Ascidians

@article{orton1913the11,
    author = "Orton, J. H",
    title = "The ciliary mechanisms on the gill and the mode of feeding in Amphioxus, Ascidians and Solenomyo togato",
    year = "1913",
    journal = "Journal of the Marine Biological Association of the United Kingdom, v. 10, p. 19-49",
    note = "talkorigins\_source = {true}; raw\_reference = {Orton, J. H., 1913, The ciliary mechanisms on the gill and the mode of feeding in Amphioxus, Ascidians and Solenomyo togato: Journal of the Marine Biological Association of the United Kingdom, v. 10, p. 19-49.}"
}

@article{berrill1947metamorphosis,
    author = "Berrill, N. J.",
    title = "Metamorphosis in ascidians",
    year = "1947",
    journal = "Journal of Morphology",
    url = "https://doi.org/10.1002/jmor.1050810207",
    doi = "10.1002/jmor.1050810207",
    number = "2",
    pages = "249-267",
    volume = "81"
}

@misc{florey1951reizphysiologie6,
    author = "Florey, E",
    title = "Reizphysiologie Untersuchungen an der Ascidie Ciona intestinatis",
    year = "1951",
    howpublished = "Biologisches Zentralblatt, v. 70, p. 523-530",
    note = "talkorigins\_source = {true}; raw\_reference = {Florey, E., 1951, Reizphysiologie Untersuchungen an der Ascidie Ciona intestinatis: Biologisches Zentralblatt, v. 70, p. 523-530.}"
}

@misc{millar1953ciona10,
    author = "Millar, R. H",
    title = "Ciona",
    year = "1953",
    howpublished = "Liverpool Marine Biological Committee Memoirs on Typical British Marine Plants and Animals, v. 35; 122 pp",
    note = "talkorigins\_source = {true}; raw\_reference = {Millar, R. H., 1953, Ciona: Liverpool Marine Biological Committee Memoirs on Typical British Marine Plants and Animals, v. 35; 122 pp.}"
}

@incollection{abbott1957ascidians,
    author = "Abbott, D. P.",
    title = "Ascidians",
    year = "1957",
    booktitle = "Geological Society of America Memoirs",
    url = "https://doi.org/10.1130/mem67v1-p1197",
    doi = "10.1130/mem67v1-p1197",
    pages = "1197-1200"
}

@misc{dodd1966an3,
    author = "Dodd, J. M. and Dodd, M. H. I",
    title = "An Experimental Investigation of the Supposed Pituitary Affinities of the Ascidian Neural Complex, in Barnes, H., ed., Some Contemporary Studies in Marine Science",
    year = "1966",
    howpublished = "London, Allen and Unwin",
    note = "talkorigins\_source = {true}; raw\_reference = {Dodd, J. M., and Dodd, M. H. I., 1966, An Experimental Investigation of the Supposed Pituitary Affinities of the Ascidian Neural Complex, in Barnes, H., ed., Some Contemporary Studies in Marine Science: London, Allen and Unwin.}"
}

@inproceedings{carlisle1968vanadium1,
    author = "Carlisle, D. B",
    title = "Vanadium and other metals in ascidians",
    year = "1968",
    booktitle = "Proceedings of the Royal Society, London B, v. 71, p. 31-42",
    note = "talkorigins\_source = {true}; raw\_reference = {Carlisle, D. B., 1968, Vanadium and other metals in ascidians: Proceedings of the Royal Society, London B, v. 71, p. 31-42.}"
}

@misc{eakin1971ultrastructure4,
    author = "Eakin, R. M. and Kuda, A",
    title = "Ultrastructure of sensory receptors in ascidian tadpoles",
    year = "1971",
    howpublished = "Zeitschrift fr Zellforschung und Mikro-skopische Anatomie, v. 112, p. 287-312",
    note = "talkorigins\_source = {true}; raw\_reference = {Eakin, R. M., and Kuda, A., 1971, Ultrastructure of sensory receptors in ascidian tadpoles: Zeitschrift fr Zellforschung und Mikro-skopische Anatomie, v. 112, p. 287-312.}"
}

@misc{goodbody1974the7,
    author = "Goodbody, I",
    title = "The physiology of acsidians",
    year = "1974",
    howpublished = "Advances in Marine Biology, v. 12, p. 1-149",
    note = "talkorigins\_source = {true}; raw\_reference = {Goodbody, I., 1974, The physiology of acsidians: Advances in Marine Biology, v. 12, p. 1-149.}"
}

@article{mackie1974behavior8,
    author = "Mackie, G. O",
    title = "Behavior of a compound ascidian",
    year = "1974",
    journal = "Canadian Journal of Zoology, v. 52, p. 23-27",
    note = "talkorigins\_source = {true}; raw\_reference = {Mackie, G. O., 1974, Behavior of a compound ascidian: Canadian Journal of Zoology, v. 52, p. 23-27.}"
}

@inproceedings{mackie1974branchial9,
    author = "Mackie, G. O. and Paul, D. H. and Singla, C. M. and Sleigh, M. A. and Williams, D. E",
    title = "Branchial innervation and ciliary control in the ascidian Corella",
    year = "1974",
    booktitle = "Proceedings of the Royal Society, London B, v. 187, p. 1-35",
    note = "talkorigins\_source = {true}; raw\_reference = {Mackie, G. O., Paul, D. H., Singla, C. M., Sleigh, M. A., and Williams, D. E., 1974, Branchial innervation and ciliary control in the ascidian Corella: Proceedings of the Royal Society, London B, v. 187, p. 1-35.}"
}

@incollection{cloney1978ascidian2,
    author = "Cloney, R. A",
    editor = "Chia, F. S. and Rice, M. E.",
    title = "Ascidian metamorphosis: review and analysis",
    year = "1978",
    booktitle = "Settlement and Metamorphosis of Marine Invertebrate Larvae",
    publisher = "New York, Elsevier, p. 255-282",
    note = "talkorigins\_source = {true}; raw\_reference = {Cloney, R. A., 1978, Ascidian metamorphosis: review and analysis, in Chia, F. S., and Rice, M. E., eds., Settlement and Metamorphosis of Marine Invertebrate Larvae: New York, Elsevier, p. 255-282.}"
}

@misc{flood1978filter5,
    author = "Flood, P. R",
    title = "Filter characteristics of appendicularian food catching nets",
    year = "1978",
    howpublished = "Experientia, v. 34, p. 173-175",
    note = "talkorigins\_source = {true}; raw\_reference = {Flood, P. R., 1978, Filter characteristics of appendicularian food catching nets: Experientia, v. 34, p. 173-175.}"
}

Particle retention in Ascidiella aspersa, Molgula manhattensis, Clavelina lepadiformis and Ciona intestinalis was determined from comparisons of particle-size distributions in the inhaled and exhaled water. Particles down to 2-3 jun were completely retained and the retention efficiency of smaller particles decreased to about 70 "/o for 1 ~u n particles. There was no indication that the ascidians were able to adjust their retention efficiency. Filtration rates (F, m1 min-l) as a function of total dry weight (W,,,,,, g) could be expressed as F = 54.4 W,0,,,'-05 in A. aspersa and F = 46.4 Wr0r,P-84 in C. intestinalis. It is concluded that undisturbed ascidians filter the water continuously at constant rates.

@article{doi103354meps001055,
    author = "Randløv, Anders and Riisgård, Hans Ulrik",
    title = "Efficiency of Particle Retention and Filtration Rate in Four Species of Ascidians",
    year = "1979",
    journal = "Marine Ecology Progress Series",
    abstract = {Particle retention in Ascidiella aspersa, Molgula manhattensis, Clavelina lepadiformis and Ciona intestinalis was determined from comparisons of particle-size distributions in the inhaled and exhaled water. Particles down to 2-3 jun were completely retained and the retention efficiency of smaller particles decreased to about 70 "/o for 1 \textasciitilde u n particles. There was no indication that the ascidians were able to adjust their retention efficiency. Filtration rates (F, m1 min-l) as a function of total dry weight (W,,,,,, g) could be expressed as F = 54.4 W,0,,,'-05 in A. aspersa and F = 46.4 Wr0r,P-84 in C. intestinalis. It is concluded that undisturbed ascidians filter the water continuously at constant rates.},
    url = "https://doi.org/10.3354/meps001055",
    doi = "10.3354/meps001055",
    openalex = "W2055314763"
}

Filter characteristics have been determined and compared in ciliary and mucus-net filter feeders. The ciliary feeders include the polychaete Sabella penicillus, the brachiopod Terebratulina retuso, the marine bivalves Monia squama, Cardiurn glaucum, and Petricola pholadiformis, and the freshwater bivalves Dreissena polymorpha, Unio pictamrn, and Anodonta cygnea. The mucus-net feeders are the polychaete Chaetopterus variopedatus, the gastropod Crepidula fomicata, and the ascidians Sfyela clava, Ciona intestinalis, Ascidia virginia, Ascidia obliqua, and Ascidia mentula. Efficiencies of particle retention as a function of particle size was determined by counting of particles in samples of inhalant and exhalant water. The lower threshold for efficient particle retention varied from about 6 p m in T. retuso to about 1 p n in D. polyrnorpha. Mucus nets efficiently retained particles down to 1 to 2 pm. Filter feeding is characterized by processing of water at low pressures (5 l mm H,O). Mechanisms of water processing and particle retention in brachiopods and bivalves are compared. It is concluded that laminar flow of through-currents and surface-currents in brachiopods is consistent with the hypothesis of capture of suspended particles by means of viscous forces acting upon the particles in the zone of contact between the 2 flow systems.

@article{doi103354meps015283,
    author = "Jørgensen, CB and Kørboe, T and Møhlenberg, F and Riisgård, Hans Ulrik",
    title = "Ciliary and mucus-net filter feeding, with special reference to fluid mechanical Characteristics",
    year = "1984",
    journal = "Marine Ecology Progress Series",
    abstract = "Filter characteristics have been determined and compared in ciliary and mucus-net filter feeders. The ciliary feeders include the polychaete Sabella penicillus, the brachiopod Terebratulina retuso, the marine bivalves Monia squama, Cardiurn glaucum, and Petricola pholadiformis, and the freshwater bivalves Dreissena polymorpha, Unio pictamrn, and Anodonta cygnea. The mucus-net feeders are the polychaete Chaetopterus variopedatus, the gastropod Crepidula fomicata, and the ascidians Sfyela clava, Ciona intestinalis, Ascidia virginia, Ascidia obliqua, and Ascidia mentula. Efficiencies of particle retention as a function of particle size was determined by counting of particles in samples of inhalant and exhalant water. The lower threshold for efficient particle retention varied from about 6 p m in T. retuso to about 1 p n in D. polyrnorpha. Mucus nets efficiently retained particles down to 1 to 2 pm. Filter feeding is characterized by processing of water at low pressures (5 l mm H,O). Mechanisms of water processing and particle retention in brachiopods and bivalves are compared. It is concluded that laminar flow of through-currents and surface-currents in brachiopods is consistent with the hypothesis of capture of suspended particles by means of viscous forces acting upon the particles in the zone of contact between the 2 flow systems.",
    url = "https://doi.org/10.3354/meps015283",
    doi = "10.3354/meps015283",
    openalex = "W1971107871",
    references = "doi101007bf00386593, doi1010160022098171900542, doi101016s0003936580800091, doi10108000785326197810425487, doi101111j109636421962tb01626x, doi101111j146363951981tb00616x, doi101128aem335122512281977, doi103354meps001055, doi103354meps005291, doi103354meps011089, doi104319lo19812661062, openalexw1549886310"
}

@article{doi1010160040816687900103,
    author = "Martinucci, G. and Dallai, R. and Burighel, P.",
    title = "A comparative study of ciliary differentiations in the branchial stigmata of ascidians.",
    year = "1987",
    journal = "Tissue \& cell",
    url = "https://www.semanticscholar.org/paper/db7e027afd2ca819aa2061de188d28c8c0b934f5",
    doi = "10.1016/0040-8166(87)90010-3",
    is_oa = "true",
    number = "2",
    pages = "251-263",
    semanticscholar_citation_count = "15",
    semanticscholar_id = "db7e027afd2ca819aa2061de188d28c8c0b934f5",
    volume = "19"
}

We present evidence that the embryo of the ascidian, Ciona intestinalis, is an easily manipulated system for investigating the establishment of basic chordate tissues and organs. Ciona has a small genome, and simple, well-defined embyronic lineages. Here, we examine the regulatory mechanisms underlying the differentiation of the notochord. Particular efforts center on the regulation of a notochord-specific Ciona Brachyury gene (Ci-Bra). An electroporation method was devised for the efficient incorporation of transgenic DNA into Ciona embryos. This method permitted the identification of a minimal, 434 bp enhancer from the Ci-Bra promoter region that mediates the notochord-restricted expression of both GFP and lacZ reporter genes. This enhancer contains a negative control region that excludes Ci-Bra expression from inappropriate embryonic lineages, including the trunk mesenchyme and tail muscles. Evidence is presented that the enhancer is activated by a regulatory element which is closely related to the recognition sequence of the Suppressor of Hairless transcription factor, thereby raising the possibility that the Notch signaling pathway plays a role in notochord differentiation. We discuss the implications of this analysis with regard to the evolutionary conservation of integrative enhancers, and the subdivision of the axial and paraxial mesoderm in vertebrates.

@article{doi101242dev1243589,
    author = "Corbo, Joseph C. and Levine, Michael and Zeller, Robert W.",
    title = "Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis",
    year = "1997",
    journal = "Development",
    abstract = "We present evidence that the embryo of the ascidian, Ciona intestinalis, is an easily manipulated system for investigating the establishment of basic chordate tissues and organs. Ciona has a small genome, and simple, well-defined embyronic lineages. Here, we examine the regulatory mechanisms underlying the differentiation of the notochord. Particular efforts center on the regulation of a notochord-specific Ciona Brachyury gene (Ci-Bra). An electroporation method was devised for the efficient incorporation of transgenic DNA into Ciona embryos. This method permitted the identification of a minimal, 434 bp enhancer from the Ci-Bra promoter region that mediates the notochord-restricted expression of both GFP and lacZ reporter genes. This enhancer contains a negative control region that excludes Ci-Bra expression from inappropriate embryonic lineages, including the trunk mesenchyme and tail muscles. Evidence is presented that the enhancer is activated by a regulatory element which is closely related to the recognition sequence of the Suppressor of Hairless transcription factor, thereby raising the possibility that the Notch signaling pathway plays a role in notochord differentiation. We discuss the implications of this analysis with regard to the evolutionary conservation of integrative enhancers, and the subdivision of the axial and paraxial mesoderm in vertebrates.",
    url = "https://doi.org/10.1242/dev.124.3.589",
    doi = "10.1242/dev.124.3.589",
    openalex = "W2181933303",
    references = "doi101242jcss27228551, openalexw1567612426, openalexw654005152"
}

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

@article{doi101126science1080049,
    author = "Dehal, Paramvir and Satou, Yutaka and Campbell, R. Keith and Chapman, Jarrod and Degnan, Bernard M. and Tomaso, Anthony De and Davidson, Brad and Gregorio, Anna Di and Gelpke, Maarten D. Sollewijn and Goodstein, David and Harafuji, Naoe and Hastings, Kenneth E.M. and Ho, Isaac and Hotta, Kohji and Huang, Wayne and Kawashima, Takeshi and Lemaire, Patrick and Martínez, Diego and Meinertzhagen, Ian A. and Necula, Simona and Nonaka, Masaru and Putnam, Nik and Rash, Sam and Saiga, Hidetoshi and Satake, Masanobu and Terry, Astrid and Yamada, Lixy and Wang, Hong‐Gang and Awazu, Satoko and Azumi, Kaoru and Boore, Jeffrey L. and Branno, Margherita and Chin-Bow, Stephen T. and Desantis, Rosaria and Doyle, Sharon A. and Francino, M. Pilar and Keys, David N. and Haga, Shinobu and Hayashi, Hiroko and Hino, Kyosuke and Imai, Kaoru S. and Inaba, Kazuo and Kano, Shungo and Kobayashi, Kenji and Kobayashi, Mari and Lee, Byung-In and Makabe, Kazuhiro W. and Manohar, Chitra and Matassi, Giorgio and Medina, Mónica and Mochizuki, Yasuaki and Mount, Steve and Morishita, Tomomi and Miura, Sachiko and Nakayama, A. and Nishizaka, Satoko and Nomoto, Hisayo and Ohta, Fumiko and Oishi, Kazuko and Rigoutsos, Isidore and Sano, Masako and Sasaki, Akane and Sasakura, Yasunori and Shoguchi, Eiichi and Shin‐I, Tadasu and Spagnuolo, Antonietta and Stainier, Didier Y. R. and Suzuki, Miho and Tassy, Olivier and Takatori, Naohito and Tokuoka, Miki and Yagi, Kasumi and Yoshizaki, Fumiko and Wada, Shuichi and Zhang, Cindy and Hyatt, P. Douglas and Larimer, Frank W. and Detter, Chris and Doggett, Norman A. and Glavina, Tijana and Hawkins, Trevor and Richardson, Paul and Lucas, Susan and Kohara, Yuji and Levine, Michael and Satoh, Nori and Rokhsar, Daniel S.",
    title = "The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins",
    year = "2002",
    journal = "Science",
    abstract = "The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.",
    url = "https://doi.org/10.1126/science.1080049",
    doi = "10.1126/science.1080049",
    openalex = "W2170258388",
    references = "doi101016s0022283605803602, doi101016s0092867400804304, doi10103835057062, doi10103835067088, doi101038370563a0, doi101093bioinformatics179847, doi101126science1058040, doi101126science28253962012, doi101126science28454181313, doi101126science28754612185, doi101186gb200123reviews3005, doi101242dev1994supplement125, openalexw1964182146"
}

