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Junghoon Yoon - One of the best experts on this subject based on the ideXlab platform.
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description of lutimonas Halocynthiae sp nov isolated from a golden sea squirt Halocynthia aurantium reclassification of aestuariicola saemankumensis as lutimonas saemankumensis comb nov and emended description of the genus lutimonas
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:: A Gram-stain-negative, non-motile, coccoid, ovoid or rod-shaped bacterial strain, designated RSS3-C1(T), was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS3-C1(T) was found to grow optimally at 20-25 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS3-C1(T) clustered with the type strains of Lutimonas vermicola and Aestuariicola saemankumensis. Strain RSS3-C1(T) exhibited 98.8% 16S rRNA gene sequence similarity to each type strain. Strain RSS3-C1(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 0), iso-C(17 : 0) 3-OH and anteiso-C(15 : 0) as the major fatty acids. The major polar lipids of strain RSS3-C1(T) were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain RSS3-C1(T) was 39.2 mol%, and DNA-DNA relatedness to the type strains of and was 21±5.3 and 26±7.5 %, respectively. The differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RSS3-C1(T) is separated from and . On the basis of the data presented, strain RSS3-C1(T) is considered to represent a novel species of the genus Lutimonas, for which the name Lutimonas Halocynthiae sp. nov. is proposed. The type strain is RSS3-C1(T) ( = KCTC 32537(T) = CECT 8444(T)). In this study, it is also proposed that Aestuariicola saemankumensis should be reclassified as a member of the genus Lutimonas, as Lutimonas saemankumensis comb. nov. (type strain SMK-142(T) = KCTC 22171(T) = CCUG 55329(T)), and the description of the genus Lutimonas is emended.
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ruegeria meonggei sp nov an alphaproteobacterium isolated from ascidian Halocynthia roretzi
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2014Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:A Gram-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated MA-E2-3T, was isolated from an ascidian (Halocynthia roretzi) collected from the South Sea, South Korea. Strain MA-E2-3T was found to grow optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MA-E2-3T fell within the clade comprising Ruegeria species, clustering consistently with the type strain of Ruegeria Halocynthiae, with which it exhibited 98.2 % sequence similarity. Sequence similarities to the type strains of the other recognized Ruegeria species were 94.7–97.7 %. Strain MA-E2-3T was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c as the predominant fatty acid. The major polar lipids of strain MA-E2-3T were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA-E2-3T was determined to be 58.0 mol%. Mean DNA–DNA relatedness values between strain MA-E2-3T and the type strains of four phylogenetically closely related Ruegeria species were in the range of 13–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MA-E2-3T is separated from other Ruegeria species. On the basis of the data presented, strain MA-E2-3T (=KCTC 32450T = CECT 8411T) represents a novel species of the genus Ruegeria, for which the name Ruegeria meonggei sp. nov. is proposed.
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litoreibacter Halocynthiae sp nov isolated from the sea squirt Halocynthia roretzi
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:A Gram-stain-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated P-MA1-7T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain P-MA1-7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain P-MA1-7T fell within the cluster comprising the type strains of four species of the genus Litoreibacter , exhibiting 16S rRNA gene sequence similarity values of 97.0–98.5 % to these four type strains and less than 95.9 % sequence similarity to the strains of the other species examined. Strain P-MA1-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids of strain P-MA1-7T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain P-MA1-7T was 58.3 mol% and DNA–DNA relatedness values of strain P-MA1-7T with the type strains of the four species of the genus Litoreibacter were in the range of 8–21 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain P-MA1-7T was separate from other species of the genus Litoreibacter . On the basis of these data, strain P-MA1-7T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter Halocynthiae sp. nov. is proposed. The type strain is P-MA1-7T ( = KCTC 32213T = CCUG 63416T).
