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2. Identification of a New Enhancer That Promotes Sox9 Expression by a Comparative Analysis of Mouse and Sry-Deficient Amami Spiny Rat.

Author

Hirata, Yurie, Mizushima, Shusei, Mitsukawa, Shoichiro, Kon, Masafumi, Kuroki, Yoko, Jogahara, Takamichi, Shinohara, Nobuo, and Kuroiwa, Asato

Subjects
GENE expression, SOX transcription factors, SEX determination, Y chromosome, SEX differentiation (Embryology), RATS, MICE, REPORTER genes
Abstract

Introduction: Testis differentiation is initiated by the SRY gene on the Y chromosome in mammalian species. However, the Amami spiny rat, Tokudaia osimensis, lacks both the Y chromosome and the Sry gene and acquired a unique Sox9 regulatory mechanism via a male-specific duplication upstream of Sox9, without Sry. In general mammalian species, the SRY protein binds to a testis-specific enhancer to promote SOX9 gene expression. Several enhancers located upstream of Sox9/SOX9 have been reported in mice and humans. In particular, the binding of SRY to the highly conserved enhancer Enh13 is thought to be a common mechanism underlying testis differentiation and sex determination in mammals. Methods: Sequences of T. osimensis homologues of three Sox9 enhancers that were previously reported in mice, Enh8, Enh14, and Enh13, were determined. We performed in vitro assays to confirm enhancer activity involved in Sox9 regulation in T. osimensis. Results:T. osimensis Enh13 showed enhancer activity when co-transfected with NR5A1 and SOX9. Mouse Enh13 was activated by NR5A1 and SRY; however, T. osimensis Enh13 did not respond to SRY, even though the binding sites of SRY and NR5A1 were conserved. To identify the key sequence that is present in mouse but absent from T. osimensis, we performed reporter gene assays using vectors in which partial sequences of T. osimensis Enh13 were replaced with mouse sequences. For T. osimensis Enh13 in which the second half (approximately 430 bp) was replaced with the corresponding mouse sequence, activity in response to NR5A1 and SRY was recovered. Further, reporter assays revealed that multiple regions in the second half of the mouse Enh13 sequence are required for the response to NR5A1 and SRY. The latter 49 bp was particularly important and contained four binding sites for three transcription factors, POU2F1, HOXA3, and GATA1. Conclusion: We showed that there are unknown sequences responsible for the interaction between NR5A1 and SRY and mEnh13 based on comparative analyses of Sry-dependent and Sry-independent species. Our comparative analyses revealed new molecular mechanisms underlying mammalian sex determination. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Genome evolution in the allotetraploid frog Xenopus laevis

Author

Session, Adam M, Uno, Yoshinobu, Kwon, Taejoon, Chapman, Jarrod A, Toyoda, Atsushi, Takahashi, Shuji, Fukui, Akimasa, Hikosaka, Akira, Suzuki, Atsushi, Kondo, Mariko, van Heeringen, Simon J, Quigley, Ian, Heinz, Sven, Ogino, Hajime, Ochi, Haruki, Hellsten, Uffe, Lyons, Jessica B, Simakov, Oleg, Putnam, Nicholas, Stites, Jonathan, Kuroki, Yoko, Tanaka, Toshiaki, Michiue, Tatsuo, Watanabe, Minoru, Bogdanovic, Ozren, Lister, Ryan, Georgiou, Georgios, Paranjpe, Sarita S, van Kruijsbergen, Ila, Shu, Shengquiang, Carlson, Joseph, Kinoshita, Tsutomu, Ohta, Yuko, Mawaribuchi, Shuuji, Jenkins, Jerry, Grimwood, Jane, Schmutz, Jeremy, Mitros, Therese, Mozaffari, Sahar V, Suzuki, Yutaka, Haramoto, Yoshikazu, Yamamoto, Takamasa S, Takagi, Chiyo, Heald, Rebecca, Miller, Kelly, Haudenschild, Christian, Kitzman, Jacob, Nakayama, Takuya, Izutsu, Yumi, Robert, Jacques, Fortriede, Joshua, Burns, Kevin, Lotay, Vaneet, Karimi, Kamran, Yasuoka, Yuuri, Dichmann, Darwin S, Flajnik, Martin F, Houston, Douglas W, Shendure, Jay, DuPasquier, Louis, Vize, Peter D, Zorn, Aaron M, Ito, Michihiko, Marcotte, Edward M, Wallingford, John B, Ito, Yuzuru, Asashima, Makoto, Ueno, Naoto, Matsuda, Yoichi, Veenstra, Gert Jan C, Fujiyama, Asao, Harland, Richard M, Taira, Masanori, and Rokhsar, Daniel S

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Animals, Chromosomes, Conserved Sequence, DNA Transposable Elements, Diploidy, Evolution, Molecular, Female, Gene Deletion, Gene Expression Profiling, Genome, Karyotype, Molecular Sequence Annotation, Mutagenesis, Phylogeny, Pseudogenes, Tetraploidy, Xenopus, Xenopus laevis, General Science & Technology
Abstract

