Dernières modifications :

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
Café
diff --git a/biblio/30535005.mdwn b/biblio/30535005.mdwn
new file mode 100644
index 00000000..b87ef5c5
--- /dev/null
+++ b/biblio/30535005.mdwn
@@ -0,0 +1,21 @@
+[[!meta title="A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates."]]
+[[!tag Oikopleura enhancer]]
+
+Nash AJ, Lenhard B.
+
+Bioinformatics. 2019 Jul 15;35(14):2354-2361. doi: 10.1093/bioinformatics/bty1014.
+
+A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates.
+
+[[!pmid 30535005 desc="“our method may have utility in the analysis of GRB developmental gene regulation in species that have undergone extreme genome compaction such as the puffer fish, Tetraodon nigroviridis, and the sea squirt, Oikopleura dioica”"]]
+
+“The kurtosis of the distribution of the lengths of all identical sequences was calculated in [30 kbp] bins across the genome.”
+
+“Runs of 100% sequence identity were [...] filtered for annotated repeats and exonic sequences.”
+
+“The kurtosis of the distribution of lengths in each bin was then calculated as [...] R(F) = q0.99(F) − q0.01(F) / G50
+where F is the distribution of the lengths of runs of perfect sequence identity in a bin, and G50 is the range of the middle 50% of the distribution of lengths of all runs of identity, from all bins (background distribution); calculated as [...] q0.75(J) − q0.25(J) where J is the distribution of the lengths of runs of perfect sequence identity across the whole genome.”
+
+“This is an adaptation of the robust kurtosis measure proposed in Ruppert (1987).”
+
+“There is a strong correlation between kurtosis and CNE density, and this correlation is greater within GRBs than outside GRBs”
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 765e0202..c5d156e9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -140,7 +140,9 @@ Genome
    ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]).
  - Proteins of O. dioica are shorter and contain less disordored domains than proteins
    from other chrodates ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]).
-
+ - [[Nash and Lenhard (2019)|biblio/30535005]] proposed a kurtosis-based measure of
+   pairwise non-coding conservation that “may have utility in the analysis of”
+   conserved non-coding elements in _Oikopleura_.
 
 Repeat elements
 ---------------

Wikipedia link to the microbial food.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 765e0202..0d5e622c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -629,21 +629,31 @@ Culture protocols (incomplete list):
 
 Food tested in laboratory (totally incomplete list):
 
- - Flagellates _Isochrysis galbana_ (4 µm width) and _Monochrysis lutheri_ (4 µm
+ - Flagellates [_Isochrysis galbana_][] (4 µm width) and _Monochrysis lutheri_ (4 µm
    width), and the diatom _Cyclotella nana_ (Thalassiosira pseudonana) which had
    a width of 5 µm ([[G.-A. Paffenhöfer, 1973|biblio/10.1007_BF00391782]]).
 
- - _Isochrysis galbana_ (5.5 µm in size), _Tetraselmis suecica_ (9.5 µm), and
+ - _Isochrysis galbana_ (5.5 µm in size), [_Tetraselmis suecica_][] (9.5 µm), and
    the chlorophyte _Chlorella sp._ (3.5 µm) [[Acuña and Kiefer,
    2000|biblio/10.4319_lo.2000.45.3.0608]].
 
- - The diatom _Chaetoceros calcitrans_, often used as a food, can be toxic at
+ - The diatom [_Chaetoceros calcitrans_][], often used as a food, can be toxic at
    high concentrations, probably because of the production of biotoxins
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
 
  - The Postlethwait lab has been feeding their animals with (_Dunaliella
-   tertiolecta_, _Isochrysis galbana_, _Rhodomonas lens_, _Nanochloropsis sp._,
+   tertiolecta_, [_Isochrysis galbana_][], _Rhodomonas lens_, _Nanochloropsis sp._,
    and _Micromonas sp._ (strain Dw-8)) [[Bassham and Postlethwait
    (2000)|biblio/10753519]]).
 
+ - The Luscombe lab ([[Masunaga and coll., 2020|biblio/32628172]]) uses
+   [_Chaetoceros calcitrans_][], [_Isochrysis galbana_],
+   [_Rhinomonas reticulata_][], and [_Synechococcus sp._][].
+
+[_Chaetoceros calcitrans_]: https://en.wikipedia.org/wiki/Chaetoceros
+[_Isochrysis galbana_]:     https://en.wikipedia.org/wiki/Isochrysis_galbana
+[_Rhinomonas reticulata_]:  https://en.wikipedia.org/wiki/Rhinomonas
+[_Synechococcus sp._]:      https://en.wikipedia.org/wiki/Synechococcus
+[_Tetraselmis suecica_]:    https://en.wikipedia.org/wiki/Tetraselmis_suecica
+
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Dnmt2
diff --git a/biblio/22140515.mdwn b/biblio/22140515.mdwn
new file mode 100644
index 00000000..c45576eb
--- /dev/null
+++ b/biblio/22140515.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2."]]
+[[!tag Oikopleura]]
+
+Jurkowski TP, Jeltsch A.
+
+On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2.
+
+PLoS One. 2011;6(11):e28104. doi:10.1371/journal.pone.0028104
+
+[[!pmid 22140515 desc="Did not find Dnmt2 in O. dioica."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3dd6b38b..765e0202 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -236,6 +236,7 @@ Genes and pathways
  - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]],
    [[Albalat, Martí-Solans and Cañestro, 2012|biblio/22389042]]).
    It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
+   [[Jurkowski and Jeltsch (2011)|bilbio/22140515]] did not find Dnmt2 in O. dioica.
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).
  - No olfactory receptors have been found in _Oikopleura_ nor in _Ciona_

Only Dnmt2 (Trdmt1) is found in Oikopleura.
diff --git a/biblio/22389042.mdwn b/biblio/22389042.mdwn
new file mode 100644
index 00000000..dcc43f93
--- /dev/null
+++ b/biblio/22389042.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates."]]
+[[!tag Oikopleura epigenetic methylation]]
+
+Albalat R, Martí-Solans J, Cañestro C
+
+Brief Funct Genomics. 2012 Mar;11(2):142-55. doi:10.1093/bfgp/els009
+
+DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates.
+
+[[!pmid 22389042 desc="Only Dnmt2 (Trdmt1) is found in Oikopleura."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cfe791d9..3dd6b38b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -233,7 +233,8 @@ Genes and pathways
 
 ### Lost
 
- - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+ - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]],
+   [[Albalat, Martí-Solans and Cañestro, 2012|biblio/22389042]]).
    It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).

Café
diff --git a/biblio/33408411.mdwn b/biblio/33408411.mdwn
new file mode 100644
index 00000000..a6dc671b
--- /dev/null
+++ b/biblio/33408411.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Platypus and echidna genomes reveal mammalian biology and evolution."]]
+[[!tag genome synteny]]
+
+Zhou Y, Shearwin-Whyatt L, Li J, Song Z, Hayakawa T, Stevens D, Fenelon JC, Peel E, Cheng Y, Pajpach F, Bradley N, Suzuki H, Nikaido M, Damas J, Daish T, Perry T, Zhu Z, Geng Y, Rhie A, Sims Y, Wood J, Haase B, Mountcastle J, Fedrigo O, Li Q, Yang H, Wang J, Johnston SD, Phillippy AM, Howe K, Jarvis ED, Ryder OA, Kaessmann H, Donnelly P, Korlach J, Lewin HA, Graves J, Belov K, Renfree MB, Grutzner F, Zhou Q, Zhang G.
+
+Nature. 2021 Jan 6. doi:10.1038/s41586-020-03039-0
+
+Platypus and echidna genomes reveal mammalian biology and evolution. 
+
+[[!pmid 33408411 desc="The ancestral mammalian genome had 30 pairs of chromosomes."]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 5899c801..1a531eab 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -9,17 +9,6 @@ were enriched near CTCF-binding events.
 distribution follows a power law and explain it with a model that requires
 breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
 
-The ancestral chordate has 17 chromosomes according to amphioxus assemblies of
-[[Putnam and coll, 2008|biblio/18563158]] and [[Simakov and coll., 2020|biblio/32313176]].
-
-The scallop genome has 19 chromosomes, which are syntenic to the 17 ancestral
-chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
-elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].  The annelid
-worm _Dimorphilus gyrociliatus_ also has
-([[Martín-Durán and coll., 2020|biblio/10.1101_2020.05.07.078311]]).
-
-The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
-
 [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints
 (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
@@ -31,4 +20,19 @@ chromosomal inversions fixed per million years in _Drosophila_.
 In insects, the Osiris gene family shows conservation of synteny over ~400
 million years ([[Sah and coll., 2012|biblio/22384409]]).
 
+### Ancestral karyotpyes
+
+ - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll., 2021|biblio/33408411]]).
+
+ - The ancestral chordate has 17 chromosomes according to amphioxus assemblies
+  ([[Putnam and coll, 2008|biblio/18563158]], [[Simakov and coll., 2020|biblio/32313176]]).
+
+ - The scallop genome has 19 chromosomes, which are syntenic to the 17 ancestral
+   chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
+   elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].  The annelid
+   worm _Dimorphilus gyrociliatus_ also has
+   ([[Martín-Durán and coll., 2020|biblio/10.1101_2020.05.07.078311]]).
+
+ - The ancestral amniote has 49 chromosomes ([[Sacerdot and coll., 2018|biblio/30333059]]).
+
 [[!inline pages="tagged(synteny)" limit=0]]

To read
diff --git a/biblio/10.1111_cla.12405.mdwn b/biblio/10.1111_cla.12405.mdwn
new file mode 100644
index 00000000..fec5609f
--- /dev/null
+++ b/biblio/10.1111_cla.12405.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea"]]
+[[!tag to_read Oikopleura]]
+
+Katrin Braun, Fanny Leubner, Thomas Stach
+
+Cladistics Volume36, Issue3, June 2020, Pages 259–300 doi:10.1111/cla.12405
+
+Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea
+
+[[!doi 10.1111/cla.12405 desc="Places appendicularians basal in tunicates."]]

Mention one more phylogeny.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7a6f9891..cfe791d9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -33,8 +33,9 @@ Parasites: _Oodinium pouchetii_ and others.
 Phylogeny
 ---------
 
- - 18S rDNA phylogeny of [[Wada and Satoh, 1994|biblio/8127885]] and [[Swalla
-   and coll., 2000|biblio/12116483]] places larvaceans sister to all tunicates.
+ - 18S rDNA phylogenies of [[Wada and Satoh, 1994|biblio/8127885]],
+   [[Wada 1998|biblio/9729883]] and [[Swalla and coll., 2000|biblio/12116483]]
+   place larvaceans sister to all tunicates.
  - Based on 18S rRNA sequences from 110 species including 4 Oikopleuridae, this
    clade is sister of Stolidobranchia (that is, not basal in Tunicates).
    Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or

Café
diff --git a/biblio/31451549.mdwn b/biblio/31451549.mdwn
new file mode 100644
index 00000000..8b60d2d9
--- /dev/null
+++ b/biblio/31451549.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2."]]
+[[!tag Ciona Oikopleura]]
+
+Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2.
+
+Confalonieri S, Colaluca IN, Basile A, Pece S, Di Fiore PP.
+
+G3 (Bethesda). 2019 Oct 7;9(10):3359-3367. doi: 10.1534/g3.119.400494.
+
+[[!pmid 31451549 desc="Ciona NUMB can inhibit ubiquitination of P53 by MDM2.  This and a phylogenetic analysis demonstrates that PTB-long isoform encoded by Exon3 is a Chordate invention. O. dioica has 2 NUMB genes, more similar to NUMB than to vertebrate-specific NUMBL.  Their intron/exon structures are different from any other organism."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7821f2c2..7a6f9891 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -227,6 +227,8 @@ Genes and pathways
    Tolstenkov and Glover 2019|biblio/30905687]]).
  - Piwi ([[Henriet and coll., 2015|biblio/25779047]]).
  - Metallothioneins _OdMT1_ and _OdMT2_ [[Calatayud and coll., 2018|biblio/30284576]].
+ - 2 NUMB genes were found; both are closer to Vertebrate NUMB than to Vertebrate NUMB-Like
+   ([[Confalonieri and coll., 2019|biblio/31451549]]).
 
 ### Lost
 

Café
diff --git a/biblio/33380456.mdwn b/biblio/33380456.mdwn
new file mode 100644
index 00000000..d1a1e904
--- /dev/null
+++ b/biblio/33380456.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="True scale-free networks hidden by finite size effects."]]
+[[!tag network power_law]]
+
+Serafino M, Cimini G, Maritan A, Rinaldo A, Suweis S, Banavar JR, Caldarelli G.
+
+Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):e2013825118. doi:10.1073/pnas.2013825118
+
+True scale-free networks hidden by finite size effects.
+
+[[!pmid 33380456 desc="Sub-sampling of 185 different networks shows that in half of them the degree distribution is scale-invariant."]]
diff --git a/tags/power_law.mdwn b/tags/power_law.mdwn
index 5d385263..a4df2b11 100644
--- a/tags/power_law.mdwn
+++ b/tags/power_law.mdwn
@@ -11,6 +11,7 @@ Bonner (2002)|biblio/12136033]] to follow a power law.  [[Balwierz et al.,
 normalisation method fitting the data to the power law.
 
 Power laws are also seen in other areas, for instance in parameters describing
-network topologies ([[Barabási & Albert, 1999|biblio/10521342]]).
+network topologies ([[Barabási & Albert, 1999|biblio/10521342]], [[Serafino and
+coll., 2021|biblio/33380456]]).
 
 [[!inline pages="tagged(power_law)" limit=0]]

Café
diff --git a/biblio/26587265.mdwn b/biblio/26587265.mdwn
new file mode 100644
index 00000000..e8b1a23c
--- /dev/null
+++ b/biblio/26587265.mdwn
@@ -0,0 +1,24 @@
+[[!meta title="MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species."]]
+[[!tag eDNA]]
+
+Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W.
+
+MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.
+
+R Soc Open Sci. 2015 Jul 22;2(7):150088. doi:10.1098/rsos.150088
+
+[[!pmid 26587265 desc="“Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera.”"]]
+
+“considering the unconventional base pairing in the T/G bond, the designed primers use G rather than A when the template is variably C or T, and T rather than C when the template is A or G;”
+
+“2 l lots of seawater from the 10 l samples were vacuum-filtered onto 47 mm diameter glass-fibre filters [and then] stored in −20°C before eDNA extraction.”  “Two litres of Milli-Q water was used as the negative control.”  ”Lysis using proteinase K [at] 56°C [...] for 30 min.”  “Six random hexamers (N) are used to enhance cluster separation on the flowcells during [basecall]”
+
+“35 cycles of a 12 μl reaction volume containing 6.0 μl 2× KAPA HiFi HotStart ReadyMix (including DNA polymerase, reaction buffer, dNTPs and MgCl2 (at a final concentration of 2.5 mM)) (KAPA Biosystems, Wilmington, MA, USA), 0.7 μl of each primer (5 μM), 2.6 μl sterile distilled H2O and 2.0 μl template. [...] The thermal cycle profile after an initial 3 min denaturation at 95°C was as follows: denaturation at 98°C for 20 s; annealing at 65°C for 15 s; and extension at 72°C for 15 s with the final extension at the same temperature for 5 min.”  “The first PCR product was diluted 10 times using Milli-Q water and used as a template for the second PCR.”
+
+“The pre-processed reads from the above custom pipeline were dereplicated using a ‘derep_fulllength’ command in UCLUST”
+
+“Optimal experimental conditions for the first PCR with these primers were achieved through trial and error, and we found that choice of a PCR kit (KAPA HiFi HotStart ReadyMix) and associated high-annealing temperatures (65–67°C) in the first PCR are the two most important factors contributing to successful amplifications showing distinct single PCR bands on the agarose gel.”
+
+“MiFish-U/E primers also amplified eDNA from a [...] spotted dolphin”
+
+“The occasional detection of [non-tank species] in the negative controls strongly suggests cross contamination in the laboratory, which seems unavoidable in eDNA studies using PCR amplifications.”
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
index 289530cb..55342d8d 100644
--- a/tags/eDNA.mdwn
+++ b/tags/eDNA.mdwn
@@ -6,4 +6,7 @@
    [[Djurhuus and coll. 2020|biblio/31937756]]
  - Oikopleuridae detected in TARA Oceans ([[Vorobev and coll., 2020|biblio/32205368]]).
 
