Dernières modifications :

software
diff --git a/biblio/28655158.mdwn b/biblio/28655158.mdwn
new file mode 100644
index 00000000..db9be0df
--- /dev/null
+++ b/biblio/28655158.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes."]]
+[[!tag mitochondrion not_read]]
+
+Bioinformatics. 2017 Nov 1;33(21):3331-3339. doi: 10.1093/bioinformatics/btx421.
+
+Noutahi E, Calderon V, Blanchette M, Lang FB, El-Mabrouk N.
+
+CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.
+
+[[!pmid desc="Not read.  For reference"]]

software
diff --git a/biblio/21653513.mdwn b/biblio/21653513.mdwn
new file mode 100644
index 00000000..6c237dc6
--- /dev/null
+++ b/biblio/21653513.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="FACIL: Fast and Accurate Genetic Code Inference and Logo."]]
+[[!tag mitochondrion software]]
+
+Bioinformatics. 2011 Jul 15;27(14):1929-33. doi:10.1093/bioinformatics/btr316
+
+Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA.
+
+FACIL: Fast and Accurate Genetic Code Inference and Logo.
+
+[[!pmid 21653513 desc="Command-line still runs fine in 2019."]]

Tag
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 2cd6d2d5..05d9de79 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Tunicates and not cephalochordates are the closest living relatives of vertebrates."]]
-[[!tag evolution Oikopleura]]
+[[!tag evolution Oikopleura tunicate]]
 
 Delsuc F, Brinkmann H, Chourrout D, Philippe H.
 

Tag
diff --git a/biblio/17051155.mdwn b/biblio/17051155.mdwn
index 8a0ced07..94d7bed3 100644
--- a/biblio/17051155.mdwn
+++ b/biblio/17051155.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida."]]
-[[!tag evolution]]
+[[!tag tunicate evolution]]
 
 Bourlat SJ1, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES, Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ.
 

Café
diff --git a/biblio/pubmedlater.mdwn b/biblio/pubmedlater.mdwn
new file mode 100644
index 00000000..f6c1e132
--- /dev/null
+++ b/biblio/pubmedlater.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ultrasound imaging of gene expression in mammalian cells"]]
+[[!tag ultrasound]]
+
+Arash Farhadi, Gabrielle H. Ho, Daniel P. Sawyer, Raymond W. Bourdeau, Mikhail G. Shapiro
+
+Science  27 Sep 2019 Vol. 365, Issue 6460, pp. 1469-1475 doi:10.1126/science.aax4804 
+
+Ultrasound imaging of gene expression in mammalian cells
+
+[[!pmid later desc="Bacillus megaterium gas vesicle genes were codon-optimised and transfected into mammalian cells.  What is detected is the collapse of the gas vesicles under ultrasound exposure."]]

OSA2016 genome on Aniseed
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index abf940d5..2e2b9b02 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -21,6 +21,7 @@ Some links:
  - Études sur les Appendiculaires du Détroit de Messine, Hermann Fol, 1872
    ([[ark:/13960/t7fr0vj77|https://archive.org/details/cbarchive_100233_etudessurlesappendiculairesdud1821]]).
  - [A day in the life of an Oikopleura lab](http://thenode.biologists.com/day-life-oikopleura-lab/).
+ - OSA2016 genome on aniseed: <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
 
 Food tested in laboratory (totally incomplete list): _Isochrysis galbana_ (5.5
 µm in size), _Tetraselmis suecica_ (9.5 µm), and the chlorophyte _Chlorella

Café
diff --git a/biblio/10.1017_S0954102003001585.mdwn b/biblio/10.1017_S0954102003001585.mdwn
new file mode 100644
index 00000000..c22eeb7c
--- /dev/null
+++ b/biblio/10.1017_S0954102003001585.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The classification of Antarctic appendicularians: the Oikopleura gaussica group"]]
+[[!tag Oikopleura]]
+
+Capitanio FL, Daponte MC and Esnal GB.
+
+Antarctic Science 15 (4): 476–482 (2003) doi:10.1017/S0954102003001585
+
+The classification of Antarctic appendicularians: the Oikopleura gaussica group
+
+[[!doi 10.1017/S0954102003001585 desc="Proposes that O. gaussica, O. valdiviae, O. drygalskii, and O. weddelli actually form a single species.  It has oral gland cells, and a variable (8~14) number of subchordal cells, on the right (ventral) side of the tail."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1780e5e2..abf940d5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -511,6 +511,9 @@ Ecology
  - Mesopelagic oikopleura were described by [[R. Fenaux
    (1993)|biblio/10.1017_S0025315400033178]] in Bahamian and Bermudian
    and in mediterranean waters.
-
+ - Oikopleuridae can be found in polar waters.  [[Capitanio, Daponte and Esnal
+   (2003)|biblio/10.1017_S0954102003001585]] proposed that _O. gaussica_, _O.
+   valdiviae_, _O. drygalskii_, and _O. weddelli_ are actually a single species
+   (with oral gland cells and ~8 to 14 subchordal cells).
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café
diff --git a/biblio/10.1017_S0025315400033178.mdwn b/biblio/10.1017_S0025315400033178.mdwn
new file mode 100644
index 00000000..b7970490
--- /dev/null
+++ b/biblio/10.1017_S0025315400033178.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A new genus of midwater appendicularian: Mesoikopleura with four species"]]
+[[!tag Oikopleura]]
+
+Robert Fenaux
+
+Journal of the Marine Biological Association of the United Kingdom. Volume 73, Issue 3, August 1993, pp. 635-646
+
+A new genus of midwater appendicularian: Mesoikopleura with four species
+
+[[!doi 10.1017/S0025315400033178 desc="Sampled at 700-900 m depth.  No buccal glands.  Trunk sizes 740~1400 µm.  Tail sizes of 7200~8750 µm.  Either numerous small amphicordal cells on both sides of the tail (M. enterospira, M. youngbluthi) or seven (4+3) fusiform amphicordal celss (gyroceanis).  Splits Oikopleurinae into two groups according to the presence or absence of buccal lips: Alabiata and Labiata."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 42a1a74c..1780e5e2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -508,5 +508,9 @@ Ecology
  - Southen sea of Cortez (Mexico), near Isla El Paradito (water temperature =
    30 °C; night dives), _O. dioica_ was found but not as abundant as other
    larvaceans ([[Galt, Grober and Sykes, 1985|biblio/10.2307_1541178]]).
+ - Mesopelagic oikopleura were described by [[R. Fenaux
+   (1993)|biblio/10.1017_S0025315400033178]] in Bahamian and Bermudian
+   and in mediterranean waters.
+
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

To read
diff --git a/biblio/15632085.mdwn b/biblio/15632085.mdwn
new file mode 100644
index 00000000..01812256
--- /dev/null
+++ b/biblio/15632085.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution."]]
+[[!tag to_read]]
+
+Genome Res. 2005 Jan;15(1):1-18 doi:10.1101/gr.3059305
+
+Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA.
+
+Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
+
+[[!pmid 15632085 desc="To read"]]

creating tag page tags/frog
diff --git a/tags/frog.mdwn b/tags/frog.mdwn
new file mode 100644
index 00000000..4fda82ce
--- /dev/null
+++ b/tags/frog.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged frog"]]
+
+[[!inline pages="tagged(frog)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/31578486.mdwn b/biblio/31578486.mdwn
new file mode 100644
index 00000000..947e0388
--- /dev/null
+++ b/biblio/31578486.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Imprinting sets the stage for speciation."]]
+[[!tag frog speciation population model]]
+
+Yang Y, Servedio MR, Richards-Zawacki CL.
+
+Nature. 2019 Oct;574(7776):99-102. doi:10.1038/s41586-019-1599-z
+
+Imprinting sets the stage for speciation.
+
+[[!pmid desc="Oophaga pumilio tadpoles learn congeneric coat color from their mother."]]

To read
diff --git a/biblio/20075246.mdwn b/biblio/20075246.mdwn
new file mode 100644
index 00000000..ce617726
--- /dev/null
+++ b/biblio/20075246.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hungry codons promote frameshifting in human mitochondrial ribosomes."]]
+[[!tag to_read]]
+
+Temperley R, Richter R, Dennerlein S, Lightowlers RN, Chrzanowska-Lightowlers ZM.
+
+Science. 2010 Jan 15;327(5963):301. doi:10.1126/science.1180674
+
+Hungry codons promote frameshifting in human mitochondrial ribosomes.
+
+[[!pmid 20075246 desc="To read"]]

To read
diff --git a/biblio/10.1016_0198-0149_92_90070-A.mdwn b/biblio/10.1016_0198-0149_92_90070-A.mdwn
new file mode 100644
index 00000000..373c1d7c
--- /dev/null
+++ b/biblio/10.1016_0198-0149_92_90070-A.mdwn
@@ -0,0 +1,9 @@
+[[!meta title="In situ observations of giant appendicularians in Monterey Bay"]]
+[[!tag to_read]]
+
+Author links open overlay panelWilliam MHamner∗†Bruce HRobison∗
+
+Volume 39, Issues 7–8, July–August 1992, Pages 1299-1313 doi:10.1016/0198-0149(92)90070-A
+
+In situ observations of giant appendicularians in Monterey Bay
+[[!doi 10.1016/0198-0149(92)90070-A desc="To read"]]

Café
diff --git a/biblio/12481130.mdwn b/biblio/12481130.mdwn
new file mode 100644
index 00000000..4d5683a7
--- /dev/null
+++ b/biblio/12481130.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins."]]
+[[!tag Ciona genome cellulose]]
+
+Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS.
+
+Science. 2002 Dec 13;298(5601):2157-67 doi: 10.1126/science.1080049
+
+The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.
+
+[[!pmid 12481130 desc="The genome of _C. intestinalis_ contains at least one cellulose synthans and multiple endoglycanases."]]
diff --git a/tags/cellulose.mdwn b/tags/cellulose.mdwn
index ee088b09..5bf15a48 100644
--- a/tags/cellulose.mdwn
+++ b/tags/cellulose.mdwn
@@ -11,4 +11,7 @@ Sasakura and coll. ([[2016|biblio/28003446]] have proposed that the GC-rich
 genome of actinobacteria might have provided an AP-2 binding site promoting
 expression in the epidermis.
 
+A cellulose synthase and several endoglycanase genes were observed in the _C.
+intestinalis_ genome by [[Dehal and coll., 2002|biblio/12481130]].
+
 [[!inline pages="tagged(cellulose)" limit=0]]

Café
diff --git a/biblio/7579513.mdwn b/biblio/7579513.mdwn
new file mode 100644
index 00000000..0af7dd3a
--- /dev/null
+++ b/biblio/7579513.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gene duplications and the origins of vertebrate development."]]
+[[!tag Oikopleura]]
+
+Holland PW, Garcia-Fernàndez J, Williams NA, Sidow A.
+
+Dev Suppl. 1994:125-33.
+
+Gene duplications and the origins of vertebrate development.
+
+[[!pmid 7579513 desc="Attempt to clone Hox genes with degenerate primers only yielded one clone."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 591388f3..42a1a74c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -174,6 +174,8 @@ Genes and pathways
    are activated by polyunsaturated aldehydes produced by diatoms
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
  - _O. dioica_ has 83 homeobox genes, according to [[Edvardsen and coll., 2005|biblio/15649342]].
+   Illustrating how diverged are the sequences, earlier attempts to clone Hox genes yielded
+   only a single clone ([[Holland and coll. 1994|biblio/7579513]]).
  - Southern blot analysis suggest the presence of a SCO-spondin gene in _O.
    dioica_ ([[Gobron and coll., 1999|biblio/10197783]]).
  - A single ortholog of _Brachyury_ (_TBXT_, or _T_) was cloned by [[Bassham

Café
diff --git a/biblio/24817302.mdwn b/biblio/24817302.mdwn
new file mode 100644
index 00000000..654f8132
--- /dev/null
+++ b/biblio/24817302.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Yellow-stained oikopleurid appendicularians are caused by bacterial parasitism"]]
+[[!tag Oikopleura]]
+
+Flood, P. R.
+
+MEPS 71:291-295 
+
+Yellow-stained oikopleurid appendicularians are caused by bacterial parasitism
+
+[Rod-shaped (0.6 or 0.4 µm-wide) bacteria observed by transmission and electron microscopy in O. dioica and O. vanhoeffeni](https://www.jstor.org/stable/24817302)
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 711c336f..591388f3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -363,7 +363,8 @@ Physiology
    the rectum.  Lipid uptake might happen in the right lobe of the stomach
    ([[Burighel, Brena, Martinucci and Cima
    (2005)|biblio/10.1111_j.1744-7410.2001.tb00038.x]]).
-
+ - Yellow color can be caused by bacterial infection.  [[Flood (1991)|biblio/24817302]]
+   observed rod-shaped bacteria (0.6 or 0.4 µm-wide) in _O. doica_ or _O. vanhoeffeni_.
 
 House
 -----

creating tag page tags/ultrasound
diff --git a/tags/ultrasound.mdwn b/tags/ultrasound.mdwn
new file mode 100644
index 00000000..4888a0b0
--- /dev/null
+++ b/tags/ultrasound.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged ultrasound"]]
+
+[[!inline pages="tagged(ultrasound)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/10.1101_785774.mdwn b/biblio/10.1101_785774.mdwn
new file mode 100644
index 00000000..df0b165a
--- /dev/null
+++ b/biblio/10.1101_785774.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The Pop-gen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses"]]
+[[!tag population]]
+
+bioRxiv,  September 30, 2019
+
+Andrew Webb, Jared Knoblauch, Nitesh Sabankar, Apeksha Sukesh Kallur, Jody Hey, Arun Sethuraman
+
+The Pop-gen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses
+
+[[!doi 10.1101/785774  desc="Python pipeline wrapping on plink, vcftools, etc."]]

