Toshie Kai, PhD
- E-mail: toshie_kaifbs.osaka-u.ac.jp
- Osaka University Reseachers
In 1998, Toshie KAI earned a Ph.D in Graduate School of Science, Department of Biological Science at Osaka University. She went on a postdoctral career in Dr. Allan Spradling's lab at Department of Embryology, Carnegie Institution of Washington/HHMI in USA, where she was first introduced to Drosophila melanogaster, fruit flies. Since then, she has been studying biology of germline cells using this excellent model organism. In 2005, she set up her own lab in Temasek Lifescience Laboratories (TLL), Singapore, as a Principal Investigator. In 2010, she was promoted to Senior Principal Investigator in TLL. She also served as an Adjunct Assistant Prof (2009-2010) and Associate Prof (2011-2015) in Department of Biological Science, National University of Singapore. In 2015, she moved her lab from Singapore to Osaka, at Graduate School of Frontier Bioscience, Osaka Univ.
- Teo RYW, Anand A, Sridhar V, Okamura K, Kai T. (2018) Heterochromatin protein 1a functions for piRNA biogenesis predominantly from pericentric and telomeric regions in Drosophila. Nat. Commun. 9:1735
- Quénerch’du E, Anand A, Kai T. (2016) The piRNA pathway is developmentally regulated during spermatogenesis in Drosophila. RNA 22(7):1044–1054
- Patil VS, Anand A, Chakrabarti, A, Kai T. (2014) The Tudor domain protein Tapas, a homolog of the vertebrate Tdrd7, functions in piRNA pathway to regulate retrotransposons in germline of Drosophila melanogaster. BMC Biol. 12:61
- Anand A, Kai T. (2014) Response to ‘Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin’ (Correspondence). EMBO J. 33(6):540–541
- Lim RSM, Anand A, Nishimiya-Fujisawa C, Kobayashi S, Kai T. (2014) Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway. Dev. Biol. 386(1):237–251
- Pek JW, Ng BF, Kai T. (2012) Polo-mediated phosphorylation of Maelstrom regulates oocyte determination. Development 139(24):4505–4513
- Anand A, Kai T. (2012) The tudor domain protein Kumo is required to assemble the nuage and to generate germline piRNAs in Drosophila. EMBO J. 31(4):870–882
- Pek JW, Kai T. (2011) DEAD-box RNA helicase Belle/DDX3 and the RNA interference pathway promote mitotic chromosome segregation. Proc. Natl. Acad. Sci. USA 108(29):12007–12012
- Pek JW, Kai T. (2011) A role for Vasa in regulating mitotic chromosome condensation in Drosophila. Curr. Biol. 21(1):39–44
- Patil VS, Kai T. (2010) Repression of retroelements in Drosophila germline via piRNA pathway by the tudor domain protein Tejas. Curr. Biol. 20(8):724–730
- Pek JW, Lim AK, Kai T. (2009) Drosophila Maelstrom Ensures Proper Germline Stem Cell Lineage Differentiation by Repressing microRNA-7. Dev. Cell 17(3):417–424
- Lim AK, Tao L, Kai T. (2009) piRNAs mediate post-transcriptional retroelement silencing and localization to pi-bodies in the Drosophila germline. J. Cell Biol. 186(3):333–342
- Lim AK, Kai T. (2007) Unique germ-line organelle, nuage, functions to repress selfish genetic elements in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 104(16):6714–6719
- Kai T, Williams D, Spradling AC. (2005) The expression profile of purified Drosophila germline stem cells. Dev. Biol. 283(2):486–502
- Kai T, Spradling A. (2004) Differentiating germ cells can revert into functional stem cells in Drosophila melanogaster ovaries. Nature 428(6982):564–569
- Kai T, Spradling A. (2003) An empty Drosophila stem cell niche reactivates the proliferation of ectopic cells. Proc. Natl. Acad. Sci. USA 100(8):4633–4638
- Niwa R, Kai T. (2020) Editorial overview: Stem cells orchestrate oogenesis: a lesson from the fruit fly, Drosophila melanogaster. Curr. Opin. Insect Sci 37:iii–v
- Gleason RJ, Anand A, *Kai T, *Chen X. (2017) Protecting and diversifying the germline. ** 208(2):435–471 (A part of FLY BOOK) *Co-corresponding
- Lim RSM, Kai T. (2015) A piece of the pi(e): the diverse roles of animal piRNAs and their PIWI partners. Sem. Cell Dev. Biol. 47–48:17–31 (Special Issue on Coding and Non-coding RNAs)