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

Published
2016

5. Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation dna sequencing

Author

Hijikata, Atsushi, primary, Suyama, Mikita, additional, Kikugawa, Shingo, additional, Matoba, Ryo, additional, Naruto, Takuya, additional, Enomoto, Yumi, additional, Kurosawa, Kenji, additional, Harada, Naoki, additional, Yanagi, Kumiko, additional, Kaname, Tadashi, additional, Miyako, Keisuke, additional, Takazawa, Masaki, additional, Sasai, Hideo, additional, Hosokawa, Junichi, additional, Itoga, Sakae, additional, Yamaguchi, Tomomi, additional, Kosho, Tomoki, additional, Matsubara, Keiko, additional, Kuroki, Yoko, additional, Fukami, Maki, additional, Adachi, Kaori, additional, Nanba, Eiji, additional, Tsuchida, Naomi, additional, Uchiyama, Yuri, additional, Matsumoto, Naomichi, additional, Nishimura, Kunihiro, additional, and Ohara, Osamu, additional

Published
2023
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7. Visualization of AMPA receptors in living human brain with positron emission tomography

Author

Miyazaki, Tomoyuki, Nakajima, Waki, Hatano, Mai, Shibata, Yusuke, Kuroki, Yoko, Arisawa, Tetsu, and Serizawa, Asami

Subjects
Brain research, PET imaging -- Methods, Neuroimaging -- Methods, Biological sciences, Health
Abstract

Although aberrations in the number and function of glutamate AMPA ([alpha]-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors are thought to underlie neuropsychiatric disorders, no methods are currently available for visualizing AMPA receptors in the living human brain. Here we developed a positron emission tomography (PET) tracer for AMPA receptors. A derivative of 4-[2-(phenylsulfonylamino)ethylthio]-2,6-difluoro-phenoxyacetamide radiolabeled with .sup.11C ([.sup.11C]K-2) showed specific binding to AMPA receptors. Our clinical trial with healthy human participants confirmed reversible binding of [.sup.11C]K-2 in the brain according to Logan graphical analysis ((https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000024205); study design: non-randomized, single arm; primary outcome: dynamics and distribution volumes of [.sup.11C]K-2 in the brain; secondary outcome: adverse events of [.sup.11C]K-2 during the 4-10 d following dosing; this trial met prespecified endpoints). In an exploratory clinical study including patients with epilepsy, we detected increased [.sup.11C]K-2 uptake in the epileptogenic focus of patients with mesial temporal lobe epilepsy, which was closely correlated with the local AMPA receptor protein distribution in surgical specimens from the same individuals ((https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000028852); study design: non-randomized, single arm; primary outcome: correlation between [.sup.11C]K-2 uptake measured with PET before surgery and AMPA receptor protein density examined by biochemical study after surgery; secondary outcome: adverse events during the 7 d following PET scan; this trial met prespecified endpoints). Thus, [.sup.11C]K-2 is a potent PET tracer for AMPA receptors, potentially providing a tool to examine the involvement of AMPA receptors in neuropsychiatric disorders. A newly developed PET tracer allows visualization of AMPA receptors in the living human brain, providing a new tool to study their potential involvement in neurological or psychiatric disorders., Author(s): Tomoyuki Miyazaki [sup.1] , Waki Nakajima [sup.1] , Mai Hatano [sup.1] , Yusuke Shibata [sup.1] , Yoko Kuroki [sup.1] , Tetsu Arisawa [sup.1] , Asami Serizawa [sup.1] , Akane [...]

Published
2020
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9. Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing

Author

Mimori, Takahiro, Yasuda, Jun, Kuroki, Yoko, Shibata, Tomoko F., Katsuoka, Fumiki, Saito, Sakae, Nariai, Naoki, Ono, Akira, Nakai-Inagaki, Naomi, Misawa, Kazuharu, Tateno, Keiko, Kawai, Yosuke, Fuse, Nobuo, Hozawa, Atsushi, Kuriyama, Shinichi, Sugawara, Junichi, Minegishi, Naoko, Suzuki, Kichiya, Kinoshita, Kengo, Nagasaki, Masao, and Yamamoto, Masayuki

Published
2019
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10. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

