).
    Some clades there scrambled a lot, and some not (sea cucumbers).
 
+ - [[Wright and coll., 2024|biblio/38383850]] found 32 ALGs in lepidopteran,
+   which they termed Merian elements.  There is a case where scrambling has
+   not erased traces of a fusion that occured 200 million years ago.
+
 ### Computational aspects
 
  - [[Rocha (2003)|biblio/14585609]] defines a Gene Order Conservation (GOC)

microsynteny mixing score
diff --git a/biblio/10.1101_2024.02.15.580425.mdwn b/biblio/10.1101_2024.02.15.580425.mdwn
new file mode 100644
index 00000000..3df64157
--- /dev/null
+++ b/biblio/10.1101_2024.02.15.580425.mdwn
@@ -0,0 +1,12 @@
+[[!meta title=" Fusion, fission, and scrambling of the bilaterian genome in Bryozoa"]]
+[[!tag bioRxiv synteny]]
+
+Thomas D. Lewin, Isabel Jiah-Yih Liao, Mu-En Chen, John D. D. Bishop, Peter W. H. Holland, Yi-Jyun Luo
+
+bioRxiv 2024.02.15.580425; doi:10.1101/2024.02.15.580425
+
+Fusion, fission, and scrambling of the bilaterian genome in Bryozoa.
+
+[[!doi 10.1101/2024.02.15.580425 desc="Defines a “microsynteny mixing score” as
+1 minus the absolute value of the spearman correlation coefficient of the
+ranked positions of orthologous genes on orthologous chromosome pairs."]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 98f5d95b..6672f561 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -105,6 +105,11 @@ can be observed in fungi even when ITS sequences are 100% identical.
    that a given gene has its orthologue in a homologous chromosome of a related
    species.
 
+ - [[Lewin and coll., 2024|biblio/10.1101_2024.02.15.580425]] defined a
+   “microsynteny mixing score” as 1 minus the Spearman correlation coefficient
+   of the ranked positional indices of orthologous genes on orthologous
+   chromosomes.
+
  - “Chains” and “nets” of pairwise alignements between two genomes are described
    in [[Kent and coll, 2003|biblio/14500911]].
 

creating tag page tags/subgenome
diff --git a/tags/subgenome.mdwn b/tags/subgenome.mdwn
new file mode 100644
index 00000000..2d8d901a
--- /dev/null
+++ b/tags/subgenome.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged subgenome"]]
+
+[[!inline pages="tagged(subgenome)" actions="no" archive="yes"
+feedshow=10]]

miel alors
diff --git a/biblio/37335429.mdwn b/biblio/37335429.mdwn
new file mode 100644
index 00000000..29e0693e
--- /dev/null
+++ b/biblio/37335429.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey."]]
+[[!tag yeast synteny subgenome]]
+
+Jia SL, Zhang M, Liu GL, Chi ZM, Chi Z.
+
+Funct Integr Genomics. 2023 Jun 19;23(3):206. doi:10.1007/s10142-023-01127-8
+
+Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey.
+
+[[!pmid 37335429 desc="A new _Aureobasidium melanogenum_ strain that has two subgenomes that diverged ~10 million years ago."]]

bioRxiv published
diff --git a/biblio/10.1101_2020.11.25.392936.mdwn b/biblio/35762203.mdwn
similarity index 65%
rename from biblio/10.1101_2020.11.25.392936.mdwn
rename to biblio/35762203.mdwn
index 5d33692b..52de2f6c 100644
--- a/biblio/10.1101_2020.11.25.392936.mdwn
+++ b/biblio/35762203.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="Robotic Search for Optimal Cell Culture in Regenerative Medicine"]]
-[[!tag bioRxiv automation]]
+[[!tag automation]]
 
 Genki N. Kanda, Taku Tsuzuki, Motoki Terada, Noriko Sakai, Naohiro Motozawa, Tomohiro Masuda, Mitsuhiro Nishida, Chihaya T. Watanabe, Tatsuki Higashi, Shuhei A. Horiguchi, Taku Kudo, Motohisa Kamei, Genshiro A. Sunagawa, Kenji Matsukuma, Takeshi Sakurada, Yosuke Ozawa, Masayo Takahashi, Koichi Takahashi, Tohru Natsume
 
-bioRxiv 2020.11.25.392936; doi: https://doi.org/10.1101/2020.11.25.392936
+Elife. 2022 Jun 28;11:e77007. doi:10.7554/eLife.77007
 
 Robotic Search for Optimal Cell Culture in Regenerative Medicine
 
-[[!doi 10.1101/2020.11.25.392936  desc="Uses the Maholo LabDroid and Batch Bayesian optimization (BBO) to screen a 7-dimensions parameter space."]]
+[[!pmid 35762203 desc="Uses the Maholo LabDroid and Batch Bayesian optimization (BBO) to screen a 7-dimensions parameter space."]]

Clarkia
diff --git a/biblio/10.1111_j.1558-5646.1958.tb02962.x.mdwn b/biblio/10.1111_j.1558-5646.1958.tb02962.x.mdwn
new file mode 100644
index 00000000..75ab5c62
--- /dev/null
+++ b/biblio/10.1111_j.1558-5646.1958.tb02962.x.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid evolution in Clarkia"]]
+[[!tag ]]
+
+Harlan Lewis and Peter H. Raven
+
+Evolution, Volume 12, Issue 3, 1 September 1958, Pages 319–336 doi:10.1111/j.1558-5646.1958.tb02962.x
+
+Rapid evolution in Clarkia
+
+[[!doi 10.1111/j.1558-5646.1958.tb02962.x desc="Frequent translocations cause bridges and circles in meiosis of hybrids."]]
diff --git a/biblio/10100754.mdwn b/biblio/10100754.mdwn
index d7d8d55d..40491a3c 100644
--- a/biblio/10100754.mdwn
+++ b/biblio/10100754.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Comparison of T-cell receptor Jβ gene usage in spleen cells of different mouse strains."]]
-[[!tag J_segment TCR mouse β_chain]]
-[[!pmid 10100754 desc="“As a possible factor responsible for this skewed TCR Jβ gene usage, rearrangement itself may be crucial”."]]
+[[!tag TCR mouse β_chain]]
+[[!pmid 10100754 desc="“As a possible factor responsible for this skewed TCR J segment Jβ gene usage, rearrangement itself may be crucial”."]]
diff --git a/biblio/22579286.mdwn b/biblio/22579286.mdwn
index 17f97448..7d25e98d 100644
--- a/biblio/22579286.mdwn
+++ b/biblio/22579286.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Nuclear Envelope Budding Enables Large Ribonucleoprotein Particle Export during Synaptic Wnt Signaling."]]
-[[!tag RNA_granule]]
+[[!tag RNP_granules]]
 
 Cell. 2012 May 11;149(4):832-46.
 
diff --git a/tags/J_segment.mdwn b/tags/J_segment.mdwn
deleted file mode 100644
index 9899bfce..00000000
--- a/tags/J_segment.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged J segment"]]
-
-[[!inline pages="tagged(J_segment)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/RNA_granule.mdwn b/tags/RNA_granule.mdwn
deleted file mode 100644
index eefe9b02..00000000
--- a/tags/RNA_granule.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged RNA granule"]]
-
-[[!inline pages="tagged(RNA_granule)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index d23fcca7..db4d006f 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -89,6 +89,11 @@ Indel-seq ([[Min and coll., 2023|biblio/37402370]]) shows insertions at
 double-strand breaks originating from donor regions possibly single-stranded by
 transcription (R-loops) or repair.  Proximity and contact appear to be important.
 
+## Translocations
+
+Translocations are frequent in _Clarkia_ ([[Lewis and Raven,
+1958|biblio/10.1111_j.1558-5646.1958.tb02962.x]]).
+
 ## Software
 
  - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long

Plastics
diff --git a/biblio/10.1101_2024.01.10.574808.mdwn b/biblio/10.1101_2024.01.10.574808.mdwn
new file mode 100644
index 00000000..5baf93d3
--- /dev/null
+++ b/biblio/10.1101_2024.01.10.574808.mdwn
@@ -0,0 +1,8 @@
+[[!meta title=" Developmental toxicity of pre-production plastic pellets affects a large swathe of invertebrate taxa"]]
+[[!tag Oikopleura microplastic]]
+
+Eva Jimenez Guri, Periklis Paganos, Claudia La Vecchia, Giovanni Annona, Filomena Caccavale, M Dolores Molina, Alfonso Ferrandez-Roldan, Rory Daniel Donnellan, Federica Salatiello, Adam N Johnstone, Maria Concetta Eliso, Antonietta Spagnuolo, Cristian Canestro, Ricard Albalat, Jose M Martin-Duran, Elisabeth A Williams, Enrico D'Aniello, Maria Ina Arnone.
+
+bioRxiv 2024.01.10.574808; doi: https://doi.org/10.1101/2024.01.10.574808 
+
+[[!doi 10.1101/2024.01.10.574808 doi desc="_O. dioica's development_ less affected by leachates than other tested animals."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3c2a35be..5d18ecf7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -637,6 +637,8 @@ Ecology
    Example(s): _B. stygius_ ([[Katija and coll., 2017b|biblio/28835922]]).  3
    to 17 microplastic particles were found in sinking houses in the Monterey Bay
    [[Choy and coll., 2019|biblio/31171833]].
+ - The development of _O. dioica_ is comparatively less affected by microplastic leachates
+   than some other invertebrates ([[Guri and coll., 2024|10.1101_2024.01.10.574808]]).
  - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus
    ([[Lawrence and coll., 2018|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.

Cleanup, simplification, consolidation.
diff --git a/biblio/18615017.mdwn b/biblio/18615017.mdwn
index 03256b31..dc995b64 100644
--- a/biblio/18615017.mdwn
+++ b/biblio/18615017.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="High-resolution mapping of meiotic crossovers and non-crossovers in yeast."]]
-[[!tag Yeast chromosome microarray genetics]]
+[[!tag yeast chromosome microarray genetics]]
 
 Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM.
 
diff --git a/biblio/20937878.mdwn b/biblio/20937878.mdwn
index c66e29a9..7e6cf7d3 100644
--- a/biblio/20937878.mdwn
+++ b/biblio/20937878.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Cell-permeable Foxp3 protein alleviates autoimmune disease associated with inflammatory bowel disease and allergic airway inflammation."]]
-[[!tag lymphocyte FoxP3 Treg therapy]]
+[[!tag lymphocyte FoxP3 therapy]]
 [[!pmid 20937878 desc=""]]
diff --git a/biblio/22761473.mdwn b/biblio/22761473.mdwn
index 316bb186..72cc0c21 100644
--- a/biblio/22761473.mdwn
+++ b/biblio/22761473.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A New Approach to Simultaneously Quantify Both TCR α- and β-Chain Diversity after Adoptive Immunotherapy."]]
-[[!tag TCR clonotype]]
+[[!tag TCR repertoire]]
 
 Zhang M, Maiti S, Bernatchez C, Huls H, Rabinovich B, Champlin RE, Vence LM, Hwu P, Radvanyi L, Cooper LJ.
 
@@ -7,4 +7,4 @@ Clin Cancer Res. 2012 Sep 1;18(17):4733-42.
 
 A New Approach to Simultaneously Quantify Both TCR α- and β-Chain Diversity after Adoptive Immunotherapy.
 
-[[!pmid 22761473 desc="Using “NanoStrings” to count α and β segments."]]
+[[!pmid 22761473 desc="Using “NanoStrings” to count α and β segments.  Clonotypes"]]
diff --git a/biblio/22933635.mdwn b/biblio/22933635.mdwn
index 1e1e7216..2cd52b7e 100644
--- a/biblio/22933635.mdwn
+++ b/biblio/22933635.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The TCR repertoires of regulatory and conventional T cells specific for the same foreign antigen are distinct."]]
-[[!tag mouse Treg TCR α_chain repertoire]]
+[[!tag mouse lymphocyte TCR α_chain repertoire]]
 
 Relland LM, Williams JB, Relland GN, Haribhai D, Ziegelbauer J, Yassai M, Gorski J, Williams CB.
 
diff --git a/biblio/23290140.mdwn b/biblio/23290140.mdwn
index 63804636..ea7d2d1f 100644
--- a/biblio/23290140.mdwn
+++ b/biblio/23290140.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Generation of rejuvenated antigen-specific T cells by reprogramming to pluripotency and redifferentiation."]]
-[[!tag iPS T_cell reprogramming]]
+[[!tag iPS lymphocyte reprogramming]]
 
 Nishimura T, Kaneko S, Kawana-Tachikawa A, Tajima Y, Goto H, Zhu D, Nakayama-Hosoya K, Iriguchi S, Uemura Y, Shimizu T, Takayama N, Yamada D, Nishimura K, Ohtaka M, Watanabe N, Takahashi S, Iwamoto A, Koseki H, Nakanishi M, Eto K, Nakauchi H.
 
diff --git a/biblio/24156252.mdwn b/biblio/24156252.mdwn
index aa7583ed..4ee8ad75 100644
--- a/biblio/24156252.mdwn
+++ b/biblio/24156252.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Temporal dynamics and transcriptional control using single-cell gene expression analysis."]]
-[[!tag single_cell OSC CLST]]
+[[!tag single_cell OSC]]
 
 Kouno T, de Hoon M, Mar JC, Tomaru Y, Kawano M, Carninci P, Suzuki H, Hayashizaki Y, Shin JW.
 
diff --git a/biblio/27071608.mdwn b/biblio/27071608.mdwn
index f3103177..69fcb3b8 100644
--- a/biblio/27071608.mdwn
+++ b/biblio/27071608.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Bioanalyzer chips can be used interchangeably for many analyses of DNA or RNA."]]
-[[!tag Bioanalyzer method]]
+[[!tag size method]]
 
 Davies J, Denyer T, Hadfield J
 
diff --git a/biblio/28623350.mdwn b/biblio/28623350.mdwn
index 49d9f8db..c696260a 100644
--- a/biblio/28623350.mdwn
+++ b/biblio/28623350.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids."]]
-[[!tag trans-splicing method random priming.]]
+[[!tag trans-splicing method random_priming]]
 
 Cuypers B, Domagalska MA, Meysman P, Muylder G, Vanaerschot M, Imamura H, Dumetz F, Verdonckt TW, Myler PJ, Ramasamy G, Laukens K, Dujardin JC.
 
diff --git a/biblio/33093512.mdwn b/biblio/33093512.mdwn
index 9e32a576..ab2bc187 100644
--- a/biblio/33093512.mdwn
+++ b/biblio/33093512.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages."]]
-[[!tag RIKEN OIST nanoCAGE HPV]]
+[[!tag OIST nanoCAGE HPV]]
 
 Taguchi A, Nagasaka K, Plessy C, Nakamura H, Kawata Y, Kato S, Hashimoto K, Nagamatsu T, Oda K, Kukimoto I, Kawana K, Carninci P, Osuga Y, Fujii T.
 
diff --git a/biblio/8894123.mdwn b/biblio/8894123.mdwn
index 10498a0f..116cd5f8 100644
--- a/biblio/8894123.mdwn
+++ b/biblio/8894123.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Zipf-scaling behavior in the immune system."]]
-[[!tag T_cell repertoire scale-free]]
+[[!tag lymphocyte repertoire scale-free]]
 
 Burgos JD, Moreno-Tovar P.
 
diff --git a/tags/Bioanalyzer.mdwn b/tags/Bioanalyzer.mdwn
deleted file mode 100644
index 05e91ae0..00000000
--- a/tags/Bioanalyzer.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged Bioanalyzer"]]
-
-[[!inline pages="tagged(Bioanalyzer)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/CLST.mdwn b/tags/CLST.mdwn
deleted file mode 100644
index 4af404bc..00000000
--- a/tags/CLST.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged CLST"]]
-
-[[!inline pages="tagged(CLST)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/RIKEN.mdwn b/tags/RIKEN.mdwn
deleted file mode 100644
index b77112a6..00000000
--- a/tags/RIKEN.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged RIKEN"]]
-
-[[!inline pages="tagged(RIKEN)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/T_cell.mdwn b/tags/T_cell.mdwn
deleted file mode 100644
index 1244a948..00000000
--- a/tags/T_cell.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged T cell"]]
-
-[[!inline pages="tagged(T_cell)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/Treg.mdwn b/tags/Treg.mdwn
deleted file mode 100644
index 744bf6a9..00000000
--- a/tags/Treg.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged Treg"]]
-
-[[!inline pages="tagged(Treg)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/clonotype.mdwn b/tags/clonotype.mdwn
deleted file mode 100644
index 25e95135..00000000
--- a/tags/clonotype.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged clonotype"]]
-
-[[!inline pages="tagged(clonotype)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/priming..mdwn b/tags/priming..mdwn
deleted file mode 100644
index bee9db76..00000000
--- a/tags/priming..mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged priming."]]
-
-[[!inline pages="tagged(priming.)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/random.mdwn b/tags/random.mdwn
deleted file mode 100644
index ee7ac848..00000000
--- a/tags/random.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged random"]]
-
-[[!inline pages="tagged(random)" actions="no" archive="yes"
-feedshow=10]]

Forgot tagging.
diff --git a/biblio/37821828.mdwn b/biblio/37821828.mdwn
index 4d4c07a6..731154f7 100644
--- a/biblio/37821828.mdwn
+++ b/biblio/37821828.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny."]]
-[[!tag ]]
+[[!tag yeast synteny]]
 
 Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny.
 
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 74ea072d..98f5d95b 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -63,6 +63,9 @@ branched at the base of the animal tree.
 At equal evolutionary distance, yeast microsynteny is lower than in animals,
 but higher than in plants ([[Li and coll., 2022|biblio/36334587]]).
 
+Kobayashi and coll ([[2023|biblio/37821828]]) showed that large structural variations
+can be observed in fungi even when ITS sequences are 100% identical.
+
 ### Ancestral karyotpyes
 
  - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll.,

Dans l'avion.
diff --git a/biblio/38130951.mdwn b/biblio/38130951.mdwn
new file mode 100644
index 00000000..aa2e426b
--- /dev/null
+++ b/biblio/38130951.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Functional specialization of Aurora kinase homologs during oogenic meiosis in the tunicate Oikopleura dioica."]]
+[[!tag Oikopleura H3S28p H3S10p]]
+
+Feng H, Thompson EM.
+
+Front Cell Dev Biol. 2023 Dec 7;11:1323378. doi:10.3389/fcell.2023.1323378
+
+Functional specialization of Aurora kinase homologs during oogenic meiosis in the tunicate Oikopleura dioica.
+
+[[!pmid 38130951 desc="“a C-terminal GFP fusion [of OdAur1] was localized on centrosomes throughout mitosis”  “a commercial phospho-Aurora antibody that can recognize the phosphorylated forms of both Aurora1 and Aurora2 in O. dioica [localised] on centrosomes and chromosomes in prophase and metaphase, and on centrosomes and the central spindle in anaphase”  “This suggests that Aurora1 and Aurora2 in O. dioica represent the polar and equatorial forms of Aurora kinases”. “[Knockdown] suggests that Aurora1 is involved in promoting the progression of prometaphase I. In all the Aur2 KD oocytes, both H3-pS10 and H3-pS28 were absent, and chromosomes were decondensed, reminiscent of INCENPa knockdown phenotypes”"]]
diff --git a/tags/H3S28p.mdwn b/tags/H3S28p.mdwn
index 1963c8f2..c1ef8182 100644
--- a/tags/H3S28p.mdwn
+++ b/tags/H3S28p.mdwn
@@ -47,4 +47,8 @@ The rat monoclonal antibody (Abcam ab10543) stains the centromere-attracting
 body in _O. dioica_, Osaka lab. strain. ([[Nishida and coll.,
 2021|biblio/34755656]]), probably by cross-reactivity.
 
+In [[Feng and Thompson, 2023|biblio/38130951], the Abcam ab10543 antibody “was
+either spread along entire chromosomes in 38% of oocytes or enriched on
+centromeres in 62% of oocytes”.
+
 [[!inline pages="tagged(H3S28p)" limit=0]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index d95bb1a3..3c2a35be 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -261,6 +261,9 @@ Genes and pathways
  - 6 FGF genes were detected by Oulion, Bertrand and Escriva ([[2012|biblio/22919541]]).
  - _Eya_, _Pitx_, _Six1/2_, _Six3/6a_ and _Six3/6b_, with expression patterns supporting
    homology of larvacean and vertebrate placodes ([[Bassham and Postlethwait, 2005|biblio/16120641]]).
+ - There are two copies of Aurora, _OdAur1_ and _OdAur2_.  In meiosis, they
+   localise to the centrosomes and the spindle respectively ([[Feng and
+   Thompson, 2023|biblio/38130951]]).
 