- Pek JW, Anand A, Kai T. (2012) Tudor domain proteins in development (Invited Review Article). Development 139:2255–2266
- Pek JW, Patil VS, Kai T. (2012) The piRNA pathway and the potential processing site, the nuage, in the Drosophila germline. Dev. Growth Differ. 54(1):66–77
- Pek JW, Kai T. (2011) Non-coding RNAs enter mitosis: functions, conservation and implications. Cell Div. 6:6
- Pek JW, Kai T. (2009) Conserved germline organelle, nuage, serves as site for processing of Piwi-interacting RNAs. (in Japanese). Exp. Med. 27:393–399
- Kai T. (2004) Germline stem cells and their niches. (in Japanese). Tanpakushitsu Kakusan Koso 49(6):710–717
- Spradling A, Drummond-Barbosa D, Kai T. (2001) Stem cells find their niche. Nature 414(6859):98–104
- Lim RS, Osato M, Kai T. (2015) Isolation of undifferentiated female germline cells from adult Drosophila ovaries. Curr. Protoc. Stem Cell Biol. 34:2E.3.1–2E.3.15
Shinichi Kawaguchi, PhD
- E-mail: shinkawafbs.osaka-u.ac.jp
In 1998, I earned a Ph.D in Graduate School of Science, Department of Biological Science at Osaka University. From 1999 to 2001, I was working as a postdoc in Dr. Shigeyuki Yokoyama's lab (Spring-8, RIKEN) to elucidate the protein function from its 3D structure. In 2001, I joined Dr. Yixian Zheng's lab as a research fellow to study the mechanism by which the microtubules are tethered to the centrosome. In 2004, I was working in NEC Soft Ltd for the collaboration with Meiji-Pharmaceutical University. From 2005 to 2014, I was working as a postdoc in Dr. Davis Ng's lab (Temasek Lifesciences Laboratory, Singapore) to study the mechanism of the protein quality control. I am working as an assistant professor in Dr. Toshie Kai’s lab at Graduate School of Frontier Bioscience (FBS), Osaka University to study the protein function which is essential for the germline development.
- Kawaguchi S, Ueki M, Kai T. (2020) Drosophila MARF1 ensures proper oocyte maturation by regulating nanos expression. PLoS One 15(4):e0231114
- Kanamori E, Kawaguchi S, Kuramitsu S, Kouyama T, Murakami M. (2015) Structural comparison between the open and closed forms of citrate synthase from Thermus thermophilus HB8. Biophys. Physicobiol. 12:47–56
- Prasad R, Kawaguchi S, Ng DT. (2012) Biosynthetic mode can determine the mechanism of protein quality control. Biochem. Biophys. Res. Commun. 425(3):689–695
- Kawaguchi S, Hsu CL, Ng DT. (2010) Interplay of substrate retention and export signals in endoplasmic reticulum quality control. PLoS One 5(11):e15532
- Prasad R, Kawaguchi S, Ng DT. (2010) A nucleus-based quality control mechanism for cytosolic proteins. Mol. Biol. Cell 21(13):2117–2127
- Ducat D, Kawaguchi S, Liu H, Yates JR 3rd, Zheng Y. (2008) Regulation of microtubule assembly and organization in mitosis by the AAA+ ATPase Pontin. Mol. Biol. Cell 19(7):3097–3110
- Ito K, Arai R, Fusatomi E, Kamo-Uchikubo T, Kawaguchi S, Akasaka R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. (2006) Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 Å resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD. Protein Sci. 15(5):1187–1192
- Tanaka Y, Tawaramoto-Sasanuma M, Kawaguchi S, Ohta T, Yoda K, Kurumizaka H, Yokoyama S. (2004) Expression and purification of recombinant human histones. Methods 33(1):3–11
- Kawaguchi S, Zheng Y. (2004) Characterization of a Drosophila centrosome protein CP309 that shares homology with Kendrin and CG-NAP. Mol. Biol. Cell 15(1):37–45
- Tanaka Y, Nureki O, Kurumizaka H, Fukai S, Kawaguchi S, Ikuta M, Iwahara J, Okazaki T, Yokoyama S. (2001) Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. EMBO J. 20(23):6612–6618
- Ura H, Nakai T, Kawaguchi S, Miyahara I, Hirotsu K, Kuramitsu S. (2001) Substrate recognition mechanism of thermophilic dual-substrate enzyme. J. Biochem. (Tokyo) 130(1):89–98
- Kawaguchi S, Muller J, Linde D, Kuramitsu S, Shibata T, Inoue Y, Vassylyev DG, Yokoyama S. (2001) The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus. EMBO J. 20(3):562–569