Achieving a real understanding of animal development obviously requires a comprehensive rather than partial identification of the genes working in each developmental process. Recent decoding of genome sequences will enable us to perform such studies. An ascidian, Ciona intestinalis, one of the animals whose genome has been sequenced, is a chordate sharing a basic body plan with vertebrates, although its genome contains less paralogs than are usually seen in vertebrates. In the present study, we discuss the genomewide approach to networks of developmental genes in Ciona embryos. We focus on transcription factor genes and some major groups of signal transduction genes. These genes are comprehensively listed and examined with regard to their embryonic expression by in situ hybridization (http://ghost.zool.kyoto-u.ac.jp/tfst.html). The results revealed that 74% of the transcription factor genes are expressed maternally and that 56% of the genes are zygotically expressed during embryogenesis. Of these, 34% of the transcription factor genes are expressed both maternally and zygotically. The number of zygotically expressed transcription factor genes increases gradually during embryogenesis. As an example, and taking advantage of this comprehensive description of gene expression profiles, we identified transcription factor genes and signal transduction genes that are expressed at the early gastrula stage and that work downstream of beta-catenin, FoxD and/or Fgf9/16/20. Because these three genes are essential for ascidian endomesoderm specification, transcription factor genes and signal transduction genes involved in each of the downstream processes can be deduced comprehensively using the present approach.

@article{doi101242dev01270,
    author = "Imai, Kaoru S. and Hino, Kyosuke and Yagi, Kasumi and Satoh, Nori and Satou, Yutaka",
    title = "Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks",
    year = "2004",
    journal = "Development",
    abstract = "Achieving a real understanding of animal development obviously requires a comprehensive rather than partial identification of the genes working in each developmental process. Recent decoding of genome sequences will enable us to perform such studies. An ascidian, Ciona intestinalis, one of the animals whose genome has been sequenced, is a chordate sharing a basic body plan with vertebrates, although its genome contains less paralogs than are usually seen in vertebrates. In the present study, we discuss the genomewide approach to networks of developmental genes in Ciona embryos. We focus on transcription factor genes and some major groups of signal transduction genes. These genes are comprehensively listed and examined with regard to their embryonic expression by in situ hybridization (http://ghost.zool.kyoto-u.ac.jp/tfst.html). The results revealed that 74\% of the transcription factor genes are expressed maternally and that 56\% of the genes are zygotically expressed during embryogenesis. Of these, 34\% of the transcription factor genes are expressed both maternally and zygotically. The number of zygotically expressed transcription factor genes increases gradually during embryogenesis. As an example, and taking advantage of this comprehensive description of gene expression profiles, we identified transcription factor genes and signal transduction genes that are expressed at the early gastrula stage and that work downstream of beta-catenin, FoxD and/or Fgf9/16/20. Because these three genes are essential for ascidian endomesoderm specification, transcription factor genes and signal transduction genes involved in each of the downstream processes can be deduced comprehensively using the present approach.",
    url = "https://doi.org/10.1242/dev.01270",
    doi = "10.1242/dev.01270",
    openalex = "W2102988868",
    references = "doi101242dev126225149"
}

@incollection{crossref2008ascidians,
    title = "Ascidians",
    year = "2008",
    booktitle = "Encyclopedia of Genetics, Genomics, Proteomics and Informatics",
    url = "https://doi.org/10.1007/978-1-4020-6754-9\_1200",
    doi = "10.1007/978-1-4020-6754-9\_1200",
    pages = "148-148"
}

Spermatozoa undergo dramatic physiological changes at fertilization. In the ascidian Ciona intestinalis, an egg-derived substance named SAAF induces both sperm activation and chemotaxis to the egg. To elucidate the molecular mechanism underlying these phenomena, whole sperm proteins before and after SAAF-treatment were analyzed by two-dimensional gel electrophoresis. By comparison of spot patterns before and after activation, we found twelve proteins that changed the isoelectric points. Seven proteins were shown to be axonemal proteins and others were suggested to be non-axonemal components. Analysis of these proteins by MS-based proteomic system revealed that components of several substructures of the axonemes underwent the changes in isoelectric point at sperm activation, including WD-repeat intermediate chains of outer and inner arm dyneins and a radial spoke protein LRR37, as well as novel axonemal proteins with armadillo repeats or SMC domain. Molecules for cell signaling such as 14-3-3 proteins, Skp1 and VCP/p97 also showed isoelectric changes at sperm activation. These results show a comprehensive feature for signaling mechanism of the activation of spermatozoa at fertilization and also shed new lights on the regulation of ciliary and flagellar movements.

@article{doi101002cm20258,
    author = "Hozumi, Akiko and Padma, P. Naga and Toda, Tosifusa and Ide, Hiroyuki and Inaba, Kazuo",
    title = "Molecular characterization of axonemal proteins and signaling molecules responsible for chemoattractant‐induced sperm activation in Ciona intestinalis",
    year = "2008",
    journal = "Cell Motility and the Cytoskeleton",
    abstract = "Spermatozoa undergo dramatic physiological changes at fertilization. In the ascidian Ciona intestinalis, an egg-derived substance named SAAF induces both sperm activation and chemotaxis to the egg. To elucidate the molecular mechanism underlying these phenomena, whole sperm proteins before and after SAAF-treatment were analyzed by two-dimensional gel electrophoresis. By comparison of spot patterns before and after activation, we found twelve proteins that changed the isoelectric points. Seven proteins were shown to be axonemal proteins and others were suggested to be non-axonemal components. Analysis of these proteins by MS-based proteomic system revealed that components of several substructures of the axonemes underwent the changes in isoelectric point at sperm activation, including WD-repeat intermediate chains of outer and inner arm dyneins and a radial spoke protein LRR37, as well as novel axonemal proteins with armadillo repeats or SMC domain. Molecules for cell signaling such as 14-3-3 proteins, Skp1 and VCP/p97 also showed isoelectric changes at sperm activation. These results show a comprehensive feature for signaling mechanism of the activation of spermatozoa at fertilization and also shed new lights on the regulation of ciliary and flagellar movements.",
    url = "https://doi.org/10.1002/cm.20258",
    doi = "10.1002/cm.20258",
    openalex = "W2066973908",
    references = "doi101006abio19769999, doi1010160003269776905273, doi101016s0014579301032884, doi101038227680a0, doi101038nature04541, doi101038nrm1471, doi101074jbcm202325200, doi101083jcb200504008, doi101083jcb913107s, doi101126science1080049"
}

@article{doi101016jydbio200810038,
    author = "Nomura, Mamoru and Nakajima, Ayako and Inaba, Kazuo",
    title = "Proteomic profiles of embryonic development in the ascidian Ciona intestinalis",
    year = "2008",
    journal = "Developmental Biology",
    url = "https://doi.org/10.1016/j.ydbio.2008.10.038",
    doi = "10.1016/j.ydbio.2008.10.038",
    openalex = "W2030393321",
    references = "doi101002cm20258"
}

The small ciliary G protein Arl13b is required for cilium biogenesis and sonic hedgehog signaling and is mutated in patients with Joubert syndrome (JS). In this study, using Caenorhabditis elegans and mammalian cell culture systems, we investigated the poorly understood ciliary and molecular basis of Arl13b function. First, we show that Arl13b/ARL-13 localization is frequently restricted to a proximal ciliary compartment, where it associates with ciliary membranes via palmitoylation modification motifs. Next, we find that loss-of-function C. elegans arl-13 mutants possess defects in cilium morphology and ultrastructure, as well as defects in ciliary protein localization and transport; ciliary transmembrane proteins abnormally accumulate, PKD-2 ciliary abundance is elevated, and anterograde intraflagellar transport (IFT) is destabilized. Finally, we show that arl-13 interacts genetically with other ciliogenic and ciliary transport-associated genes in maintaining cilium structure/morphology and anterograde IFT stability. Together, these data implicate a role for JS-associated Arl13b at ciliary membranes, where it regulates ciliary transmembrane protein localizations and anterograde IFT assembly stability.

@article{doi101083jcb200908133,
    author = "Cevik, Sebiha and Hori, Yuji and Kaplan, Oktay I. and Kida, Katarzyna and Toivenon, Tiina and Foley-Fisher, Christian and Cottell, David C. and Katada, Toshiaki and Kontani, Kenji and Blacque, Oliver E.",
    title = "Joubert syndrome Arl13b functions at ciliary membranes and stabilizes protein transport in Caenorhabditis elegans",
    year = "2010",
    journal = "The Journal of Cell Biology",
    abstract = "The small ciliary G protein Arl13b is required for cilium biogenesis and sonic hedgehog signaling and is mutated in patients with Joubert syndrome (JS). In this study, using Caenorhabditis elegans and mammalian cell culture systems, we investigated the poorly understood ciliary and molecular basis of Arl13b function. First, we show that Arl13b/ARL-13 localization is frequently restricted to a proximal ciliary compartment, where it associates with ciliary membranes via palmitoylation modification motifs. Next, we find that loss-of-function C. elegans arl-13 mutants possess defects in cilium morphology and ultrastructure, as well as defects in ciliary protein localization and transport; ciliary transmembrane proteins abnormally accumulate, PKD-2 ciliary abundance is elevated, and anterograde intraflagellar transport (IFT) is destabilized. Finally, we show that arl-13 interacts genetically with other ciliogenic and ciliary transport-associated genes in maintaining cilium structure/morphology and anterograde IFT stability. Together, these data implicate a role for JS-associated Arl13b at ciliary membranes, where it regulates ciliary transmembrane protein localizations and anterograde IFT assembly stability.",
    url = "https://doi.org/10.1083/jcb.200908133",
    doi = "10.1083/jcb.200908133",
    openalex = "W2062938087"
}

@incollection{ali2012marine,
    author = "Ali, H and Tamilselvi, M",
    title = "Marine Ascidians",
    year = "2012",
    booktitle = "Marine Pharmacognosy",
    url = "https://doi.org/10.1201/b13868-16",
    doi = "10.1201/b13868-16",
    pages = "173-190"
}

BACKGROUND: The dorsally located central nervous system (CNS) is an important hallmark of chordates. Among chordates, tunicate ascidians change their CNS remarkably by means of a metamorphosis from a highly regionalized larval CNS to an oval-shaped juvenile CNS without prominent morphological features. The neuronal organization of the CNS of ascidian tadpole larvae has been well described, but that in the CNS of postmetamorphosis juveniles has not been characterized well. RESULTS: We investigated the number of neural cells, the number and position of differentiated neurons, and their axonal trajectories in the juvenile CNS of the ascidian Ciona intestinalis. The cell bodies of cholinergic, glutamatergic, and GABAergic/glycinergic neurons exhibited different localization patterns along the anterior-posterior axis in the juvenile CNS. Cholinergic neurons extended their axons toward the oral, atrial and body wall muscles and pharyngeal gill to regulate muscle contraction and ciliary movement. CONCLUSIONS: Unlike its featureless shape, the juvenile CNS is highly patterned along the anterior-posterior axis. This patterning may be necessary for exerting multiple roles in the regulation of adult tissues distributed throughout the body. This basic information of the juvenile CNS of Ciona will allow in-depth studies of molecular mechanisms underlying the reconstruction of the CNS during ascidian metamorphosis.

@article{doi101002dvdy24317,
    author = "Hozumi, Akiko and Horie, Takeo and Sasakura, Yasunori",
    title = "Neuronal map reveals the highly regionalized pattern of the juvenile central nervous system of the ascidian Ciona intestinalis.",
    year = "2015",
    journal = "Developmental dynamics: an official publication of the American Association of Anatomists",
    abstract = "BACKGROUND: The dorsally located central nervous system (CNS) is an important hallmark of chordates. Among chordates, tunicate ascidians change their CNS remarkably by means of a metamorphosis from a highly regionalized larval CNS to an oval-shaped juvenile CNS without prominent morphological features. The neuronal organization of the CNS of ascidian tadpole larvae has been well described, but that in the CNS of postmetamorphosis juveniles has not been characterized well. RESULTS: We investigated the number of neural cells, the number and position of differentiated neurons, and their axonal trajectories in the juvenile CNS of the ascidian Ciona intestinalis. The cell bodies of cholinergic, glutamatergic, and GABAergic/glycinergic neurons exhibited different localization patterns along the anterior-posterior axis in the juvenile CNS. Cholinergic neurons extended their axons toward the oral, atrial and body wall muscles and pharyngeal gill to regulate muscle contraction and ciliary movement. CONCLUSIONS: Unlike its featureless shape, the juvenile CNS is highly patterned along the anterior-posterior axis. This patterning may be necessary for exerting multiple roles in the regulation of adult tissues distributed throughout the body. This basic information of the juvenile CNS of Ciona will allow in-depth studies of molecular mechanisms underlying the reconstruction of the CNS during ascidian metamorphosis.",
    url = "https://pubmed.ncbi.nlm.nih.gov/26250096/",
    doi = "10.1002/dvdy.24317",
    openalex = "W2152549204",
    pmid = "26250096",
    references = "doi101016s0959437x02003222, doi101038nature04336, doi101038nature06967, doi101038nmeth936, doi101073pnas202320599, doi101126science1080049, doi101242dev048975, doi101242dev1243589, doi101242dev12771349, doi101523jneurosci1823097331998"
}

Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.

@article{doi101093nargkv966,
    author = "Brozovic, Matija and Martin, Cyril and Dantec, Christelle Le and Dauga, Delphine and Mendez, Mickaël and Simion, Paul and Percher, Madeline and Laporte, Baptiste and Scornavacca, Céline and Gregorio, Anna Di and Fujiwara, Shigeki and Gineste, Mathieu and Lowe, Elijah K. and Piette, Jacques and Racioppi, Claudia and Ristoratore, Filomena and Sasakura, Yasunori and Takatori, Naohito and Brown, Titus and Delsuc, Frédéric and Douzery, Emmanuel and Gissi, Carmela and McDougall, Alex and Nishida, Hiroki and Sawada, Hitoshi and Swalla, Billie J. and Yasuo, Hitoyoshi and Lemaire, Patrick",
    title = "ANISEED 2015: a digital framework for the comparative developmental biology of ascidians",
    year = "2015",
    journal = "Nucleic Acids Research",
    abstract = "Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.",
    url = "https://doi.org/10.1093/nar/gkv966",
    doi = "10.1093/nar/gkv966",
    openalex = "W1900418691",
    references = "doi101002dvdy24317"
}

The motility of eukaryotic cilia and flagella is modulated in response to several extracellular stimuli. Ca(2+) is the most critical intracellular factor for these changes in motility, directly acting on the axonemes and altering flagellar asymmetry. Calaxin is an opisthokont-specific neuronal calcium sensor protein first described in the sperm of the ascidian Ciona intestinalis. It binds to a heavy chain of two-headed outer arm dynein in a Ca(2+)-dependent manner and regulates 'asymmetric' wave propagation at high concentrations of Ca(2+). A Ca(2+)-binding subunit of outer arm dynein in Chlamydomonas reinhardtii, the light chain 4 (LC4), which is a Ca(2+)-sensor phylogenetically different from calaxin, shows Ca(2+)-dependent binding to a heavy chain of three-headed outer arm dynein. However, LC4 appears to participate in 'symmetric' wave propagation at high concentrations of Ca(2+). LC4-type dynein light chain is present in bikonts, except for some subclasses of the Excavata. Thus, flagellar asymmetry-symmetry conversion in response to Ca(2+) concentration represents a 'mirror image' relationship between Ciona and Chlamydomonas. Phylogenetic analyses indicate the duplication, divergence, and loss of heavy chain and Ca(2+)-sensors of outer arm dynein among excavate species. These features imply a divergence point with respect to Ca(2+)-dependent regulation of outer arm dynein in cilia and flagella during the evolution of eukaryotic supergroups.

