ホヤを用いた初期発生メカニズムの分子·進化発生学的研究 (ホヤ, 母性因子, 局在RNA, genome, EST, 転写因子ネットワーク, 小分子RNA)
Book / Paper
Book:
1.
宮島 郁子, 奥田 晶彦, 村松 正實, 濱田 博司 and Kazuhiro W. Makabe : 調節するゲノム, 西村書店,
2.
Kazuhiro W. Makabe : ウイルト発生生物学, Tokyo Kagaku Dozin C., Ltd., Tokyo, Feb. 2006.
3.
Kazuhiro W. Makabe and 西方 敬人 : 「超実践バイオ実験イラストレイテッド レッスン1.キットも活用遺伝子実験」 秀潤社, 2005.
4.
Kazuhiro W. Makabe and T. Kawashima : MAGEST:a database of MAboya Gene Expression patterns and Sequence Tags., John Wiley&Sons,Weinheim, 2002.
5.
Kazuhiro W. Makabe, T. Kawashima, S. Kawashima, Y. Sasakura, H. Ishikawa, H. Kawamura, M. Kanehisa, T. Nishikata and H. Nishida : Maternal genetic information stored in fertilized eggs of the ascidian,Halocynthia roretzi., Springer-Verlag Tokyo, Tokyo, 2001.
6.
Kazuhiro W. Makabe and 西駕 俊秀 : 発生における遺伝子発現, University of Tokyo Press, Tokyo, 1998.
7.
Kazuhiro W. Makabe : 苦労なしのクローニング, Shujunsha Co.Ltd., Tokyo, Jun. 1997.
8.
Kazuhiro W. Makabe, N. Satoh and S. Fujiwara : Cell lineeage and differentiation of muscle cells in prochordate embryos., Frontiers in Muscle Research(eds.by E.Ozawa,T.Masaki&Y.Nabeshima), 1991.
9.
Kazuhiro W. Makabe and 佐藤 矩行 : ホヤの筋肉細胞はどのようにしてできるか, University of Tokyo Press, 1990.
Academic Paper (Judged Full Paper):
1.
Kazuhiro W. Makabe and Swalla W Makabe Hannah I Jensen Alexander C A Fodor Jennifer Hsu William R Jeffery Noriyuki Satoh Billie J Kazuhiro : Cymric, a Maternal and Zygotic HTK-16-Like SHARK Family Tyrosine Kinase Gene, Is Disrupted in Molgula occulta, a Tailless Ascidian, The Biological Bulletin, Vol.245, No.1, 1-8, 2023.
(Summary)
AbstractWe describe the cloning and expression of a nonreceptor tyrosine kinase, (), a () gene, identified in a subtractive screen for maternal ascidian cDNAs in , an ascidian species with a tadpole larva. The gene encodes a 4-kb mRNA expressed in gonads, eggs, and embryos in the tailed but is not detected in eggs or embryos of the closely related tailless species . There is a large insertion in in the genome, as shown by transcriptome and genome analyses, resulting in it becoming a pseudogene. The amino acid sequence encodes a nonreceptor tyrosine kinase with an N-terminal region containing two SH2 domains and five ankyrin repeats, similar to the gene found in other ascidians. Thus, the ascidian genes are members of the SHARK (Src-homology ankyrin-repeat containing tyrosine kinase) family of nonreceptor tyrosine kinases, which are found throughout invertebrates and missing from vertebrates. We show that is lacking the tyrosine kinase domain in the tailless , although the truncated mRNA is still expressed in transcriptome data. This maternal and zygotic tyrosine kinase is another described pseudogene from and appears not to be necessary for adult development.
Kazuhiro W. Makabe and Hiroki Nishida : Cytoplasmic localization and reorganization in ascidian eggs: role of postplasmic/PEM RNAs in axis formation and fate determination., Wiley Interdisciplinary Reviews. Developmental Biology, Vol.1, No.4, 501-518, 2012.
(Summary)
Localization of maternal molecules in eggs and embryos and cytoplasmic movements to relocalize them are fundamental for the orderly cellular and genetic processes during early embryogenesis. Ascidian embryos have been known as 'mosaic eggs' because of their autonomous differentiation abilities based on localized cell fate determinants. This review gives a historical overview of the concept of cytoplasmic localization, and then explains the key features such as ooplasmic movements and cell lineages that are essential to grasp the process of ascidian development mediated by localized determinant activities. These activities are partly executed by localized molecules named postplasmic/PEM RNAs, originating from approximately 50 genes, of which the muscle determinant, macho-1, is an example. The cortical domain containing these RNAs is relocalized to the posterior-vegetal region of the egg by cytoskeletal movements after fertilization, and plays crucial roles in axis formation and cell fate determination. The cortical domain contains endoplasmic reticulum and characteristic granules, and gives rise to a subcellular structure called the centrosome-attracting body (CAB), in which postplasmic/PEM RNAs are highly concentrated. The CAB is responsible for a series of unequal partitionings of the posterior-vegetal cytoplasmic domain and the postplasmic/PEM RNAs at the posterior pole during cleavage. Some components of this domain, which is rich in granules, are eventually inherited by prospective germline cells with particular postplasmic/PEM RNAs such as vasa. The postplasmic/PEM RNAs are classified into two groups according to their final cellular destinations and localization pathways. Localization of these RNAs is regulated by specific nucleotide sequences in the 3' untranslated regions (3'UTRs).
Olivier Tassy, Delphine Dauga, Fabrice Daian, Daniel Sobral, François Robin, Pierre Khoueiry, David Salgado, Vanessa Fox, Danièle Caillol, Renaud Schiappa, Baptiste Laporte, Anne Rios, Guillaume Luxardi, Takehiro Kusakabe, Jean-Stéphane Joly, Sébastien Darras, Lionel Christiaen, Magali Contensin, Hélène Auger, Clément Lamy, Clare Hudson, Ute Rothbächer, Michael J. Gilchrist, Kazuhiro W. Makabe, Kohji Hotta, Shigeki Fujiwara, Nori Satoh, Yutaka Satou and Patrick Lemaire : The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program., Genome Research, Vol.20, No.10, 1459-1468, 2010.
(Summary)
Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions.
Kazuhiro W. Makabe and Hiroshi Wada : Genome duplications of early vertebrates as a possible chronicle of the evolutionary history of the neural crest., International Journal of Biological Sciences, Vol.2, No.3, 133-141, 2006.
(Summary)
It is now accepted that ancestral vertebrates underwent two rounds of genome duplication. Here we test the possible utility of these genome duplication events as a reference time for the evolutionary history of vertebrates, by tracing the molecular evolutionary history of the genes involved in vertebrate neural crest development. For most transcription factors that are involved in neural crest specification, more than two paralogs are involved in that process. These were likely involved in the specification of the neural crest before the genome duplications occurred in ancestral vertebrates, although FoxD3 may have acquired that role after the genome duplications. By contrast, the epithelial-mesenchymal transition of neural crest cells is controlled by genes that evolved after the genome duplications, such as cadherin6, cadherin7, cadherin11, and rhoB. This suggests that primitive neural crest cells control their delamination by using a small or distinct set of cell adhesion molecules. Alternatively, these observations suggest that delamination of the neural crest evolved after the genome duplications. In that case, the neural crest might have evolved in sequential steps; the specification of the neural crest occurred before the genome duplications, and the neural crest acquired a new cell migration property after the genome duplications.