- Renault L, Kerjan P, Pasqualato S, Menetrey J, Robinson JC, Kawaguchi S, Vassylyev DG, Yokoyama S, Mirande M, Cherfils J. (2001) Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry. EMBO J. 20(3):570–578
- Ishijima J, Nakai T, Kawaguchi S, Hirotsu K, Kuramitsu S. (2000) Free energy requirement for domain movement of an enzyme. J. Biol. Chem. 275(25):18939–18945
- Matsui I, Matsui E, Sakai Y, Kikuchi H, Kawarabayasi Y, Ura H, Kawaguchi S, Kuramitsu S, and Harata K. (2000) The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii. J. Biol. Chem. 275(7):4871–4879
- Nakai T, Okada K, Akutsu S, Miyahara I, Kawaguchi S, Kato R, Kuramitsu S, Hirotsu K. (1999) Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate. Biochemistry 38(8):2413–2424
- Nobe Y, Kawaguchi S, Ura H, Nakai T, Hirotsu K, Kato R, Kuramitsu S. (1998) The novel substrate recognition mechanism utilized by aspartate aminotransferase of the extreme thermophile Thermus thermophilus HB8. J. Biol. Chem. 273(45):29554–29564
- Kawaguchi S, Kuramitsu S. (1998) Thermodynamics and molecular simulation analysis of hydrophobic substrate recognition by aminotransferases. J. Biol. Chem. 273(29):18353–18364
- Nakai T, Okada K, Kawaguchi S, Kato R, Kuramitsu S, Hirotsu K. (1998) Crystallization and preliminary X-ray characterization of aspartate aminotransferase from an extreme thermophile, Thermus thermophilus HB8. Acta Cryst. D54(Pt 5):1032–1034
- Hiramatsu Y, Kato R, Kawaguchi S, Kuramitsu S. (1997) Cloning and characterization of the uvrD gene from an extremely thermophilic bacterium, Thermus thermophilus HB8. Gene 199:77–82
- Kawaguchi S, Nobe Y, Yasuoka J, Wakamiya T, Kusumoto S, Kuramitsu S. (1997) Enzyme flexibility: new concept in recognition of hydrophobic substrates. J. Biochem. 122(1):55–63
- Kawaguchi S, Kuramitsu S. (1995) Separation of heat-stable proteins from Thermus thermophilus HB8 by two-dimensional electrophoresis. Electophoresis 16:1060–1066
- Kawaguchi S, Kuramitsu S. (1994) Homologus ligation. Trends Genet. 10(12):420
- Miyazawa K, Kawaguchi S, Okamoto A, Kato R, Ogawa T, Kuramitsu S. (1994) Construction of aminotransferase chimeras and analysis of their substrate specificity. J. Biochem. 115(3):568–577
- Kawaguchi S, Ng DT. (2007) SnapShot: ER-associated protein degradation pathways. Cell 129(6):1230
- Kanehara K, Kawaguchi S, Ng DT. (2007) The EDEM and Yos9p families of lectin-like ERAD factors. Semin Cell Dev. Biol. 18(6):743–750
- Yokoyama S, Matsuo Y, Hirota H, Kigawa T, Shirouzu M, Kuroda Y, Kurumizaka H, Kawaguchi S, Ito Y, Shibata T, Kainosho M, Nishimura Y, Inoue Y, Kuramitsu S. (2000) Structural genomics projects in Japan. Prog. Biophys. Mol. Biol. 73(5):363–376
- Kawaguchi S, Kuramitsu S. (1994) Mechanism of enzyme reaction. (in Japanese). Tanpakushitsu Kakusan Koso 39(7):1083–1090
Taichiro Iki, PhD
- E-mail: ikitfbs.osaka-u.ac.jp
In 2008, I earned my Ph.D in Dr. Hiroshi Oyaizu’s lab in the graduate school of the university of Tokyo. My research focus was on one of symbiotic bacteria, Azorhizobium caulinodans, which induces nodules on a leguminous plant Sesbania rostrata. In the symbiotic organ, A. caulinodans converts atmospheric N2 to ammonium to serve it to the host plants. I was studying of the nif gene clusters essential for N2 fixation, especially of the regulatory mechanisms on their expression.
From 2008 to 2012, I was working as a postdoc in Dr. Masayuki Ishikawa’s lab in the National Institute of Agrobiological Sciences (NIAS). One of my research objectives was to elucidate the molecular mechanisms by which small non-coding RNAs repress target gene expression in plants. We have developed a cell-free system that recapitulates the assembly and activity of RNA-induced silencing complex (RISC), the effector of posttranscriptional gene silencing. The findings include the dependence of RISC assembly on molecular chaperone machinery comprising HSP90 and the co-chaperone cyclophilin 40/SQUINT.