Café
diff --git a/biblio/29300010.mdwn b/biblio/29300010.mdwn
new file mode 100644
index 00000000..ad203709
--- /dev/null
+++ b/biblio/29300010.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts."]]
+[[!tag method imaging ultrasound]]
+
+Bourdeau RW, Lee-Gosselin A, Lakshmanan A, Farhadi A, Kumar SR, Nety SP, Shapiro MG.
+
+Nature. 2018 Jan 3;553(7686):86-90. doi:10.1038/nature25021
+
+Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts.
+
+[[!pmid 29300010 desc="Bacterial gas containers reflect ultrasounds.  Introduced by transgenesis, they were used to non-invasively detect bacteria in the gut of live animals."]]

Users !
diff --git a/biblio/31519912.mdwn b/biblio/31519912.mdwn
new file mode 100644
index 00000000..081be278
--- /dev/null
+++ b/biblio/31519912.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells."]]
+[[!tag nanoCAGE not_read]]
+
+Tan L, Lacko LA, Zhou T, Tomoiaga D, Hurtado R, Zhang T, Sevilla A, Zhong A, Mason CE, Noggle S, Evans T, Stuhlmann H, Schwartz RE, Chen S.
+
+Nat Commun. 2019 Sep 13;10(1):4155. doi:10.1038/s41467-019-12063-2
+
+Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells.
+
+[[!pmid desc="Uses nanoCAGE"]]

To read
diff --git a/biblio/10.4067_S0716-078X2002000200005.mdwn b/biblio/10.4067_S0716-078X2002000200005.mdwn
new file mode 100644
index 00000000..a377b27f
--- /dev/null
+++ b/biblio/10.4067_S0716-078X2002000200005.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Taxonomic identification of appendicularians collected in the epipelagic waters off northern Chile (Tunicata, Appendicularia)"]]
+[[!tag to_read]]
+
+Guillermo Aravena & Sergio Palma
+
+Rev. chil. hist. nat. v.75 n.2 Santiago jun. 2002
+
+Taxonomic identification of appendicularians collected in the epipelagic waters off northern Chile (Tunicata, Appendicularia)
+
+[[!doi 10.4067/S0716-078X2002000200005 desc="to_read"]]

To read.
diff --git a/biblio/28854623.mdwn b/biblio/28854623.mdwn
new file mode 100644
index 00000000..2687ee27
--- /dev/null
+++ b/biblio/28854623.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Extreme Mitogenomic Variation in Natural Populations of Chaetognaths."]]
+[[!tag to_read]]
+
+Genome Biol Evol. 2017 Jun 1;9(6):1374-1384. doi:10.1093/gbe/evx090
+
+Marlétaz F, Le Parco Y, Liu S, Peijnenburg KTCA.
+
+Extreme Mitogenomic Variation in Natural Populations of Chaetognaths.
+
+[[!pmid 28854623 desc="To read"]]

To read
diff --git a/biblio/10.1093_plankt_21.12.2421.mdwn b/biblio/10.1093_plankt_21.12.2421.mdwn
new file mode 100644
index 00000000..da1862b6
--- /dev/null
+++ b/biblio/10.1093_plankt_21.12.2421.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Production of Oikopleura longicauda (Tunicata: Appendicularia) in Toyama Bay, southern Japan Sea"]]
+[[!tag to_read]]
+
+Mika Tomita, Tsutomu Ikeda, Naonobu Shiga
+
+Journal of Plankton Research, Volume 21, Issue 12, December 1999, Pages 2421–2430, doi:10.1093/plankt/21.12.2421
+
+Production of Oikopleura longicauda (Tunicata: Appendicularia) in Toyama Bay, southern Japan Sea
+
+[[!doi 10.1093/plankt/21.12.2421 desc="To read"]]

To read
diff --git a/biblio/30635418.mdwn b/biblio/30635418.mdwn
new file mode 100644
index 00000000..efcd07b2
--- /dev/null
+++ b/biblio/30635418.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Symbiotic organs shaped by distinct modes of genome evolution in cephalopods."]]
+[[!tag to_read]]
+
+Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez 
+S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S,
+Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai
+M, Simakov O, Foster JS, Nyholm SV.
+
+Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3030-3035. doi:10.1073/pnas.1817322116
+
+Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.
+
+[[!pmid 30635418 desc="To read"]]

To read
diff --git a/biblio/10.1093_plankt_fbn064.mdwn b/biblio/10.1093_plankt_fbn064.mdwn
new file mode 100644
index 00000000..03ba17af
--- /dev/null
+++ b/biblio/10.1093_plankt_fbn064.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Temporal and vertical distributions of three appendicularian species (Tunicata) in Conception Bay, Newfoundland"]]
+[[!tag to_read]]
+
+Nami Choe, Don Deibel
+
+Journal of Plankton Research, Volume 30, Issue 9, September 2008, Pages 969–979, doi:10.1093/plankt/fbn064
+
+Temporal and vertical distributions of three appendicularian species (Tunicata) in Conception Bay, Newfoundland
+
+[[!doi 10.1093/plankt/fbn064 desc="To read"]]

To read
diff --git a/biblio/10.1093_plankt_25.6.579.mdwn b/biblio/10.1093_plankt_25.6.579.mdwn
new file mode 100644
index 00000000..be5c6a7f
--- /dev/null
+++ b/biblio/10.1093_plankt_25.6.579.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Seasonal occurrence and vertical distribution of appendicularians in Toyama Bay, southern Japan Sea"]]
+[[!tag to_read]]
+
+Mika Tomita, Naonobu Shiga, Tsutomu Ikeda
+
+Journal of Plankton Research, Volume 25, Issue 6, June 2003, Pages 579–589, doi:10.1093/plankt/25.6.579
+
+Seasonal occurrence and vertical distribution of appendicularians in Toyama Bay, southern Japan Sea
+
+[[!doi 10.1093/plankt/25.6.579 desc="To read"]]

To read
diff --git a/biblio/10.1093_plankt_23.4.415.mdwn b/biblio/10.1093_plankt_23.4.415.mdwn
new file mode 100644
index 00000000..70abeb49
--- /dev/null
+++ b/biblio/10.1093_plankt_23.4.415.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=" House Production by Oikopleura dioica (Tunicata, Appendicularia) Under Laboratory Conditions"]]
+[[!tag to_read]]
+
+Riki Sato, Yuji Tanaka, Takashi Ishimaru
+
+Journal of Plankton Research, Volume 23, Issue 4, April 2001, Pages 415–423, doi:10.1093/plankt/23.4.415
+
+House Production by Oikopleura dioica (Tunicata, Appendicularia) Under Laboratory Conditions
+
+[[!doi 10.1093/plankt/23.4.415 desc="To read"]]

To read
diff --git a/biblio/21186941.mdwn b/biblio/21186941.mdwn
new file mode 100644
index 00000000..fa8c8456
--- /dev/null
+++ b/biblio/21186941.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Simple procedure for sperm cryopreservation in the larvacean tunicate Oikopleura dioica."]]
+[[!tag to_read]]
+
+Zoolog Sci. 2011 Jan;28(1):8-11. doi:10.2108/zsj.28.8
+
+Ouchi K, Nishino A, Nishida H.
+
+Simple procedure for sperm cryopreservation in the larvacean tunicate Oikopleura dioica.
+
+[[!pmid 21186941 desc="to read"]]

To read
diff --git a/biblio/26399483.mdwn b/biblio/26399483.mdwn
new file mode 100644
index 00000000..0af374e7
--- /dev/null
+++ b/biblio/26399483.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans."]]
+[[!tag to_read]]
+
+Rogers RL
+
+Mol Biol Evol. 2015 Dec;32(12):3064-78. doi:10.1093/molbev/msv204
+
+Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.
+
+[[!pmid 26399483 desc="To read"]]

Caéf
diff --git a/biblio/31511699.mdwn b/biblio/31511699.mdwn
new file mode 100644
index 00000000..fc7355ab
--- /dev/null
+++ b/biblio/31511699.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Genome architecture and stability in the Saccharomyces cerevisiae knockout collection."]]
+[[!tag yeast variants]]
+
+Puddu F, Herzog M, Selivanova A, Wang S, Zhu J, Klein-Lavi S, Gordon M,
+Meirman R, Millan-Zambrano G, Ayestaran I, Salguero I, Sharan R, Li R, Kupiec M, 
+Jackson SP.
+
+Nature. 2019 Sep;573(7774):416-420. doi:10.1038/s41586-019-1549-9
+
+Genome architecture and stability in the Saccharomyces cerevisiae knockout collection.
+
+[[!pmid 31511699 desc="Loss of short chromosomes and gains of long chromosomes, changes in rDNA and telomere repeats, ..."]]

To read
diff --git a/biblio/10.1007_BF00280746.mdwn b/biblio/10.1007_BF00280746.mdwn
new file mode 100644
index 00000000..63114350
--- /dev/null
+++ b/biblio/10.1007_BF00280746.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="La couche öikoplastique de l'Appendiculaire Oïkopleura albicans (Leuckart) (Tunicata)"]]
+[[!tag Oikopleura to_read]]
+
+La couche öikoplastique de l'Appendiculaire Oïkopleura albicans (Leuckart) (Tunicata)
+
+Morph. Tiere (1971) 69: 184. https://doi.org/10.1007/BF00280746 
+
+Fenaux, R. Z.
+
+[[!doi 10.1007/BF00280746 desc="À lire"]]

Good discussion with with B. Ryabko and N. Savina.
diff --git a/biblio/10.1109_ISIT.2017.8006502.mdwn b/biblio/10.1109_ISIT.2017.8006502.mdwn
new file mode 100644
index 00000000..63db6625
--- /dev/null
+++ b/biblio/10.1109_ISIT.2017.8006502.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Using data-compressors for statistical analysis of problems on homogeneity testing and classification"]]
+[[!tag software method comparison]]
+
+2017 IEEE International Symposium on Information Theory (ISIT), 25-30 June 2017, ISSN: 2157-8117, INSPEC Accession Number: 17100050, DOI: 10.1109/ISIT.2017.8006502
+
+Boris Ryabko ; Andrey Guskov ; Irina Selivanova
+
+Using data-compressors for statistical analysis of problems on homogeneity testing and classification
+
+[[!doi 10.1109/ISIT.2017.8006502 desc="Sequences more similar to each other are more efficiently compressed together.  First, test for difference, and if appropriate, compute distance."]]

creating tag page tags/to_read
diff --git a/tags/to_read.mdwn b/tags/to_read.mdwn
new file mode 100644
index 00000000..de06bc0c
--- /dev/null
+++ b/tags/to_read.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged to read"]]
+
+[[!inline pages="tagged(to_read)" actions="no" archive="yes"
+feedshow=10]]

To read
diff --git a/biblio/17629909.mdwn b/biblio/17629909.mdwn
new file mode 100644
index 00000000..58579d3d
--- /dev/null
+++ b/biblio/17629909.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment."]]
+[[!tag to_read]]
+
+Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G.
+
+BMC Bioinformatics. 2007 Jul 13;8:252 doi:10.1186/1471-2105-8-252
+
+Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
+
+[[!pmid 17629909 desc="to read"]]

Café
diff --git a/biblio/10.2307_1541178.mdwn b/biblio/10.2307_1541178.mdwn
new file mode 100644
index 00000000..03c59db3
--- /dev/null
+++ b/biblio/10.2307_1541178.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Taxonomic correlates of bioluminescence among appendicularians (urochordata: larvacea)"]]
+[[!tag Oikopleura]]
+
+Charles P. Galt, Matthew S. Grober and Paul F. Sykes
+
+The Biological Bulletin 168, no. 1 (February 1985): 125-134. 
+
+Taxonomic correlates of bioluminescence among appendicularians (urochordata: larvacea)
+
+[[!doi 10.2307/1541178 desc="Bioluminescence stimulated by agitation.  Field-collected houses of species that lack oral glands also sometimes emit light, possibly because of bioluminescent dinoflagellates.  O. dioica has oral glands and bioluminescent rudiment inclusions.  Neither O. longicauda nor Bathochordaeus charon have oral glands and bioluminescence.  O. dioica not as abundant as other oiks in the Southen sea of Cortez (Mexico), near Isla El Paradito (water temperature = 30 °C; night dives)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 4e7517a0..711c336f 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -391,6 +391,10 @@ House
  - _Mesochordaeus erythrocephalus_ [[(Hopcroft and Robinson,
    1999)|biblio/10.1093_plankt_21.10.1923]]: mesopelagic species with a large
    (~30 cm) house.
+ - Houses of _O. dioica_ and related species that have oral glands have
+   granular inclusions that are bioluminescent ([[Galt, Grober and Sykes,
+   1985|biblio/10.2307_1541178]]).  In species without oral glands, bioluminescence
+   might be caused by dinoflagellates.
 
 
 Phenotypes
@@ -498,5 +502,8 @@ Ecology
  - South Atlantic: found all year near Mar del Plata in 2000—1, where it was
    most abundant in summer ([[Viñas and coll.,
    2013|biblio/10.1080_17451000.2012.745003]]).
+ - Southen sea of Cortez (Mexico), near Isla El Paradito (water temperature =
+   30 °C; night dives), _O. dioica_ was found but not as abundant as other
+   larvaceans ([[Galt, Grober and Sykes, 1985|biblio/10.2307_1541178]]).
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café
diff --git a/biblio/31171833.mdwn b/biblio/31171833.mdwn
new file mode 100644
index 00000000..340f012f
--- /dev/null
+++ b/biblio/31171833.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column."]]
+[[!tag Oikopleura microplastic]]
+
+Choy CA, Robison BH, Gagne TO, Erwin B, Firl E, Halden RU, Hamilton JA, Katija K, Lisin SE, Rolsky C, S Van Houtan K.
+
+Sci Rep. 2019 Jun 6;9(1):7843. doi: 10.1038/s41598-019-44117-2.
+
+The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column.
+
+[[!pmid 31171833 desc="“The number of microplastic particles contained within a [Bathochordaeus] sinker ranged from 3 to 17 (mean 10.7 microplastic particles ± 5.3 particles standard deviation).”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 979858f4..4e7517a0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -406,6 +406,7 @@ Phenotypes
    binding to protein from the lipocalin family, to change the color from
    red to blue ([[Mojib and coll., 2014|biblio/24803335]]).
 