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tenacibaculum Halocynthiae sp nov a member of the family flavobacteriaceae isolated from sea squirt Halocynthia roretzi
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2013Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:A Gram-negative, non-spore-forming, aerobic, non-flagellated, non-gliding and rod-shaped bacterial strain, designated P-R2A1-2T, was isolated from sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. It grew optimally at 25–28 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that the strain fell within the clade comprising Tenacibaculum species. Strain P-R2A1-2T exhibited the highest 16S rRNA gene sequence similarity values of 97.6, 97.2 and 97.0 % to Tenacibaculum aestuarii SMK-4T, T. lutimaris TF-26T and T. aiptasiae a4T, respectively, and of 94.5–96.8 % to the type strains of the other Tenacibaculum species. Strain P-R2A1-2T contained MK-6 as the predominant menaquinone and C16:1 ω7c and/or iso-C15:0 2-OH, iso-C15:0 3-OH and iso-C15:0 as the major fatty acids. The DNA G + C content of strain P-R2A1-2T was 30.7 mol % and its DNA–DNA relatedness values with the type strains of T. aestuarii, T. lutimaris and T. aiptasiae were 17 ± 4.2, 21 ± 6.1 and 16 ± 5.2 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that the novel strain is separate from other Tenacibaculum species. On the basis of the data presented, strain P-R2A1-2T is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum Halocynthiae sp. nov. is proposed. The type strain is P-R2A1-2T (=KCTC 32262T = CCUG 63681T).
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ruegeria Halocynthiae sp nov isolated from the sea squirt Halocynthia roretzi
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Sooyeon Park, Sojung Kang, Taekwang Oh, Junghoon YoonAbstract:A Gram-negative, motile, ovoid- to rod-shaped bacterial strain, designated MA1-10T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain MA1-10T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain MA1-10T clustered with Roseovarius crassostreae CV919-312T, with which it exhibited 97.1 % sequence similarity, at a bootstrap resampling value of 96.2 %. It exhibited 93.3–95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized Roseovarius species. Strain MA1-10T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid, which is consistent with data for the genus Roseovarius . The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-10T was 55.4 mol%. Mean DNA–DNA relatedness between strain MA1-10T and R. crassostreae DSM 16950T was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain MA1-10T could be distinguished from all recognized Roseovarius species. On the basis of the data presented, strain MA1-10T is considered to represent a novel species of the genus Roseovarius , for which the name Roseovarius Halocynthiae sp. nov. is proposed; the type strain is MA1-10T ( = KCTC 23462T = CCUG 60745T).
Kazuhiro W Makabe - One of the best experts on this subject based on the ideXlab platform.
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characterization of a novel member of the fgfr family hrfgfr in Halocynthia roretzi
Biochemical and Biophysical Research Communications, 2000Co-Authors: Shuichi Kamei, Hiroaki Yamamoto, Kazuhiro W Makabe, Ichiro Yajima, Ako Kobayashi, Hidetoshi Yamazaki, Shinichi Hayashi, Takahiro KunisadaAbstract:Abstract The cDNA for a novel member of the FGFR family, named HrFGFR, was isolated from a Halocynthia roretzi cDNA library prepared at the mid-tailbud stage. This cDNA was 3507b long, and the deduced amino acid sequence contained a motif characteristic of the vertebrate FGFRs. The existence of a single copy of the FGFR homologue gene in H. roretzi was suggested by restriction site analysis of multiple clones. HrFGFR mRNA was expressed strongly in the posterior region in the epidermis from the middle neurula stage. By contrast, Xenopus FGFR homologues are expressed in the anterior region and are known to induce anterior neural formation. A transition of the region expressing FGFR might have induced the more complicated brain or head formation characteristic of vertebrates.
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expression patterns of musashi homologs of the ascidians Halocynthia roretzi and ciona intestinalis
Development Genes and Evolution, 2000Co-Authors: Takeshi Kawashima, Yasunori Sasakura, Michio Ogasawara, Akikazu R Murakami, Kimio J Tanaka, Ryuji Isoda, Takahito Nishikata, Hideyuki Okano, Kazuhiro W MakabeAbstract:The gene family encoding RNA-binding proteins includes important regulators involved in the neurogenesis in both protostomes and deuterostomes. We isolated cDNAs of the ascidian homolog of one of the RNA-binding proteins, MUSASHI, from Halocynthia roretzi and Ciona intestinalis. The predicted amino acid sequences contained two RNA-recognition and RNA-binding motifs in the N-terminus and an ascidian-specific YG-rich domain in the C-terminus. Maternal transcripts of musashi were ubiquitous in early cleavage-stage embryos. Ascidian musashi had three domains of zygotic expression: the brain, nerve cord, and mesenchyma. The temporal order of the onset in these domains was highly divergent between the two species of ascidian examined.