Kazuhiro W. Makabe, Y Nakamura and Hiriki Nishida : The functional analysis of Type postplasmic/PEM mRNAs in embryos of the ascidian Halocynthia roretzi., Development Genes and Evolution, Vol.216, No.2, 69-80, 2005.
(Summary)
Maternal factors, such as a muscle determinant macho-1 mRNA that is localized to the posterior-vegetal cortex (PVC) of fertilized ascidian eggs, are crucial for embryonic axis formation and cell fate specification. Maternal mRNAs that show an identical posterior localization pattern to that of macho-1 in eggs and embryos are called Type I postplasmic/PEM mRNAs. We investigated the functions of five of the nine Type I mRNAs so far known in Halocynthia roretzi: Hr-Wnt-5, Hr-GLUT, Hr-PEM3, Hr-PEN1, and Hr-PEN2. Suppression of their functions with specific antisense morpholino oligonucleotides (MOs) had effects on the formation of various tissues: Hr-Wnt-5 on notochord, muscle, and mesenchyme, although zygotic function of Hr-Wnt-5 is responsible for notochord formation; Hr-GLUT on notochord, mesenchyme, and endoderm; and Hr-PEN2 on muscle, mesenchyme, and endoderm. On the other hand, Hr-PEM3 and Hr-PEN1 MOs seemed to have no effect. We conclude that the functions of at least some localized maternal Type I postplasmic/PEM mRNAs are necessary for early embryonic patterning in ascidians.
Kazuhiro W. Makabe, Y. Nakamura and H. Nishida : POPK-1/Sad-1 kinase is required for the proper translocation of maternal mRNAs and putative germ plasm at the posterior pole of the ascidian embryo., Development, Vol.132, No.21, 4731-4742, 2005.
(Summary)
Maternal mRNAs localized to specific regions in eggs play important roles in the establishment of embryonic axes and germ layers in various species. Type I postplasmic/PEM mRNAs, which are localized to the posterior-vegetal cortex (PVC) of fertilized ascidian eggs, such as the muscle determinant macho-1 mRNA, play key roles in embryonic development. In the present study, we analyzed the function of the postplasmic/PEM RNA Hr-POPK-1, which encodes a kinase of Halocynthia roretzi. When the function of POPK-1 was suppressed by morpholino antisense oligonucleotides, the resulting malformed larvae did not form muscle or mesenchyme, as in macho-1-deficient embryos. Epistatic analysis indicated that POPK-1 acts upstream of macho-1. When POPK-1 was knocked down, localization of every Type I postplasmic/PEM mRNA examined, including macho-1, was perturbed, showing diffuse early distribution and eventual concentration into a smaller area. This is the probable reason for the macho-1 dysfunction. The postplasmic/PEM mRNAs such as macho-1 and Hr-PEM1 are co-localized with the cortical endoplasmic reticulum (cER) and move with it after fertilization. Eventually they become highly concentrated into a subcellular structure, the centrosome-attracting body (CAB), at the posterior pole of the cleaving embryos. The suppression of POPK-1 function reduced the size of the domain of concentrated cER at the posterior pole, indicating that POPK-1 is involved in the movement of postplasmic/PEM RNAs via relocalization of cER. The CAB also shrank. These results suggest that Hr-POPK-1 plays roles in concentration and positioning of the cER, as well as in the concentration of CAB materials, such as putative germ plasm, in the posterior blastomeres.
Kazuhiro W. Makabe, K. Takahasshi, Y. Tokuzawa, M. Maruyama and Y. Oda : Evolutionarily conserved Non-AUG translation in NAT1/p97/DAP5(ELF4G3), Genomics 85, Vol.85, 360-371, 2005.
Kazuhiro W. Makabe, C.A. Shepherdley, W. Klootwijk and T.J. Visser : An ascidian homelog of vertebrate iodothyronine deiodonases., Endocrinology, Vol.145, No.3, 1255-1268, 2003.
(Summary)
In all classes of vertebrates, the deiodination of the prohormone T(4) to T(3) represents an essential activation step in thyroid hormone action. The possible presence of iodothyronine deiodinase activity in protochordates has been demonstrated in vivo. Recent molecular cloning of the genomes and transcripts of several ascidian species allows further investigation into thyroid-related processes in ascidians. A cDNA clone from Halocynthia roretzi (hrDx) was found to have significant homology (30% amino acid identity) with the iodothyronine deiodinase gene sequences from vertebrates, including the presence of an in-frame UGA codon that might encode a selenocysteine (SeC) in the active site. Because it was not certain that the 3' untranslated region (UTR) contained a SeC insertion sequence (SECIS) element essential for SeC incorporation, a chimeric expression vector of the hrDx coding sequence and the rat deiodinase SECIS element was produced, as well as an expression vector containing the intact hrDx cDNA. COS, CHO, and HEK cells were transfected with these vectors, and deiodinase activity was measured in cell homogenates. Outer-ring deiodinase activity was detected using both T(4) and reverse T(3) as substrates, and activity was enhanced by the presence of the reductive cofactor dithiothreitol. The enzyme activity was optimal during incubation between 20 and 30 C (pH 6-7) and was strongly inhibited by gold-thioglucose. The Halocynthia deiodinase appears to be a high Michaelis-Menten constant (K(m)) enzyme (K(m) reverse T(3), 2 microM; and K(m) T(4), 4 microM). Deiodinase activity was completely lost upon the substitution of the SeC residue in the putative catalytic center by either cysteine or alanine. Transfection of the full-length hrDx cDNA produced deiodinase activity confirming the presence of a SECIS element in the 3'UTR, as revealed by the SECISearch program. In conclusion, our results show, for the first time, the existence of an ascidian iodothyronine outer-ring deiodinase. This raises the hypothesis that, in protochordates, the prohormone T(4) is activated by enzymatic outer-ring deiodination to T(3).
Kazuhiro W. Makabe, S. J. Kauffman, A. Zinovyeva, K. Yagi and A. R. Raff : Neural Expression of the Huntington's Disease Gene as a Chordate Evolutionary Novelty., Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution, Vol.297, No.1, 57-64, 2003.
(Summary)
Huntington's disease is a progressive neuro-degenerative disorder in humans, which is scharacterized by onset of dementia, muscular ataxia, and death. Huntington's disease is caused by the expansion of the polyglutamine (polyQ) tract in the N-terminus of the HD protein (Huntingtin). CAG expansion is a dominant gain of function mutation that affects striated neurons in the brain (Cattaneo, 2003, News Physiol Sci 18:34). The evolutionary origins of the vertebrate Hd gene are not well understood. In order to address the evolutionary history of the Hd gene, we have cloned and characterized the expression of the Hd gene in two invertebrate deuterostomes, an echinoderm and an ascidian, and have examined the expression patterns in a phylogenetic context. Echinoderms are basal deuterostomes and ascidians are basal chordates; both are useful for understanding the origins of and evolutionary trends in genes important in vertebrates such as the Huntigton's disease gene. Expression of Hd RNA is detected at all stages of development in both the echinoderm and ascidian studied. In the echinoderm Heliocidaris erythrogramma, Hd is expressed in coelomic mesodermal tissue derivatives, but not in the central nervous system. In the ascidian Halocynthia roretzi expression is located in both mesoderm and nervous tissue. We suggest that the primitive deuterostome expression pattern is not neural. Thus, neural expression of the Hd gene in deuterostomes may be a novel feature of the chordate lineage, and the original role(s) of HD in deuterostomes may have been non-neural.
