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1 lating embryos of a simple proto-vertebrate (Ciona).
2 egies in the elucidation of gene function in Ciona.
3 ebrates to basal chordates like the ascidian Ciona.
4 o form the atrium and atrial siphon of adult Ciona.
5 nomic organisation, albeit more divergent in Ciona.
6 participate in notochord differentiation in Ciona.
7 midline dynamics during NTC in the tunicate Ciona.
8 cis-regulatory sequences between Molgula and Ciona.
9 llow for rapid screening of gene function in Ciona.
10 xplain and reproduce the neuronal pattern in Ciona.
11 iple classes of MRF-regulated genes exist in Ciona.
13 encoded at four loci (i.e., VCBPA-VCBPD) in Ciona, a urochordate, and are expressed by distinct epit
20 any genes expressed in B4.1 lineages in both Ciona and the distantly related ascidian Halocynthia.
21 Finally, cross-species comparisons between Ciona and the mouse evoke the deep evolutionary origins
22 gulatory and functional conservation between Ciona and vertebrate Hmx, and point to bipolar tail neur
25 ordates including chicken, axolotl, lamprey, Ciona, and amphioxus, revealing a universal upstream LPM
26 gest that a midbrain homologue is missing in Ciona, and argue that midbrain development is a novelty
27 enomic comparisons restricted to Drosophila, Ciona, and humans (protostomes, urochordates, and verteb
28 sential notochord gene regulatory network of Ciona, and provide a reference for studies of transcript
31 l number of binding motifs are necessary for Ciona betagamma-crystallin expression, and narrow down t
40 bp enhancer from the promoter region of the Ciona Brachyury gene (Ci-Bra), which is sufficient to di
42 Invertebrate chordates, such as the tunicate Ciona, can offer insight into the evolution of the chord
48 ng with visuomotor circuits predicted by the Ciona connectome, we used expression maps of neurotransm
51 ndicate that notochord cell intercalation in Ciona does not require the progressive signals which coo
53 itary master regulator in the model chordate Ciona Ectopic Bra expression only partially reprograms o
54 , we applied a drug treatment approach using Ciona eggs and found that inhibition of casein kinase 2
58 gle-cell RNA-seq to the 16-cell stage of the Ciona embryo, a marine chordate and performed a computat
60 homeobox gene bix in notochord or muscle of Ciona embryos as a means of interfering with development
62 h mediates expression in the neural plate of Ciona embryos in response to fibroblast growth factor (F
63 re, we develop an expression assay in living Ciona embryos that captures the liquid behavior of indiv
70 yogenesis in the tail of the simple chordate Ciona exhibits a similar reliance on its single MRF-fami
73 The notochord of the invertebrate chordate Ciona forms a tapered rod at tailbud stages consisting o
74 , techniques, and resources available to the Ciona geneticist, citing examples of studies that employ
77 sequencing of staged EST libraries make the Ciona genome one of the best annotated among those that
78 as clusters of identical sites found in the Ciona genome with different arrangements are unable to a
79 spects of creating a regulatory atlas of the Ciona genome, whereby every enhancer is identified for e
85 These observations provide evidence that Ciona has a neurogenic proto-placode, which forms neuron
89 on analyses was used to demonstrate that the Ciona HNF-3beta homologue is expressed in the ventralmos
92 Caenorhabditis elegans (Ce), the sea squirt Ciona intestinalis (Ci) and amphioxus Branchiostoma flor
95 euterostomian invertebrate - the urochordate Ciona intestinalis - that is orthologous to vertebrate c
96 eart progenitor cells of the simple chordate Ciona intestinalis also generate precursors of the atria
98 enotype was rescued by ectopic expression of Ciona intestinalis alternative oxidase (AOX)(12), which
99 yces cerevisiae NADH dehydrogenase (NDI1) or Ciona intestinalis alternative oxidase, which can comple
101 D family gene was identified in the ascidian Ciona intestinalis and designated CiMDF (Ciona intestina
102 lated organisms that make cellulose, such as Ciona intestinalis and Dictyostelium discoideum, reveale
103 sms, Drosophila melanogaster, Daphnia pulex, Ciona intestinalis and Strongylocentrotus purpuratus.