+
 Ecology
 -------
 
@@ -433,8 +434,10 @@ Ecology
    Kiefer, 2000|biblio/10.4319_lo.2000.45.3.0608.mdwn]]).
  - Gravid _B mcnutti_ individuals are found at down to 800 m, but spawning is supposed to
    happen closer to the surface ([[Sherlock and coll., 2017|biblio/28042175]]).
- - Oikopleuridae have been reported to be able to ingest microplastics.  Example(s):
-   _B. stygius_ ([[Katija and coll., 2017b|biblio/28835922]]).
+ - Oikopleuridae have been reported to be able to ingest microplastics.
+   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]].
  - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus
    ([[Lawrence and coll., 2017|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.

Café
diff --git a/biblio/15947183.mdwn b/biblio/15947183.mdwn
new file mode 100644
index 00000000..1b67602b
--- /dev/null
+++ b/biblio/15947183.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Giant larvacean houses: rapid carbon transport to the deep sea floor."]]
+[[!tag Oikopleura]]
+
+Robison BH, Reisenbichler KR, Sherlock RE.
+
+Science. 2005 Jun 10;308(5728):1609-11 doi:10.1126/science.1109104
+
+Giant larvacean houses: rapid carbon transport to the deep sea floor.
+
+[[!pmid 15947183 desc="Bathochordaeus species may produce one house per day.  Sinking houses are an important contribution to the carbon flux to the sea floor."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 2567d0b4..979858f4 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -386,6 +386,12 @@ House
    ([[Katija and coll., 2018|biblio/28508058]]).
  - Filter-feeding in marine animals has been reviewed by [[Conley, Lombard and
    Sutherland (2018)|biblio/29720410]].
+ - _Bathochordaeus_ may produce one house per day ([[Robison, Reisenbichler and
+   Sherlock, 2005|biblio/15947183]]).
+ - _Mesochordaeus erythrocephalus_ [[(Hopcroft and Robinson,
+   1999)|biblio/10.1093_plankt_21.10.1923]]: mesopelagic species with a large
+   (~30 cm) house.
+
 
 Phenotypes
 ----------
@@ -490,12 +496,4 @@ Ecology
    most abundant in summer ([[Viñas and coll.,
    2013|biblio/10.1080_17451000.2012.745003]]).
 
-Other appendicularians
-----------------------
-
- - _Mesochordaeus erythrocephalus_ [[(Hopcroft and Robinson,
-   1999)|biblio/10.1093_plankt_21.10.1923]]: mesopelagic species with a large
-   (~30 cm) house.
-
-
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5ac9d5bb..2567d0b4 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -445,7 +445,7 @@ Ecology
  - Two blooms taking place in summer 1997 in the Seto inland sea, Japan, were reported
    by [[Nakamura (1998)|biblio/10.1023_A_1003531812536]].
  - _O. dioica_ was found all year in the Fukuyama harbour, Japan in 1986—7
-   [[Uye and Ichino, 1995|biblio/10.1016_0022-0981_95_00004-B]]).  Mature stages were also
+   ([[Uye and Ichino, 1995|biblio/10.1016_0022-0981_95_00004-B]]).  Mature stages were also
    found all year, and trunk length was shorter in summer.
  - In 1972, 1976, 1977, 1978, 1982 or 1986, _O. dioica_ was rare but relatively
    more abundant in slope waters, compared with Kuroshio and subtropical
@@ -472,13 +472,11 @@ Ecology
 
 ### Elsewhere in the Pacific ocean
 
- - In California, _O. dioica_ was reported by C. Essenberg
-   ([[1922|biblio/1929090]]) to be rare in summer's warm (> 20ºC) waters and
-   more abundant in winter's cool (13~16 ºC) waters.
- - _O. dioica_ was found throurought the North Pacific by ([[Tokioka
-   (1960)|biblio/10.5134_174644]]).
- - _O. dioica_ was reported in Alaska, where it is more abundant in summer
-   and near the coast ([[Doubleday and Hopcroft, 2015|biblio/10.1093_plankt_fbu092]]).
+ - California  ([[C. Essenbergm, 1922|biblio/1929090]]); rare in summer's warm
+   (> 20ºC) waters and more abundant in winter's cool (13~16 ºC) waters.
+ -  Throurought the North Pacific ([[Tokioka, 1960|biblio/10.5134_174644]]).
+ - Alaska, where it is more abundant in summer and near the coast ([[Doubleday
+   and Hopcroft, 2015|biblio/10.1093_plankt_fbu092]]).
 
 ### Elsewhere in the World
 
@@ -489,14 +487,14 @@ Ecology
  - Jamaica, where it was less abundant than _O. longicauda_ ([[Hopcroft and
    Roff, 1998|biblio/10.1093_plankt_20.3.557]]).
  - South Atlantic: found all year near Mar del Plata in 2000—1, where it was
-   most abundant in summer [[Viñas and coll.,
+   most abundant in summer ([[Viñas and coll.,
    2013|biblio/10.1080_17451000.2012.745003]]).
 
 Other appendicularians
 ----------------------
 
- - _Mesochordaeus erythrocephalus_ [[Hopcroft and Robinson,
-   1999|biblio/10.1093_plankt_21.10.1923]]: mesopelagic species with a large
+ - _Mesochordaeus erythrocephalus_ [[(Hopcroft and Robinson,
+   1999)|biblio/10.1093_plankt_21.10.1923]]: mesopelagic species with a large
    (~30 cm) house.
 
 

Café
diff --git a/biblio/10.1080_17451000.2012.745003.mdwn b/biblio/10.1080_17451000.2012.745003.mdwn
new file mode 100644
index 00000000..624c083f
--- /dev/null
+++ b/biblio/10.1080_17451000.2012.745003.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=" Seasonal succession of zooplankton in coastal waters of the Argentine Sea (Southwest Atlantic Ocean): prevalence of classical or microbial food webs"]]
+[[!tag Oikopleura]]
+
+María Delia Viñas, Rubén Mario Negri, Georgina Daniela Cepeda, Daniel Hernández, Ricardo Silva, María Cristina Daponte & Fabiana Lía Capitanio
+
+Marine Biology Research, 2013 Vol. 9, No. 4, 371—382, http://dx.doi.org/10.1080/17451000.2012.745003
+
+Seasonal succession of zooplankton in coastal waters of the Argentine Sea (Southwest Atlantic Ocean): prevalence of classical or microbial food webs
+
+[[!doi 10.1080/17451000.2012.745003 desc="_O. dioica_ found all year near Mar del Plata in 2000—1, where it was most abundant in summer."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cfd48b3e..5ac9d5bb 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -482,13 +482,15 @@ Ecology
 
 ### Elsewhere in the World
 
- - _O. dioica_ was reported in the bay of Bengal by [[Bhavanarayana and
-   Ganapati in 1972|biblio/10.1007_BF03045329]].
+ - Bay of Bengal ([[Bhavanarayana and Ganapati in 1972|biblio/10.1007_BF03045329]]).
  - While _O. dioica_ was not reported on the atlantic and pacific coasts of Costa Rica, its
    presence is considered plausible ([[Castellanos, Morales-Ramírez and Suárez-Morales,
    2009|biblio/10.1007_978-1-4020-8278-8_41]]).
- - _O. dioica_ was reported in Jamaica, where it was less abundant than _O. longicauda_
-   ([[Hopcroft and Roff, 1998|biblio/10.1093_plankt_20.3.557]]).
+ - Jamaica, where it was less abundant than _O. longicauda_ ([[Hopcroft and
+   Roff, 1998|biblio/10.1093_plankt_20.3.557]]).
+ - South Atlantic: found all year near Mar del Plata in 2000—1, where it was
+   most abundant in summer [[Viñas and coll.,
+   2013|biblio/10.1080_17451000.2012.745003]]).
 
 Other appendicularians
 ----------------------

Café
diff --git a/biblio/10.1093_plankt_20.3.557.mdwn b/biblio/10.1093_plankt_20.3.557.mdwn
new file mode 100644
index 00000000..bdfccce9
--- /dev/null
+++ b/biblio/10.1093_plankt_20.3.557.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Production of tropical larvaceans in Kingston Harbour, Jamaica: are we ignoring an important secondary producer?"]]
+[[!tag Oikopleura]]
+
+Russell R. Hopcroft, John C. Roff
+
+Journal of Plankton Research, Volume 20, Issue 3, 1998, Pages 557–569, doi:10.1093/plankt/20.3.557
+
+Production of tropical larvaceans in Kingston Harbour, Jamaica: are we ignoring an important secondary producer?
+
+[[!doi 10.1093/plankt/20.3.557 desc="O. longicauda was usually more abundant than O. dioica."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8aed996e..cfd48b3e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -155,7 +155,7 @@ Genes and pathways
    genes (6 H4, 10 H3, 15 H2A, 11 H2B and 5 H1 genes) encoding 31 different
    histone proteins (2 H4, 6 H3, 11 H2A, 7 H2B and 5 H1) were identified”.
    The centromeric CenH3 is present ([[Moosmann and coll., 2011|biblio/21756361]]).
- - 2 cellulose synthase genes, possibly acquired by horizontal gene transfer
+ - 2 cellulose synthase genes CesA1 and CesA2, possibly acquired by horizontal gene transfer
    from an actinobacteria ([[Nakashima and coll., 2004|biblio/14740209]]), were
    found by [[Sagane et al. (2010)|biblio/20335363]] and [[Nakashima et al.
    (2011)|biblio/20972815]].  They are used to produce different crystalline forms
@@ -487,6 +487,8 @@ Ecology
  - While _O. dioica_ was not reported on the atlantic and pacific coasts of Costa Rica, its
    presence is considered plausible ([[Castellanos, Morales-Ramírez and Suárez-Morales,
    2009|biblio/10.1007_978-1-4020-8278-8_41]]).
+ - _O. dioica_ was reported in Jamaica, where it was less abundant than _O. longicauda_
+   ([[Hopcroft and Roff, 1998|biblio/10.1093_plankt_20.3.557]]).
 
 Other appendicularians
 ----------------------

Intercistronic regions.
diff --git a/biblio/15314184.mdwn b/biblio/15314184.mdwn
index b45e7b36..f03ae638 100644
--- a/biblio/15314184.mdwn
+++ b/biblio/15314184.mdwn
@@ -7,4 +7,4 @@ Mol Cell Biol. 2004 Sep;24(17):7795-805. doi:10.1128/MCB.24.17.7795-7805.2004
 
 Spliced-Leader RNA trans Splicing in a Chordate, Oikopleura dioica, with a Compact Genome.
 
-[[!pmid 15314184 desc="5′ splice leader (SL) found in 90/158 ESTs containing a start codon.  The SL RNA is found downstream of the 5S RNA in at least 40 occurences, and aproximately 2/3 of all the 5S rRNA genes.  Its sequence is ACTCATCCCATTTTTGAGTCCGATTTCGATTGTCTAACAG. O. doica is the first chordate where gene operons have been described."]]
+[[!pmid 15314184 desc="5′ splice leader (SL) found in 90/158 ESTs containing a start codon.  The SL RNA is found downstream of the 5S RNA in at least 40 occurences, and aproximately 2/3 of all the 5S rRNA genes.  Its sequence is ACTCATCCCATTTTTGAGTCCGATTTCGATTGTCTAACAG. O. doica is the first chordate where gene operons have been described.  Intercistronic regions are very short (<30 nt)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 116075fa..8aed996e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -236,8 +236,8 @@ Transcriptome
  - O. dioica is the first chordate where gene operons have been described.  A
    40-nt 5′ [[splice leader|tags/trans-splicing]] (SL) bearing a trimethylated cap is found in some RNAs.
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
-   times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus
-   ([[Ganot et al., 2004|biblio/15314184]]).
+   times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus.
+   Reported intercistronic regions are short (<30 nt) ([[Ganot et al., 2004|biblio/15314184]]).
  - The splice leader found in the Norwegian strain by ([[Ganot et al., 2004|biblio/15314184]])
    was found indentical in a Japanese strain by ([[Wang and coll., 2015|biblio/26032664]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the

Omura bay and reorganisation
diff --git a/biblio/10069_30542.mdwn b/biblio/10069_30542.mdwn
new file mode 100644
index 00000000..94c73c81
--- /dev/null
+++ b/biblio/10069_30542.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Studies on the Zooplankton in Omura Bay―II Seasonal Occurrences of Rotatoria, Cladocera, Sagittoidea, Appendiculata and Benthos Larvae"]]
+[[!tag Oikopleura]]
+
+伊藤,栄樹/飯塚,昭二 (Itoh, Hideki / Iizuka, Shoji)
+
+大村湾における動物プランクトンに関する研究―II 輪虫類,枝角類,矢虫類,尾虫類 および底生生物幼生の季節的出現
+
+Studies on the Zooplankton in Omura Bay―II Seasonal Occurrences of Rotatoria, Cladocera, Sagittoidea, Appendiculata and Benthos Larvae
+
+長崎大学水産学部研究報告, v.49, pp.1-10; 1980
+
+[[!handle 10069/30542 desc="O. dioica found in the Omura (Nagasaki) bay."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c21eb5c9..116075fa 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -404,33 +404,20 @@ Ecology
 -------
 