Kazuhiro W. Makabe, Y. Nakamura and H. Nishida : Localization and expression pattern of type I postplasmic mRNAs in embryos of the ascidian Halocynthia roretzi., Gene Expression Patterns, Vol.3, No.1, 71-75, 2003.
(Summary)
The posterior-vegetal cytoplasm (PVC) of fertilized ascidian eggs plays important roles in embryo development. It has been reported that some maternal RNAs are localized to the PVC. We identified four novel type I postplasmic mRNAs that are localized to the PVC through the use of data from a cDNA project of maternal mRNAs in the eggs of Halocynthia roretzi (MAGEST database). The mRNAs are HrGLUT, HrPEN-1, and HrPEM-3, which show similarity to a glucose transporter, a g1-related protein, and Ciona pem-3, respectively; and HrPEN-2, with no similarity. Maternal mRNAs of all four genes were identically localized to the PVC after ooplasmic segregation. During cleavage, they were concentrated in the centrosome-attracting body (CAB) and were then segregated into the small blastomeres located at the posterior pole. This localization pattern is common to all known type I postplasmic mRNAs found so far. HrGLUT, HrPEN-1, and HrPEM-3 were expressed zygotically in various tissues later in embryogenesis: HrGLUT and HrPEM-3 in the mesenchyme and nervous system, and HrPEN-1 in the ectodermal cells.
Kazuhiro W. Makabe, C-P. Wang, K. Yagi, J. P. Lin, Y. D. Jin and W. D. Stafford : Identification of a gene encoding a typical gamma-carboxyglutamic acid domain in the tunicate Halocynthia roretzi., Journal of Thrombosis and Haemostasis, Vol.1, No.1, 118-123, 2003.
(Summary)
We report the identification of a gene capable of encoding a novel Gla (gamma-carboxyglutamic acid) protein from the tunicate Halocynthia roretzi, a primitive member of the phylum Chordata. We call this new hypothetical protein Gla-RTK; it has a Gla domain typical of human vitamin K-dependent coagulation factors, a transmembrane domain, and a receptor tyrosine kinase domain. The receptor tyrosine kinase domain is very similar to the ARK (adhesion-related kinase) family of receptor tyrosine kinases. The ARK family includes Axl, Tyro3, and c-Mer. This gene also encodes a propeptide that binds to the human gamma-glutamyl carboxylase within a range of affinities observed for mammalian propeptides. The cDNA for this putative protein is found distributed throughout the oocyte and embryo but the cDNA is apparently not transcribed except during oogenesis. One of the most interesting aspects of this hypothetical protein is that its Gla domain is highly homologous to the Gla domain of Gas6, a ligand for Axl, while its receptor tyrosine kinase domain is highly homologous to Axl.
(Keyword)
1-Carboxyglutamic Acid / Amino Acid Sequence / Animals / Base Sequence / Blood Coagulation Factors / DNA, Complementary / In Situ Hybridization / Molecular Sequence Data / Oogenesis / Peptides / Protein Structure, Tertiary / Receptor Protein-Tyrosine Kinases / Sequence Homology, Amino Acid / Tissue Distribution / Transcription, Genetic / Urochordata / Vitamin K
Kazuhiro W. Makabe, Paramvir Dehal, Yutaka Satoh, Kaoru Azumi, Margherita Branno, Robert K. Campbell, Bernard Degnan, Rosaria DeSantis, Anthony De Tomaso, Brad Davidson, Anna Di Gregorio, Naoe Harafuji, David N. Keys, Kenneth M. E. Hastings, Kohji Hotta, Kazuo Inaba, Shungo Kano, Takeshi Kawashima and Patrick Lemaire : The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins, Science, Vol.298, No.5601, 2157-2167, 2002.
(Summary)
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 approximately 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.
(Keyword)
Alleles / Animals / Apoptosis / Base Sequence / Cellulose / Central Nervous System / Ciona intestinalis / Computational Biology / Endocrine System / Gene Dosage / Gene Duplication / Genes / Genes, Homeobox / Genome / Heart / Immunity / Molecular Sequence Data / Multigene Family / Muscle Proteins / Organizers, Embryonic / Phylogeny / Polymorphism, Genetic / Proteins / Sequence Analysis, DNA / Sequence Homology, Nucleic Acid / Species Specificity / Thyroid Gland / Urochordata / Vertebrates
Kazuhiro W. Makabe and Y. Sasakura : Identification of the cis elements which direct the localization of maternal mRNAs to the posterior pole of ascidian embryos., Developmental Biology, Vol.250, No.1, 128-144, 2002.
(Summary)
During ascidian embryogenesis, some mRNAs show clear localization at the posterior-most region. These postplasmic mRNAs are divided into two groups (type I and type II) according to their pattern of localization. To elucidate how these localization patterns are achieved, we attempted to identify the localization elements of these mRNAs. When in vitro synthesized postplasmic mRNAs were introduced into eggs, these mRNAs showed posterior localization similar to the endogenous mRNAs. The posterior localization of these mRNAs was mediated by their 3' untranslated regions (3' UTRs), as is the case for several localized Drosophila and Xenopus mRNAs. We identified smaller fragments of the 3' UTRs of HrWnt-5 and HrPOPK-1 mRNAs (type I) and HrPet-3 mRNA (type II) that were sufficient to direct green fluorescent protein mRNA to the posterior pole. For the localization of HrWnt-5 mRNA, two UG dinucleotide repetitive elements were essential. Motifs similar to these small elements also exist within the HrPOPK-1 mRNA localization element and 3' UTR of HrZF-1 mRNA, suggesting the conservation of localization elements among type I mRNAs. In contrast, the smallest sequence that suffices for the posterior localization of HrPet-3 (a type II mRNA) has different features from those of type I mRNAs; indeed, it does not have an identifiable critical element. This difference may distinguish type II mRNAs from type I mRNAs. These findings, especially the identification of the small localization element of HrWnt-5 mRNA, provide new insights into the localization of mRNAs during ascidian embryogenesis.
Kazuhiro W. Makabe and Kasumi Yagi : Neural marker genes differently expressed in subsets of embryonic neural cells of the ascidian Halocynthia roretzi., Zoological Science, Vol.19, No.8, 885-889, 2002.
(Summary)
Ascidians are lower chordates that possess a possible prototype of the vertebrate nervous system. The central and peripheral nervous systems of ascidian larvae are composed of only a few hundred cells (Nicol and Meinertzhagen, 1991). To investigate how these ascidian nervous systems develop, dissection at the molecular level using subset-specific markers is essential. Here we describe four new genes zygotically expressed in subsets of the ascidian neural cells. The spatial expression domains of these genes overlap in some parts but not in other parts of the nervous systems. Our results suggest that there are functionally different regions in the nervous systems owing to the gene expression differences. Further analyses of these genes will enable us to determine the molecular neuro-developmental characteristics of various clusters of neural cells.
Kazuhiro W. Makabe and Kasumi Yagi : Retinoic acid differently affects the formation of palps and surrounding neurons in the ascidian tadpole., Development Genes and Evolution, Vol.212, No.6, 288-292, 2002.