+ - Primer design “considering the unconventional base pairing in the T/G bond”
+   instead of using degenerate bases: [[Miya and coll (2015)|biblio/26587265]].
+
 [[!inline pages="tagged(eDNA)" limit=0]]

Syntax
diff --git a/biblio/10.1101_2020.12.23.423594.mdwn b/biblio/10.1101_2020.12.23.423594.mdwn
index 3c2f8fbf..77093509 100644
--- a/biblio/10.1101_2020.12.23.423594.mdwn
+++ b/biblio/10.1101_2020.12.23.423594.mdwn
@@ -7,4 +7,4 @@ bioRxiv 2020.12.23.423594; doi:10.1101/2020.12.23.423594
 
 SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
 
-[[!doi 10.1101/2020.12.23.423594 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two "gene" annotations."]]
+[[!doi 10.1101/2020.12.23.423594 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two “gene” annotations."]]

Café
diff --git a/biblio/10.1101_2020.12.23.423594.mdwn b/biblio/10.1101_2020.12.23.423594.mdwn
new file mode 100644
index 00000000..3c2f8fbf
--- /dev/null
+++ b/biblio/10.1101_2020.12.23.423594.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data"]]
+[[!tag Oikopleura bioRxiv]]
+
+Marius Wenzel, Berndt Mueller, Jonathan Pettitt
+
+bioRxiv 2020.12.23.423594; doi:10.1101/2020.12.23.423594
+
+SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
+
+[[!doi 10.1101/2020.12.23.423594 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two "gene" annotations."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ab0d6eb5..7821f2c2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -282,7 +282,8 @@ Transcriptome
    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.
-   Reported intercistronic regions are short (<30 nt) ([[Ganot et al., 2004|biblio/15314184]]).
+   Reported intercistronic regions are short: <30 nt ([[Ganot et al., 2004|biblio/15314184]])
+   or ~33 nt ([[Wenzel, Mueller and Pettitt, 2020|biblio/10.1101_2020.12.23.423594]]).
  - 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

Kaffe
diff --git a/biblio/23523957.mdwn b/biblio/23523957.mdwn
new file mode 100644
index 00000000..dd732bea
--- /dev/null
+++ b/biblio/23523957.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A remote-controlled adaptive medchem lab: an innovative approach to enable drug discovery in the 21st Century."]]
+[[!tag automation]]
+
+Godfrey AG, Masquelin T, Hemmerle H.
+
+Drug Discov Today. 2013 Sep;18(17-18):795-802. doi:10.1016/j.drudis.2013.03.001
+
+A remote-controlled adaptive medchem lab: an innovative approach to enable drug discovery in the 21st Century.
+
+[[!pmid 23523957 desc="Automated Synthesis Laboratory (ASL)"]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 44c50ffc..c6d23e90 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -2,6 +2,8 @@
 
 “Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery” ([[Kitano 2016|biblio/AI_37_2642]]).
 
+Automated synthesis laboratory (ASL): [[Godfrey, Masquelin and Hemmerle (2013)|biblio/23523957]]
+
 “A mobile robotic chemist” ([[Burger and coll., 2020|biblio/32641813]]).
 
 Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).

Café
diff --git a/biblio/30498165.mdwn b/biblio/30498165.mdwn
new file mode 100644
index 00000000..30ed5a92
--- /dev/null
+++ b/biblio/30498165.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Organic synthesis in a modular robotic system driven by a chemical programming language."]]
+[[!tag automation]]
+
+Steiner S, Wolf J, Glatzel S, Andreou A, Granda JM, Keenan G, Hinkley T, Aragon-Camarasa G, Kitson PJ, Angelone D, Cronin L.
+
+Science. 2019 Jan 11;363(6423):eaav2211. doi: 10.1126/science.aav2211.
+
+Organic synthesis in a modular robotic system driven by a chemical programming language.
+
+[[!pmid 30498165 desc="“The physical routing that links the connected modules is described in [GraphML]”.  Hardware-unknowing domain-specific language (DSL) is compiled in robot commands, so that the same DSL instructions can be executed on robots with different layouts but same equipment.  The commands are first simulated to check for potential issues such as overfilling, etc.  Valves etc. are connected to and commanded by the computer."]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 3851ef67..44c50ffc 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -6,6 +6,10 @@
 
 Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).
 
+Computational control of an organic chemistry system.  Position of the
+instruments are stored relative to each other in a graph.
+([[Steiner and coll., 2019|biblio/30498165]])
+
 Computational planning of compounts for a robotic platform that can assemble an run flow chemistry modules: [[Coley and coll., 2019|biblio/31395756]].
 
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].

Café
diff --git a/biblio/31395756.mdwn b/biblio/31395756.mdwn
new file mode 100644
index 00000000..f7fe14f3
--- /dev/null
+++ b/biblio/31395756.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A robotic platform for flow synthesis of organic compounds informed by AI planning."]]
+[[!tag automation]]
+
+Coley CW, Thomas DA 3rd, Lummiss JAM, Jaworski JN, Breen CP, Schultz V, Hart T, Fishman JS, Rogers L, Gao H, Hicklin RW, Plehiers PP, Byington J, Piotti JS, Green WH, Hart AJ, Jamison TF, Jensen KF.
+
+Science. 2019 Aug 9;365(6453):eaax1566. doi:10.1126/science.aax1566
+
+A robotic platform for flow synthesis of organic compounds informed by AI planning.
+
+[[!pmid  31395756 desc="An algorithm proposes a synthetic route for a robotic flow chemistry platform, an expect makes practical amendments for safety or efficiency, and the robot assembles the flow platform and runs the synthesis.  Practical challenges remain, such as predicting solubility of the products to avoid clogging the pipes with precipitates."]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index fd4fcf0b..3851ef67 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -6,6 +6,8 @@
 
 Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).
 
+Computational planning of compounts for a robotic platform that can assemble an run flow chemistry modules: [[Coley and coll., 2019|biblio/31395756]].
+
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
 
 Synthetic sequences that have the same function in a genome need to differ from each other, to prevent from spurious homologous recombinations.  Hossain and coll ([[2020|biblio/32661437]]) optimised an algorithm for producing libraries of "nonrepetitive" elements such as promoters.

Café
diff --git a/biblio/32661437.mdwn b/biblio/32661437.mdwn
new file mode 100644
index 00000000..1f0a37b6
--- /dev/null
+++ b/biblio/32661437.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Automated design of thousands of nonrepetitive parts for engineering stable genetic systems."]]
+[[!tag synthetic]]
+
+Hossain A, Lopez E, Halper SM, Cetnar DP, Reis AC, Strickland D, Klavins E, Salis HM.
+
+Nat Biotechnol. 2020 Dec;38(12):1466-1475. doi: 10.1038/s41587-020-0584-2
+
+Automated design of thousands of nonrepetitive parts for engineering stable genetic systems.
+
+[[!pmid 32661437 desc="To avoid homologous recombinations, synthetic parts of a genome that have the same function (promoter, ...) need to have a different sequence.  Constructing a set of functional synthetic sequences that never share k-mers of a given length (10 to 20) is difficult because the graph of related sequences is very dense.  Therefore, the authors have optimised an algorithm for very dense graph."]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 082ef04b..fd4fcf0b 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -8,4 +8,6 @@ Computational planning of the synthesis of complex natural products. ([[Mikulak-
 
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
 
+Synthetic sequences that have the same function in a genome need to differ from each other, to prevent from spurious homologous recombinations.  Hossain and coll ([[2020|biblio/32661437]]) optimised an algorithm for producing libraries of "nonrepetitive" elements such as promoters.
+
 [[!inline pages="tagged(automation)" limit=0]]

Café
diff --git a/biblio/33049755.mdwn b/biblio/33049755.mdwn
new file mode 100644
index 00000000..598e30d8
--- /dev/null
+++ b/biblio/33049755.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Computational planning of the synthesis of complex natural products."]]
+[[!tag automation]]
+
+Mikulak-Klucznik B, Gołębiowska P, Bayly AA, Popik O, Klucznik T, Szymkuć S, Gajewska EP, Dittwald P, Staszewska-Krajewska O, Beker W, Badowski T, Scheidt KA, Molga K, Mlynarski J, Mrksich M, Grzybowski BA.
+
+Nature. 2020 Dec;588(7836):83-88. doi:10.1038/s41586-020-2855-y
+
+Computational planning of the synthesis of complex natural products.
+
+[[!pmid 33049755 desc="Searches for the shortest path in a graph of compounds.  “computational synthesis planning”.  “the program has been taught [100,000] mechanism-based reaction rules”  “inclusion of [...] heuristics that prescribe how to strategize over multiple steps, taking into account how certain reaction choices imply succession (or elimination) of other transformations.”  “allowing [...] to overcome local maxima”  In a “Turing test“, evaluators could not distinguish plannings made by human and those made by the program.  “When needed, organic chemists performing the syntheses were allowed to adjust reaction conditions [...] for the sake of optimization.”"]]
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 6dc18731..082ef04b 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -4,6 +4,8 @@
 
 “A mobile robotic chemist” ([[Burger and coll., 2020|biblio/32641813]]).
 
+Computational planning of the synthesis of complex natural products. ([[Mikulak-Klucznik and coll., 2020|biblio/33049755]]).
+
 The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
 
 [[!inline pages="tagged(automation)" limit=0]]

Café
diff --git a/biblio/32810209.mdwn b/biblio/32810209.mdwn
new file mode 100644
index 00000000..113da47d
--- /dev/null
+++ b/biblio/32810209.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform."]]
+[[!tag sequencing]]
+
+Hirose Y, Shiozaki T, Hamano I, Yoshihara S, Tokumoto H, Eki T, Harada N.
+
+DNA Res. 2020 Aug 1;27(4):dsaa017. doi:10.1093/dnares/dsaa017
+
+A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform.
+
+[[!pmid 32810209 desc="N704/S507 index pair considered harmful on MiSeq."]]

creating tag page tags/karyotype
diff --git a/tags/karyotype.mdwn b/tags/karyotype.mdwn
new file mode 100644
index 00000000..a81787cf
--- /dev/null
+++ b/tags/karyotype.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged karyotype"]]
+
+[[!inline pages="tagged(karyotype)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/10.1101_2020.09.08.286724.mdwn b/biblio/10.1101_2020.09.08.286724.mdwn
new file mode 100644
index 00000000..9cea5b64
--- /dev/null
+++ b/biblio/10.1101_2020.09.08.286724.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cell culture-based shark karyotyping as a resource for chromosome-scale genome analysis"]]
+[[!tag bioRxiv cell_culture karyotype]]
+
+Yoshinobu Uno, Ryo Nozu, Itsuki Kiyatake, Nobuyuki Higashiguchi, Shuji Sodeyama, Kiyomi Murakumo, Keiichi Sato, Shigehiro Kuraku
+
+bioRxiv 2020.09.08.286724; doi: https://doi.org/10.1101/2020.09.08.286724
+
+Cell culture-based shark karyotyping as a resource for chromosome-scale genome analysis
+
+[[!doi 10.1101/2020.09.08.286724 desc="Primary cell culture of fibroblasts and lymphocytes.  Mitogens were used to stimulate lymphocyte growth. “2n = 102 for the whale shark (Rhincodon typus) and zebra shark (Stegostoma fasciatum), and 2n = 106 for the brownbanded bamboo shark (Chiloscyllium punctatum) and whitespotted bamboo shark (C. plagiosum)”.  In comparison with teleost cell culture medium, shark cells needed a higher osmolarity and the medium was supplemented with 333 mM urea, 188 mM NaCl and 54 mM trimethylamine N-oxide."]]

re-read
diff --git a/biblio/10471753.mdwn b/biblio/10471753.mdwn
index 495da5a4..fc24caa9 100644
--- a/biblio/10471753.mdwn
+++ b/biblio/10471753.mdwn
@@ -7,6 +7,7 @@ Shagin DA, Lukyanov KA, Vagner LL, Matz MV.
 
 Regulation of average length of complex PCR product.
 
-[[!pmid 10471753 desc="Amplify preferentially long PCR product with a single
-primer. Shorter molecules have a higher probability of undergoing
-inhibitory intramolecular interactions. (suppressive PCR)"]]
+[[!pmid 10471753 desc="Suppression PCR amplification of a phage lambda digested
+by HindII on which inverted terminal repeats were ligated.  Suppression effect
+is stronger when the PCR primer is shorter than the terminal repeats, and
+when the PCR primer molarity is lower (tested in a 750–0 nM range)."]]
diff --git a/tags/amplification.mdwn b/tags/amplification.mdwn
index 531fee71..798fcbaf 100644
--- a/tags/amplification.mdwn
+++ b/tags/amplification.mdwn
@@ -5,6 +5,10 @@ _work in progress..._
 ‘Suppression PCR’ was first published in English in [[Siebert and coll.,
 1995|biblio/7731798]].  Figure 1B shows a ‘panhandle’ structure.
 
+Primer concentration (lower -> stronger suppression) and length ratio between
+inverted tandem repeats and PCR primer (shorter PCR primer -> stronger
+suppression) were investigated by Shagin and coll ([[1999|biblio/10471753]]).
+
 Suppression PCR usually does not affect long (6~8 kbp) DNA molecules
 (mentionned in [[Lukyanov and coll., 2007|biblio/10.1007_978-1-4020-6040-3_2]]).
 