  - _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
-    Azam, 1980|biblio/10.1007_BF00390593]])
- - In a rRNA metabarcoding study [[López-Escardó and coll, 2018|biblio/29904074]] report that 28 %
-   of the RNA reads in oxic micro/mesoplanktonic samples originate from tunicates, mostly appendicularian.
+   of its own diet, but the grazing has only “minimal influence on the
+   population dynamics of the free-living bacteria” ([[King, Hollibaugh and
+   Azam, 1980|biblio/10.1007_BF00390593]])
+ - In a rRNA metabarcoding study [[López-Escardó and coll,
+   2018|biblio/29904074]] report that 28 % of the RNA reads in oxic
+   micro/mesoplanktonic samples originate from tunicates, mostly appendicularian.
  - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans
    ([[Bouquet et al., 2018|biblio/29298334]]).  Another mesocosm study that took place
    in the Gullmar Fjord ([[Algueró-Muñiz M and coll., 2017|biblio/28410436]])
    did not predict major changes in mesozooplankton community structure and provides raw data
    including _O. dioica_, for which no significant changes are visible.
- - In California, _O. dioica_ was reported by C. Essenberg
-   ([[1922|biblio/1929090]]) to be rare in summer's warm (> 20ºC) waters and
-   more abundant in winter's cool (13~16 ºC) waters.
- - _O. dioica_ was found throurought the North Pacific by ([[Tokioka (1960)|biblio/10.5134_174644]]).
  - _O. dioica_ has “a very large mutation rate, and/or a very large effective
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).
- - It was already reported to be frequent in Japanese waters [[in 1907 by T. Aida|biblio/AA0069577]].
- - _O. dioica_ was found all year in the Fukuyama harbour, Japan in 1986—7
-   [[Uye and Ichino, 1995|biblio/10.1016_0022-0981_95_00004-B]]).  Mature stages were also
-   found all year, and trunk length was shorter in summer.
- - In 1972, 1976, 1977, 1978, 1982 or 1986, _O. dioica_ was rare but relatively
-   more abundant in slope waters, compared with Kuroshio and subtropical
-   waters, on the Pacific side of the Japan coast ([[Hidaka,
-   2008|biblio/10.3800_pbr.3.152]]).
- - Two blooms taking place in summer 1997 in the Seto inland sea, Japan, were reported
-   by [[Nakamura (1998)|biblio/10.1023_A_1003531812536]].
  - Meta-transcriptomic analysis in the Red sea showed a decrease of appendicularians during
    a Trichodesmium bloom in 2012 ([[Mojib and coll., 2017|biblio/10.1002_lno.10395]]).
  - As of August 2018, _O. dioica_ is not yet found in the [BOLD](http://www.boldsystems.org/)
@@ -438,9 +425,6 @@ Ecology
  - Carbon output of _O. dioica_ is either their house or fecal pellets, the
    ratio of which may depend on food concentration ([[Acuña and
    Kiefer, 2000|biblio/10.4319_lo.2000.45.3.0608.mdwn]]).
- - Oikopleuridae can be found in the deep see.  For instance, [[Lindsay and
-   coll., 2014|biblio/10.1007_978-4-431-54865-2_51]] reported _Oikopleura_, _Mesochordaeus_
-   and _Bathochordaeus_ individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.
  - Gravid _B mcnutti_ individuals are found at down to 800 m, but spawning is supposed to
    happen closer to the surface ([[Sherlock and coll., 2017|biblio/28042175]]).
  - Oikopleuridae have been reported to be able to ingest microplastics.  Example(s):
@@ -448,13 +432,28 @@ Ecology
  - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus
    ([[Lawrence and coll., 2017|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.
- - While _O. dioica_ was not reported on the atlantic and pacific coasts of Costa Rica, its
-   presence is considered plausible ([[Castellanos, Morales-Ramírez and Suárez-Morales,
-   2009|biblio/10.1007_978-1-4020-8278-8_41]]).
- - _O. dioica_ and _O. longicauda_ were found throurought 2006-2007 in the Yellow sea
-   ([[Franco, Chen and Li, 2014|biblio/10.1007_s11802-014-2376-0]]).  Abundance peaked
-   is spring, but the animals could also be found in winter when water temperature
-   went below 10°C.
+
+### Distribution near Japan
+
+ - _O. dioica_ was reported in the Omura (Nagasaki) bay by [[Ito and Iizuka
+   (1980)|biblio/10069_30542]].
+ - It was already reported to be frequent in Japanese waters [[in 1907 by T.
+   Aida|biblio/AA0069577]].
+ - Oikopleuridae can be found in the deep see.  For instance, [[Lindsay and
+   coll., 2014|biblio/10.1007_978-4-431-54865-2_51]] reported _Oikopleura_, _Mesochordaeus_
+   and _Bathochordaeus_ individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.
+ - Two blooms taking place in summer 1997 in the Seto inland sea, Japan, were reported
+   by [[Nakamura (1998)|biblio/10.1023_A_1003531812536]].
+ - _O. dioica_ was found all year in the Fukuyama harbour, Japan in 1986—7
+   [[Uye and Ichino, 1995|biblio/10.1016_0022-0981_95_00004-B]]).  Mature stages were also
+   found all year, and trunk length was shorter in summer.
+ - In 1972, 1976, 1977, 1978, 1982 or 1986, _O. dioica_ was rare but relatively
+   more abundant in slope waters, compared with Kuroshio and subtropical
+   waters, on the Pacific side of the Japan coast ([[Hidaka,
+   2008|biblio/10.3800_pbr.3.152]]).
+
+### Distribution near Taiwan and China
+
  - In Taiwan, _O. dioica_ was reported in north east costal waters in summar
    2005 by [[Hsiao and coll.|biblio/10.1007/s10750-011-0628-1]] and in 2009
    (plus near the Kueishan island) by [[Kâ and Hwang,
@@ -466,11 +465,29 @@ Ecology
  - In the northern south China sea, _O. longicauda_ and _O. rufescens_ were
    reported to be more abundant than _O. dioica_ in 2006 by ([[Li and coll.,
    2012|biblio/10.1007_s13131-012-0243-7]]).
- - _O. dioica_ was reported in the bay of Bengal by [[Bhavanarayana and
-   Ganapati in 1972|biblio/10.1007_BF03045329]].
+ - _O. dioica_ and _O. longicauda_ were found throurought 2006-2007 in the Yellow sea
+   ([[Franco, Chen and Li, 2014|biblio/10.1007_s11802-014-2376-0]]).  Abundance peaked
+   is spring, but the animals could also be found in winter when water temperature
+   went below 10°C.
+
+### Elsewhere in the Pacific ocean
+
+ - In California, _O. dioica_ was reported by C. Essenberg
+   ([[1922|biblio/1929090]]) to be rare in summer's warm (> 20ºC) waters and
+   more abundant in winter's cool (13~16 ºC) waters.
+ - _O. dioica_ was found throurought the North Pacific by ([[Tokioka
+   (1960)|biblio/10.5134_174644]]).
  - _O. dioica_ was reported in Alaska, where it is more abundant in summer
    and near the coast ([[Doubleday and Hopcroft, 2015|biblio/10.1093_plankt_fbu092]]).
 
+### Elsewhere in the World
+
+ - _O. dioica_ was reported in the bay of Bengal by [[Bhavanarayana and
+   Ganapati in 1972|biblio/10.1007_BF03045329]].
+ - While _O. dioica_ was not reported on the atlantic and pacific coasts of Costa Rica, its
+   presence is considered plausible ([[Castellanos, Morales-Ramírez and Suárez-Morales,
+   2009|biblio/10.1007_978-1-4020-8278-8_41]]).
+
 Other appendicularians
 ----------------------
 

Café
diff --git a/biblio/31477934.mdwn b/biblio/31477934.mdwn
new file mode 100644
index 00000000..2dacd5fd
--- /dev/null
+++ b/biblio/31477934.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Inferring whole-genome histories in large population datasets."]]
+[[!tag software method haplotype]]
+
+Kelleher J, Wong Y, Wohns AW, Fadil C, Albers PK, McVean G.
+
+Nat Genet. 2019 Sep;51(9):1330-1338. doi:10.1038/s41588-019-0483-y
+
+Inferring whole-genome histories in large population datasets.
+
+[[!pmid 31477934 desc="Primary paper for the tskit and tsinfer libraries.  Uses succinct tree sequence instead of ancestral recombination graphs."]]

Café
diff --git a/tags/cellulose.mdwn b/tags/cellulose.mdwn
index 3d2e97dd..ee088b09 100644
--- a/tags/cellulose.mdwn
+++ b/tags/cellulose.mdwn
@@ -7,4 +7,8 @@ weavable fibers for wearable sensors ([[Cho and coll., 2019|biblio/31369239]]).
 
 CesA from _C savignyi_ can rescue _A. tumefaciens_ mutants ([[Matthysse and coll., 2004|biblio/14722352]]).
 
+Sasakura and coll. ([[2016|biblio/28003446]] have proposed that the GC-rich
+genome of actinobacteria might have provided an AP-2 binding site promoting
+expression in the epidermis.
+
 [[!inline pages="tagged(cellulose)" limit=0]]

Café
diff --git a/biblio/28003446.mdwn b/biblio/28003446.mdwn
new file mode 100644
index 00000000..97a036f1
--- /dev/null
+++ b/biblio/28003446.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Transcriptional regulation of a horizontally transferred gene from bacterium to chordate."]]
+[[!tag tunicate cellulose]]
+
+Sasakura Y, Ogura Y, Treen N, Yokomori R, Park SJ, Nakai K, Saiga H, Sakuma T,
+Yamamoto T, Fujiwara S, Yoshida K.
+
+Proc Biol Sci. 2016 Dec 28;283(1845). pii: 20161712. doi:10.1098/rspb.2016.1712
+
+Transcriptional regulation of a horizontally transferred gene from bacterium to chordate.
+
+[[!pmid 28003446 desc="GC-rich DNA from Actinobacteria contains AP-2 binding
+sites, which triggers expression in the epidermis.  This might have facilitated
+horizontal transfer of the CesA gene."]]

creating tag page tags/tunic
diff --git a/tags/tunic.mdwn b/tags/tunic.mdwn
new file mode 100644
index 00000000..3c7ece5a
--- /dev/null
+++ b/tags/tunic.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged tunic"]]
+
+[[!inline pages="tagged(tunic)" actions="no" archive="yes"
+feedshow=10]]

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diff --git a/biblio/25575391.mdwn b/biblio/25575391.mdwn
new file mode 100644
index 00000000..6edd1c2e
--- /dev/null
+++ b/biblio/25575391.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tunic morphology and cellulosic components of pyrosomas, doliolids, and salps (thaliacea, urochordata)."]]
+[[!tag tunic cellulose]]
+
+Hirose E, Kimura S, Itoh T, Nishikawa J.
+
+Biol Bull. 1999 Feb;196(1):113-20 doi:10.2307/1543173
+
+Tunic morphology and cellulosic components of pyrosomas, doliolids, and salps (thaliacea, urochordata).
+
+[[!pmid 25575391 desc="Shows synaptomorphy of the tunic in ascidians and thaliaceans."]]

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diff --git a/biblio/10.4282_sosj.35.21.mdwn b/biblio/10.4282_sosj.35.21.mdwn
new file mode 100644
index 00000000..34c67add
--- /dev/null
+++ b/biblio/10.4282_sosj.35.21.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cellulose production and the evolution of the sessile lifestyle in ascidians"]]
+[[!tag review cellulose]]
+
+Yasunori Sasakura
+
+Sessile Organisms 2018 Volume 35 Issue 2 Pages 21-29
+
+Cellulose production and the evolution of the sessile lifestyle in ascidians
+
+[[!doi 10.4282/sosj.35.21 desc="Includes a discussion on the horizontal gene transfer."]]

cellulose
diff --git a/biblio/14722352.mdwn b/biblio/14722352.mdwn
index 652f9118..0b08800b 100644
--- a/biblio/14722352.mdwn
+++ b/biblio/14722352.mdwn
@@ -7,4 +7,4 @@ A functional cellulose synthase from ascidian epidermis.
 
 Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):986-91.
 
-[[!pmid 14722352 desc="The CesA mRNA is trans-spliced in Ciona intestinalis."]]
+[[!pmid 14722352 desc="The CesA mRNA is trans-spliced in Ciona savignyi.  C. sav CesA can rescue mutant A. tumefaciens bacteria."]]
diff --git a/tags/cellulose.mdwn b/tags/cellulose.mdwn
index 870867f3..3d2e97dd 100644
--- a/tags/cellulose.mdwn
+++ b/tags/cellulose.mdwn
@@ -5,4 +5,6 @@
 Tunicate cellulose has potential applications, such as the synthesis of
 weavable fibers for wearable sensors ([[Cho and coll., 2019|biblio/31369239]]).
 