(Summary)
The anterior-most surface of the ascidian tadpole larvae is composed of specialized complex structures, including adhesive organs (palps) and the surrounding sensory neurons (RTENs) connected to neurons inside the palps. These are derived from a-line blastomeres by inductive effects from A-line blastomeres. The induction is reported to coordinate the expression of homeobox genes in the anterior epidermis, which can be affected by all- trans retinoic acid (RA). RA treatment also results in failure of the morphological formation of palps. Here we first isolated a gene intensely expressed in the cells of the anterior structure from the time of their lineage restriction, and then found that the RA treatment did not affect the specific gene expression in the presumptive palp cells but did affect that in the RTENs. These results suggest that the palp formation involves at least two different processes, a RA-insensitive cell-type specification process and a RA-sensitive morphogenetic process. RA treatment also affects the morphogenetic process of the palp formation and also disturbs the precise patterning of the surrounding epidermis, which may contribute to the regulation of RTEN development.
Takeshi Kawashima, Shuichi Kawashima, Yuji Kohara, Minoru Kanehisa and Kazuhiro W. Makabe : Update of MAGEST: MAboya Gene Expression patterns and Sequence Tags., Nucleic Acids Research, Vol.30, No.1, 119-120, 2002.
(Summary)
MAGEST is a database for maternal gene expression information for an ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows a simple developmental process, and belongs to one of the chordate groups. Various data are deposited into the MAGEST database, e.g. the 3'- and 5'-tag sequences from the fertilized egg cDNA library, the results of similarity searches against GenBank and the expression data from whole mount in situ hybridization. Over the last 2 years, the data retrieval systems have been improved in several aspects, and the tag sequence entries have increased to over 20 000 clones. Additionally, we constructed a database, translated MAGEST, for the amino acid fragment sequences predicted from the EST data sets. Using this information comprehensively, we should obtain new information on gene functions. The MAGEST database is accessible via the Internet at http://www.genome.ad.jp/magest/.
Kazuhiro W. Makabe and Y. Sasakura : Ascidian Wnt-5 gene is involved in the morphogenetic movement of notochord cells., Development Growth & Differentiation, Vol.43, No.5, 573-582, 2001.
(Summary)
Wnt proteins play important roles in many developmental events. Wnts are divided into two groups according to biological function. The Wnt-5a class proteins function in morphogenetic movement during embryogenesis. Previously, a Wnt-5 homolog has been isolated from the ascidian, Halocynthia roretzi. HrWnt-5 is expressed in the notochord until the tail-bud stage, implying a role in the notochord. In this study, the function of HrWnt-5 was investigated. When HrWnt-5 mRNA was injected into fertilized eggs, the embryos showed morphologic defects at around the neurula stage. The anterior-posterior axis was shorter than in control embryos. These defects were caused by the abnormal movement of notochord cells. However, the overexpression of HrWnt-5 mRNA did not affect the differentiation of tissues, suggesting that HrWnt-5 solely regulates the morphogenetic movement. Although endogenous HrWnt-5 is expressed in the notochord, the overexpression of HrWnt-5 mRNA caused the defects, suggesting that the amount of HrWnt-5 mRNA in the notochord is strictly regulated. These results suggest that HrWnt-5 regulates the morphogenetic movement of notochord cells during ascidian embryogenesis.
Kazuhiro W. Makabe, Michio Ogasawara, Takuya Minokawa, Yasunori Sasakura and Hiroki Nishida : A large-scale whole-mount in situ hybridization system: rapid one-tube preparation of DIG-labeled RNA probes and high throughput hybridization using 96-well silent screen plates., Zoological Science, Vol.18, No.2, 187-193, 2001.
(Summary)
Recent progress in multiple and automated-sequencing technology allows large-scale random cDNA sequencing, the so-called EST project, in various fields. In addition to the EST collection, the cDNA project requires analysis of spatiotemporal patterns of gene expression of a large number of clones by whole-mount in situ hybridization (WISH). To facilitate the multiple WISH procedures, we developed a protocol for rapid and uniform synthesis of multiple probes and multi-well based WISH processing. A DIG-labeled RNA probe for WISH was synthesized from a PCR-amplified template which contained an RNA promoter. All reactions of PCR and subsequent RNA synthesis were performed in a single tube by sequential addition of the reagents without phenol extraction or ethanol precipitation steps. An RNA probe was purified and condensed by a centrifugal ultrafilter to achieve high and stable purification efficiency. WISH of 96 samples were performed simultaneously in a 96-well plate attached to silent screen filters that were connected with a vacuum exhausting system. These processes eliminated the labor-intensive steps of WISH and provided opportunities to search for novel genes.
Kazuhiro W. Makabe and Ako Kobayashi : Expression patterns of smad family members during embryogenesis of the ascidian Halocynthia roretzi., Zoological Science, Vol.18, No.6, 833-842, 2001.
(Summary)
The ascidian embryo has been long thought to show a mosaic mode of development. However, recent studies revealed significance of cell-cell communication during cleavage stages of embryogenesis. FGF and BMP signalings play critical roles in determination of cell types. Little is, however, known about regulation of competence of cells to the signals. Here we report the isolation of ascidian smad genes ; Hrsmad4 which encodes a homolog of smad4 of vertebrates, Hrsmad6/7 which encodes a homologous gene of smad 6 and smad7 of vertebrates, and Hrsmad2/3 which encodes a homolog of smad2 and smad3 of vertebrates. The mRNAs of the isolated smad family genes were maternally inherited in egg and early embryos. While Hrsmad4 and Hrsmad6/7 RNAs distributed broadly in the early embryos, Hrsmad2/3 RNA was preferentially accumulated in the animal hemisphere.
Kazuhiro W. Makabe, T. Kawashima, S. Kawashima, T. Minokawa, A. Adachi, H. Kawamura, H. Ishikawa, R. Yasuda, H. Yamamoto, K. Kondoh and S. Arioka : Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development., Development, Vol.128, No.13, 2555-2567, 2001.
(Summary)
The ascidian egg is a well-known mosaic egg. In order to investigate the molecular nature of the maternal genetic information stored in the egg, we have prepared cDNAs from the mRNAs in the fertilized eggs of the ascidian, Halocynthia roretzi. The cDNAs of the ascidian embryo were sequenced, and the localization of individual mRNA was examined in staged embryos by whole-mount in situ hybridization. The data obtained were stored in the database MAGEST (http://www.genome.ad.jp/magest) and further analyzed. A total of 4240 cDNA clones were found to represent 2221 gene transcripts, including at least 934 different protein-coding sequences. The mRNA population of the egg consisted of a low prevalence, high complexity sequence set. The majority of the clones were of the rare sequence class, and of these, 42% of the clones showed significant matches with known peptides, mainly consisting of proteins with housekeeping functions such as metabolism and cell division. In addition, we found cDNAs encoding components involved in different signal transduction pathways and cDNAs encoding nucleotide-binding proteins. Large-scale analyses of the distribution of the RNA corresponding to each cDNA in the eight-cell, 110-cell and early tailbud embryos were simultaneously carried out. These analyses revealed that a small fraction of the maternal RNAs were localized in the eight-cell embryo, and that 7.9% of the clones were exclusively maternal, while 40.6% of the maternal clones showed expression in the later stages. This study provides global insights about the genes expressed during early development.
Yasunori Sasakura and Kazuhiro W. Makabe : A gene encoding a new ONECUT class homeodomain protein in the ascidian Halocynthia roretzi functions in the differentiation and specification of neural cells in a scidian embryogenesis., Mechanisms of Development, Vol.104, No.1-2, 37-48, 2001.