@article{doi101186s136300150015z,
    author = "Inaba, Kazuo",
    title = "Calcium sensors of ciliary outer arm dynein: functions and phylogenetic considerations for eukaryotic evolution.",
    year = "2015",
    journal = "Cilia",
    abstract = "The motility of eukaryotic cilia and flagella is modulated in response to several extracellular stimuli. Ca(2+) is the most critical intracellular factor for these changes in motility, directly acting on the axonemes and altering flagellar asymmetry. Calaxin is an opisthokont-specific neuronal calcium sensor protein first described in the sperm of the ascidian Ciona intestinalis. It binds to a heavy chain of two-headed outer arm dynein in a Ca(2+)-dependent manner and regulates 'asymmetric' wave propagation at high concentrations of Ca(2+). A Ca(2+)-binding subunit of outer arm dynein in Chlamydomonas reinhardtii, the light chain 4 (LC4), which is a Ca(2+)-sensor phylogenetically different from calaxin, shows Ca(2+)-dependent binding to a heavy chain of three-headed outer arm dynein. However, LC4 appears to participate in 'symmetric' wave propagation at high concentrations of Ca(2+). LC4-type dynein light chain is present in bikonts, except for some subclasses of the Excavata. Thus, flagellar asymmetry-symmetry conversion in response to Ca(2+) concentration represents a 'mirror image' relationship between Ciona and Chlamydomonas. Phylogenetic analyses indicate the duplication, divergence, and loss of heavy chain and Ca(2+)-sensors of outer arm dynein among excavate species. These features imply a divergence point with respect to Ca(2+)-dependent regulation of outer arm dynein in cilia and flagella during the evolution of eukaryotic supergroups.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC4415241/",
    doi = "10.1186/s13630-015-0015-z",
    openalex = "W2123428823",
    pmcid = "PMC4415241",
    pmid = "25932323",
    references = "doi1010079783642164835778, doi1010079783642866593, doi101007bf00336662, doi101016jcub201302007, doi101016s002192581944043x, doi101073pnas0807880106, doi101083jcb913107s, doi101093humupddmn029, doi101093nargkn750, doi10109900207713522297, openalexw2772099086"
}

Histamine is a biogenic molecule that plays a role in many physiological pathways via binding to a specific receptor. Histaminergic receptors belong to the large family of seven-transmembrane α-helix domain receptors classified in mammals into four distinct classes: H1, H2, H3, and H4. Despite being widely studied in vertebrates, few data are available on the invertebrate receptors, with only predicted H1 and H2 sequences for nonchordate deuterostomes. Here, we report the first characterized transcript sequence for an H2 receptor from the colonial ascidian Botryllus schlosseri, describing the localization of both transcript and protein during blastogenic development through in situ hybridization and immunohistochemistry. Its phylogenetic relationships with deuterostome orthologous proteins are reported, its role in ciliary beat frequency (CBF) in cultured stigma cells of the branchial basket is outlined, and the effects of histamine and its receptor agonists and antagonists are analyzed. In the presence of increasing concentrations of histamine in the medium, CBF increases similarly to the selective H2 receptor agonist dimaprit. In contrast, ranitidine, which is an inhibitor of the H2 receptor, causes a significant inhibition of CBF, similar to that observed after preincubation with the specific anti-BsHRH2 or the anti-human HRH2 antibody. In cells bordering the branchial basket stigmata, both antibodies colocalize in the proximal region of the ciliary plasmalemma, and histamine is present inside vesicles of the apical region, thus supporting the hypothesis of a histamine-binding H2 receptor control of the pharyngeal mucociliary transport similar to that of the upper respiratory tract and middle ear in mammals.

@article{doi101002jezb22675,
    author = "Cima, Francesca and Franchi, Nicola",
    title = "Histamine Stimulates Ciliary Beat Frequency via the H2 Receptor in the Protochordate Botryllus schlosseri",
    year = "2016",
    journal = "Journal of Experimental Zoology Part B Molecular and Developmental Evolution",
    abstract = "Histamine is a biogenic molecule that plays a role in many physiological pathways via binding to a specific receptor. Histaminergic receptors belong to the large family of seven-transmembrane α-helix domain receptors classified in mammals into four distinct classes: H1, H2, H3, and H4. Despite being widely studied in vertebrates, few data are available on the invertebrate receptors, with only predicted H1 and H2 sequences for nonchordate deuterostomes. Here, we report the first characterized transcript sequence for an H2 receptor from the colonial ascidian Botryllus schlosseri, describing the localization of both transcript and protein during blastogenic development through in situ hybridization and immunohistochemistry. Its phylogenetic relationships with deuterostome orthologous proteins are reported, its role in ciliary beat frequency (CBF) in cultured stigma cells of the branchial basket is outlined, and the effects of histamine and its receptor agonists and antagonists are analyzed. In the presence of increasing concentrations of histamine in the medium, CBF increases similarly to the selective H2 receptor agonist dimaprit. In contrast, ranitidine, which is an inhibitor of the H2 receptor, causes a significant inhibition of CBF, similar to that observed after preincubation with the specific anti-BsHRH2 or the anti-human HRH2 antibody. In cells bordering the branchial basket stigmata, both antibodies colocalize in the proximal region of the ciliary plasmalemma, and histamine is present inside vesicles of the apical region, thus supporting the hypothesis of a histamine-binding H2 receptor control of the pharyngeal mucociliary transport similar to that of the upper respiratory tract and middle ear in mammals.",
    url = "https://doi.org/10.1002/jez.b.22675",
    doi = "10.1002/jez.b.22675",
    openalex = "W2346269057",
    references = "doi101002dvdy24317, martinucci1987a"
}

Ascidians are marine invertebrate chordates. Their tadpole larvae contain a dorsal tubular nervous system, resulting from the rolling up of a neural plate. Along the anterior-posterior (A-P) axis, the central nervous system (CNS) is organized into a sensory vesicle, neck, trunk ganglion, and tail nerve cord and consists of approximately only 330 cells, of which around 100 are thought to be neurons. The organization of distinct neuronal cell types and neurotransmitter gene expression within the CNS has been described. The unique developmental mode of ascidians, with a small number of cells and a fixed cell division pattern, allows individual cells to be traced throughout development. This feature has led to the complete documentation of the cell lineages of certain cell types in the CNS. Thus, a step-by-step understanding of nervous system development from the initial stages of neural induction to the neurogenesis of individual neurons is a feasible goal. The genetic control of neural fate induction and early neural plate patterning are now well understood. The molecular mechanisms specifying the cholinergic neurons of the trunk ganglion as well as the pigment cells of the sensory organs are also well elucidated. In addition, studies have begun on the morphogenetic processes of neurulation. Remaining challenges include building an embryonic atlas integrating gene expression patterns, cell lineage, and neuronal cell types as well as developing the gene regulatory networks of cell fate specification and integrating them with the genetic control of morphogenesis. WIREs Dev Biol 2016, 5:538-561. doi: 10.1002/wdev.239 For further resources related to this article, please visit the WIREs website.

@article{doi101002wdev239,
    author = "Hudson, C. S.",
    title = "The central nervous system of ascidian larvae",
    year = "2016",
    journal = "Wiley Interdisciplinary Reviews Developmental Biology",
    abstract = "Ascidians are marine invertebrate chordates. Their tadpole larvae contain a dorsal tubular nervous system, resulting from the rolling up of a neural plate. Along the anterior-posterior (A-P) axis, the central nervous system (CNS) is organized into a sensory vesicle, neck, trunk ganglion, and tail nerve cord and consists of approximately only 330 cells, of which around 100 are thought to be neurons. The organization of distinct neuronal cell types and neurotransmitter gene expression within the CNS has been described. The unique developmental mode of ascidians, with a small number of cells and a fixed cell division pattern, allows individual cells to be traced throughout development. This feature has led to the complete documentation of the cell lineages of certain cell types in the CNS. Thus, a step-by-step understanding of nervous system development from the initial stages of neural induction to the neurogenesis of individual neurons is a feasible goal. The genetic control of neural fate induction and early neural plate patterning are now well understood. The molecular mechanisms specifying the cholinergic neurons of the trunk ganglion as well as the pigment cells of the sensory organs are also well elucidated. In addition, studies have begun on the morphogenetic processes of neurulation. Remaining challenges include building an embryonic atlas integrating gene expression patterns, cell lineage, and neuronal cell types as well as developing the gene regulatory networks of cell fate specification and integrating them with the genetic control of morphogenesis. WIREs Dev Biol 2016, 5:538-561. doi: 10.1002/wdev.239 For further resources related to this article, please visit the WIREs website.",
    url = "https://doi.org/10.1002/wdev.239",
    doi = "10.1002/wdev.239",
    openalex = "W2475024994",
    references = "doi101002dvdy24317, doi101242jcss310363393"
}

The Ciona intestinalis larva has two distinct photoreceptor organs, a conventional pigmented ocellus and a nonpigmented ocellus, that are asymmetrically situated in the brain. The ciliary photoreceptor cells of these ocelli resemble visual cells of the vertebrate retina. Precise elucidation of the lineage of the photoreceptor cells will be key to understanding the developmental mechanisms of these cells as well as the evolutionary relationships between the photoreceptor organs of ascidians and vertebrates. Photoreceptor cells of the pigmented ocellus have been thought to develop from anterior animal (a-lineage) blastomeres, whereas the developmental origin of the nonpigmented ocellus has not been determined. Here, we show that the photoreceptor cells of both ocelli develop from the right anterior vegetal hemisphere: those of the pigmented ocellus from the right A9.14 cell and those of the nonpigmented ocellus from the right A9.16 cell. The pigmented ocellus is formed by a combination of two lineages of cells with distinct embryonic origins: the photoreceptor cells originate from a medial portion of the A-lineage neural plate, while the pigment cell originates from the lateral edge of the a-lineage neural plate. In light of the recently proposed close evolutionary relationship between the ocellus pigment cell of ascidians and the cephalic neural crest of vertebrates, the ascidian ocellus may represent a prototypic contribution of the neural crest to a cranial sensory organ.

@article{doi101016jydbio201610014,
    author = "Oonuma, Kouhei and Tanaka, Moeko and Nishitsuji, Koki and Kato, Yumiko and Shimai, Kotaro and Kusakabe, Takehiro G",
    title = "Revised lineage of larval photoreceptor cells in Ciona reveals archetypal collaboration between neural tube and neural crest in sensory organ formation.",
    year = "2016",
    journal = "Developmental biology",
    abstract = "The Ciona intestinalis larva has two distinct photoreceptor organs, a conventional pigmented ocellus and a nonpigmented ocellus, that are asymmetrically situated in the brain. The ciliary photoreceptor cells of these ocelli resemble visual cells of the vertebrate retina. Precise elucidation of the lineage of the photoreceptor cells will be key to understanding the developmental mechanisms of these cells as well as the evolutionary relationships between the photoreceptor organs of ascidians and vertebrates. Photoreceptor cells of the pigmented ocellus have been thought to develop from anterior animal (a-lineage) blastomeres, whereas the developmental origin of the nonpigmented ocellus has not been determined. Here, we show that the photoreceptor cells of both ocelli develop from the right anterior vegetal hemisphere: those of the pigmented ocellus from the right A9.14 cell and those of the nonpigmented ocellus from the right A9.16 cell. The pigmented ocellus is formed by a combination of two lineages of cells with distinct embryonic origins: the photoreceptor cells originate from a medial portion of the A-lineage neural plate, while the pigment cell originates from the lateral edge of the a-lineage neural plate. In light of the recently proposed close evolutionary relationship between the ocellus pigment cell of ascidians and the cephalic neural crest of vertebrates, the ascidian ocellus may represent a prototypic contribution of the neural crest to a cranial sensory organ.",
    url = "https://pubmed.ncbi.nlm.nih.gov/27789227/",
    doi = "10.1016/j.ydbio.2016.10.014",
    openalex = "W2537046125",
    pmid = "27789227",
    references = "doi1010160012160685901010, doi101016jcub200912006, doi101016s0021925818823195, doi10103714088000, doi10103835093002, doi101073pnas202320599, doi101074jbcm009030200, doi101242dev01270, doi105962bhltitle4801, doi105962bhltitle68064"
}

Left-right asymmetries in brains are usually minor or cryptic. We report brain asymmetries in the tiny, dorsal tubular nervous system of the ascidian tadpole larva, Ciona intestinalis. Chordate in body plan and development, the larva provides an outstanding example of brain asymmetry. Although early neural development is well studied, detailed cellular organization of the swimming larva's CNS remains unreported. Using serial-section EM we document the synaptic connectome of the larva's 177 CNS neurons. These formed 6618 synapses including 1772 neuromuscular junctions, augmented by 1206 gap junctions. Neurons are unipolar with at most a single dendrite, and few synapses. Some synapses are unpolarised, others form reciprocal or serial motifs; 922 were polyadic. Axo-axonal synapses predominate. Most neurons have ciliary organelles, and many features lack structural specialization. Despite equal cell numbers on both sides, neuron identities and pathways differ left/right. Brain vesicle asymmetries include a right ocellus and left coronet cells.

@article{doi107554elife16962,
    author = "Ryan, Kerrianne and Lu, Zhiyuan and Meinertzhagen, Ian A.",
    title = "The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling",
    year = "2016",
    journal = "eLife",
    abstract = "Left-right asymmetries in brains are usually minor or cryptic. We report brain asymmetries in the tiny, dorsal tubular nervous system of the ascidian tadpole larva, Ciona intestinalis. Chordate in body plan and development, the larva provides an outstanding example of brain asymmetry. Although early neural development is well studied, detailed cellular organization of the swimming larva's CNS remains unreported. Using serial-section EM we document the synaptic connectome of the larva's 177 CNS neurons. These formed 6618 synapses including 1772 neuromuscular junctions, augmented by 1206 gap junctions. Neurons are unipolar with at most a single dendrite, and few synapses. Some synapses are unpolarised, others form reciprocal or serial motifs; 922 were polyadic. Axo-axonal synapses predominate. Most neurons have ciliary organelles, and many features lack structural specialization. Despite equal cell numbers on both sides, neuron identities and pathways differ left/right. Brain vesicle asymmetries include a right ocellus and left coronet cells.",
    url = "https://doi.org/10.7554/elife.16962",
    doi = "10.7554/elife.16962",
    openalex = "W2559748052",
    references = "doi1010079783642182624, doi101007bf02584045, doi101016jpreteyeres201306001, doi101016jydbio201610014, doi101017cbo9780511546372, doi101038383407a0, doi101046j14697580200119910063x, doi101098rspb19660086, doi101098rstb19860056, doi101111j13652818200501466x, doi101126science1080049, doi101126science341314, doi101242jcss27228551, doi101242jcss310363393, doi101371journalpcbi1001066, openalexw1618384257"
}

The representative characteristic of ascidians is their vertebrate-like, tadpole shape at the larval stage. Ascidians lose the tadpole shape through metamorphosis to become adults with a nonmotile, sessile body and a shape generally considered distinct from that of vertebrates. Solitary ascidians including Ciona species are extensively studied to understand the developmental mechanisms of ascidians, and to compare these mechanisms with their counterparts in vertebrates. In these ascidian species, the digestive and circulatory systems are not well developed in the larval trunk and the larvae do not take food. This is in contrast with the inner conditions of vertebrate tadpoles, which have functional organs comparable to those of adults. The adult organs and tissues of these ascidians become functional during metamorphosis that is completed quickly, suggesting that the ascidian larvae of solitary species are a transient stage of development. We here discuss how the cells and tissues in the ascidian larval body are converted into those of adults. The hearts of ascidians and vertebrates use closely related cellular and molecular mechanisms that suggest their shared origin. Hox genes of ascidians are essential for forming adult endodermal structures. To fully understand the development and evolution of chordates, a complete elucidation of the mechanisms underlying the adult tissue/organ formation of ascidians will be needed. WIREs Dev Biol 2018, 7:e304. doi: 10.1002/wdev.304 This article is categorized under: Comparative Development and Evolution > Body Plan Evolution Early Embryonic Development > Development to the Basic Body Plan.