+CesA from _C savignyi_ can rescue _A. tumefaciens_ mutants ([[Matthysse and coll., 2004|biblio/14722352]]).
+
 [[!inline pages="tagged(cellulose)" limit=0]]

Café
diff --git a/biblio/10.1023_A_1003531812536.mdwn b/biblio/10.1023_A_1003531812536.mdwn
new file mode 100644
index 00000000..7745d020
--- /dev/null
+++ b/biblio/10.1023_A_1003531812536.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Blooms of tunicates Oikopleura spp. and Dolioletta gegenbauri in the Seto Inland Sea, Japan, during summer"]]
+[[!tag Oikopleura]]
+
+Nakamura, Y.
+
+Hydrobiologia (1998) 385: 183. doi:10.1023/A:1003531812536 
+
+Blooms of tunicates Oikopleura spp. and Dolioletta gegenbauri in the Seto Inland Sea, Japan, during summer
+
+[[!doi 10.1023/A:1003531812536 desc="O. dioica was dominant in a first bloom, but O. longicauda dominated the second one.  Population decrease between the blooms might have been caused by predation by anchovy larvae."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b103db7c..c21eb5c9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -429,6 +429,8 @@ Ecology
    more abundant in slope waters, compared with Kuroshio and subtropical
    waters, on the Pacific side of the Japan coast ([[Hidaka,
    2008|biblio/10.3800_pbr.3.152]]).
+ - Two blooms taking place in summer 1997 in the Seto inland sea, Japan, were reported
+   by [[Nakamura (1998)|biblio/10.1023_A_1003531812536]].
  - Meta-transcriptomic analysis in the Red sea showed a decrease of appendicularians during
    a Trichodesmium bloom in 2012 ([[Mojib and coll., 2017|biblio/10.1002_lno.10395]]).
  - As of August 2018, _O. dioica_ is not yet found in the [BOLD](http://www.boldsystems.org/)

Café
diff --git a/biblio/31114914.mdwn b/biblio/31114914.mdwn
new file mode 100644
index 00000000..6bc84b19
--- /dev/null
+++ b/biblio/31114914.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging."]]
+[[!tag method ligase]]
+
+Nucleic Acids Res. 2019 May 22. pii: gkz435. doi:10.1093/nar/gkz435
+
+Miura F, Shibata Y, Miura M, Sangatsuda Y, Hisano O, Araki H, Ito T.
+
+Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
+
+[[!pmid desc="Add a A-tail with TdT before ligation, because ligase prefers As."]]
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index c05a18a6..527c63a3 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -29,7 +29,7 @@ On T4 RNL2:
    linker to RNA ends, thus prevents unwanted ligation products
    ([[Viollet et al., 2011|biblio/21722378]]).
 
-DNA and RNA ligases can be used to adenylylate a substrate.
+DNA and RNA ligases can be used to [[adenylylate|adenylylation]] a substrate.
 
  - [[McLaughlin, Piel and Graeser (1985)|biblio/3978074]] noted that
    adenylylated RNA is a better substrate for T4 RNA ligase, and that
@@ -60,8 +60,13 @@ DNA and RNA ligases can be used to adenylylate a substrate.
    better tolerated with higher GC content and lower temperature.  Surprisingly,
    TNA overhangs were especially hard to ligate.
 
-[[!inline pages="tagged(ligase)" limit=0]]
-[[!meta title="pages tagged adenylylation"]]
+## Methods using ligases:
+
+(works continuously in progress)
 
+ - TACS (terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate
+   connector-mediated ssDNA) tails DNA with As using the TdT, in order to
+   benefit from the ligase's preference for As ([[Miura and coll.,
+   2019|biblio/31114914]]).
 
-[[!inline pages="tagged(adenylylation)" limit=0]]
+[[!inline pages="tagged(ligase)" limit=0]]

creating tag page tags/pig
diff --git a/tags/pig.mdwn b/tags/pig.mdwn
new file mode 100644
index 00000000..a4f18053
--- /dev/null
+++ b/tags/pig.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged pig"]]
+
+[[!inline pages="tagged(pig)" actions="no" archive="yes"
+feedshow=10]]

Mesochordaeus
diff --git a/biblio/10.1093_plankt_21.10.1923.mdwn b/biblio/10.1093_plankt_21.10.1923.mdwn
new file mode 100644
index 00000000..bb877d09
--- /dev/null
+++ b/biblio/10.1093_plankt_21.10.1923.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="A new mesopelagic larvacean, Mesochordaeus erythrocephalus, sp. nov., from Monterey Bay, with a description of its filtering house"]]
+[[!tag Oikopleura]]
+
+Russell R.Hopcroft and Bruce H.Robison
+
+Journal of Plankton Research, Volume 21, Issue 10, 1 October 1999, Pages 1923–1937, doi:10.1093/plankt/21.10.1923
+
+A new mesopelagic larvacean, _Mesochordaeus erythrocephalus_, sp. nov., from Monterey Bay, with a description of its filtering house 
+
+[[!doi 10.1093/plankt/21.10.1923 desc="House is ~30cm ø; ~2 tail beats per s.
+Heavily pigmented digestive tract.  “Although we are inclined to ally this
+genus most closely to Bathochordaeus, we note several features that raise
+questions with regard to its placement within the subfamily Bathochordaeinae
+(represented only by the genus Bathochordaeus) as opposed to the
+Oikopleurinae.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 58c41be5..b103db7c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -469,4 +469,12 @@ Ecology
  - _O. dioica_ was reported in Alaska, where it is more abundant in summer
    and near the coast ([[Doubleday and Hopcroft, 2015|biblio/10.1093_plankt_fbu092]]).
 
+Other appendicularians
+----------------------
+
+ - _Mesochordaeus erythrocephalus_ [[Hopcroft and Robinson,
+   1999|biblio/10.1093_plankt_21.10.1923]]: mesopelagic species with a large
+   (~30 cm) house.
+
+
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

O. dioica's mitochondrial sequences.
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index a523aac3..bf68f92c 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -30,6 +30,8 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
  - Sequence of a thaliacean (_Doliolum nationalis_) mitochondrial genome
    suggests they also decode AGR as glycine ([[Yokobori, Oshima and Wada,
    2005|biblio/15619441]]).
+ - [[Deneoud and coll, 2010|biblio/21097902]] reported that mitochondrial
+   genes of _O. dioica_ translate well with the ascidian code.
  - Another case, unrelated, of reassignment to glycin is know: UGA → Gly in
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
  - In the hemichordate _Balanoglossus carnosus_ ([[Castresana and coll.,
@@ -38,8 +40,9 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
 ```
                      AGA   AGG   ATA   AAA   TGA
 Vertebrates           *     *     M     K     W
-Tunicates             G     G     M     K     W
-Cephalochordates
+Tunicates             G     G     M     K     W   (O. di, salps, ascidians)
+ O. lon and B. char?  G     G     I     K     W
+Cephalochordates      S    S,ø?   M     K     W   (standard invertebrate)
 Hemichordates         S     ø     I     ø     W
 Echinoderms           S     S     I     N     W
 ```

creating tag page tags/hemichordate
diff --git a/tags/hemichordate.mdwn b/tags/hemichordate.mdwn
new file mode 100644
index 00000000..e41aff62
--- /dev/null
+++ b/tags/hemichordate.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged hemichordate"]]
+
+[[!inline pages="tagged(hemichordate)" actions="no" archive="yes"
+feedshow=10]]

Hemichordates
diff --git a/biblio/9799263.mdwn b/biblio/9799263.mdwn
new file mode 100644
index 00000000..d6d24519
--- /dev/null
+++ b/biblio/9799263.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria."]]
+[[!tag mitochondrion hemichordate]]
+
+Genetics. 1998 Nov;150(3):1115-23.
+
+Castresana J, Feldmaier-Fuchs G, Yokobori S, Satoh N, Pääbo S.
+
+The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria.
+
+[[!pmid 9799263 desc="AGA encodes Ser, AGG is absent, ATA encodes Ile, AAA is absent. “…out of the 69 ATA hemichordate codons, 20 occur in positions where Ile is conserved in >55% of the sequences (eight of these positions have Ile in >90% of the sequences), while none of them occur at positions where Met is conserved. Of the 19 AGA codons, 6 occur at positions where Ser is conserved in >55% of the sequences (3 of them with Ser in >90% of the sequences), whereas they are never used as stop codons.”"]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 8f318f34..a523aac3 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -17,7 +17,7 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    ATA and TGA are likely to code for M and W like in vertebtates.
    [[Durrheim and coll. |biblio/8393993]] also translated that way,
    but did not report it explicitely.
- - [[Delarbre and coll, 1997|biblio/9254918]] proposed an AGR -> Gly
+ - [[Delarbre and coll, 1997|biblio/9254918]] proposed an AGR → Gly
    reassignment in amphioxus, based on a AGG/GGG polymorphism, and
    [[Spruyt and coll, 1998|biblio/9628930]] found a putative TCT (Gly) tRNA
    in the mitochondrial genome of the amphioxus (in which they also show
@@ -30,9 +30,19 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
  - Sequence of a thaliacean (_Doliolum nationalis_) mitochondrial genome
    suggests they also decode AGR as glycine ([[Yokobori, Oshima and Wada,
    2005|biblio/15619441]]).
- - Another case, unrelated, of reassignment to glycin is know: UGA -> Gly in
+ - Another case, unrelated, of reassignment to glycin is know: UGA → Gly in
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
+ - In the hemichordate _Balanoglossus carnosus_ ([[Castresana and coll.,
+   1998|biblio/9799263]]): ATA → Ile, AGA → Ser, AGG → ø and AAA → ø.
 
+```
+                     AGA   AGG   ATA   AAA   TGA
+Vertebrates           *     *     M     K     W
+Tunicates             G     G     M     K     W
+Cephalochordates
+Hemichordates         S     ø     I     ø     W
+Echinoderms           S     S     I     N     W
+```
 
 ### Genes 
 

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diff --git a/biblio/31405970.mdwn b/biblio/31405970.mdwn
new file mode 100644
index 00000000..296613bd
--- /dev/null
+++ b/biblio/31405970.mdwn
@@ -0,0 +1,25 @@
+[[!meta title="Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe."]]
+[[!tag pig genetics]]
+
+Proc Natl Acad Sci U S A. 2019 Aug 12. pii: 201901169. doi:10.1073/pnas.1901169116
+
+Frantz LAF, Haile J, Lin AT, Scheu A, Geörg C, Benecke N, Alexander M,
+Linderholm A, Mullin VE, Daly KG, Battista VM, Price M, Gron KJ, Alexandri P,
+Arbogast RM, Arbuckle B, Bӑlӑşescu A, Barnett R, Bartosiewicz L, Baryshnikov G,
+Bonsall C, Borić D, Boroneanţ A, Bulatović J, Çakirlar C, Carretero JM, Chapman
+J, Church M, Crooijmans R, De Cupere B, Detry C, Dimitrijevic V, Dumitraşcu V, du
+Plessis L, Edwards CJ, Erek CM, Erim-Özdoğan A, Ervynck A, Fulgione D, Gligor M, 
+Götherström A, Gourichon L, Groenen MAM, Helmer D, Hongo H, Horwitz LK,
+Irving-Pease EK, Lebrasseur O, Lesur J, Malone C, Manaseryan N, Marciniak A,
+Martlew H, Mashkour M, Matthews R, Matuzeviciute GM, Maziar S, Meijaard E,
+McGovern T, Megens HJ, Miller R, Mohaseb AF, Orschiedt J, Orton D, Papathanasiou 
+A, Pearson MP, Pinhasi R, Radmanović D, Ricaut FX, Richards M, Sabin R, Sarti L, 
+Schier W, Sheikhi S, Stephan E, Stewart JR, Stoddart S, Tagliacozzo A, Tasić N,
+Trantalidou K, Tresset A, Valdiosera C, van den Hurk Y, Van Poucke S, Vigne JD,
+Yanevich A, Zeeb-Lanz A, Triantafyllidis A, Gilbert MTP, Schibler J, Rowley-Conwy
+P, Zeder M, Peters J, Cucchi T, Bradley DG, Dobney K, Burger J, Evin A,
+Girdland-Flink L, Larson G.
+
+Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.
+
+[[!pmid 31405970 desc="Near-total replacement of the genetic background of the domesticated pig in Europe, except for at least one selection marker on the coat color, Melanocortin 1 Receptor (MC1R)."]]

Karyotype
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 09dc703f..58c41be5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -54,19 +54,27 @@ Phylogeny
  - CO1 DNA of _B. mcnutti_ and _B. strygius_ are ~12% different ([[Sherlock and coll., 2017|biblio/28042175]]).
 
 
-Genome
+Karyotype
 ------
 
- - Germ cells contain 3 haploid chromosomes ([[Körner, 1952|biblio/43261846]]).
+ - In individuals sampled in the Wadden sea, [[Körner, 1952|biblio/43261846]]
+   reported that germ cells contain 3 haploid chromosomes.
    This is a low number in the animal reign, although at least one mammal has
    a similar number ([[Wurster and Benirschke 1970|biblio/5444269]]), and some insects have even less.
-   There are also intriguing observations of somatic mitotic cells with 7
-   chromosomes ([[Körner, 1952|biblio/43261846]]) and meiotic cells with
-   8 haploid chromosomes ([[Colombera & Fenaux, 1973|biblio/10.1080_11250007309429248]]).
+ - There are also intriguing observations of somatic mitotic cells with 7
+   chromosomes ([[Körner, 1952|biblio/43261846]])
+ - In individuals captured in Villefranche-sur-Mer (Mediterranean sea),
+   meiotic cells were reported to have8 haploid chromosomes
+   by [[Colombera & Fenaux, 1973|biblio/10.1080_11250007309429248]].
  - Several manuscripts using animals from the SARS laboratory include
    fluorescent microscopy pictures supporting the 3 × 2 karyotype.  For instance:
    centromere marking in [[Feng and coll., 2019|biblio/31306061]].
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
+
+
+Genome
+------
+
  - Genome size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al,
    2001|biblio/11752568]].  A 70.4 Mb genome "reference assembly" was later
    produced from the shotgun sequencing of sperm DNA from ~200 partially inbred

Quote relative to the karyotype.
diff --git a/biblio/10.1080_11250007309429248.mdwn b/biblio/10.1080_11250007309429248.mdwn
index 5c9a46e8..66f3ae1c 100644
--- a/biblio/10.1080_11250007309429248.mdwn
+++ b/biblio/10.1080_11250007309429248.mdwn
@@ -3,8 +3,24 @@
 
 Colombera D. & Fenaux R.
 
-Italian Journal of Zoology, 40:3-4, 347-353
+Italian Journal of Zoology, 1973, 40:3-4, 347-353
 
 Chromosome form and number in the larvacea
 
+“In 10 anaphase plates (fig. 10) a chromosome number of 16 was
+regularly found. I n another five anaphase plates, presumably because of
+chromosome losses during the squashing, a lower number mas found.
+
+These chromosomes are exceedingly small, without morphologically
+differentiated structures. They are rod-shape, with a sharp bend in a
+medial or submedial position ; of the two arms individuated by the bend,
+one is often thinner than the other.
+
+As is often the result of squashing, the direction of tlie chromosome
+movement is clearly altered for some chromosomes. Since none of the
+chromosomes appears to be homologous we consider such chromosomes
+to be meiotic and in consequence we mould assign a haploid number of
+eight to 0. dioica, with the reservation that the above mentioned plates
+might be mitotic in which case the true haploid number would be four.”
+
 [[!doi 10.1080/11250007309429248 desc="Reports 16 chromosomes in meiotic cells (8 haploid chromosomes)."]]