(Summary)
Genes encoding a novel group of homeodomain transcription factors, ONECUT class homeodomain proteins, have previously been isolated from vertebrate and insect. Among them, vertebrate HNF-6 is expressed in hepatocytes and the central nervous system during embryogenesis. Although the functions of HNF-6 in hepatocytes have been well studied, the functions of HNF-6 in the central nervous system remain unknown. In this study, we isolated HrHNF-6, which encodes a new ONECUT class homeodomain protein, from an ascidian, Halocynthia roretzi. HrHNF-6 mRNA was expressed exclusively in neural cells, just posterior to the expression of Hroth during embryogenesis. One of the functions of HrHNF-6 in neural cells is the activation of the expression of HrTBB2, the ascidian beta-tubulin gene. Another is the restriction of the expression of HrPax-258 (which is expressed in the neural tube), suggesting that HrHNF-6 functions in the specification of the neural tube. These results indicate that HrHNF-6 functions in the differentiation and regional specification of neural cells during ascidian embryogenesis.
Kazuhiro W. Makabe, T. Minokawa, K. Yagi and H. Nishida : Binary specification of nerve cord and notochord cell fates in ascidian embryos., Development, Vol.128, No.11, 2007-2017, 2001.
(Summary)
In the ascidian embryo, the nerve cord and notochord of the tail of tadpole larvae originate from the precursor blastomeres for both tissues in the 32-cell-stage embryo. Each fate is separated into two daughter blastomeres at the next cleavage. We have examined mechanisms that are responsible for nerve cord and notochord specification through experiments involving blastomere isolation, cell dissociation, and treatment with basic fibroblast growth factor (bFGF) and inhibitors for the mitogen-activated protein kinase (MAPK) cascade. It has been shown that inductive cell interaction at the 32-cell stage is required for notochord formation. Our results show that the nerve cord fate is determined autonomously without any cell interaction. Presumptive notochord blastomeres also assume a nerve cord fate when they are isolated before induction is completed. By contrast, not only presumptive notochord blastomeres but also presumptive nerve cord blastomeres forsake their default nerve cord fate and choose the notochord fate when they are treated with bFGF. When the FGF-Ras-MAPK signaling cascade is inhibited, both blastomeres choose the default nerve cord pathway, supporting the results of blastomere isolation. Thus, binary choice of alternative fates and asymmetric division are involved in this nerve cord/notochord fate determination system, mediated by FGF signaling.
(Keyword)
Animals / Blastomeres / Butadienes / Cell Differentiation / Central Nervous System / Fibroblast Growth Factor 2 / Mitogen-Activated Protein Kinases / Nitriles / Notochord / Pyrroles / Receptors, Fibroblast Growth Factor / Signal Transduction / Urochordata
(Link to Search Site for Scientific Articles)
● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 11493523
Kazuhiro W. Makabe and K. Yagi : Isolation of an early neural maker gene abundantly expressed in the nervous system of the ascidian, Halocynthia roretzi., Development Genes and Evolution, Vol.211, No.1, 49-53, 2001.
(Summary)
Ascidian tadpole larvae possess a primitive nervous system, which is a prospective prototype of the chordate nervous system. It is composed of relatively few cells but sufficient for complex larval behavior. Here we report on HrETR-1, a gene zygotically expressed in a large proportion of the developing neural cells of the ascidian, Halocynthia roretzi. HrETR-1 is an early neural marker which can be used for analyzing neural differentiation. HrETR-1 expression intensified in most neural cells of genes isolated to date, in both central and peripheral nervous systems including palps as early as the 110-cell stage. Using this gene as a probe, we characterized neural cells in the nervous system as well as confirming their origins. Also, we recognized three types of peripheral epidermal neurons which presumably correlate to the larval neurons previously reported for another ascidian. Among these, five bilateral neurons located in the anterior region of the trunk appeared to be derived from a8.26 blastomeres.
Kazuhiro W. Makabe and Y. Sasakura : Ascidian Wnt-7 gene is expressed exclusively in the tail neural tube of tailbud embryos., Development Genes and Evolution, Vol.210, No.12, 641-643, 2000.
(Summary)
In vertebrate embryogenesis, many Wnt genes are expressed in the neural tube and play important roles in regional specifications. There are many subfamilies of Wnt, and each subfamily shows distinct expression patterns in the neural tube. Ascidian larvae have a dorsal hollow neural tube similar to that of vertebrates. To date, the degree of correspondence between regionality of the neural tubes of ascidians and vertebrates remains unclear. To compare cellular differences in neural tubes, Wnt genes can be used as molecular probes. We report here that a new member of the ascidian Wnt gene family, HrWnt-7, was expressed in the tail neural tube at the early tailbud stage. Moreover, in cross-section, HrWnt-7 was expressed in the dorsal and ventral ependymal cells.
Kazuhiro W. Makabe, Shuichi Kamei, Ichiro Yajima, Hiroaki Yamamoto, Ako Kobayashi, Hidetoshi Yamazaki, Shin-Ichi Hayashi and Takahiro Kunisada : Characterization of a novel member of the FGFR family ,HrFGFR ,in Halocynthia roretzi., Biochemical and Biophysical Research Communications, Vol.275, No.2, 503-508, 2000.
(Summary)
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.
Kazuhiro W. Makabe, Y. Sasakura and M. Ogasawara : Two pathways of maternal RNA localization at the posterior-vegetal cytoplasm in early ascidian embryos., Developmental Biology, Vol.220, No.2, 365-378, 2000.
(Summary)
A cDNA library prepared from fertilized eggs of the ascidian Halocynthia roretzi was screened for prelocalized mRNAs in the early embryo by means of whole-mount in situ hybridization using a digoxigenin-labeled antisense RNA of each clone. Random mass screening of 150 cDNAs in a fertilized egg yielded six different clones which showed mRNA localization in the posterior-vegetal cytoplasm of the 8-cell embryo. An in situ hybridization study of the detailed spatial distribution of each mRNA in embryos of various stages revealed that there are, in contrast to the identical localization in embryos after the 16-cell stage, two distinct patterns of RNA distribution at earlier stages. One is colocalization with the myoplasm from the prefertilization stage to the 8-cell stage (type I postplasmic RNAs). The other is delayed accumulation of RNA at the posterior-vegetal cytoplasm after fertilization (type II postplasmic RNAs). We found that both types of RNAs associate with the cytoskeleton, but that they show different sensitivities to inhibitors of the cytoskeleton; translocation of the type I RNAs is dependent upon microfilaments during the first phase of ooplasmic segregation and dependent upon microtubules during the second phase of segregation, whereas translocation of the type II RNAs is dependent upon microfilaments throughout ooplasmic segregation. These results show that there are two pathways for the localization of the RNAs at the posterior-vegetal cytoplasm in the 8-cell embryo of the ascidian H. roretzi.
Kazuhiro W. Makabe, T. Kawashima, S. Kawashima, M. Kaneshisa and H. Nishida : Expression of musashi homologs of the ascidian, Halocynthia roretzi and Ciona intestinalis., Development Genes and Evolution, Vol.210, No.3, 162-165, 2000.
(Summary)
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.
Takeshi Kawashima, Shuichi Kawashima, Minoru Kaneshisa, Hiroki Nishida and Kazuhiro W. Makabe : MAGEST: MAboya Gene Expression patterns and Sequence Tags., Nucleic Acids Research, Vol.28, No.1, 133-135, 2000.