 ### Lost
 

creating tag page tags/calcium
diff --git a/tags/calcium.mdwn b/tags/calcium.mdwn
new file mode 100644
index 00000000..b21e1368
--- /dev/null
+++ b/tags/calcium.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged calcium"]]
+
+[[!inline pages="tagged(calcium)" actions="no" archive="yes"
+feedshow=10]]

En avion
diff --git a/biblio/37821828.mdwn b/biblio/37821828.mdwn
new file mode 100644
index 00000000..4d4c07a6
--- /dev/null
+++ b/biblio/37821828.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny."]]
+[[!tag ]]
+
+Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny.
+
+BMC Genomics. 2023 Oct 11;24(1):609. doi:10.1186/s12864-023-09718-2.
+
+Kobayashi Y, Kayamori A, Aoki K, Shiwa Y, Matsutani M, Fujita N, Sugita T, Iwasaki W, Tanaka N, Takashima M.
+
+[[!pmid 37821828 desc="_Cutaneotrichosporon cavernicola_ sister species with same karyotype, ITS sequence similarity above the usual threshold for species boundaries, but scrambling of large-width regions.  “If [mating infertility caused by genome rearrangement] is universal, chromosome synteny should be considered the determinant of biological species”"]]

Tag fixup
diff --git a/biblio/15786810.mdwn b/biblio/15786810.mdwn
index 15b4888e..610f21c9 100644
--- a/biblio/15786810.mdwn
+++ b/biblio/15786810.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="cDNA library construction from a small amount of RNA: adaptor-ligation approach for two-round cRNA amplification using T7 and SP6 RNA polymerases."]]
-[[!tag ]]
+[[!tag library amplification]]
 
 Biotechniques. 2005 Mar;38(3):451-8.
 
diff --git a/biblio/26001965.mdwn b/biblio/26001965.mdwn
index dc319085..e73f2eac 100644
--- a/biblio/26001965.mdwn
+++ b/biblio/26001965.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing."]]
-[[!tag ]]
+[[!tag mRNA]]
 
 Peach SE, York K, Hesselberth JR.
 
diff --git a/biblio/31857067.mdwn b/biblio/31857067.mdwn
index 19b1826a..0d4aac24 100644
--- a/biblio/31857067.mdwn
+++ b/biblio/31857067.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica."]]
-[[!tag ]]
+[[!tag Oikopleura calcium]]
+
+Matsuo M, Onuma TA, Omotezako T, Nishida H.
 
 Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica.
 
 Dev Biol. 2020 Apr 15;460(2):155-163. doi:10.1016/j.ydbio.2019.12.005
 
-Matsuo M, Onuma TA, Omotezako T, Nishida H.
-
 [[!pmid 31857067 desc="“PP2A is essential for the maintenance of meiotic arrest and prevention of parthenogenesis at spawning event in O. dioica. When PP2Ac is lost, the pH rise at spawning brings about an aberrant Ca burst by still unknown molecular mechanisms, and it activates eggs via CaMK II, reinitiates meiosis, and eventually results in improper initiation of embryogenesis.” Okadaic acid also induced parthenogenesis.  Termination of parthenogenetic migth be explain by failure to complete the cleavages because of the absence of the centrosome that should have been brought by the sperm."]]
diff --git a/biblio/m088p297.mdwn b/biblio/m088p297.mdwn
index 859a8104..a12defd4 100644
--- a/biblio/m088p297.mdwn
+++ b/biblio/m088p297.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Lipid and lipid class content of the pelagic tunicate Oikopleura vanhoeffeni"]]
-[[!tag ]]
+[[!tag Oikopleura ]]
 
 Deibel, D., Cavaletto, J. F., Riehl, M., Gardner, W. S.
 

En avion
diff --git a/biblio/37945377.mdwn b/biblio/37945377.mdwn
new file mode 100644
index 00000000..32645c12
--- /dev/null
+++ b/biblio/37945377.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The human genome contains over a million autonomous exons."]]
+[[!tag splicing]]
+
+Stepankiw N, Yang AWH, Hughes TR.
+
+Genome Res. 2023 Nov 9. doi:10.1101/gr.277792.123
+
+The human genome contains over a million autonomous exons.
+
+[[!pmid 37945377 desc="“∼4.2 billion paired end reads [...] mapped to ∼6 million clusters [which] encompassed ∼9% of the genome.”  “Internal exons from protein-coding genes [...] had an average of 10,636 reads, [...] encompassing 32% of all reads.”  “exon clusters with at least 100 reads [captured] 1,245,947 exons in total, encompassing 3.2% of the stranded genome (i.e., 6.2 Gb)“. “5.3% of all intergenic region bases [...] are part of a trapped exon [424,632], corresponding to an exon every 3311 bases on average”. “52% of GENCODE lncRNA internal exons were trapped with at least 100 reads, a figure comparable to that of mRNA internal exons (61%).”  “Known alternative cassette exons displayed, on average, 2.5-fold lower inclusion rates when compared to all internal mRNA exons.”  “the trapped exons are very significantly depleted from introns, but not the mRNA antisense strand, and trapped exons that are detected in introns tend to have low read counts”"]]

Café
diff --git a/biblio/10.1101_2023.10.30.564762.mdwn b/biblio/10.1101_2023.10.30.564762.mdwn
new file mode 100644
index 00000000..8146af0f
--- /dev/null
+++ b/biblio/10.1101_2023.10.30.564762.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The brittle star genome illuminates the genetic basis of animal appendage regeneration"]]
+[[!tag synteny]]
+
+bioRxiv 2023.10.30.564762; doi:10.1101/2023.10.30.564762
+
+Elise Parey, Olga Ortega-Martinez, Jérôme Delroisse, Laura Piovani, Anna Czarkwiani, David Dylus, Srishti Arya, Samuel Dupont, Michael Thorndyke, Tomas Larsson, Kerstin Johannesson, Katherine M. Buckley, Pedro Martinez, Paola Oliveri, Ferdinand Marlétaz
+
+The brittle star genome illuminates the genetic basis of animal appendage regeneration
+
+[[!doi 10.1101/2023.10.30.564762 desc="“We showed that the ‘Eleutherozoa Linkage Groups’ descend from a single fusion of ancestral bilaterian linkages (B2+C2).”  “Interestingly, sea cucumbers have the lowest rate of inter-chromosomal rearrangements, yet the most derived echinoderm body plan (Rahman et al. 2019), which highlights the uncoupling of global genomic rearrangements from morphological evolution.”  “In contrast with its sea star sister-group, the A. filiformis genome is highly rearranged: our analyses identified 26 inter-chromosomal rearrangements since the Eleutherozoa ancestor.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index f1b16968..74ea072d 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -85,6 +85,10 @@ but higher than in plants ([[Li and coll., 2022|biblio/36334587]]).
  - The ancestral bilaterian had 24 linkage groups according to [[Simakov and
    coll., 2022|biblio/35108053]].
 
+ - The Eleutherozoa Linkage Groups descend from a single fusion of ancestral
+   bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/10.1101_2023.10.30.564762]]).
+   Some clades there scrambled a lot, and some not (sea cucumbers).
+
 ### Computational aspects
 
  - [[Rocha (2003)|biblio/14585609]] defines a Gene Order Conservation (GOC)

Café
diff --git a/biblio/37947122.mdwn b/biblio/37947122.mdwn
new file mode 100644
index 00000000..7fafe168
--- /dev/null
+++ b/biblio/37947122.mdwn
@@ -0,0 +1,25 @@
+[[!meta title="The appendicularian Oikopleura dioica can enhance carbon export in a high CO2 ocean."]]
+[[!tag Oikopleura]]
+
+Taucher J, Lechtenbörger AK, Bouquet JM, Spisla C, Boxhammer T, Minutolo F, Bach LT, Lohbeck KT, Sswat M, Dörner I, Ismar-Rebitz SMH, Thompson EM, Riebesell U.
+
+The appendicularian _Oikopleura dioica_ can enhance carbon export in a high CO2 ocean.
+
+Glob Chang Biol. 2023 Nov 10:e17020. doi: 10.1111/gcb.17020.
+
+[[!pmid 37947122 desc=" “pelagic mesocosms [...], each extending to a depth of
+21 m (19 m cylindrical bag and 2 m full size/diameter conical sediment trap
+attached to the bottom of the bag) and enclosing about 60 m3 of the natural
+water column.”  “Average pCO2 during the experiment ranged between ~320
+(“ambient”) and 1700 μatm (“high CO2,” corresponding to a drop in pH by
+0.57 units compared to ambient conditions).”  “a custom-built net (50 μm mesh
+size; 20 cm in diameter) with a modified, non-filtering cod end (3.8 L clear
+polycarbonate beaker) and reduced towing speeds (0.15 m s−1) was applied in
+order to collect alive and undamaged O. dioica specimen.”  “The peak biomass of
+O. dioica was approximately twice as high in the high CO2 mesocosms (2.5 vs.
+1.3 μgC L−1) and occurred earlier (days 13–17) than under ambient conditions
+(day 21)”. “female O. dioica were cultured in mesocosm water (pre-filtered
+through a 50-μm mesh) of the respective CO2 conditions until they achieved
+maturity and produced eggs.”   “The fecundity of O. dioica was significantly
+elevated under lower pH, with females producing 278 (±107) eggs under ambient
+and 334 (±14) eggs in the OA treatment“"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ea44efba..d95bb1a3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -390,9 +390,11 @@ Development
    2014|biblio/24695788]]).
  - Meiosis is resumed by change of extracellular pH when the oocytes are released
    in seawater.  Partenogenesis starts if PP2A is inhibited by DNAi or with
-   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]).
+   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]]).
  - Colchicine treatment induced early differenciation of the oocytes
    ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
+ - In mesocosms under high-CO2 (low-pH) conditions, femals produce more eggs
+   (278 ±11 vs 334 ±14), Taucher and coll. ([[2023|biblio/37947122]]).
 
 ### Fertilization and early stages
 

Café
diff --git a/biblio/37989229.mdwn b/biblio/37989229.mdwn
new file mode 100644
index 00000000..e41c4776
--- /dev/null
+++ b/biblio/37989229.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The hydrodynamics and kinematics of the appendicularian tail underpin peristaltic pumping."]]
+[[!tag Oikopleura]]
+
+Hiebert TC, Gemmell BJ, von Dassow G, Conley KR, Sutherland KR.
+
+J R Soc Interface. 2023 Nov;20(208):20230404. doi:10.1098/rsif.2023.0404
+
+The hydrodynamics and kinematics of the appendicularian tail underpin peristaltic pumping.
+
+[[!pmid 37989229 desc="“Flow tracers consisted of live, unicellular microalgae. Rhinomonas reticulata was used for observations at low magnifications (4×) and Isochrysis galbana was used for observations at high magnifications (40×).”  “Our micro-videography confirms that the beating tail in O. dioica acts as a positive displacement peristaltic pump when filtering”   “Temperature had a significant effect on tail beat frequency, which increased by 366% from 5 to 25°C.”  “Likewise, inlet particle speeds increased with increasing temperature”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6c4d1336..ea44efba 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -581,6 +581,9 @@ House
  - Temperature and food availability increase house production from ~0.2 /h to ~0.4 / h
    ([[Fenaux 1985|biblio/WOSA1985AYN8600012]], of from ~0.4 /h to ~0.8 / h
    [[Sato, Tanaka and Ishimaru, 2001|biblio/10.1093_plankt_23.4.415]].
+ - The tail acts as a peristaltic pump to generate the flow in the house.  Tail
+   beat and particule speed increased with temperature (5, 15 and 25 ºC)
+   ([[Hiebert and coll., 2023|biblio/37989229]]).
 
 Phenotypes
 ----------

cocorrico
diff --git a/biblio/1571417125678584576.mdwn b/biblio/1571417125678584576.mdwn
new file mode 100644
index 00000000..5c630a82
--- /dev/null
+++ b/biblio/1571417125678584576.mdwn
@@ -0,0 +1,14 @@
+[[!meta title="Cycle vital d'un Appendiculaire Oikopleura dioica Fol, 1872 : description et chronologie"]]
+[[!tag Oikopleura]]
+
+Robert Fenaux
+
+Cycle vital d'un Appendiculaire _Oikopleura dioica_ Fol, 1872 : description et chronologie
+
+Ann. Inst. Oceanogr. Paris (1976) 52, 89-101 https://cir.nii.ac.jp/crid/1571417125678584576
+
+[[!url https://cir.nii.ac.jp/crid/1571417125678584576 desc="High sperm
+concentration leads to polyspermia, aborted cell divisions, and early
+developmental arrest.  Egg diameter between 97 and 107 µm.  The trunk / tail
+length ratio varies with age and can be matched with a Bertalanffy model.  Fed
+with _Nannochloris occulata_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index eea3da10..6c4d1336 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -367,6 +367,8 @@ Tools
 Development
 -----------
 
+### Gametes
+
  - 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]]).
@@ -378,18 +380,34 @@ Development
  - 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]]).
+ - Egg diameter in females from (probably) Villefranche-sur-mer: 97 to 107 µm
+   ([[Fenaux, 1976|biblio/1571417125678584576]]). 
+ - Increased food abundance increases egg number but does not change diameter nor
+   generation time ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).
+   Food reduction before day 4 causes growth arrest (GA), in which all cell cycles
+   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]]).
+ - Meiosis is resumed by change of extracellular pH when the oocytes are released
+   in seawater.  Partenogenesis starts if PP2A is inhibited by DNAi or with
+   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]).
+ - Colchicine treatment induced early differenciation of the oocytes
+   ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
+
+### Fertilization and early stages
+
  - The sperm's mitochondrion enters the oocyte together with the nucleus
    ([[Holland, Gorsky and Fenaux, 1988|biblio/10.1007_BF00312223]]).
  - 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]]).
- - Meiosis is resumed by change of extracellular pH when the oocytes are released
-   in seawater.  Partenogenesis starts if PP2A is inhibited by DNAi or with
-   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]).
  - 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]]).
+ - Fertilization in high sperm concentration leads to polyspermia
+   ([[Fenaux, 1976|biblio/1571417125678584576]]).
+
+### Other
+
  - 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
@@ -402,12 +420,6 @@ Development
    1995|biblio/10.1016_0022-0981_95_00004-B]]).  Tôkyô bay _O. dioica_ under
    laboratory condiditons:  6 days at 15°C, 4 days at 20°C and 3 days at 25°C
    ([[Sato, Tanaka and Ishimaru, 2001|biblio/10.1093_plankt_23.4.415]]).
- - Increased food abundance increases egg number but does not change diameter nor
-   generation time ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).
-   Food reduction before day 4 causes growth arrest (GA), in which all cell cycles
-   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]]).
  - Large animals (~5 mm body length) could be cultivated when provided with large
    amounts of food ([[Li and Zhang, 2021|biblio/10.1007_s00343-020-0071-0]]).
  - Telomeres are localised at the nuclear envelope and do not overlap with nuclear
@@ -746,6 +758,9 @@ Culture protocols (incomplete list):
 
 Food tested in laboratory (totally incomplete list):
 
+ - [[Fenaux 1976|biblio/1571417125678584576]] reported the use of [_Nanochloropsis oceanica_][]
+   (under the name _Nanochloris occulata_) (2 to 3 µm according to Wikipedia).
+
  - Flagellates [_Isochrysis galbana_][] (4 µm width) and _Monochrysis lutheri_ (4 µm
    width), and the diatom _Cyclotella nana_ (Thalassiosira pseudonana) which had
    a width of 5 µm ([[G.-A. Paffenhöfer, 1973|biblio/10.1007_BF00391782]]).
@@ -776,5 +791,6 @@ Food tested in laboratory (totally incomplete list):
 [_Rhinomonas reticulata_]:  https://en.wikipedia.org/wiki/Rhinomonas
 [_Synechococcus sp._]:      https://en.wikipedia.org/wiki/Synechococcus
 [_Tetraselmis suecica_]:    https://en.wikipedia.org/wiki/Tetraselmis_suecica
+[_Nanochloropsis oceanica_]: https://en.wikipedia.org/wiki/Nannochloropsis
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Curry
diff --git a/biblio/37819006.mdwn b/biblio/37819006.mdwn
new file mode 100644
index 00000000..c08cbcd2
--- /dev/null
+++ b/biblio/37819006.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution."]]
+[[!tag splicing]]
+
+Larue GE, Roy SW.
+
+Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution.
+
+Nucleic Acids Res. 2023 Nov 10;51(20):10884-10908. doi: 10.1093/nar/gkad797
+
+[[!pmid 37819006 desc="Reports possible loss of the minor spliceosome in the
+Dipteran clade Chironomidae (_Clunio marinus_, _Polypedilum vanderplanki_ and
+_Belgica antarctica_) and in the copepod crustaceans _Tigriopus californicus_
+and _Eurytemora affinis_."]]

Café
diff --git a/biblio/10.1016_j.slast.2023.10.004.mdwn b/biblio/10.1016_j.slast.2023.10.004.mdwn
new file mode 100644
index 00000000..c13fde4d
--- /dev/null
+++ b/biblio/10.1016_j.slast.2023.10.004.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Robotic cell processing facility for clinical research of retinal cell therapy"]]
+[[!tag robot]]
+
+Motoki Terada, Yu Kogawa, Yumiko Shibata, Michinori Kitagawa, Shinya Kato, Tomomitsu Iida, Tsuyoshi Yorimitsu, Akari Kato, Kenji Matsukuma, Tadao Maeda, Masayo Takahashi, Genki N. Kanda,
+
+SLAS Technology, 2023, ISSN 2472-6303, doi.org:10.1016/j.slast.2023.10.004
+
+Robotic cell processing facility for clinical research of retinal cell therapy
+
+[[!doi 10.1016/j.slast.2023.10.004 desc="10-day culture of iPS cells to be implanted in patients."]]

mito
diff --git a/biblio/10.1007_BF00312223.mdwn b/biblio/10.1007_BF00312223.mdwn
new file mode 100644
index 00000000..821fd471
--- /dev/null
+++ b/biblio/10.1007_BF00312223.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Fertilization in Oikopleura dioica (Tunicata, Appendicularia): Acrosome reaction, cortical reaction and sperm-egg fusion."]]
+[[!tag Oikopleura]]
+
+Holland, L.Z., Gorsky, G. & Fenaux, R.
+
+Zoomorphology 108, 229–243 (1988). doi:10.1007/BF00312223
+
+Fertilization in Oikopleura dioica (Tunicata, Appendicularia): Acrosome reaction, cortical reaction and sperm-egg fusion.
+
+[[!doi 10.1007/BF00312223 desc="“Males [...] were placed in cold (4° C) seawater to induce testicular rupture.”  “Each egg is about 80-100 µm in diameter and is surrounded by a thin vitelline layer 80-100 nm thick [...] There is an asymmetrical perivitelline space ranging from 2 to 7 µm in width”. “The maximal diameter of the chromosomes in our section is about 150 nm”. “By 60 s after insemination, when the egg is regaining its spherical shape, the sperm nucleus, centriole, axoneme and mitochondrion have moved into the egg cortex”. “Fertilization [...] occurs almost simultaneously throughout an egg population after the addition of sperm”. “The central cytoplasm of the unfertilized appendicularian egg contains a preponderance of multivesicular bodies and the periphery has alternating areas rich in mitochondria and rich in endoplasmic reticulum”. “the anterior portion of the nuclear envelope evaginates together with the acrosomal membrane and may help to stiffen the resulting acrosomal tubule. The lumen of the tubule, which is consequently lined by the nuclear envelope, contains some fine fibrils that extend back into the nucleus.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index fa7ea4e7..eea3da10 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -378,6 +378,8 @@ Development
  - 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 sperm's mitochondrion enters the oocyte together with the nucleus
+   ([[Holland, Gorsky and Fenaux, 1988|biblio/10.1007_BF00312223]]).
  - 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]]).
  - Meiosis is resumed by change of extracellular pH when the oocytes are released

syntaxserrorr
diff --git a/biblio/34824214.mdwn b/biblio/34824214.mdwn
index 4725c16d..fcc4b8b7 100644
--- a/biblio/34824214.mdwn
+++ b/biblio/34824214.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer"]
+[[!meta title="Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer"]]
 [[!tag genome synteny chromosome epigenetic evolution]]
 
 Yin Y, Fan H, Zhou B, Hu Y, Fan G, Wang J, Zhou F, Nie W, Zhang C, Liu L, Zhong Z, Zhu W, Liu G, Lin Z, Liu C, Zhou J, Huang G, Li Z, Yu J, Zhang Y, Yang Y, Zhuo B, Zhang B, Chang J, Qian H, Peng Y, Chen X, Chen L, Li Z, Zhou Q, Wang W, Wei F.

ANI
diff --git a/biblio/29506021.mdwn b/biblio/29506021.mdwn
index e3cb72ad..b527789a 100644
--- a/biblio/29506021.mdwn
+++ b/biblio/29506021.mdwn
@@ -7,4 +7,8 @@ Bioinformatics. 2018 Jul 15;34(14):2371-2375. doi:10.1093/bioinformatics/bty113
 
 Updating the 97% identity threshold for 16S ribosomal RNA OTUs.
 
