Some bibliography

2Ome 3′ UTR 3′ end 454 5′ UTR 5mC 7SK 8-oxo-G 96-wells AI Alu BCR Bioconductor Biotechnology Brenner C33a CAGE CDR3 COVID-19 CRISPR CaSki ChIP Ciona CpG Crick DGT DNA DNAi DNAse I DNase-hypersensitivity DTT Dictyostelium Drosophila EBV ENCODE ES EcoP15I EpiSC Fluidigm FoxP3 Fritillaria Fucci H2AX H3K27ac H3K27me3 H3K36me3 H3K4me1 H3K4me2 H3K4me3 H3K4me4 H3K9ac H3K9me2 H3K9me3 H3S10p H3S28p H3S31p H3T3p H42K20me2 H4K16Ac H4K20me2 H4K8Ac HDAC HIV HPV HeLa Helicos HepG2 LAST LNA LPA LTR MHC MRI OIST OSC Oikopleura Okinawa Olf-1 Oxford plot PCR PEG PETM PKR PLA PRDM9 Parkinson’s disease QTL RACE RNA RNA-inheritance RNA-protein RNA-seq RNA polymerase RNAse R RNP granules RT-PCR RdRP SAGE SARS-CoV-2 SNP SRA STRT Sanger SiHa TATA-box TCR TFBS Taq Trizol UTR adenylylation adipocyte agarose ageing alignment allelic expression amplification analysis annotation antibody antisense application aptamer arabidopsis archaea artefact assembly auto immunity automation bHLH bacteria barcode bat beads benchmark betaine bias bidirectional bioRxiv biochemistry biotin bistable blood brain buffer cDNA calcium cancer cap capture catecholaminergic cell-cell interaction cell conversion cell culture cell cycle cell type cellulose centromere cephalopod cerebellum chicken chimeric transcript chimpanzee chromatin chromosome chromothripsis circuit circular RNA click climate clock cloning clustering comparison compartment complex-loci copy number coral cytometry cytoplasm damage database degradation demethylase dendrite detection development diagnostic differentiation dog dosage droplet drug drug delivery dsRNA eDNA eQTL editing education electrophoresis elongation embryo embryoid body emulsion endosymbiosis enhancer environment enzyme epicentre epigenetic evolution exon painting exonuclease exosome experiment design expression factory fingerprint fish fixation floor-plate flow cytometry fluorescence format fractionation frog function fusion transcript genetics genome germ line global warming graft granule growth guanylation hair hairpin haplotype heart heavy chain hemichordate heterodimer heterogeneity high-throughput histone historical human hybridisation iPS imaging immune-system immunity immunoglobulin imprinting in situ in vivo infection information inhibition inosine integration intellectual-property intron isoform isothermal journal club karyotype knock-out labelling lamin lariat laser-capture library ligase lineage lipid live liver localisation locus boundary loop lymphocyte lysis m6A mC mRNA machine learning manganese mangrove mass spectroscopy maternal mechanical force mechanism medaka meiosis metabolism metabolome methanol method methylation miRNA microarray microfluidic microplastic microscopy missing-method mitochondrion model modification modified base monkey mosquito motif mouse muller element multiplex muscle mutation mycoplasma nanoCAGE nanopore natural selection nematode network neurogenin neuron nick noise nomenclature non-coding non-polyadenylated non coding normalisation not read nuclear body nucleolus nucleosome nucleotides nucleus occupancy ocean acidification ocular-dominance olfaction oligo-capping oligonucleotides open data open science organoid outreach pH paired-end parasite parvalbumin patent peak peroxydase pharmacology pheromones phosphatase phosphorylation phylogeny physiology piRNA pig plankton plant plasticity policy polony poly-A polymerase polyploid polysome population population transcriptomics post translational modification power law primase prion privacy product profile program prokaryote promoter promotome protein proteome proteomics publishing purification purkinje pyrophosphatase qPCR radioisotope random priming rat recombination recycle regulation repair repeat repertoire replication repression reprogramming reticulocyte reverse transcription review ribosome ribozyme richness robot sRNA scale-free screen selection selex sequence tags sequencing sex siRNA silencing single cell single chain single gene single molecule single strand size small RNA small samples snoRNA software somatic mutation sorting speciation spike splicing ssbp statistics stem cell storage structure subgenome superfamily supergene synapse synteny synthetic systems biology tRNA tag taxonomy telomere temperature template switching termination theory therapy thermo-enhancement thymus to read trans-splicing transcript transcript count transcription transcription factor transcriptome translation translatome transolcation transport transposase transposon trehalose triple helix tunicate turnover ultraconserved ultrasound unicellular unnatural base vaccine vanadium variants virus visual cortex yeast zebrafish α chain αβ chains β chain γH2AX μORF