(Summary)
MAGEST is a database for newly identified maternal cDNAs of the ascidian, Halocynthia roretzi, which aims to examine the population of the mRNAs. We have collected 3' and 5' tag sequences of mRNAs and their expression data from whole-mount in situ hybridi-zation in early embryos. To date, we have determined more than 2000 tag-sequences of H.roretzi cDNAs and input them into public databases. The tag sequences and the expression data as well as additional information can be obtained through MAGEST via the WWW at http://www.genome.ad.jp/magest/
Kazuhiro W. Makabe, A. Kobayashi, M. Ogasawara and Y. Sasakura : A maternal RNA encoding smadl 1/5 is segregated to the animal blastomeres during ascidian development, Development Growth & Differentiation, Vol.41, 419-427, 1999.
30.
Yasunori Sasakura, Michio Ogasawara and Kazuhiro W. Makabe : Maternally localized RNA encoding a serine/threonine protein kinase in the ascidian,Halocynthia roretzi., Mechanisms of Development, Vol.76, No.1-2, 161-163, 1998.
31.
Kazuhiro W. Makabe, Y. Sasakura and M. Ogasawara : Hr Wnt-5:a maternally expressed ascidian Wnt gene with posterior localization in early embryos., The International Journal of Developmental Biology, Vol.42, No.4, 573-580, 1998.
(Summary)
Ascidians show a highly determinate mode of development. In particular, components of the posterior-vegetal cytoplasm of fertilized eggs are responsible for the establishment of the embryonic axis. Recent studies have, however, also revealed significant roles of cell-cell interactions during embryogenesis. Proteins encoded by the Wnt family of genes act as signals and have been shown to play important roles in a wide range of developmental processes. Here we have isolated and characterized an ascidian Wnt gene, HrWnt-5, from Halocynthia roretzi. HrWnt-5 mRNA is present in the vegetal cortex in unfertilized eggs. After fertilization, HrWnt-5 mRNA moves to the equatorial region to form a crescent-like structure, after which the mRNA is concentrated in the posteriormost region of the embryo. This early pattern of HrWnt-5 mRNA localization coincides with another posterior-vegetally localized mRNA, pem, isolated from Ciona savignyi. In the gastrula, the zygotic HrWnt-5 mRNA is found in a variety of blastomeres, suggesting multiple roles of the gene.
Kazuhiro W. Makabe, H. Takahashi, K. Ishida and N. Satoh : Isolation of cDNA clones for genes that are expressed in the tail region of the ascidiantailbud embryo., The International Journal of Developmental Biology, Vol.41, No.5, 691-698, 1997.
(Summary)
An ascidian tailbud embryo is comprised of the anterior trunk and posterior tail. We constructed cDNA libraries of the tail region and trunk region of the ascidian Halocynthia roretzi. The screening of the tail library by tail single-stranded cDNA minus the trunk library RNA as a probe, yielded cDNA clones for genes that are expressed in the tail epidermis, visceral ganglion, trunk lateral cells, muscle cells, and certain regions of the tail. Among them, a cDNA clone for a gene designated HrPost-1 is described in detail. HrPost-1 encodes a novel, possible secreted protein of 238 amino acids. The expression of the gene is zygotic. HrPost-1 transcript was first evident in the posterior B-line blastomeres including muscle cells and endodermal strand cells of the gastrula-stage embryo, and the expression in these regions disappeared by the early tailbud stage. Around neurulation, the HrPost-1 transcript appeared in epidermal cells of the posterior-most region of the embryo. As development proceeded, the gene expression spread anteriorly in the epidermal cells of the neurula and tailbud embryo, and thus at the early-to-mid tailbud stage, HrPost-1 expression appeared to define the boundary between the trunk and tail epidermis. These results suggest that, in addition to tissue-specific genes, the activities of a set of region-specific genes are associated with tail formation in the ascidian embryo.
Kazuhiro W. Makabe, S. Hori and T. Saitoh : Notch homologue from Halocynthia roretzi is preferentially expressed in the central nervous system during ascidian embryogenesis, Development Genes and Evolution, Vol.207, No.6, 371-380, 1997.
Kazuhiro W. Makabe, E. Yasuda, T. Goto and N. Satoh : Expression of actin genes in the arrow worm Paraspadellagotoi(Chaetognatha.), Zoological Science, Vol.14, 953-960, 1997.
35.
Kazuhiro W. Makabe, Michio Ogasawara, Kimio J Tanaka and Noriyuki Satoh : Expression of endostyle-specific gene in the ascidian Halocynthia roretzi, Development Genes and Evolution, Vol.206, No.3, 227-235, 1996.
(Summary)
The endostyle is a special organ in the pharynx of Urochordata, Cephalochordata and Cyclostomata. This organ may have arisen in their common ancestor with a shift to internal feeding for extracting suspended food from the water. In addition, the endostyle has functional homology to the vertebrate thyroid gland. The endostyle is therefore another key structure in the understanding of the origin and evolution of chordates. Following a previous report of the pharyngeal gill-specific genes, we report here the isolation and characterization of cDNA clones for endostyle-specific genes HrEnds1 and HrEnds2 of the ascidian Halocynthia roretzi. These cDNA clones were obtained by differential screening of an endostyle cDNA library and a pharyngeal gill cDNA library with total endostyle cDNA probes. Both transcripts were abundant in the library; each represented about 10% of the cDNA clones of the library. The HrEnds1 transcript was small in size, about 600 bp in length. Although the predicted amino acid sequence of the gene product showed no similarity to known proteins, mean hydropathy profiles suggested that HrENDS1 is a type Ib protein or secreted protein. The HrEnds2 transcript was about 2.5 kb in length. Although the HrEnds2 gene product showed no sequence similarity to known proteins, mean hydropathy profiles suggested that HrENDS2 is a secreted protein. The transcripts of both genes were not detected in embryos, larvae and early juveniles but were evident in 1-month-old young adult after several compositional zones were organized in the endostyle. In situ hybridization revealed that distribution of transcripts of both genes was restricted to zone 6, the protein-secreting glandular element of the endostyle. These genes may be useful for further analysis of molecular mechanisms involved in endostyle development.
Kazuhiro W. Makabe, Kimio J Tanaka, Michio Ogasawara and Noriyuki Satoh : Expression of Phryngeal gill-specific gene in the ascidian Halocynthia roretzi., Development Genes and Evolution, Vol.206, No.3, 218-226, 1996.
(Summary)
The most primitive chordates may have arisen with a shift to internal feeding through the use of the pharyngeal gill slits and endostyle for extracting suspended food from the water. Therefore, the pharyngeal gill and endostyle, in addition to notochord and nerve cord, are structures key to an understanding of the molecular developmental mechanisms underlying the origin and evolution of chordates. In this and a following study, isolation of cDNA clones for genes that are specifically expressed in the pharyngeal gill or endostyle in the ascidian Halocynthia roretzi was attempted. Differential screening of a pharyngeal gill cDNA library and an endostyle cDNA library with total pharyngeal-gill cDNA probes yielded cDNA clones for two pharyngeal gill-specific genes, HrPhG1 and HrPhG2. Northern blot analysis showed a 3.0-kb transcript of HrPhG1 and a 2.0-kb transcript of HrPhG2. Predicted amino acid sequences of the gene products suggested that both genes encode secretory proteins with no significant match to known proteins. In adults, both HrPhG1 and HrPhG2 genes were only expressed in the pharyngeal gill and not in other tissues including the endostyle, body-wall muscle, gonad, gut and digestive gland. HrPhG1 and HrPhG2 transcripts were undetectable in embryos and larvae, and were first detected in juveniles 3 days after initiation of metamorphosis. In situ hybridization revealed that the expression of HrPhG1 and HrPhG2 was restricted to differentiating pharyngeal-wall epithelium, with intense signals in the area surrounding the stigma or gill slit. These genes may serve as probes for further analyses of molecular mechanisms underlying the occurrence of pharyngeal gill and formation of gill slits during chordate evolution.