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maternally localized rna encoding a serine threonine protein kinase in the ascidian Halocynthia roretzi
Mechanisms of Development, 1998Co-Authors: Yasunori Sasakura, Michio Ogasawara, Kazuhiro W MakabeAbstract:Abstract Maternally localized cytoplasmic determinants play important roles in the embryogenesis of many animals, including ascidians. Cytoplasmic determinants are particularly important in the determination of cell fates, and in the establishment of the embryonic axes. Ascidians, which show mosaic development, are good models for the study of maternal cytoplasmic determinants. Here we report the isolation and characterization of HrPOPK-1 ( Halocynthia roretzi posterior protein kinase-1), a putative protein serine/threonine kinase. HrPOPK-1 cDNA was obtained from a Halocynthia roretzi fertilized egg cDNA library by screening for localized RNAs using whole-mount in situ hybridization. HrPOPK-1 mRNA is strongly localized at the posterior pole of embryos. The pattern of HrPOPK-1 mRNA localization during early embryogenesis is identical to that of HrWnt-5 in Halocynthia roretzi , and to those of the posterior end mark ( pem ) transcripts of Ciona savignyi . In addition, HrPOPK-1 shows zygotic expression in neural tissues at the tailbud stage. These results show that the temporal regulation of HrPOPK-1 transcription is complex.
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Maternally localized RNA encoding a serine/threonine protein kinase in the ascidian, Halocynthia roretzi
Mechanisms of Development, 1998Co-Authors: Yasunori Sasakura, Michio Ogasawara, Kazuhiro W MakabeAbstract:Abstract Maternally localized cytoplasmic determinants play important roles in the embryogenesis of many animals, including ascidians. Cytoplasmic determinants are particularly important in the determination of cell fates, and in the establishment of the embryonic axes. Ascidians, which show mosaic development, are good models for the study of maternal cytoplasmic determinants. Here we report the isolation and characterization of HrPOPK-1 ( Halocynthia roretzi posterior protein kinase-1), a putative protein serine/threonine kinase. HrPOPK-1 cDNA was obtained from a Halocynthia roretzi fertilized egg cDNA library by screening for localized RNAs using whole-mount in situ hybridization. HrPOPK-1 mRNA is strongly localized at the posterior pole of embryos. The pattern of HrPOPK-1 mRNA localization during early embryogenesis is identical to that of HrWnt-5 in Halocynthia roretzi , and to those of the posterior end mark ( pem ) transcripts of Ciona savignyi . In addition, HrPOPK-1 shows zygotic expression in neural tissues at the tailbud stage. These results show that the temporal regulation of HrPOPK-1 transcription is complex.
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Introduction and Expression of Recombinant Genes in Ascidian Embryos
Development Growth & Differentiation, 1992Co-Authors: Akira Hikosaka, Takehiro Kusakabe, Noriyuki Satoh, Kazuhiro W MakabeAbstract:In order to examine the expression of exogenous genes introduced into ascidian eggs, two recombinant plasmids pmiwZ and pHrMA4aCAT were microinjected into the cytoplasm of fertilized eggs of Ciona savignyi and Halocynthia roretzi, respectively. The plasmid pmiwZ contains the coding sequence of bacterial β-galactosidase gene (lac-Z) fused with animal gene promoters, while pHrMA4aCAT was constructed by fusing about 1.4-kb long 5′ flanking region of H. roretzi muscle actin gene HrMA4a with bacterial chloramphenicol acetyltransferase gene (CAT). Injection of approximately 160 pl of 10 μg/ml pmiwZ DNA into Ciona eggs did not affect the embryogenesis, although introduction of the same volume of 30 μg/ml pmiwZ DNA resulted in abnormal development of injected eggs. When the expression of lac-Z was examined by histochemical detection of the enzyme activity, the expression was evident in the early tailbud embryos and later stage embryos, and larvae, irrespective of linear or circular form of the plasmid. The enzyme activity appeared in various cell-types including epidermis, nervous system, endoderm, mesenchyme, notochord, and muscle. In contrast, when pHrMA4aCAT was introduced into Halocynthia eggs and the appearance of CAT protein was examined later by the anti-CAT antibody, the CAT expression was restricted to muscle cells. These results indicate that the recombinant genes introduced into ascidian eggs could express during embryogenesis and that the 1.4-kb long 5′ flanking region of HrMA4a contains regulatory sequences enough for the appropriate spatial and temporal expression of the gene.