@article{doi101002wdev304,
    author = "Sasakura, Yasunori and Hozumi, Akiko",
    title = "Formation of adult organs through metamorphosis in ascidians",
    year = "2017",
    journal = "Wiley Interdisciplinary Reviews Developmental Biology",
    abstract = "The representative characteristic of ascidians is their vertebrate-like, tadpole shape at the larval stage. Ascidians lose the tadpole shape through metamorphosis to become adults with a nonmotile, sessile body and a shape generally considered distinct from that of vertebrates. Solitary ascidians including Ciona species are extensively studied to understand the developmental mechanisms of ascidians, and to compare these mechanisms with their counterparts in vertebrates. In these ascidian species, the digestive and circulatory systems are not well developed in the larval trunk and the larvae do not take food. This is in contrast with the inner conditions of vertebrate tadpoles, which have functional organs comparable to those of adults. The adult organs and tissues of these ascidians become functional during metamorphosis that is completed quickly, suggesting that the ascidian larvae of solitary species are a transient stage of development. We here discuss how the cells and tissues in the ascidian larval body are converted into those of adults. The hearts of ascidians and vertebrates use closely related cellular and molecular mechanisms that suggest their shared origin. Hox genes of ascidians are essential for forming adult endodermal structures. To fully understand the development and evolution of chordates, a complete elucidation of the mechanisms underlying the adult tissue/organ formation of ascidians will be needed. WIREs Dev Biol 2018, 7:e304. doi: 10.1002/wdev.304 This article is categorized under: Comparative Development and Evolution > Body Plan Evolution Early Embryonic Development > Development to the Basic Body Plan.",
    url = "https://doi.org/10.1002/wdev.304",
    doi = "10.1002/wdev.304",
    openalex = "W2766825054",
    references = "doi101002dvdy24317"
}

The nervous system of ascidians is an excellent model system to provide insights into the evolutionary process of the chordate nervous system due to their phylogenetic positions as the sister group of vertebrates. However, the entire nervous system of adult ascidians has yet to be functionally and anatomically investigated. In this study, we have revealed the whole dorsal and siphon nervous system of the transgenic adult ascidian of Ciona intestinalis Type A (Ciona robusta) in which a Kaede reporter gene is expressed in a pan-neuronal fashion. The fluorescent signal of Kaede revealed the innervation patterns and distribution of neurons in the nervous system of Ciona. Precise microscopic observation demonstrated the clear innervation of the anterior and posterior main nerves to eight and six lobes of the oral and atrial siphons, respectively. Moreover, visceral nerves, previously identified as unpaired nerves, were found to be paired; one nerve was derived from the posterior end of the cerebral ganglion and the other from the right posterior nerve. This study further revealed the full trajectory of the dorsal strand plexus and paired visceral nerves on either side from the cerebral ganglion to the ovary, and precise innervation between the cerebral ganglion and the peripheral organs including the gonoduct, cupular organ, rectum and ovary. The differential innervation patterns of visceral nerves and the dorsal strand plexus indicate that the peripheral organs including the ovary undergo various neural regulations. Collectively, the present anatomical analysis revealed the major innervation of the dorsal and siphon nervous systems of adult Ciona.

@article{doi101371journalpone0180227,
    author = "Osugi, Tomohiro and Sasakura, Yasunori and Satake, Honoo",
    title = "The nervous system of the adult ascidian Ciona intestinalis Type A (Ciona robusta): Insights from transgenic animal models",
    year = "2017",
    journal = "PLoS ONE",
    abstract = "The nervous system of ascidians is an excellent model system to provide insights into the evolutionary process of the chordate nervous system due to their phylogenetic positions as the sister group of vertebrates. However, the entire nervous system of adult ascidians has yet to be functionally and anatomically investigated. In this study, we have revealed the whole dorsal and siphon nervous system of the transgenic adult ascidian of Ciona intestinalis Type A (Ciona robusta) in which a Kaede reporter gene is expressed in a pan-neuronal fashion. The fluorescent signal of Kaede revealed the innervation patterns and distribution of neurons in the nervous system of Ciona. Precise microscopic observation demonstrated the clear innervation of the anterior and posterior main nerves to eight and six lobes of the oral and atrial siphons, respectively. Moreover, visceral nerves, previously identified as unpaired nerves, were found to be paired; one nerve was derived from the posterior end of the cerebral ganglion and the other from the right posterior nerve. This study further revealed the full trajectory of the dorsal strand plexus and paired visceral nerves on either side from the cerebral ganglion to the ovary, and precise innervation between the cerebral ganglion and the peripheral organs including the gonoduct, cupular organ, rectum and ovary. The differential innervation patterns of visceral nerves and the dorsal strand plexus indicate that the peripheral organs including the ovary undergo various neural regulations. Collectively, the present anatomical analysis revealed the major innervation of the dorsal and siphon nervous systems of adult Ciona.",
    url = "https://doi.org/10.1371/journal.pone.0180227",
    doi = "10.1371/journal.pone.0180227",
    openalex = "W2661387851",
    references = "doi101002dvdy24317"
}

@book{crossref2018transgenic,
    title = "Transgenic Ascidians",
    year = "2018",
    booktitle = "Advances in Experimental Medicine and Biology",
    url = "https://doi.org/10.1007/978-981-10-7545-2",
    doi = "10.1007/978-981-10-7545-2"
}

Tadpole larvae of the ascidian, Halocynthia roretzi, show morphological left-right asymmetry in the brain structures and the orientation of tail bending within the vitelline membrane. Neurula embryos rotate along the anterior-posterior axis in a counterclockwise direction, and then this rotation stops when the left side of the embryo is oriented downwards. Contact of the left-side epidermis with the vitelline membrane promotes nodal gene expression in the left-side epidermis. This is a novel mechanism in which rotation of whole embryos provides the initial cue for breaking left-right symmetry. Here we show that epidermal monocilia, which appear at the neurula rotation stage, generate the driving force for rotation. A ciliary protein, Arl13b, fused with Venus YFP was used for live imaging of ciliary movements. Although overexpression of wild-type Arl13b fusion protein resulted in aberrant movements of the cilia and abrogation of neurula rotation, mutant Arl13b fusion protein, in which the GTPase and coiled-coil domains were removed, did not affect the normal ciliary movements and neurula rotation. Epidermis cilia moved in a wavy and serpentine way like sperm flagella but not in a rotational way or beating way with effective stroke and recovery stroke. They moved very slowly, at 1/7 Hz, consistent with the low angular velocity of neurula rotation (ca. 43°/min). The tips of most cilia pointed in the opposite direction of embryonic rotation. Similar motility was also observed in Ciona robusta embryos. When embryos were treated with a dynein inhibitor, Ciliobrevin D, both ciliary movements and neurula rotation were abrogated, showing that ciliary movements drive neurula rotation in Halocynthia. The drug also inhibited Ciona neurula rotation. Our observations suggest that the driving force of rotation is generated using the vitelline membrane as a substrate but not by making a water current around the embryo. It is of evolutionary interest that ascidians use ciliary movements to break embryonic left-right symmetry, like in many vertebrates. Meanwhile, ascidian embryos rotate as a whole, similar to embryos of non-vertebrate deuterostomes, such as echinoderm, hemichordate, and amphioxus, while swimming.

@article{doi101016jydbio201807023,
    author = "Yamada, Shiori and Tanaka, Yuka and Imai, Kaoru S and Saigou, Motohiko and Onuma, Takeshi A and Nishida, Hiroki",
    title = "Wavy movements of epidermis monocilia drive the neurula rotation that determines left-right asymmetry in ascidian embryos.",
    year = "2019",
    journal = "Developmental biology",
    abstract = "Tadpole larvae of the ascidian, Halocynthia roretzi, show morphological left-right asymmetry in the brain structures and the orientation of tail bending within the vitelline membrane. Neurula embryos rotate along the anterior-posterior axis in a counterclockwise direction, and then this rotation stops when the left side of the embryo is oriented downwards. Contact of the left-side epidermis with the vitelline membrane promotes nodal gene expression in the left-side epidermis. This is a novel mechanism in which rotation of whole embryos provides the initial cue for breaking left-right symmetry. Here we show that epidermal monocilia, which appear at the neurula rotation stage, generate the driving force for rotation. A ciliary protein, Arl13b, fused with Venus YFP was used for live imaging of ciliary movements. Although overexpression of wild-type Arl13b fusion protein resulted in aberrant movements of the cilia and abrogation of neurula rotation, mutant Arl13b fusion protein, in which the GTPase and coiled-coil domains were removed, did not affect the normal ciliary movements and neurula rotation. Epidermis cilia moved in a wavy and serpentine way like sperm flagella but not in a rotational way or beating way with effective stroke and recovery stroke. They moved very slowly, at 1/7 Hz, consistent with the low angular velocity of neurula rotation (ca. 43°/min). The tips of most cilia pointed in the opposite direction of embryonic rotation. Similar motility was also observed in Ciona robusta embryos. When embryos were treated with a dynein inhibitor, Ciliobrevin D, both ciliary movements and neurula rotation were abrogated, showing that ciliary movements drive neurula rotation in Halocynthia. The drug also inhibited Ciona neurula rotation. Our observations suggest that the driving force of rotation is generated using the vitelline membrane as a substrate but not by making a water current around the embryo. It is of evolutionary interest that ascidians use ciliary movements to break embryonic left-right symmetry, like in many vertebrates. Meanwhile, ascidian embryos rotate as a whole, similar to embryos of non-vertebrate deuterostomes, such as echinoderm, hemichordate, and amphioxus, while swimming.",
    url = "https://pubmed.ncbi.nlm.nih.gov/30059669/",
    doi = "10.1016/j.ydbio.2018.07.023",
    openalex = "W2884515397",
    pmid = "30059669",
    references = "doi101016jcell200504008, doi101016jcub200610067, doi101016jydbio201303021, doi101016s0092867400817055, doi101038nature00849, doi101038nature10936, doi101083jcb200908133, doi101242dev01772, doi101242dev100560, doi101242jcs02818"
}

@misc{arumugam2020ascidians,
    author = "Arumugam, Velusamy and Venkatesan, Manigandan and Ramachandran, Karthik and Sundaresan, Umamaheswari and Ramachandran, Saravanan",
    title = "Ascidians",
    year = "2020",
    booktitle = "Encyclopedia of Marine Biotechnology",
    url = "https://doi.org/10.1002/9781119143802.ch113",
    doi = "10.1002/9781119143802.ch113",
    pages = "2487-2508"
}

Ciona robusta (Ciona intestinalis type A), a model organism for biological studies, belongs to ascidians, the main class of tunicates, which are the closest relatives of vertebrates. In Ciona, a project on the ontology of both development and anatomy is ongoing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified until the hatching larva stage. Here, we present its extension throughout the swimming larva stages, the metamorphosis, until the juvenile stages. For standardizing the developmental ontology, we acquired different time-lapse movies, confocal microscope images and histological serial section images for each developmental event from the hatching larva stage (17.5 h post fertilization) to the juvenile stage (7 days post fertilization). Combining these data, we defined 12 new distinct developmental stages (from Stage 26 to Stage 37), in addition to the previously defined 26 stages, referred to embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile. To build the anatomical ontology, 203 anatomical entities were identified, defined according to the literature, and annotated, taking advantage from the high resolution and the complementary information obtained from confocal microscopy and histology. The ontology describes the anatomical entities in hierarchical levels, from the cell level (cell lineage) to the tissue/organ level. Comparing the number of entities during development, we found two rounds on entity increase: in addition to the one occurring after fertilization, there is a second one during the Body Axis Rotation Period, when juvenile structures appear. Vice versa, one-third of anatomical entities associated with the embryo/larval life were significantly reduced at the beginning of metamorphosis. Data was finally integrated within the web-based resource "TunicAnatO", which includes a number of anatomical images and a dictionary with synonyms. This ontology will allow the standardization of data underpinning an accurate annotation of gene expression and the comprehension of mechanisms of differentiation. It will help in understanding the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.

@article{doi101038s41598020735449,
    author = "Hotta, K. and Dauga, Delphine and Manni, L.",
    title = "The ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis",
    year = "2020",
    journal = "Scientific Reports",
    abstract = {Ciona robusta (Ciona intestinalis type A), a model organism for biological studies, belongs to ascidians, the main class of tunicates, which are the closest relatives of vertebrates. In Ciona, a project on the ontology of both development and anatomy is ongoing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified until the hatching larva stage. Here, we present its extension throughout the swimming larva stages, the metamorphosis, until the juvenile stages. For standardizing the developmental ontology, we acquired different time-lapse movies, confocal microscope images and histological serial section images for each developmental event from the hatching larva stage (17.5 h post fertilization) to the juvenile stage (7 days post fertilization). Combining these data, we defined 12 new distinct developmental stages (from Stage 26 to Stage 37), in addition to the previously defined 26 stages, referred to embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile. To build the anatomical ontology, 203 anatomical entities were identified, defined according to the literature, and annotated, taking advantage from the high resolution and the complementary information obtained from confocal microscopy and histology. The ontology describes the anatomical entities in hierarchical levels, from the cell level (cell lineage) to the tissue/organ level. Comparing the number of entities during development, we found two rounds on entity increase: in addition to the one occurring after fertilization, there is a second one during the Body Axis Rotation Period, when juvenile structures appear. Vice versa, one-third of anatomical entities associated with the embryo/larval life were significantly reduced at the beginning of metamorphosis. Data was finally integrated within the web-based resource "TunicAnatO", which includes a number of anatomical images and a dictionary with synonyms. This ontology will allow the standardization of data underpinning an accurate annotation of gene expression and the comprehension of mechanisms of differentiation. It will help in understanding the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.},
    url = "https://www.nature.com/articles/s41598-020-73544-9.pdf",
    doi = "10.1038/s41598-020-73544-9",
    is_oa = "true",
    number = "1",
    semanticscholar_citation_count = "44",
    semanticscholar_id = "5d4626a8cfef73e4d3673532c431a1c0fedf2c31",
    volume = "10",
    references = "doi101007s004270050011, doi101093icb224817"
}

Ciliary movement is a fundamental process to support animal life, and the movement pattern may be altered in response to external stimuli under the control of nervous systems. Juvenile and adult ascidians have ciliary arrays around their pharyngeal gill slits (stigmata), and continuous beating is interrupted for seconds by mechanical stimuli on other parts of the body. Although it has been suggested that neural transmission to evoke ciliary arrest is cholinergic, its molecular basis has not yet been elucidated in detail. Here, we attempted to clarify the molecular mechanisms underlying this neurociliary transmission in the model ascidian Ciona Acetylcholinesterase histochemical staining showed strong signals on the laterodistal ciliated cells of stigmata, hereafter referred to as trapezial cells. The direct administration of acetylcholine (ACh) and other agonists of nicotinic ACh receptors (nAChRs) onto ciliated cells reliably evoked ciliary arrest that persisted for seconds in a dose-dependent manner. While the Ciona genome encodes ten nAChRs, only one of these called nAChR-A7/8-1, a relative of vertebrate α7 nAChRs, was found to be expressed by trapezial cells. Exogenously expressed nAChR-A7/8-1 on Xenopus oocytes responded to ACh and other agonists with consistent pharmacological traits to those observed in vivo Further efforts to examine signaling downstream of this receptor revealed that an inhibitor of phospholipase C (PLC) hampered ACh-induced ciliary arrest. We propose that homomeric α7-related nAChR-A7/8-1 mediates neurociliary transmission in Ciona stigmata to elicit persistent ciliary arrest by recruiting intracellular Ca2+ signaling.