Café
diff --git a/biblio/17194496.mdwn b/biblio/17194496.mdwn
index 0b068de4..495ae4f4 100644
--- a/biblio/17194496.mdwn
+++ b/biblio/17194496.mdwn
@@ -1,3 +1,19 @@
 [[!meta title="PCR-suppression effect: kinetic analysis and application to representative or long-molecule biased PCR-based amplification of complex samples."]]
-[[!tag template_switching]]
-[[!pmid 17194496 desc="Uses a 3′ phosphate to prevent the template switching oligonucleotide to prime a first strand cDNA."]]
+[[!tag amplification template_switching]]
+
+Dai ZM, Zhu XJ, Chen Q, Yang WJ.
+
+J Biotechnol. 2007 Feb 20;128(3):435-43. doi:10.1016/j.jbiotec.2006.10.018
+
+PCR-suppression effect: kinetic analysis and application to representative or long-molecule biased PCR-based amplification of complex samples.
+
+[[!pmid 17194496 desc="PCR amplification of a GeneRuler 1kb DNA Ladder (Fermentas) on which adatpers were ligated.  Investigates “parameters which affect ITR self-annealing: (i) the length  of PCR  products [...] (ii) Primer concentration [...] (iii)  The  ratio of ITR  length to  primer length [and] (iv) [annealing temperature]”.  Uses a 3′ phosphate to prevent the template switching oligonucleotide to prime a first strand cDNA."]]
+
+“The 10 µl final [RT] reaction mixture contained 50 mM Tris–Cl (pH 8.3 at 25°C), 75 mM KCl,6 mM MgCl2, 2 mM MnCl2, 0.2 mg/ml BSA, 10 mM DTT, 1 mM dNTPs, 1µM TS-oligo, 1µM oligo(dT) adaptor (, 10 U RNase Inhibitor, and 150 U SuperScript II [and] was incubated at 42 °C for 1 h, followed by 45 °C for 30 min, and 50 °C for 10 min.”
+
+
+“Using [...] the shortest adaptor, whose length is equal to [the PCR primer], short fragments corresponding to 0.25 kb were efficiently amplified, while longer fragments (>3.5 kb) could not be distinguished from the background.  Using [...] the longest adaptor, whose length is more than twice [the PCR primer], fragments shorter than 1.5 kb were suppressed, while fragments up to 10 kb were efficiently amplified.” [My comment: this analysis does not take into account the overall reduction of PCR efficiency with increasing and the fact that mass of shortest fragments were also lower in the GeneRuler ladder.  This also contributes to the disappearance of these bands on the electrophoresis pictures.  This might explain why the high-length fragments could not resolve in the amplifications with highest yields.]
+
+“Lower [annealing temperature] enhanced the PS-effect under any condition.  [Annealing temperature] greatly affected the PS-effect when the primer concentration was low (P2 = 0.04M).  [The] average length  of  the products was longer at lower [annealing temperature].  [...] From 50 to 61.2°C), longer products (up to 10 kb) wer eefficiently amplified. When [annealing temperature] was higher (>65.9°C), much shorter products (<4 kb) were efficiently amplified and longer products disappeared. [Annealing temperature] also affected the PS-effect when primer concentration was 15-fold higher [...]  The average product length between higher (70◦C) and lower (60◦C) [annealing temperature] was significantly different, regardless of adaptors used.”
+
+“[Only] with the longest adaptor [...] we were able to amplify products in a wide range (from 0.25 to 10 kb) simultaneously with a slight over-representation of longer molecules.  [To] representatively amplify a complex sample, relatively long ITR (compared to primer length), high [annealing temperature], and high concentratio nof primer should be used.”
diff --git a/tags/amplification.mdwn b/tags/amplification.mdwn
index 995b611f..531fee71 100644
--- a/tags/amplification.mdwn
+++ b/tags/amplification.mdwn
@@ -8,4 +8,10 @@ _work in progress..._
 Suppression PCR usually does not affect long (6~8 kbp) DNA molecules
 (mentionned in [[Lukyanov and coll., 2007|biblio/10.1007_978-1-4020-6040-3_2]]).
 
+4 parameters (template length, inverted repeat length vs primer length, primer
+concentration and annealing temperature) were investigated by [[Dai and coll.,
+2020|biblio/17194496]], who concluded that to “representatively amplify a
+complex sample, relatively long ITR (compared to primer length), high
+[annealing temperature], and high concentration of primer should be used.”.
+
 [[!inline pages="tagged(amplification)" limit=0]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index a0f28cf8..1d0d7a0b 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -78,7 +78,8 @@ as a replacement for RNA.
  - 3′ phosphate or biotin blocking groups abolish template-switching
    ([[Turchinovich et al (2014)|biblio/24922482]] and others).  However,
    [[Pinto & Lindblad (2010)|biblio/19837043]] report the use of a
-   3′ C3 spacer (on all-DNA TSOs).
+   3′ C3 spacer (on all-DNA TSOs) and [[Dai and coll. 2020|biblio/17194496]].
+   report successful use of a phosphorylated TSO.
 
  - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
    of the TSO, and therefore blocks concatenation

Café
diff --git a/biblio/29712911.mdwn b/biblio/29712911.mdwn
new file mode 100644
index 00000000..cadf5c3b
--- /dev/null
+++ b/biblio/29712911.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty."]]
+[[!tag evolution]]
+
+Paps J, Holland PWH.
+
+Nat Commun. 2018 Apr 30;9(1):1730. doi:10.1038/s41467-018-04136-5
+
+Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty
+
+[[!pmid 29712911 desc="“[Homology groups] derived from the first animal genome were abundant in protein classes implicated in gene regulation [...] and catalytic activities [...]. The most abundant GO pathways include many signalling pathways.”"]]

Café
diff --git a/biblio/33057197.mdwn b/biblio/33057197.mdwn
new file mode 100644
index 00000000..ee8112f1
--- /dev/null
+++ b/biblio/33057197.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Dense and pleiotropic regulatory information in a developmental enhancer."]]
+[[!tag Drosophila enhancer automation]]
+
+Fuqua T, Jordan J, van Breugel ME, Halavatyi A, Tischer C, Polidoro P, Abe N, Tsai A, Mann RS, Stern DL, Crocker J.
+
+Nature. 2020 Nov;587(7833):235-239. doi:10.1038/s41586-020-2816-5
+
+Dense and pleiotropic regulatory information in a developmental enhancer
+
+[[!pmid 33057197 desc="Study of the E3N enhancer of the shavenbaby (svb) gene.  Immunohistochemistry automated with liquid handling robots.  “sequence conservation is not an accurate predictor of the quantitative roles of individual sites in the E3N enhancer”  “most mutations in E3N led to changes in transcriptional outputs, suggesting that regulatory information is distributed densely within this enhancer”"]]

Bière et tchidjimi.
diff --git a/biblio/10.1073_pnas.1003250107.mdwn b/biblio/10.1073_pnas.1003250107.mdwn
new file mode 100644
index 00000000..4b756aea
--- /dev/null
+++ b/biblio/10.1073_pnas.1003250107.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Universal robotic gripper based on the jamming of granular material"]]
+[[!tag robot]]
+
+Eric Brown, Nicholas Rodenberg, John Amend, Annan Mozeika, Erik Steltz, Mitchell R. Zakin, Hod Lipson, and Heinrich M. Jaeger
+
+Proc Natl Acad Sci U S A. 2010 Nov 2; 107(44): 18809–18814. doi:10.1073/pnas.1003250107
+
+Universal robotic gripper based on the jamming of granular material
+
+[[!doi 10.1073/pnas.1003250107 desc="Doraemon !"]]
diff --git a/tags/robot.mdwn b/tags/robot.mdwn
index e671a3a9..01b6c733 100644
--- a/tags/robot.mdwn
+++ b/tags/robot.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged robot"]]
 
-[[!inline pages="tagged(robot)" actions="no" archive="yes"
-feedshow=10]]
+(work in progress)
+
+ - A ball gripper that reminds me Doraemon's hand: [[Brown and coll.,
+   2010|biblio/10.1073_pnas.1003250107]].
+
+[[!inline pages="tagged(robot)" limit=0]]

Café
diff --git a/biblio/10.1007_978-1-4020-6040-3_2.mdwn b/biblio/10.1007_978-1-4020-6040-3_2.mdwn
new file mode 100644
index 00000000..db71efa6
--- /dev/null
+++ b/biblio/10.1007_978-1-4020-6040-3_2.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Selective Suppression of Polymerase Chain Reaction and Its Most Popular Applications."]]
+[[!tag amplification]]
+
+Lukyanov S.A., Lukyanov K.A., Gurskaya N.G., Bogdanova E.A., Buzdin A.A.
+
+(2007)
+
+Selective Suppression of Polymerase Chain Reaction and Its Most Popular Applications.
+
+In: Buzdin A.A., Lukyanov S.A. (eds) Nucleic Acids Hybridization Modern Applications. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6040-3_2
+
+[[!doi 10.1007/978-1-4020-6040-3_2 desc="Mentions that the “SSP [selective suppression PCR] effect does not inhibit, or inhibits sparingly, amplification of very long DNA ([...] usually 6–8 kbp).” "]]
diff --git a/tags/amplification.mdwn b/tags/amplification.mdwn
index f5162ec2..995b611f 100644
--- a/tags/amplification.mdwn
+++ b/tags/amplification.mdwn
@@ -5,4 +5,7 @@ _work in progress..._
 ‘Suppression PCR’ was first published in English in [[Siebert and coll.,
 1995|biblio/7731798]].  Figure 1B shows a ‘panhandle’ structure.
 
+Suppression PCR usually does not affect long (6~8 kbp) DNA molecules
+(mentionned in [[Lukyanov and coll., 2007|biblio/10.1007_978-1-4020-6040-3_2]]).
+
 [[!inline pages="tagged(amplification)" limit=0]]

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index ee50f858..78892dd7 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-11-02 03:50+0000\n"
+"POT-Creation-Date: 2020-11-02 06:36+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"
@@ -71,17 +71,18 @@ msgstr ""
 #. type: Plain text
 msgid ""
 "I have complemented my work on CAGE with the development of a gene-centred "
-"technique for detecting promoters, termed Deep-RACE ([Olivarius and coll., "
-"2009](https://pubmed.gov/19317658), [Plessy and coll., 2012](http://dx.doi."
-"org/10.1002/9783527644582.ch4)), which we used to validate our discovery of "
-"the pervasive expression of retrotransposons detected by CAGE ([Faulkner and "
-"coll., 2009](https://pubmed.gov/19377475)). To study transcription start "
-"activity at nucleotide resolution in zebrafish transfected with chimeric "
-"transgenes containing a copy of an endogenous promoter, I combined Deep-"
-"RACE, CAGE and paired-end sequencing in a technology that we called “Single-"
-"Locus CAGE” ([Haberle and coll., 2014](https://pubmed.gov/24531765)). With "
-"my contributions related to CAGE development and analysis, I have been a "
-"**member of the FANTOM consortium** since FANTOM3."
+"technique for detecting promoters, termed **Deep-RACE** ([Olivarius and "
+"coll., 2009](https://pubmed.gov/19317658), [Plessy and coll., 2012](http://"
+"dx.doi.org/10.1002/9783527644582.ch4)), which we used to validate our "
+"discovery of the pervasive expression of retrotransposons detected by CAGE "
+"([Faulkner and coll., 2009](https://pubmed.gov/19377475)). To study "
+"transcription start activity at nucleotide resolution in zebrafish "
+"transfected with chimeric transgenes containing a copy of an endogenous "
+"promoter, I combined Deep-RACE, CAGE and paired-end sequencing in a "
+"technology that we called “Single-Locus CAGE” ([Haberle and coll., 2014]"
+"(https://pubmed.gov/24531765)). With my contributions related to CAGE "
+"development and analysis, I have been a **member of the FANTOM consortium** "
+"since FANTOM3."
 msgstr ""
 
 #. type: Plain text
@@ -96,17 +97,23 @@ msgid ""
 "(https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory "
 "epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with "
 "this promoter-centric work, I have also explored the huge repertoire of the "
-"T cell antigen receptors.  I also applied the nanoCAGE technology to patient "
-"samples infected with the human papillomavirus (HPV) ([Taguchi and coll., "
-"2020](https://pubmed.gov/33093512))."
+"**T cell antigen receptors**.  I also applied the nanoCAGE technology to "
+"patient samples infected with the **human papillomavirus** (HPV) ([Taguchi "
+"and coll., 2020](https://pubmed.gov/33093512))."
 msgstr ""
 
 #. type: Plain text
 msgid ""
 "I joined OIST in 2018, to study **the genetic structure and population "
-"variations** of an animal plankton, _Oikopleura dioica_, that has a genome "
-"50 time more compact than the human one, which empowers us to sequence at "
-"chromosomal resolution many individual sampled from all over the World."
+"variations** of an animal plankton, **_Oikopleura dioica_**, that has a "
+"genome 50 time more compact than the human one, which empowers us to "
+"sequence at chromosomal resolution many individual sampled from all over the "
+"World.  Its mitochondria use a different genetic code than ours ([Pichon and "
+"coll., 2019](https://pubmed.gov/32148763)).  We assembled whole-chromosome "
+"sequences for the Okinawan _O. dioica_ population ([Bliznina and coll., 2020]"
+"(https://doi.org/10.1101/2020.09.11.292656)), which has 3 pairs of "
+"chromosomes ([Liu and coll, 2020](https://f1000research.com/articles/9-780/"
+"v1))  like the other dioceous species."
 msgstr ""
 
 #. type: Plain text

Emphasis and papers.
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index a7cabb82..dc03f0ad 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -41,7 +41,7 @@ for FACS-isolated cells, and one for the Fluidigm C1 platform ([Kouno and coll.,
 2019](https://pubmed.gov/30664627)).
 
 I have complemented my work on CAGE with the development of a gene-centred
-technique for detecting promoters, termed Deep-RACE ([Olivarius and coll.,
+technique for detecting promoters, termed **Deep-RACE** ([Olivarius and coll.,
 2009](https://pubmed.gov/19317658), [Plessy and coll.,
 2012](http://dx.doi.org/10.1002/9783527644582.ch4)), which we used to validate
 our discovery of the pervasive expression of retrotransposons detected by CAGE
@@ -63,16 +63,21 @@ demonstrate the expression of haemoglobin in the midbrain ([Biagioli and coll.,
 localisation of RNA in **Purkinje neurons** ([Kratz and coll.,
 2014](https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory
 epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with
-this promoter-centric work, I have also explored the huge repertoire of the T
-cell antigen receptors.  I also applied the nanoCAGE technology to patient
-samples infected with the human papillomavirus (HPV) ([Taguchi and coll.,
+this promoter-centric work, I have also explored the huge repertoire of the **T
+cell antigen receptors**.  I also applied the nanoCAGE technology to patient
+samples infected with the **human papillomavirus** (HPV) ([Taguchi and coll.,
 2020](https://pubmed.gov/33093512)).
 
 I joined OIST in 2018, to study **the genetic structure and population
-variations** of an animal plankton, _Oikopleura dioica_, that has a genome
-50 time more compact than the human one, which empowers us to sequence
-at chromosomal resolution many individual sampled from all over the
-World.
+variations** of an animal plankton, **_Oikopleura dioica_**, that has a genome
+50 time more compact than the human one, which empowers us to sequence at
+chromosomal resolution many individual sampled from all over the World.  Its
+mitochondria use a different genetic code than ours ([Pichon and coll.,
+2019](https://pubmed.gov/32148763)).  We assembled whole-chromosome sequences
+for the Okinawan _O. dioica_ population ([Bliznina and coll.,
+2020](https://doi.org/10.1101/2020.09.11.292656)), which has 3 pairs of
+chromosomes ([Liu and coll, 2020](https://f1000research.com/articles/9-780/v1))
+like the other dioceous species.
 