Figure legends related to the karyotype.
diff --git a/biblio/43261846.mdwn b/biblio/43261846.mdwn
index 8b8d9fd0..2e8a24d4 100644
--- a/biblio/43261846.mdwn
+++ b/biblio/43261846.mdwn
@@ -7,4 +7,12 @@ Zeitschrift für Morphologie und Ökologie der Tiere Vol. 41, No. 1 (20.Mai 1952
 
 Untersuchungen über die Gehäusebildung bei Appendicularien (Oikopleura dioica Fol)
 
+Figure legends:
+
+Abb. 18. Oikopleura dioica Fol. Anaphase aus dem Ektoderm der Larve. Maßstab 10 µ.
+
+Abb. 19a u. b. Oikopleura dioica Fol. a Äquatorialplatte aus einer Spermiocyte I. Ordnung.
+Nach Karmin-Essigsäurepräparaten. b Oogenetische Meiose mit 3 Chromosomentetraden.
+Maßstab 10 µ.
+
 [Reports 3 haploid chromosomes in sperm and oocytes, one beign longer than the others.  Also reports an observation of 7 chromosomes in a somatic mitotic cell. “Die zur Untersuchung benutzten Tiere stammten ausschließlich aus dem Wattenmeer der Deutschen Bucht.” (all animals were collected from the Wadden sea)](https://www.jstor.org/stable/43261846)

ATA and TGA in ascidians.
diff --git a/biblio/8381878.mdwn b/biblio/8381878.mdwn
index bd7a6b94..c0dd2d7f 100644
--- a/biblio/8381878.mdwn
+++ b/biblio/8381878.mdwn
@@ -7,4 +7,4 @@ Yokobori S, Ueda T, Watanabe K.
 
 Codons AGA and AGG are read as glycine in ascidian mitochondria.
 
-[[!pmid 8381878 desc="Analysis of Halocynthia roretzi cox1 cDNA sequence suggests a different genetic code for ascidian mitochodria."]]
+[[!pmid 8381878 desc="Analysis of _Halocynthia roretzi_ Cox1 cDNA sequence suggests that in the ascidian mitochondrial genetic code, AGR code for Gly (unlike other animals), ATA for Met (like vertebrates and invertebrates) and TGA for Trp (like vertebrates and invertebrates)."]]
diff --git a/biblio/8393993.mdwn b/biblio/8393993.mdwn
index 17e93094..d81ad632 100644
--- a/biblio/8393993.mdwn
+++ b/biblio/8393993.mdwn
@@ -7,4 +7,4 @@ Nucleic Acids Res. 1993 Jul 25;21(15):3587-8.
 
 Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: evidence that AGR encodes glycine.
 
-[[!pmid 8393993 desc="AGR -> Gly in another tunicate"]]
+[[!pmid 8393993 desc="AGR -> Gly in another tunicate.  Protein tranlated assuming ATA -> Met and TGA -> Trp like in vertebrates and invertebrates."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 693212d7..8f318f34 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -10,9 +10,13 @@ https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgenco
 https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
 
  - [[Yokobori and coll, 1993|biblio/8381878]] sequenced _cox1_ in
-   _Halocynthia roretzi_ and suggested that it may use a different
-   genetic code.  The same year, [[Durrheim and coll. |biblio/8393993]] made
+   _Halocynthia roretzi_ and proposed that AGR codes for Gly.
+   The same year, [[Durrheim and coll. |biblio/8393993]] made
    the same observation on the _cox3_ sequence of _Pyura stolonifera_.
+ - [[Yokobori and coll, 1993|biblio/8381878]] also noted that
+   ATA and TGA are likely to code for M and W like in vertebtates.
+   [[Durrheim and coll. |biblio/8393993]] also translated that way,
+   but did not report it explicitely.
  - [[Delarbre and coll, 1997|biblio/9254918]] proposed an AGR -> Gly
    reassignment in amphioxus, based on a AGG/GGG polymorphism, and
    [[Spruyt and coll, 1998|biblio/9628930]] found a putative TCT (Gly) tRNA

Café
diff --git a/biblio/29741723.mdwn b/biblio/29741723.mdwn
new file mode 100644
index 00000000..a752a8b9
--- /dev/null
+++ b/biblio/29741723.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining."]]
+[[!tag enzyme ligase]]
+
+Nucleic Acids Res. 2018 Jul 27;46(13):e79. doi:10.1093/nar/gky303
+
+Potapov V, Ong JL, Langhorst BW, Bilotti K, Cahoon D, Canton B, Knight TF,
+Evans TC Jr, Lohman GJS.
+
+A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining.
+
+[[!pmid 29741723 desc="TNA overhangs are very inefficient to ligate.  However ANT are not harder to ligate than similar mismatches.  GC-rich overhangs better tolerate mismatches than AT-rich ones.  Increasing temperature reduced mismatched ligations.  5′-G mismatches are much better tolerated than 5′-T mismatches."]]
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 2ba035e9..c05a18a6 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -51,6 +51,15 @@ DNA and RNA ligases can be used to adenylylate a substrate.
  - [[Torchia, Takagi and Ho (2008)|biblio/18829718]] reported the use
    of the Methanobacterium RNA ligase (MthRnl) to adenylylate RNA.
 
+## Sequence biases
+
+(work in progress)
+
+ - Potapov and coll. ([[2018|biblio/29741723]]) studied in details the tolerance
+   to mismatches of T4 DNA ligase when ligating 3' overhangs.  Mismatches were
+   better tolerated with higher GC content and lower temperature.  Surprisingly,
+   TNA overhangs were especially hard to ligate.
+
 [[!inline pages="tagged(ligase)" limit=0]]
 [[!meta title="pages tagged adenylylation"]]
 

Alaska
diff --git a/biblio/10.1093_plankt_fbu092.mdwn b/biblio/10.1093_plankt_fbu092.mdwn
new file mode 100644
index 00000000..d70b96f0
--- /dev/null
+++ b/biblio/10.1093_plankt_fbu092.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Interannual patterns during spring and late summer of larvaceans and pteropods in the coastal Gulf of Alaska, and their relationship to pink salmon survival"]]
+[[!tag Oikopleura]]
+
+Ayla J. Doubleday, Russell R. Hopcroft
+
+Journal of Plankton Research, Volume 37, Issue 1, January/February 2015, Pages 134–150
+
+Interannual patterns during spring and late summer of larvaceans and pteropods in the coastal Gulf of Alaska, and their relationship to pink salmon survival
+
+[[!doi 10.1093/plankt/fbu092 desc="“Across seasons, O. labradoriensis and F. borealis abundance were negatively related to temperature.”  “O. dioica occurred in highest abundance during late summer relative to spring. During this time, O. dioica abundance was positively related to temperature and chlorophyll-a, but negatively related to salinity, and had a maximum abundance at nearshore stations.”  “When season and year were pooled, the 150-µm net collected 34% of the abundance that the 53-µm net collected for Oikopleura spp., 34% of the abundance for Fritillaria spp. and 30% of the abundance for L. helicina. If we assume, time-of-day has no impact on the distribution of either group (i.e. no diel vertical migrations), then the 505-µm net captures 10% of the 53-µm net.”  “The 505-µm mesh nets indicate that Oikopleura spp. had highest abundance at the surface”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 365af405..09dc703f 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -458,5 +458,7 @@ Ecology
    2012|biblio/10.1007_s13131-012-0243-7]]).
  - _O. dioica_ was reported in the bay of Bengal by [[Bhavanarayana and
    Ganapati in 1972|biblio/10.1007_BF03045329]].
+ - _O. dioica_ was reported in Alaska, where it is more abundant in summer
+   and near the coast ([[Doubleday and Hopcroft, 2015|biblio/10.1093_plankt_fbu092]]).
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café
diff --git a/biblio/28280153.mdwn b/biblio/28280153.mdwn
new file mode 100644
index 00000000..ab50fef4
--- /dev/null
+++ b/biblio/28280153.mdwn
@@ -0,0 +1,8 @@
+[[!meta title="Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome."]]
+[[!tag yeast synthethic chromosome]]
+
+Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi:10.1126/science.aaf4791
+
+Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.
+
+[[!pmid 28280153 desc="Repaired structural variants by engeneering duplications and forcing their resolution by I-SceI cleavage."]]

creating tag page tags/variations
diff --git a/tags/variations.mdwn b/tags/variations.mdwn
new file mode 100644
index 00000000..47fe6435
--- /dev/null
+++ b/tags/variations.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged variations"]]
+
+[[!inline pages="tagged(variations)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/16136133.mdwn b/biblio/16136133.mdwn
new file mode 100644
index 00000000..aa16959c
--- /dev/null
+++ b/biblio/16136133.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication."]]
+[[!tag chromosome variations]]
+
+Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ.
+
+Nature. 2005 Sep 1;437(7055):94-100 doi:10.1038/nature04029
+
+Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication.
+
+[[!pmid 16136133 desc="New segments are exchanged between chromosomes via the NHEJ pathway.  Segments exchange internal sequences via homologous recombinations.  The rate of gene creation is higher in subtelomers (and centromeres...) than in chromosomal cores."]]

Café
diff --git a/biblio/28416820.mdwn b/biblio/28416820.mdwn
new file mode 100644
index 00000000..2d874f04
--- /dev/null
+++ b/biblio/28416820.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Contrasting evolutionary genome dynamics between domesticated and wild yeasts."]]
+[[!tag yeast chromosome variants]]
+
+Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G.
+
+Nat Genet. 2017 Jun;49(6):913-924. doi:10.1038/ng.3847
+
+Contrasting evolutionary genome dynamics between domesticated and wild yeasts.
+
+[[!pmid 28416820 desc="Yeast subtelomeres accumulate structural variants."]]

Café hier
diff --git a/biblio/31308546.mdwn b/biblio/31308546.mdwn
new file mode 100644
index 00000000..fd5b98d7
--- /dev/null
+++ b/biblio/31308546.mdwn
@@ -0,0 +1,14 @@
+[[!meta title="Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression."]]
+[[!tag Drosophila chromosome variants]]
+
+Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM.
+
+Nat Genet. 2019 Aug;51(8):1272-1282. doi:10.1038/s41588-019-0462-3
+
+Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.
+
+[[!pmid 31308546 desc="Sequencing of balancer chromosomes.  Allele-specific
+RNA-seq, Hi-C and Capture-C.  “Genes with changes in their expression have a
+small but significant enrichment for differential promoter contacts”, but the
+converse is not true.  “Loss of long-range chromatin loops has little impact on
+gene expression.”"]]

Tunicate cellulose.
diff --git a/biblio/31369239.mdwn b/biblio/31369239.mdwn
new file mode 100644
index 00000000..7b8f19f7
--- /dev/null
+++ b/biblio/31369239.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Continuous Meter-Scale Synthesis of Weavable Tunicate Cellulose/Carbon Nanotube Fibers for High-Performance Wearable Sensors."]]
+[[!tag cellulose]]
+
+Cho SY, Yu H, Choi J, Kang H, Park S, Jang JS, Hong HJ, Kim ID, Lee SK, Jeong HS, Jung HT.
+
+ACS Nano. 2019 Aug 2. doi:10.1021/acsnano.9b03971
+
+Continuous Meter-Scale Synthesis of Weavable Tunicate Cellulose/Carbon Nanotube Fibers for High-Performance Wearable Sensors.
+
+[[!pmid 31369239 desc="Application of tunicate cellulose to wearable sensors."]]
diff --git a/tags/cellulose.mdwn b/tags/cellulose.mdwn
index b6209c32..870867f3 100644
--- a/tags/cellulose.mdwn
+++ b/tags/cellulose.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged cellulose"]]
 
-[[!inline pages="tagged(cellulose)" actions="no" archive="yes"
-feedshow=10]]
+** In construction **
+
+Tunicate cellulose has potential applications, such as the synthesis of
+weavable fibers for wearable sensors ([[Cho and coll., 2019|biblio/31369239]]).
+
+[[!inline pages="tagged(cellulose)" limit=0]]

Add details.
diff --git a/biblio/43261846.mdwn b/biblio/43261846.mdwn
index 73a7f772..8b8d9fd0 100644
--- a/biblio/43261846.mdwn
+++ b/biblio/43261846.mdwn
@@ -7,4 +7,4 @@ Zeitschrift für Morphologie und Ökologie der Tiere Vol. 41, No. 1 (20.Mai 1952
 
 Untersuchungen über die Gehäusebildung bei Appendicularien (Oikopleura dioica Fol)
 
-[Reports 3 haploid chromosomes in sperm and oocytes, one beign longer than the others.  Also reports an observation of 7 chromosomes in a somatic mitotic cell.](https://www.jstor.org/stable/43261846)
+[Reports 3 haploid chromosomes in sperm and oocytes, one beign longer than the others.  Also reports an observation of 7 chromosomes in a somatic mitotic cell. “Die zur Untersuchung benutzten Tiere stammten ausschließlich aus dem Wattenmeer der Deutschen Bucht.” (all animals were collected from the Wadden sea)](https://www.jstor.org/stable/43261846)

Dans le train.
diff --git a/biblio/31366885.mdwn b/biblio/31366885.mdwn
new file mode 100644
index 00000000..8d89daa4
--- /dev/null
+++ b/biblio/31366885.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids."]]
+[[!tag HPV evolution]]
+
+Kazlauskas D, Varsani A, Koonin EV, Krupovic M.
+
+Nat Commun. 2019 Jul 31;10(1):3425. doi:10.1038/s41467-019-11433-0
+
+Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids.
+
+[[!pmid 31366885 desc="Suggests that papillomaviruses evolved from single-strand DNA viruses, which evolved from bacterial plasmids."]]