An improved cultivation device for appendicularians with notes on the biology of Fritillaria sp. collected in Sagami Bay, Japan.

Sato Riki

Journal of the Marine Biological Association of the United Kingdom. 2023;103:e68. doi:10.1017/S0025315423000541

Uses rotating cylinders to circulate water in buckets. The cultivated Fritillaria sp. do not survive the use of rotating paddles. Its house covered the body entirely.

Li S, Liang Y, Zhang G.

J Hazard Mater. 2024 Aug 16;479:135552. doi:10.1016/j.jhazmat.2024.135552.

Growth and reproductive toxicity of bisphenol A in Oikopleura dioica at environmentally relevant concentrations.

“Evaluation of the toxicity of environmentally relevant levels of BPA [(bisphenol a)] (2.5–150 μg/L) on the appendicularian Oikopleura dioica” LC50 of 142 μg/L. “125 μg/L BPA significantly inhibited the somatic growth, gonadal development and reproduction” ”exposure to an environmentally safe concentration (2.5 μg/L) affected female fecundity and fitness” “BPA exposure […] led to abnormal secretion of digestive enzymes and phospholipase A2”

Nat Ecol Evol. 2024 Aug;8(8):1505-1521. doi:10.1038/s41559-024-02456-y

Elise Parey, Olga Ortega-Martinez, Jérôme Delroisse, Laura Piovani, Anna Czarkwiani, David Dylus, Srishti Arya, Samuel Dupont, Michael Thorndyke, Tomas Larsson, Kerstin Johannesson, Katherine M. Buckley, Pedro Martinez, Paola Oliveri, Ferdinand Marlétaz

The brittle star genome illuminates the genetic basis of animal appendage regeneration

“We showed that the ‘Eleutherozoa Linkage Groups’ descend from a single fusion of ancestral bilaterian linkages (B2+C2).” “Interestingly, sea cucumbers have the lowest rate of inter-chromosomal rearrangements, yet the most derived echinoderm body plan (Rahman et al. 2019), which highlights the uncoupling of global genomic rearrangements from morphological evolution.” “In contrast with its sea star sister-group, the A. filiformis genome is highly rearranged: our analyses identified 26 inter-chromosomal rearrangements since the Eleutherozoa ancestor.”

David Lagman, Anthony Leon, Nadia Cieminska, Wei Deng, Marios Chatzigeorgiou, Simon Henriet, Daniel Chourrout

Dev Biol. 2024 Aug 22:S0012-1606(24)00217-3. doi:10.1016/j.ydbio.2024.08.012.

Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory

Knock-out of Pax37B and Pax37A using CRISPR-Cas9. Pax37B is essential to the proper patterning of the oikoblastic epithelium but not Pax37A. Based on the analysis of single-cell and transcriptomic data in Oikopleura and Ciona, the authors propose a parallel between oikoblastic cells in Oikopleura and the neuroepithelial cells that produce gluing collocytes in Ciona.

Tracing Homopolymers in Oikopleura dioica's mitogenome.

Dierckxsens N, Watanabe K, Tan Y, Masunaga A, Mansfield MJ, Miao J, Luscombe NM, Plessy C.

Genome Biol Evol. 2024 Aug 20:evae182. doi: 10.1093/gbe/evae182

Our PacBio I25 assembly

Klirs Y, Novosolov M, Gissi C, Garic R, Pupko T, Stach T, Huchon D.

Genome Biol Evol. 2024 Aug 20:evae181. doi:10.1093/gbe/evae181

Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.

“the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal“ Cs are occasionally found in edited poly-T regions.