-[[!pmid 29506021 desc="Following a benchmark on V4 regions of the 16S rRNA, proposes to raise the threshold to 99% or to just use sequence variants (also called ZOTUS, Zero-radius OTUs."]]
+[[!pmid 29506021 desc="Following a benchmark on V4 regions of the 16S rRNA,
+proposes to raise the threshold to 99% or to just use sequence variants (also
+called ZOTUS, Zero-radius OTUs.  Identity computed as the number of columns
+containing identical letters divided by the number of columns containing at
+least one letter."]]

Muntjak
diff --git a/biblio/34824214.mdwn b/biblio/34824214.mdwn
new file mode 100644
index 00000000..4725c16d
--- /dev/null
+++ b/biblio/34824214.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer"]
+[[!tag genome synteny chromosome epigenetic evolution]]
+
+Yin Y, Fan H, Zhou B, Hu Y, Fan G, Wang J, Zhou F, Nie W, Zhang C, Liu L, Zhong Z, Zhu W, Liu G, Lin Z, Liu C, Zhou J, Huang G, Li Z, Yu J, Zhang Y, Yang Y, Zhuo B, Zhang B, Chang J, Qian H, Peng Y, Chen X, Chen L, Li Z, Zhou Q, Wang W, Wei F.
+
+Nat Commun. 2021 Nov 25;12(1):6858. doi:10.1038/s41467-021-27091-0
+
+Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer
+
+[[!pmid 34824214 desc="“we identified the rapidly evolving genes (REGs) and positively selected genes (PSGs) in the _M. crinifrons_, _M. gongshanensis_, and _M. muntjak vaginalis_ with large fused chromosomes, as well in their common ancestor node. The results showed that the PSGs and REGs in these lineages are enriched in GOs and pathways related to the maintenance of genomic stability.”  “the occurrence/frequency of genomic rearrangements (>10 kb) of _M. crinifrons_ and _M. gongshanensis_ (3.06~3.89 events/Mb) are not significantly higher than those in _M. reevesi_, _E. davidianus_, and _C. albirostris_ (3.11~4.56 events/Mb)”"]]

creating tag page tags/publishing
diff --git a/tags/publishing.mdwn b/tags/publishing.mdwn
new file mode 100644
index 00000000..3f7655ae
--- /dev/null
+++ b/tags/publishing.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged publishing"]]
+
+[[!inline pages="tagged(publishing)" actions="no" archive="yes"
+feedshow=10]]

Tidy bioRxiv tags
diff --git a/biblio/29145518.mdwn b/biblio/29145518.mdwn
index 38ea5c74..9166c13c 100644
--- a/biblio/29145518.mdwn
+++ b/biblio/29145518.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The prehistory of biology preprints: A forgotten experiment from the 1960s."]]
-[[!tag bioRxiv]]
+[[!tag publishing]]
 
 Cobb M.
 
diff --git a/biblio/10.1101_2020.03.10.985549.mdwn b/biblio/33906962.mdwn
similarity index 95%
rename from biblio/10.1101_2020.03.10.985549.mdwn
rename to biblio/33906962.mdwn
index 791bf8ac..5b9cb08c 100644
--- a/biblio/10.1101_2020.03.10.985549.mdwn
+++ b/biblio/33906962.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants"]]
-[[!tag bioRxiv genome]]
+[[!tag genome]]
 
 Jing Xia, Aarthi Venkat, Karine Le Roch, Ferhat Ay and Jon P. Boyle
 

Café, avion, ...
diff --git a/biblio/10.1101_2023.07.18.549157v1.mdwn b/biblio/10.1101_2023.07.18.549157v1.mdwn
new file mode 100644
index 00000000..d46ce5e8
--- /dev/null
+++ b/biblio/10.1101_2023.07.18.549157v1.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory"]]
+[[!tag Oikopleura bioRxiv]]
+
+David Lagman, Anthony Leon, Nadia Cieminska, Wei Deng, Marios Chatzigeorgiou, Simon Henriet, Daniel Chourrout
+
+bioRxiv 2023.07.18.549157; doi:10.1101/2023.07.18.549157
+
+Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory
+
+[[!doi 2023.07.18.549157v1 desc="Knock-out of Pax37B and Pax37A using
+CRISPR-Cas9.  Pax37B is essential to the proper patterning of the oikoblastic
+epithelium but not Pax37A.  Based on the analysis of single-cell and
+transcriptomic data in Oikopleura and Ciona, the authors propose a parallel
+between oikoblastic cells in Oikopleura and the neuroepithelial cells that
+produce gluing collocytes in Ciona."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 774f1cac..fa7ea4e7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -464,7 +464,8 @@ Development
  - Endocycling cells show no polytenisation nor _in loco_ amplifications.  Deep invaginations
    of the nuclear envelopper are shown by simultaneous staining of DNA, RNA and membranes
    ([[Spada and coll., 2007|biblio/17288541]]).
-
+ - Knock-out of _Pax37B_ shows it is essential to the proper patterning of the oikoblastic
+   epithelium ([[Langma an coll., 2023|biblio/10.1101_2023.07.18.549157v1]]). 
 
 Anatomy
 -------

Dans le bus
diff --git a/biblio/29325078.mdwn b/biblio/29325078.mdwn
new file mode 100644
index 00000000..50ac319b
--- /dev/null
+++ b/biblio/29325078.mdwn
@@ -0,0 +1,21 @@
+[[!meta title="Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni."]]
+[[!tag nematode]]
+
+Ren X, Li R, Wei X, Bi Y, Ho VWS, Ding Q, Xu Z, Zhang Z, Hsieh CL, Young A, Zeng J, Liu X, Zhao Z.
+
+Nucleic Acids Res. 2018 Feb 16;46(3):1295-1307. doi:10.1093/nar/gkx1277
+
+Genomic basis of recombination suppression in the hybrid between _Caenorhabditis briggsae_ and _C. nigoni_.
+
+[[!pmid 29325078 desc="”the coding sequences of [the] one-to-one orthologs
+exhibited only around a 90% identity, and most of [the] introns and intergenic
+regions were not alignable” “we produced [15,157] one-to-one orthologous gene
+pairs between C. briggsae and C. nigoni.”  “we extracted all of the best hits
+between the two genomes that were >1 kb in size [and] observed over 400
+interchromosomal translocations”  “[we produced] produce homozygous viable
+introgressions representing ∼28% of the C. briggsae genome”   “We observed a
+significantly higher [alignment score] in recombination sites than in genomic
+background”  “Nearly half of the reduced genome in C. briggsae could be
+explained by its lost repeats relative to the C. nigoni genome. These
+differences in genome size and repeat content are expected to create gaps in
+the sequence alignment or make the syntenic sequences not alignable.”"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index 626da130..6d3c50ef 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -65,4 +65,8 @@ Nematode chromosomes have been called “Nigon elements” by [[Tandonnet and co
    of neighboring genes are rearranged in the selfers compared with 15.0% in the
    outcrossers)” ([[Stevens and coll., 2022|biblio/35348662]]).
 
+ - When comparing _C. briggsae_ and _C. nigoni_, most of the introns and
+   intergenic regions are not alignable.  The aligned regions are ~90%
+   identical ([[Ren and coll., 2018|biblio/29325078]]).
+
 [[!inline pages="tagged(nematode)" limit=0]]

Nigon elements
diff --git a/biblio/30770412.mdwn b/biblio/30770412.mdwn
new file mode 100644
index 00000000..5fe1c8e5
--- /dev/null
+++ b/biblio/30770412.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis."]]
+[[!tag nematode]]
+
+Tandonnet S, Koutsovoulos GD, Adams S, Cloarec D, Parihar M, Blaxter ML, Pires-daSilva A.
+
+Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis.
+
+G3 (Bethesda). 2019 Apr 9;9(4):1211-1230. doi: 10.1534/g3.119.0011
+
+[[!pmid 30770412 desc="Nigon elements"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index d79694c9..626da130 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -2,6 +2,9 @@
 
 ... in progress ...
 
+Nematode chromosomes have been called “Nigon elements” by [[Tandonnet and coll,
+2019|biblio/30770412]].
+
 ### _C. inopinata_
 
  - _C. inopinata_ was discovered in 2018 to be the closest species to _C.

Nematodes
diff --git a/biblio/31007946.mdwn b/biblio/31007946.mdwn
new file mode 100644
index 00000000..62c4cfcb
--- /dev/null
+++ b/biblio/31007946.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative genomics of 10 new _Caenorhabditis_ species."]]
+[[!tag nematode]]
+
+Stevens L, Félix MA, Beltran T, Braendle C, Caurcel C, Fausett S, Fitch D, Frézal L, Gosse C, Kaur T, Kiontke K, Newton MD, Noble LM, Richaud A, Rockman MV, Sudhaus W, Blaxter M.
+
+Evol Lett. 2019 Apr 2;3(2):217-236. doi:10.1002/evl3.110
+
+Comparative genomics of 10 new _Caenorhabditis_ species.
+
+[[!pmid 31007946 desc="“Phylogenetic relationships of 32 Caenorhabditis species”"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index 001fd69c..d79694c9 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -29,6 +29,10 @@
 
 ### Other nematodes
 
+ - A phylogeny of 32 _Caenorhabditis_ species shows [ (_briggsae_ | _nigoni_) |
+   (_latens_ | _remanei_) ] | (_elegans_ | _inopinata_) ([[Stevens and coll.,
+   2019|biblio/31007946]]).
+
  - _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]]).

rm refs
diff --git a/biblio/37726270.mdwn b/biblio/37726270.mdwn
index d427e9ce..491b1d5c 100644
--- a/biblio/37726270.mdwn
+++ b/biblio/37726270.mdwn
@@ -7,4 +7,4 @@ Nat Commun. 2023 Sep 19;14(1):5617. doi:10.1038/s41467-023-41220-x
 
 Evolutionary origin of genomic structural variations in domestic yaks.
 
-[[!pmid 37726270 desc="“assemblies were constructed for 6 wild and 15 domestic yaks”  “we used a uniform standard pipeline to annotate these 47 bovine genomes. We identified an average of 24,368 protein-coding genes for each assembly” “1,048,639 high-confidence SNPs were detected and used in phylogenetic analyses with the water buffalo genome as outgroup”  “We further constructed a species tree on the basis of 8428 single-copy core genes through selecting one representative individual of each species”  “Pangenomes were constructed for yaks and cattle and a super-pangenome for the 7 Bovini species. For the yak pangenome the total gene set approached saturation at n = 20. The percentages of core (present in all 22 genomes), near-core (present in 20–21 genomes) and variable (found in 1–19 genomes) gene families were 50.18, 10.91, 38.91%, respectively.”  “ In pairwise comparisons of the assemblies constituting the pangenome, each assembly possessed 123 to 2113 genes not present in the other genome”   we constructed a multi-assembly graph-based genome of the 47 genomes used in the phylogenomic and super-pangenome analyses. This comprised 3.14 gigabases (Gb) spread across 5,449,222 nodes (the number of fragments of sequences) and connected by 4,889,530 edges (the connections between nodes), with non-reference nodes spanning 387.0 Mb. The core (shared by all genomes), near-core (in 46 or 45 genomes) and variable nodes (in 44 or less samples) accounted for 60.8, 17.0, 22.2% of all nodes.”  “We detected SVs ( ≥ 50 bp) in the graph-based genome using the bubble popping algorithm of gfatools25 and retained 293,712 SVs (81.7% <500 bp, 99.76% <10 kb) that could be genotyped in the BosMut3.0 yak reference genome or at least one other genome”  “Next, we used the graph-genotyping software Vg (v1.36.0)26 on 386 bovines (233 yaks, 140 cattle, 4 bison, 8 wisent and one gaur, including the novel genome sequences for assembling the super-pangenome) for which resequencing data with >6× coverage were available (Supplementary Data 1, 2)2,3,8,20,21,27,28,29,30,31,32,33,34,35,36. This yielded 610,921 genotyped SVs, from which 57,432 were retained after quality filtering”"]]
+[[!pmid 37726270 desc="“assemblies were constructed for 6 wild and 15 domestic yaks”  “we used a uniform standard pipeline to annotate these 47 bovine genomes. We identified an average of 24,368 protein-coding genes for each assembly” “1,048,639 high-confidence SNPs were detected and used in phylogenetic analyses with the water buffalo genome as outgroup”  “We further constructed a species tree on the basis of 8428 single-copy core genes through selecting one representative individual of each species”  “Pangenomes were constructed for yaks and cattle and a super-pangenome for the 7 Bovini species. For the yak pangenome the total gene set approached saturation at n = 20. The percentages of core (present in all 22 genomes), near-core (present in 20–21 genomes) and variable (found in 1–19 genomes) gene families were 50.18, 10.91, 38.91%, respectively.”  “ In pairwise comparisons of the assemblies constituting the pangenome, each assembly possessed 123 to 2113 genes not present in the other genome”   we constructed a multi-assembly graph-based genome of the 47 genomes used in the phylogenomic and super-pangenome analyses. This comprised 3.14 gigabases (Gb) spread across 5,449,222 nodes (the number of fragments of sequences) and connected by 4,889,530 edges (the connections between nodes), with non-reference nodes spanning 387.0 Mb. The core (shared by all genomes), near-core (in 46 or 45 genomes) and variable nodes (in 44 or less samples) accounted for 60.8, 17.0, 22.2% of all nodes.”  “We detected SVs ( ≥ 50 bp) in the graph-based genome using the bubble popping algorithm of gfatools25 and retained 293,712 SVs (81.7% <500 bp, 99.76% <10 kb) that could be genotyped in the BosMut3.0 yak reference genome or at least one other genome”  “Next, we used the graph-genotyping software Vg (v1.36.0) on 386 bovines (233 yaks, 140 cattle, 4 bison, 8 wisent and one gaur, including the novel genome sequences for assembling the super-pangenome) for which resequencing data with >6× coverage were available. This yielded 610,921 genotyped SVs, from which 57,432 were retained after quality filtering”"]]

Café
diff --git a/biblio/37726270.mdwn b/biblio/37726270.mdwn
new file mode 100644
index 00000000..d427e9ce
--- /dev/null
+++ b/biblio/37726270.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolutionary origin of genomic structural variations in domestic yaks."]]
+[[!tag variants]]
+
+Liu X, Liu W, Lenstra JA, Zheng Z, Wu X, Yang J, Li B, Yang Y, Qiu Q, Liu H, Li K, Liang C, Guo X, Ma X, Abbott RJ, Kang M, Yan P, Liu J.
+
+Nat Commun. 2023 Sep 19;14(1):5617. doi:10.1038/s41467-023-41220-x
+
+Evolutionary origin of genomic structural variations in domestic yaks.
+
+[[!pmid 37726270 desc="“assemblies were constructed for 6 wild and 15 domestic yaks”  “we used a uniform standard pipeline to annotate these 47 bovine genomes. We identified an average of 24,368 protein-coding genes for each assembly” “1,048,639 high-confidence SNPs were detected and used in phylogenetic analyses with the water buffalo genome as outgroup”  “We further constructed a species tree on the basis of 8428 single-copy core genes through selecting one representative individual of each species”  “Pangenomes were constructed for yaks and cattle and a super-pangenome for the 7 Bovini species. For the yak pangenome the total gene set approached saturation at n = 20. The percentages of core (present in all 22 genomes), near-core (present in 20–21 genomes) and variable (found in 1–19 genomes) gene families were 50.18, 10.91, 38.91%, respectively.”  “ In pairwise comparisons of the assemblies constituting the pangenome, each assembly possessed 123 to 2113 genes not present in the other genome”   we constructed a multi-assembly graph-based genome of the 47 genomes used in the phylogenomic and super-pangenome analyses. This comprised 3.14 gigabases (Gb) spread across 5,449,222 nodes (the number of fragments of sequences) and connected by 4,889,530 edges (the connections between nodes), with non-reference nodes spanning 387.0 Mb. The core (shared by all genomes), near-core (in 46 or 45 genomes) and variable nodes (in 44 or less samples) accounted for 60.8, 17.0, 22.2% of all nodes.”  “We detected SVs ( ≥ 50 bp) in the graph-based genome using the bubble popping algorithm of gfatools25 and retained 293,712 SVs (81.7% <500 bp, 99.76% <10 kb) that could be genotyped in the BosMut3.0 yak reference genome or at least one other genome”  “Next, we used the graph-genotyping software Vg (v1.36.0)26 on 386 bovines (233 yaks, 140 cattle, 4 bison, 8 wisent and one gaur, including the novel genome sequences for assembling the super-pangenome) for which resequencing data with >6× coverage were available (Supplementary Data 1, 2)2,3,8,20,21,27,28,29,30,31,32,33,34,35,36. This yielded 610,921 genotyped SVs, from which 57,432 were retained after quality filtering”"]]

WFH
diff --git a/biblio/37277269.mdwn b/biblio/37277269.mdwn
new file mode 100644
index 00000000..69875eb4
--- /dev/null
+++ b/biblio/37277269.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Gelatinous larvacean zooplankton can enhance trophic transfer and carbon sequestration."]]
+[[!tag Oikopleura review]]
+
+Jaspers C, Hopcroft RR, Kiørboe T, Lombard F, López-Urrutia Á, Everett JD, Richardson AJ.
+
+Trends Ecol Evol. 2023 Oct;38(10):980-993. doi:10.1016/j.tree.2023.05.005
+
+Gelatinous larvacean zooplankton can enhance trophic transfer and carbon sequestration.
+
+[[!pmid 37277269 desc="Role of appendicularians in the biological pump to the
+sea floor.  “Larvacean shunt” in the food chain."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 4c1d660f..774f1cac 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -584,6 +584,8 @@ Phenotypes
 Ecology
 -------
 
+ - The ecological role of appendicularians was reviewed by [[Jaspers and coll,
+   2023|biblio/37277269]].
  - _O. dioica_ grazes on bacterioplankton, which can be a significant share
    of its own diet, but the grazing has only “minimal influence on the
    population dynamics of the free-living bacteria” ([[King, Hollibaugh and

add a tag
diff --git a/biblio/36867684.mdwn b/biblio/36867684.mdwn
index 3a99120f..9d8b2f7f 100644
--- a/biblio/36867684.mdwn
+++ b/biblio/36867684.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. "]]
-[[!tag genome clock]]
+[[!tag genome clock phylogeny]]
 
 Huang Z, Xu L, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis ED, Li G, Lin G, Zhang Q, Zhou Q. 
 

Café
diff --git a/biblio/37402370.mdwn b/biblio/37402370.mdwn
new file mode 100644
index 00000000..d51cc30d
--- /dev/null
+++ b/biblio/37402370.mdwn
@@ -0,0 +1,39 @@
+[[!meta title="Mechanisms of insertions at a DNA double-strand break."]]
+[[!tag variants]]
+
+Min J, Zhao J, Zagelbaum J, Lee J, Takahashi S, Cummings P, Schooley A, Dekker J, Gottesman ME, Rabadan R, Gautier J. 
+
+Mol Cell. 2023 Jul 20;83(14):2434-2448.e7. doi: 10.1016/j.molcel.2023.06.016
+
+Mechanisms of insertions at a DNA double-strand break.
+
+[[!pmid 37402370 desc="Indel-seq: double-strand breaks are induced with the
+AsiSI endonuclease or CRISPR, and a target locus is studied by targeted
+sequencing of PCR amplicons.  “the median size of inserts is 120 bp [...] 39%
+of inserts originate from repetitive sequences, including telomeres,
+centromeres, Alu, and retrotransposon elements”  “Inhibition [with NU7441] of
+DNA-PK catalytic activity [involved in NHEJ] significantly decreased insertion
+events. In contrast, the size and number of deletions increased.”  “POLQ
+inhibition did not reduce [...] insertions, indicating that insertions were
+largely independent of microhomology-mediated end joining (MMEJ)”  “Treatment
+with CK-666, a small-molecule inhibitor that stabilizes the Arp2/3 complex in
+an inactive conformation, resulted in a significant decrease in insertion
+events originating from AsiSI-proximal donor sequences”  “siRNA-mediated
+downregulation of RAD51 did not affect the overall number of insertions but
+dramatically [increased] distal (class 3) insertions”.  “8.7% of insertions
+originated from multiple genomic loci on different chromosomes”  “more than 70%
+of donor sequences originated from promoters and transcribed gene body regions”
+“Donor sequences are spread around the AsiSI sites and span the TSS; however,
+insertions preferentially originate from the transcribed side [...]. In
+contrast, donor sequences originating from AsiSI-cleaved DSBs within a gene
+body or distal intergenic regions did not show any bias”  ”[Insertions in] a
+Cas9 DSB near the TSS of the BCL6 locus in a [the OCI-Ly7 cell line] were
+markedly enriched in the direction of transcription.”  “alpha-amanitin
+decreased the frequency of insertions, preferentially those originating from
+promoter-proximal DSBs [...]. Furthermore, donor sequences in
+alpha-amanitin-treated cells were no longer preferentially derived from the
+transcribed side.” “[Upregulating transcription of telomeric repeat-containing
+RNA at telomerse via] FANCM downregulation resulted in a significant increase
+in telomeric insertions.”  “RNA-DNA hybrid disruption by RNaseH1 suppressed the
+bias of donor sequences that originate preferentially from the direction of
+transcription”"]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index c86aa2db..d23fcca7 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -83,6 +83,12 @@ the same transposon participate in an aberrant transposition event to a new
 site”.  They give an example where the two transposons are identical copies
 on sister chromatids in G2 phase.
 