Syntax
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 4060c0c5..365af405 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -455,7 +455,7 @@ Ecology
    2017|biblio/10.1080_00222933.2017.1293180]]).
  - In the northern south China sea, _O. longicauda_ and _O. rufescens_ were
    reported to be more abundant than _O. dioica_ in 2006 by ([[Li and coll.,
-   2012|biblio/10.1007_s13131-012-0243-7.mdwn]]).
+   2012|biblio/10.1007_s13131-012-0243-7]]).
  - _O. dioica_ was reported in the bay of Bengal by [[Bhavanarayana and
    Ganapati in 1972|biblio/10.1007_BF03045329]].
 

Café
diff --git a/biblio/18490654.mdwn b/biblio/18490654.mdwn
new file mode 100644
index 00000000..bd197ea2
--- /dev/null
+++ b/biblio/18490654.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Embryology of a planktonic tunicate reveals traces of sessility."]]
+[[!tag Oikopleura]]
+
+Proc Natl Acad Sci U S A. 2008 May 20;105(20):7229-34. doi:10.1073/pnas.0710196105
+
+Stach T, Winter J, Bouquet JM, Chourrout D, Schnabel R.
+
+Embryology of a planktonic tunicate reveals traces of sessility.
+
+[[!pmid 18490654 desc="“Clonal organization of the tissues is essentially invariant among individuals”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b06aabd6..4060c0c5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -259,6 +259,9 @@ Tools
 Development
 -----------
 
+ - First embryonic cleavages are deterministic and “Clonal organization of the
+   tissues is essentially invariant among individuals” ([[Stach and coll.,
+   2008|biblio/18490654]]).
  - 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

Café
diff --git a/biblio/30905687.mdwn b/biblio/30905687.mdwn
new file mode 100644
index 00000000..3994342a
--- /dev/null
+++ b/biblio/30905687.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gap junction-dependent coordination of intercellular calcium signalling in the developing appendicularian tunicate Oikopleura dioica."]]
+[[!tag Oikopleura]]
+
+Dev Biol. 2019 Jun 1;450(1):9-22. doi:10.1016/j.ydbio.2019.03.006
+
+Mikhaleva Y, Tolstenkov O, Glover JC.
+
+Gap junction-dependent coordination of intercellular calcium signalling in the developing appendicularian tunicate Oikopleura dioica.
+
+[[!pmid 30905687 desc="Calcium waves observed with GCaMP6.  Each wave is preceded by a “minipeak”.  Two connexins (CxA and CxB) are expressed during embyogenesis.  ”Knockdown of both CxA and CxB mRNA severely disrupts Ca2+ wave propagation and thereby also synchronization.“"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3e23f267..b06aabd6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -178,6 +178,8 @@ Genes and pathways
  - Duplications in the Rab family: Rab5/17, Rab6, Rab7, Rab10, Rab35.  The EF-Rab chimera
    Rab46 is kept ([[Coppola and coll., 2019|biblio/31028425]]).  See below for the losses. 
  - INCENP and Plk1 are duplicated ([[Feng and coll., 2019|biblio/31306061]]).
+ - Two connexins, CxA and CxB are expressed during embyogenesis ([[Mikhaleva,
+   Tolstenkov and Glover 2019|biblio/30905687]]).
 
 ### Lost
 
@@ -286,6 +288,9 @@ Development
    who noted that it is exceptional in invertebrates, and hypothethise that it may
    be caused by neofunctionalisation (house production, ...) or by the small size of
    the genome (doubling the genes would then double the amount of regulatory sequences).
+ - Regular calcium waves are pulsing during embyogenesis.  Their propagation and
+   synchronicity is severly disrupted by the knockdown of the connexins CxA and CxB
+   ([[Mikhaleva, Tolstenkov and Glover 2019|biblio/30905687]]).
  - The tandem _propA_ and _propB_ genes control directly or indirectly _oik41a_
    and proper development of the house-secreting epithelium ([[Mikhaleva et
    al., 2018|biblio/30217597]]).

Café aujourdhui
diff --git a/biblio/10.1007_BF03045329.mdwn b/biblio/10.1007_BF03045329.mdwn
new file mode 100644
index 00000000..d94bddea
--- /dev/null
+++ b/biblio/10.1007_BF03045329.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Distribution of pelagic tunicates in the western part of the Bay of Bengal"]]
+[[!tag Oikopleura]]
+
+P. V. Bhavanarayana, P. N. Ganapati
+
+Proceedings of the Indian Academy of Sciences - Section B (1972) 75: 1.
+
+Distribution of pelagic tunicates in the western part of the Bay of Bengal
+
+[[!doi 10.1007/BF03045329 desc="O. dioica reported in the bay of Bengal."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7267b640..3e23f267 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -448,5 +448,7 @@ Ecology
  - In the northern south China sea, _O. longicauda_ and _O. rufescens_ were
    reported to be more abundant than _O. dioica_ in 2006 by ([[Li and coll.,
    2012|biblio/10.1007_s13131-012-0243-7.mdwn]]).
+ - _O. dioica_ was reported in the bay of Bengal by [[Bhavanarayana and
+   Ganapati in 1972|biblio/10.1007_BF03045329]].
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café aujourdhui
diff --git a/biblio/10.5134_174644.mdwn b/biblio/10.5134_174644.mdwn
new file mode 100644
index 00000000..20f9c4f9
--- /dev/null
+++ b/biblio/10.5134_174644.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Studies on the distribution of appendicularians and some thaliaceans of the North Pacific, with some morphological notes."]]
+[[!tag Oikopleura]]
+
+Tokioka, Takasi
+
+Seto Mar. Biol. Lab., 1960, 3, 130–221.
+
+Studies on the distribution of appendicularians and some thaliaceans of the North Pacific, with some morphological notes.
+
+[[!doi 10.5134/174644 desc="Multiple records of O. dioica in the North Pacific."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index daa9cf3e..7267b640 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -401,6 +401,7 @@ Ecology
  - In California, _O. dioica_ was reported by C. Essenberg
    ([[1922|biblio/1929090]]) to be rare in summer's warm (> 20ºC) waters and
    more abundant in winter's cool (13~16 ºC) waters.
+ - _O. dioica_ was found throurought the North Pacific by ([[Tokioka (1960)|biblio/10.5134_174644]]).
  - _O. dioica_ has “a very large mutation rate, and/or a very large effective
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).

creating tag page tags/H3S31p
diff --git a/tags/H3S31p.mdwn b/tags/H3S31p.mdwn
new file mode 100644
index 00000000..19a310aa
--- /dev/null
+++ b/tags/H3S31p.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H3S31p"]]
+
+[[!inline pages="tagged(H3S31p)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/H3T3p
diff --git a/tags/H3T3p.mdwn b/tags/H3T3p.mdwn
new file mode 100644
index 00000000..444999ab
--- /dev/null
+++ b/tags/H3T3p.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged H3T3p"]]
+
+[[!inline pages="tagged(H3T3p)" actions="no" archive="yes"
+feedshow=10]]

Café hier
diff --git a/biblio/31306061.mdwn b/biblio/31306061.mdwn
new file mode 100644
index 00000000..5c63f377
--- /dev/null
+++ b/biblio/31306061.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Switching of INCENP paralogs controls transitions in mitotic chromosomal passenger complex functions."]]
+[[!tag Oikopleura centromere H3T3p H3S28p H3S10p H3S31p H3K4me2 H3K9me3]]
+
+Cell Cycle. 2019 Jul 15:1-20. doi:10.1080/15384101.2019.1634954
+
+Feng H, Raasholm M, Moosmann A, Campsteijn C, Thompson EM.
+
+Switching of INCENP paralogs controls transitions in mitotic chromosomal passenger complex functions.
+
+[[!pmid 31306061 desc="Components of the constitutive centromere-associated network (CCAN) at the inner kinetochore seem to be missing in the genome.  H3T3p and H3S28p mark inner centromeric regions (single spots) and H3T11p mark outer centromeric regions (pairs of spots).  Fluorescent microscopy pictures supporting a 2 × 3 karyotype."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 805ba5da..daa9cf3e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -63,6 +63,9 @@ Genome
    There are also intriguing observations of somatic mitotic cells with 7
    chromosomes ([[Körner, 1952|biblio/43261846]]) and meiotic cells with
    8 haploid chromosomes ([[Colombera & Fenaux, 1973|biblio/10.1080_11250007309429248]]).
+ - Several manuscripts using animals from the SARS laboratory include
+   fluorescent microscopy pictures supporting the 3 × 2 karyotype.  For instance:
+   centromere marking in [[Feng and coll., 2019|biblio/31306061]].
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
  - Genome size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al,
    2001|biblio/11752568]].  A 70.4 Mb genome "reference assembly" was later
@@ -174,6 +177,7 @@ Genes and pathways
    retrotransposition.
  - Duplications in the Rab family: Rab5/17, Rab6, Rab7, Rab10, Rab35.  The EF-Rab chimera
    Rab46 is kept ([[Coppola and coll., 2019|biblio/31028425]]).  See below for the losses. 
+ - INCENP and Plk1 are duplicated ([[Feng and coll., 2019|biblio/31306061]]).
 
 ### Lost
 
@@ -198,7 +202,9 @@ Genes and pathways
  - More than 50 % of the Rab family is lost ([[Coppola and coll., 2019|biblio/31028425]]):
    Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, RabX1 and the
    the EF-rab chimera Rasef and EFcab4/Rab44.
-
+ - Components of the constitutive centromere-associated network (CCAN) of the
+   inner kinetochore cound not be found in the genome by ([[Feng and coll.,
+   2019|biblio/31306061]]).
 
 Epigenome
 ---------

Café
diff --git a/biblio/16354750.mdwn b/biblio/16354750.mdwn
new file mode 100644
index 00000000..c47b96a1
--- /dev/null
+++ b/biblio/16354750.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis."]]
+[[!tag Ciona chromosome]]
+
+Genome Res. 2006 Feb;16(2):297-303 doi:10.1101/gr.4156606
+
+Shoguchi E, Kawashima T, Satou Y, Hamaguchi M, Sin-I T, Kohara Y, Putnam N, Rokhsar DS, Satoh N.
+
+Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.
+
+[[!pmid 16354750 desc="The short arm of chromosome 4, 5 and 6 contains rDNA clusters."]]

Karyotyping in Ciona
diff --git a/biblio/14993826.mdwn b/biblio/14993826.mdwn
new file mode 100644
index 00000000..a33525b8
--- /dev/null
+++ b/biblio/14993826.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Fluorescent in situ hybridization to ascidian chromosomes."]]
+[[!tag Ciona chromosome]]
+
+Zoolog Sci. 2004 Feb;21(2):153-7 doi:10.2108/zsj.21.153
+
+Shoguchi E1, Ikuta T, Yoshizaki F, Satou Y, Satoh N, Asano K, Saiga H, Nishikata T.
+
+Fluorescent in situ hybridization to ascidian chromosomes.
+
+[[!pmid 14993826 desc="“Embryos at three different developmental stages (32-cell embryos, 64-cell embryos and gastrulae) were used to produce metaphase spreads, although treatment of 32-cell embryos and 64-cell embryos with 0.05% colchicine (Sigma) in seawater caused aggregated and disorganized chromosomes. After treatment with colchicine for 20–30 min, embryos were transferred to a 1.5-ml microfuge tube, to which cold methanol:glacial acetic acid (3:1) fixative was added (chilled on ice). The fixative was changed twice over a period of 1 hr and once after overnight (embryos kept at 4°C). The specimens were then stored in fixative at 4°C.”"]]

privés de dessert
diff --git a/biblio/24695788.mdwn b/biblio/24695788.mdwn
new file mode 100644
index 00000000..43ef5d1a
--- /dev/null
+++ b/biblio/24695788.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Lifespan extension in a semelparous chordate occurs via developmental growth arrest just prior to meiotic entry."]]
+[[!tag Oikopleura H3S28p]]
+
+PLoS One. 2014 Apr 2;9(4):e93787. doi:10.1371/journal.pone.0093787
+
+Subramaniam G, Campsteijn C, Thompson EM.
+
+Lifespan extension in a semelparous chordate occurs via developmental growth arrest just prior to meiotic entry.
+
+[[!pmid 24695788 desc="Growth arrest (GA) discovered by culturing animals in crowded conditions, but can also be striggered by reduction of food intake before D4.  After that, starvation reduces the number of gametes produced instead of inducing GA.  In GA, cell cycle stops in both the somatic and germ lines.  GA can also be induced by the TOR inhibitor CCI-779.  Animals in GA can survice up to ~18 days at 15°C."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ab9ad739..805ba5da 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -260,6 +260,10 @@ Development
    culture conditions might differ.
  - 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]]).
  - Colchicine treatment induced early differenciation of the oocytes
    ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
  - Telomeres are localised at the nuclear envelope and do not overlap with nuclear

Et pendant ce temps, Maholo travaille...
diff --git a/biblio/15114417.mdwn b/biblio/15114417.mdwn
new file mode 100644
index 0000000..5d7c41a
--- /dev/null
+++ b/biblio/15114417.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians."]]
+[[!tag mitochondrion]]
+
+J Mol Evol. 2004 Apr;58(4):376-89 doi:10.1007/s00239-003-2559-6
+
+Gissi C, Iannelli F, Pesole G.
+
+Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians.
+
+[[!pmid 15114417 desc="Gene order varies even within the _Ciona_ genus.  A short _atp8_ gene is found in _Ciona_ and _Halocynthia_."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 3238950..eee0685 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -39,6 +39,9 @@ Speciation is estimated to have happened during the Pliocene (≈ 3.8 Ma); a
 recent introgression then happened 15,000 years ago ([[Roux and coll.,
 2013|biblio/23564941]]).
 