@article{doi101242jeb209320,
    author = "Jokura, Kei and Nishino, Junko M and Ogasawara, Michio and Nishino, Atsuo",
    title = "An α7-related nicotinic acetylcholine receptor mediates the ciliary arrest response in pharyngeal gill slits of Ciona.",
    year = "2020",
    journal = "The Journal of experimental biology",
    abstract = "Ciliary movement is a fundamental process to support animal life, and the movement pattern may be altered in response to external stimuli under the control of nervous systems. Juvenile and adult ascidians have ciliary arrays around their pharyngeal gill slits (stigmata), and continuous beating is interrupted for seconds by mechanical stimuli on other parts of the body. Although it has been suggested that neural transmission to evoke ciliary arrest is cholinergic, its molecular basis has not yet been elucidated in detail. Here, we attempted to clarify the molecular mechanisms underlying this neurociliary transmission in the model ascidian Ciona Acetylcholinesterase histochemical staining showed strong signals on the laterodistal ciliated cells of stigmata, hereafter referred to as trapezial cells. The direct administration of acetylcholine (ACh) and other agonists of nicotinic ACh receptors (nAChRs) onto ciliated cells reliably evoked ciliary arrest that persisted for seconds in a dose-dependent manner. While the Ciona genome encodes ten nAChRs, only one of these called nAChR-A7/8-1, a relative of vertebrate α7 nAChRs, was found to be expressed by trapezial cells. Exogenously expressed nAChR-A7/8-1 on Xenopus oocytes responded to ACh and other agonists with consistent pharmacological traits to those observed in vivo Further efforts to examine signaling downstream of this receptor revealed that an inhibitor of phospholipase C (PLC) hampered ACh-induced ciliary arrest. We propose that homomeric α7-related nAChR-A7/8-1 mediates neurociliary transmission in Ciona stigmata to elicit persistent ciliary arrest by recruiting intracellular Ca2+ signaling.",
    url = "https://pubmed.ncbi.nlm.nih.gov/32220975/",
    doi = "10.1242/jeb.209320",
    openalex = "W3013390895",
    pmid = "32220975",
    references = "doi101007s00441019030355, doi101016089662739090344f, doi101016jceca200308006, doi101016s0021925818543623, doi101016s0022356525130346, doi101016s0022356525229676, doi101073pnas90156971, doi101113jphysiol1987sp016883, doi101126science1080049, doi101177123219, doi101523jneurosci1302005961993"
}

A mucous secreting organ in ascidians, the endostyle, consists of several epithelial zones with different ciliary length, density, and beating direction. Here we found by transmission electron microscopy that long cilia in endostyle zone 1 showed 9 + 2 axonemal structures but completely lacked the outer arm dynein. In contrast, cilia in other zones bore both outer and inner dynein arms. Western blotting and immunofluorescence microscopy further revealed that zone 1 appeared to lack not only outer arm dynein but also two-headed inner arm dynein. These results suggest a mechanism for a region-specific gene suppression that causes the limited loss of two-headed axonemal dyneins in the endostyle epithelium. The loss of these dyneins in zone 1 is considered to contribute to the generation of undulating ciliary movement that is essential for a unique circuit of mucus flow in the endostyle.

@article{doi102108zs200095,
    author = "Konno, Alu and Inaba, Kazuo",
    title = "Region-Specific Loss of Two-Headed Ciliary Dyneins in Ascidian Endostyle.",
    year = "2020",
    journal = "Zoological science",
    abstract = "A mucous secreting organ in ascidians, the endostyle, consists of several epithelial zones with different ciliary length, density, and beating direction. Here we found by transmission electron microscopy that long cilia in endostyle zone 1 showed 9 + 2 axonemal structures but completely lacked the outer arm dynein. In contrast, cilia in other zones bore both outer and inner dynein arms. Western blotting and immunofluorescence microscopy further revealed that zone 1 appeared to lack not only outer arm dynein but also two-headed inner arm dynein. These results suggest a mechanism for a region-specific gene suppression that causes the limited loss of two-headed axonemal dyneins in the endostyle epithelium. The loss of these dyneins in zone 1 is considered to contribute to the generation of undulating ciliary movement that is essential for a unique circuit of mucus flow in the endostyle.",
    url = "https://pubmed.ncbi.nlm.nih.gov/33269866/",
    doi = "10.2108/zs200095",
    openalex = "W3096892882",
    pmid = "33269866",
    references = "doi101002cm970080110, doi101016jcub200607012, doi101038227680a0, doi101038nature07471, doi101038ng1106, doi101038ng2707, doi101083jcb1515f37, doi101083jcb913107s, doi101093molehrgar034, doi101126science1084576"
}

The spatiotemporal expression of zygotic genes is regulated by transcription factors, which mediate cell fate decision and morphogenesis. Investigation of the expression patterns and their transcriptional regulatory relationships is crucial to understand embryonic development. Staged RNA-seq of the ascidian Halocynthia roretzi has previously shown that nine genes encoding transcription factors are transiently expressed at the blastula stage, which is the stage at which cell fates are specified and differentiation starts. Six of these transcription factors have already been found to play important roles during early development. However, the functions of the other transcription factors (FoxJ-r, SoxF, and SP8/9) remain unknown. The study of the spatial and temporal expression patterns showed that all three genes were expressed in the animal hemisphere as early as the 16-cell stage. This is likely due to transcription factor genes that are expressed in the vegetal hemisphere, which have been extensively and comprehensively analyzed in previous studies of ascidians. Functional analyses using FoxJ-r morphants showed that they resulted in the disruption of laterality and the absence of epidermal mono-cilia, suggesting FoxJ-r functions in cilia formation and, consequently, in the generation of left-right asymmetry, as observed in vertebrates. SoxF knockdown resulted in incomplete epiboly by the ectoderm during gastrulation, while SP8/9 knockdown showed no phenotype until the tailbud stage in the present study, although it was expressed during blastula stages. Our results indicate that transcription factor genes expressed at the cleavage stages play roles in diverse functions, and are not limited to cell fate specification.

@article{doi102108zs200128,
    author = "Shih, Yu and Wang, Kai and Kumano, Gaku and Nishida, Hiroki",
    title = "Expression and Functional Analyses of Ectodermal Transcription Factors FoxJ-r, SoxF, and SP8/9 in Early Embryos of the Ascidian Halocynthia roretzi",
    year = "2020",
    journal = "ZOOLOGICAL SCIENCE",
    abstract = "The spatiotemporal expression of zygotic genes is regulated by transcription factors, which mediate cell fate decision and morphogenesis. Investigation of the expression patterns and their transcriptional regulatory relationships is crucial to understand embryonic development. Staged RNA-seq of the ascidian Halocynthia roretzi has previously shown that nine genes encoding transcription factors are transiently expressed at the blastula stage, which is the stage at which cell fates are specified and differentiation starts. Six of these transcription factors have already been found to play important roles during early development. However, the functions of the other transcription factors (FoxJ-r, SoxF, and SP8/9) remain unknown. The study of the spatial and temporal expression patterns showed that all three genes were expressed in the animal hemisphere as early as the 16-cell stage. This is likely due to transcription factor genes that are expressed in the vegetal hemisphere, which have been extensively and comprehensively analyzed in previous studies of ascidians. Functional analyses using FoxJ-r morphants showed that they resulted in the disruption of laterality and the absence of epidermal mono-cilia, suggesting FoxJ-r functions in cilia formation and, consequently, in the generation of left-right asymmetry, as observed in vertebrates. SoxF knockdown resulted in incomplete epiboly by the ectoderm during gastrulation, while SP8/9 knockdown showed no phenotype until the tailbud stage in the present study, although it was expressed during blastula stages. Our results indicate that transcription factor genes expressed at the cleavage stages play roles in diverse functions, and are not limited to cell fate specification.",
    url = "https://doi.org/10.2108/zs200128",
    doi = "10.2108/zs200128",
    openalex = "W3113189041",
    references = "doi101016jydbio201807023"
}

@article{doi101016jfsi202110022,
    author = "Longo, Valeria and Parrinello, Daniela and Longo, Alessandra and Parisi, Maria Giovanna and Parrinello, Nicolò and Colombo, Paolo and Cammarata, Matteo",
    title = "The conservation and diversity of ascidian cells and molecules involved in the inflammatory reaction: The Ciona robusta model",
    year = "2021",
    journal = "Fish \& Shellfish Immunology",
    url = "https://doi.org/10.1016/j.fsi.2021.10.022",
    doi = "10.1016/j.fsi.2021.10.022",
    openalex = "W3205664997",
    references = "doi1010160022175977900552"
}

Cionin is a homolog of vertebrate cholecystokinin/gastrin that has been identified in the ascidian Ciona intestinalis type A. The phylogenetic position of ascidians as the closest living relatives of vertebrates suggests that cionin can provide clues to the evolution of endocrine/neuroendocrine systems throughout chordates. Here, we show the biological role of cionin in the regulation of ovulation. In situ hybridization demonstrated that the mRNA of the cionin receptor, Cior2, was expressed specifically in the inner follicular cells of pre-ovulatory follicles in the Ciona ovary. Cionin was found to significantly stimulate ovulation after 24-h incubation. Transcriptome and subsequent Real-time PCR analyses confirmed that the expression levels of receptor tyrosine kinase (RTK) signaling genes and a matrix metalloproteinase (MMP) gene were significantly elevated in the cionin-treated follicles. Of particular interest is that an RTK inhibitor and MMP inhibitor markedly suppressed the stimulatory effect of cionin on ovulation. Furthermore, inhibition of RTK signaling reduced the MMP gene expression in the cionin-treated follicles. These results provide evidence that cionin induces ovulation by stimulating MMP gene expression via the RTK signaling pathway. This is the first report on the endogenous roles of cionin and the induction of ovulation by cholecystokinin/gastrin family peptides in an organism.

@article{doi101038s41598021902953,
    author = "Osugi, Tomohiro and Miyasaka, Natsuko and Shiraishi, A. and Matsubara, Shin and Satake, H.",
    title = "Cionin, a vertebrate cholecystokinin/gastrin homolog, induces ovulation in the ascidian Ciona intestinalis type A",
    year = "2021",
    journal = "Scientific Reports",
    abstract = "Cionin is a homolog of vertebrate cholecystokinin/gastrin that has been identified in the ascidian Ciona intestinalis type A. The phylogenetic position of ascidians as the closest living relatives of vertebrates suggests that cionin can provide clues to the evolution of endocrine/neuroendocrine systems throughout chordates. Here, we show the biological role of cionin in the regulation of ovulation. In situ hybridization demonstrated that the mRNA of the cionin receptor, Cior2, was expressed specifically in the inner follicular cells of pre-ovulatory follicles in the Ciona ovary. Cionin was found to significantly stimulate ovulation after 24-h incubation. Transcriptome and subsequent Real-time PCR analyses confirmed that the expression levels of receptor tyrosine kinase (RTK) signaling genes and a matrix metalloproteinase (MMP) gene were significantly elevated in the cionin-treated follicles. Of particular interest is that an RTK inhibitor and MMP inhibitor markedly suppressed the stimulatory effect of cionin on ovulation. Furthermore, inhibition of RTK signaling reduced the MMP gene expression in the cionin-treated follicles. These results provide evidence that cionin induces ovulation by stimulating MMP gene expression via the RTK signaling pathway. This is the first report on the endogenous roles of cionin and the induction of ovulation by cholecystokinin/gastrin family peptides in an organism.",
    url = "https://www.nature.com/articles/s41598-021-90295-3.pdf",
    doi = "10.1038/s41598-021-90295-3",
    is_oa = "true",
    number = "1",
    semanticscholar_citation_count = "10",
    semanticscholar_id = "aa3678451ba997b1e9606a005be4f2989934bfcd",
    volume = "11"
}

ABSTRACT Background Left-right asymmetries are a common feature of metazoan nervous systems. This is particularly pronounced in the comparatively simple larval central nervous system (CNS) of the tunicate Ciona, whose swimming tadpole larva shows a clear chordate ground plan. While common pathway elements for specifying the left-right axis are found in the chordates, particularly a requirement for Nodal signaling, Ciona differs from its vertebrate cousins by specifying its axis at the neurula stage, rather than at gastrula. Additionally, Ciona, and other ascidians, have a requirement for an intact chorionic membrane for proper left/right specification. Results We present here results showing that left-right asymmetry disruptions caused by removal of the chorion (dechorionation) are highly variable and present throughout the Ciona larval nervous system. While previous studies have documented disruptions to the conspicuously asymmetric sensory systems in the anterior brain vesicle, we document asymmetries in seemingly symmetric structures such as the posterior brain vesicle and motor ganglion. Moreover, defects caused by dechorionation include misplaced or absent neuron classes, loss of asymmetric gene expression, aberrant synaptic connectivity, and abnormal behaviors. In the motor ganglion, a brain structure that has been equated with the vertebrate hindbrain, we find that despite the apparent left/right symmetric distribution of interneurons and motor neurons, AMPA receptors are expressed exclusively on the left side, which equates with asymmetric swimming behaviors. We also find that within a population of dechorionated larvae, there is a small percentage with apparently normal left-right specification, and approximately equal population with inverted (mirror-image) asymmetry. We present a method based on a behavioral assay for isolating these larvae. When these two classes of larvae (normal and inverted) are assessed in a light dimming assay they display mirror-image behaviors, with normal larvae responding with counterclockwise swims, while inverted larvae respond with clockwise swims. Conclusions Our findings highlight the importance of left-right specification pathways not only for proper CNS anatomy, but also for correct synaptic connectivity and behavior.

@misc{doi10110120210303433807,
    author = "Kourakis, Matthew J. and Bostwick, Michaela and Zabriskie, Amanda and Smith, William C.",
    title = "Left/right asymmetry disruptions and mirror-image reversals to behavior and brain anatomy in Ciona",
    year = "2021",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "ABSTRACT Background Left-right asymmetries are a common feature of metazoan nervous systems. This is particularly pronounced in the comparatively simple larval central nervous system (CNS) of the tunicate Ciona, whose swimming tadpole larva shows a clear chordate ground plan. While common pathway elements for specifying the left-right axis are found in the chordates, particularly a requirement for Nodal signaling, Ciona differs from its vertebrate cousins by specifying its axis at the neurula stage, rather than at gastrula. Additionally, Ciona, and other ascidians, have a requirement for an intact chorionic membrane for proper left/right specification. Results We present here results showing that left-right asymmetry disruptions caused by removal of the chorion (dechorionation) are highly variable and present throughout the Ciona larval nervous system. While previous studies have documented disruptions to the conspicuously asymmetric sensory systems in the anterior brain vesicle, we document asymmetries in seemingly symmetric structures such as the posterior brain vesicle and motor ganglion. Moreover, defects caused by dechorionation include misplaced or absent neuron classes, loss of asymmetric gene expression, aberrant synaptic connectivity, and abnormal behaviors. In the motor ganglion, a brain structure that has been equated with the vertebrate hindbrain, we find that despite the apparent left/right symmetric distribution of interneurons and motor neurons, AMPA receptors are expressed exclusively on the left side, which equates with asymmetric swimming behaviors. We also find that within a population of dechorionated larvae, there is a small percentage with apparently normal left-right specification, and approximately equal population with inverted (mirror-image) asymmetry. We present a method based on a behavioral assay for isolating these larvae. When these two classes of larvae (normal and inverted) are assessed in a light dimming assay they display mirror-image behaviors, with normal larvae responding with counterclockwise swims, while inverted larvae respond with clockwise swims. Conclusions Our findings highlight the importance of left-right specification pathways not only for proper CNS anatomy, but also for correct synaptic connectivity and behavior.",
    url = "https://doi.org/10.1101/2021.03.03.433807",
    doi = "10.1101/2021.03.03.433807",
    openalex = "W3135056905",
    references = "doi101016jydbio201807023"
}

ABSTRACT Swimming locomotion in aquatic vertebrates, such as fish and tadpoles, is expressed through orchestrated operations of central pattern generators. These parallel neuronal circuits are ubiquitously distributed and mutually coupled along the spinal cord to express undulation patterns accommodated to efferent and afferent inputs. While such sets of schemes have been shown in vertebrates, the evolutionary origin of those mechanisms along the chordate phylogeny remains unclear. Ascidians, representing a sister group of vertebrates, give rise to tadpole larvae that freely swim in seawater. In this study, we tried to locate the swimming pattern generator in larvae of the ascidian Ciona by examining locomotor ability of segmented body fragments. Our experiments demonstrated necessary and sufficient pattern generator activity in a short region (∼10% of the body length as the longest estimation) including the trunk-tail junction but excluding most of the trunk and tail with major sensory apparatuses therein. Moreover, we found that these “mid-piece” body fragments express periodic tail beating bursts with ∼20-s intervals without any exogenous stimuli. Comparisons among temporal patterns of tail beating bursts expressed by the mid-piece fragments and by whole larvae placed under different sensory conditions suggested that the presence of parts other than the critical mid-piece had effects to shorten swimming burst intervals, especially in the dark, and also to expand the variance in burst durations. We propose that Ciona larvae perform swimming as modified representations of autonomous and periodic pattern generator drives, which operate locally in the region of the trunk-tail junction. Summary statement Mid-piece fragments of tadpole larvae of the ascidian Ciona, lacking most of the anterior trunk and posterior tail, autonomously and periodically express tail beating bursts.