Kazuhiro W. Makabe, C. V. Kirchhamer, R. J. Britten and E. H. Davidson : Cis-regulatory control of the SM50 gene,an early marker of skeletogenic lineage specification in the sea urchin embryo., Development, Vol.121, No.7, 1957-1970, 1995.
(Summary)
The SM50 gene encodes a minor matrix protein of the sea urchin embryo spicule. We carried out a detailed functional analysis of a cis-regulatory region of this gene, extending 440 bp upstream and 120 bp downstream of the transcription start site, that had been shown earlier to confer accurate skeletogenic expression of an injected expression vector. The distal portion of this fragment contains elements controlling amplitude of expression, while the region from -200 to +105 contains spatial control elements that position expression accurately in the skeletogenic lineages of the embryo. A systematic mutagenesis analysis of this region revealed four adjacent regulatory elements, viz two copies of a positively acting sequence (element D) that are positioned just upstream of the transcription start site; an indispensable spatial control element (element C) that is positioned downstream of the start site; and further downstream, a second positively acting sequence (element A). We then constructed a series of synthetic expression constructs. These contained oligonucleotides representing normal and mutated versions of elements D, C, and A, in various combinations. We also changed the promoter of the SM50 gene from a TATA-less to a canonical TATA box form, without any effect on function. Perfect spatial regulation was also produced by a final series of constructs that consisted entirely of heterologous enhancers from the CyIIIa gene, the SV40 early promoter, and synthetic D, C, and A elements. We demonstrate that element C exercises the primary spatial control function of the region we analyzed. We term this a 'locator' element. This differs from conventional 'tissue-specific enhancers' in that while it is essential for expression, it has no transcriptional activity on its own, and it requires other, separable, positive regulatory elements for activity. In the normal configuration these ancillary positive functions are mediated by elements A and D. Only positively acting control elements were observed in the SM50 regulatory domain throughout this analysis.
Kazuhiro W. Makabe, H. Saiga, N. Satoh and I. Araki : Expression of AMDI, a gene for a MyoD1-related factor in the ascidian Halocynthia roretzi., Roux's Archives of Developmental Biology, Vol.203, 320-327, 1994.
39.
Kazuhiro W. Makabe, T. Miya and N. Satoh : Expression of a gene for major mitochondrial protein, ADP/ATP translocase, during embryo gnesis in the ascidian Halocynthia roretzi., Development Growth & Differentiation, Vol.36, 39-48, 1994.
40.
Kazuhiro W. Makabe, Shigeki Fujiwara, Hiroyuki Kawahara and Noriyuki Satoh : A complementary DNA for an ascidian embryonic nuclear antigen closely related to the amphibian histone-binding protein N1., The Journal of Biochemistry, Vol.113, No.2, 189-195, 1993.
41.
Kazuhiro W. Makabe, A. Hikosaka and N. Satoh : Regulated spatial expression of fusion gene constructs with the 5' upstream region of Halocynthia roretzi muscle actin gene in Ciona savignvi embryos., Roux's Archives of Developmental Biology, Vol.203, 104-112, 1993.
42.
Kazuhiro W. Makabe, B. J. Swalla, N. Satoh and W. R. Jeffery : Novel genes expression differentially in ascidians with alternate modes of development., Development, Vol.119, 307-318, 1993.
43.
Takehiro Kusakabe, Noriyuki Satoh and Kazuhiro W. Makabe : Tunicate muscle actin gene. Structure and organization as a gene cluster., Journal of Molecular Biology, Vol.227, No.3, 955-960, 1992.
44.
Kazuhiro W. Makabe, H. Wada, M. Nakauchi and N. Satoh : Phylogenetic relationships between solitary and colonial ascidians,as inferred from the sequence of the central region o their respective 18S rDNAs., Biol.Bull., Vol.183, 448-455, 1992.
45.
Kazuhiro W. Makabe, A. hikosaka, T. Kusakabe and N. Satoh : Introduction and expression of recombinant gene in ascidian embryos., Development Growth & Differentiation, Vol.34, 627-634, 1992.
46.
Kazuhiro W. Makabe, S. Fujiwara, H. Nishida and S. Satoh : Failue of muscle myosin heavy-chain gene expression in quarter from the secondary muscle lineage cells., Zoological Science, Vol.9, 569-573, 1992.
47.
Kazuhiro W. Makabe, T. Ueki and N. Satoh : Isolation of cDNA clones for epidermis-specific genes of the ascidian embryo., Development Growth & Differentiation, Vol.33, 307-313, 1991.
48.
Kazuhiro W. Makabe, T. Kusakabe, J. Suzuki, H. Saiga, W. E. Jeffery and N. Satoh : Temporal and spatial expression of a muscle actin gene during embryo genesis of the ascidian Halocynthia roretzi, Development Growth & Differentiation, Vol.33, 227-234, 1991.
49.
Kazuhiro W. Makabe, H. Saiga, A. Mizokami, N. Satoh and T. Mita : Molecular cloning and expression of a novel homeobox gene AHoxl of the ascidia,Halocynthia roretzi., Deveropment, Vol.111, 821-828, 1991.
50.
Kazuhiro W. Makabe, S. Fujiwara, H. Saiga and N. Satoh : Specific expression of myosin heavy chain gene in muscle lineage cells of the ascidian embryo, Roux's Archives of Developmental Biology, Vol.199, 307-313, 1990.
51.
Kazuhiro W. Makabe and N. Satoh : temporal expression of myosin heavy chain gene during ascidian embryo genesis, Development Growth & Differentiation, Vol.31, 71-77, 1989.
Academic Paper (Unrefereed Paper):
1.
山中 瑞江, 脇加 奈子, 尾崎 絵里香, 金井 拓, 金井 悠一郎, 中辻 嵩, 谷川 和代, 橋本 美城子, 森 由美子, 倉林 陽子, 岸本 慎哉, 水本 浩太, Minoru Watanabe, Masaya Satoh, Kazuhiro W. Makabe, Makoto Ohashi and Toshio Gotoh : Comparative study on the primary structure of globin chains of the extracellular giant hemoglobin from the polychaet Perinereis aibuhitensis and Tylonrrhynchus heterochaetus, Natural Science Research, Faculty of Integrated Arts and Sciences, The University of Tokushima, Vol.19, 63-92, 2005.
Kazuhiro W. Makabe and H. Nishida : Maternal information in egg cytoplasm and localized maternal mRNAs in early embryos of the ascidian Halocynthia roretzi., Inverte.Repro.Dev., Vol.36, 41-49, 1999.
3.
Kazuhiro W. Makabe, N. Satoh, Y. Katsuyama, S. Wada and H. Saiga : The ascidian An experimental system for studying genetic circuitry for embryonic cell specification and morphogenesis., Development Growth & Differentiation, Vol.38, 325-340, 1996.
4.
Kazuhiro W. Makabe, N. Satoh and T. Nishikata : Egg cytoplasmic components responsible for larval muscle cell differentiation of ascidian embryos., Developmental Biology,UCLA Symposia Mol. Cell.Biol. (eds. by E.H. Davidson,J.V. Ruderman&J.W.Posakony.), Vol.125, 143-151, 1990.