+Mitochondrial gene order differs even within the _Ciona_ genus ([[Gissi,
+Iannelli and Pesole 2004|biblio/15114417]]).
+
 _Ciona savignyi_ uses the same mitochodrial genetic code as of other ascidians
 studied before ([[Yokobori, Watanabe and Oshima, 2003|biblio/14738316]]).
 
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index ebde925..693212d 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -29,12 +29,18 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
  - Another case, unrelated, of reassignment to glycin is know: UGA -> Gly in
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
 
-### Gene order
 
+### Genes 
+
+ - All protein-coding genes are transcribed from the same strand.  See for
+   instance ([[Gissi, Iannelli and Pesole, 2004|biblio/15114417]]).
  - _cox2_ and _cytb_ are usually adjascent in tunicates, but they were found
    to be separated in the ascidians _Herdmania momus_ ([[Singh and coll,
    2009|biblio/19922605]]) or _Lissoclinum patella_ ([[Kwan and coll,
    2014|biblio/24788869]]).
+ - Contrary to statements in some early publication, the _atp8_ gene can be
+   found in ascidians ([[Gissi, Iannelli and Pesole, 2004|biblio/15114417]]).
+
 
 ### Transcription
 

Pendant que LabDroid travaille...
diff --git a/biblio/12915488.mdwn b/biblio/12915488.mdwn
new file mode 100644
index 0000000..0cd3248
--- /dev/null
+++ b/biblio/12915488.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcript mapping and genome annotation of ascidian mtDNA using EST data."]]
+[[!tag mitochondrion]]
+
+Genome Res. 2003 Sep;13(9):2203-12. doi:10.1101/gr.1227803
+
+Gissi C, Pesole G.
+
+Transcript mapping and genome annotation of ascidian mtDNA using EST data.
+
+[[!pmid 12915488 desc="Observation of polycistronic precursor and mature RNAs in ascidians."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 7c9a5b6..ebde925 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -1,14 +1,14 @@
 [[!meta title="pages tagged mitochondrion"]]
 
-The ascidian genetic code
--------------------------
+The tunicate mitochondrial genome
+---------------------------------
+
+### Genetic code
 
 https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG13
 
 https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
 
-(work in progress)
-
  - [[Yokobori and coll, 1993|biblio/8381878]] sequenced _cox1_ in
    _Halocynthia roretzi_ and suggested that it may use a different
    genetic code.  The same year, [[Durrheim and coll. |biblio/8393993]] made
@@ -29,11 +29,17 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
  - Another case, unrelated, of reassignment to glycin is know: UGA -> Gly in
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
 
+### Gene order
+
  - _cox2_ and _cytb_ are usually adjascent in tunicates, but they were found
    to be separated in the ascidians _Herdmania momus_ ([[Singh and coll,
    2009|biblio/19922605]]) or _Lissoclinum patella_ ([[Kwan and coll,
    2014|biblio/24788869]]).
 
-To read: Durrheim/8393993 (P. stol code),  Gissi/12915488 (alt. start codon)
+### Transcription
+
+ - EST data shows the presence of polycistronic precursor and mature RNAs
+   ([[Gissi & Pessole, 2003|biblio/12915488]]).
+
 
 [[!inline pages="tagged(mitochondrion)" limit=0]]

Café
diff --git a/biblio/8393993.mdwn b/biblio/8393993.mdwn
new file mode 100644
index 0000000..17e9309
--- /dev/null
+++ b/biblio/8393993.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: evidence that AGR encodes glycine."]]
+[[!tag mitochondrion]]
+
+Durrheim GA, Corfield VA, Harley EH, Ricketts MH.
+
+Nucleic Acids Res. 1993 Jul 25;21(15):3587-8.
+
+Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: evidence that AGR encodes glycine.
+
+[[!pmid 8393993 desc="AGR -> Gly in another tunicate"]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index cbf7c60..7c9a5b6 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -11,7 +11,8 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
 
  - [[Yokobori and coll, 1993|biblio/8381878]] sequenced _cox1_ in
    _Halocynthia roretzi_ and suggested that it may use a different
-   genetic code.
+   genetic code.  The same year, [[Durrheim and coll. |biblio/8393993]] made
+   the same observation on the _cox3_ sequence of _Pyura stolonifera_.
  - [[Delarbre and coll, 1997|biblio/9254918]] proposed an AGR -> Gly
    reassignment in amphioxus, based on a AGG/GGG polymorphism, and
    [[Spruyt and coll, 1998|biblio/9628930]] found a putative TCT (Gly) tRNA

updated PO files
diff --git "a/Debian/debi\303\242neries/inboxZero.en.po" "b/Debian/debi\303\242neries/inboxZero.en.po"
index d9d4b4c..74b76c8 100644
--- "a/Debian/debi\303\242neries/inboxZero.en.po"
+++ "b/Debian/debi\303\242neries/inboxZero.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-07-04 12:53+0000\n"
+"POT-Creation-Date: 2019-07-04 12:58+0000\n"
 "PO-Revision-Date: 2019-07-04 21:57+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
-"Language-Team: \n"
 "X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text

Inbox zero
diff --git "a/Debian/debi\303\242neries/inboxZero.en.po" "b/Debian/debi\303\242neries/inboxZero.en.po"
index c1610ac..d9d4b4c 100644
--- "a/Debian/debi\303\242neries/inboxZero.en.po"
+++ "b/Debian/debi\303\242neries/inboxZero.en.po"
@@ -3,38 +3,38 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2019-07-04 12:53+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2019-07-04 21:57+0900\n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Thu, 04 Jul 2019 21:52:28 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Thu, 04 Jul 2019 21:52:28 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Thu, 04 Jul 2019 21:52:28 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Thu, 04 Jul 2019 21:52:28 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Zéro inbox\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Inbox zero\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -44,3 +44,7 @@ msgid ""
 "l'ai fait, ça ne m'a pas servi à grand chose au final.  Alors envoyez-moi un "
 "rappel si vous attendez une réponse de ma part !"
 msgstr ""
+"I accidentally erased all the emails in my inbox.  This is very easy with "
+"[mutt](http://www.mutt.org/).  I have some experience in recovering files, "
+"but last time I did, it was not so useful in the end.  So please send me a "
+"reminder if you were expecting some answer from me!"

updated PO files
diff --git "a/Debian/debi\303\242neries/inboxZero.en.po" "b/Debian/debi\303\242neries/inboxZero.en.po"
new file mode 100644
index 0000000..c1610ac
--- /dev/null
+++ "b/Debian/debi\303\242neries/inboxZero.en.po"
@@ -0,0 +1,46 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2019-07-04 12:53+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, 04 Jul 2019 21:52:28 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Thu, 04 Jul 2019 21:52:28 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Zéro inbox\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'ai effacé par accident toute la boîte de réception de mes courriels.  "
+"C'est très facile avec [mutt](http://www.mutt.org/).  J'ai quelque "
+"expérience dans la récupération de fichiers mais la dernière fois que je "
+"l'ai fait, ça ne m'a pas servi à grand chose au final.  Alors envoyez-moi un "
+"rappel si vous attendez une réponse de ma part !"
+msgstr ""

zéro courriel.
diff --git "a/Debian/debi\303\242neries/inboxZero.mdwn" "b/Debian/debi\303\242neries/inboxZero.mdwn"
new file mode 100644
index 0000000..8eb3299
--- /dev/null
+++ "b/Debian/debi\303\242neries/inboxZero.mdwn"
@@ -0,0 +1,11 @@
+[[!meta date="Thu, 04 Jul 2019 21:52:28 +0900"]]
+[[!meta updated="Thu, 04 Jul 2019 21:52:28 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Zéro inbox"]]
+
+J'ai effacé par accident toute la boîte de réception de mes courriels.  C'est
+très facile avec [mutt](http://www.mutt.org/).  J'ai quelque expérience dans la
+récupération de fichiers mais la dernière fois que je l'ai fait, ça ne m'a pas
+servi à grand chose au final.  Alors envoyez-moi un rappel si vous attendez une
+réponse de ma part !

Another broken cox2-cytb pair.
diff --git a/biblio/24788869.mdwn b/biblio/24788869.mdwn
new file mode 100644
index 0000000..598272a
--- /dev/null
+++ b/biblio/24788869.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Host Control of Symbiont Natural Product Chemistry in Cryptic Populations of the Tunicate Lissoclinum patella"]]
+[[!tag mitochondrion]]
+
+Kwan JC, Tianero MD, Donia MS, Wyche TP, Bugni TS, Schmidt EW.
+
+PLoS One. 2014 May 2;9(5):e95850. doi:10.1371/journal.pone.0095850
+
+Host Control of Symbiont Natural Product Chemistry in Cryptic Populations of the Tunicate Lissoclinum patella
+
+[[!pmid 24788869 desc="Another ascidian where cox2 and cytb are not adjascent.  This ascidian has an endosymbiont."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index f4b8903..cbf7c60 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -29,7 +29,9 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
 
  - _cox2_ and _cytb_ are usually adjascent in tunicates, but they were found
-   to be separated in ([[Singh and coll, 2009|biblio/19922605]]).
+   to be separated in the ascidians _Herdmania momus_ ([[Singh and coll,
+   2009|biblio/19922605]]) or _Lissoclinum patella_ ([[Kwan and coll,
+   2014|biblio/24788869]]).
 
 To read: Durrheim/8393993 (P. stol code),  Gissi/12915488 (alt. start codon)
 

The cox2 cytb pair.
diff --git a/biblio/19922605.mdwn b/biblio/19922605.mdwn
new file mode 100644
index 0000000..cbbd154
--- /dev/null
+++ b/biblio/19922605.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny"]]
+[[!tag mitochondrion]]
+
+Tiratha Raj Singh, Georgia Tsagkogeorga, Frédéric Delsuc, Samuel Blanquart, Noa Shenkar, Yossi Loya, Emmanuel JP Douzery and Dorothée Huchon
+
+BMC Genomics. 2009 Nov 17;10:534. doi: 10.1186/1471-2164-10-534
+
+Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny
+
+[[!pmid 19922605 desc="The cox2-cytb pair, usually found in tunicates, is separated in the solitary ascidian _Herdmania momus_."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 6204677..f4b8903 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -28,6 +28,9 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
  - Another case, unrelated, of reassignment to glycin is know: UGA -> Gly in
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
 
+ - _cox2_ and _cytb_ are usually adjascent in tunicates, but they were found
+   to be separated in ([[Singh and coll, 2009|biblio/19922605]]).
+
 To read: Durrheim/8393993 (P. stol code),  Gissi/12915488 (alt. start codon)
 
 [[!inline pages="tagged(mitochondrion)" limit=0]]

thaliaceans
diff --git a/biblio/15619441.mdwn b/biblio/15619441.mdwn
new file mode 100644
index 0000000..56192e7
--- /dev/null
+++ b/biblio/15619441.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates."]]
+[[!tag mitochondrion]]
+
+Yokobori S, Oshima T, Wada H.
+
+Mol Phylogenet Evol. 2005 Feb;34(2):273-83. Epub 2004 Nov 19 doi:10.1016/j.ympev.2004.10.002
+
+Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates.
+
+[[!pmid 15619441 desc="Suggests that taliaceans also decode AGR as glycine."]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 4419ddc..6204677 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -22,6 +22,9 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    in _Halocynthia roretzi._.
  - [[Yokobori and coll, 1999|biblio/10581290]] sequenced the mitochondrial
    genome of _Halocynthia roretzi_ and found the predicted Gly tRNA.
+ - Sequence of a thaliacean (_Doliolum nationalis_) mitochondrial genome
+   suggests they also decode AGR as glycine ([[Yokobori, Oshima and Wada,
+   2005|biblio/15619441]]).
  - Another case, unrelated, of reassignment to glycin is know: UGA -> Gly in
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
 

Café
diff --git a/biblio/10.1111_bij.12915.mdwn b/biblio/10.1111_bij.12915.mdwn
new file mode 100644
index 0000000..926b3c9
--- /dev/null
+++ b/biblio/10.1111_bij.12915.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="One tunic but more than one barcode: evolutionary insights from dynamic mitochondrial DNA in Salpa thompsoni (Tunicata: Salpida)"]]
+[[!tag mitochondrion]]
+
+William P. Goodall-Copestake
+
+Biological Journal of the Linnean Society, Volume 120, Issue 3, 1 March 2017, Pages 637–648, https://doi.org/10.1111/bij.12915
+
+One tunic but more than one barcode: evolutionary insights from dynamic mitochondrial DNA in Salpa thompsoni (Tunicata: Salpida)
+
+[[!doi 10.1111/bij.12915 desc="Found ”inverse PCR amplicons [that] could occur in vivo as single circular DNAs and/or as tandem repeats within a larger circular or linear molecule”"]]

Café
diff --git a/biblio/23509275.mdwn b/biblio/23509275.mdwn
new file mode 100644
index 0000000..17f4636
--- /dev/null
+++ b/biblio/23509275.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota."]]
+[[!tag mitochondrion]]
+
+Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5540-5. doi:10.1073/pnas.1303090110
+
+Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M.
+
+UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.
+
+[[!pmid 23509275 desc="“Coexpression of SR1 glycyl-tRNA synthetase and tRNA(Gly)UCA in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an in-frame TGA codon.”"]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 0ed77ef..4419ddc 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -22,6 +22,8 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    in _Halocynthia roretzi._.
  - [[Yokobori and coll, 1999|biblio/10581290]] sequenced the mitochondrial
    genome of _Halocynthia roretzi_ and found the predicted Gly tRNA.
+ - Another case, unrelated, of reassignment to glycin is know: UGA -> Gly in
+   SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
 
 To read: Durrheim/8393993 (P. stol code),  Gissi/12915488 (alt. start codon)