 I am also a **Free Software** enthusiast, and contribute to the Debian Med
 project, by **packaging bioinformatics tools**, which are redistributed in

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 1788c12c..ee50f858 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-16 01:18+0000\n"
+"POT-Creation-Date: 2020-11-02 03:50+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"
@@ -28,10 +28,9 @@ msgid ""
 "enhancers ([Blader and coll., 2003](https://pubmed.gov/12559493)) and their "
 "evolutionary conservation ([Plessy and coll., 2005](https://pubmed."
 "gov/15797614)). This gave me a strong interest for whole-transcriptome "
-"analysis and technology. For that purpose, I have joined RIKEN in 2004, "
-"where have worked on high-throughput methods for **profiling promoters and "
-"inferring gene networks**, and in particular on CAGE (Cap Analysis Gene "
-"Expression)."
+"analysis and technology. For that purpose, I have worked at RIKEN in 2004–18 "
+"on high-throughput methods for **profiling promoters and inferring gene "
+"networks**, and in particular on CAGE (Cap Analysis Gene Expression)."
 msgstr ""
 
 #. type: Plain text
@@ -47,25 +46,26 @@ msgid ""
 "gov/23180801)), combining multiple cap-enrichment steps ([Batut and coll., "
 "2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic "
 "acids for template switching ([Harbers and coll., 2013](https://pubmed."
-"gov/24079827)), and reducing the number of primer artefacts and unwanted "
+"gov/24079827)), reducing the number of primer artefacts and unwanted "
 "sequences generated by ribosomal RNAs using low-complexity “pseudo-random” "
 "reverse-transcription primers ([Arnaud and coll., 2016](https://pubmed."
-"gov/27071605))."
+"gov/27071605)), and screening for optimal parameters of the template-"
+"switching reaction ([Poulain and coll., 2020](https://pubmed.gov/32025730))."
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"On April 2013, I started a new development cycle as the leader of the "
-"Genomics Miniaturization Technology Unit at RIKEN Center for Life Sciences, "
-"Division of Genomics Technology, to expand this work on single cells "
-"following a **population transcriptomics** approach ([Plessy and coll., 2013]"
-"(https://pubmed.gov/23281054)) focused on sampling the largest possible "
-"number of cells. In our ongoing developments, we have reached **single-cell "
-"and single molecule resolution** through the introduction of transposase "
-"fragmentation and unique molecular identifiers ([Poulain and coll., 2017]"
-"(https://pubmed.gov/28349422)). The protocol exists in two versions, one for "
-"FACS-isolated cells, and one for the Fluidigm C1 platform ([Kouno and coll., "
-"2019](https://pubmed.gov/30664627))."
+"In 2013–8, I lead a new development cycle at the Genomics Miniaturization "
+"Technology Unit in RIKEN's Center for Life Sciences, Division of Genomics "
+"Technology, to expand this work on single cells following a **population "
+"transcriptomics** approach ([Plessy and coll., 2013](https://pubmed."
+"gov/23281054)) focused on sampling the largest possible number of cells. In "
+"our ongoing developments, we have reached **single-cell and single molecule "
+"resolution** through the introduction of transposase fragmentation and "
+"unique molecular identifiers ([Poulain and coll., 2017](https://pubmed."
+"gov/28349422)). The protocol exists in two versions, one for FACS-isolated "
+"cells, and one for the Fluidigm C1 platform ([Kouno and coll., 2019](https://"
+"pubmed.gov/30664627))."
 msgstr ""
 
 #. type: Plain text
@@ -96,7 +96,9 @@ msgid ""
 "(https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory "
 "epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with "
 "this promoter-centric work, I have also explored the huge repertoire of the "
-"**T cell antigen receptors**."
+"T cell antigen receptors.  I also applied the nanoCAGE technology to patient "
+"samples infected with the human papillomavirus (HPV) ([Taguchi and coll., "
+"2020](https://pubmed.gov/33093512))."
 msgstr ""
 
 #. type: Plain text

creating tag page tags/RIKEN
diff --git a/tags/RIKEN.mdwn b/tags/RIKEN.mdwn
new file mode 100644
index 00000000..b77112a6
--- /dev/null
+++ b/tags/RIKEN.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged RIKEN"]]
+
+[[!inline pages="tagged(RIKEN)" actions="no" archive="yes"
+feedshow=10]]

More papers !
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index 41a4ad95..a7cabb82 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -6,9 +6,9 @@ and zebrafish**, where I studied the activity of transcription enhancers
 ([Blader and coll., 2003](https://pubmed.gov/12559493)) and their evolutionary
 conservation ([Plessy and coll., 2005](https://pubmed.gov/15797614)). This gave
 me a strong interest for whole-transcriptome analysis and technology. For that
-purpose, I have joined RIKEN in 2004, where have worked on high-throughput
-methods for **profiling promoters and inferring gene networks**, and in
-particular on CAGE (Cap Analysis Gene Expression).
+purpose, I have worked at RIKEN in 2004–18  on high-throughput methods for
+**profiling promoters and inferring gene networks**, and in particular on CAGE
+(Cap Analysis Gene Expression).
 
 I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to
 analyse small samples yielding only nanograms of RNA ([Plessy and coll.,
@@ -21,13 +21,15 @@ the molecular barcodes ([Tang and coll., 2013](https://pubmed.gov/23180801)),
 combining multiple cap-enrichment steps ([Batut and coll.,
 2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic
 acids for template switching ([Harbers and coll.,
-2013](https://pubmed.gov/24079827)), and reducing the number of primer
-artefacts and unwanted sequences generated by ribosomal RNAs using
-low-complexity “pseudo-random” reverse-transcription primers ([Arnaud and
-coll., 2016](https://pubmed.gov/27071605)).
+2013](https://pubmed.gov/24079827)), reducing the number of primer artefacts
+and unwanted sequences generated by ribosomal RNAs using low-complexity
+“pseudo-random” reverse-transcription primers ([Arnaud and coll.,
+2016](https://pubmed.gov/27071605)), and screening for optimal parameters of
+the template-switching reaction ([Poulain and coll.,
+2020](https://pubmed.gov/32025730)).
 
-On April 2013, I started a new development cycle as the leader of the Genomics
-Miniaturization Technology Unit at RIKEN Center for Life Sciences, Division of
+In 2013–8, I lead a new development cycle at the Genomics
+Miniaturization Technology Unit in RIKEN's Center for Life Sciences, Division of
 Genomics Technology, to expand this work on single cells following a
 **population transcriptomics** approach ([Plessy and coll.,
 2013](https://pubmed.gov/23281054)) focused on sampling the largest possible
@@ -61,8 +63,10 @@ demonstrate the expression of haemoglobin in the midbrain ([Biagioli and coll.,
 localisation of RNA in **Purkinje neurons** ([Kratz and coll.,
 2014](https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory
 epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with
-this promoter-centric work, I have also explored the huge repertoire of the **T
-cell antigen receptors**.
+this promoter-centric work, I have also explored the huge repertoire of the T
+cell antigen receptors.  I also applied the nanoCAGE technology to patient
+samples infected with the human papillomavirus (HPV) ([Taguchi and coll.,
+2020](https://pubmed.gov/33093512)).
 
 I joined OIST in 2018, to study **the genetic structure and population
 variations** of an animal plankton, _Oikopleura dioica_, that has a genome

nanoCAGE on HPV patient samples.
diff --git a/biblio/33093512.mdwn b/biblio/33093512.mdwn
new file mode 100644
index 00000000..9e32a576
--- /dev/null
+++ b/biblio/33093512.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages."]]
+[[!tag RIKEN OIST nanoCAGE HPV]]
+
+Taguchi A, Nagasaka K, Plessy C, Nakamura H, Kawata Y, Kato S, Hashimoto K, Nagamatsu T, Oda K, Kukimoto I, Kawana K, Carninci P, Osuga Y, Fujii T.
+
+Sci Rep. 2020 Oct 22;10(1):17991. doi:10.1038/s41598-020-75133-2
+
+Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages.
+
+[[!pmid 33093512 desc="nanoCAGE in HPV patient samples."]]
diff --git a/tags/nanoCAGE.mdwn b/tags/nanoCAGE.mdwn
index fd96652b..031609dd 100644
--- a/tags/nanoCAGE.mdwn
+++ b/tags/nanoCAGE.mdwn
@@ -1,4 +1,3 @@
 [[!meta title="pages tagged nanoCAGE"]]
 
-[[!inline pages="tagged(nanoCAGE)" actions="no" archive="yes"
-feedshow=10]]
+[[!inline pages="tagged(nanoCAGE)" limit=0]]

Syntax
diff --git a/biblio/US5759822.mdwn b/biblio/US5759822.mdwn
index 749d6074..c6a2b499 100644
--- a/biblio/US5759822.mdwn
+++ b/biblio/US5759822.mdwn
@@ -1,4 +1,6 @@
 [[!meta title="Method for suppressing DNA fragment amplification during PCR."]]
 [[!tag patent amplification]]
-[[https://patents.google.com/patent/US5759822A|Suppressive PCR]]
-See also patent [[https://patents.google.com/patent/US5565340|US5565340]].
+
+[Suppressive PCR](https://patents.google.com/patent/US5759822A).
+
+See also patent [US5565340](https://patents.google.com/patent/US5565340).

Syntax
diff --git a/biblio/US5759822.mdwn b/biblio/US5759822.mdwn
index 72b60138..749d6074 100644
--- a/biblio/US5759822.mdwn
+++ b/biblio/US5759822.mdwn
@@ -1,4 +1,4 @@
 [[!meta title="Method for suppressing DNA fragment amplification during PCR."]]
 [[!tag patent amplification]]
-[[https://patents.google.com/patent/US5759822A desc="Suppressive PCR."]]
-See also patent [[https://patents.google.com/patent/US5565340 desc="US5565340"]].
+[[https://patents.google.com/patent/US5759822A|Suppressive PCR]]
+See also patent [[https://patents.google.com/patent/US5565340|US5565340]].
diff --git a/tags/patent.mdwn b/tags/patent.mdwn
index fd30c0a2..f3e265bc 100644
--- a/tags/patent.mdwn
+++ b/tags/patent.mdwn
@@ -2,7 +2,7 @@
 
 Expired:
 
- - [[Method for suppressing DNA fragment amplification during PCR (1996)|bilbio/US5565340]]
+ - [[Method for suppressing DNA fragment amplification during PCR (1996)|bilbio/US5759822]]
  - [[Method for suppressing DNA fragment amplification during PCR (1998)|biblio/US5759822]]
 
 [[!inline pages="tagged(patent)" limit=0]]

Expired
diff --git a/biblio/US5759822.mdwn b/biblio/US5759822.mdwn
index eff3b18f..72b60138 100644
--- a/biblio/US5759822.mdwn
+++ b/biblio/US5759822.mdwn
@@ -1,4 +1,4 @@
 [[!meta title="Method for suppressing DNA fragment amplification during PCR."]]
 [[!tag patent amplification]]
-[[!gpatent Ak0jAAAAEBAJ desc="Suppressive PCR."]]
-See also patent [[!gpatent L-ccAAAAEBAJ desc="5565340"]].
+[[https://patents.google.com/patent/US5759822A desc="Suppressive PCR."]]
+See also patent [[https://patents.google.com/patent/US5565340 desc="US5565340"]].
diff --git a/tags/patent.mdwn b/tags/patent.mdwn
index 3ad87a82..fd30c0a2 100644
--- a/tags/patent.mdwn
+++ b/tags/patent.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged patent"]]
 
-[[!inline pages="tagged(patent)" actions="no" archive="yes"
-feedshow=10]]
+Expired:
+
+ - [[Method for suppressing DNA fragment amplification during PCR (1996)|bilbio/US5565340]]
+ - [[Method for suppressing DNA fragment amplification during PCR (1998)|biblio/US5759822]]
+
+[[!inline pages="tagged(patent)" limit=0]]

Café
diff --git a/biblio/33055213.mdwn b/biblio/33055213.mdwn
new file mode 100644
index 00000000..c7c6ba4d
--- /dev/null
+++ b/biblio/33055213.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts."]]
+[[!tag cap method]]
+
+Culjkovic-Kraljacic B, Skrabanek L, Revuelta MV, Gasiorek J, Cowling VH, Cerchietti L, Borden KLB.
+
+Proc Natl Acad Sci U S A. 2020 Oct 27;117(43):26773-26783. doi:10.1073/pnas.2002360117
+
+The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts.
+
+[[!pmid 33055213 desc="Some RNAs have more than half of their molecules non-capped.  Increasing expression of eIF4E increases their capped proportion to similar levels as other genes.  Enzymatic (cap quantification; CapQ) and quantitative cap immunoprecipitation (CapIP) methods.  Uses the mouse IgG2aκ anti-7-methylguanosine (m7G)-Cap antibody of MBL (RN016M). The maker's site notes that “This antibody (Clone 150-15) reacts with 5′-terminal 7-methylguanosine (m7G) cap structure of RNA and partially cross-reacts with m7G within RNA”.  Overexpression of eIF4E-Flag in  RNA immunoprecipitation experiments increased enrichment of RNA export targets such as RNMT or RNGTT, but export-deficient S53A-eIF4E-Flag mutants did not.  Overexpression also shifted RNA translation to heavier polysomal fractions and elevated m7G levels in the nuclear and cytoplasmic compartments. This elevation is reduced by RNMT knockdown and stronger on specific target, for instance from the capping machinery and the Myc pathway.  A CapQ assay (sequencing an oligo-capping library and a control PNK library) confirmed the observations made by immunoprecipitation.  In control conditions, the capping rate of the targets of eIF4E capping are lower than those of the non-targets."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 2b911981..552aa76d 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -72,4 +72,11 @@ Atypical caps (work in progress)
  - Mass spectroscopy and molecular biology detected dinucleoside polyphosphate caps
    in bacteria ([[Hudeček and coll., 2020|biblio/32103016]]).
 
+Cap physiology (work in progress)
+---------------------------------
+
+Some RNAs have more than half of their molecules non-capped.  Increasing
+expression of eIF4E increases their capped proportion to similar levels as
+other genes.  [[Culjkovic-Kraljacic and coll, 2020|biblio/33055213]]
+
 [[!inline pages="tagged(cap)" limit=0]]

Café
diff --git a/biblio/33020265.mdwn b/biblio/33020265.mdwn
new file mode 100644
index 00000000..59138c90
--- /dev/null
+++ b/biblio/33020265.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Dynamic evolution of great ape Y chromosomes."]]
+[[!tag chromosome]]
+
+Cechova M, Vegesna R, Tomaszkiewicz M, Harris RS, Chen D, Rangavittal S, Medvedev P, Makova KD.
+
+Proc Natl Acad Sci U S A. 2020 Oct 20;117(42):26273-26280. doi:10.1073/pnas.2001749117
+
+Dynamic evolution of great ape Y chromosomes.
+
+[[!pmid 33020265 desc="“Unexpectedly, the rates of gene death were similar between ampliconic and X-degenerate genes.”"]]

Café
diff --git a/biblio/10.1101_2020.05.07.078311.mdwn b/biblio/10.1101_2020.05.07.078311.mdwn
new file mode 100644
index 00000000..be6a0ea9
--- /dev/null
+++ b/biblio/10.1101_2020.05.07.078311.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conservative route to genome compaction in a miniature annelid"]]
+[[!tag genome synteny]]
+
+José M. Martín-Durán, Bruno C. Vellutini, Ferdinand Marlétaz, Viviana Cetrangolo, Nevena Cvetesic, Daniel Thiel, Simon Henriet, Xavier Grau-Bové, Allan M. Carrillo-Baltodano, Wenjia Gu, Alexandra Kerbl, Yamile Marquez, Nicolas Bekkouche, Daniel Chourrout, Jose Luis Gómez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol
+
+bioRxiv 2020.05.07.078311; doi:10.1101/2020.05.07.078311 
+
+Conservative route to genome compaction in a miniature annelid
+
+[[!doi 10.1101/2020.05.07.078311 desc="Genome assembly (PacBio, 73.8 Mb, 95.8% BUSCO genes, 2.24 Mb N50, 4.87% transposable elements, 14,203 protein-coding genes) for the annelid Dimorphilus gyrociliatus, a meiobenthic segmented worm.  Synteny with the scallop genome is visible.  The Hox cluster is present and lacks only one gene, post1.  However, in situ hybridisation suggests lack of temporal colinearity.  The Myc pathway  “lacks the regulators mad (in D. gyrociliatus) and mnt (in all Dinophilidae), a condition also shared with the appendicularian O. dioica”.  “Open chromatin regions [ATAC-seq peaks] are short and mostly found in promoters.”  “Promoters [CAGE] are narrow (<150 bp) and use pyrimidine-purine dinucleotides as preferred initiators.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 9b27c1df..5899c801 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -14,7 +14,9 @@ The ancestral chordate has 17 chromosomes according to amphioxus assemblies of
 
 The scallop genome has 19 chromosomes, which are syntenic to the 17 ancestral
 chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
-elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].
+elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].  The annelid
+worm _Dimorphilus gyrociliatus_ also has
+([[Martín-Durán and coll., 2020|biblio/10.1101_2020.05.07.078311]]).
 