+## Indels
+
+Indel-seq ([[Min and coll., 2023|biblio/37402370]]) shows insertions at
+double-strand breaks originating from donor regions possibly single-stranded by
+transcription (R-loops) or repair.  Proximity and contact appear to be important.
+
 ## Software
 
  - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long

Café
diff --git a/biblio/37407817.mdwn b/biblio/37407817.mdwn
new file mode 100644
index 00000000..054c1d2a
--- /dev/null
+++ b/biblio/37407817.mdwn
@@ -0,0 +1,22 @@
+[[!meta title="Hepatitis C virus RNA is 5'-capped with flavin adenine dinucleotide"]]
+[[!tag cap]]
+
+Sherwood AV, Rivera-Rangel LR, Ryberg LA, Larsen HS, Anker KM, Costa R, Vågbø CB, Jakljevič E, Pham LV, Fernandez-Antunez C, Indrisiunaite G, Podolska-Charlery A, Grothen JER, Langvad NW, Fossat N, Offersgaard A, Al-Chaer A, Nielsen L, Kuśnierczyk A, Sølund C, Weis N, Gottwein JM, Holmbeck K, Bottaro S, Ramirez S, Bukh J, Scheel TKH, Vinther J. Hepatitis C virus RNA is 5'-capped with flavin adenine dinucleotide. 
+
+Nature. 2023 Jul;619(7971):811-818. doi:10.1038/s41586-023-06301-3.
+
+Hepatitis C virus RNA is 5'-capped with flavin adenine dinucleotide.
+
+[[!pmid 37407817 desc="Arabidopsis thaliana Nudix pyrophosphohydrolase 23
+(AtNUDX23) decapping followed with adapter ligation results in libraries
+enriched in HCV(+) and HCV(-) RNAs.  75% of the HCV RNAs are capped and most of
+the rest is 5′ triphosphate.  FAD capping was not found in “bovine viral
+diarrhea virus (BVDV) and the ortho flavivirus tick-borne encephalitis virus
+(TBEV), both from the Flaviviridae family, as well as chikungunya virus
+(CHIKV), an alphavirus of the Togaviridae family“.  “no replication of
+JFH1-SGR-Feo was observed upon riboflavin depletion, whereas replication was
+rescued by supplementing exogenous riboflavin or FAD”  “inclusion of FAD as the
+priming nucleotide resulted in efficient de novo initiation of replication and
+production of an initiation product consisting of FAD linked to CMP”
+“Incubation of 5′-ppp RNA with recombinant NS5B and flavin mononucleotide (FMN)
+did not result in 5′-FAD capping”"]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 175d7267..4b5f3495 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -77,6 +77,9 @@ Atypical caps (work in progress)
  - Mass spectroscopy and molecular biology detected dinucleoside polyphosphate caps
    in bacteria ([[Hudeček and coll., 2020|biblio/32103016]]).
 
+ - Hepatitis C virus RNA is 5′-capped with flavin adenine dinucleotide
+   ([[Sherwood and coll., 2023|biblio/37407817]]).
+
 Cap physiology (work in progress)
 ---------------------------------
 

Ce matin
diff --git a/biblio/32761142.mdwn b/biblio/32761142.mdwn
new file mode 100644
index 00000000..d7488c72
--- /dev/null
+++ b/biblio/32761142.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="NCBI Taxonomy: a comprehensive update on curation, resources and tools."]]
+[[!tag taxonomy database]]
+
+Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I.
+
+Database (Oxford). 2020 Jan 1;2020:baaa062. doi:10.1093/database/baaa062
+
+NCBI Taxonomy: a comprehensive update on curation, resources and tools.
+
+[[!pmid 32761142 desc="83% of the know invertebrate species are still not in the database."]]

creating tag page tags/priming.
diff --git a/tags/priming..mdwn b/tags/priming..mdwn
new file mode 100644
index 00000000..bee9db76
--- /dev/null
+++ b/tags/priming..mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged priming."]]
+
+[[!inline pages="tagged(priming.)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/random
diff --git a/tags/random.mdwn b/tags/random.mdwn
new file mode 100644
index 00000000..ee7ac848
--- /dev/null
+++ b/tags/random.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged random"]]
+
+[[!inline pages="tagged(random)" actions="no" archive="yes"
+feedshow=10]]

Dans l'avion
diff --git a/biblio/28623350.mdwn b/biblio/28623350.mdwn
new file mode 100644
index 00000000..49d9f8db
--- /dev/null
+++ b/biblio/28623350.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids."]]
+[[!tag trans-splicing method random priming.]]
+
+Cuypers B, Domagalska MA, Meysman P, Muylder G, Vanaerschot M, Imamura H, Dumetz F, Verdonckt TW, Myler PJ, Ramasamy G, Laukens K, Dujardin JC.
+
+Sci Rep. 2017 Jun 16;7(1):3725. doi:10.1038/s41598-017-03987-0
+
+Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids.
+
+[[!pmidi 28623350 desc="1 µg total RNA reverse-transcribed with SuperScript III and 2 µM random primer (GTATAAGAGACAGNNNNNNN).  The RNA strand degraded with 2U RNAse H for 20 mi at 37 °C.  The DNA strand was purified with Agencourt AMPure XP beads.  0.6 mM of SL primer (TCAGTTTCTGTA) was annealed to 25 µL of DNA from the previous step in 1x NEB buffer at 98 °C for 5 minutes and cooled down to room temperature for min.  Second-strand synthesis with 5U Klenow fragment and 0.4 mM dNTPs in 50 µL at 37 °C for 60 minutes."]]
diff --git a/tags/random_priming.mdwn b/tags/random_priming.mdwn
index 8cc4d277..7a0b1d9a 100644
--- a/tags/random_priming.mdwn
+++ b/tags/random_priming.mdwn
@@ -1,4 +1,7 @@
 [[!meta title="pages tagged random priming"]]
 
-[[!inline pages="tagged(random_priming)" actions="no" archive="yes"
-feedshow=10]]
+Work in progress.
+
+ - 2 µM N7, 1 µg total RNA, SuperScript III ([[Cuypers and coll., 2017|biblio/28623350]]), 
+
+[[!inline pages="tagged(random_priming)" actions="no" limit=0]]

creating tag page tags/archaea
diff --git a/tags/archaea.mdwn b/tags/archaea.mdwn
new file mode 100644
index 00000000..ed4ddb19
--- /dev/null
+++ b/tags/archaea.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged archaea"]]
+
+[[!inline pages="tagged(archaea)" actions="no" archive="yes"
+feedshow=10]]

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
oburo
diff --git a/biblio/37307447.mdwn b/biblio/37307447.mdwn
new file mode 100644
index 00000000..4aa63d1a
--- /dev/null
+++ b/biblio/37307447.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease."]]
+[[!tag repeat]]
+
+Craig RJ
+
+Proc Natl Acad Sci U S A. 2023 Jun 20;120(25):e2301424120. doi:10.1073/pnas.2301424120
+
+Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease.
+
+[[!pmid 37307447 desc="Copy-and-paste mechanism.  The transposon has short tandem repeats at its end, inserts a short copy of its downstream sequences in the new copy, and creates an even shorter duplication of its insertion site."]]

Misudo
diff --git a/biblio/37313762.mdwn b/biblio/37313762.mdwn
new file mode 100644
index 00000000..74c6c3a4
--- /dev/null
+++ b/biblio/37313762.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolutionary traces of miniaturization in a giant-Comparative anatomy of brain and brain nerves in Bathochordaeus stygius (Tunicata, Appendicularia)."]]
+[[!tag Oikopleura]]
+
+Zemann B, Le MV, Sherlock RE, Baum D, Katija K, Stach T.
+
+J Morphol. 2023 Jul;284(7):e21598. doi:10.1002/jmor.21598
+
+Evolutionary traces of miniaturization in a giant-Comparative anatomy of brain and brain nerves in _Bathochordaeus stygius_ (Tunicata, Appendicularia).
+
+[[!pmid 37313762 desc="102 cells in the brain, a number comparable to one in _O. doica_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3791499b..404e868d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -487,6 +487,8 @@ Anatomy
    are lost in appendicularians ([[Ferrández-Roldán and coll., 2021|biblio/34789899]]).
  - A 3D reconstitution of hatchlings and jufeniles was done by SEM tomography by
    [[Nishida and coll., 2021|biblio/33649401]].
+ - The brain of _B. stygius_ contains a number of cells comparable to the one of
+   _O. dioica_ ([[Zemann and coll., 2003|biblio/37313762]]).
 
 Physiology
 ----------

List culture paper of Paffenhöfer, 1973
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3791499b..c0d7356e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -725,6 +725,7 @@ Laboratory culture
 
 Culture protocols (incomplete list):
 
+ - [[G.-A. Paffenhöfer, 1973|biblio/10.1007_BF00391782]].
  - [[Fenaux and Gorsky (1985)|biblio/art0358]] published a method using a
    helicoidal paddle to stir the culture.
  - Rotating vessels: [[Sato and coll, 1999|biblio/10005415955]].

radio taiso
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 12f886c3..f1b16968 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -55,7 +55,10 @@ chromosomes, but with randomized orders and orientations“ and call that
 phenomenon “mesosynteny”.
 
 Squid chromosomes still have synteny with scallop, but gene order is scrambled
-([[Albertin and coll., 2022|biblio/35508532]]).
+([[Albertin and coll., 2022|biblio/35508532]]).  Sets of syntenic orthologues
+present in separate chromosomes in some clades but irreversibly mixed in others
+allowed [[Schultz and coll. (2023)|biblio/37198475]] to predict that cnidarians
+branched at the base of the animal tree.
 
 At equal evolutionary distance, yeast microsynteny is lower than in animals,
 but higher than in plants ([[Li and coll., 2022|biblio/36334587]]).

Science is in the air...
diff --git a/biblio/26166067.mdwn b/biblio/26166067.mdwn
new file mode 100644
index 00000000..4fb52d73
--- /dev/null
+++ b/biblio/26166067.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes"]]
+[[!tag bacteria variants]]
+
+Matteo Cossu, Violette Da Cunha, Claire Toffano-Nioche, Patrick Forterre, Jacques Oberto
+
+Biochimie. 2015 Nov;118:313-21. doi:10.1016/j.biochi.2015.07.008
+
+Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes
+
+[[!pmid 26166067 desc="“The comparative genomics analysis presented here
+confirms the initial observation that Thermococcales chromosomes are highly
+rearranged. In these genomes, DNA sequence scrambling has reached such a high
+level that commonly observed prokaryotic chromosomal landmarks such as oriC and
+terC are no longer readily identifiable by measuring DNA composition
+biases.”"]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index fea90940..c86aa2db 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -67,7 +67,9 @@ The state of the art in bacterial genomics in 2000 was reviewed by
 
 A mixture of X-shaped dot-plot pattern and scrambling was reported by
 [[Zivanovic and coll. (2002)|biblio/11972326]] in a study of _Pyrococcus_
-genomes.
+genomes.  Scrambling in _Thermococcales_ appears to be fast enough that
+the usual compositional biases on both sides of the origin of replication
+do not have time to establish ([[Cossu and coll., 2015|biblio/26166067]]).
 
 ### Mechanism
 

Et ensuite, des râmen
diff --git a/biblio/11972326.mdwn b/biblio/11972326.mdwn
new file mode 100644
index 00000000..6793a9bf
--- /dev/null
+++ b/biblio/11972326.mdwn
@@ -0,0 +1,20 @@
+[[!meta title="Pyrococcus genome comparison evidences chromosome shuffling-driven evolution."]]
+[[!tag archaea variants]]
+
+Zivanovic Y, Lopez P, Philippe H, Forterre P.
+
+Nucleic Acids Res. 2002 May 1;30(9):1902-10. doi:10.1093/nar/30.9.1902
+
+Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. 
+
+[[!pmid 11972326 desc="“the extent of rearrangement that occurred after the
+three species diverged is much lower between _P. abyssi_ and _P. horikoshii_
+than between these two species and _P. furiosus_.”  “[In _P. furiosus_, the
+distribution of IS elements] is clearly non-random, since 16 of them are
+located near shuffled segments boundaries, five are in completely scrambled
+regions and only two are found within an undisturbed segment.”  “the AT3 skew
+was less upset than the word skew (here GGTT), which was itself, as expected,
+less perturbed than the gene orientation skew”.  Coding genes were weakly
+colinear with the replication direction in _P. abissi_ and P. horikoshii_,
+especially for highly expressed genes, but this correlation was less evident or
+absent for _P. furiosus_."]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index 4cd0a25e..fea90940 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -65,6 +65,10 @@ this phenomenon was confirmed by [[D'Iorio and Dewar, 2022|biblio/36261227]].
 The state of the art in bacterial genomics in 2000 was reviewed by
 [[Hughes|biblio/11380986]].
 
+A mixture of X-shaped dot-plot pattern and scrambling was reported by
+[[Zivanovic and coll. (2002)|biblio/11972326]] in a study of _Pyrococcus_
+genomes.
+
 ### Mechanism
 
 _Staggered breaks_ ([[Ranz and coll., 2007|bilbio/17550304]]) caused

Dans le train.
diff --git a/biblio/11380986.mdwn b/biblio/11380986.mdwn
new file mode 100644
index 00000000..50d61b35
--- /dev/null
+++ b/biblio/11380986.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes."]]
+[[!tag bacteria variants review]]
+
+Hughes D.
+
+Genome Biol. 2000;1(6):REVIEWS0006. doi: 10.1186/gb-2000-1-6-reviews0006.
+
+Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes.
+
+[[!pmid 11380986 desc="Review reporting that “almost all rearrangements conserve the axis of chromosome replication”."]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index 9826c13b..4cd0a25e 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -62,6 +62,8 @@ in dot-plots by [[Eisen and coll (2000)|biblio/11178265]] and [[Tillier and
 Collins (2000)|biblio/11017076]].  Both reports suggest that the patterns are
 generated by inversions centered on origins and termini.  The prevalence of
 this phenomenon was confirmed by [[D'Iorio and Dewar, 2022|biblio/36261227]].
+The state of the art in bacterial genomics in 2000 was reviewed by
+[[Hughes|biblio/11380986]].
 
 ### Mechanism
 

Assis dans un parc
diff --git a/biblio/11017076.mdwn b/biblio/11017076.mdwn
new file mode 100644
index 00000000..a0bc955f
--- /dev/null
+++ b/biblio/11017076.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="Genome rearrangement by replication-directed translocation."]]
+[[!tag bacteria variants]]
+
+Tillier ER, Collins RA
+
+Nat Genet. 2000 Oct;26(2):195-7. doi:10.1038/79918
+
+Genome rearrangement by replication-directed translocation.
+
+[[!pmid 11017076 desc="X-shaped patterns in whole-genome comparisons dot plots.
+“Single-gene inversions occurred at 12 of 44 boundaries [of repositioned blocks
+of genes] identified in _Chlamydia_, compared with only 13 local inversions
+adjacent to any of the 643 genes not at a boundary”  Proposes that
+origin-centered inversions caused by replication forks can generate the
+patterns."]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index 285f087a..9826c13b 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -58,10 +58,10 @@ inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
 human/mouse comparisons, median length 814. 
 
 In bacteria, rearrangements have been reported to generate a X-shaped pattern
-in dot-plots by [[Eisen and coll (2000)|biblio/11178265]].  The authors suggest
-that the patterns are generated by inversions centered on origins and termini.
-The prevalence of this phenomenon was confirmed by [[D'Iorio and Dewar,
-2022|biblio/36261227]].
+in dot-plots by [[Eisen and coll (2000)|biblio/11178265]] and [[Tillier and
+Collins (2000)|biblio/11017076]].  Both reports suggest that the patterns are
+generated by inversions centered on origins and termini.  The prevalence of
+this phenomenon was confirmed by [[D'Iorio and Dewar, 2022|biblio/36261227]].
 
 ### Mechanism
 

Dans le train
diff --git a/biblio/36261227.mdwn b/biblio/36261227.mdwn
new file mode 100644
index 00000000..65f63bcb
--- /dev/null
+++ b/biblio/36261227.mdwn
@@ -0,0 +1,18 @@
+[[!meta title="Replication-associated inversions are the dominant form of bacterial chromosome structural variation."]]
+[[!tag bacteria variants]]
+
+D'Iorio M, Dewar K.
+
+Life Sci Alliance. 2022 Oct 19;6(1):e202201434. doi:10.26508/lsa.202201434
+
+Replication-associated inversions are the dominant form of bacterial chromosome structural variation.
+
+[[!pmid 36261227 desc="“We assessed a total of 313 species that were
+represented by 10 or more complete genome sequences”  “A genoform in this work
+refers to a group of collinear chromosomal sequences within a species with at
+least 80% sequence similarity and without an inversion spanning more than 50
+Kb.”  “In Gammaproteobacteria, the species Haemophilus influenzae, Haemophilus
+parainfluenzae, and Mannheimia haemolytica all contained inversions that were
+predominantly located away from the replication origin. We also observed
+species that were consistently offset from symmetry in one direction such as in
+B. pertussis”"]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index 015b7c21..285f087a 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -60,6 +60,8 @@ human/mouse comparisons, median length 814.
 In bacteria, rearrangements have been reported to generate a X-shaped pattern
 in dot-plots by [[Eisen and coll (2000)|biblio/11178265]].  The authors suggest
 that the patterns are generated by inversions centered on origins and termini.
+The prevalence of this phenomenon was confirmed by [[D'Iorio and Dewar,
+2022|biblio/36261227]].
 
 ### Mechanism
 

Encore plus de café
diff --git a/biblio/11178265.mdwn b/biblio/11178265.mdwn
index 17aec71b..848e9444 100644
--- a/biblio/11178265.mdwn
+++ b/biblio/11178265.mdwn
@@ -7,4 +7,4 @@ Genome Biol. 2000;1(6):RESEARCH0011. doi:10.1186/gb-2000-1-6-research0011
 
 Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
 
-[[!pmid 11178265 desc="X-shaped pattern observed in line plots of pairwise comparisons between E. coli and V. cholerae, or Streptococcus or Mycobacterium species."]]
+[[!pmid 11178265 desc="X-shaped pattern observed in line plots of pairwise comparisons between E. coli and V. cholerae, or Streptococcus or Mycobacterium species.  The patterns might have been generated by inversions centered on origins and termini of replication."]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index a89e2583..015b7c21 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -58,7 +58,8 @@ inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
 human/mouse comparisons, median length 814. 
 
 In bacteria, rearrangements have been reported to generate a X-shaped pattern
-in dot-plots by [[Eisen and coll (2000)|biblio/11178265]].
+in dot-plots by [[Eisen and coll (2000)|biblio/11178265]].  The authors suggest
+that the patterns are generated by inversions centered on origins and termini.
 
 ### Mechanism
 

Café
diff --git a/biblio/11178265.mdwn b/biblio/11178265.mdwn
new file mode 100644
index 00000000..17aec71b
--- /dev/null
+++ b/biblio/11178265.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evidence for symmetric chromosomal inversions around the replication origin in bacteria."]]
+[[!tag variants bacteria]]
+
+Eisen JA, Heidelberg JF, White O, Salzberg SL.
+
+Genome Biol. 2000;1(6):RESEARCH0011. doi:10.1186/gb-2000-1-6-research0011
+
+Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
+
+[[!pmid 11178265 desc="X-shaped pattern observed in line plots of pairwise comparisons between E. coli and V. cholerae, or Streptococcus or Mycobacterium species."]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index 222faccd..a89e2583 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -57,6 +57,9 @@ inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
 [[Kent and coll., 2003|biblio/14500911]] reported 2 inversions per Mbp in
 human/mouse comparisons, median length 814. 
 
