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Fundamental structural characteristics of planar granular assemblies
The microstructural organization of a granular system is the most important determinant of its macroscopic behavior. Here we identify the fundamental factors that determine the statistics of such microstructures, using numerical...
The spatial organization of non-homologous end joining
Non-homologous end joining (NHEJ) repairs DNA double-strand breaks generated by DNA damage and also those occurring in V(D)J recombination in immunoglobulin and T cell receptor production in the immune system. In NHEJ DNA-PKcs...
Artemis DNA ligase IV Cernunnus DNA-PKcs LIG4 syndrome Non-homologous end joining XLF XRCC4 Binding Sites DNA Breaks Double-Stranded DNA End-Joining Repair DNA Ligases DNA Repair Enzymes DNA-Activated Protein Kinase DNA-Binding Proteins Endonucleases Humans Models Molecular Multiprotein Complexes Nuclear Proteins Protein Binding
Design, Synthesis, and Chemical and Biological Properties of Cyclic ADP-4-Thioribose as a Stable Equivalent of Cyclic ADP-Ribose
T. Tsuzuki, S. Takano, N. Sakaguchi, T Kudoh, Takashi Murayama, Takashi Sakurai, Haruhiro Higashida, K Weber, A H Guse, T. Kameda, T. Hirokawa, Y. Kumaki, M Arisawa, Barry Potter, Satoshi Shuto
Jun 01, 2015
Here we describe the successful synthesis of cyclic ADP-4-thioribose (cADPtR, 3), designed as a stable mimic of cyclic ADP-ribose (cADPR, 1), a Ca2+-mobilizing second messenger, in which the key N1-β-thioribosyladenosine...
Single-molecule fluorescence polarization study of conformational change in archaeal group II chaperonin.
Group II chaperonins found in archaea and in eukaryotic cytosol mediate protein folding without a GroES-like cofactor. The function of the cofactor is substituted by the helical protrusion at the tip of the apical domain, which...
Structure of the catalytic region of DNA ligase IV in complex with an Artemis fragment sheds light on double-strand break repair.
Nonhomologous end joining (NHEJ) is central to the repair of double-stranded DNA breaks throughout the cell cycle and plays roles in the development of the immune system. Although three-dimensional structures of most components...
Asymmetric division of contractile domains couples cell positioning and fate specification.
Jean-Léon Maître, Hervé Turlier, Rukshala Illukkumbura, Björn Eismann, Ritsuya Niwayama, François Nédélec, Takashi Hiiragi
Aug 06, 2020
During pre-implantation development, the mammalian embryo self-organizes into the blastocyst, which consists of an epithelial layer encapsulating the inner-cell mass (ICM) giving rise to all embryonic tissues. In mice, oriented...
Adaptor Proteins Signal Transducing Animals Blastocyst Blastocyst Inner Cell Mass Blastomeres Cell Cycle Proteins Cell Differentiation Cell Division Cell Lineage Cell Movement Cell Polarity Embryo Mammalian Embryonic Development Female Male Mice Phosphoproteins Protein Transport Reproducibility of Results YAP-Signaling Proteins
Comparison of Hi-C results using in-solution versus in-nucleus ligation.
Takashi Nagano, Csilla Várnai, Stefan Schoenfelder, Biola-Maria Javierre, Steven W Wingett, Peter Fraser
Jul 15, 2019
BACKGROUND: Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods employ...
Design, Synthesis, and Chemical and Biological Properties of Cyclic ADP-4-Thioribose as a Stable Equivalent of Cyclic ADP-Ribose
T. Tsuzuki, S. Takano, N. Sakaguchi, T Kudoh, Takashi Murayama, Takashi Sakurai, Haruhiro Higashida, K Weber, A H Guse, T. Kameda, T. Hirokawa, Y. Kumaki, M Arisawa, Barry Potter, Satoshi Shuto
Jun 01, 2015
Here we describe the successful synthesis of cyclic ADP-4-thioribose (cADPtR, 3), designed as a stable mimic of cyclic ADP-ribose (cADPR, 1), a Ca2+-mobilizing second messenger, in which the key N1-β-thioribosyladenosine...
HiCUP
Steven Wingett, Philip Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon Andrews
Jul 15, 2019
HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified...
Structural biology of DNA repair
Takashi Ochi, Lynn Sibanda, Qian Wu, Dima Chirgadze, Victor M Bolanos-Garcia, Tom Blundell
Mar 12, 2021
Published by: Journal of nucleic acids
Engineering a novel multifunctional green fluorescent protein tag for a wide variety of protein research.
Takuya Kobayashi, Nobuhiro Morone, Taku Kashiyama, Hideto Oyamada, Nagomi Kurebayashi, Takashi Murayama
May 28, 2019
BACKGROUND: Genetically encoded tag is a powerful tool for protein research. Various kinds of tags have been developed: fluorescent proteins for live-cell imaging, affinity tags for protein isolation, and epitope tags for...
Putting High-Index Cu on the Map for High-Yield, Dry-Transferred CVD Graphene.
Oliver J Burton, Zachary Winter, Kenji Watanabe, Takashi Taniguchi, Bernd Beschoten, Christoph Stampfer, Stephan Hofmann
Feb 02, 2023
Reliable, clean transfer and interfacing of 2D material layers are technologically as important as their growth. Bringing both together remains a challenge due to the vast, interconnected parameter space. We introduce a...
Structural insights into the role of domain flexibility in human DNA ligase IV.