Author

Rensing, Stefan A., Lang, Daniel, Zimmer, Andreas D., Terry, Astrid, Salamov, Asaf, Shapiro, Harris, Nishiyama, Tomaoki, Perroud, Pierre-Francois, Lindquist, Erika A., Kamisugi, Yasuko, Tanahashi, Takako, Sakakibara, Keiko, Fujita, Tomomichi, Oishi, Kazuko, Shin, Tadasu, Kuroki, Yoko, Toyoda, Atsushi, Suzuki, Yutaka, Hashimoto, Shin-ichi, Yamaguchi, Kazuo, Sugano, Sumio, Kohara, Yuji, Fujiyama, Asao, Anterola, Aldwin, Aoki, Setsuyuki, Ashton, Neil, Barbazuk, W. Brad, Barker, Elizabeth, Bennetzen, Jeffrey L., Blankenship, Robert, Cho, Sung Hyun, Dutcher, Susan K., Estelle, Mark, Fawcett, Jeffrey A., Gundlach, Heidrum, Hanada, Kousuke, Melkozernov, Alexander, Murata, Takashi, Nelson, David R., Pils, Birgit, Prigge, Michael, Reiss, Bernd, Renner, Tanya, Rombauts, Stephane, Rushton, Paul J., Sanderfoot, Anton, Schween, Gabriele, Shiu, Shin-Han, Stueber, Kurt, Theodoulou, Frederica L., Tu, Hank, Peer, Yves Van de, Verrier, Paul J., Waters, Elizabeth, Wood, Andrew, Yang, Lixing, Cove, David, Cuming, Andrew C., Hasebe, Mitsayasu, Lucas, Susan, Mishler, Brent D., Reski, Ralf, Grigoriev, Igor V., Quatrano, Rakph S., and Boore, Jeffrey L.

Abstract

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

Published
2007

12. Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing

Author

Nagasaki, Masao, Kuroki, Yoko, Shibata, Tomoko F., Katsuoka, Fumiki, Mimori, Takahiro, Kawai, Yosuke, Minegishi, Naoko, Hozawa, Atsushi, Kuriyama, Shinichi, Suzuki, Yoichi, Kawame, Hiroshi, Nagami, Fuji, Takai-Igarashi, Takako, Ogishima, Soichi, Kojima, Kaname, Misawa, Kazuharu, Tanabe, Osamu, Fuse, Nobuo, Tanaka, Hiroshi, Yaegashi, Nobuo, Kinoshita, Kengo, Kure, Shiego, Yasuda, Jun, and Yamamoto, Masayuki

Published
2019
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14. Identification of CD34’ and CD34− leukemia-initiating cells in MLL-rearranged human acute lymphoblastic leukemia

Author

Aoki, Yuki, Watanabe, Takashi, Saito, Yoriko, Kuroki, Yoko, Hijikata, Atsushi, Takagi, Masatoshi, Tomizawa, Daisuke, Eguchi, Mariko, Eguchi-Ishimae, Minenori, Kaneko, Akiko, Ono, Rintaro, Sato, Kaori, Suzuki, Nahoko, Fujiki, Saera, Koh, Katsuyoshi, Ishii, Eiichi, Shultz, Leonard D., Ohara, Osamu, Mizutani, Shuki, and Ishikawa, Fumihiko

Published
2015
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15. Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing

Author

Hijikata, Atsushi, primary, Suyama, Mikita, additional, Kikugawa, Shingo, additional, Matoba, Ryo, additional, Naruto, Takuya, additional, Enomoto, Yumi, additional, Kurosawa, Kenji, additional, Harada, Naoki, additional, Yanagi, Kumiko, additional, Kaname, Tadashi, additional, Miyako, Keisuke, additional, Takazawa, Masaki, additional, Sasai, Hideo, additional, Hosokawa, Junichi, additional, Itoga, Sakae, additional, Yamaguchi, Tomomi, additional, Kosho, Tomoki, additional, Matsubara, Keiko, additional, Kuroki, Yoko, additional, Fukami, Maki, additional, Adachi, Kaori, additional, Nanba, Eiji, additional, Tsuchida, Naomi, additional, Uchiyama, Yuri, additional, Matsumoto, Naomichi, additional, Nishimura, Kunihiro, additional, and Ohara, Osamu, additional

Published
2022
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18. Monitoring of minimal residual disease in early T‐cell precursor acute lymphoblastic leukaemia by next‐generation sequencing

Author

Pan, Xiaoqing, Nariai, Naoki, Fukuhara, Noriko, Saito, Sakae, Sato, Yukuto, Katsuoka, Fumiki, Kojima, Kaname, Kuroki, Yoko, Danjoh, Inaho, Saito, Rumiko, Hasegawa, Shin, Okitsu, Yoko, Kondo, Aiko, Onishi, Yasushi, Nagami, Fuji, Kiyomoto, Hideyasu, Hozawa, Atsushi, Fuse, Nobuo, Nagasaki, Masao, Shimizu, Ritsuko, Yasuda, Jun, Harigae, Hideo, and Yamamoto, Masayuki

Published
2017
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19. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Author