+In bacteria, rearrangements have been reported to generate a X-shaped pattern
+in dot-plots by [[Eisen and coll (2000)|biblio/11178265]].
+
 ### Mechanism
 
 _Staggered breaks_ ([[Ranz and coll., 2007|bilbio/17550304]]) caused

Café
diff --git a/biblio/37137302.mdwn b/biblio/37137302.mdwn
new file mode 100644
index 00000000..5b0ccce0
--- /dev/null
+++ b/biblio/37137302.mdwn
@@ -0,0 +1,29 @@
+[[!meta title="Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells"]]
+[[!tag yeast synthetic]]
+
+Gvozdenov Z, Barcutean Z, Struhl K
+
+Mol Cell. 2023 Apr 24:S1097-2765(23)00254-X. 10.1016/j.molcel.2023.04.010
+
+Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells
+
+[[!pmid 37137302 desc="Circular chromosome of 27 kbp comprising 18 kbp of random
+sequences.  “the major class of nucleosomes average 147 bp (range 143–180),
+i.e., the expected size”  “nucleosome occupancy on [the artificial chromosome]
+is 1.42-fold higher than on yeast genomic DNA”  “when compared with yeast
+genomic chromatin, [artificial] chro- matin is characterized by fewer
+[nucleotide-depleted regions], fewer highly positioned nucleosomes, and little
+nucleosome phasing, although nucleosome positioning is nonrandom.”
+“Transcription from all regions of random-sequence DNA leads to similar RNA
+levels that are roughly comparable to that of the majority of mRNA expressed
+from yeast genomic DNA”  “transcription from randomsequence DNA is more
+variable than from genomic DNA”  “decay rates of RNAs expressed from
+randomsequence DNA are 3-fold faster”  “RNAs expressed from [the artificial
+chrmosome] are polyadenylated throughout the entire region of random-sequence
+DNA”  “the choice of poly(A) sites by the cleavage/polyadenylation machinery is
+roughly similar for RNAs expressed from random-sequence and genomic DNAs.” “The
+50 isoform pattern from random-sequence DNA resembles that observed from yeast
+genomic regions not corresponding to 50 UTRs”  “The level of newly synthesized
+RNA from random-sequence DNA is in excellent accord with calculated estimates
+that only 10%–20% of elongating RNA Pol II molecules generate mRNAs, such the
+remaining 80%–90% represent transcriptional noise”"]]
diff --git a/tags/synthetic.mdwn b/tags/synthetic.mdwn
index 120fc94d..07a6d002 100644
--- a/tags/synthetic.mdwn
+++ b/tags/synthetic.mdwn
@@ -12,8 +12,12 @@ Example of neochromosome synthesis in yeast: [[Postma and coll., 2021|biblio/334
 
 Artificial genome scrambling in yeast 2.0 with loxPsym sites: [[Brooks and coll, 2022|biblio/35239377]].
 
+Artificial 18 kbp random chromosome in yeast: [[Gvozdenov, Barcutean and Struhl, 2023|biblio/37137302]].
+
 ## Pathway
 
-Increasing the copy number of the endogenous aldehyde dehydrogenase Hfd1 allowed [[Hu, Yu and Ye, 2022|biblio/35880393]] to obtain the best yield of conversion of retinol to retinoic acid..
+Increasing the copy number of the endogenous aldehyde dehydrogenase Hfd1
+allowed [[Hu, Yu and Ye, 2022|biblio/35880393]] to obtain the best yield of
+conversion of retinol to retinoic acid.
 
 [[!inline pages="tagged(synthethic)" limit=0]]

Dans l'avion
diff --git a/biblio/36161960.mdwn b/biblio/36161960.mdwn
new file mode 100644
index 00000000..38c577af
--- /dev/null
+++ b/biblio/36161960.mdwn
@@ -0,0 +1,33 @@
+[[!meta title="Evolution of the ancestral mammalian karyotype and syntenic regions."]]
+[[!tag synteny]]
+
+Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, Ryder OA, Steiner C, Houck ML, Hall S, Shiue L, Thomas S, Swale T, Daly M, Korlach J, Uliano-Silva M, Mazzoni CJ, Birren BW, Genereux DP, Johnson J, Lindblad-Toh K, Karlsson EK, Nweeia MT, Johnson RN; Zoonomia Consortium; Lewin HA.
+
+Proc Natl Acad Sci U S A. 2022 Oct 4;119(40):e2209139119. doi: 10.1073/pnas.2209139119
+
+Evolution of the ancestral mammalian karyotype and syntenic regions.
+
+[[!pmid 36161960 desc="Analyses the number of breakpoints between nodes of the
+phylogenetic tree, thanks to ancestral genome reconstruction.  “2 extant
+mammals (Dataset S1), representing all 19 eutherian, 3 marsupial, and the
+monotreme orders, were used to reconstruct ancestral karyotypes at 16 nodes of
+the mammalian phylogeny”  “We used DESCHRAMBLER to generate reconstructed
+ancestral chromosome fragments (RACFs) for each of 16 mammalian ancestors at
+300-kbp syntenic fragment (SF) resolution”  “The reconstructed mammalian
+ancestor karyotype has 19 autosomes plus X, except for the cattle genome-based
+reconstruction, which has two fewer chromosomes and the lowest total
+reconstruction length”  “The differences between the mammalian and therian (n =
+17 + X) ancestors’ chromosomes resulted from 96 chromosomal rearrangements over
+18 My.”  “The eutherian ancestor (n = 19 + X) is the most recent common
+ancestor of the three lineages represented by the reference genomes. Its
+karyotype evolved from that of the therian ancestor as a result of 124
+chromosomal rearrangements over 53 My.”  “We identified 323, 262, and 257 EBRs
+that occurred along the lineage from the mammalian ancestor to the human,
+sloth, and cattle genomes, respectively”  “Inversions were most frequent,
+accounting for 76 to 85% of all rearrangements identified for each lineage”
+“The highest number of interchromosomal rearrangements (i.e., fissions and
+fusions) was observed on the branch from the therian to the eutherian ancestor
+(n = 30)”  “We observed that 9 of 14 small MAMs have 1:1 orthology to chicken
+chromosomes (GGA) and reconstructed chromosomes of the avian and amniote
+ancestors”  “EBRs were found to have a significantly higher density of
+repeats”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index d9fd0d0f..12f886c3 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -62,7 +62,9 @@ but higher than in plants ([[Li and coll., 2022|biblio/36334587]]).
 
 ### Ancestral karyotpyes
 
- - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll., 2021|biblio/33408411]]).
+ - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll.,
+   2021|biblio/33408411]]), or 19 + X ([[Damas and coll.,
+   2022|biblio/36161960]]).
 
  - The ancestral chordate has 17 chromosomes according to amphioxus assemblies
   ([[Putnam and coll, 2008|biblio/18563158]], [[Simakov and coll., 2020|biblio/32313176]]).

Café
diff --git a/biblio/37198475.mdwn b/biblio/37198475.mdwn
new file mode 100644
index 00000000..9be501f8
--- /dev/null
+++ b/biblio/37198475.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ancient gene linkages support ctenophores as sister to other animals."]]
+[[!tag synteny]]
+
+Schultz DT, Haddock SHD, Bredeson JV, Green RE, Simakov O, Rokhsar DS. 
+
+Nature. 2023 May 17. doi:10.1038/s41586-023-05936-6
+
+Ancient gene linkages support ctenophores as sister to other animals.
+
+[[!pmid 37198475 desc="Gene linkages found in all metazoans and single-celled outgroups are irreversibly merged (fusion followed by mixing) in Porifera, Cnidaria and Bilateria, supporting the idea that Ctenophora are sister to them."]]

CAGE
diff --git a/biblio/10.1101_2023.04.27.538568.mdwn b/biblio/10.1101_2023.04.27.538568.mdwn
new file mode 100644
index 00000000..07acf6f9
--- /dev/null
+++ b/biblio/10.1101_2023.04.27.538568.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Abundant capped RNAs are derived from mRNA cleavage at 3’UTR G-Quadruplexes"]]
+[[!tag CAGE 3′_UTR]]
+
+Nejc Haberman, Holly Digby, Rupert Faraway, Rebecca Cheung, Andrew M Jobbins, Callum Parr, Kayoko Yasuzawa, Takeya Kasukawa, Chi Wai Yip, Masaki Kato, Hazuki Takahashi, Piero Carninci, Santiago Vernia, Jernej Ule, Christopher R Sibley, Aida Martinez-Sanchez, Boris Lenhard
+
+bioRxiv 2023.04.27.538568; doi:10.1101/2023.04.27.538568
+
+Abundant capped RNAs are derived from mRNA cleavage at 3’UTR G-Quadruplexes
+
+[[!doi 10.1101/2023.04.27.538568  desc="3′ peaks colocalising with a G-rich motif are now explained by AGO2-mediated cleavage of G-quadruplex regions and recapping.  The 3′ fragments and the mRNA did not localise equally in the cell when imaged by in-situ hybridisation."]]

po
diff --git "a/Debian/debi\303\242neries/markdown2.en.po" "b/Debian/debi\303\242neries/markdown2.en.po"
index 9773d7d7..da40e345 100644
--- "a/Debian/debi\303\242neries/markdown2.en.po"
+++ "b/Debian/debi\303\242neries/markdown2.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2023-05-11 00:02+0000\n"
-"PO-Revision-Date: 2023-05-11 08:58+0900\n"
+"PO-Revision-Date: 2023-05-11 09:03+0900\n"
 "Last-Translator: \n"
 "Language-Team: \n"
 "Language: en\n"
@@ -32,8 +32,7 @@ msgid "[[!tag Debian]]\n"
 msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta title=\"Plussez pour patcher Firefox pour afficher du Markdown ?\"]]\n"
+#, no-wrap
 msgid "[[!meta title=\"Plussez pour patcher Firefox pour afficher du Markdown.\"]]\n"
 msgstr "[[!meta title=\"Upvote to patch Firefox to render Markdown\"]]\n"
 

updated PO files
diff --git "a/Debian/debi\303\242neries/markdown2.en.po" "b/Debian/debi\303\242neries/markdown2.en.po"
index b85db619..9773d7d7 100644
--- "a/Debian/debi\303\242neries/markdown2.en.po"
+++ "b/Debian/debi\303\242neries/markdown2.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2023-05-10 23:51+0000\n"
+"POT-Creation-Date: 2023-05-11 00:02+0000\n"
 "PO-Revision-Date: 2023-05-11 08:58+0900\n"
 "Last-Translator: \n"
 "Language-Team: \n"
@@ -32,24 +32,27 @@ msgid "[[!tag Debian]]\n"
 msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta title=\"Plussez pour patcher Firefox pour afficher du Markdown ?\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta title=\"Plussez pour patcher Firefox pour afficher du Markdown ?\"]]\n"
+msgid "[[!meta title=\"Plussez pour patcher Firefox pour afficher du Markdown.\"]]\n"
 msgstr "[[!meta title=\"Upvote to patch Firefox to render Markdown\"]]\n"
 
 #. type: Plain text
 msgid ""
-"J'ai [[écrit auparavant|markdown]] que quand Firefox reçoit un fichier dont le type média est "
-"_text/markdown_, il le propose au téléchargement, alors que les autres navigateurs l'affichent "
-"comme un fichier texte."
+"J'ai [[écrit auparavant|markdown]] que quand Firefox reçoit un fichier dont "
+"le type média est _text/markdown_, il le propose au téléchargement, alors "
+"que les autres navigateurs l'affichent comme un fichier texte."
 msgstr ""
-"I [[previously wrote|markdown]] that when Firefox receives a file whose media type is _text/"
-"markdown_, it prompts the user to download it, whereas other browsers display rendered results."
+"I [[previously wrote|markdown]] that when Firefox receives a file whose "
+"media type is _text/markdown_, it prompts the user to download it, whereas "
+"other browsers display rendered results."
 
 #. type: Plain text
 msgid ""
-"Il est maintenant possible de plusser sur [connect.mozilla.org](https://connect.mozilla.org/t5/"
-"ideas/display-markdown-files/idi-p/6000)  pour demander que Firefox formatte le _markdown_ par "
-"défaut."
+"Il est maintenant possible de plusser sur [connect.mozilla.org](https://"
+"connect.mozilla.org/t5/ideas/display-markdown-files/idi-p/6000)  pour "
+"demander que Firefox formatte le _markdown_ par défaut."
 msgstr ""
-"Now it is possible to upvote a proposal on [connect.mozilla.org](https://connect.mozilla.org/"
-"t5/ideas/display-markdown-files/idi-p/6000) asking that Firefox renders Markdown by default."
+"Now it is possible to upvote a proposal on [connect.mozilla.org](https://"
+"connect.mozilla.org/t5/ideas/display-markdown-files/idi-p/6000) asking that "
+"Firefox renders Markdown by default."

Correction du titre.
diff --git "a/Debian/debi\303\242neries/markdown2.mdwn" "b/Debian/debi\303\242neries/markdown2.mdwn"
index 4191be52..cc9d9ceb 100644
--- "a/Debian/debi\303\242neries/markdown2.mdwn"
+++ "b/Debian/debi\303\242neries/markdown2.mdwn"
@@ -2,7 +2,7 @@
 [[!meta updated="Thu, 11 May 2023 08:43:33 +0900"]]
 [[!tag Debian]]
 
-[[!meta title="Plussez pour patcher Firefox pour afficher du Markdown ?"]]
+[[!meta title="Plussez pour patcher Firefox pour afficher du Markdown."]]
 
 J'ai [[écrit auparavant|markdown]] que quand Firefox reçoit un fichier dont le
 type média est _text/markdown_, il le propose au téléchargement, alors que les

upvote !
diff --git "a/Debian/debi\303\242neries/markdown2.en.po" "b/Debian/debi\303\242neries/markdown2.en.po"
index ad915ae4..b85db619 100644
--- "a/Debian/debi\303\242neries/markdown2.en.po"
+++ "b/Debian/debi\303\242neries/markdown2.en.po"
@@ -3,51 +3,53 @@
 # 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: 2023-05-10 23:51+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: 2023-05-11 08:58+0900\n"
+"Last-Translator: \n"
+"Language-Team: \n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"X-Generator: Poedit 3.2.2\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Thu, 11 May 2023 08:43:33 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Thu, 11 May 2023 08:43:33 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Thu, 11 May 2023 08:43:33 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Thu, 11 May 2023 08:43:33 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
-msgid ""
-"[[!meta title=\"Plussez pour patcher Firefox pour afficher du "
-"Markdown ?\"]]\n"
-msgstr ""
+msgid "[[!meta title=\"Plussez pour patcher Firefox pour afficher du Markdown ?\"]]\n"
+msgstr "[[!meta title=\"Upvote to patch Firefox to render Markdown\"]]\n"
 
 #. type: Plain text
 msgid ""
-"J'ai [[écrit auparavant|markdown]] que quand Firefox reçoit un fichier dont "
-"le type média est _text/markdown_, il le propose au téléchargement, alors "
-"que les autres navigateurs l'affichent comme un fichier texte."
+"J'ai [[écrit auparavant|markdown]] que quand Firefox reçoit un fichier dont le type média est "
+"_text/markdown_, il le propose au téléchargement, alors que les autres navigateurs l'affichent "
+"comme un fichier texte."
 msgstr ""
+"I [[previously wrote|markdown]] that when Firefox receives a file whose media type is _text/"
+"markdown_, it prompts the user to download it, whereas other browsers display rendered results."
 
 #. type: Plain text
 msgid ""
-"Il est maintenant possible de plusser sur "
-"[connect.mozilla.org](https://connect.mozilla.org/t5/ideas/display-markdown-files/idi-p/6000)  "
-"pour demander que Firefox formatte le _markdown_ par défaut."
+"Il est maintenant possible de plusser sur [connect.mozilla.org](https://connect.mozilla.org/t5/"
+"ideas/display-markdown-files/idi-p/6000)  pour demander que Firefox formatte le _markdown_ par "
+"défaut."
 msgstr ""
+"Now it is possible to upvote a proposal on [connect.mozilla.org](https://connect.mozilla.org/"
+"t5/ideas/display-markdown-files/idi-p/6000) asking that Firefox renders Markdown by default."

updated PO files
diff --git "a/Debian/debi\303\242neries/markdown2.en.po" "b/Debian/debi\303\242neries/markdown2.en.po"
new file mode 100644
index 00000000..ad915ae4
--- /dev/null
+++ "b/Debian/debi\303\242neries/markdown2.en.po"
@@ -0,0 +1,53 @@
+# 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: 2023-05-10 23:51+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Thu, 11 May 2023 08:43:33 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Thu, 11 May 2023 08:43:33 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"[[!meta title=\"Plussez pour patcher Firefox pour afficher du "
+"Markdown ?\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'ai [[écrit auparavant|markdown]] que quand Firefox reçoit un fichier dont "
+"le type média est _text/markdown_, il le propose au téléchargement, alors "
+"que les autres navigateurs l'affichent comme un fichier texte."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Il est maintenant possible de plusser sur "
+"[connect.mozilla.org](https://connect.mozilla.org/t5/ideas/display-markdown-files/idi-p/6000)  "
+"pour demander que Firefox formatte le _markdown_ par défaut."
+msgstr ""
diff --git a/Joules.en.po b/Joules.en.po
index e0ffd0e2..51cf028b 100644
--- a/Joules.en.po
+++ b/Joules.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2023-05-09 13:37+0000\n"
+"POT-Creation-Date: 2023-05-10 23:51+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"
@@ -43,6 +43,39 @@ msgid ""
 "Joules) sur Framapiaf."
 msgstr ""
 
+#. type: Title ##
+#, no-wrap
+msgid "En bref, par an:"
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid "Travail: 100 ~ 350 GJ."
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid "Avion: 20 ~ 40 GJ."
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid "Voiture: 10 ~ 15 GJ."
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid "Électricité: 5 GJ."
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid "Nourriture (métabolisme): 3 GJ."
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid "Gaz: 2 GJ."
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid "Télécoms: 1 ~ 5 GJ (arrondis à la louche)"
+msgstr ""
+
 #. type: Title ##
 #, no-wrap
 msgid "Les transports"
@@ -62,7 +95,10 @@ msgid ""
 "Je roule en **voiture** 30 kilomètres par jour pour aller travailler, "
 "environ 20 jours par mois.  Avec une voiture hybride parcourant 25 "
 "kilomètres par litre, ça fait 24 litres par mois, donc environ 800 MJ par "
-"mois."
+"mois ou environ 10 GJ par an.  J'achète environ 50 litres d'essence par mois "
+"et hormis mes trajets aller travailler, nous sommes souvents trois dans la "
+"voiture.  Donc aller au travail représente les trois quarts de ce que je "
+"dépense en essence à titre individuel."
 msgstr ""
 
 #. type: Bullet: ' - '
@@ -89,7 +125,8 @@ msgid ""
 "litre (43 MJ/kg pour densité de 0.8).  La différence avec la voiture, c'est "
 "qu'on fait beaucoup plus de kilomètres en avion.  Je fais environ un voyage "
 "intercontinental (20 000 km) et quatre voyages domestiques entre Okinawa et "
-"Tôkyô (4 × 2000 km).  Donc environ 840 litres par an, donc 2 400 MJ."
+"Tôkyô (4 × 3000 km).  Donc environ 600 et 1200 litres par an, donc entre 20 "
+"et 40 GJ par an."
 msgstr ""
 
 #. type: Bullet: ' - '
@@ -195,9 +232,9 @@ msgid ""
 "serait plus que la moyenne au Japon ou en Amérique, on voit que la "
 "consommation résidentielle reste négligeable dans l'équation.  Entre 1000 et "
 "2000 personnes travaillent sur le campus.  On peut donc dire que chacun "
-"d'entre nous consomme de l'ordre de 360 GJ / an en moyenne, et que c'est "
-"probablement un peu surestimé.  En comparaison, je consomme 800 MJ * 12 ~= "
-"10 GJ d'énergie en carburant pour aller travailler."
+"d'entre nous consomme de l'ordre de 100 à 360 GJ / an en moyenne, et que "
+"c'est probablement un peu surestimé.  En comparaison, je consomme 800 MJ * "
+"12 ~= 10 GJ d'énergie en carburant pour aller travailler."
 msgstr ""
 
 #. type: Title ##
@@ -229,3 +266,35 @@ msgid ""
 "Le coût énergétique de la synthèse et manufacture du plastique est estimé à "
 "18 MJ / kg de plastique."
 msgstr ""
+
+#. type: Plain text
+msgid "le vin"
+msgstr ""
+
+#. type: Plain text
+msgid "Aller au travail en vélo"
+msgstr ""
+
+#. type: Plain text
+msgid "une vie plus bourgeoise ? Une vie plus maigre ?"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Consommation annuelle de pétrole (4.2 10e20 J)/ Énergie envoyée par le "
+"soleil: 6,2 × 1020 J \tl'énergie totale du Soleil qui atteint la Terre en "
+"une heure. (https://fr.wikipedia.org/wiki/Ordres_de_grandeur_d"
+"%27%C3%A9nergie)"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"L'énergie cinétique d'un 1kg de matière à la vitesse de libération (7.9 km/"
+"s)  est d'un peu plus de 30 MJ.  Il faut brûler un litre d'essence pour "
+"dégager cette énergie.  Malheureusement, comme on n'a pas encore inventé "
+"mieux, il faut aussi transporter l'essence et le moteur, ce qui alourdit "
+"considérablement l'ensemble, au point de doubler le poids et donc l'énergie "
+"demandée, et donc le poids, et donc l'énergie demandée, etc.  Note: la "
+"différence d'énergie potentielle dans le champs de gravité terrestre est "
+"largement inférieure à la quantité d'énergie cinétique nécessaire."
+msgstr ""

Plussons!
diff --git "a/Debian/debi\303\242neries/markdown2.mdwn" "b/Debian/debi\303\242neries/markdown2.mdwn"
new file mode 100644
index 00000000..4191be52
--- /dev/null
+++ "b/Debian/debi\303\242neries/markdown2.mdwn"
@@ -0,0 +1,13 @@
+[[!meta date="Thu, 11 May 2023 08:43:33 +0900"]]
+[[!meta updated="Thu, 11 May 2023 08:43:33 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Plussez pour patcher Firefox pour afficher du Markdown ?"]]
+
+J'ai [[écrit auparavant|markdown]] que quand Firefox reçoit un fichier dont le
+type média est _text/markdown_, il le propose au téléchargement, alors que les
+autres navigateurs l'affichent comme un fichier texte.
+
+Il est maintenant possible de plusser sur
+[connect.mozilla.org](https://connect.mozilla.org/t5/ideas/display-markdown-files/idi-p/6000)
+pour demander que Firefox formatte le _markdown_ par défaut.