Hiroki Nishida - One of the best experts on this subject based on the ideXlab platform.
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genome wide survey of mirnas and their evolutionary history in the ascidian Halocynthia roretzi
BMC Genomics, 2017Co-Authors: Christelle Dantec, Kai Wang, Patrick Lemaire, Takeshi A Onuma, Hiroki NishidaAbstract:Abstract Background miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona . Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi , has become available, but miRNAs in H. roretzi have not been previously studied. Results We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods. Experimental validation suggests that more than half of these candidate miRNAs are expressed during embryogenesis. The majority of predicted H. roretzi miRNAs appear specific to ascidians or tunicates, and only 32 candidates, belonging to 25 families, are widely conserved across metazoans. Conclusion Our study presents a comprehensive identification of candidate H. roretzi miRNAs. This resource will facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidian development. Further, our analysis suggests that the majority of Halocynthia miRNAs are specific to ascidian or tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the general notion that animal miRNAs are less conserved between taxa than plant ones.
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FGF9/16/20 and Wnt-5α signals are involved in specification of secondary muscle fate in embryos of the ascidian, Halocynthia roretzi
Development Genes and Evolution, 2007Co-Authors: Miki Tokuoka, Gaku Kumano, Hiroki NishidaAbstract:The tail muscle cells of the ascidian tadpole larva originate from two different lineages, the B- (primary) and A- and b- (secondary) line blastomeres of the eight-cell stage embryo. The primary muscle cells assume muscle fate cell-autonomously with the involvement of a localized muscle determinant, macho-1. On the other hand, fate determination of secondary muscle cells is a non-cell-autonomous process that depends on cellular interactions. In this paper, we investigated the mechanisms underlying fate specification of secondary muscle cells in Halocynthia roretzi . We found that FGF and Wnt5 signals were required. In contrast, the Nodal signal, which is required for specification of A-line muscle cells in another ascidian, Ciona intestinalis , was not necessary for the formation of any secondary muscle cells in Halocynthia embryo. Therefore, Halocynthia and Ciona show distinctly different mechanisms for generation of the secondary lineages, despite the fact that embryogenesis appears very similar between these species. We also found that the mechanisms involved in specification of A- and b-line muscle cells were distinct in that the required timing of the FGF signal for the A-line muscle cells preceded that for the b-line. Moreover, the inducer blastomeres for specification of these two lineages were different.
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fgf9 16 20 and wnt 5α signals are involved in specification of secondary muscle fate in embryos of the ascidian Halocynthia roretzi
Development Genes and Evolution, 2007Co-Authors: Miki Tokuoka, Gaku Kumano, Hiroki NishidaAbstract:The tail muscle cells of the ascidian tadpole larva originate from two different lineages, the B- (primary) and A- and b- (secondary) line blastomeres of the eight-cell stage embryo. The primary muscle cells assume muscle fate cell-autonomously with the involvement of a localized muscle determinant, macho-1. On the other hand, fate determination of secondary muscle cells is a non-cell-autonomous process that depends on cellular interactions. In this paper, we investigated the mechanisms underlying fate specification of secondary muscle cells in Halocynthia roretzi. We found that FGF and Wnt5 signals were required. In contrast, the Nodal signal, which is required for specification of A-line muscle cells in another ascidian, Ciona intestinalis, was not necessary for the formation of any secondary muscle cells in Halocynthia embryo. Therefore, Halocynthia and Ciona show distinctly different mechanisms for generation of the secondary lineages, despite the fact that embryogenesis appears very similar between these species. We also found that the mechanisms involved in specification of A- and b-line muscle cells were distinct in that the required timing of the FGF signal for the A-line muscle cells preceded that for the b-line. Moreover, the inducer blastomeres for specification of these two lineages were different.
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Developmental roles of nuclear complex factors released during oocyte maturation in the ascidians Halocynthia roretzi and Boltenia villosa.