104 erived pharyngeal epithelium of the ascidian Ciona intestinalis and the amphioxus Branchiostoma lance
105 macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the
106 t absent from the genomes of the urochordate Ciona intestinalis and the lower eukaryotes D. melanogas
107 using a simple method to introduce DNA into Ciona intestinalis and the several available tissue-spec
111 ique phylogenetic position of the sea squirt Ciona intestinalis as part of the sister group to the ve
112 nderlying basis of enhancer activity for the Ciona intestinalis betagamma-crystallin gene, which driv
115 sed to improve and enrich the description of Ciona intestinalis embryonic development, based on an im
119 POUIV gene families to examine the tunicate Ciona intestinalis for evidence of structures homologous
120 s, making for a direct orthology between the Ciona intestinalis gene CiPax6 and Pax6 in mammals.
122 we estimated that the invertebrate chordate Ciona intestinalis has 15,500 protein-coding genes (+/-3
124 A forward genetic screen in the ascidian Ciona intestinalis identified a mutant line (frimousse)
126 t specification in the invertebrate chordate Ciona intestinalis is similar to that of vertebrates but
131 estigate this process in the simple chordate Ciona intestinalis Previous studies have implicated Noda
132 s trunk ventral cells, TVCs) of the ascidian Ciona intestinalis provide a simple chordate model with
133 the CNS of the tadpole larva of the ascidian Ciona intestinalis provides us with a chordate nervous s
134 ans and even a highly divergent invertebrate Ciona intestinalis qualitatively and quantitatively supp
135 motivated by our experiments in the ascidian Ciona intestinalis showing that the peripheral sensory n
138 ed several cDNAs derived from the sea squirt Ciona intestinalis that encode vitamin K-dependent prote
139 -induced short-tailed mutant in the ascidian Ciona intestinalis that is the product of a premature st
140 identified in the primitive ascidian species Ciona intestinalis that possesses the characteristic fea
141 Here, we employ the invertebrate chordate Ciona intestinalis to delineate an essential in vivo rol
142 rphological simplicity of the basal chordate Ciona intestinalis to elucidate Mesp regulation and func
143 loit wild populations of the marine chordate Ciona intestinalis to show that levels of buffering are
144 invasive tunicates, Ciona robusta (formerly Ciona intestinalis type A) and C. intestinalis (formerly
145 inalis type A) and C. intestinalis (formerly Ciona intestinalis type B), globally distributed and sym
147 reduced the sensitivity of Kv7.5 channels to Ciona intestinalis voltage-sensing phosphatase (Ci-VSP)-
148 results suggest that the native S4 from the Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP
150 voltage-sensing membrane proteins using the Ciona intestinalis voltage-sensitive phosphatase (CiVSP)
151 ht consists of the voltage-sensing domain of Ciona intestinalis voltage-sensitive phosphatase and sup
152 2 K(+) channel and the voltage sensor of the Ciona intestinalis voltage-sensitive phosphatase, agains
154 The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of me
156 ogs transcribed in eggs of Xenopus laevis or Ciona intestinalis were found, pinpointing evolutionary
160 identified ABC proteins from the sea squirt (Ciona intestinalis), zebrafish (Danio rerio), and chicke
161 -3beta and snail homologues in the ascidian, Ciona intestinalis, a member of the subphylum Urochordat
162 We have examined ASICs from the ascidian Ciona intestinalis, a simple chordate organism whose ner
163 ting the ARNTL gene family in the genomes of Ciona intestinalis, amphioxus, zebrafish, and human.