@misc{doi10110120210412439438,
    author = "Hara, T and Hasegawa, Shuya and Iwatani, Yasushi and Nishino, Atsuo",
    title = "An autonomous tail-beating cycle period expressed by a region- specific swimming pattern generator in the Ciona larva",
    year = "2021",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "ABSTRACT Swimming locomotion in aquatic vertebrates, such as fish and tadpoles, is expressed through orchestrated operations of central pattern generators. These parallel neuronal circuits are ubiquitously distributed and mutually coupled along the spinal cord to express undulation patterns accommodated to efferent and afferent inputs. While such sets of schemes have been shown in vertebrates, the evolutionary origin of those mechanisms along the chordate phylogeny remains unclear. Ascidians, representing a sister group of vertebrates, give rise to tadpole larvae that freely swim in seawater. In this study, we tried to locate the swimming pattern generator in larvae of the ascidian Ciona by examining locomotor ability of segmented body fragments. Our experiments demonstrated necessary and sufficient pattern generator activity in a short region (∼10\% of the body length as the longest estimation) including the trunk-tail junction but excluding most of the trunk and tail with major sensory apparatuses therein. Moreover, we found that these “mid-piece” body fragments express periodic tail beating bursts with ∼20-s intervals without any exogenous stimuli. Comparisons among temporal patterns of tail beating bursts expressed by the mid-piece fragments and by whole larvae placed under different sensory conditions suggested that the presence of parts other than the critical mid-piece had effects to shorten swimming burst intervals, especially in the dark, and also to expand the variance in burst durations. We propose that Ciona larvae perform swimming as modified representations of autonomous and periodic pattern generator drives, which operate locally in the region of the trunk-tail junction. Summary statement Mid-piece fragments of tadpole larvae of the ascidian Ciona, lacking most of the anterior trunk and posterior tail, autonomously and periodically express tail beating bursts.",
    url = "https://doi.org/10.1101/2021.04.12.439438",
    doi = "10.1101/2021.04.12.439438",
    openalex = "W3156475079",
    references = "doi101242jeb209320"
}

Based on transcription factor expression, location, and developmental origin, we conclude that the sea urchin larval photoreceptors constitute a cell type that is likely homologous to the ciliary photoreceptors present in chordates.

@article{doi101186s1291502101194y,
    author = "Valencia, Jonathan E. and Feuda, Roberto and Mellott, Dan O and Burke, Robert D. and Peter, Isabelle S.",
    title = "Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation",
    year = "2021",
    journal = "BMC Biology",
    abstract = "Based on transcription factor expression, location, and developmental origin, we conclude that the sea urchin larval photoreceptors constitute a cell type that is likely homologous to the ciliary photoreceptors present in chordates.",
    url = "https://doi.org/10.1186/s12915-021-01194-y",
    doi = "10.1186/s12915-021-01194-y",
    openalex = "W4225759254",
    references = "doi101016jydbio201610014"
}

During evolution, new characters are designed by modifying pre-existing structures already present in ancient organisms. In this perspective, the Central Nervous System (CNS) of ascidian larva offers a good opportunity to analyze a complex phenomenon with a simplified approach. As sister group of vertebrates, ascidian tadpole larva exhibits a dorsal CNS, made up of only about 330 cells distributed into the anterior sensory brain vesicle (BV), connected to the motor ganglion (MG) and a caudal nerve cord (CNC) in the tail. Low number of cells does not mean, however, low complexity. The larval brain contains 177 neurons, for which a documented synaptic connectome is now available, and two pigmented organs, the otolith and the ocellus, controlling larval swimming behavior. The otolith is involved in gravity perception and the ocellus in light perception. Here, we specifically review the studies focused on the development of the building blocks of ascidians pigmented sensory organs, namely pigment cells and photoreceptor cells. We focus on what it is known, up to now, on the molecular bases of specification and differentiation of both lineages, on the function of these organs after larval hatching during pre-settlement period, and on the most cutting-edge technologies, like single cell RNAseq and genome editing CRISPR/CAS9, that, adapted and applied to Ciona embryos, are increasingly enhancing the tractability of Ciona for developmental studies, including pigmented organs formation.

@article{doi103389fcell2021701779,
    author = "Olivo, Paola and Palladino, A. and Ristoratore, F. and Spagnuolo, A.",
    title = "Brain Sensory Organs of the Ascidian Ciona robusta: Structure, Function and Developmental Mechanisms",
    year = "2021",
    journal = "Frontiers in Cell and Developmental Biology",
    abstract = "During evolution, new characters are designed by modifying pre-existing structures already present in ancient organisms. In this perspective, the Central Nervous System (CNS) of ascidian larva offers a good opportunity to analyze a complex phenomenon with a simplified approach. As sister group of vertebrates, ascidian tadpole larva exhibits a dorsal CNS, made up of only about 330 cells distributed into the anterior sensory brain vesicle (BV), connected to the motor ganglion (MG) and a caudal nerve cord (CNC) in the tail. Low number of cells does not mean, however, low complexity. The larval brain contains 177 neurons, for which a documented synaptic connectome is now available, and two pigmented organs, the otolith and the ocellus, controlling larval swimming behavior. The otolith is involved in gravity perception and the ocellus in light perception. Here, we specifically review the studies focused on the development of the building blocks of ascidians pigmented sensory organs, namely pigment cells and photoreceptor cells. We focus on what it is known, up to now, on the molecular bases of specification and differentiation of both lineages, on the function of these organs after larval hatching during pre-settlement period, and on the most cutting-edge technologies, like single cell RNAseq and genome editing CRISPR/CAS9, that, adapted and applied to Ciona embryos, are increasingly enhancing the tractability of Ciona for developmental studies, including pigmented organs formation.",
    url = "https://www.frontiersin.org/articles/10.3389/fcell.2021.701779/pdf",
    doi = "10.3389/fcell.2021.701779",
    is_oa = "true",
    semanticscholar_citation_count = "12",
    semanticscholar_id = "a66c1a941a2e8c11d77a89364f8f4c9856b289fa",
    volume = "9"
}

The locomotor system is highly bilateral at the macroscopic level. Homochirality of biological molecules is fully compatible with the bilateral body. However, whether and how single-handed cells contribute to the bilateral locomotor system is obscure. Here, exploiting the small number of cells in the swimming tadpole larva of the ascidian Ciona, we analyzed morphology of the tail at cellular and subcellular scales. Quantitative phase-contrast X-ray tomographic microscopy revealed a high-density midline structure ventral to the notochord in the tail. Muscle cell nuclei on each side of the notochord were roughly bilaterally aligned. However, fluorescence microscopy detected left-right asymmetry of myofibril inclination relative to the longitudinal axis of the tail. Zernike phase-contrast X-ray tomographic microscopy revealed the presence of left-handed helices of myofibrils in muscle cells on both sides. Therefore, the locomotor system of ascidian larvae harbors symmetry-breaking left-handed helical cells, while maintaining bilaterally symmetrical cell alignment. These results suggest that bilateral animals can override cellular homochirality to generate the bilateral locomotor systems at the supracellular scale.

@article{doi103389fcell2021800455,
    author = "Matsuo, Koichi and Tamura, Ryota and Hotta, Kohji and Okada, Mayu and Takeuchi, Akihisa and Wu, Yanlin and Hashimoto, Koh and Takano, Hidekazu and Momose, Atsushi and Nishino, Atsuo",
    title = "Bilaterally Asymmetric Helical Myofibrils in Ascidian Tadpole Larvae",
    year = "2021",
    journal = "Frontiers in Cell and Developmental Biology",
    abstract = "The locomotor system is highly bilateral at the macroscopic level. Homochirality of biological molecules is fully compatible with the bilateral body. However, whether and how single-handed cells contribute to the bilateral locomotor system is obscure. Here, exploiting the small number of cells in the swimming tadpole larva of the ascidian Ciona, we analyzed morphology of the tail at cellular and subcellular scales. Quantitative phase-contrast X-ray tomographic microscopy revealed a high-density midline structure ventral to the notochord in the tail. Muscle cell nuclei on each side of the notochord were roughly bilaterally aligned. However, fluorescence microscopy detected left-right asymmetry of myofibril inclination relative to the longitudinal axis of the tail. Zernike phase-contrast X-ray tomographic microscopy revealed the presence of left-handed helices of myofibrils in muscle cells on both sides. Therefore, the locomotor system of ascidian larvae harbors symmetry-breaking left-handed helical cells, while maintaining bilaterally symmetrical cell alignment. These results suggest that bilateral animals can override cellular homochirality to generate the bilateral locomotor systems at the supracellular scale.",
    url = "https://doi.org/10.3389/fcell.2021.800455",
    doi = "10.3389/fcell.2021.800455",
    openalex = "W4200404911",
    references = "doi101016jydbio201807023"
}

Oxytocin (OT) and vasopressin (VP) superfamily neuropeptides are distributed in not only vertebrates but also diverse invertebrates. However, no VPergic innervation of invertebrates has ever been documented. In the ascidian, Ciona intestinalis Type A (Ciona robusta), an OT/VP superfamily peptide was identified, and the Ciona vasopressin (CiVP) induces oocyte maturation and ovulation. In the present study, we characterize the innervation and phenotypes of genetically modified Ciona: CiVP promoter-Venus transgenic and CiVP mutants. CiVP promoter-Venus transgenic Ciona demonstrated that CiVP gene was highly expressed in the cerebral ganglion and several nerves. Fluorescence was also detected in the ovary of young CiVP promoter-Venus transgenic ascidians, suggesting that the CiVP gene is also expressed temporarily in the ovary of young ascidians. Furthermore, a marked decrease of post-vitellogenic (stage III) follicles was observed in the ovary of CiVP mutants, whereas pre-vitellogenic (stage I) and vitellogenic (stage II) follicles were increased in the mutant ovary, compared with that of wildtype Ciona. Gene expression profiles showed that the expression of various genes, including genes related to ovarian follicle growth, was altered in the ovary of CiVP mutants. Altogether, these results indicated that CiVP, mainly as a neuropeptide, plays pivotal roles in diverse biological functions, including growth of early-stage ovarian follicles via regulation of the expression of a wide variety of genes. This is the first report describing a VP gene promoter-transgenic and VP gene-edited invertebrate and also on its gene expression profiles and phenotypes.

@article{doi103389fendo2021668564,
    author = "Kawada, T. and Shiraishi, A. and Matsubara, Shin and Hozumi, Akiko and Horie, T. and Sasakura, Y. and Satake, H.",
    title = "Vasopressin Promoter Transgenic and Vasopressin Gene-Edited Ascidian, Ciona intestinalis Type A (Ciona robusta): Innervation, Gene Expression Profiles, and Phenotypes",
    year = "2021",
    journal = "Frontiers in Endocrinology",
    abstract = "Oxytocin (OT) and vasopressin (VP) superfamily neuropeptides are distributed in not only vertebrates but also diverse invertebrates. However, no VPergic innervation of invertebrates has ever been documented. In the ascidian, Ciona intestinalis Type A (Ciona robusta), an OT/VP superfamily peptide was identified, and the Ciona vasopressin (CiVP) induces oocyte maturation and ovulation. In the present study, we characterize the innervation and phenotypes of genetically modified Ciona: CiVP promoter-Venus transgenic and CiVP mutants. CiVP promoter-Venus transgenic Ciona demonstrated that CiVP gene was highly expressed in the cerebral ganglion and several nerves. Fluorescence was also detected in the ovary of young CiVP promoter-Venus transgenic ascidians, suggesting that the CiVP gene is also expressed temporarily in the ovary of young ascidians. Furthermore, a marked decrease of post-vitellogenic (stage III) follicles was observed in the ovary of CiVP mutants, whereas pre-vitellogenic (stage I) and vitellogenic (stage II) follicles were increased in the mutant ovary, compared with that of wildtype Ciona. Gene expression profiles showed that the expression of various genes, including genes related to ovarian follicle growth, was altered in the ovary of CiVP mutants. Altogether, these results indicated that CiVP, mainly as a neuropeptide, plays pivotal roles in diverse biological functions, including growth of early-stage ovarian follicles via regulation of the expression of a wide variety of genes. This is the first report describing a VP gene promoter-transgenic and VP gene-edited invertebrate and also on its gene expression profiles and phenotypes.",
    url = "https://www.frontiersin.org/articles/10.3389/fendo.2021.668564/pdf",
    doi = "10.3389/fendo.2021.668564",
    is_oa = "true",
    semanticscholar_citation_count = "11",
    semanticscholar_id = "568cc74ebef80e931d381d65fa6a647161cd203d",
    volume = "12"
}

Conserved transcription factors termed "terminal selectors" regulate neuronal sub-type specification and differentiation through combinatorial transcriptional regulation of terminal differentiation genes. The unique combinations of terminal differentiation gene products in turn contribute to the functional identities of each neuron. One well-characterized terminal selector is COE (Collier/Olf/Ebf), which has been shown to activate cholinergic gene batteries in C. elegans motor neurons. However, its functions in other metazoans, particularly chordates, is less clear. Here we show that the sole COE ortholog in the non-vertebrate chordate Ciona robusta, Ebf, controls the expression of the cholinergic locus VAChT/ChAT in a single dorsal interneuron of the larval Motor Ganglion, which is presumed to be homologous to the vertebrate spinal cord. We propose that, while the function of Ebf as a regulator of cholinergic neuron identity conserved across bilaterians, its exact role may have diverged in different cholinergic neuron subtypes (e.g., interneurons vs. motor neurons) in chordate-specific motor circuits.

@article{doi103389fnins2021784649,
    author = "Popsuj, Sydney and Stolfi, Alberto",
    title = "Ebf Activates Expression of a Cholinergic Locus in a Multipolar Motor Ganglion Interneuron Subtype in Ciona",
    year = "2021",
    journal = "Frontiers in Neuroscience",
    abstract = {Conserved transcription factors termed "terminal selectors" regulate neuronal sub-type specification and differentiation through combinatorial transcriptional regulation of terminal differentiation genes. The unique combinations of terminal differentiation gene products in turn contribute to the functional identities of each neuron. One well-characterized terminal selector is COE (Collier/Olf/Ebf), which has been shown to activate cholinergic gene batteries in C. elegans motor neurons. However, its functions in other metazoans, particularly chordates, is less clear. Here we show that the sole COE ortholog in the non-vertebrate chordate Ciona robusta, Ebf, controls the expression of the cholinergic locus VAChT/ChAT in a single dorsal interneuron of the larval Motor Ganglion, which is presumed to be homologous to the vertebrate spinal cord. We propose that, while the function of Ebf as a regulator of cholinergic neuron identity conserved across bilaterians, its exact role may have diverged in different cholinergic neuron subtypes (e.g., interneurons vs. motor neurons) in chordate-specific motor circuits.},
    url = "https://doi.org/10.3389/fnins.2021.784649",
    doi = "10.3389/fnins.2021.784649",
    openalex = "W4200276734",
    references = "doi101242jeb209320"
}

@incollection{krasovec2021solitary,
    author = "Krasovec, Gabriel and Biasuz, Kilian and Thomann, Lisa M. and Chambon, Jean-Philippe",
    title = "Solitary Ascidians",
    year = "2021",
    booktitle = "Handbook of Marine Model Organisms in Experimental Biology",
    url = "https://doi.org/10.1201/9781003217503-20",
    doi = "10.1201/9781003217503-20",
    pages = "357-384"
}

@article{doi101007s0030002203100w,
    author = "Giachetti, C. and Tatián, M. and Schwindt, E.",
    title = "Differences in the gonadal cycle between two ascidians species, Ascidiella aspersa and Ciona robusta, help to explain their invasion success in a cold temperate port",
    year = "2022",
    journal = "Polar Biology",
    url = "https://www.semanticscholar.org/paper/0e4722fac2bfff890ea1864e11638d132a643f79",
    doi = "10.1007/s00300-022-03100-w",
    is_oa = "true",
    number = "12",
    pages = "1689-1701",
    semanticscholar_citation_count = "6",
    semanticscholar_id = "0e4722fac2bfff890ea1864e11638d132a643f79",
    volume = "45"
}

Swimming locomotion in aquatic vertebrates, such as fish and tadpoles, is expressed through neuron networks in the spinal cord. These networks are arranged in parallel, ubiquitously distributed and mutually coupled along the spinal cord to express undulation patterns accommodated to various inputs into the networks. While these systems have been widely studied in vertebrate swimmers, their evolutionary origin along the chordate phylogeny remains unclear. Ascidians, representing a sister group of vertebrates, give rise to tadpole larvae that swim freely in seawater. In the present study, we examined the locomotor ability of the anterior and posterior body fragments of larvae of the ascidian Ciona that had been cut at an arbitrary position. Examination of more than 200 fragments revealed a necessary and sufficient body region that spanned only ∼10% of the body length and included the trunk-tail junction. 'Mid-piece' body fragments, which included the trunk-tail junctional region, but excluded most of the anterior trunk and posterior tail, autonomously expressed periodic tail-beating bursts at ∼20 s intervals. We compared the durations and intervals of tail-beating bursts expressed by mid-piece fragments, and also by whole larvae under different sensory conditions. The results suggest that body parts outside the mid-piece effect shortening of swimming intervals, particularly in the dark, and vary the burst duration. We propose that Ciona larvae express swimming behaviors by modifying autonomous and periodic locomotor drives that operate locally in the trunk-tail junctional region.