 The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
 

Endosymbiosis.
diff --git a/biblio/33080189.mdwn b/biblio/33080189.mdwn
index 2fe0e343..742c2210 100644
--- a/biblio/33080189.mdwn
+++ b/biblio/33080189.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Oikopleura."]]
-[[!tag Oikopleura review]]
+[[!tag Oikopleura review endosymbiosis]]
 
 Glover JC.
 
@@ -7,4 +7,4 @@ Curr Biol. 2020 Oct 19;30(20):R1243-R1245. doi:10.1016/j.cub.2020.07.075
 
 Oikopleura.
 
-[[!pmid 33080189 desc="Introduction for non-specialists."]]
+[[!pmid 33080189 desc="Introduction for non-specialists.  Mentions the ideas that the CesA gene could have been transferred from an endosymbion."]]

PETase.
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index 0b513673..e59edbf2 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -1,8 +1,12 @@
 [[!meta title="pages tagged microplastic"]]
 
+# Microplastics
+
 [[Oikopleura]] can ingest microplastics and participate to their sedimentation
 ([[Katija and coll., 2017|biblio/28835922]], [[Choy and coll., 2019|biblio/31171833]]).
 
+# [[PETase|https://en.wikipedia.org/wiki/PETase]]
+
 To read: A bacterium that degrades and assimilates poly(ethylene terephthalate)
 Shosuke Yoshida1,2,*, Kazumi Hiraga1, Toshihiko Takehana3, Ikuo Taniguchi4, Hironao Yamaji1, Yasuhito Maeda5, Kiyotsuna Toyohara5, Kenji Miyamoto2,†, Yoshiharu Kimura4, Kohei Oda1,† Science  11 Mar 2016: Vol. 351, Issue 6278, pp. 1196-1199 DOI: 10.1126/science.aad6359 
 

Café
diff --git a/biblio/33080189.mdwn b/biblio/33080189.mdwn
new file mode 100644
index 00000000..2fe0e343
--- /dev/null
+++ b/biblio/33080189.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oikopleura."]]
+[[!tag Oikopleura review]]
+
+Glover JC.
+
+Curr Biol. 2020 Oct 19;30(20):R1243-R1245. doi:10.1016/j.cub.2020.07.075
+
+Oikopleura.
+
+[[!pmid 33080189 desc="Introduction for non-specialists."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7770a977..ab0d6eb5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -13,6 +13,7 @@ for feeding (and perhaps defending).  The main house proteins are called
 _oikosins_ and half or them are unique to Oikopleura and related animals
 ("_Appendicularia_").  The japanese name of _O. dioica_ is
 [ワカレオタマボヤ](https://www.godac.jamstec.go.jp/bismal/j/view/9018229).
+Review for non-specialists: [[Glover, 2020|biblio/33080189]].
 
 Some links:
 

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
Paper to read.
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index b94dae10..a97370dc 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -3,6 +3,9 @@
 [[Oikopleura]] can ingest microplastics and participate to their sedimentation
 ([[Katija and coll., 2017|biblio/28835922]], [[Choy and coll., 2019|biblio/31171833]]).
 
+To read: A bacterium that degrades and assimilates poly(ethylene terephthalate)
+Shosuke Yoshida1,2,*, Kazumi Hiraga1, Toshihiko Takehana3, Ikuo Taniguchi4, Hironao Yamaji1, Yasuhito Maeda5, Kiyotsuna Toyohara5, Kenji Miyamoto2,†, Yoshiharu Kimura4, Kohei Oda1,† Science  11 Mar 2016: Vol. 351, Issue 6278, pp. 1196-1199 DOI: 10.1126/science.aad6359 
+
 To do: read Furukawa M, Kawakami N, Oda K, Miyamoto K (2018) Acceleration of
 enzymatic degradation of poly(ethylene terephthalate) by surface coating with
 anionic surfactants. Chem Sus Chem 11: 4018–4025

Café hier.
diff --git a/biblio/33087570.mdwn b/biblio/33087570.mdwn
new file mode 100644
index 00000000..fb62d375
--- /dev/null
+++ b/biblio/33087570.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Liquid drop of DNA libraries reveals total genome information."]]
+[[!tag emulsion PCR]]
+
+Terekhov SS, Eliseev IE, Ovchinnikova LA, Kabilov MR, Prjibelski AD, Tupikin AE, Smirnov IV, Belogurov AA Jr, Severinov KV, Lomakin YA, Altman S, Gabibov AG.
+
+Proc Natl Acad Sci U S A. 2020 Oct 21:202017138. doi:10.1073/pnas.2017138117.
+
+Liquid drop of DNA libraries reveals total genome information.
+
+[[!pmid 33087570 desc="“[...] either 3% of Abil EM 180 (A-oil) or a mixture of 4.5% Span 80/0.4% Tween 80/0.05% Triton X-100 (T-oil) was used [...] The homogeneity of the amplified DNA was much better in the case of A-oil, whereas ePCR in T-oil resulted in the formation of high-molecular-weight by-products [...] Thirty-five cycles of ePCR in A-oil were sufficient to reach saturation in the majority of the droplets. T-oil was less stable, displaying droplet coalescence after 25 cycles [...].”  “Appearance of clear amplicon bands on electropherograms does not correlate with the uniformity of amplification during ePCR.”  “ePCR clearly outperformed bulk PCR, reducing the number of reads with gross errors by twofold [and] resulted in a more uniform distribution of amplified sequences”"]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 55eb466a..577847f6 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -21,6 +21,7 @@ Different kinds of surfactants:
  - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])
  - DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]]
  - 3% fluorosurfactant (RAN Biotechnologies) in Novec HFE-7500 / 0.015% Tween 80 for double emulsions in [[Masted and coll., 2018|biblio/10.1101_409086]].
+ - 3% of Abil EM 180 or 4.5% Span 80/0.4% Tween 80/0.05% Triton X-100 were compared for ePCR by [[Terekhov and coll., 2020|biblio/33087570]]. “T-oil was less stable, displaying droplet coalescence after 25 cycles.”  “ePCR clearly outperformed bulk PCR, reducing the number of reads with gross errors by twofold [and] resulted in a more uniform distribution of amplified sequences”
 
 Reactive droplets:
 

PETase et Hi-C
diff --git a/biblio/32968280.mdwn b/biblio/32968280.mdwn
new file mode 100644
index 00000000..a9106713
--- /dev/null
+++ b/biblio/32968280.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conformation of sister chromatids in the replicated human genome."]]
+[[!tag H3K27me3 method tags chromosome structure]]
+
+Mitter M, Gasser C, Takacs Z, Langer CCH, Tang W, Jessberger G, Beales CT, Neuner E, Ameres SL, Peters JM, Goloborodko A, Micura R, Gerlich DW.
+
+Nature. 2020 Oct;586(7827):139-144. doi:10.1038/s41586-020-2744-4
+
+Conformation of sister chromatids in the replicated human genome.
+
+[[!pmid 32968280 desc="Sister-chromatid-sensitive Hi-C (scsHi-C) “4-thio-thymidine (4sT) converted into 5mC by OsO4/NH4Cl”  “A read was assigned to the Watson strand if it contained two or more A-to-G mutations and no T-to-C mutations. Similarly, if a read contained two or more T-to-C mutations, but no A-to-G mutations it was assigned to the Crick strand. Then, contacts were classified as cis sister contacts if (after correcting for the opposite read-strandedness of Illumina sequencing of the two mates) both mates mapped to the same strand. Conversely, contacts were classified as trans sister contacts if the two mates mapped to opposing strands.”“Highly paired TADs were markedly enriched in trimethylation of lysine 27 of histone 3 (H3K27me3).”  “Trans sister contacts were particularly enriched at many TAD boundaries.“  The cohesin loading factor NIPBL was homozygously tagged with auxin-inducible degrons to deplete loop-forming cohesin.  “Loop-forming cohesin is necessary to separate sister chromatids within TADs, resulting in locally enriched sister-chromatid contacts at TAD boundaries.”   Sororin was homozygously tagged with AID to deplete the pool of cohesin that mediates sister-chromatid cohesion.  “The sororin-stabilized pool of cohesin is [...] not required to form intra-chromatid loops or TADs in G2, but it is required to prevent the separation of sister chromatids and to maintain their global alignment during the G2 phase.”"]]
diff --git a/biblio/32989159.mdwn b/biblio/32989159.mdwn
new file mode 100644
index 00000000..0ae5dbff
--- /dev/null
+++ b/biblio/32989159.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Characterization and engineering of a two-enzyme system for plastics depolymerization."]]
+[[!tag microplastic structure]]
+
+Knott BC, Erickson E, Allen MD, Gado JE, Graham R, Kearns FL, Pardo I, Topuzlu E, Anderson JJ, Austin HP, Dominick G, Johnson CW, Rorrer NA, Szostkiewicz CJ, Copié V, Payne CM, Woodcock HL, Donohoe BS, Beckham GT, McGeehan JE.
+
+Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25476-25485. doi:10.1073/pnas.2006753117
+
+Characterization and engineering of a two-enzyme system for plastics depolymerization.
+
+[[!pmid 32989159 desc="“No MHETase activity was detected for [mono(2-hydroxyethyl)-isophthalate (MHEI) and mono(2-hydroxyethyl)-furanoate (MHEF)].”  “Degradation scales with PETase loading and the presence of MHETase, even at low concentrations relative to PETase, improves total degradation.”  “Chimeric proteins covalently linking the C terminus of MHETase to the N terminus of PETase, using flexible glycine-serine linkers of 8, 12, and 20 total glycine and serine residues, were generated.”  “When comparing the extent of degradation achieved by PETase alone, MHETase alone, and an equimolar mix of PETase and MHETase, the chimeric proteins outperform PETase, as well as the mixed reaction containing both PETase and MHETase unlinked in solution.”"]]
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index b94dae10..a788a748 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -12,4 +12,7 @@ Hiraga, Taniguchi, Yoshida, Kimura and Oda K proposed in
 a biological recycling of plastic.  They also underlined that salt-tolerating
 enzymes would be needed for bioremediation of oceans.
 
+[[Knott and coll, 2020|biblio/32989159]] showed that a chimeric MHETase:PETase
+protein is more efficient than the two free enzymes.
+
 [[!inline pages="tagged(microplastic)" limit=0]]

creating tag page tags/PETM
diff --git a/tags/PETM.mdwn b/tags/PETM.mdwn
new file mode 100644
index 00000000..83645ecb
--- /dev/null
+++ b/tags/PETM.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged PETM"]]
+
+[[!inline pages="tagged(PETM)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32877528.mdwn b/biblio/32877528.mdwn
new file mode 100644
index 00000000..76c5b5ea
--- /dev/null
+++ b/biblio/32877528.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Eighteen coral genomes reveal the evolutionary origin of Acropora strategies to accommodate environmental changes."]]
+[[!tag PETM coral genome OIST]]
+
+Shinzato C, Khalturin K, Inoue J, Zayasu Y, Kanda M, Kawamitsu M, Yoshioka Y, Yamashita H, Suzuki G, Satoh N.
+
+Mol Biol Evol. 2020 Sep 2:msaa216 doi:10.1093/molbev/msaa216
+
+Eighteen coral genomes reveal the evolutionary origin of _Acropora_ strategies to accommodate environmental changes.
+
+[[!pmid 32877528 desc="“Our data suggest that the Acropora common ancestor originated and survived in warm environments during the mid–late Cretaceous and the Paleocene–Eocene Thermal Maximum.”  “[cystathionine ß-synthase] was lost in the common ancestor of the Acroporidae.”  “Our analysis shows that DMSP lyase [DiMethlySulfonioProprionate lyase] gene expansions occurred first in the common ancestor of Acropora and again after divergence of the basal clade.”"]]
diff --git a/biblio/32973093.mdwn b/biblio/32973093.mdwn
index 29d3a186..93c35c4e 100644
--- a/biblio/32973093.mdwn
+++ b/biblio/32973093.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle."]]
-[[!tag OIST climate phylogeny]]
+[[!tag OIST PETM climate phylogeny]]
 
 Peijnenburg KTCA, Janssen AW, Wall-Palmer D, Goetze E, Maas AE, Todd JA, Marlétaz F.
 

creating tag page tags/climate
diff --git a/tags/climate.mdwn b/tags/climate.mdwn
new file mode 100644
index 00000000..6852f1bb
--- /dev/null
+++ b/tags/climate.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged climate"]]
+
+[[!inline pages="tagged(climate)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32973093.mdwn b/biblio/32973093.mdwn
new file mode 100644
index 00000000..29d3a186
--- /dev/null
+++ b/biblio/32973093.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle."]]
+[[!tag OIST climate phylogeny]]
+
+Peijnenburg KTCA, Janssen AW, Wall-Palmer D, Goetze E, Maas AE, Todd JA, Marlétaz F.
+
+Proc Natl Acad Sci U S A. 2020 Sep 24:201920918. doi:10.1073/pnas.1920918117
+
+The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle.
+
+[[!pmid 32973093 desc="Pteropods survived the Paleocene–Eocene Thermal Maximum (PETM)."]]

creating tag page tags/bat
diff --git a/tags/bat.mdwn b/tags/bat.mdwn
new file mode 100644
index 00000000..bb0c66f7
--- /dev/null
+++ b/tags/bat.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged bat"]]
+
+[[!inline pages="tagged(bat)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/33029010.mdwn b/biblio/33029010.mdwn
new file mode 100644
index 00000000..2296ef5f
--- /dev/null
+++ b/biblio/33029010.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Relatives of rubella virus in diverse mammals."]]
+[[!tag bat virus]]
+
+Bennett AJ, Paskey AC, Ebinger A, Pfaff F, Priemer G, Höper D, Breithaupt A, Heuser E, Ulrich RG, Kuhn JH, Bishop-Lilly KA, Beer M, Goldberg TL.
+
+Nature. 2020 Oct 7. doi: 10.1038/s41586-020-2812-9
+
+Relatives of rubella virus in diverse mammals.
+
+[[!pmid 33029010 desc="Ruhugu virus and rustrela virus are the closest know relatives of rubella virus and have animal reservoirs (cyclops leaf-nosed bats and yellow-necked field mice respectively)."]]

Oikopleura sequences in GenBank.
diff --git a/biblio/9729883.mdwn b/biblio/9729883.mdwn
new file mode 100644
index 00000000..67e15f13
--- /dev/null
+++ b/biblio/9729883.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolutionary history of free-swimming and sessile lifestyles in urochordates as deduced from 18S rDNA molecular phylogeny."]]
+[[!tag Oikopleura]]
+
+Wada H.
+
+Mol Biol Evol. 1998 Sep;15(9):1189-94. doi:10.1093/oxfordjournals.molbev.a026026
+
+Evolutionary history of free-swimming and sessile lifestyles in urochordates as deduced from 18S rDNA molecular phylogeny.
+
+[[!pmid 9729883 desc="Phylogenetic study that places _Oikopleura_ at the base of the tunicate tree.  Two _Oikopleura_ 18S sequences were recovered from screening an _O. dioica_ genomic DNA library: a major one (7/8 clones, AB013014), labelled as _O. dioica_ and a minor (1/8 clones, AB013015), interpreted as a contamination an unknown species similar to the one of D14366."]]