From 2012 to 2016, I was working as a postdoc in Dr. Olivier Voinnet’s lab in ETH Zürich, and experienced the European academic cultures. During the period of 2013 to 2015, my research was funded by Marie Curie International Incoming Fellowships. The research topics include the dissection of viral suppressors of RNA silencing which have been developed by diverse viral genera as a counter defensive strategy against host antiviral RNA silencing activities. Also, I was studying of microRNA (miRNA) structures and the cellular impacts.
From February in 2016, I am working as an assistant professor in Dr. Toshie Kai’s lab at Graduate School of Frontier Bioscience (FBS), Osaka University. Our research objective is to decipher the mechanisms underlying the maintenance and differentiation of germ cells in animals. We are using a model organism Drosophila melanogaster. Of my particular interest, if not all, are the non-coding RNA-mediated processes in oogenesis or spermatogenesis.
- Iki T, Tschopp MA, and Voinnet O (2017) Biochemical and genetic functional dissection of the P38 viral suppressor of RNA silencing. RNA 23(5):639–654
- Yoshikawa M, Iki T, Tsutsui Y, Miyashita K, Poethig S, Habu Y, Ishikawa M (2013) 3’ fragment of miR173-programmed RISC-cleaved RNA is protected from degradation in a complex with RISC and SGS3. Proc. Nat. Acad. Sci. USA. 110(10):4117-22
- Ye R, Wang W, Iki T, Liu C, Wu Y, Ishikawa M, Zhou X, Qi Y (2012) Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes. Molecular Cell 46(6):859-870
- Iki T, Yoshikawa M, Meshi T, Ishikawa M (2012) Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants. EMBO Journal 31(2):267-278
- Iki T, Yoshikawa M, Nishikiori M, Jaudal MC, Matsumoto-Yokoyama E, Mitsuhara I, Meshi T, Ishikawa M (2010) In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90. Molecular Cell 39(2):282-291
- Suzuki T, Aono T, Liu C. T, Suzuki S, Iki T, Yokota K, and Oyaizu H (2008) An outer membrane autotransporter, AoaA, of Azorhizobium caulinodans is required for sustaining high N2-fixing activity of stem nodules. FEMS Microbiology Letters 285:16-24.
- Suzuki, S, Aono T, Lee KB, Suzuki T, Liu C. T, Miwa H, Wakao S, Iki T, and Oyaizu H (2007) Rhizobial factors required for stem nodule maturation and maintenance in Sesbania rostrata-Azorhizobium caulinodans ORS571 symbiosis. Applied and Environmental Microbiology 73:6650-6659
- Iki T, Aono T, and Oyaizu H (2007) Evidence for functional differentiation of duplicated nifH genes in Azorhizobium caulinodans. FEMS Microbiology Letters 274(2):173-9
- Liu, CT, Aono T, Kinoshita M, Miwa H, Iki T, Lee KB, and Oyaizu H (2006) Isolation and differential expression of beta-1,3-glucanase messenger RNAs, SrGLU3 and SrGLU4, following inoculation of Sesbania rostrata. Functional Plant Biology 33:983-990
- Iki T (2017) Messages on small RNA duplexes in plants. J. Plant Res. 130:7–16
Ritsuko Suyama, PhD
- E-mail: rrsuyamafbs.osaka-u.ac.jp
In 2003, I earned my Ph.D. in Graduate School of Medicine, Department of Medicine at Kyushu University. From 2000 to 2007, I worked as a technician/postdoc in Dr. Anne Ephrussi’s lab at European Molecular Biology Laboratory (EMBL). The research topic is Drosophila oogenesis. We revealed a new mechanism of retaining Oskar protein in the oocyte cortex employing the germline and body axis formation. From 2007 to 2009, I worked in Dr. Asifa Akhtar’s lab and investigated dosage compensation mechanism in Drosophila. We identified the loci on X-chromosomes that bind to nucleoporins and their spatial position in the nucleus. From 2009 to 2012, I worked as a postdoc in Dr. Tadashi Uemura’s lab in Kyoto University and investigated the mechanism of dendrite formation in sensory neurons during fly metamorphosis. From 2012-2018, I worked as a staff scientist in Dr. Nicholas Luscombe’s lab. We established a single-cell RNA-seq technique in Ciona embryos to detail gene dynamics involved in tissue and cell lineage specification. Since 2018, I have been working as an assistant professor in Dr. Toshie Kai’s lab at Graduate School of Frontier Bioscience (FBS), Osaka University and focus the developmental mechanism of Drosophila oogenesis and the relevant environmental effect.