Rensing, Stefan A., Lang, Daniel, Zimmer, Andreas D., Terry, Astrid, Salamov, Asaf, Shapiro, Harris, Nishiyama, Tomoaki, Perroud, Pierre-François, Lindquist, Erika A., Kamisugi, Yasuko, Tanahashi, Takako, Sakakibara, Keiko, Fujita, Tomomichi, Oishi, Kazuko, Shin-I, Tadasu, Kuroki, Yoko, Toyoda, Atsushi, Suzuki, Yutaka, Hashimoto, Shin-ichi, Yamaguchi, Kazuo, Sugano, Sumio, Kohara, Yuji, Fujiyama, Asao, Anterola, Aldwin, Aoki, Setsuyuki, Ashton, Neil, Barbazuk, W. Brad, Barker, Elizabeth, Bennetzen, Jeffrey L., Blankenship, Robert, Cho, Sung Hyun, Dutcher, Susan K., Estelle, Mark, Fawcett, Jeffrey A., Gundlach, Heidrun, Hanada, Kousuke, Heyl, Alexander, Hicks, Karen A., Hughes, Jon, Lohr, Martin, Mayer, Klaus, Melkozernov, Alexander, Murata, Takashi, Nelson, David R., Pils, Birgit, Prigge, Michael, Reiss, Bernd, Renner, Tanya, Rombauts, Stephane, Rushton, Paul J., Sanderfoot, Anton, Schween, Gabriele, Shiu, Shin-Han, Stueber, Kurt, Theodoulou, Frederica L., Tu, Hank, Van de Peer, Yves, Verrier, Paul J., Waters, Elizabeth, Wood, Andrew, Yang, Lixing, Cove, David, Cuming, Andrew C., Hasebe, Mitsuyasu, Lucas, Susan, Mishler, Brent D., Reski, Ralf, Grigoriev, Igor V., Quatrano, Ralph S., and Boore, Jeffrey L.

Published
2008
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23. The amphioxus genome and the evolution of the chordate karyotype

Author

Putnam, Nicholas H., Butts, Thomas, Ferrier, David E.K., Furlong, Rebecca F., Hellsten, Uffe, Kawashima, Takeshi, Robinson-Rechavi, Marc, Shoguchi, Eiichi, Terry, Astrid, Yu, Jr-Kai, Benito-Gutierrez, Elia, Dubchak, Inna, Garcia-Fernandez, Jordi, Gibson-Brown, Jeremy J., Grigoriev, Igor V., Horton, Amy C., de Jong, Pieter J., Jurka, Jerzy, Kapitonov, Vladimir V., Kohara, Yuji, Kuroki, Yoko, Lindquist, Erika, Lucas, Susan, Osoegawa, Kazutoyo, Pennacchio, Len A., Salamov, Asaf A., Satou, Yutaka, Sauka-Spengler, Tatjana, Schmutz, Jeremy, Shin-I, Tadasu, Toyoda, Atsushi, Bronner-Fraser, Marianne, Fujiyama, Asao, Holland, Linda Z., Holland, Peter W.H., Satoh, Nori, and Rokhsar, Daniel S.

Subjects
Genomes -- Identification and classification -- Genetic aspects, Genetic variation -- Evaluation -- Genetic aspects, Karyotypes -- Identification and classification -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Identification and classification, Evaluation, Genetic aspects, Natural history
Abstract

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of [...]

Published
2008

24. The medaka draft genome and insights into vertebrate genome evolution

Author

Kasahara, Masahiro, Naruse, Kiyoshi, Sasaki, Shin, Nakatani, Yoichiro, Qu, Wei, Ahsan, Budrul, Yamada, Tomoyuki, Nagayasu, Yukinobu, Doi, Koichiro, Kasai, Yasuhiro, Jindo, Tomoko, Kobayashi, Daisuke, Shimada, Atsuko, Toyoda, Atsushi, Kuroki, Yoko, Fujiyama, Asao, Sasaki, Takashi, Shimizu, Atsushi, Asakawa, Shuichi, Shimizu, Nobuyoshi, Hashimoto, Shin-ichi, Yang, Jun, Lee, Yongjun, Matsushima, Kouji, Sugano, Sumio, Sakaizumi, Mitsuru, Narita, Takanori, Ohishi, Kazuko, Haga, Shinobu, Ohta, Fumiko, Nomoto, Hisayo, Nogata, Keiko, Morishita, Tomomi, Endo, Tomoko, Shin-I, Tadasu, Takeda, Hiroyuki, Morishita, Shinichi, and Kohara, Yuji

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Masahiro Kasahara [1, 10]; Kiyoshi Naruse [2, 10]; Shin Sasaki [1, 10]; Yoichiro Nakatani [1, 10]; Wei Qu [1]; Budrul Ahsan [1]; Tomoyuki Yamada [1]; Yukinobu Nagayasu [1]; Koichiro [...]

Published
2007
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25. Human chromosome 11 DNA sequence and analysis including novel gene identification

Author

Taylor, Todd D., Noguchi, Hideki, Totoki, Yasushi, Toyoda, Atsushi, Kuroki, Yoko, Dewar, Ken, Lloyd, Christine, Itoh, Takehiko, Takeda, Tadayuki, Kim, Dae-Won, She, Xinwei, Barlow, Karen F., Bloom, Toby, Bruford, Elspeth, Chang, Jean L., Cuomo, Christina A., Eichler, Evan, FitzGerald, Michael G., Jaffe, David B., LaButti, Kurt, Nicol, Robert, Park, Hong-Seog, Seaman, Christopher, Sougnez, Carrie, Yang, Xiaoping, Zimmer, Andrew R., Zody, Michael C., Birren, Bruce W., Nusbaum, Chad, Fujiyama, Asao, Hattori, Masahira, Rogers, Jane, Lander, Eric S., and Sakaki, Yoshiyuki

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Todd D. Taylor (corresponding author) [1]; Hideki Noguchi [1, 10]; Yasushi Totoki [1]; Atsushi Toyoda [1]; Yoko Kuroki [1]; Ken Dewar [2, 10]; Christine Lloyd [3]; Takehiko Itoh [4]; [...]