En bref par an.
diff --git a/Joules.md b/Joules.md
index 9b55565f..4ff4901a 100644
--- a/Joules.md
+++ b/Joules.md
@@ -13,6 +13,16 @@ l'unité du Système International, pour mieux comparer.  Je vais poster chacun
 de mes calculs avec le tag [#Joules](https://framapiaf.org/tags/Joules) sur
 Framapiaf.
 
+## En bref, par an:
+
+ - Travail: 100 ~ 350 GJ.
+ - Avion: 20 ~ 40 GJ.
+ - Voiture: 10 ~ 15 GJ.
+ - Électricité: 5 GJ.
+ - Nourriture (métabolisme): 3 GJ.
+ - Gaz: 2 GJ.
+ - Télécoms: 1 ~ 5 GJ (arrondis à la louche)
+
 ## Les transports
 
  - « _L'énergie contenue dans l'essence est d'environ 33 600 000 joules par
@@ -22,7 +32,11 @@ Framapiaf.
 
  - Je roule en **voiture** 30 kilomètres par jour pour aller travailler,
    environ 20 jours par mois.  Avec une voiture hybride parcourant 25
-   kilomètres par litre, ça fait 24 litres par mois, donc environ 800 MJ par mois.
+   kilomètres par litre, ça fait 24 litres par mois, donc environ 800 MJ par
+   mois ou environ 10 GJ par an.  J'achète environ 50 litres d'essence
+   par mois et hormis mes trajets aller travailler, nous sommes souvents
+   trois dans la voiture.  Donc aller au travail représente les trois quarts
+   de ce que je dépense en essence à titre individuel.
 
  - Pour parcourir un kilomètre en **train** je dois dépenser entre 10 et 20 yens.
    Çela me côute environ autant en essence quand je pends la voiture, mais
@@ -40,7 +54,8 @@ Framapiaf.
    litre (43 MJ/kg pour densité de 0.8).  La différence avec la voiture, c'est
    qu'on fait beaucoup plus de kilomètres en avion.  Je fais environ un voyage
    intercontinental (20 000 km) et quatre voyages domestiques entre Okinawa et
-   Tôkyô (4 × 2000 km).  Donc environ 840 litres par an, donc 2 400 MJ.
+   Tôkyô (4 × 3000 km).  Donc environ 600 et 1200 litres par an, donc entre 20
+   et 40 GJ par an.
 
  - Article intéressant comparant la dépense énergétique de chaque moyen de
    transport.  La dépense du corps humain est estmiée via la consommation
@@ -112,7 +127,7 @@ Framapiaf.
    plus que la moyenne au Japon ou en Amérique, on voit que la consommation
    résidentielle reste négligeable dans l'équation.  Entre 1000 et 2000 personnes
    travaillent sur le campus.  On peut donc dire que chacun d'entre nous consomme
-   de l'ordre de 360 GJ / an en moyenne, et que c'est probablement un peu
+   de l'ordre de 100 à 360 GJ / an en moyenne, et que c'est probablement un peu
    surestimé.  En comparaison, je consomme 800 MJ * 12 ~= 10 GJ d'énergie en
    carburant pour aller travailler.
 
@@ -129,3 +144,20 @@ estimé à 1/2 ou 1/3 du coût total. (à vérifier)
 
 Le coût énergétique de la synthèse et manufacture du plastique est
 estimé à 18 MJ / kg de plastique.
+
+le vin
+
+Aller au travail en vélo
+
+une vie plus bourgeoise ?  Une vie plus maigre ?
+
+Consommation annuelle de pétrole (4.2 10e20 J)/ Énergie envoyée par le soleil: 6,2 × 1020 J 	l'énergie totale du Soleil qui atteint la Terre en une heure. (https://fr.wikipedia.org/wiki/Ordres_de_grandeur_d%27%C3%A9nergie)
+
+L'énergie cinétique d'un 1kg de matière à la vitesse de libération (7.9 km/s)
+est d'un peu plus de 30 MJ.  Il faut brûler un litre d'essence pour dégager
+cette énergie.  Malheureusement, comme on n'a pas encore inventé mieux, il faut
+aussi transporter l'essence et le moteur, ce qui alourdit considérablement
+l'ensemble, au point de doubler le poids et donc l'énergie demandée, et donc le
+poids, et donc l'énergie demandée, etc.  Note: la différence d'énergie
+potentielle dans le champs de gravité terrestre est largement inférieure à la
+quantité d'énergie cinétique nécessaire.

updated PO files
diff --git a/Joules.en.po b/Joules.en.po
index 75b3cab6..e0ffd0e2 100644
--- a/Joules.en.po
+++ b/Joules.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2023-05-09 13:35+0000\n"
+"POT-Creation-Date: 2023-05-09 13:37+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"
@@ -229,35 +229,3 @@ msgid ""
 "Le coût énergétique de la synthèse et manufacture du plastique est estimé à "
 "18 MJ / kg de plastique."
 msgstr ""
-
-#. type: Plain text
-msgid "le vin"
-msgstr ""
-
-#. type: Plain text
-msgid "Aller au travail en vélo"
-msgstr ""
-
-#. type: Plain text
-msgid "une vie plus bourgeoise ? Une vie plus maigre ?"
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Consommation annuelle de pétrole (4.2 10e20 J)/ Énergie envoyée par le "
-"soleil: 6,2 × 1020 J \tl'énergie totale du Soleil qui atteint la Terre en "
-"une heure. (https://fr.wikipedia.org/wiki/Ordres_de_grandeur_d"
-"%27%C3%A9nergie)"
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"L'énergie cinétique d'un 1kg de matière à la vitesse de libération (7.9 km/"
-"s)  est d'un peu plus de 30 MJ.  Il faut brûler un litre d'essence pour "
-"dégager cette énergie.  Malheureusement, comme on n'a pas encore inventé "
-"mieux, il faut aussi transporter l'essence et le moteur, ce qui alourdit "
-"considérablement l'ensemble, au point de doubler le poids et donc l'énergie "
-"demandée, et donc le poids, et donc l'énergie demandée, etc.  Note: la "
-"différence d'énergie potentielle dans le champs de gravité terrestre est "
-"largement inférieure à la quantité d'énergie cinétique nécessaire."
-msgstr ""

On enlève le brouillon
diff --git a/Joules.md b/Joules.md
index 8194cf9e..9b55565f 100644
--- a/Joules.md
+++ b/Joules.md
@@ -129,20 +129,3 @@ estimé à 1/2 ou 1/3 du coût total. (à vérifier)
 
 Le coût énergétique de la synthèse et manufacture du plastique est
 estimé à 18 MJ / kg de plastique.
-
-le vin
-
-Aller au travail en vélo
-
-une vie plus bourgeoise ?  Une vie plus maigre ?
-
-Consommation annuelle de pétrole (4.2 10e20 J)/ Énergie envoyée par le soleil: 6,2 × 1020 J 	l'énergie totale du Soleil qui atteint la Terre en une heure. (https://fr.wikipedia.org/wiki/Ordres_de_grandeur_d%27%C3%A9nergie)
-
-L'énergie cinétique d'un 1kg de matière à la vitesse de libération (7.9 km/s)
-est d'un peu plus de 30 MJ.  Il faut brûler un litre d'essence pour dégager
-cette énergie.  Malheureusement, comme on n'a pas encore inventé mieux, il faut
-aussi transporter l'essence et le moteur, ce qui alourdit considérablement
-l'ensemble, au point de doubler le poids et donc l'énergie demandée, et donc le
-poids, et donc l'énergie demandée, etc.  Note: la différence d'énergie
-potentielle dans le champs de gravité terrestre est largement inférieure à la
-quantité d'énergie cinétique nécessaire.

updated PO files
diff --git a/Joules.en.po b/Joules.en.po
index 2183e164..75b3cab6 100644
--- a/Joules.en.po
+++ b/Joules.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2022-12-16 12:58+0000\n"
+"POT-Creation-Date: 2023-05-09 13:35+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"
@@ -43,6 +43,11 @@ msgid ""
 "Joules) sur Framapiaf."
 msgstr ""
 
+#. type: Title ##
+#, no-wrap
+msgid "Les transports"
+msgstr ""
+
 #. type: Bullet: ' - '
 msgid ""
 "« _L'énergie contenue dans l'essence est d'environ 33 600 000 joules par "
@@ -54,42 +59,75 @@ msgstr ""
 
 #. type: Bullet: ' - '
 msgid ""
-"Je roule 30 kilomètres par jour pour aller travailler, environ 20 jours par "
-"mois, avec une voiture parcourant 25 kilomètres par litre, ça fait 24 litres "
-"par mois, donc environ 800 MJ par mois."
+"Je roule en **voiture** 30 kilomètres par jour pour aller travailler, "
+"environ 20 jours par mois.  Avec une voiture hybride parcourant 25 "
+"kilomètres par litre, ça fait 24 litres par mois, donc environ 800 MJ par "
+"mois."
 msgstr ""
 
 #. type: Bullet: ' - '
 msgid ""
-"Je n'ai aucune idée précise de la quantité d'énergie que j'ingère chaque "
-"jour.  Mon pèse-personne, calibré pour une masse corporelle japonaise, me "
-"recommande de manger 1700 kilocalories par jour.  C'est gross-modo mon "
-"métabolisme de base d'après les chiffres résumés par l'ANSES dans on avis "
-"suivant la saisine 2012-SA-0103.  Dans ce même document, les besoins d'un "
-"homme de mon age « modérément actif » sont un peu au dessus de 2500 kcal par "
-"jour.  Une calorie vaut environ 4.2 Joules.  10 000 kJoules valent un peu "
-"moins de 2400 kcal.  En approximant ça à ma consommation quotidienne, j'en "
-"déduis que je consomme environ 300 MJ par mois.  Reste à savoir: l'énergie "
-"dépensée pour me fournir cette nourriture…"
+"Pour parcourir un kilomètre en **train** je dois dépenser entre 10 et 20 "
+"yens.  Çela me côute environ autant en essence quand je pends la voiture, "
+"mais c'est sans compter la rentabilisation de la voiture et les taxes sur la "
+"propriété et le contrôle technique (et pour d'autres, le prix du parking).  "
+"Mes trajets en voiture consomment (voir plus haut) 1/25 L par km, c'est à "
+"dire environ 825 kJ par km, ou 825 J / m.  C'est très proche des chiffres "
+"annoncés par Die Bahn pour les transports par train régionaux en Allemagne."
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "   https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/progress-in-climate-protection/energy-efficiency-increased/\n"
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid ""
+"On estime la consommation des **avions** modernes entre 2 et 4 litres de "
+"kérosène par 100 kilomètres et par passager.  Son pouvoir calorifique n'est "
+"pas très différent ce celui de l'essence de nos voitures, mettons 34 MJ par "
+"litre (43 MJ/kg pour densité de 0.8).  La différence avec la voiture, c'est "
+"qu'on fait beaucoup plus de kilomètres en avion.  Je fais environ un voyage "
+"intercontinental (20 000 km) et quatre voyages domestiques entre Okinawa et "
+"Tôkyô (4 × 2000 km).  Donc environ 840 litres par an, donc 2 400 MJ."
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid ""
+"Article intéressant comparant la dépense énergétique de chaque moyen de "
+"transport.  La dépense du corps humain est estmiée via la consommation "
+"d'oxygène, bien étudiée.  Le rendement musculaire n'est pas très haut : les "
+"trois quarts de l'énergie dépensée se dissipent en chaleur, et le reste est "
+"disponible pour le mouvement."
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "   http://www.economiematin.fr/news-consommation-transports-industrie-services-energie\n"
+msgstr ""
+
+#. type: Title ##
+#, no-wrap
+msgid "Le logement"
 msgstr ""
 
 #. type: Bullet: ' - '
 msgid ""
 "Pour nous chauffer et nous rafraîchir, pour utiliser nos appareils électro-"
 "ménagers, et nos médias à écrans, nous consommons environ 300 kWh "
-"d'électricité par mois.  Mettons que ça fait 100 pour moi.  Une puissance de "
-"1 Watt, c'est 1 Joule par seconde.  Donc 100 kWh font 360 MJ.  Une grande "
-"partie de cette énergie provient de centrales à charbon et il faut de "
-"l'énergie pour l'extraire et le transporter.  Une partie de l'électricité "
-"produite se dissipe en chaleur dans le réseau électrique.  Ma consommation "
-"réelle est donc supérieure à ce que m'annonce le compteur."
+"d'**électricité** par mois.  Mettons que ça fait 100 pour moi.  Une "
+"puissance de 1 Watt, c'est 1 Joule par seconde.  Donc 100 kWh font 360 MJ.  "
+"Une grande partie de cette énergie provient de centrales à charbon et il "
+"faut de l'énergie pour l'extraire et le transporter.  Une partie de "
+"l'électricité produite se dissipe en chaleur dans le réseau électrique.  Ma "
+"consommation réelle est donc supérieure à ce que m'annonce le compteur."
 msgstr ""
 
 #. type: Bullet: ' - '
 msgid ""
 "Pour cuisiner, chauffer notre eau de lavage, et sécher nos habits, nous "
-"utilisons environ 12 mètres cube de gaz par mois, donc 4 pour ma part.  Il "
-"existe différents types de gaz domestique, et une partie de l'énergie "
+"utilisons environ 12 mètres cube de **gaz** par mois, donc 4 pour ma part.  "
+"Il existe différents types de gaz domestique, et une partie de l'énergie "
 "dégagée par la combustion se perd par l'émission de vapeur d'eau.  Les "
 "chiffres donnés sur Wikipédia sont pour une température ambiante de zéro "
 "degrés, ce qui n'est pas le cas dans notre appartement.  Néanmoins, une "
@@ -101,19 +139,8 @@ msgstr ""
 
 #. type: Bullet: ' - '
 msgid ""
-"On estime la consommation des avions modernes entre 2 et 4 litres de "
-"kérosène par 100 kilomètres et par passager.  Son pouvoir calorifique n'est "
-"pas très différent ce celui de l'essence de nos voitures, mettons 34 MJ par "
-"litre (43 MJ/kg pour densité de 0.8).  La différence avec la voiture, c'est "
-"qu'on fait beaucoup plus de kilomètres en avion.  Je fais environ un voyage "
-"intercontinental (20 000 km) et quatre voyages domestiques entre Okinawa et "
-"Tôkyô (4 × 2000 km).  Donc environ 840 litres par an, donc 2 400 MJ."
-msgstr ""
-
-#. type: Bullet: ' - '
-msgid ""
-"Ma part dans la facture télécoms familiale, internet plus téléphonie mobile, "
-"est d'environ 5000 yens.  Je n'ai aucune idée précise de la quantité "
+"Ma part dans la facture **télécoms** familiale, internet plus téléphonie "
+"mobile, est d'environ 5000 yens.  Je n'ai aucune idée précise de la quantité "
 "d'énergie utilisée.  Mais on peut estimer une limite supérieure: si cet "
 "argent était entièrement dépensé en électricité par les opérateurs, et "
 "qu'ils la payaient au même prix que nous cela ferait environ 160 kWh, ou "
@@ -125,19 +152,44 @@ msgstr ""
 
 #. type: Bullet: ' - '
 msgid ""
-"Je consomme entre 6 et 7 mètres cubes d'eau par mois pour un prix d'environ "
-"1000 yens, qui include la production et le retraitement.  Un rapport de "
-"l'observatoire de l'eau de la Seine-et-Marne sur les enjeux énergétiques de "
-"l'eau potable et de l'assainissement, de 2016, estime entre 1.6 et 16 % la "
-"part énergétique de la facture d'eau.  En extrapolant avec ma facture "
-"d'électricité, 100 yens font environ 11 MJ.  L'eau est précieuse et les "
-"effets de son gaspillage sont différents de ceux du gaspillage de l'énergie."
+"Je consomme entre 6 et 7 mètres cubes d'**eau** par mois pour un prix "
+"d'environ 1000 yens, qui include la production et le retraitement.  Un "
+"rapport de l'observatoire de l'eau de la Seine-et-Marne sur les enjeux "
+"énergétiques de l'eau potable et de l'assainissement, de 2016, estime entre "
+"1.6 et 16 % la part énergétique de la facture d'eau.  En extrapolant avec ma "
+"facture d'électricité, 100 yens font environ 11 MJ.  L'eau est précieuse et "
+"les effets de son gaspillage sont différents de ceux du gaspillage de "
+"l'énergie."
+msgstr ""
+
+#. type: Title ##
+#, no-wrap
+msgid "La vie quotidienne"
+msgstr ""
+
+#. type: Bullet: ' - '
+msgid ""
+"Je n'ai aucune idée précise de la quantité d'énergie que j'ingère chaque "
+"jour.  Mon pèse-personne, calibré pour une masse corporelle japonaise, me "
+"recommande de manger 1700 kilocalories par jour.  C'est gross-modo mon "
+"**métabolisme** de base d'après les chiffres résumés par l'ANSES dans on "
+"avis suivant la saisine 2012-SA-0103.  Dans ce même document, les besoins "
+"d'un homme de mon age « modérément actif » sont un peu au dessus de 2500 "
+"kcal par jour.  Une calorie vaut environ 4.2 Joules.  10 000 kJoules valent "
+"un peu moins de 2400 kcal.  En approximant ça à ma consommation quotidienne, "
+"j'en déduis que je consomme environ 300 MJ par mois.  Reste à savoir: "
+"l'énergie dépensée pour me fournir cette nourriture…"
+msgstr ""
+
+#. type: Title ##
+#, no-wrap
+msgid "Le travail"
 msgstr ""
 
 #. type: Bullet: ' - '
 msgid ""
-"Je travaille sur un campus qui consomme 100 000 000 kWh / an, c'est à dire "
-"360 000 000 MJ / an ou 360 TJ / an.  Cela inclut la consommation des "
+"Je **travaille** sur un campus qui consomme 100 000 000 kWh / an, c'est à "
+"dire 360 000 000 MJ / an ou 360 TJ / an.  Cela inclut la consommation des "
 "résidences de quelques centaines d'étudiants et de chercheurs.  Imaginons "
 "qu'une personne consomme 10 000 kWh par an, c'est à dire 36 GJ, ce qui "
 "serait plus que la moyenne au Japon ou en Amérique, on voit que la "
@@ -147,3 +199,65 @@ msgid ""
 "probablement un peu surestimé.  En comparaison, je consomme 800 MJ * 12 ~= "

(Diff truncated)
Réorganisation et ajouts.
diff --git a/Joules.md b/Joules.md
index 29ec81ac..8194cf9e 100644
--- a/Joules.md
+++ b/Joules.md
@@ -13,16 +13,18 @@ l'unité du Système International, pour mieux comparer.  Je vais poster chacun
 de mes calculs avec le tag [#Joules](https://framapiaf.org/tags/Joules) sur
 Framapiaf.
 
+## Les transports
+
  - « _L'énergie contenue dans l'essence est d'environ 33 600 000 joules par
    litre, ou 46 700 000 joules par kilogramme (de pouvoir calorifique
    supérieur)._ » ([Wikipedia](https://fr.wikipedia.org/wiki/Essence_(hydrocarbure)).
    Reste à savoir: l'énergie consommée pour produire ce litre d'essence…
 
- - Je roule 30 kilomètres par jour pour aller travailler, environ 20 jours par
-   mois, avec une voiture parcourant 25 kilomètres par litre, ça fait 24 litres
-   par mois, donc environ 800 MJ par mois.
+ - Je roule en **voiture** 30 kilomètres par jour pour aller travailler,
+   environ 20 jours par mois.  Avec une voiture hybride parcourant 25
+   kilomètres par litre, ça fait 24 litres par mois, donc environ 800 MJ par mois.
 