@article{doi101242jeb243828,
    author = "Hara, T and Hasegawa, Shuya and Iwatani, Yasushi and Nishino, Atsuo",
    title = "The trunk–tail junctional region in Ciona larvae autonomously expresses tail-beating bursts at ∼20 second intervals",
    year = "2022",
    journal = "Journal of Experimental Biology",
    abstract = "Swimming locomotion in aquatic vertebrates, such as fish and tadpoles, is expressed through neuron networks in the spinal cord. These networks are arranged in parallel, ubiquitously distributed and mutually coupled along the spinal cord to express undulation patterns accommodated to various inputs into the networks. While these systems have been widely studied in vertebrate swimmers, their evolutionary origin along the chordate phylogeny remains unclear. Ascidians, representing a sister group of vertebrates, give rise to tadpole larvae that swim freely in seawater. In the present study, we examined the locomotor ability of the anterior and posterior body fragments of larvae of the ascidian Ciona that had been cut at an arbitrary position. Examination of more than 200 fragments revealed a necessary and sufficient body region that spanned only ∼10\% of the body length and included the trunk-tail junction. 'Mid-piece' body fragments, which included the trunk-tail junctional region, but excluded most of the anterior trunk and posterior tail, autonomously expressed periodic tail-beating bursts at ∼20 s intervals. We compared the durations and intervals of tail-beating bursts expressed by mid-piece fragments, and also by whole larvae under different sensory conditions. The results suggest that body parts outside the mid-piece effect shortening of swimming intervals, particularly in the dark, and vary the burst duration. We propose that Ciona larvae express swimming behaviors by modifying autonomous and periodic locomotor drives that operate locally in the trunk-tail junctional region.",
    url = "https://doi.org/10.1242/jeb.243828",
    doi = "10.1242/jeb.243828",
    openalex = "W4281609119",
    references = "doi101242jeb209320"
}

The last decades have seen an increase in the isolation and characterization of anticancer compounds derived from marine organisms, especially invertebrates, and their use in clinical trials. In this regard, ascidians, which are included in the subphylum Tunicata, represent successful examples with two drugs, Aplidine© and Yondelis©, that reached the market as orphan drugs against several malignancies. Here, we report that an organic extract prepared from homogenized tissues of the Mediterranean ascidian Ciona robusta inhibited cell proliferation in HT-29, Hep G2, and U2 OS human cells with the former resulting as the most sensitive to the extract (EC50 = 250 µg/ml). We demonstrated that the ascidian organic extract was not cytotoxic on HT-29 cells induced to differentiate with sodium butyrate, suggesting a preference for the mixture for the malignant phenotype. Finally, we reported that the cell death induced by the organic extract was mediated by the activation of a process of cytotoxic autophagy as a result of the increased expression of the LC3-II marker and the number of autophagic vacuoles, which almost doubled in treated HT-29 cells. In summary, although the detailed chemical composition of the Ciona robusta extract is still undetermined, our data suggest the presence in it of bioactive compounds possessing anticancer activity.

@article{doi103389fchem20241322558,
    author = "Gallo, A. and Penna, Ylenia Maria and Russo, M. and Rosapane, Marco and Tosti, E. and Russo, G.",
    title = "An organic extract from ascidian Ciona robusta induces cytotoxic autophagy in human malignant cell lines",
    year = "2023",
    journal = "Frontiers in Chemistry",
    abstract = "The last decades have seen an increase in the isolation and characterization of anticancer compounds derived from marine organisms, especially invertebrates, and their use in clinical trials. In this regard, ascidians, which are included in the subphylum Tunicata, represent successful examples with two drugs, Aplidine© and Yondelis©, that reached the market as orphan drugs against several malignancies. Here, we report that an organic extract prepared from homogenized tissues of the Mediterranean ascidian Ciona robusta inhibited cell proliferation in HT-29, Hep G2, and U2 OS human cells with the former resulting as the most sensitive to the extract (EC50 = 250 µg/ml). We demonstrated that the ascidian organic extract was not cytotoxic on HT-29 cells induced to differentiate with sodium butyrate, suggesting a preference for the mixture for the malignant phenotype. Finally, we reported that the cell death induced by the organic extract was mediated by the activation of a process of cytotoxic autophagy as a result of the increased expression of the LC3-II marker and the number of autophagic vacuoles, which almost doubled in treated HT-29 cells. In summary, although the detailed chemical composition of the Ciona robusta extract is still undetermined, our data suggest the presence in it of bioactive compounds possessing anticancer activity.",
    url = "https://www.frontiersin.org/articles/10.3389/fchem.2024.1322558/pdf?isPublishedV2=False",
    doi = "10.3389/fchem.2024.1322558",
    is_oa = "true",
    semanticscholar_citation_count = "2",
    semanticscholar_id = "b21b1def329a40f23807e994d7fe6ecf0970709b",
    volume = "12"
}

The endostyle is a pharyngeal organ with an opening groove and cilia in invertebrate chordates (amphioxus and ascidian) and cyclostomate (lamprey), serving as a filter-feeding tract and thyroid-secreting location. Emerging evidence implies its complex cellular composition and potentially versatile functions. Multiple cell types in the endostyle have been thought to be progenitors of complex organs in advanced vertebrates. To describe the expression profile and the potential functions, bulk RNA sequencing on the endostyle in ascidian Styela clava was conducted and distinct markers were selected by multileveled comparative analysis. Transcriptional data assay and qRT-PCR-verified results showed the regional expression patterns of Hox genes in the longitudinal axis. Organ-specific markers of the endostyle was proposed by comparing expression with the main organs of the ascidian. A cross-species transcriptional profile projection between the endostyle and organs from Danio rerio and Homo sapiens indicates a robust homogenous relationship to the thyroid and digestive system of the endostyle. The high similarity between the endostyle and the head kidney in zebrafish/the bone marrow in human implies uniquely profound functions of the pharyngeal organ in proto-vertebrates. Our result revealed that the transcriptional profile of the human parathyroid gland was similar to the ascidian endostyle, indicating the evolutionary origin of vertebrate hormone secretion organs.

@article{doi103390biology12020245,
    author = "Jiang, An and Zhang, Wei and Wei, Jiankai and Liu, Penghui and Dong, Bo",
    title = "Transcriptional Analysis of the Endostyle Reveals Pharyngeal Organ Functions in Ascidian",
    year = "2023",
    journal = "Biology",
    abstract = "The endostyle is a pharyngeal organ with an opening groove and cilia in invertebrate chordates (amphioxus and ascidian) and cyclostomate (lamprey), serving as a filter-feeding tract and thyroid-secreting location. Emerging evidence implies its complex cellular composition and potentially versatile functions. Multiple cell types in the endostyle have been thought to be progenitors of complex organs in advanced vertebrates. To describe the expression profile and the potential functions, bulk RNA sequencing on the endostyle in ascidian Styela clava was conducted and distinct markers were selected by multileveled comparative analysis. Transcriptional data assay and qRT-PCR-verified results showed the regional expression patterns of Hox genes in the longitudinal axis. Organ-specific markers of the endostyle was proposed by comparing expression with the main organs of the ascidian. A cross-species transcriptional profile projection between the endostyle and organs from Danio rerio and Homo sapiens indicates a robust homogenous relationship to the thyroid and digestive system of the endostyle. The high similarity between the endostyle and the head kidney in zebrafish/the bone marrow in human implies uniquely profound functions of the pharyngeal organ in proto-vertebrates. Our result revealed that the transcriptional profile of the human parathyroid gland was similar to the ascidian endostyle, indicating the evolutionary origin of vertebrate hormone secretion organs.",
    url = "https://doi.org/10.3390/biology12020245",
    doi = "10.3390/biology12020245",
    openalex = "W4319317139",
    references = "doi101186s12915022012827, doi102108zs200095"
}

The cholecystokinin (CCK)/gastrin family peptides are involved in regulation of feeding and digestion in vertebrates. In the ascidian Ciona intestinalis type A (Ciona robusta), cionin, a CCK/gastrin family peptide, has been identified. Cionin is expressed exclusively in the central nervous system (CNS). In contrast, cionin receptor expression has been detected in the CNS, digestive tract, and ovary. Although cionin has been reported to be involved in ovulation, its physiological function in the CNS remains to be investigated. To elucidate its neural function, in the present study, we analyzed the expression of cionin and cionin receptors in the CNS. Cionin was expressed mainly in neurons residing in the anterior region of the cerebral ganglion. In contrast, the gene expressin of the cionin receptor gene CioR1, was detected in the middle part of the cerebral ganglion and showed a similar expression pattern to that of VACHT, a cholinergic neuron marker gene. Moreover, CioR1 was found to be expressed in cholinergic neurons. Consequently, these results suggest that cionin interacts with cholinergic neurons as a neurotransmitter or neuromodulator via CioR1. This study provides insights into a biological role of a CCK/gastrin family peptide in the CNS of ascidians.

@article{doi101038s41598024559087,
    author = "Taniguchi, Shiho and Nakayama, Satoshi and Iguchi, Rin and Sasakura, Yasunori and Satake, Honoo and Wada, Shuichi and Suzuki, Nobuo and Ogasawara, Michio and Sekiguchi, Toshio",
    title = "Distribution of cionin, a cholecystokinin/gastrin family peptide, and its receptor in the central nervous system of Ciona intestinalis type A",
    year = "2024",
    journal = "Scientific Reports",
    abstract = "The cholecystokinin (CCK)/gastrin family peptides are involved in regulation of feeding and digestion in vertebrates. In the ascidian Ciona intestinalis type A (Ciona robusta), cionin, a CCK/gastrin family peptide, has been identified. Cionin is expressed exclusively in the central nervous system (CNS). In contrast, cionin receptor expression has been detected in the CNS, digestive tract, and ovary. Although cionin has been reported to be involved in ovulation, its physiological function in the CNS remains to be investigated. To elucidate its neural function, in the present study, we analyzed the expression of cionin and cionin receptors in the CNS. Cionin was expressed mainly in neurons residing in the anterior region of the cerebral ganglion. In contrast, the gene expressin of the cionin receptor gene CioR1, was detected in the middle part of the cerebral ganglion and showed a similar expression pattern to that of VACHT, a cholinergic neuron marker gene. Moreover, CioR1 was found to be expressed in cholinergic neurons. Consequently, these results suggest that cionin interacts with cholinergic neurons as a neurotransmitter or neuromodulator via CioR1. This study provides insights into a biological role of a CCK/gastrin family peptide in the CNS of ascidians.",
    url = "https://doi.org/10.1038/s41598-024-55908-7",
    doi = "10.1038/s41598-024-55908-7",
    openalex = "W4392869396",
    references = "doi101242jeb209320"
}

The heart of ascidians (marine invertebrate chordates) has a tubular structure, and heartbeats propagate from one end to the other. The direction of pulsation waves intermittently reverses in the heart of ascidians and their relatives; however, the underlying mechanisms remain unclear. We herein performed a series of experiments to characterize the pacemaker systems in isolated hearts and their fragments, and applied a mathematical model to examine the conditions leading to heart reversals. The isolated heart of Ciona robusta autonomously generated pulsation waves at ∼20 to 25 beats min-1 with reversals at ∼1 to 10 min intervals. Experimental bisections of isolated hearts revealed that independent pacemakers resided on each side and also that their beating frequencies periodically changed as they expressed bimodal rhythms, which comprised an ∼1.25 to 5.5 min acceleration/deceleration cycle of a beating rate of between 0 and 25 beats min-1. Only fragments including 5% or shorter terminal regions of the heart tube maintained autonomous pulsation rhythms, whereas other regions did not. Our mathematical model, based on FitzHugh-Nagumo equations applied to a one-dimensional alignment of cells, demonstrated that the difference between frequencies expressed by the two independent terminal pacemakers determined the direction of propagated waves. Changes in the statuses of terminal pacemakers between the excitatory and oscillatory modes as well as in their endogenous oscillation frequencies were sufficient to lead to heart reversals. These results suggest that the directions of pulsation waves in the Ciona heart reverse according to the changing rhythms independently expressed by remotely coupled terminal pacemakers.

@article{doi101242jeb246810,
    author = "Fujikake, Yuma and Fukuda, Kéita and Matsushita, Katsuyoshi and Iwatani, Yasushi and Fujimoto, Koichi and Nishino, Atsuo",
    title = "Pulsation waves along the Ciona heart tube reverse by bimodal rhythms expressed by a remote pair of pacemakers",
    year = "2024",
    journal = "Journal of Experimental Biology",
    abstract = "The heart of ascidians (marine invertebrate chordates) has a tubular structure, and heartbeats propagate from one end to the other. The direction of pulsation waves intermittently reverses in the heart of ascidians and their relatives; however, the underlying mechanisms remain unclear. We herein performed a series of experiments to characterize the pacemaker systems in isolated hearts and their fragments, and applied a mathematical model to examine the conditions leading to heart reversals. The isolated heart of Ciona robusta autonomously generated pulsation waves at ∼20 to 25 beats min-1 with reversals at ∼1 to 10 min intervals. Experimental bisections of isolated hearts revealed that independent pacemakers resided on each side and also that their beating frequencies periodically changed as they expressed bimodal rhythms, which comprised an ∼1.25 to 5.5 min acceleration/deceleration cycle of a beating rate of between 0 and 25 beats min-1. Only fragments including 5\% or shorter terminal regions of the heart tube maintained autonomous pulsation rhythms, whereas other regions did not. Our mathematical model, based on FitzHugh-Nagumo equations applied to a one-dimensional alignment of cells, demonstrated that the difference between frequencies expressed by the two independent terminal pacemakers determined the direction of propagated waves. Changes in the statuses of terminal pacemakers between the excitatory and oscillatory modes as well as in their endogenous oscillation frequencies were sufficient to lead to heart reversals. These results suggest that the directions of pulsation waves in the Ciona heart reverse according to the changing rhythms independently expressed by remotely coupled terminal pacemakers.",
    url = "https://doi.org/10.1242/jeb.246810",
    doi = "10.1242/jeb.246810",
    openalex = "W4396229527",
    references = "doi101242jeb209320"
}

The ascidian larvae, which display a chordate ground body plan, are left-right asymmetric in several structures, including the brain vesicle. In ascidian larvae, the ocellus and otolith pigment cells, which are thought to detect light and gravity respectively, are located on the right side of the brain vesicle, while the coronet cells, which are presumed to be dopaminergic, are located on the left side. To study how left-right asymmetry of the brain vesicle in the ascidian Halocynthia roretzi larva is determined, I attempted to isolate a gene that is expressed in the brain vesicle. As a result, an ascidian Parkin co-regulated gene (PACRG) orthologue was cloned. Expression of PACRG begins weakly in the head region of the late tailbud embryos, and it thereafter is observed on the left side of the brain vesicle of the larvae just before hatching. The location of PACRG expression is estimated to overlap with the area stained by the coronet cell-specific antibody. Thus, it is suggested that PACRG might be involved in the formation of the left-side structures of the brain vesicle, including coronet cells, during ascidian embryogenesis.