Takashi Ochi, Qian Wu, Dimitri Y Chirgadze, J Günter Grossmann, Victor M Bolanos-Garcia, Tom L Blundell
Mar 12, 2021
Knowledge of the architecture of DNA ligase IV (LigIV) and interactions with XRCC4 and XLF-Cernunnos is necessary for understanding its role in the ligation of double-strand breaks during nonhomologous end joining. Here we...
Catalytic Domain Chromatography Gel DNA DNA Breaks Double-Stranded DNA Ligase ATP DNA Ligases DNA Nucleotidyltransferases DNA Repair DNA Repair Enzymes DNA-Binding Proteins Escherichia coli Humans Models Molecular Protein Binding Protein Structure Secondary Protein Structure Tertiary Recombinant Proteins SCATTERING Small Angle X-Ray Diffraction
Putting High-Index Cu on the Map for High-Yield, Dry-Transferred CVD Graphene.
Oliver J Burton, Zachary Winter, Kenji Watanabe, Takashi Taniguchi, Bernd Beschoten, Christoph Stampfer, Stephan Hofmann
Jan 25, 2023
Reliable, clean transfer and interfacing of 2D material layers are technologically as important as their growth. Bringing both together remains a challenge due to the vast, interconnected parameter space. We introduce a...
Understanding the structure and role of DNA-PK in NHEJ
Qian Wu, Shikang Liang, Takashi Ochi, Dimitri Y Chirgadze, Juha T Huiskonen, Tom L Blundell
Apr 15, 2019
DNA double-strand breaks (DSBs), generated by ionizing radiation, reactive oxygen species and DNA replication across nicks, are the most severe DNA damage in eukaryotic cells. Non-Homologous End Joining repairs DNA double-strand...
Insights into gene expression profiles induced by Socs3 depletion in keratinocytes.
Archana Bajpai, Takashi Ishii, Kosuke Miyauchi, Vipul Gupta, Yuka Nishio-Masaike, Yuki Shimizu-Yoshida, Masato Kubo, Hiroaki Kitano
Jul 11, 2019
Specific deletion of suppressor of cytokine signaling 3 (Socs3) in keratinocytes can cause severe skin inflammation with infiltration of immune cells. The molecular mechanisms and key regulatory pathways involved in these...
Tunable Fermi surface topology and Lifshitz transition in bilayer graphene
Anastasia Varlet, Marcin Mucha-Kruczynski, Dominik Bischoff, Pauline Simonet, Takashi Taniguchi, Kenji Watanabe, Vladimir Fal'ko, Thomas Ihn, Klaus Ensslin
Dec 01, 2015
Bilayer graphene is a highly tunable material: not only can one tune the Fermi energy using standard gates, as in single-layer graphene, but the band structure can also be modified by external perturbations such as transverse...
Anomalous sequence of quantum hall liquids revealing a tunable Lifshitz transition in bilayer graphene
Anastasia Varlet, Dominik Bischoff, Pauline Simonet, Kenji Watanabe, Takashi Taniguchi, Thomas Ihn, Klaus Ensslin, Marcin Mucha-Kruczynski, Vladimir I. Fal’ko
Sep 12, 2014
Bilayer graphene is a unique system where both the Fermi energy and the low-energy electron dispersion can be tuned. This is brought about by an interplay between trigonal warping and the band gap opened by a transverse electric...
High-throughput screening identifies suppressors of mitochondrial fragmentation in OPA1 fibroblasts.
Emma Cretin, Priscilla Lopes, Elodie Vimont, Takashi Tatsuta, Thomas Langer, Anastasia Gazi, Martin Sachse, Patrick Yu-Wai-Man, Pascal Reynier, Timothy Wai
Jun 21, 2021
Mutations in OPA1 cause autosomal dominant optic atrophy (DOA) as well as DOA+, a phenotype characterized by more severe neurological deficits. OPA1 deficiency causes mitochondrial fragmentation and also disrupts cristae...
Published by: EMBO molecular medicine
The Naming of Names
John L Bowman, Takashi Araki, Mario A Arteaga-Vazquez, Frederic Berger, Liam Dolan, Jim Haseloff, Kimitsune Ishizaki, Junko Kyozuka, Shih-Shun Lin, Hideki Nagasaki, Hirofumi Nakagami, Keiji Nakajima, Yasukazu Nakamura, Kyoko Ohashi-Ito, Shinichiro Sawa, Masaki Shimamura, Roberto Solano, Hirokazu Tsukaya, Takashi Ueda, Yuichiro Watanabe, Katsuyuki T Yamato, Sabine Zachgo, Takayuki Kohchi
Sep 15, 2021
While Marchantia polymorpha has been utilized as a model system to investigate fundamental biological questions for over almost two centuries, there is renewed interest in M. polymorpha as a model genetic organism in the...
High-throughput screening identifies suppressors of mitochondrial fragmentation in OPA1 fibroblasts.
Emma Cretin, Priscilla Lopes, Elodie Vimont, Takashi Tatsuta, Thomas Langer, Anastasia Gazi, Martin Sachse, Patrick Yu-Wai-Man, Pascal Reynier, Timothy Wai
Jun 28, 2021
Mutations in OPA1 cause autosomal dominant optic atrophy (DOA) as well as DOA+, a phenotype characterized by more severe neurological deficits. OPA1 deficiency causes mitochondrial fragmentation and also disrupts cristae...
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