- - Pour parcourir un kilomètre en train je dois dépenser entre 10 et 20 yens.
+ - Pour parcourir un kilomètre en **train** je dois dépenser entre 10 et 20 yens.
    Çela me côute environ autant en essence quand je pends la voiture, mais
    c'est sans compter la rentabilisation de la voiture et les taxes sur la
    propriété et le contrôle technique (et pour d'autres, le prix du parking).
@@ -30,22 +32,29 @@ Framapiaf.
    dire environ 825 kJ par km, ou 825 J / m.  C'est très proche des chiffres
    annoncés par Die Bahn pour les transports par train régionaux en Allemagne.
 
-https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/progress-in-climate-protection/energy-efficiency-increased/
+   https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/progress-in-climate-protection/energy-efficiency-increased/
 
- - Je n'ai aucune idée précise de la quantité d'énergie que j'ingère chaque jour.
-   Mon pèse-personne, calibré pour une masse corporelle japonaise, me recommande de
-   manger 1700 kilocalories par jour.  C'est gross-modo mon métabolisme de base
-   d'après les chiffres résumés par l'ANSES dans on avis suivant la saisine
-   2012-SA-0103.  Dans ce même document, les besoins d'un homme de mon age
-   « modérément actif » sont un peu au dessus de 2500 kcal par jour.  Une calorie
-   vaut environ 4.2 Joules.  10 000 kJoules valent un peu moins de 2400 kcal.
-   En approximant ça à ma consommation quotidienne, j'en déduis que je consomme
-   environ 300 MJ par mois.  Reste à savoir: l'énergie dépensée pour me fournir
-   cette nourriture…
+ - On estime la consommation des **avions** modernes entre 2 et 4 litres de
+   kérosène par 100 kilomètres et par passager.  Son pouvoir calorifique n'est
+   pas très différent ce celui de l'essence de nos voitures, mettons 34 MJ par
+   litre (43 MJ/kg pour densité de 0.8).  La différence avec la voiture, c'est
+   qu'on fait beaucoup plus de kilomètres en avion.  Je fais environ un voyage
+   intercontinental (20 000 km) et quatre voyages domestiques entre Okinawa et
+   Tôkyô (4 × 2000 km).  Donc environ 840 litres par an, donc 2 400 MJ.
+
+ - Article intéressant comparant la dépense énergétique de chaque moyen de
+   transport.  La dépense du corps humain est estmiée via la consommation
+   d'oxygène, bien étudiée.  Le rendement musculaire n'est pas très haut : les
+   trois quarts de l'énergie dépensée se dissipent en chaleur, et le reste est
+   disponible pour le mouvement.
+   
+   http://www.economiematin.fr/news-consommation-transports-industrie-services-energie
+
+## Le logement
 
  - Pour nous chauffer et nous rafraîchir, pour utiliser nos appareils
    électro-ménagers, et nos médias à écrans, nous consommons environ 300 kWh
-   d'électricité par mois.  Mettons que ça fait 100 pour moi.  Une puissance de
+   d'**électricité** par mois.  Mettons que ça fait 100 pour moi.  Une puissance de
    1 Watt, c'est 1 Joule par seconde.  Donc 100 kWh font 360 MJ.  Une grande
    partie de cette énergie provient de centrales à charbon et il faut de l'énergie
    pour l'extraire et le transporter.  Une partie de l'électricité produite se
@@ -53,7 +62,7 @@ https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/pr
    supérieure à ce que m'annonce le compteur.
 
  - Pour cuisiner, chauffer notre eau de lavage, et sécher nos habits, nous
-   utilisons environ 12 mètres cube de gaz par mois, donc 4 pour ma part.
+   utilisons environ 12 mètres cube de **gaz** par mois, donc 4 pour ma part.
    Il existe différents types de gaz domestique, et une partie de l'énergie
    dégagée par la combustion se perd par l'émission de vapeur d'eau.  Les chiffres
    donnés sur Wikipédia sont pour une température ambiante de zéro degrés, ce
@@ -63,15 +72,7 @@ https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/pr
    sais pas combien d'énergie supplémentaire il faut dépenser pour me fournir
    ce gaz.
 
- - On estime la consommation des avions modernes entre 2 et 4 litres de
-   kérosène par 100 kilomètres et par passager.  Son pouvoir calorifique n'est
-   pas très différent ce celui de l'essence de nos voitures, mettons 34 MJ par
-   litre (43 MJ/kg pour densité de 0.8).  La différence avec la voiture, c'est
-   qu'on fait beaucoup plus de kilomètres en avion.  Je fais environ un voyage
-   intercontinental (20 000 km) et quatre voyages domestiques entre Okinawa et
-   Tôkyô (4 × 2000 km).  Donc environ 840 litres par an, donc 2 400 MJ.
-
- - Ma part dans la facture télécoms familiale, internet plus téléphonie
+ - Ma part dans la facture **télécoms** familiale, internet plus téléphonie
    mobile, est d'environ 5000 yens.  Je n'ai aucune idée précise de la quantité
    d'énergie utilisée.  Mais on peut estimer une limite supérieure: si cet
    argent était entièrement dépensé en électricité par les opérateurs, et qu'ils
@@ -81,7 +82,7 @@ https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/pr
    entendu, ces chiffres ne tiennent pas compte du fait que côté centres de
    données qui nous fournissent le « contenu », la dépense énergétique est énorme.
 
- - Je consomme entre 6 et 7 mètres cubes d'eau par mois pour un prix d'environ
+ - Je consomme entre 6 et 7 mètres cubes d'**eau** par mois pour un prix d'environ
    1000 yens, qui include la production et le retraitement.  Un rapport de
    l'observatoire de l'eau de la Seine-et-Marne sur les enjeux énergétiques
    de l'eau potable et de l'assainissement, de 2016, estime entre 1.6 et 16 %
@@ -89,7 +90,22 @@ https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/pr
    d'électricité, 100 yens font environ 11 MJ.  L'eau est précieuse et les effets
    de son gaspillage sont différents de ceux du gaspillage de l'énergie.
 
- - Je travaille sur un campus qui consomme 100 000 000 kWh / an, c'est à dire
+## La vie quotidienne
+
+ - Je n'ai aucune idée précise de la quantité d'énergie que j'ingère chaque jour.
+   Mon pèse-personne, calibré pour une masse corporelle japonaise, me recommande de
+   manger 1700 kilocalories par jour.  C'est gross-modo mon **métabolisme** de base
+   d'après les chiffres résumés par l'ANSES dans on avis suivant la saisine
+   2012-SA-0103.  Dans ce même document, les besoins d'un homme de mon age
+   « modérément actif » sont un peu au dessus de 2500 kcal par jour.  Une calorie
+   vaut environ 4.2 Joules.  10 000 kJoules valent un peu moins de 2400 kcal.
+   En approximant ça à ma consommation quotidienne, j'en déduis que je consomme
+   environ 300 MJ par mois.  Reste à savoir: l'énergie dépensée pour me fournir
+   cette nourriture…
+
+## Le travail
+
+ - Je **travaille** sur un campus qui consomme 100 000 000 kWh / an, c'est à dire
    360 000 000 MJ / an ou 360 TJ / an.  Cela inclut la consommation des
    résidences de quelques centaines d'étudiants et de chercheurs.  Imaginons
    qu'une personne consomme 10 000 kWh par an, c'est à dire 36 GJ, ce qui serait
@@ -100,3 +116,33 @@ https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/pr
    surestimé.  En comparaison, je consomme 800 MJ * 12 ~= 10 GJ d'énergie en
    carburant pour aller travailler.
 
+## Le plastique
+
+ - Le **plastique** en général: http://large.stanford.edu/courses/2010/ph240/hamman1/
+
+La plupart du plastique est produit à partir de pétrole ou de gaz.  L'énergie
+de combusion du polyéthylène est d'environ 45 MJ / kg.  En 2008, le monde a
+produit environ 80 Tg de plastique.
+
+Le coût énergétique de la synthèse et manufacture du plastique est
+estimé à 1/2 ou 1/3 du coût total. (à vérifier)
+
+Le coût énergétique de la synthèse et manufacture du plastique est
+estimé à 18 MJ / kg de plastique.
+
+le vin
+
+Aller au travail en vélo
+
+une vie plus bourgeoise ?  Une vie plus maigre ?
+
+Consommation annuelle de pétrole (4.2 10e20 J)/ Énergie envoyée par le soleil: 6,2 × 1020 J 	l'énergie totale du Soleil qui atteint la Terre en une heure. (https://fr.wikipedia.org/wiki/Ordres_de_grandeur_d%27%C3%A9nergie)
+
+L'énergie cinétique d'un 1kg de matière à la vitesse de libération (7.9 km/s)
+est d'un peu plus de 30 MJ.  Il faut brûler un litre d'essence pour dégager
+cette énergie.  Malheureusement, comme on n'a pas encore inventé mieux, il faut
+aussi transporter l'essence et le moteur, ce qui alourdit considérablement
+l'ensemble, au point de doubler le poids et donc l'énergie demandée, et donc le
+poids, et donc l'énergie demandée, etc.  Note: la différence d'énergie
+potentielle dans le champs de gravité terrestre est largement inférieure à la
+quantité d'énergie cinétique nécessaire.

Train
diff --git a/Joules.md b/Joules.md
index cecfb116..29ec81ac 100644
--- a/Joules.md
+++ b/Joules.md
@@ -22,6 +22,16 @@ Framapiaf.
    mois, avec une voiture parcourant 25 kilomètres par litre, ça fait 24 litres
    par mois, donc environ 800 MJ par mois.
 
+ - Pour parcourir un kilomètre en train je dois dépenser entre 10 et 20 yens.
+   Çela me côute environ autant en essence quand je pends la voiture, mais
+   c'est sans compter la rentabilisation de la voiture et les taxes sur la
+   propriété et le contrôle technique (et pour d'autres, le prix du parking).
+   Mes trajets en voiture consomment (voir plus haut) 1/25 L par km, c'est à
+   dire environ 825 kJ par km, ou 825 J / m.  C'est très proche des chiffres
+   annoncés par Die Bahn pour les transports par train régionaux en Allemagne.
+
+https://ibir.deutschebahn.com/ib2018/en/group-management-report/environmental/progress-in-climate-protection/energy-efficiency-increased/
+
  - Je n'ai aucune idée précise de la quantité d'énergie que j'ingère chaque jour.
    Mon pèse-personne, calibré pour une masse corporelle japonaise, me recommande de
    manger 1700 kilocalories par jour.  C'est gross-modo mon métabolisme de base

APEX2 / APE2
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 475eb22c..3791499b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -276,6 +276,8 @@ Genes and pathways
    ([[Niimura, 2009|biblio/20333175]]).
  - Most members of retinoic acid pathway gene network (biosynthesis, signalling
    and degradation) are lost in _O. dioica_ ([[Martí-Solans et al., 2016|biblio/27406791]]).
+ - APEX2 (encoding for the APE2 protein involved in base excision repair and microhomology
+   mediated end-joining (MMEJ) was not found, but APEX1 was found ([[Denoeud et al., 2010|biblio/21097902]]).
  - The entire machinery required for performing classical NHEJ repair of DSB (which is
    conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
    An alternative or microhomology (MH)-driven end joining pathway is active

larvacea
diff --git a/biblio/biostor-236874.mdwn b/biblio/biostor-236874.mdwn
new file mode 100644
index 00000000..a001e3bb
--- /dev/null
+++ b/biblio/biostor-236874.mdwn
@@ -0,0 +1,21 @@
+[[!meta title="A revised classification of the Tunicata, with definitions of the orders, sub-orders, families, sub-families and genera, and analytical keys to the species"]]
+[[!tag Oikopleura]]
+
+William Abbott Herdman
+
+Journal of The Linnean Society of London, Zoology, vol 23, 558-652, Feb 5th 1891.  ark:/13960/t5q898f4x, biostor-236874.
+
+A revised classification of the Tunicata, with definitions of the orders, sub-orders, families, sub-families and genera, and analytical keys to the species
+
+Defines:
+
+ - Order Larvacea, Herdman, 1882
+   - Family Appendiculariidae, Bronn, 1862
+     - Genus Appendicularia (Chamisso 1821), Fol, 1874
+     - Genus Oikopoleura (Mertens 1831), Fol, 1872
+             synonym: Vexillaria, J. Müller
+     - Genus Stegosoma, Chun 1888
+     - Genus Fritillaria (Q. & G. 1833), Fol, 1872
+             synonym: Eurycercus, Busch
+     - Genus Kowalvskia, Fol, 1872
+             Herdman speculates that it may be a Family.

outliers
diff --git a/biblio/22925495.mdwn b/biblio/22925495.mdwn
new file mode 100644
index 00000000..6669e60c
--- /dev/null
+++ b/biblio/22925495.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage."]]
+[[!tag genome chromosome repeats]]
+
+Moreau H, Verhelst B, Couloux A, Derelle E, Rombauts S, Grimsley N, Van Bel M, Poulain J, Katinka M, Hohmann-Marriott MF, Piganeau G, Rouzé P, Da Silva C, Wincker P, Van de Peer Y, Vandepoele K.
+
+Genome Biol. 2012 Aug 24;13(8):R74. doi:10.1186/gb-2012-13-8-r74
+
+Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage.
+
+[[!pmid 22925495 desc="7,847 genes, no transposons.  Two “outlier” chromosomes are found with lower GC content, like in _Ostreococcus_ and _Micromonas_.  Genes in the big outlier chromosomes have a high number of small AT-rich introns with no apparent conserved motifs."]]
diff --git a/tags/chromosome.mdwn b/tags/chromosome.mdwn
index 288710cd..ac6a4887 100644
--- a/tags/chromosome.mdwn
+++ b/tags/chromosome.mdwn
@@ -6,7 +6,9 @@ _in progressss_
 
 Two (out of 20) chromosomes in the genome of the unicellular green alga
 _Ostreococcus tauri_ have a markedly different GC and transposable element
-content compared to the others. [[Derelle et al., 2003|biblio/16868079]].
+content compared to the others. [[Derelle and coll., 2003|biblio/16868079]].
+The same phenomeon has then been reported in _Bathycoccus prasinos_ ([[Moreau
+and coll., 2012|biblio/22925495]]) and other species.
 
 Chr4 in _Polypedilum vanderplanki_ has lower GC content than the others
 ([[Yoshida et al., 2022|biblio/35387384]]), and it has been speculated that it

creating tag page tags/mangrove
diff --git a/tags/mangrove.mdwn b/tags/mangrove.mdwn
new file mode 100644
index 00000000..e47229d1
--- /dev/null
+++ b/tags/mangrove.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged mangrove"]]
+
+[[!inline pages="tagged(mangrove)" actions="no" archive="yes"
+feedshow=10]]

WGD
diff --git a/biblio/31258950.mdwn b/biblio/31258950.mdwn
new file mode 100644
index 00000000..ce8c747b
--- /dev/null
+++ b/biblio/31258950.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing."]]
+[[!tag mangrove genome]]
+
+Xu, S., He, Z., Zhang, Z., Guo, Z., Guo, W., Lyu, H., Li, J., Yang, M., Du, Z., Huang, Y., Zhou, R., Zhong, C., Boufford, D. E., Lerdau, M., Wu, C. I., Duke, N. C., International Mangrove Consortium, & Shi, S.
+
+National science review, 4(5), 721–734, 2017. doi:10.1093/nsr/nwx065
+
+The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing 
+
+[[!pmid 31258950 desc="Analysis of the genome sequence of _Rhizophora
+apiculata_ suggests a whole-genome duplication.  dN/dS analysis of the
+paralogues and comparisons to outgroups suggest that the duplication took place
+in the ancestors of _Rhizophoreae_."]]

PBS
diff --git a/biblio/25828383.mdwn b/biblio/25828383.mdwn
new file mode 100644
index 00000000..bbffdb84
--- /dev/null
+++ b/biblio/25828383.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot"]]
+[[!tag PCR]]
+
+Zhu Y, Zhang YX, Liu WW, Ma Y, Fang Q, Yao B.
+
+Sci Rep. 2015 Apr 1;5:9551. doi:10.1038/srep09551
+
+Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot
+
+[[!pmid 25828383 desc="For the amplification of a miRNA, the authors reported a
+98.03% efficiency in standard conditions.  It dropped to 90.94% with 0.5 mM
+49.99% PBS, 86.96% with 2 mM, 80.47% with 10 mM (1×), and 49.99% with 50 mM.
+The PCR was done in TaqMan universal PCR master mix."]]

Fungi
diff --git a/tags/yeast.mdwn b/tags/yeast.mdwn
index da1870c0..2e16ab37 100644
--- a/tags/yeast.mdwn
+++ b/tags/yeast.mdwn
@@ -1,4 +1,6 @@
 [[!meta title="pages tagged yeast"]]
 
+# Yeast and other unicellular fungi
+
 [[!inline pages="tagged(yeast)" actions="no" archive="yes"
 feedshow=10]]

Café hier
diff --git a/biblio/30618839.mdwn b/biblio/30618839.mdwn
new file mode 100644
index 00000000..bec42c55
--- /dev/null
+++ b/biblio/30618839.mdwn
@@ -0,0 +1,17 @@
+[[!meta title="A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus."]]
+[[!tag phylogeny]]
+
+Front Physiol. 2018 Dec 18;9:1833. doi:10.3389/fphys.2018.01833
+
+Zhang QL, Zhang GL, Yuan ML, Dong ZX, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB.
+
+A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus. 
+
+[[!pmid 30618839 desc="Supports “a phylogeny of [(B. belcheri + B. japonicum) +
+(B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus”.
+Estimates that “the most recent common ancestor of the living amphioxus species
+(the divergence time between _Asymmetron_ and _Branchiostoma_) was estimated to
+be ∼104 Mya [23.74—211.63]; the early splits within each main clade occurred at
+∼87 Mya [41.02—162.19]; _B. lanceolatum_ diverged from _B. floridae_ at ∼72 Mya
+[31.93—149.68], and the divergence time between _B. belcheri_ and _B.
+japonicum_ was ∼61 Mya [10.21—136.41]”."]]

Fritillaria
diff --git a/biblio/36307829.mdwn b/biblio/36307829.mdwn
index 4598663c..18eb634f 100644
--- a/biblio/36307829.mdwn
+++ b/biblio/36307829.mdwn
@@ -8,9 +8,10 @@ Front Zool. 2022 Oct 28;19(1):26. doi:10.1186/s12983-022-00471-y
 Laboratory study of Fritillaria lifecycle reveals key morphogenetic events leading to genus-specific anatomy.
 
 [[!pmid 36307829 desc="Possibly parasited by a Syndiniale from the genus
-_Sphaeripara_ and _Oodinium_.  Fed with _Micromonas_, _Phaeocystis_ and
-_Synechococcus_ in culture. 4 chromosomes are visible in oocytes by DAPI
-staining.  Self-fertilization was never observed.  In vitro fertilized oocytes
-frequently aborted development when left in vessels without water flow.
-Embryos hatch between 4 and 6 h at 15 °C. Cellulose-producing cells identified
-by staining with a carbohydrate-binding-module (CBM)."]]
+_Sphaeripara_ and _Oodinium_.  Fed with _Micromonas pusilla_ or _Synechococcus
+sp_ in culture at a density between 2 and 8 × 10<sup>7</sup> depending on the
+developmental stage. 4 chromosomes are visible in oocytes by DAPI staining.
+Self-fertilization was never observed.  In vitro fertilized oocytes frequently
+aborted development when left in vessels without water flow.  Embryos hatch
+between 4 and 6 h at 15 °C. Cellulose-producing cells identified by staining
+with a carbohydrate-binding-module (CBM)."]]
diff --git a/tags/Fritillaria.mdwn b/tags/Fritillaria.mdwn
index ed9d0dc3..84d424a9 100644
--- a/tags/Fritillaria.mdwn
+++ b/tags/Fritillaria.mdwn
@@ -4,6 +4,12 @@ _in progress_
 
  - _Fritillaria borealis_ can swim with its house deflated ([[Flood, 2003|biblio/10.1007_s00227-003-1075-y]]).
 