Published
2006
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26. DNA sequence and analysis of human chromosome 18

Author

Nusbaum, Chad, Zody, Michael C., Borowsky, Mark L., Kamal, Michael, Kodira, Chinnappa D., Taylor, Todd D., Whittaker, Charles A., Chang, Jean L., Cuomo, Christina A., Dewar, Ken, FitzGerald, Michael G., Yang, Xiaoping, Abouelleil, Amr, Allen, Nicole R., Anderson, Scott, Bloom, Toby, Bugalter, Boris, Butler, Jonathan, Cook, April, DeCaprio, David, Engels, Reinhard, Garber, Manuel, Gnirke, Andreas, Hafez, Nabil, Hall, Jennifer L., Norman, Catherine Hosage, Itoh, Takehiko, Jaffe, David B., Kuroki, Yoko, Lehoczky, Jessica, Lui, Annie, Macdonald, Pendexter, Mauceli, Evan, Mikkelsen, Tarjei S., Naylor, Jerome W., Nicol, Robert, Nguyen, Cindy, Noguchi, Hideki, O'Leary, Sinead B., Piqani, Bruno, L Smith, Cherylyn, Talamas, Jessica A., Topham, Kerri, Totoki, Yasushi, Toyoda, Atsushi, Wain, Hester M., Young, Sarah K., Zeng, Qiandong, Zimmer, Andrew R., Fujiyama, Asao, Hattori, Masahira, Birren, Bruce W., Sakaki, Yoshiyuki, and Lander, Eric S.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Chad Nusbaum (corresponding author) [1]; Michael C. Zody [1]; Mark L. Borowsky [1]; Michael Kamal [1]; Chinnappa D. Kodira [1]; Todd D. Taylor [2]; Charles A. Whittaker [1, 8]; [...]

Published
2005
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27. Suppression of Non-Random Fertilization by MHC Class I Antigens

Author

Kamiya, Junki, primary, Kang, Woojin, additional, Yoshida, Keiichi, additional, Takagi, Ryota, additional, Kanai, Seiya, additional, Hanai, Maito, additional, Nakamura, Akihiro, additional, Yamada, Mitsutoshi, additional, Miyamoto, Yoshitaka, additional, Miyado, Mami, additional, Kuroki, Yoko, additional, Hayashi, Yoshiki, additional, Umezawa, Akihiro, additional, Kawano, Natsuko, additional, and Miyado, Kenji, additional

Published
2020
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30. UTGB/medaka: genomic resource database for medaka biology

Author

Ahsan, Budrul, Kobayashi, Daisuke, Yamada, Tomoyuki, Kasahara, Masahiro, Sasaki, Shin, Saito, Taro L., Nagayasu, Yukinobu, Doi, Koichiro, Nakatani, Yoichiro, Qu, Wei, Jindo, Tomoko, Shimada, Atsuko, Naruse, Kiyoshi, Toyoda, Atsushi, Kuroki, Yoko, Fujiyama, Asao, Sasaki, Takashi, Shimizu, Atsushi, Asakawa, Shuichi, Shimizu, Nobuyoshi, Hashimoto, Shin-ichi, Yang, Jun, Lee, Yongjun, Matsushima, Kouji, Sugano, Sumio, Sakaizumi, Mitsuru, Narita, Takanori, Ohishi, Kazuko, Haga, Shinobu, Ohta, Fumiko, Nomoto, Hisayo, Nogata, Keiko, Morishita, Tomomi, Endo, Tomoko, Shin-I, Tadasu, Takeda, Hiroyuki, Kohara, Yuji, and Morishita, Shinichi

Published
2008

33. The identification and functional implications of human-specific 'fixed' amino acid substitutions in the glutamate receptor family

Author

Fujiyama Asao, Sakaki Yoshiyuki, Hattori Masahira, Toyoda Atsushi, Kuroki Yoko, Tanaka Kunika, Kageyama Rui, Araragi Naozumi, Watanabe Kazunori, Goto Hiroki, Fukumaki Yasuyuki, and Shibata Hiroki