@article{doi1012717dr2024284121,
    author = "Kim, Gil Jung",
    title = "PACRG is Expressed on the Left Side of the Brain Vesicle in the Ascidian Halocynthia Larva",
    year = "2024",
    journal = "Development \& Reproduction",
    abstract = "The ascidian larvae, which display a chordate ground body plan, are left-right asymmetric in several structures, including the brain vesicle. In ascidian larvae, the ocellus and otolith pigment cells, which are thought to detect light and gravity respectively, are located on the right side of the brain vesicle, while the coronet cells, which are presumed to be dopaminergic, are located on the left side. To study how left-right asymmetry of the brain vesicle in the ascidian Halocynthia roretzi larva is determined, I attempted to isolate a gene that is expressed in the brain vesicle. As a result, an ascidian Parkin co-regulated gene (PACRG) orthologue was cloned. Expression of PACRG begins weakly in the head region of the late tailbud embryos, and it thereafter is observed on the left side of the brain vesicle of the larvae just before hatching. The location of PACRG expression is estimated to overlap with the area stained by the coronet cell-specific antibody. Thus, it is suggested that PACRG might be involved in the formation of the left-side structures of the brain vesicle, including coronet cells, during ascidian embryogenesis.",
    url = "https://doi.org/10.12717/dr.2024.28.4.121",
    doi = "10.12717/dr.2024.28.4.121",
    openalex = "W4406601527",
    references = "doi101016jydbio201807023"
}

The notochord is an axial structure required for the development of all chordate embryos, from sea squirts to humans. Over the course of more than half a billion years of chordate evolution, in addition to its structural function, the notochord has acquired increasingly relevant patterning roles for its surrounding tissues. This process has involved the co-option of signaling pathways and the acquisition of novel molecular mechanisms responsible for the precise timing and modalities of their deployment. To reconstruct this evolutionary route, we surveyed the expression of signaling molecules in the notochord of the tunicate Ciona, an experimentally amenable and informative chordate. We found that several genes encoding for candidate components of diverse signaling pathways are expressed during notochord development, and in some instances, display distinctive regionalized and/or lineage-specific patterns. We identified and deconstructed notochord enhancers associated with TGF-β and Ctgf, two evolutionarily conserved signaling genes that are expressed dishomogeneously in the Ciona notochord, and shed light on the cis -regulatory origins of their peculiar expression patterns.

@article{doi103390ijms252413631,
    author = "Negrón-Piñeiro, Lenny J. and Wu, Yushi and Mehta, Ravij and Maguire, Julie E. and Chou, Cindy and Lee, Joyce M. and Dahia, Chitra Lekha and Gregorio, Anna Di",
    title = "Fine-Tuned Expression of Evolutionarily Conserved Signaling Molecules in the Ciona Notochord",
    year = "2024",
    journal = "International Journal of Molecular Sciences",
    abstract = "The notochord is an axial structure required for the development of all chordate embryos, from sea squirts to humans. Over the course of more than half a billion years of chordate evolution, in addition to its structural function, the notochord has acquired increasingly relevant patterning roles for its surrounding tissues. This process has involved the co-option of signaling pathways and the acquisition of novel molecular mechanisms responsible for the precise timing and modalities of their deployment. To reconstruct this evolutionary route, we surveyed the expression of signaling molecules in the notochord of the tunicate Ciona, an experimentally amenable and informative chordate. We found that several genes encoding for candidate components of diverse signaling pathways are expressed during notochord development, and in some instances, display distinctive regionalized and/or lineage-specific patterns. We identified and deconstructed notochord enhancers associated with TGF-β and Ctgf, two evolutionarily conserved signaling genes that are expressed dishomogeneously in the Ciona notochord, and shed light on the cis -regulatory origins of their peculiar expression patterns.",
    url = "https://doi.org/10.3390/ijms252413631",
    doi = "10.3390/ijms252413631",
    openalex = "W4405649523",
    references = "doi101016jydbio201807023"
}

Nanoplastics are known to represent a threat to marine ecosystems. Their combination with other contaminants of emerging concerns (CECs) may amplify ecotoxic effects, with unknown impacts on marine biodiversity. This study investigates the effects, single and combined, of bisphenol A (BPA)-one of the most hazardous CECs-and polystyrene nanoparticles (PS NPs)-as a proxy for nanoplastics, being among the most commonly found asmarine debris-on cholinesterase (ChE) activities of the ascidian Ciona robusta. ChE activity was first measured in the siphons, tunic, and viscera of wild-caught adult specimens and exposed in vitro to BPA (0.01, 0.21, 0.69 mM) and PS NPs (0.0096-0.096 mM; 8.096 × 10 9 -10 10 particles, respectively) alone and combined for 15 min of incubation. PS NPs' behavior in milliQ water and in the ChE assay reaction buffer was characterized alone, combined with BPA, and analyzed through ζ-potential measurements via Dynamic Light Scattering. The results revealed that ChE activity was predominant in the viscera and siphons of C. robusta; PS NPs did not affect the ChE activity alone or combined, while BPA caused a concentration-dependent inhibition of ChE activity in the viscera. No changes in ζ-potential were observed for PS NPs alone or combined with BPA in the ChE buffer, suggesting no interaction. Further investigations are needed to understand the potential neurotoxic consequences for C. robusta and ecological risk scenarios due to exposure to BPA and nanoplastics in marine coastal waters.

@article{doi103390jox14040103,
    author = "Melki, Safa and Ferrari, Emma and Ahmed, Raja Ben and Spagnuolo, Antonietta and Corsi, Ilaria",
    title = "Single but Not Combined In Vitro Exposure to Bisphenol A and Nanoplastics Affects the Cholinergic Function of the Ascidian Ciona robusta",
    year = "2024",
    journal = "Journal of Xenobiotics",
    abstract = "Nanoplastics are known to represent a threat to marine ecosystems. Their combination with other contaminants of emerging concerns (CECs) may amplify ecotoxic effects, with unknown impacts on marine biodiversity. This study investigates the effects, single and combined, of bisphenol A (BPA)-one of the most hazardous CECs-and polystyrene nanoparticles (PS NPs)-as a proxy for nanoplastics, being among the most commonly found asmarine debris-on cholinesterase (ChE) activities of the ascidian Ciona robusta. ChE activity was first measured in the siphons, tunic, and viscera of wild-caught adult specimens and exposed in vitro to BPA (0.01, 0.21, 0.69 mM) and PS NPs (0.0096-0.096 mM; 8.096 × 10 9 -10 10 particles, respectively) alone and combined for 15 min of incubation. PS NPs' behavior in milliQ water and in the ChE assay reaction buffer was characterized alone, combined with BPA, and analyzed through ζ-potential measurements via Dynamic Light Scattering. The results revealed that ChE activity was predominant in the viscera and siphons of C. robusta; PS NPs did not affect the ChE activity alone or combined, while BPA caused a concentration-dependent inhibition of ChE activity in the viscera. No changes in ζ-potential were observed for PS NPs alone or combined with BPA in the ChE buffer, suggesting no interaction. Further investigations are needed to understand the potential neurotoxic consequences for C. robusta and ecological risk scenarios due to exposure to BPA and nanoplastics in marine coastal waters.",
    url = "https://doi.org/10.3390/jox14040103",
    doi = "10.3390/jox14040103",
    openalex = "W4405070819",
    references = "doi101242jeb209320"
}

Although the differentiation of cardiac progenitors during embryogenesis has been characterized in detail in the ascidian Ciona robusta, heart development after metamorphosis remains unclear. The sub-terminal regions at both ends of the Ciona heart harbor pacemaker cells, as well as undifferentiated cells located within the growth zone. We performed an RNA-Seq analysis to identify transcription factors predominantly expressed in the sub-terminal regions of the Ciona heart. Among the 17 transcription factors predominantly expressed in one or both of the sub-terminal regions, Hox3 showed the strongest expression in both. Since the role of Hox3 during Ciona heart development remained unknown, we investigated the spatial expression and function of Hox3. In situ hybridization revealed the expression of Hox3 in undifferentiated cells within the growth zone at both ends of the heart tube. The TALEN-mediated disruption of Hox3 in cardiac progenitors resulted in irregularly swollen or shortened heart tubes. These results suggest that Hox3 plays a crucial role in heart tube formation by regulating the activity of growth zone cells. Similar Hox3 expression in the terminal regions of ascidian and vertebrate hearts suggests the partial conservation of cardiac patterning and pacemaker localization.

@article{doi101111dgd70028,
    author = "Saito, Ryota and Hyodo, Tatsuki and Kamakura, Nene and Fujikake, Yuma and Nishino, Junko M. and Sasakura, Yasunori and Nishino, Atsuo and Fujiwara, Shigeki",
    title = "Hox3 Is Required for Post‐Metamorphic Heart Development in Adult Ciona",
    year = "2025",
    journal = "Development Growth \& Differentiation",
    abstract = "Although the differentiation of cardiac progenitors during embryogenesis has been characterized in detail in the ascidian Ciona robusta, heart development after metamorphosis remains unclear. The sub-terminal regions at both ends of the Ciona heart harbor pacemaker cells, as well as undifferentiated cells located within the growth zone. We performed an RNA-Seq analysis to identify transcription factors predominantly expressed in the sub-terminal regions of the Ciona heart. Among the 17 transcription factors predominantly expressed in one or both of the sub-terminal regions, Hox3 showed the strongest expression in both. Since the role of Hox3 during Ciona heart development remained unknown, we investigated the spatial expression and function of Hox3. In situ hybridization revealed the expression of Hox3 in undifferentiated cells within the growth zone at both ends of the heart tube. The TALEN-mediated disruption of Hox3 in cardiac progenitors resulted in irregularly swollen or shortened heart tubes. These results suggest that Hox3 plays a crucial role in heart tube formation by regulating the activity of growth zone cells. Similar Hox3 expression in the terminal regions of ascidian and vertebrate hearts suggests the partial conservation of cardiac patterning and pacemaker localization.",
    url = "https://doi.org/10.1111/dgd.70028",
    doi = "10.1111/dgd.70028",
    openalex = "W4416223790",
    references = "doi101242jeb209320"
}

Understanding the mechanisms that determine invasion success requires evaluating both abiotic constraints and biotic interactions acting on introduced species. In this study we analyzed the role of environmental filtering, understood as the capacity of organisms to tolerate physical conditions such as temperature and oxygen availability, and biotic resistance, defined as the effects of native consumers in limiting establishment. These processes were evaluated in two solitary ascidians, Corella eumyota (Phlebobranchia: Corellidae) and Asterocarpa humilis (Stolidobranchia: Styelidae), collected from settlement plates deployed at approximately 1 m depth in Coliumo Bay (36°32'S, 72°56'W), central Chile. Both species exhibited broad thermal tolerance, maintaining survival between 12 and 20 °C, tolerating cooling to 4 °C, and showing mortality at 24 °C. They also displayed high resistance to hypoxic conditions, with critical oxygen tension (Pcrit) values of 0.64 ± 0.35 kPa for Corella eumyota and 2.01 ± 0.74 kPa for Asterocarpa humilis, indicating physiological capacity to persist in low oxygen environments. Predation assays conducted with native consumers observed in the plates revealed contrasting effects, as the crab Romaleon setosum consumed a high proportion of individuals, whereas the fish Hypsoblennius sordidus showed limited consumption. Adult ascidians were used in the experiments, allowing the assessment of local consumers to prey on settled organisms rather than early life stages. Overall, the results indicate that invasion success in these ascidians emerges from the combined action of broad physiological tolerance that enables persistence under broad environmental conditions and context dependent biotic resistance that may limit their expansion into adjacent natural habitats.

@article{doi101016jmarenvres2026108044,
    author = "Pinochet, Javier and Barrios-Figueroa, Rocío and Jorquera, Erika and Molina-Valdivia, Víctor and Lagos-Oróstica, Marcelo and Urbina, Mauricio A and Brante, Antonio",
    title = "Physiological tolerance and predator-mediated resistance as critical factors influencing the invasion success in two solitary ascidians.",
    year = "2026",
    journal = "Marine environmental research",
    abstract = "Understanding the mechanisms that determine invasion success requires evaluating both abiotic constraints and biotic interactions acting on introduced species. In this study we analyzed the role of environmental filtering, understood as the capacity of organisms to tolerate physical conditions such as temperature and oxygen availability, and biotic resistance, defined as the effects of native consumers in limiting establishment. These processes were evaluated in two solitary ascidians, Corella eumyota (Phlebobranchia: Corellidae) and Asterocarpa humilis (Stolidobranchia: Styelidae), collected from settlement plates deployed at approximately 1 m depth in Coliumo Bay (36°32'S, 72°56'W), central Chile. Both species exhibited broad thermal tolerance, maintaining survival between 12 and 20 °C, tolerating cooling to 4 °C, and showing mortality at 24 °C. They also displayed high resistance to hypoxic conditions, with critical oxygen tension (Pcrit) values of 0.64 ± 0.35 kPa for Corella eumyota and 2.01 ± 0.74 kPa for Asterocarpa humilis, indicating physiological capacity to persist in low oxygen environments. Predation assays conducted with native consumers observed in the plates revealed contrasting effects, as the crab Romaleon setosum consumed a high proportion of individuals, whereas the fish Hypsoblennius sordidus showed limited consumption. Adult ascidians were used in the experiments, allowing the assessment of local consumers to prey on settled organisms rather than early life stages. Overall, the results indicate that invasion success in these ascidians emerges from the combined action of broad physiological tolerance that enables persistence under broad environmental conditions and context dependent biotic resistance that may limit their expansion into adjacent natural habitats.",
    url = "https://pubmed.ncbi.nlm.nih.gov/41955794/",
    doi = "10.1016/j.marenvres.2026.108044",
    pmid = "41955794"
}

The development of the central nervous system (CNS) depends on tightly regulated gene expression programs that guide neural progenitor differentiation and neuronal subtype specification. The tunicate Ciona robusta provides a powerful and simplified model for dissecting the genetic control of nervous system development, with a larval CNS composed of just over 200 neurons and sensory cells. Although CRISPR/Cas9-mediated mutagenesis is now routinely used in Ciona, validated single-guide RNAs (sgRNAs) have yet to be validated for key neural genes. Here, we report the design and experimental validation of 25 novel sgRNAs targeting eight conserved genes encoding conserved proteins involved in neurodevelopment and neural function, including six transcription factors (Cdx, Foxb, Sox1/2/3, Dmbx, Engrailed, and Mnx) and two neural effector genes (Tyrosinase and Slc18a3/VAChT). Candidate sgRNAs were selected using CRISPOR and tested for mutagenesis efficiency using Illumina-based target site amplicon sequencing. All sgRNAs induced insertions or deletions at their target loci, with most genes yielding at least one sgRNA with mutagenesis efficacy exceeding 30%, with the exception of Dmbx, for which maximal efficacy reached 25%. We further compared measured mutagenesis rates with predicted Doench '16 and Doench Ruleset 3 (RS3) scores, observing a modest but improved correlation with RS3 predictions. Based on these results, we recommend considering both scoring algorithms, with RS3 potentially offering improved predictive value for Ciona.

@article{doi106489820260325711585,
    author = "Popsuj, Sydney and Kalsang, Tenzin and Kim, Kwantae and Drummond, Erica and Manekar, Pooja and Munagapati, Pranavvarma V. and Oleti, Manasi and Sato, Hiroki and Vickery, Izabella and Gigante, Eduardo D. and Stolfi, Alberto",
    title = "Validated CRISPR/Cas9 guide RNAs targeting neurodevelopmental genes in the tunicate Ciona robusta",
    year = "2026",
    journal = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "The development of the central nervous system (CNS) depends on tightly regulated gene expression programs that guide neural progenitor differentiation and neuronal subtype specification. The tunicate Ciona robusta provides a powerful and simplified model for dissecting the genetic control of nervous system development, with a larval CNS composed of just over 200 neurons and sensory cells. Although CRISPR/Cas9-mediated mutagenesis is now routinely used in Ciona, validated single-guide RNAs (sgRNAs) have yet to be validated for key neural genes. Here, we report the design and experimental validation of 25 novel sgRNAs targeting eight conserved genes encoding conserved proteins involved in neurodevelopment and neural function, including six transcription factors (Cdx, Foxb, Sox1/2/3, Dmbx, Engrailed, and Mnx) and two neural effector genes (Tyrosinase and Slc18a3/VAChT). Candidate sgRNAs were selected using CRISPOR and tested for mutagenesis efficiency using Illumina-based target site amplicon sequencing. All sgRNAs induced insertions or deletions at their target loci, with most genes yielding at least one sgRNA with mutagenesis efficacy exceeding 30\%, with the exception of Dmbx, for which maximal efficacy reached 25\%. We further compared measured mutagenesis rates with predicted Doench '16 and Doench Ruleset 3 (RS3) scores, observing a modest but improved correlation with RS3 predictions. Based on these results, we recommend considering both scoring algorithms, with RS3 potentially offering improved predictive value for Ciona.",
    url = "https://doi.org/10.64898/2026.03.25.711585",
    doi = "10.64898/2026.03.25.711585",
    openalex = "W7141812979",
    references = "doi101242jeb209320"
}