5.
Kazuhiro W. Makabe, N. Satoh, T. Deno, H. Nishida and T. Nishikata : Cellular and molecular mechanisms of muscle cell differentiation in ascidian embryos., Int.Rev.Cytol., Vol.122, 221-258, 1990.
Review, Commentary:
1.
Kazuhiro W. Makabe and 佐藤 矩行 : 発生と遺伝情報, 数理科学「DNA:紐の物理ー分子情報から時空構造へのシナリオー」, Vol.40, No.6, 13-18, 2002.
2.
Kazuhiro W. Makabe and 川島 武士 : ホヤ卵内の母性遺伝子情報の網羅的解析, 蛋白質核酸酵素増刊「ゲノムサイエンスの新たなる挑戦」, 2246-2450, 2001.
3.
Kazuhiro W. Makabe : 間充織細胞のみに発現する遺伝子の制御, 遺伝「ウニの発生学-新展開を迎えたウニの生物学」, Vol.48, No.4, 29-33, 1994.
4.
Kazuhiro W. Makabe and 嶋田 拓 : 日米セミナー「海産無脊椎動物発生の分子生物学」に参加して, The Cell, Vol.23, No.12, 50-51, 1991.
5.
Kazuhiro W. Makabe : 日米セミナーに出席して, 生物科学ニュース, No.235, 50-51, 1991.
6.
Kazuhiro W. Makabe : ホヤ胚の筋細胞系列と筋細胞分化機構, The Cell, Vol.18, No.12, 393-397, 1986.
Kazuhiro W. Makabe, 田端 義厳, 荒木 良子, 安倍 真澄 and 西田 宏紀 : The 15th International Society of Developmental Biologists Congress,Sydney,Australia,2005,
(Summary)
A Sensitive Transcriptome Analysis of Divergence of the embryonic Epidermal and Neural fates of Ascidian Halocynthia roretzi
2.
Kazuhiro W. Makabe, 田端 義厳, 荒木 良子, 安倍 真澄 and 西田 宏紀 : The 2nd International Symposium and Annual Meeting of Dynamics of Developmental Systems, 千葉, 2005.
(Summary)
A Sensitive Transcriptome Analysis of Divergence of the embryonic Epidermal and Neural fates of the Ascidian Halocynthia roretzi.
3.
Kazuhiro W. Makabe : Genome Science of Halocynthia:toward Comparative Genomics., 4th Workshop of Anton Dohrn,Naple,Zoological Station,New Perpective in Tunicate Biology., Ischia(Italy), 2001.
4.
Kazuhiro W. Makabe : Maternal mRNA repatoir in Ascidian Egg, Developmental Biology of the Sea Urchin XIII, Woods Hole(USA), 2000.
5.
Kazuhiro W. Makabe : Maternal Genetic Information in Ascidian Egg., AEARU Meeting on Molecular Biology., Pohang(Korea), 2000.
6.
Kazuhiro W. Makabe : Maternal Genetic Information Stored in the Ascidian Egg, International Symposium on the Biology of Ascidians., Sapporo, 2000.
7.
Kazuhiro W. Makabe : Two Pathways of RNA Localization at the Posterior Pole of Ascidian Embryo., FASEB Summer Reseach Conference,RNA Sorting in Development, Colorado(USA), 2000.
8.
Kazuhiro W. Makabe : Maternal mRNA in Ascidian Egg, Reseach for the Future Symposium,Cell Fate Specification during Early Embryogenesis., Tokyo, 2000.
9.
Kazuhiro W. Makabe : Maternal Factors in the Ascidian Egg, New Hampshire(USA), 1998.
10.
Kazuhiro W. Makabe : Cis-regulatory Elements of the SM50 promoter, Woods Hole(USA), 1994.
11.
Kazuhiro W. Makabe and Noriyuki Sato : Exprssion of Muscle Specific Genes during Development of Ascidian, Hawaii(USA), 1991.
12.
Kazuhiro W. Makabe and Noriyuki Sato : Muscle Cell Differentiation in Ascidian Embryos:Molecular Biological Approach, Aomori, 1988.
Proceeding of Domestic Conference:
1.
Minoru Watanabe, 水本 浩太, 山中 瑞恵, Kazuhiro W. Makabe and Toshio Gotoh : アオゴカイ巨大ヘモグロビンのグロビンmRNAとその発現組織, 平成18年度生物系三学会中国四国支部大会，会報, 18, May 2006.
2.
Kazuhiro W. Makabe, 水本 浩太, 山中 瑞江, 渡部 稔 and 後藤 寿夫 : アオゴカイ細胞外へヘモグロビンのグロビン鎖に含まれるCyc残基の位置とグロビン鎖の共通名, 第116回徳島生物学会会報, 15, Dec. 2005.
3.
水本 浩太, 山中 瑞江, Kazuhiro W. Makabe, Minoru Watanabe and Toshio Gotoh : アオゴカイ細胞外ヘモグロビンのグロビン鎖に含まれるCyc残基の位置とグロビン鎖の共通名, 第116回徳島生物学会会報, 15, Dec. 2005.
4.
Kazuhiro W. Makabe, 田端 義厳, 西田 宏記, 荒井 良子 and 安倍 真澄 : 第76回 日本動物学会大会, Oct. 2005.
(Summary)
マボヤ初期胚の表皮・神経分化運命分岐における高感度トランスクリプトーム解析
5.
Kazuhiro W. Makabe, 後藤 寿夫, 尾崎 絵里香, 野網 明子, 金井 拓, 水本 浩太 and 渡部 稔 : アオゴカイPerinereis aibuhitensis巨大ヘモグロビンのアミノ酸配列, 平成17年度生物系三学会中国四国支部大会岡山大会,会報, 18, May 2005.
6.
Toshio Gotoh, 尾崎 絵理香, 野網 明子, 金井 拓, 水本 浩太, Minoru Watanabe and Kazuhiro W. Makabe : アオゴカイPerinereis aibuhitensis巨大ヘモグロビンのアミノ酸配列, 平成17年度生物系三学会中国四国支部大会岡山大会，会報, 18, May 2005.
7.
中村 依子, Kazuhiro W. Makabe and 西田 宏記 : 第37回 日本発生生物学会大会, 第37回日本発生生物学会大会, Jun. 2004.
(Summary)
kinase HrPOPK-1はホヤ胚後極でのmRNA局在化に関与する
Et cetera, Workshop:
1.
Kohji Nakashima, Masanori Miyata, Kazuhiro W. Makabe, Donald Sturge, Meredith Anne Stephens and Kayoko Ueno : Preparation and Use of ``Authentic English'' Web Materials at The University of Tokushima (Tokushima, Japan), Journal of University Education Research, Vol.1, No.5, 116-122, Mar. 2008.
(Summary)
This paper outlines a pilot project funded by The President's Fund of the University of Tokushima that was designed to create English educational material to motivate students to acquire ``Authentic English.'' Recording was at sites in Honolulu (Hawaii, USA), Storrs (Connecticut, USA), Montreal (Canada) and Brisbane (Australia). Material was designed for use in teaching EFL students at our university who are mainly taking general language courses. Section One of this paper refers to the aims and process of making English educational material for the Web. Sections Two, Three, and Four refer to how materials were created. Section Five introduces technical aspects of the Web application. Sections Six and Seven discuss merits and problems related to the ``Authentic English'' material and its production.
(Keyword)
English Education / Authentic English / web application