Subjects
Evolution, QH359-425
Abstract

Abstract Background The glutamate receptors (GluRs) play a vital role in the mediation of excitatory synaptic transmission in the central nervous system. To clarify the evolutionary dynamics and mechanisms of the GluR genes in the lineage leading to humans, we determined the complete sequences of the coding regions and splice sites of 26 chimpanzee GluR genes. Results We found that all of the reading frames and splice sites of these genes reported in humans were completely conserved in chimpanzees, suggesting that there were no gross structural changes in humans after their divergence from the human-chimpanzee common ancestor. We observed low KA/KS ratios in both humans and chimpanzees, and we found no evidence of accelerated evolution. We identified 30 human-specific "fixed" amino acid substitutions in the GluR genes by analyzing 80 human samples of seven different populations worldwide. Grantham's distance analysis showed that GRIN2C and GRIN3A are the most and the second most diverged GluR genes between humans and chimpanzees. However, most of the substitutions are non-radical and are not clustered in any particular region. Protein motif analysis assigned 11 out of these 30 substitutions to functional regions. Two out of these 11 substitutions, D71G in GRIN3A and R727H in GRIN3B, caused differences in the functional assignments of these genes between humans and other apes. Conclusion We conclude that the GluR genes did not undergo drastic changes such as accelerated evolution in the human lineage after the divergence of chimpanzees. However, there remains a possibility that two human-specific "fixed" amino acid substitutions, D71G in GRIN3A and R727H in GRIN3B, are related to human-specific brain function.

Published
2009
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35. Identification of somatic mutations in postmortem human brains by whole genome sequencing and their implications for psychiatric disorders

Author

Nishioka, Masaki, primary, Bundo, Miki, additional, Ueda, Junko, additional, Katsuoka, Fumiki, additional, Sato, Yukuto, additional, Kuroki, Yoko, additional, Ishii, Takao, additional, Ukai, Wataru, additional, Murayama, Shigeo, additional, Hashimoto, Eri, additional, Nagasaki, Masao, additional, Yasuda, Jun, additional, Kasai, Kiyoto, additional, Kato, Tadafumi, additional, and Iwamoto, Kazuya, additional

Published
2018
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36. Biallelic mutations in SZT2 cause a discernible clinical entity with epilepsy, developmental delay, macrocephaly and a dysmorphic corpus callosum

Author

Nakamura, Yuji, primary, Togawa, Yasuko, additional, Okuno, Yusuke, additional, Muramatsu, Hideki, additional, Nakabayashi, Kazuhiko, additional, Kuroki, Yoko, additional, Ieda, Daisuke, additional, Hori, Ikumi, additional, Negishi, Yutaka, additional, Togawa, Takao, additional, Hattori, Ayako, additional, Kojima, Seiji, additional, and Saitoh, Shinji, additional

Published
2018
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37. Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing

Author

Mimori, Takahiro, primary, Yasuda, Jun, additional, Kuroki, Yoko, additional, Shibata, Tomoko F., additional, Katsuoka, Fumiki, additional, Saito, Sakae, additional, Nariai, Naoki, additional, Ono, Akira, additional, Nakai-Inagaki, Naomi, additional, Misawa, Kazuharu, additional, Tateno, Keiko, additional, Kawai, Yosuke, additional, Fuse, Nobuo, additional, Hozawa, Atsushi, additional, Kuriyama, Shinichi, additional, Sugawara, Junichi, additional, Minegishi, Naoko, additional, Suzuki, Kichiya, additional, Kinoshita, Kengo, additional, Nagasaki, Masao, additional, and Yamamoto, Masayuki, additional

Published
2018
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39. Additional file 3: of Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki

Author

Murata, Chie, Kuroki, Yoko, Imoto, Issei, Tsukahara, Masaru, Ikejiri, Naoto, and Asato Kuroiwa

Abstract

File_1 and File_2 include each gene sequence alignment of non-coding and coding region among T. muenninki , mouse, and rat, respectively. File_3 includes each gene sequence alignment of coding region among the three species with guinea pig. (DOC 21 kb)

Published
2015
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40. Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare.

Author

Yasuda, Jun, Kinoshita, Kengo, Katsuoka, Fumiki, Danjoh, Inaho, Sakurai-Yageta, Mika, Motoike, Ikuko N, Kuroki, Yoko, Saito, Sakae, Kojima, Kaname, Shirota, Matsuyuki, Saigusa, Daisuke, Otsuki, Akihito, Kawashima, Junko, Yamaguchi-Kabata, Yumi, Tadaka, Shu, Aoki, Yuichi, Mimori, Takahiro, Kumada, Kazuki, Inoue, Jin, and Makino, Satoshi

Subjects
INDIVIDUALIZED medicine, HUMAN genome, MEDICAL genetics, SINGLE nucleotide polymorphisms, NUCLEOTIDE sequencing
Abstract

Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC. [ABSTRACT FROM AUTHOR]

Published
2019
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41. Genome evolution in the allotetraploid frog Xenopus laevis.