Zoological Science, 1998Co-Authors: William R. Bates, Hiroki NishidaAbstract:Abstract The developmental roles of factors associated with the nuclear complex of Halocynthia roretzi and Boltenia villosa oocytes were investigated by cutting mature oocytes into animal and vegetal merogons before and during GVBD. Animal and vegetal merogons were cultured in sea water until the GV cytoplasm had dispersed within the cytoplasm of control oocytes and then they were cross-fertilized and scored for their ablility to undergo normal development. Halocynthia oocyte fragments produced from the animal region of oocytes containing intact GVs exhibited a low frequency of polyspermy, a high frequency of fertilization and cleavage, and a high frequency of expressing an epidermal antigen, Epi-2. In contrast, merogons produced from the vegetal region of Halocynthia oocytes in which GVs were intact exhibited a high frequency of polyspermy, did not undergo cell division, and expressed a high frequency of Epi-2 expression. When vegetal fragments were produced after the dispersal of approximately 50-70% of...
Sooyeon Park - One of the best experts on this subject based on the ideXlab platform.
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description of lutimonas Halocynthiae sp nov isolated from a golden sea squirt Halocynthia aurantium reclassification of aestuariicola saemankumensis as lutimonas saemankumensis comb nov and emended description of the genus lutimonas
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:: A Gram-stain-negative, non-motile, coccoid, ovoid or rod-shaped bacterial strain, designated RSS3-C1(T), was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS3-C1(T) was found to grow optimally at 20-25 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS3-C1(T) clustered with the type strains of Lutimonas vermicola and Aestuariicola saemankumensis. Strain RSS3-C1(T) exhibited 98.8% 16S rRNA gene sequence similarity to each type strain. Strain RSS3-C1(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 0), iso-C(17 : 0) 3-OH and anteiso-C(15 : 0) as the major fatty acids. The major polar lipids of strain RSS3-C1(T) were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain RSS3-C1(T) was 39.2 mol%, and DNA-DNA relatedness to the type strains of and was 21±5.3 and 26±7.5 %, respectively. The differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RSS3-C1(T) is separated from and . On the basis of the data presented, strain RSS3-C1(T) is considered to represent a novel species of the genus Lutimonas, for which the name Lutimonas Halocynthiae sp. nov. is proposed. The type strain is RSS3-C1(T) ( = KCTC 32537(T) = CECT 8444(T)). In this study, it is also proposed that Aestuariicola saemankumensis should be reclassified as a member of the genus Lutimonas, as Lutimonas saemankumensis comb. nov. (type strain SMK-142(T) = KCTC 22171(T) = CCUG 55329(T)), and the description of the genus Lutimonas is emended.
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ruegeria meonggei sp nov an alphaproteobacterium isolated from ascidian Halocynthia roretzi
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2014Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:A Gram-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated MA-E2-3T, was isolated from an ascidian (Halocynthia roretzi) collected from the South Sea, South Korea. Strain MA-E2-3T was found to grow optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MA-E2-3T fell within the clade comprising Ruegeria species, clustering consistently with the type strain of Ruegeria Halocynthiae, with which it exhibited 98.2 % sequence similarity. Sequence similarities to the type strains of the other recognized Ruegeria species were 94.7–97.7 %. Strain MA-E2-3T was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c as the predominant fatty acid. The major polar lipids of strain MA-E2-3T were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA-E2-3T was determined to be 58.0 mol%. Mean DNA–DNA relatedness values between strain MA-E2-3T and the type strains of four phylogenetically closely related Ruegeria species were in the range of 13–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MA-E2-3T is separated from other Ruegeria species. On the basis of the data presented, strain MA-E2-3T (=KCTC 32450T = CECT 8411T) represents a novel species of the genus Ruegeria, for which the name Ruegeria meonggei sp. nov. is proposed.
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litoreibacter Halocynthiae sp nov isolated from the sea squirt Halocynthia roretzi
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:A Gram-stain-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated P-MA1-7T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain P-MA1-7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain P-MA1-7T fell within the cluster comprising the type strains of four species of the genus Litoreibacter , exhibiting 16S rRNA gene sequence similarity values of 97.0–98.5 % to these four type strains and less than 95.9 % sequence similarity to the strains of the other species examined. Strain P-MA1-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids of strain P-MA1-7T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain P-MA1-7T was 58.3 mol% and DNA–DNA relatedness values of strain P-MA1-7T with the type strains of the four species of the genus Litoreibacter were in the range of 8–21 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain P-MA1-7T was separate from other species of the genus Litoreibacter . On the basis of these data, strain P-MA1-7T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter Halocynthiae sp. nov. is proposed. The type strain is P-MA1-7T ( = KCTC 32213T = CCUG 63416T).