- Ilsley GR*, Suyama R*, Noda T, Satoh N, Luscombe NM (2020) Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq. Sci. Rep. 10(1):4961
- Suyama R (2015) Meeting report for single cell genomics conference. Jikken-Igaku, 33, 44-4
- Satoh D*, Suyama R*, Kimura K and Uemura T (2012) High-resolution in vivo imaging of regenerating dendrites of Drosophila sensory neurons during metamorphosis: local filopodial degeneration and heterotypic dendrite-dendrite contacts. Genes to Cells, 12, 939-51, equally contribution (*)
Vaquerizas JM*, Suyama R*, Kind J*, Miura K, Luscombe NM and Akhtar A (2010) Nuclear pore proteins Nup153 and Megator define transcription ally active regions in the Drosophila genome. PLoS Genet 12, 6, (2) equally contribution (*)
- Suyama R*, Jenney A*, Curado S* and Ephrussi A (2009) The actin binding protein Lasp promotes Oskar accumulation at the posterior pole of the Drosophila embryo. Development 136, 95-105, equally contribution (*)
- Arima K, Umeshita-Suyama R, Sakata Y, Akaiwa M, Mao XQ, Enomoto T, Dake Y, Shimazu S, Yamashita T, Sugawara N, Brodeur S, Geha R, Puri RK, Sayegh MH, Adra CN, Hamasaki N, Hamasaki N, Hopkin JM, Shirakawa T and Izuhara K (2002) Upregulation of IL-13 concentration in vivo by the IL-13 variant associated with bronchial asthma. Journal of Allergy and Clinical Immunology 109, 6, 980-987.
- Umeshita-Suyama R, Sugimoto R, Akaiwa M, Arima K, Hamasaki N and Izuhara K (2000) Characterization of IL-4 and IL-13 signals dependent on the human IL-13 receptor alpha chain 1. Imternational Immunology 12, 1499-1509,
- Ohshima K, Akaiwa M, Umeshita R, Suzumiya J, Izuhara K and Kikuchi M (2001) Interleukin-13 and Interluekin-13 receptor in Hodgkin’s disease : possible autocrine and involvement in fibrosis. Histopathology 38, 368-375.
- Akaiwa M, Yu B, Umeshita R, Terada N, Suto H, Koga T, Arima K, Matsushita S, Saito H, Ogawa H, Furue M, Hamasaki N, Ohshima K and Izuhara K (2001) Localization of Human Interleukin-13 Receptor in Non Hematopoietic Cells. Cytokine 13,75-84.
- Heinzmann A, Mao X-Q, Akaiwa M, Kremor R T, Gao P-S,Ohshima K, Umeshita R, Abe Y, Braun S, Yamashita,T, Roberts M H, Sugimoto R, Arima K, Arinobu Y, Yu B, Kruse S, Enomoto T, Dake Y, Kawai M, Shimazu S, Sasaki S, Addra C N, Hamasaki N, Izuhara K, Shirakawa T and Hopkin J M (2000) Genetic variants of IL-13 signaling and human asthma and atopy. Human Molecular genetics 9, 549-559.
- Izuhara K, Umeshita R, Akaiwa M, Shirakawa T, Deichmann A, Arima K, Yu,B, Hamasaki N and Hopkin J M (2000) Recent advances in understanding how interleukin-13 signals are involved in pathogenesis of bronchial asthma (review). Arch Immunol Ther Exp 505-512.
- Izuhara K, Sugimoto R, Akaiwa M, Umeshita R, Arima K, Bin Yu and Hamasaki N (2000) Signal transduction of IL-4 and IL-13: its correlation with the pathogenesis of allergic diseases. Molecular target for Hematological Malignancies and Cancer 95-102.
- Umeshita R and Izuhara K (2000) IL-13 receptor (review in Japanese). RINSHO MEN-EKI 34, 608-612.
- Sawa M, Imaeda Y, Hiratake J, Fujii R, Umeshita R, Watanabe M, Kondo H and Oda J (1998) Toward the antibody-catalyzed chemiluminescence: Design and synthesis of hapten. Bioorg. med. chem. 8:647-652.
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PhD Student D5/D5 (FBS RA)
Lin Xenia Lim
PhD Student D3/D5 (MEXT)
PhD Student D2/D5
Adrian Duncan Lene
PhD Student D1/D5
Undergraduate Part-time Assistant