Primer sequences.
diff --git a/biblio/8127885.mdwn b/biblio/8127885.mdwn
index 909ff968..04e86a1c 100644
--- a/biblio/8127885.mdwn
+++ b/biblio/8127885.mdwn
@@ -7,4 +7,4 @@ Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1801-4 doi:10.1073/pnas.91.5.1801
 
 Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA.
 
-[[!pmid 8127885 desc="Source for the 18S sequence D14360"]]
+[[!pmid 8127885 desc="Source for the 18S sequence D14360 (Oikopleura sp, provenance not described). Primer sequences: 5'-CTGGTTGATCCTGCCAG-3' and 5'-CACCTACGGA(AT)ACCTTG-3'"]]

creating tag page tags/Okinawa
diff --git a/tags/Okinawa.mdwn b/tags/Okinawa.mdwn
new file mode 100644
index 00000000..25e02620
--- /dev/null
+++ b/tags/Okinawa.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Okinawa"]]
+
+[[!inline pages="tagged(Okinawa)" actions="no" archive="yes"
+feedshow=10]]

Jus de tomate.
diff --git a/biblio/31988781.mdwn b/biblio/31988781.mdwn
new file mode 100644
index 00000000..ec2dc76d
--- /dev/null
+++ b/biblio/31988781.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Clinical characteristics of jellyfish stings in Japan."]]
+[[!tag Okinawa]]
+
+Hifumi T, Fukuchi Y, Otani N, Kondo Y, Kitamoto T, Kobayashi K, Nakaya N, Tomioka J.
+
+Acute Med Surg. 2019 Nov 25;7(1):e469. doi:10.1002/ams2.469
+
+Clinical characteristics of jellyfish stings in Japan.
+
+[[!pmid 31988781 desc="Stung tourists faster to go to the hospital."]]

Frère Saint-Jacques...
diff --git a/biblio/28812685.mdwn b/biblio/28812685.mdwn
new file mode 100644
index 00000000..30d06da9
--- /dev/null
+++ b/biblio/28812685.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Scallop genome provides insights into evolution of bilaterian karyotype and development."]]
+[[!tag genome synteny]]
+
+Wang S, Zhang J, Jiao W, Li J, Xun X, Sun Y, Guo X, Huan P, Dong B, Zhang L, Hu X, Sun X, Wang J, Zhao C, Wang Y, Wang D, Huang X, Wang R, Lv J, Li Y, Zhang Z, Liu B, Lu W, Hui Y, Liang J, Zhou Z, Hou R, Li X, Liu Y, Li H, Ning X, Lin Y, Zhao L, Xing Q, Dou J, Li Y, Mao J, Guo H, Dou H, Li T, Mu C, Jiang W, Fu Q, Fu X, Miao Y, Liu J, Yu Q, Li R, Liao H, Li X, Kong Y, Jiang Z, Chourrout D, Li R, Bao Z.
+
+Nat Ecol Evol. 2017 Apr 3;1(5):120. doi:10.1038/s41559-017-0120
+
+Scallop genome provides insights into evolution of bilaterian karyotype and development.
+
+[[!pmid 28812685 desc="“The final [SOAPdenovo] assembly is 988 Mb, with a contig N50 size of 38 kb and a scaffold N50 size of 804 kb.”  “With the aid of a high-density linkage map (7,489 markers) constructed by using the 2b-RAD methodology, 1,419 scaffolds (covering ~81% of the assembly) are assigned to the 19 haploid chromosomes.”  “The scallop genome encodes 26,415 protein-coding genes.”  “Phylogenetic analysis with 482 highly conserved, single-copy genes show that the scallop lineage diverged around ~425 Ma from the lineage leading to Pacific oyster and pearl oyster. Based on the sister taxon relationship between Bivalvia and Gastropoda, our phylogenetic analysis gives an estimation of 504 Ma for the appearance of the bivalve lineage or its divergence from the gastropod lineage.”  “Chromosome-based macrosynteny analysis reveals a near-perfect correspondence between the 19 scallop chromosomes and the 17 presumed bilaterian ancestral linkage groups.”  “ParaHox and Hox clusters are well-preserved and remain intact in the scallop genome.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index eb31c383..9b27c1df 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -12,6 +12,10 @@ breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
 The ancestral chordate has 17 chromosomes according to amphioxus assemblies of
 [[Putnam and coll, 2008|biblio/18563158]] and [[Simakov and coll., 2020|biblio/32313176]].
 
+The scallop genome has 19 chromosomes, which are syntenic to the 17 ancestral
+chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
+elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].
+
 The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
 
 [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints

Café
diff --git a/tags/synthetic.mdwn b/tags/synthetic.mdwn
index d8a82e40..c1548515 100644
--- a/tags/synthetic.mdwn
+++ b/tags/synthetic.mdwn
@@ -2,6 +2,8 @@
 
 _in progress_
 
-Sc3.0 roadmap: [[Dai and coll., 2020|32791980]].
+Sc3.0 roadmap: [[Dai and coll., 2020|biblio/32791980]].
+
+“Biosynthesis of medicinal tropane alkaloids in yeast”: [[Srinivasan and Smolke and coll., 2020|biblio/32879484]]
 
 [[!inline pages="tagged(synthethic)" limit=0]]

Café
diff --git a/biblio/32879484.mdwn b/biblio/32879484.mdwn
new file mode 100644
index 00000000..a49aacb0
--- /dev/null
+++ b/biblio/32879484.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Biosynthesis of medicinal tropane alkaloids in yeast."]]
+[[!tag yeast synthetic]]
+
+Srinivasan P, Smolke CD.
+
+Nature. 2020 Sep;585(7826):614-619. doi:10.1038/s41586-020-2650-9
+
+Biosynthesis of medicinal tropane alkaloids in yeast.
+
+[[!pmid 32879484 desc="“Our final strain comprises 34 chromosomal modifications (26 genes, 8 gene disruptions), resulting in an integrated whole-cell system that expresses enzymes and transporters in diverse sub-cellular locations (cytosol, mitochondria, peroxisome, vacuole, ER and vacuolar membranes)”  Screened a plant RNA-seq to discover one of the enzymes.  Protein sequence needed modifications for proper trans-compartment transport and maturation in the yeast cells."]]

ptidéj
diff --git a/biblio/32938798.mdwn b/biblio/32938798.mdwn
new file mode 100644
index 00000000..bb84454b
--- /dev/null
+++ b/biblio/32938798.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reconstruction of the birth of a male sex chromosome present in Atlantic herring."]]
+[[!tag chromosome sex fish]]
+
+Rafati N, Chen J, Herpin A, Pettersson ME, Han F, Feng C, Wallerman O, Rubin CJ, Péron S, Cocco A, Larsson M, Trötschel C, Poetsch A, Korsching K, Bönigk W, Körschen HG, Berg F, Folkvord A, Kaupp UB, Schartl M, Andersson L.
+
+Proc Natl Acad Sci U S A. 2020 Sep 16:202009925. doi:10.1073/pnas.2009925117
+
+Reconstruction of the birth of a male sex chromosome present in Atlantic herring.
+
+[[!pmid 32938798 desc="A ~500-kbp region on Chr8 is sex-associated, and within it, two ~100 kbp windows are only found in males in a single copy.  Thus the Chr8 is an X/Y pair.  The Y chromosome does not lack genes present on the X chromosome.  It is estimated that it evolved prior the divergence of the Atlantic and Pacific species 2 My ago."]]

Cleanup
diff --git a/biblio/20133776.mdwn b/biblio/20133776.mdwn
index 0d6d6011..f0d7ea72 100644
--- a/biblio/20133776.mdwn
+++ b/biblio/20133776.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Synthetic design of strong promoters."]]
-[[!tag promoter synthethic oligonucleotides method]]
+[[!tag promoter synthetic oligonucleotides method]]
 [[!pmid 20133776 desc="The sequence library was created by printing oligonucleotides with restriction sites on a microarray, and releasing them by cleavage."]]
diff --git a/biblio/22820316.mdwn b/biblio/22820316.mdwn
index 091e390d..95dc1994 100644
--- a/biblio/22820316.mdwn
+++ b/biblio/22820316.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A tissue-engineered jellyfish with biomimetic propulsion."]]
-[[!tag synthethic]]
+[[!tag synthetic]]
 
 Nawroth JC, Lee H, Feinberg AW, Ripplinger CM, McCain ML, Grosberg A, Dabiri JO, Parker KK.
 
diff --git a/biblio/23354052.mdwn b/biblio/23354052.mdwn
index d0ef0589..b5994a93 100644
--- a/biblio/23354052.mdwn
+++ b/biblio/23354052.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Towards practical, high-capacity, low-maintenance information storage in synthesized DNA."]]
-[[!tag synthethic DNA sequencing]]
+[[!tag synthetic DNA sequencing]]
 
 Goldman N, Bertone P, Chen S, Dessimoz C, Leproust EM, Sipos B, Birney E.
 
diff --git a/biblio/25417166.mdwn b/biblio/25417166.mdwn
index cfb8e0f9..055c81ff 100644
--- a/biblio/25417166.mdwn
+++ b/biblio/25417166.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Toehold switches: de-novo-designed regulators of gene expression."]]
-[[!tag not_read synthethic]]
+[[!tag not_read synthetic]]
 
 Cell. 2014 Nov 6;159(4):925-39. doi:10.1016/j.cell.2014.10.002
 
diff --git a/biblio/28280153.mdwn b/biblio/28280153.mdwn
index ab50fef4..ac6a30d3 100644
--- a/biblio/28280153.mdwn
+++ b/biblio/28280153.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome."]]
-[[!tag yeast synthethic chromosome]]
+[[!tag yeast synthetic chromosome]]
 
 Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi:10.1126/science.aaf4791
 
diff --git a/biblio/30069045.mdwn b/biblio/30069045.mdwn
index 0e604bc9..3e46cb5f 100644
--- a/biblio/30069045.mdwn
+++ b/biblio/30069045.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Creating a functional single-chromosome yeast."]]
-[[!tag yeast genome synthethic]]
+[[!tag yeast genome synthetic]]
 
 Nature. 2018 Aug 1. doi:10.1038/s41586-018-0382-x
 
diff --git a/biblio/31719208.mdwn b/biblio/31719208.mdwn
index 00673cc8..d2607ee7 100644
--- a/biblio/31719208.mdwn
+++ b/biblio/31719208.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Definitive demonstration by synthesis of genome annotation completeness."]]
-[[!tag synthethic]]
+[[!tag synthetic]]
 
 Jaschke PR, Dotson GA, Hung KS, Liu D, Endy D.
 
diff --git a/biblio/31932426.mdwn b/biblio/31932426.mdwn
index 21a308d9..de22bd84 100644
--- a/biblio/31932426.mdwn
+++ b/biblio/31932426.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A scalable pipeline for designing reconfigurable organisms."]]
-[[!tag synthethic]]
+[[!tag synthetic]]
 
 Kriegman S, Blackiston D, Levin M, Bongard J
 
diff --git a/biblio/32103016.mdwn b/biblio/32103016.mdwn
index 4aa7f3da..24adcc82 100644
--- a/biblio/32103016.mdwn
+++ b/biblio/32103016.mdwn
@@ -12,6 +12,6 @@ transcription with N(p)nN cap analogs at mM concentrations.  LC-MS analysis of
 sRNAs digested with Nuclease P1 detects N(p)nN caps.  Existence of the internal
 polyphosphate chain demonstrated by the fact that the N(p)nN caps are not
 fragmented by ionization, like GppppG and unlike pppGpG.  m7Gp4Gm and m6Ap3A
-were further identified using synthethic standards.  The RppH and ApaH enzymes
+were further identified using synthetic standards.  The RppH and ApaH enzymes
 cleaved caps, leaving 5′-p or 5′-ppp ends respectively.  Cap methylation
 protects from RppH cleavage but not from ApaH."]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 9a374f6b..eb31c383 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -19,6 +19,9 @@ The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
 are highly significant”
 
+[[Ranz and coll., 2001|biblio/11157786]] estimate an evolution rate of 0.9–1.4
+chromosomal inversions fixed per million years in _Drosophila_.
+
 In insects, the Osiris gene family shows conservation of synteny over ~400
 million years ([[Sah and coll., 2012|biblio/22384409]]).
 
diff --git a/tags/synthethic.mdwn b/tags/synthethic.mdwn
deleted file mode 100644
index d8a82e40..00000000
--- a/tags/synthethic.mdwn
+++ /dev/null
@@ -1,7 +0,0 @@
-[[!meta title="pages tagged synthethic"]]
-
-_in progress_
-
-Sc3.0 roadmap: [[Dai and coll., 2020|32791980]].
-
-[[!inline pages="tagged(synthethic)" limit=0]]
diff --git a/tags/synthetic.mdwn b/tags/synthetic.mdwn
index 0f4fd49c..d8a82e40 100644
--- a/tags/synthetic.mdwn
+++ b/tags/synthetic.mdwn
@@ -1,4 +1,7 @@
-[[!meta title="pages tagged synthetic"]]
+[[!meta title="pages tagged synthethic"]]
 
-[[!inline pages="tagged(synthetic)" actions="no" archive="yes"
-feedshow=10]]
+_in progress_
+
+Sc3.0 roadmap: [[Dai and coll., 2020|32791980]].
+
+[[!inline pages="tagged(synthethic)" limit=0]]

Cleanup
diff --git a/biblio/22384409.mdwn b/biblio/22384409.mdwn
index e93282ee..29d822bd 100644
--- a/biblio/22384409.mdwn
+++ b/biblio/22384409.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Evolution of a large, conserved, and syntenic gene family in insects."]]
-[[!tag syntenty]]
+[[!tag synteny]]
 
 Shah N, Dorer DR, Moriyama EN, Christensen AC.
 
diff --git a/tags/syntenty.mdwn b/tags/syntenty.mdwn
deleted file mode 100644
index 6c1e458c..00000000
--- a/tags/syntenty.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged syntenty"]]
-
-[[!inline pages="tagged(syntenty)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/11157786.mdwn b/biblio/11157786.mdwn
new file mode 100644
index 00000000..ef430d86
--- /dev/null
+++ b/biblio/11157786.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila."]]
+[[!tag Drosophila muller_element synteny chromosome]]
+
+Ranz JM, Casals F, Ruiz A.
+
+Genome Res. 2001 Feb;11(2):230-9. doi:10.1101/gr.162901
+
+How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila.
+
+[[!pmid 11157786 desc="186 DNA probes on Muller element E (density: 1 / 175 kbp in D. mel and 1 
+/ 219 in D. rep) for comparing gene order in _D. repleta_ and _D. melanogaster_.  Random distribution of breakpoints.  “177.07 (±28.88) breakpoints or 89 (±14) paracentric inversions fixed in this chromosomal element between D. melanogaster and D. repleta.”  “Application of [a] ML method [...] yielded an estimate of 228 (±28) fixed breakpoints, that is, 114 ± 14 fixed inversions.”  “We estimate an evolution rate of 0.9–1.4 chromosomal inversions fixed per million years.”  “A significant correlation of gene order was found.” “If large inversions have a low probability of fixation because of their fertility effects (Navarro et al. 1997), which seems to be the case (Cáceres et al. 1997), then the randomization of gene order would proceed at a slower rate than is implied in Figure 2.”"]]

creating tag page tags/syntenty
diff --git a/tags/syntenty.mdwn b/tags/syntenty.mdwn
new file mode 100644
index 00000000..6c1e458c
--- /dev/null
+++ b/tags/syntenty.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged syntenty"]]
+
+[[!inline pages="tagged(syntenty)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/22384409.mdwn b/biblio/22384409.mdwn
new file mode 100644
index 00000000..e93282ee
--- /dev/null
+++ b/biblio/22384409.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution of a large, conserved, and syntenic gene family in insects."]]
+[[!tag syntenty]]
+
+Shah N, Dorer DR, Moriyama EN, Christensen AC.
+
+G3 (Bethesda). 2012 Feb;2(2):313-9. doi:10.1534/g3.111.001412
+
+Evolution of a large, conserved, and syntenic gene family in insects.
+
+[[!pmid 22384409 desc="The Osiris gene family, specific to insects, shows strong conservation of synteny over ~400 million years"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 364c601e..9a374f6b 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -19,4 +19,7 @@ The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
 are highly significant”
 
+In insects, the Osiris gene family shows conservation of synteny over ~400
+million years ([[Sah and coll., 2012|biblio/22384409]]).
+
 [[!inline pages="tagged(synteny)" limit=0]]

Café
diff --git a/biblio/10.1093_plankt_fbn001.mdwn b/biblio/10.1093_plankt_fbn001.mdwn
new file mode 100644
index 00000000..b26046ac
--- /dev/null
+++ b/biblio/10.1093_plankt_fbn001.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Productivity and grazing impact of Oikopleura dioica (Tunicata, Appendicularia) in Tokyo Bay"]]
+[[!tag Oikopleura]]
+
+Riki Sato, Yukiko Ishibashi, Yuji Tanaka, Takashi Ishimaru, Michael J. Dagg.
+
+Journal of Plankton Research, Volume 30, Issue 3, March 2008, Pages 299–309 doi: 10.1093/plankt/fbn001
+
+Productivity and grazing impact of _Oikopleura dioica_ (Tunicata, Appendicularia) in Tokyo Bay
+
+[[!doi 10.1093/plankt/fbn001 desc="Rare in July to September, where surface temperatures are higher than 25 °C.  Homogeneously distributed from 0 to 25 m in the water column from December to March, when temperatures were around 10 °C or below.  Rarity in summer interpreted as the result of predation."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index bf2df3f6..7770a977 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -526,8 +526,10 @@ Ecology
    ([[Lawrence and coll., 2018|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.
 