Author

Uno, Yoshinobu, Uno, Yoshinobu, Kwon, Taejoon, Chapman, Jarrod, Toyoda, Atsushi, Takahashi, Shuji, Fukui, Akimasa, Hikosaka, Akira, Suzuki, Atsushi, Kondo, Mariko, van Heeringen, Simon, Quigley, Ian, Ogino, Hajime, Ochi, Haruki, Hellsten, Uffe, Lyons, Jessica, Simakov, Oleg, Putnam, Nicholas, Stites, Jonathan, Kuroki, Yoko, Tanaka, Toshiaki, Michiue, Tatsuo, Watanabe, Minoru, Bogdanovic, Ozren, Lister, Ryan, Georgiou, Georgios, Paranjpe, Sarita, van Kruijsbergen, Ila, Shu, Shengquiang, Miller, Kelly, Haudenschild, Christian, Kitzman, Jacob, Nakayama, Takuya, Izutsu, Yumi, Robert, Jacques, Fortriede, Joshua, Burns, Kevin, Lotay, Vaneet, Karimi, Kamran, Yasuoka, Yuuri, Dichmann, Darwin, Flajnik, Martin, Houston, Douglas, Shendure, Jay, DuPasquier, Louis, Vize, Peter, Zorn, Aaron, Ito, Michihiko, Marcotte, Edward, Wallingford, John, Ito, Yuzuru, Asashima, Makoto, Ueno, Naoto, Matsuda, Yoichi, Veenstra, Gert, Fujiyama, Asao, Kinoshita, Tsutomu, Ohta, Yuko, Mawaribuchi, Shuuji, Jenkins, Jerry, Grimwood, Jane, Schmutz, Jeremy, Mozaffari, Sahar, Suzuki, Yutaka, Haramoto, Yoshikazu, Yamamoto, Takamasa, Takagi, Chiyo, Taira, Masanori, Rokhsar, Daniel, Harland, Richard, Heald, Rebecca, Heinz, Sven, Session, Adam, Carlson, Joseph, Mitros, Therese, Uno, Yoshinobu, Uno, Yoshinobu, Kwon, Taejoon, Chapman, Jarrod, Toyoda, Atsushi, Takahashi, Shuji, Fukui, Akimasa, Hikosaka, Akira, Suzuki, Atsushi, Kondo, Mariko, van Heeringen, Simon, Quigley, Ian, Ogino, Hajime, Ochi, Haruki, Hellsten, Uffe, Lyons, Jessica, Simakov, Oleg, Putnam, Nicholas, Stites, Jonathan, Kuroki, Yoko, Tanaka, Toshiaki, Michiue, Tatsuo, Watanabe, Minoru, Bogdanovic, Ozren, Lister, Ryan, Georgiou, Georgios, Paranjpe, Sarita, van Kruijsbergen, Ila, Shu, Shengquiang, Miller, Kelly, Haudenschild, Christian, Kitzman, Jacob, Nakayama, Takuya, Izutsu, Yumi, Robert, Jacques, Fortriede, Joshua, Burns, Kevin, Lotay, Vaneet, Karimi, Kamran, Yasuoka, Yuuri, Dichmann, Darwin, Flajnik, Martin, Houston, Douglas, Shendure, Jay, DuPasquier, Louis, Vize, Peter, Zorn, Aaron, Ito, Michihiko, Marcotte, Edward, Wallingford, John, Ito, Yuzuru, Asashima, Makoto, Ueno, Naoto, Matsuda, Yoichi, Veenstra, Gert, Fujiyama, Asao, Kinoshita, Tsutomu, Ohta, Yuko, Mawaribuchi, Shuuji, Jenkins, Jerry, Grimwood, Jane, Schmutz, Jeremy, Mozaffari, Sahar, Suzuki, Yutaka, Haramoto, Yoshikazu, Yamamoto, Takamasa, Takagi, Chiyo, Taira, Masanori, Rokhsar, Daniel, Harland, Richard, Heald, Rebecca, Heinz, Sven, Session, Adam, Carlson, Joseph, and Mitros, Therese

Abstract

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of fossil transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

Published
2016

42. Monitoring of minimal residual disease in early T‐cell precursor acute lymphoblastic leukaemia by next‐generation sequencing

Author

Pan, Xiaoqing, primary, Nariai, Naoki, additional, Fukuhara, Noriko, additional, Saito, Sakae, additional, Sato, Yukuto, additional, Katsuoka, Fumiki, additional, Kojima, Kaname, additional, Kuroki, Yoko, additional, Danjoh, Inaho, additional, Saito, Rumiko, additional, Hasegawa, Shin, additional, Okitsu, Yoko, additional, Kondo, Aiko, additional, Onishi, Yasushi, additional, Nagami, Fuji, additional, Kiyomoto, Hideyasu, additional, Hozawa, Atsushi, additional, Fuse, Nobuo, additional, Nagasaki, Masao, additional, Shimizu, Ritsuko, additional, Yasuda, Jun, additional, Harigae, Hideo, additional, and Yamamoto, Masayuki, additional

Published
2016
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43. Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki

Author

Murata, Chie, Kuroki, Yoko, Imoto, Issei, Tsukahara, Masaru, Ikejiri, Naoto, Kuroiwa, Asato, Murata, Chie, Kuroki, Yoko, Imoto, Issei, Tsukahara, Masaru, Ikejiri, Naoto, and Kuroiwa, Asato