+ - Fed in culture with _Micromonas pusilla_ or _Synechococcus sp_ in culture at
+   a density between 2 and 8 × 10<sup>7</sup> depending on the developmental
+   stage ([[Henriet, Asajord and Chourrout, 2022|biblio/36307829]]).
+
+ - Karyotype of 4 chromosomes ([[Henriet, Asajord and Chourrout, 2022|biblio/36307829]]).
+
 # Found in:
 
 ## Antarctica

creating tag page tags/clock
diff --git a/tags/clock.mdwn b/tags/clock.mdwn
new file mode 100644
index 00000000..50f3f75d
--- /dev/null
+++ b/tags/clock.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged clock"]]
+
+[[!inline pages="tagged(clock)" actions="no" archive="yes"
+feedshow=10]]

Details on the molecular clock analysis.
diff --git a/biblio/36867684.mdwn b/biblio/36867684.mdwn
index 76e76691..3a99120f 100644
--- a/biblio/36867684.mdwn
+++ b/biblio/36867684.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. "]]
-[[!tag genome]]
+[[!tag genome clock]]
 
 Huang Z, Xu L, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis ED, Li G, Lin G, Zhang Q, Zhou Q. 
 
@@ -7,4 +7,28 @@ Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2201504120. doi:10.1073/pnas.22015
 
 Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. 
 
-[[!pmid 36867684 desc="Chromosomal assembly of _Branchiostoma floridae_ (Bf), _Branchiostoma belcheri_ (Bb) and _Branchiostoma japonicum_ (Bj).  ”we devised an interspecific trio sequencing strategy [...] for the F1 hybrids derived from Bf-Bb or Bf-Bj crosses. [...] the hybrids contain two haploid parental genomes that have become too diverged in sequences to form cross-species chimeric assembly”  “The three amphioxus genomes show a highly conserved chromosomal synteny to each other, with  most  chromosomes  showing  a  one-to-one  homologous  relationship except for a few chromosome fusions.”  ”genome-wide heterozygosity [estimated to] range from 3.2 to 4.2%”  ”Based on 3,653 single-copy orthologous genes, we estimated that different chordate lineages diverged about 592.5 Mya, and three amphioxus  species  diverged  about  99.9  Mya”.  “Using whole-genome resequencing data of between 10 and 48 individuals per sex per species, we identified the sexually differentiated regions (SDR) that harbor [...] excessive  female heterozygotes, and are not shared between the three amphioxus species.  In particular, the SDR of Bf is located on Chr16 and harbors 194 genes; and those of Bj and Bb are located at two different genomic loci of Chr3, harboring 35 genes and one gene with unknown function respectively. Bf Chr16 is not homologous with Chr3 of Bj or Bb.”"]]
+[[!pmid 36867684 desc="Chromosomal assembly of _Branchiostoma floridae_ (Bf),
+_Branchiostoma belcheri_ (Bb) and _Branchiostoma japonicum_ (Bj).  ”we devised
+an interspecific trio sequencing strategy [...] for the F1 hybrids derived from
+Bf-Bb or Bf-Bj crosses. [...] the hybrids contain two haploid parental genomes
+that have become too diverged in sequences to form cross-species chimeric
+assembly”  “The three amphioxus genomes show a highly conserved chromosomal
+synteny to each other, with most chromosomes showing a one-to-one homologous
+relationship except for a few chromosome fusions.”  ”genome-wide heterozygosity
+[estimated to] range from 3.2 to 4.2%”  ”Based on 3,653 single-copy orthologous
+genes, we estimated that different chordate lineages diverged about 592.5 Mya,
+and three amphioxus species diverged about 99.9 Mya”.  “Using whole-genome
+resequencing data of between 10 and 48 individuals per sex per species, we
+identified the sexually differentiated regions (SDR) that harbor [...]
+excessive female heterozygotes, and are not shared between the three amphioxus
+species.  In particular, the SDR of Bf is located on Chr16 and harbors 194
+genes; and those of Bj and Bb are located at two different genomic loci of
+Chr3, harboring 35 genes and one gene with unknown function respectively. Bf
+Chr16 is not homologous with Chr3 of Bj or Bb.”"]]
+
+Mean and confidence interval for divergence times given in Table S2:
+
+ - _B. belcheri_ and _B. japonicum_: 59.3 [12.2, 132.0].
+ - all _Branchiostoma_: 99.9 [22.1, 211.7].
+ - all chordates: 592.5 [530.8, 640.3].  Prior: [514, 636.1].
+ - Euarchontoglires: 116.1 [72.1, 163.1].  Prior: [65.6, 164.6].

Résolu
diff --git a/dh.txt b/dh.txt
deleted file mode 100644
index e02faf22..00000000
--- a/dh.txt
+++ /dev/null
@@ -1,21 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
-
-Hello DreahHost Customer Service I am Charles Plessy and we are discussing in the email thread 226139527 
-
------BEGIN PGP SIGNATURE-----
-
-iQIzBAEBCgAdFiEEc0cUmcxg7Z7ugFlGxb1sjyKV1QIFAmPwFvMACgkQxb1sjyKV
-1QImoRAAob7ZPH9T3/AG6p96RSulnOXfCxEcq7rDc3pFZdgIgsI9e0od0CFIlUtT
-Dnbwycgd+RFOwk+VeEbj0eWAFb4PBEZO1G3X4YEiQDLVv5aNsLEdenNC9+H0x6XT
-NigFIHTILvHwpcdtUfOHnUZe+1vwo8DsZHNrc3FQ3uOrygcDvzzXdmQY1blRpq37
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-9+8l5gDAHxmk0pB9/Wu5J5IAlX+fZ2bjqSRZK+GvfxNjnoEZyUtWVZ1YF5iKKiq0
-0862YnDBrR9ajRtCVskiZ3ML6ySujbo8gnMYBe36JqyhtZNbEM2DvQtdCzac47Ep
-CSmFR7mYO3vidH8ETqKiMPAErq27lAaYzdq7MWwWaLVxqu/w0b6D7+Npc9d1lx52
-j4Qv693SVLU9GvYxHZZ0HJWSmYIPMR13ldXOR8t/88M7ANQ2tGDYG1cVIqMwl7OH
-88WUrJ8aBnZPwi2lq5Up956wFg7JQqtb/O8S7SS9LumXZJAXC4qOfN2AsDkoxEr/
-aVqtKLNJBPky7kn1o21dbUpilz70jjoU46KFZIe//njwsnebqq+bB/Y4HDlXxBKz
-cX9jlPji2MCqg7LfH/5rJAeCKhtCBXyF4EdyxJsU87TlE+uKikw=
-=WBtm
------END PGP SIGNATURE-----

Café
diff --git a/biblio/36867684.mdwn b/biblio/36867684.mdwn
new file mode 100644
index 00000000..76e76691
--- /dev/null
+++ b/biblio/36867684.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. "]]
+[[!tag genome]]
+
+Huang Z, Xu L, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis ED, Li G, Lin G, Zhang Q, Zhou Q. 
+
+Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2201504120. doi:10.1073/pnas.2201504120
+
+Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. 
+
+[[!pmid 36867684 desc="Chromosomal assembly of _Branchiostoma floridae_ (Bf), _Branchiostoma belcheri_ (Bb) and _Branchiostoma japonicum_ (Bj).  ”we devised an interspecific trio sequencing strategy [...] for the F1 hybrids derived from Bf-Bb or Bf-Bj crosses. [...] the hybrids contain two haploid parental genomes that have become too diverged in sequences to form cross-species chimeric assembly”  “The three amphioxus genomes show a highly conserved chromosomal synteny to each other, with  most  chromosomes  showing  a  one-to-one  homologous  relationship except for a few chromosome fusions.”  ”genome-wide heterozygosity [estimated to] range from 3.2 to 4.2%”  ”Based on 3,653 single-copy orthologous genes, we estimated that different chordate lineages diverged about 592.5 Mya, and three amphioxus  species  diverged  about  99.9  Mya”.  “Using whole-genome resequencing data of between 10 and 48 individuals per sex per species, we identified the sexually differentiated regions (SDR) that harbor [...] excessive  female heterozygotes, and are not shared between the three amphioxus species.  In particular, the SDR of Bf is located on Chr16 and harbors 194 genes; and those of Bj and Bb are located at two different genomic loci of Chr3, harboring 35 genes and one gene with unknown function respectively. Bf Chr16 is not homologous with Chr3 of Bj or Bb.”"]]

updated PO files
diff --git "a/Debian/debi\303\242neries/dreamhost.en.po" "b/Debian/debi\303\242neries/dreamhost.en.po"
index 414ac52e..101ff943 100644
--- "a/Debian/debi\303\242neries/dreamhost.en.po"
+++ "b/Debian/debi\303\242neries/dreamhost.en.po"
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2023-03-09 13:38+0000\n"
+"POT-Creation-Date: 2023-03-10 03:07+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"
@@ -36,6 +36,15 @@ msgstr ""
 msgid "[[!meta title=\"If you work at Dreamhost, can you help us?\"]]\n"
 msgstr ""
 
+#. type: Plain text
+#, no-wrap
+msgid ""
+"***Update: thanks to the very kind involvment of the widow of our wemaster, we\n"
+"could provide enough private information to Dreamhost, who finally accepted to\n"
+"reset the password and the MFA.  We have recovered evrything!  Many thanks to\n"
+"everybody who helped us!***\n"
+msgstr ""
+
 #. type: Plain text
 msgid ""
 "Due to tragic circumstances, one association that I am part of, "

Bonne nouvelle.
diff --git "a/Debian/debi\303\242neries/dreamhost.mdwn" "b/Debian/debi\303\242neries/dreamhost.mdwn"
index f4e52e6d..bddf20cc 100644
--- "a/Debian/debi\303\242neries/dreamhost.mdwn"
+++ "b/Debian/debi\303\242neries/dreamhost.mdwn"
@@ -4,6 +4,11 @@
 
 [[!meta title="If you work at Dreamhost, can you help us?"]]
 
+***Update: thanks to the very kind involvment of the widow of our wemaster, we
+could provide enough private information to Dreamhost, who finally accepted to
+reset the password and the MFA.  We have recovered evrything!  Many thanks to
+everybody who helped us!***
+
 Due to tragic circumstances, one association that I am part of,
 [Sciencescope](https://www.sciencescope.org) got locked out of its account at
 Dreamhost.  Locked out, we can not pay the annual bill.  Dreamhost contacted us

updated PO files
diff --git "a/Debian/debi\303\242neries/dreamhost.en.po" "b/Debian/debi\303\242neries/dreamhost.en.po"
new file mode 100644
index 00000000..414ac52e
--- /dev/null
+++ "b/Debian/debi\303\242neries/dreamhost.en.po"
@@ -0,0 +1,68 @@
+# 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: 2023-03-09 13:38+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Thu, 09 Mar 2023 22:35:00 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Thu, 09 Mar 2023 22:35:00 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"If you work at Dreamhost, can you help us?\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Due to tragic circumstances, one association that I am part of, "
+"[Sciencescope](https://www.sciencescope.org) got locked out of its account "
+"at Dreamhost.  Locked out, we can not pay the annual bill.  Dreamhost "
+"contacted us about the payment, but will not let us recover the access to "
+"our account in order to pay.  So they will soon close the account.  Our "
+"website, mailing lists and archives, will be erased.  We provided plenty of "
+"evidence that we are not scammers and that we are the legitimate owners of "
+"the account, but reviewing it is above the pay grade of the custommer "
+"support (I don't blame them) and I could not convince them to let somebody "
+"higher have a look at our case."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"If you work at Dreamhost and want to keep us as custommers instead of "
+"kicking us like that, please ask the support service in charge of ticket "
+"225948648 to send the recovery URL to the _secondary_ email adddresses (the "
+"ones you used to contact us about the bill!) in addition to the _primary_ "
+"one (which nobody will read anymore).  You can encrypt it for my Debian "
+"Developer key 73471499CC60ED9EEE805946C5BD6C8F2295D502 if you worry it gets "
+"in wrong hands.  If you still have doubts I am available for calls any time."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"If you know somebody working at Dreamhost can you pass them the message? "
+"This would be a big, big, relief for our non-profit association."
+msgstr ""

help
diff --git "a/Debian/debi\303\242neries/dreamhost.mdwn" "b/Debian/debi\303\242neries/dreamhost.mdwn"
new file mode 100644
index 00000000..f4e52e6d
--- /dev/null
+++ "b/Debian/debi\303\242neries/dreamhost.mdwn"
@@ -0,0 +1,26 @@
+[[!meta date="Thu, 09 Mar 2023 22:35:00 +0900"]]
+[[!meta updated="Thu, 09 Mar 2023 22:35:00 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="If you work at Dreamhost, can you help us?"]]
+
+Due to tragic circumstances, one association that I am part of,
+[Sciencescope](https://www.sciencescope.org) got locked out of its account at
+Dreamhost.  Locked out, we can not pay the annual bill.  Dreamhost contacted us
+about the payment, but will not let us recover the access to our account in
+order to pay.  So they will soon close the account.  Our website, mailing lists
+and archives, will be erased.  We provided plenty of evidence that we are not
+scammers and that we are the legitimate owners of the account, but reviewing it
+is above the pay grade of the custommer support (I don't blame them) and I
+could not convince them to let somebody higher have a look at our case.
+
+If you work at Dreamhost and want to keep us as custommers instead of kicking
+us like that, please ask the support service in charge of ticket 225948648 to
+send the recovery URL to the _secondary_ email adddresses (the ones you used to
+contact us about the bill!) in addition to the _primary_ one (which nobody will
+read anymore).  You can encrypt it for my Debian Developer key
+73471499CC60ED9EEE805946C5BD6C8F2295D502 if you worry it gets in wrong hands.
+If you still have doubts I am available for calls any time.
+
+If you know somebody working at Dreamhost can you pass them the message?
+This would be a big, big, relief for our non-profit association.

Hello DreamHost
diff --git a/dh.txt b/dh.txt
new file mode 100644
index 00000000..e02faf22
--- /dev/null
+++ b/dh.txt
@@ -0,0 +1,21 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
+Hello DreahHost Customer Service I am Charles Plessy and we are discussing in the email thread 226139527 
+
+-----BEGIN PGP SIGNATURE-----
+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+=WBtm
+-----END PGP SIGNATURE-----

Café
diff --git a/biblio/21685081.mdwn b/biblio/21685081.mdwn
new file mode 100644
index 00000000..3a9ffeb7
--- /dev/null
+++ b/biblio/21685081.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions."]]
+[[!tag genome alignment]]
+
+Lin MF, Jungreis I, Kellis M.
+
+Bioinformatics. 2011 Jul 1;27(13):i275-82. doi: 10.1093/bioinformatics/btr209
+
+PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.
+
+[[!pmid 21685081 desc="Classifies coding and non-coding regions using multiple genome sequence alignments and the fit with separate codon score matrices for coding an non-coding."]]
diff --git a/tags/alignment.mdwn b/tags/alignment.mdwn
index 89b1ef03..b98b01be 100644
--- a/tags/alignment.mdwn
+++ b/tags/alignment.mdwn
@@ -21,4 +21,8 @@ see [[LAST]] for a detailed bibliography.
    an iterative approach where ancestral genomes are reconstituted using 2-5 pairs
    of in- and out-group comparisons, and then progressively aligned to each other.
 
+## Consumers of multiple genome sequence alignments
+
+ - PhyloCSF ([[Lin, Jungreis and Kellis (2011)|biblio/21685081]]).
+
 [[!inline pages="tagged(alignment)" limit=0]]

Café
diff --git a/biblio/34853330.mdwn b/biblio/34853330.mdwn
new file mode 100644
index 00000000..f7aec4dd
--- /dev/null
+++ b/biblio/34853330.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Metabarcoding analysis of trophic sources and linkages in the plankton community of the Kuroshio and neighboring waters."]]
+[[!tag eDNA]]
+
+Kobari T, Tokumo Y, Sato I, Kume G, Hirai J.
+
+Sci Rep. 2021 Dec 1;11(1):23265 doi:10.1038/s41598-021-02083-8
+
+Metabarcoding analysis of trophic sources and linkages in the plankton community of the Kuroshio and neighboring waters.
+
+[[!pmid 34853330 desc="eDNA analysis of “the diets of 22 higher taxonomic groups, 13 copepod families and 35 species, that dominate in the Kuroshio food web”.  Larvacean DNA was more frequent in predator gut contents than in water samples.  “The 18S rRNA V9 region was amplified using eukaryotic universal primers 1389F and 1510R.”"]]
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
index 3aa11f94..f284280c 100644
--- a/tags/eDNA.mdwn
+++ b/tags/eDNA.mdwn
@@ -16,6 +16,9 @@
  - Edgar ([[2018|biblio/29506021]] proposes to raise the threshold to 99% or to
    just use sequence variants (also called ZOTUS, Zero-radius OTUs. 
 
+ - Larvacean DNA found more frequently in predator gut than in water samples
+   ([[Kobari and coll., 2021|biblio/34853330]]).  Uses the V9 region 18S primers.
+
 ### Published primers
 
 ```

Details on mechanism.
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index 65fbf91b..222faccd 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -51,6 +51,9 @@ Flanking an inversion in _D. buzzati_ between two _Galileo_ elements, the
 exchange of Target-Site Duplication sequences was observed by Cáceres and
 coll., [[(1999|biblio/10411506]]). 
 
+Ectopic recombination of a Galileo element may have caused a recent large-scale
+inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
+
 [[Kent and coll., 2003|biblio/14500911]] reported 2 inversions per Mbp in
 human/mouse comparisons, median length 814. 
 
@@ -60,8 +63,11 @@ _Staggered breaks_ ([[Ranz and coll., 2007|bilbio/17550304]]) caused
 by inverted duplications.  The duplicated sequnces may be coding genes or
 pseudogenes, not just transposable elements.
 
-Ectopic recombination of a Galileo element may have caused a recent large-scale
-inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
+([[Delprat and coll, 2009|biblio/19936241]]) proposed that “Chromosomal
+inversions may be generated by transposons when two ends that are not part of
+the same transposon participate in an aberrant transposition event to a new
+site”.  They give an example where the two transposons are identical copies
+on sister chromatids in G2 phase.
 
 ## Software
 

Reorganise avec du café
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index dc41893b..65fbf91b 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -5,7 +5,9 @@ _in progress_
 Long read sequencing data from 3,622 Icelanders identified a median of 22,636
 SVs per individual (insertios: 13,353; deletions: 9,474) [[Beyter and coll, 2021|biblio/33972781]].
 
-### Inversions
+## Inversions
+
+### Within-population
 
 SNP analysis in >1400 seaweed flies identified known and candidate genomic inversions
 ([[Mérot and coll, 2021|biblio/33963409]]).
@@ -14,6 +16,15 @@ SV analysis of 31 diploid assemblies of _Theobroma cacao_ showed relaxed
 selection and increased genetic load in inversions and other types of variants
 [[Hämälä and coll., 2021|biblio/34408075]].
 
+[[Stefansson and coll, 2005||biblio/15654335]] found an inversion in the human
+genome and calculated that it appeared ~3 million years ago, before the
+speciation of _Homo sapiens_.  Low-copy repeated sequences were found in the
+vicinity.  [[Donelly and coll., 2010|biblio/20116045]] gave a radically lower
+time estimate of 13,600 to 108,400 years, but an ancient origin was again
+supported by [[Steinberg and coll in 2012|biblio/22751100]].
+
+### Between-species
+
 ~1100 small-scale inversions are estimated to have happened between _S.
 cerevisiae_ and _C. albicans_ ([[Seoighe and coll., 2000|biblio/11087826]]).  The authors propose that
 “successive multigene inversions” have “distrupted” the “precise arrangement”
@@ -36,16 +47,6 @@ isochromatid or chromatid, and that this, rather than ectopic exchange between
 inverted repetitive sequences, is the prevalent mechanism for the generation of
 inversions in the melanogaster species group”. 
 
-[[Stefansson and coll, 2005||biblio/15654335]] found an inversion in the human
-genome and calculated that it appeared ~3 million years ago, before the
-speciation of _Homo sapiens_.  Low-copy repeated sequences were found in the
-vicinity.  [[Donelly and coll., 2010|biblio/20116045]] gave a radically lower
-time estimate of 13,600 to 108,400 years, but an ancient origin was again
-supported by [[Steinberg and coll in 2012|biblio/22751100]].
-
-Ectopic recombination of a Galileo element may have caused a recent large-scale
-inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
-
 Flanking an inversion in _D. buzzati_ between two _Galileo_ elements, the
 exchange of Target-Site Duplication sequences was observed by Cáceres and
 coll., [[(1999|biblio/10411506]]). 
@@ -53,7 +54,16 @@ coll., [[(1999|biblio/10411506]]).
 [[Kent and coll., 2003|biblio/14500911]] reported 2 inversions per Mbp in
 human/mouse comparisons, median length 814. 
 
-### Software
+### Mechanism
+
+_Staggered breaks_ ([[Ranz and coll., 2007|bilbio/17550304]]) caused
+by inverted duplications.  The duplicated sequnces may be coding genes or
+pseudogenes, not just transposable elements.
+
+Ectopic recombination of a Galileo element may have caused a recent large-scale
+inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
+
+## Software
 
  - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long
    reads aligned to a reference genome with last-split