-### Distribution near Japan
+### Distribution in and near Japan
 
+ - _O. dioica_ was reported to be abundant in Tokyo bay except in summer
+   ([[Sato and coll, 2008|biblio/10.1093_plankt_fbn001]]).
  - _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.

Tagmentation.
diff --git a/biblio/21143862.mdwn b/biblio/21143862.mdwn
new file mode 100644
index 00000000..968690eb
--- /dev/null
+++ b/biblio/21143862.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition."]]
+[[!tag transposase]]
+
+Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, Shendure J.
+
+Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.
+
+Genome Biol. 2010;11(12):R119. doi: 10.1186/gb-2010-11-12-r119
+
+[[!pmid 21143862 desc="Tn5 tagmentation: in vitro transposase-catalyzed adaptor insertion."]]
diff --git a/tags/transposase.mdwn b/tags/transposase.mdwn
index 4e839843..0075de9f 100644
--- a/tags/transposase.mdwn
+++ b/tags/transposase.mdwn
@@ -2,6 +2,9 @@
 
 _work in progress_
 
+ - Tn5 tagmentation (“in vitro transposase-catalyzed adaptor insertion”):
+   [[Adey and coll., 2010|biblio/21143862]].
+
  - Method to produce Tn5 in a laboratory: [[Picelli and coll., 2014|biblio/25079858]].
 
  - Tn5 can tagment RNA/DNA hybrids ([[Di and coll., 2020|biblio/31988135]]),  but it is

transposase
diff --git a/tags/transposase.mdwn b/tags/transposase.mdwn
index 4101ec2a..4e839843 100644
--- a/tags/transposase.mdwn
+++ b/tags/transposase.mdwn
@@ -7,4 +7,6 @@ _work in progress_
  - Tn5 can tagment RNA/DNA hybrids ([[Di and coll., 2020|biblio/31988135]]),  but it is
    not efficient on hyperbranched DNA ([[Gole and coll., 2013|biblio/24213699]]).
 
+ - Tn5 still binds after ligating its payload ([[Amini and coll., 2014|biblio/25326703]]).
+
 [[!inline pages="tagged(transposase)" limit=0]]

updated PO files
diff --git "a/Debian/debi\303\242neries/X61.en.po" "b/Debian/debi\303\242neries/X61.en.po"
new file mode 100644
index 00000000..c8c1078d
--- /dev/null
+++ "b/Debian/debi\303\242neries/X61.en.po"
@@ -0,0 +1,49 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2020-09-21 01:43+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=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Merci, VAIO\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'utilise tous les jours un VAIO Pro 13 mk2 acheté il y a 5 ans avec 3 ans "
+"de guarantie.  Cela faisait quelques mois que j'avais remarqué que quelque "
+"chose enflait lentement à l'intérieur.  Et en juillet, tout s'est accéléré "
+"au point qu'il a doublé d'épaisseur.  Après avoir appelé le service "
+"après-vente de VAIO, quelqu'un est passé le prendre pour faire une "
+"estimation du coût de la réparation.  Et ensuite on nous a annoncé que ça "
+"serait gratuit.  Le voici de retour dans mes mains en moins de deux "
+"semaines.  Bravo VAIO !"
+msgstr ""

transposase
diff --git a/biblio/31988135.mdwn b/biblio/31988135.mdwn
index 962a94a6..4e62598f 100644
--- a/biblio/31988135.mdwn
+++ b/biblio/31988135.mdwn
@@ -7,4 +7,4 @@ Proc Natl Acad Sci U S A. 2020 Jan 27. pii: 201919800. doi:10.1073/pnas.19198001
 
 RNA sequencing by direct tagmentation of RNA/DNA hybrids.
 
-[[!pmid 31988135 desc="Impact on size profile is much harder to notice compared with DNA/DNA tagmentation (Figs S9 and S10)."]]
+[[!pmid 31988135 desc="Sequencing HEteRo RNA-DNA-hYbrid (SHERRY).  Impact on size profile is much harder to notice compared with DNA/DNA tagmentation (Figs S9 and S10)."]]
diff --git a/tags/transposase.mdwn b/tags/transposase.mdwn
index f8db17c5..4101ec2a 100644
--- a/tags/transposase.mdwn
+++ b/tags/transposase.mdwn
@@ -1,4 +1,10 @@
 [[!meta title="pages tagged transposase"]]
 
-[[!inline pages="tagged(transposase)" actions="no" archive="yes"
-feedshow=10]]
+_work in progress_
+
+ - Method to produce Tn5 in a laboratory: [[Picelli and coll., 2014|biblio/25079858]].
+
+ - Tn5 can tagment RNA/DNA hybrids ([[Di and coll., 2020|biblio/31988135]]),  but it is
+   not efficient on hyperbranched DNA ([[Gole and coll., 2013|biblio/24213699]]).
+
+[[!inline pages="tagged(transposase)" limit=0]]

Café hier.
diff --git a/biblio/32669707.mdwn b/biblio/32669707.mdwn
new file mode 100644
index 00000000..c315b18a
--- /dev/null
+++ b/biblio/32669707.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nucleolar RNA polymerase II drives ribosome biogenesis."]]
+[[!tag transcription ribosome nucleolus]]
+
+Abraham KJ, Khosraviani N, Chan JNY, Gorthi A, Samman A, Zhao DY, Wang M, Bokros M, Vidya E, Ostrowski LA, Oshidari R, Pietrobon V, Patel PS, Algouneh A, Singhania R, Liu Y, Yerlici VT, De Carvalho DD, Ohh M, Dickson BC, Hakem R, Greenblatt JF, Lee S, Bishop AJR, Mekhail K.
+
+Nature. 2020 Sep;585(7824):298-302. doi: 10.1038/s41586-020-2497-0
+
+Nucleolar RNA polymerase II drives ribosome biogenesis.
+
+[[!pmid 32669707 desc="Active (S2p) Pol II is enriched at InterGenic Spacer (IGS) regions.  Pol II inhibition with α-amanitin (AMN) or flavopiridol for 30 min was sufficient to disrupt rRNA processing.  IGS noncoding RNAs (ncRNAs) decreased in abundance following Pol I inhibition and increased with Pol II inhibition.  Double inhibition decreased their abundance.  Pol I transcribed sense intergenic ncRNAs (sincRNAs) and Pol II antisense intergenic ncRNAs (asincRNAs)."]]

Café
diff --git a/biblio/32211845.mdwn b/biblio/32211845.mdwn
new file mode 100644
index 00000000..be4874ee
--- /dev/null
+++ b/biblio/32211845.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata."]]
+[[!tag Oikopleura]]
+
+DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. 
+
+Genome Biol Evol. 2020 Jun 1;12(6):948-964. doi:10.1093/gbe/evaa060
+
+Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata.
+
+[[!pmid 32211845 desc="210 single-copy orthogroups from 37 tunicates + 10 outgroups.  Questions the annotation (gene name) of the Hox genes in Oikopleura."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 66ac8c68..bf2df3f6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -40,8 +40,10 @@ Phylogeny
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
  - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]]),
    on 798 genes in 28 species ([[Kocot and coll., 2018|biblio/29330139]]),
-   and 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
-   show that Oikopleuridae is sister to all other tunicates.
+   258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]]),
+   and 210 single-copy orthogroups from 37 tunicates + 10 outgroups
+   [[DeBiasse and coll., 2020|biblio/32211845]] show that appendicularians are
+   sister to all other tunicates.
  - “The difference between coding sequences was considerably higher in
    comparisons between strains of different oceans than within the Bergen gene
    pool.  We ignore whether and how Oikopleura dioica is subdivided into multiple

Café
diff --git a/biblio/29330139.mdwn b/biblio/29330139.mdwn
new file mode 100644
index 00000000..79ea63b7
--- /dev/null
+++ b/biblio/29330139.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Phylogenomics offers resolution of major tunicate relationships."]]
+[[!tag Oikopleura tunicate evolution]]
+
+Kocot KM, Tassia MG, Halanych KM, Swalla BJ.
+
+Mol Phylogenet Evol. 2018 Apr;121:166-173. doi:10.1016/j.ympev.2018.01.005
+
+Phylogenomics offers resolution of major tunicate relationships.
+
+[[!pmid 29330139 desc="A matrix of 798 genes totaling 254,865 amino acid positions places appendicularians as the sister group to all other tunicates."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ce6665c1..66ac8c68 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -38,8 +38,9 @@ Phylogeny
    clade is sister of Stolidobranchia (that is, not basal in Tunicates).
    Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
- - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]])
-   and then 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
+ - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]]),
+   on 798 genes in 28 species ([[Kocot and coll., 2018|biblio/29330139]]),
+   and 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
    show that Oikopleuridae is sister to all other tunicates.
  - “The difference between coding sequences was considerably higher in
    comparisons between strains of different oceans than within the Bergen gene

Shasta
diff --git a/biblio/32686750.mdwn b/biblio/32686750.mdwn
new file mode 100644
index 00000000..5b53d3c0
--- /dev/null
+++ b/biblio/32686750.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes."]]
+[[!tag assembly method software]]
+
+Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B.
+
+Nat Biotechnol. 2020 Sep;38(9):1044-1053. doi:10.1038/s41587-020-0503-6
+
+Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
+
+[[!pmid 32686750 desc="Runs in memory (no disk IO) and requires terabyte amounts for human genome.  Designed for Nanopore data.  Reads are run length encoded before assembling.  Assemblies are more fragmented, but with less disagreements to the reference.  The estimated cost of running is lower than for competitors."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 259f50eb..6ff69435 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -15,6 +15,14 @@ contings and increase their accuracy.  (The predecessor of Flye, ABruijn, was
 reported by [[Istace and coll. (2017)|biblio/28369459]] to be able to assemble
 mitochondrial genomes, unlike Canu and other assemblers.)
 
+The Shasta assembler [[Shafin and coll., 2020|biblio/32686750]] is designed for
+Nanopore data. Reads are run length encoded before assembly, to mitigate the
+impact of errors in homopolymer tracts.  The assembly runs entirely in memory;
+it needs terabyte amounts for a human genome, but as a consequence it runs
+fast. Shasta assemblies tend to be more fragmented, but have less disagreement
+with the reference.  Shasta also comes with polishing modules similar to Racon
+and Medaka, but also  to be faster. 
+
 After assembly, the contigs can be further polished with Racon ([[Vaser, Sović,
 Nagarajan and Šikić, 2017|biblio/28100585]]).
 

Ptitdéj
diff --git a/biblio/32500941.mdwn b/biblio/32500941.mdwn
new file mode 100644
index 00000000..c27da783
--- /dev/null
+++ b/biblio/32500941.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Highly active rubiscos discovered by systematic interrogation of natural sequence diversity."]]
+[[!tag screen]]
+
+Davidi D, Shamshoum M, Guo Z, Bar-On YM, Prywes N, Oz A, Jablonska J, Flamholz A, Wernick DG, Antonovsky N, de Pins B, Shachar L, Hochhauser D, Peleg Y, Albeck S, Sharon I, Mueller-Cajar O, Milo R.
+
+EMBO J. 2020 Jun 5:e104081. doi:10.15252/embj.2019104081
+
+Highly active rubiscos discovered by systematic interrogation of natural sequence diversity.
+
+[[!pmid 32500941 desc="A faster enzyme was found, but its specificity to CO2 is lower."]]

creating tag page tags/COVID-19
diff --git a/tags/COVID-19.mdwn b/tags/COVID-19.mdwn
new file mode 100644
index 00000000..87e460c2
--- /dev/null
+++ b/tags/COVID-19.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged COVID-19"]]
+
+[[!inline pages="tagged(COVID-19)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/SARS-CoV-2
diff --git a/tags/SARS-CoV-2.mdwn b/tags/SARS-CoV-2.mdwn
new file mode 100644
index 00000000..f3dce043
--- /dev/null
+++ b/tags/SARS-CoV-2.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged SARS-CoV-2"]]
+
+[[!inline pages="tagged(SARS-CoV-2)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32868442.mdwn b/biblio/32868442.mdwn
new file mode 100644
index 00000000..6ddf9c9a
--- /dev/null
+++ b/biblio/32868442.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid isothermal amplification and portable detection system for SARS-CoV-2."]]
+[[!tag SARS-CoV-2 COVID-19 microfluidic isothermal]]
+
+Ganguli A, Mostafa A, Berger J, Aydin MY, Sun F, Ramirez SAS, Valera E, Cunningham BT, King WP, Bashir R.
+
+Proc Natl Acad Sci U S A. 2020 Aug 31:202014739. doi:10.1073/pnas.2014739117
+
+Rapid isothermal amplification and portable detection system for SARS-CoV-2.
+
+[[!pmid 32868442 desc="RT-LAMP assay on gene N.  Amplification in a microfluidic device.  LEDs (λpeak = 485 nm, XPEBBL, Cree) used to excite the EvaGreen fluorescent dye.  Signal read on a smartphone camera after going through a custom long-pass filter.]]

Café
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 1cda6a7d..6dc18731 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -1,4 +1,9 @@
 [[!meta title="pages tagged automation"]]
 
-[[!inline pages="tagged(automation)" actions="no" archive="yes"
-feedshow=10]]
+“Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery” ([[Kitano 2016|biblio/AI_37_2642]]).
+
+“A mobile robotic chemist” ([[Burger and coll., 2020|biblio/32641813]]).
+
+The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
+
+[[!inline pages="tagged(automation)" limit=0]]

Café
diff --git a/biblio/32904024.mdwn b/biblio/32904024.mdwn
new file mode 100644
index 00000000..981c1018
--- /dev/null
+++ b/biblio/32904024.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Changing Infrastructural Practices: Routine and Reproducibility in Automated Interdisciplinary Bioscience."]]
+[[!tag automation]]
+
+Meckin R.
+
+Sci Technol Human Values. 2020 Nov;45(6):1220-1241. doi:10.1177/0162243919893757
+
+Changing Infrastructural Practices: Routine and Reproducibility in Automated Interdisciplinary Bioscience.
+
+[[!pmid 32904024 desc="Synthetic biologists studied by a sociologist."]]