Abstract

Background: Sex chromosomes of extant eutherian species are too ancient to reveal the process that initiated sex-chromosome differentiation. By contrast, the neo-sex chromosomes generated by sex-autosome fusions of recent origin in Tokudaia muenninki are expected to be evolutionarily ‘young’, and therefore provide a good model in which to elucidate the early phases of eutherian sex chromosome evolution. Here we describe the genomic evolution of T. muenninki in neo-sex chromosome differentiation. Results: FISH mapping of a T. muenninki male, using 50 BAC clones as probes, revealed no chromosomal rearrangements between the neo-sex chromosomes. Substitution-direction analysis disclosed that sequence evolution toward GC-richness, which positively correlates with recombination activity, occurred in the peritelomeric regions, but not middle regions of the neo-sex chromosomes. In contrast, the sequence evolution toward AT-richness was observed in those pericentromeric regions. Furthermore, we showed genetic differentiation between the pericentromeric regions as well as an accelerated rate of evolution in the neo-Y region through the detection of male-specific substitutions by gene sequencing in multiple males and females, and each neo-sex–derived BAC sequencing. Conclusions: Our results suggest that recombination has been suppressed in the pericentromeric region of neo-sex chromosomes without chromosome rearrangement, whereas high levels of recombination activity is limited in the peritelomeric region of almost undifferentiated neo-sex chromosomes. We conclude that PAR might have been formed on the peritelomeric region of sex chromosomes as an independent event from spread of recombination suppression during the early stages of sex chromosome differentiation.

Published
2015

46. Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation

Author

Urushihara, Hideko, primary, Kuwayama, Hidekazu, additional, Fukuhara, Kensuke, additional, Itoh, Takehiko, additional, Kagoshima, Hiroshi, additional, Shin-I, Tadasu, additional, Toyoda, Atsushi, additional, Ohishi, Kazuyo, additional, Taniguchi, Tateaki, additional, Noguchi, Hideki, additional, Kuroki, Yoko, additional, Hata, Takashi, additional, Uchi, Kyoko, additional, Mohri, Kurato, additional, King, Jason S, additional, Insall, Robert H, additional, Kohara, Yuji, additional, and Fujiyama, Asao, additional

Published
2015
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47. Mutations in the Testis-Specific Enhancer of SOX9 in the SRY Independent Sex-Determining Mechanism in the Genus Tokudaia

Author

Kimura, Ryutaro, Murata, Chie, Kuroki, Yoko, 1000020372261, Kuroiwa, Asato, Kimura, Ryutaro, Murata, Chie, Kuroki, Yoko, 1000020372261, and Kuroiwa, Asato

Abstract

SRY (sex-determining region Y) is widely conserved in eutherian mammals as a sex-determining gene located on the Y chromosome. SRY proteins bind to the testis-specific enhancer of SOX9 (TES) with SF1 to upregulate SOX9 expression in undifferentiated gonads of XY embryos of humans and mice. The core region within TES, named TESCO, is an important enhancer for mammalian sex determination. We show that TESCO of the genus Tokudaia lost enhancer activity caused by mutations in its SRY and SF1 binding sites. Two species of Tokudaia do not have the Y chromosome or SRY, and one species has multiple SRYs located on the neo-Y chromosome consisting of the Y fused with an autosome. The sequence of Tokudaia TESCO exhibited more than 83% identity with mouse TESCO, however, nucleotide substitution(s) were found in two out of three SRY binding sites and in five out of six SF1 binding sites. TESCO of all species showed low enhancer activity in cells co-transfected with SRY and SF1, and SOX9 and SF1 in reporter gene assays. Mutated TESCO, in which nucleotide substitutions found in SRY and SF1 binding sites were replaced with mouse sequence, recovered the activity. Furthermore, SRYs of the SRY-positive species could not activate the mutated TESCO or mouse TESCO, suggesting that SRYs lost function as a sex-determining gene any more. Our results indicate that the SRY dependent sex-determining mechanism was lost in a common ancestor of the genus Tokudaia caused by nucleotide substitutions in SRY and SF1 binding sites after emergence of a new sex-determining gene. We present the first evidence for an intermediate stage of the switchover from SRY to a new sex-determining gene in the evolution of mammalian sex-determining mechanism.

Published
2014

48. [Comparative studies on human and chimpanzee genomes]

Author

Kuroki, Yoko, Toyoda, Atsushi, Noguchi, Hideki, and Fujiyama, Asao

Subjects
Evolution, Molecular, Genome, Base Sequence, Pan troglodytes, Genome, Human, Animals, Humans, DNA, Genomics, Gene Library, Repetitive Sequences, Nucleic Acid
Published
2006

50. Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena

Author

Takehana, Yusuke, primary, Matsuda, Masaru, additional, Myosho, Taijun, additional, Suster, Maximiliano L., additional, Kawakami, Koichi, additional, Shin-I, Tadasu, additional, Kohara, Yuji, additional, Kuroki, Yoko, additional, Toyoda, Atsushi, additional, Fujiyama, Asao, additional, Hamaguchi, Satoshi, additional, Sakaizumi, Mitsuru, additional, and Naruse, Kiyoshi, additional

Published
2014
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