164 the zebrafish (Danio rerio) and the ascidian Ciona intestinalis, an invertebrate chordate belonging t
167 subsequently identified in human, mouse, and Ciona intestinalis, but their existence in dinoflagellat
168 mo sapiens, Mus musculus, Takifugu rubripes, Ciona intestinalis, Caenorhabditis elegans, Drosophila m
169 he voltage sensor of the prototypic VSP from Ciona intestinalis, Ci-VSP, we generated chimeric protei
171 the genome of a urochordate, the sea squirt, Ciona intestinalis, did not turn up any genuine ortholog
172 anglion development and that in the tunicate Ciona intestinalis, Hmx is necessary and sufficient to d
173 nt evidence that the embryo of the ascidian, Ciona intestinalis, is an easily manipulated system for
175 e demonstrate that, in the chordate ascidian Ciona intestinalis, miR-124 plays an extensive role in p
176 of the gene for the FlgCK from the tunicate Ciona intestinalis, providing support for the linkage of
177 rithm on simulated next-generation data from Ciona intestinalis, real next-generation data from Droso
179 ll type in the tadpole larva of the tunicate Ciona intestinalis, the bipolar tail neuron, shares a se
182 tic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intraspecies sequence com
183 tion and streamlined genome of the ascidian, Ciona intestinalis, to investigate heart development in
184 on pattern of CiMDF, the MyoD-family gene of Ciona intestinalis, was analyzed in unmanipulated and mi
186 anogaster and in the non-vertebrate chordate Ciona intestinalis, which each have only one talin gene,
216 In some chordates, including the ascidian Ciona, members of the Tbx2 subfamily of T-box genes are
217 zation of a minimal cardiac enhancer for the Ciona Mesp gene demonstrated direct activation by the T-
218 gulatory elements that drive coexpression of Ciona muscle genes and obtained quantitative estimates o
229 changed and then restored, underscoring the Ciona notochord's amenability for in vivo studies of PCP
232 RPE65 nor LRAT orthologs occur in tunicates (Ciona) or cephalochordates (Branchiostoma), but occur in
233 diac genes were analyzed, including the sole Ciona ortholog of the Drosophila tinman gene, and tissue
237 closest invertebrate relatives, the tunicate Ciona, processes light and gravity cues through a simple
239 ession of Dmbx genes from amphioxus and from Ciona, representing the two most closely related lineage
240 in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF, MyoD a
241 ibility that the PPE-derived GnRH neurons of Ciona resemble an ancestral cell type, a progenitor to t
242 tions of these proteins in Branchiostoma and Ciona, respectively, providing an insight into the ances
243 h MEK or Fgfr inhibitor at tailbud stages in Ciona results in a larva which fails to form atrial plac
244 Comparisons to the homologous lineage in Ciona revealed identical cell division and fate specific
245 is is exemplified by two invasive tunicates, Ciona robusta (formerly Ciona intestinalis type A) and C
246 define the identity of blood cell states in Ciona robusta, a member of the tunicate subphylum, the s
247 intricate pathway is remarkably conserved in Ciona robusta, a non-vertebrate chordate in the tunicate
248 mmonly found within the pharyngeal basket of Ciona robusta, a pivotal model species in marine biology
249 sion during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interact
255 nificant progress has been made in utilizing Ciona's genomic and morphological simplicity to better u
258 Here we show that the recessive short-tailed Ciona savignyi mutation chongmague (chm) has a novel def
259 affecting early development in the ascidian Ciona savignyi resulted in the isolation of a number of
260 l mutation in the gene dmrt1 in the ascidian Ciona savignyi results in profound abnormalities in the
264 ped to assemble the genome of the sea squirt Ciona savignyi, which was sequenced to a depth of 12.7 x
269 ied two potential neural crest cell types in Ciona, sensory pigment cells and bipolar tail neurons(5,
270 pendymal cells of the neural tube, while the Ciona snail homologue is expressed at the junction betwe
271 omparative sequence analysis between the two Ciona species for guiding gene regulatory experiments.
275 es are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ances
276 turbation of the FGF pathway in the ascidian Ciona support a similar role for this pathway: inhibitio
282 determined that the notochord expression of Ciona Tbx2/3 (Ci-Tbx2/3) requires Ci-Bra, and identified
287 tochord intercalation are cell-autonomous in Ciona, though such defects have nonautonomous effects in
288 ident community in limiting the abundance of Ciona through experiments conducted on fertilization, la
289 veraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereot
290 e-cell genomics in the simple chordate model Ciona to reconstruct developmental trajectories forming
294 tion between CiMRF and an essential E-box of Ciona Troponin I is required for the expression of this
295 cation of Xbp1-downstream notochord genes in Ciona, we found evidence of the early co-option of genes
297 cardiopharyngeal mesoderm in the urochordate Ciona, where a related gene regulatory network determine
298 ional analyses in zebrafish and the tunicate Ciona, which has a single GATA4/5/6 homolog, revealed th
299 e from embryonic development in the ascidian Ciona, which is dependent upon the transcription factors