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tenacibaculum Halocynthiae sp nov a member of the family flavobacteriaceae isolated from sea squirt Halocynthia roretzi
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2013Co-Authors: Sooyeon Park, Yongtaek Jung, Junghoon YoonAbstract:A Gram-negative, non-spore-forming, aerobic, non-flagellated, non-gliding and rod-shaped bacterial strain, designated P-R2A1-2T, was isolated from sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. It grew optimally at 25–28 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that the strain fell within the clade comprising Tenacibaculum species. Strain P-R2A1-2T exhibited the highest 16S rRNA gene sequence similarity values of 97.6, 97.2 and 97.0 % to Tenacibaculum aestuarii SMK-4T, T. lutimaris TF-26T and T. aiptasiae a4T, respectively, and of 94.5–96.8 % to the type strains of the other Tenacibaculum species. Strain P-R2A1-2T contained MK-6 as the predominant menaquinone and C16:1 ω7c and/or iso-C15:0 2-OH, iso-C15:0 3-OH and iso-C15:0 as the major fatty acids. The DNA G + C content of strain P-R2A1-2T was 30.7 mol % and its DNA–DNA relatedness values with the type strains of T. aestuarii, T. lutimaris and T. aiptasiae were 17 ± 4.2, 21 ± 6.1 and 16 ± 5.2 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that the novel strain is separate from other Tenacibaculum species. On the basis of the data presented, strain P-R2A1-2T is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum Halocynthiae sp. nov. is proposed. The type strain is P-R2A1-2T (=KCTC 32262T = CCUG 63681T).
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ruegeria Halocynthiae sp nov isolated from the sea squirt Halocynthia roretzi
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Sooyeon Park, Sojung Kang, Taekwang Oh, Junghoon YoonAbstract:A Gram-negative, motile, ovoid- to rod-shaped bacterial strain, designated MA1-10T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain MA1-10T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain MA1-10T clustered with Roseovarius crassostreae CV919-312T, with which it exhibited 97.1 % sequence similarity, at a bootstrap resampling value of 96.2 %. It exhibited 93.3–95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized Roseovarius species. Strain MA1-10T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid, which is consistent with data for the genus Roseovarius . The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-10T was 55.4 mol%. Mean DNA–DNA relatedness between strain MA1-10T and R. crassostreae DSM 16950T was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain MA1-10T could be distinguished from all recognized Roseovarius species. On the basis of the data presented, strain MA1-10T is considered to represent a novel species of the genus Roseovarius , for which the name Roseovarius Halocynthiae sp. nov. is proposed; the type strain is MA1-10T ( = KCTC 23462T = CCUG 60745T).
Gaku Kumano - One of the best experts on this subject based on the ideXlab platform.
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h3k27me3 suppresses sister lineage somatic gene expression in late embryonic germline cells of the ascidian Halocynthia roretzi
Developmental Biology, 2020Co-Authors: Tao Zheng, Ayaki Nakamoto, Gaku KumanoAbstract:Abstract Protection of the germline from somatic differentiation programs is crucial for germ cell development. In many animals, whose germline development relies on the maternally inherited germ plasm, such protection in particular at early stages of embryogenesis is achieved by maternally localized global transcriptional repressors, such as PIE-1 of Caenorhabditis elegans, Pgc of Drosophila melanogaster and Pem of ascidians. However, zygotic gene expression starts in later germline cells eventually and mechanisms by which somatic gene expression is selectively kept under repression in the transcriptionally active cells are poorly understood. By using the ascidian species Halocynthia roretzi, we found that H3K27me3, a repressive transcription-related chromatin mark, became enriched in germline cells starting at the 64-cell stage when Pem protein level and its contribution to transcriptional repression decrease. Interestingly, inhibition of H3K27me3 together with Pem knockdown resulted in ectopic expression in germline cells of muscle developmental genes Muscle actin (MA4) and Snail, and of Clone 22 (which is expressed in all somatic but not germline cells), but not of other tissue-specific genes such as the notochord gene Brachyury, the nerve cord marker ETR-1 and a heart precursor gene Mesp, at the 110-cell stage. Importantly, these ectopically expressed genes are normally expressed in the germline sister cells (B7.5), the last somatic lineage separated from the germline. Also, the ectopic expression of MA4 was dependent on a maternally localized muscle determinant Macho-1. Taken together, we propose that H3K27me3 may be responsible for selective transcriptional repression for somatic genes in later germline cells in Halocynthia embryos and that the preferential repression of germline sister-lineage genes may be related to the mechanism of germline segregation in ascidian embryos, where the germline is segregated progressively by successive asymmetric cell divisions during cell cleavage stages. Together with findings from C. elegans and D. melanogaster, our data for this urochordate animal support the proposal for a mechanism, conserved widely throughout the animal kingdom, where germline transcriptional repression is mediated initially by maternally localized factors and subsequently by a chromatin-based mechanism.