Café
diff --git a/biblio/32817535.mdwn b/biblio/32817535.mdwn
new file mode 100644
index 00000000..2aef39ef
--- /dev/null
+++ b/biblio/32817535.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Vianna JA, Fernandes FAN, Frugone MJ, Figueiró HV, Pertierra LR, Noll D, Bi K, Wang-Claypool CY, Lowther A, Parker P, Le Bohec C, Bonadonna F, Wienecke B, Pistorius P, Steinfurth A, Burridge CP, Dantas GPM, Poulin E, Simison WB, Henderson J, Eizirik E, Nery MF, Bowie RCK."]]
+[[!tag genome]]
+
+Vianna JA, Fernandes FAN, Frugone MJ, Figueiró HV, Pertierra LR, Noll D, Bi K, Wang-Claypool CY, Lowther A, Parker P, Le Bohec C, Bonadonna F, Wienecke B, Pistorius P, Steinfurth A, Burridge CP, Dantas GPM, Poulin E, Simison WB, Henderson J, Eizirik E, Nery MF, Bowie RCK.
+
+Genome-wide analyses reveal drivers of penguin diversification.
+
+Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22303-22310. doi:10.1073/pnas.2006659117
+
+[[!pmid 32817535 desc="Assemblies guided by the reference empreor penguin genome."]]

Add tag.
diff --git a/biblio/17333540.mdwn b/biblio/17333540.mdwn
index 56ea8e2e..24076ba1 100644
--- a/biblio/17333540.mdwn
+++ b/biblio/17333540.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica."]]
-[[!tag Oikopleura histone telomere H3S28p]]
+[[!tag Oikopleura histone telomere H3S28p H3S31p]]
 
 Chromosome Res. 2007;15(2):189-201. doi:10.1007/s10577-006-1112-z
 

Café
diff --git a/biblio/12453460.mdwn b/biblio/12453460.mdwn
new file mode 100644
index 00000000..a646de14
--- /dev/null
+++ b/biblio/12453460.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Patterning through differential endoreduplication in epithelial organogenesis of the chordate, Oikopleura dioica."]]
+[[!tag Oikopleura cell_cycle]]
+
+Ganot P, Thompson EM.
+
+Patterning through differential endoreduplication in epithelial organogenesis of the chordate, _Oikopleura dioica_.
+
+Dev Biol. 2002 Dec 1;252(1):59-71. doi:10.1006/dbio.2002.0834
+
+[[!pmid 12453460 desc="In the epithelial cells, “endoreduplication begins before tailshift and stops during gamete differentiation.”  “Endocycles are asynchronous within a given field of oikoplastic cells, but the replication pattern is bilaterally symmetrical.”  “In mature animals, final ploidy levels ranged from a low of 34 C in chain of pearl nuclei to 1300 C in giant Eisen nuclei.”  Cells with higher ploidy had shorter gap phases."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f3ed4dc6..ce6665c1 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -392,6 +392,10 @@ Development
    ([[Bassham and Postlethwait (2000)|biblio/10753519]]).
  - Expression of development genes is retarded by polyunsaturated aldehydes produced
    by diatoms ([[Torres-Águila and coll., 2018|biblio/30272001]]).
+ - Epithelial cells divide by mitosis during embryogenesis.  Once the final number
+   of cells is produce, they grow by endomitosis, with final ploidy ranging between
+   ~30 to ~1300 C. Cells with higher ploidy have shorter gap phases.  Endomitoses
+   stop when gamete differentiation starts.  [[Ganot and Thompson, 2002|biblio/12453460]]
  - Endocycling cells show no polytenisation nor _in loco_ amplifications.  Deep invaginations
    of the nuclear envelopper are shown by simultaneous staining of DNA, RNA and membranes
    ([[Spada and coll., 2007|biblio/17288541]]).

Published.
diff --git a/biblio/10.1101_831495.mdwn b/biblio/32788667.mdwn
similarity index 50%
rename from biblio/10.1101_831495.mdwn
rename to biblio/32788667.mdwn
index b21a6829..7bd4e28c 100644
--- a/biblio/10.1101_831495.mdwn
+++ b/biblio/32788667.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="High throughput, error corrected Nanopore single cell transcriptome sequencing"]]
-[[!tag bioRxiv Nanopore single_cell]]
+[[!tag Nanopore single_cell]]
 
 Kevin Lebrigand, Virginie Magnone, Pascal Barbry and Rainer Waldmann
 
-Posted November 05, 2019
+Nat Commun. 2020 Aug 12;11(1):4025. doi:10.1038/s41467-020-17800-6.
 
 High throughput, error corrected Nanopore single cell transcriptome sequencing
 
-[[!doi 10.1101/831495 desc="Sequences libraries with Illumina first, to find UMI and cell barcode sequences, and then sequences again with Nanopore."]]
+[[!pmid 32788667 desc="Sequences libraries with Illumina first, to find UMI and cell barcode sequences, and then sequences again with Nanopore."]]

Café
diff --git a/biblio/10.1101_2020.03.10.985549.mdwn b/biblio/10.1101_2020.03.10.985549.mdwn
new file mode 100644
index 00000000..791bf8ac
--- /dev/null
+++ b/biblio/10.1101_2020.03.10.985549.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants"]]
+[[!tag bioRxiv genome]]
+
+Jing Xia, Aarthi Venkat, Karine Le Roch, Ferhat Ay and Jon P. Boyle
+
+bioRxiv 2020.03.10.985549; doi:https://doi.org/10.1101/2020.03.10.985549
+
+Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.
+
+[[!doi 10.1101/2020.03.10.985549 desc="Long-read sequencing leads to revision of the karyotype."]]

Centromeres.
diff --git a/biblio/23832878.mdwn b/biblio/23832878.mdwn
new file mode 100644
index 00000000..e7c17334
--- /dev/null
+++ b/biblio/23832878.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Quantitative analysis of centromeric FISH spots during the cell cycle by image cytometry."]]
+[[!tag cell_cycle centromere microscopy]]
+
+Amakawa G, Ikemoto K, Ito H, Furuya T, Sasaki K.
+
+J Histochem Cytochem. 2013 Oct;61(10):699-705. doi:10.1369/0022155413498754
+
+Quantitative analysis of centromeric FISH spots during the cell cycle by image cytometry.
+
+[[!pmid 23832878 desc="Fluorescence in situ hybridization (FISH) using chromosome enumeration DNA probes (CEPs) labeling centromeric regions.  The intensity of the staining increases as the cell progresses in the cell cycle.  On the published pictures, it is rare to be able to resolve the centromeric regions of the sister chromatids."]]
diff --git a/tags/centromere.mdwn b/tags/centromere.mdwn
index 40284a22..6a3d6ca9 100644
--- a/tags/centromere.mdwn
+++ b/tags/centromere.mdwn
@@ -2,17 +2,27 @@
 
 _Work in progress_
 
+## Sequence
+
  - Brute-force analysis to find the most abundant large tandem repeat can find
    centromeres ([[Melters and coll., 2013|biblio/23363705]]).
- - In medaka, study of homologous pairs of centromeres suggest that the
-   acrocentric ones evolve slower ([[Ichikawa and coll., 2017|biblio/29184138]]).
+ - In the three-spine stickleback, the centromere sequence of chrX differs from
+   the one of chrY ([[Peichel and coll., 2020|biblio/32684159]]).
+
+## Visualisation
+
  - In Oikopleura (and many others) H3S28p marks mitotic centromeres [[Fent and
    coll., 2019|biblio/31306061]].
+ - Centromeric regions of sister chromatids are rarely resolved in FISH.  Instead,
+   the intensity of the spot increases ([[Amakawa and coll., 2013|biblio/23832878]]).
+
+## Evolution
+
+ - In medaka, study of homologous pairs of centromeres suggest that the
+   acrocentric ones evolve slower ([[Ichikawa and coll., 2017|biblio/29184138]]).
  - Centromere breakage and inactivation in yeast: [[Sankaranarayanan and coll.,
    2020|biblio/31958060]].
  - Centromere relocation to a transcribed region in yeast, detected by ChIP of
    centromeric H3 [[Ola and coll., 2020|biblio/32424070]].
- - In the three-spine stickleback, the centromere sequence of chrX differs from
-   the one of chrY ([[Peichel and coll., 2020|biblio/32684159]]).
 
 [[!inline pages="tagged(centromere)" limit="0"]]

Café
diff --git a/biblio/32313176.mdwn b/biblio/32313176.mdwn
new file mode 100644
index 00000000..614e184a
--- /dev/null
+++ b/biblio/32313176.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Deeply conserved synteny resolves early events in vertebrate evolution."]]
+[[!tag evolution synteny chromosome]]
+
+Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS.
+
+Nat Ecol Evol. 2020 Jun;4(6):820-830. doi:10.1038/s41559-020-1156-z
+
+Deeply conserved synteny resolves early events in vertebrate evolution.
+
+[[!pmid 32313176 desc="Most of the 19 amphioxus (lancelet) chromosomes directly correspond to one of the 17 ancestral chordate linkage groups.  Pattern of paralogue elimination show that autotetraploidy was followed by allotetraploidy in bony vertebrates."]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 9bd08b3a..364c601e 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -9,7 +9,8 @@ were enriched near CTCF-binding events.
 distribution follows a power law and explain it with a model that requires
 breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
 
-The ancestral chordate has 17 chromosomes according to [[Putnam and coll, 2008|biblio/18563158]].
+The ancestral chordate has 17 chromosomes according to amphioxus assemblies of
+[[Putnam and coll, 2008|biblio/18563158]] and [[Simakov and coll., 2020|biblio/32313176]].
 
 The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
 

Café
diff --git a/biblio/32845085.mdwn b/biblio/32845085.mdwn
new file mode 100644
index 00000000..1449e819
--- /dev/null
+++ b/biblio/32845085.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="SBML Level 3: an extensible format for the exchange and reuse of biological models."]]
+[[!tag software systems_biology]]
+
+Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members.
+
+Mol Syst Biol. 2020 Aug;16(8):e9110. doi:10.15252/msb.20199110
+
+SBML Level 3: an extensible format for the exchange and reuse of biological models.
+
+[[!pmid  32845085 desc="Modularisation of SBML."]]

Café
diff --git a/biblio/25940625.mdwn b/biblio/25940625.mdwn
new file mode 100644
index 00000000..4e6edbf0
--- /dev/null
+++ b/biblio/25940625.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Accurate identification of centromere locations in yeast genomes using Hi-C."]]
+[[!tag assembly software]]
+
+Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS.
+
+Nucleic Acids Res. 2015 Jun 23;43(11):5331-9. doi:10.1093/nar/gkv424.
+
+Accurate identification of centromere locations in yeast genomes using Hi-C.
+
+[[!pmid 25940625 desc="Tested on yeast and Plasmodium falciparium.  First, detects regions enriched in Hi-C contacts.  Then, prioritises local maxima enriched in trans-contacts."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index b999bbb0..259f50eb 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -51,6 +51,9 @@ that most contact points are due to local (same-chromosome) proximity.  Version
 2 of SALSA uses unitigs and the assembly graph as input ([[Ghurye and coll.,
 2019|biblio/31433799]]).
 
+The Hi-C data can also be used to call the location of centromeres ([[Varoquaux
+and coll., 2015|biblio/25940625]], Marie-Nelly and coll., 2014(not read)).
+
 Assemblies can be aligned with [[last-dotplot|LAST]] or, for SVG export and
 interactive browsing with D-GENIES ([[Cabanettes and Klopp
 2018|biblio/29888139]]).

creating tag page tags/synthetic
diff --git a/tags/synthetic.mdwn b/tags/synthetic.mdwn
new file mode 100644
index 00000000..0f4fd49c
--- /dev/null
+++ b/tags/synthetic.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged synthetic"]]
+
+[[!inline pages="tagged(synthetic)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32791980.mdwn b/biblio/32791980.mdwn
new file mode 100644
index 00000000..c1f0bb10
--- /dev/null
+++ b/biblio/32791980.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Sc3.0: revamping and minimizing the yeast genome"]]
+[[!tag yeast synthetic]]
+
+Dai J, Boeke JD, Luo Z, Jiang S, Cai Y.
+
+Genome Biol. 2020 Aug 13;21(1):205. doi:10.1186/s13059-020-02130-z
+
+Sc3.0: revamping and minimizing the yeast genome
+
+[[!pmid 32791980 desc="Proposes to build a core “essential gene array (eArray)” as a centromeric chromosome that can be linearised to serve as a base to build more complex genomes."]]
diff --git a/tags/synthethic.mdwn b/tags/synthethic.mdwn
index 9ec53efc..d8a82e40 100644
--- a/tags/synthethic.mdwn
+++ b/tags/synthethic.mdwn
@@ -1,4 +1,7 @@
 [[!meta title="pages tagged synthethic"]]
 
-[[!inline pages="tagged(synthethic)" actions="no" archive="yes"
-feedshow=10]]
+_in progress_
+
+Sc3.0 roadmap: [[Dai and coll., 2020|32791980]].
+
+[[!inline pages="tagged(synthethic)" limit=0]]

Café
diff --git a/biblio/1465136.mdwn b/biblio/1465136.mdwn
new file mode 100644
index 00000000..1039f0b1
--- /dev/null
+++ b/biblio/1465136.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells."]]
+[[!tag trans-splicing]]
+
+Bruzik JP, Maniatis T.
+
+Nature. 1992 Dec 17;360(6405):692-5. doi:10.1038/360692a0
+
+Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells.
+
+[[!pmid 1465136 desc="Trans-splicing in vivo in COS cells and in vitro in HeLa cell extracts, using splice leaders and actin genes from C. elegans and Leptomonas colosoma, and also using an adenoviral RNA as acceptor."]]
diff --git a/tags/trans-splicing.mdwn b/tags/trans-splicing.mdwn
index 7ded5bdd..0a750e29 100644
--- a/tags/trans-splicing.mdwn
+++ b/tags/trans-splicing.mdwn
@@ -1,5 +1,8 @@
 [[!meta title="pages tagged trans-splicing"]]
 
+Trans-spplicing of a splice leader from a nematode and a trypanosome was shown
+to be possible in COS cells and HeLa cell extracts by [[Bruzik and Maniatis, 1992|biblio/1465136]].
+
 Trans-splicing was discovered in tunicates by [[Vandenberghe, Meedel and Hastings, 2001|biblio/11159910]].
 
 The splice leader is 16-nt in C. intestinalis ([[Satou et al, 2006|biblio/16822859]]) and 40-nt in O. dioica ([[Ganot et al., 2004|biblio/15314184]]).

Café
diff --git a/biblio/32763167.mdwn b/biblio/32763167.mdwn
new file mode 100644
index 00000000..8ae9cd71
--- /dev/null
+++ b/biblio/32763167.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes."]]
+[[!tag genome evolution mutation]]
+
+Bourguignon T, Kinjo Y, Villa-Martín P, Coleman NV, Tang Q, Arab DA, Wang Z, Tokuda G, Hongoh Y, Ohkuma M, Ho SYW, Pigolotti S, Lo N.
+
+Curr Biol. 2020 Jul 29:S0960-9822(20)31026-5. doi:10.1016/j.cub.2020.07.034
+
+Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes.
+
+[[!pmid 32763167 desc="”gene-loss rate strongly correlated with synonymous substitution rate”"]]