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microinjection of exogenous dna into eggs of Halocynthia roretzi
Advances in Experimental Medicine and Biology, 2018Co-Authors: Gaku KumanoAbstract:Exogenous gene expression assays during development, including reporters under the control of 5′ upstream enhancer regions of genes, constitute a powerful technique for understanding the mechanisms of tissue-specific gene expression regulation and determining the characteristics, behaviors, and functions of cells that express these genes. The simple marine chordate Halocynthia roretzi has been used for these transgenic analyses for a long time and is an excellent model system for such studies, especially in comparative analyses with other ascidians. In this study, I describe simple methods for microinjecting H. roretzi eggs with exogenous DNA, such as a promoter construct consisting of a 5′ upstream region and a reporter gene, which are prerequisites for transgenic analyses. I also describe basic knowledge regarding this ascidian species, providing reasons why it is an ideal subject for developmental biology studies.
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FGF9/16/20 and Wnt-5α signals are involved in specification of secondary muscle fate in embryos of the ascidian, Halocynthia roretzi
Development Genes and Evolution, 2007Co-Authors: Miki Tokuoka, Gaku Kumano, Hiroki NishidaAbstract:The tail muscle cells of the ascidian tadpole larva originate from two different lineages, the B- (primary) and A- and b- (secondary) line blastomeres of the eight-cell stage embryo. The primary muscle cells assume muscle fate cell-autonomously with the involvement of a localized muscle determinant, macho-1. On the other hand, fate determination of secondary muscle cells is a non-cell-autonomous process that depends on cellular interactions. In this paper, we investigated the mechanisms underlying fate specification of secondary muscle cells in Halocynthia roretzi . We found that FGF and Wnt5 signals were required. In contrast, the Nodal signal, which is required for specification of A-line muscle cells in another ascidian, Ciona intestinalis , was not necessary for the formation of any secondary muscle cells in Halocynthia embryo. Therefore, Halocynthia and Ciona show distinctly different mechanisms for generation of the secondary lineages, despite the fact that embryogenesis appears very similar between these species. We also found that the mechanisms involved in specification of A- and b-line muscle cells were distinct in that the required timing of the FGF signal for the A-line muscle cells preceded that for the b-line. Moreover, the inducer blastomeres for specification of these two lineages were different.
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fgf9 16 20 and wnt 5α signals are involved in specification of secondary muscle fate in embryos of the ascidian Halocynthia roretzi
Development Genes and Evolution, 2007Co-Authors: Miki Tokuoka, Gaku Kumano, Hiroki NishidaAbstract:The tail muscle cells of the ascidian tadpole larva originate from two different lineages, the B- (primary) and A- and b- (secondary) line blastomeres of the eight-cell stage embryo. The primary muscle cells assume muscle fate cell-autonomously with the involvement of a localized muscle determinant, macho-1. On the other hand, fate determination of secondary muscle cells is a non-cell-autonomous process that depends on cellular interactions. In this paper, we investigated the mechanisms underlying fate specification of secondary muscle cells in Halocynthia roretzi. We found that FGF and Wnt5 signals were required. In contrast, the Nodal signal, which is required for specification of A-line muscle cells in another ascidian, Ciona intestinalis, was not necessary for the formation of any secondary muscle cells in Halocynthia embryo. Therefore, Halocynthia and Ciona show distinctly different mechanisms for generation of the secondary lineages, despite the fact that embryogenesis appears very similar between these species. We also found that the mechanisms involved in specification of A- and b-line muscle cells were distinct in that the required timing of the FGF signal for the A-line muscle cells preceded that for the b-line. Moreover, the inducer blastomeres for specification of these two lineages were different.
