Search
Results: 136
Specification and epigenetic programming of the human germ line.
Primordial germ cells (PGCs), the precursors of sperm and eggs, are established in perigastrulation-stage embryos in mammals. Signals from extra-embryonic tissues induce a unique gene regulatory network in germline-competent...
Germ cell specification and pluripotency in mammals
Germ cells are unique cell types that generate a totipotent zygote upon fertilization, giving rise to the next generation in mammals and many other multicellular organisms. How germ cells acquire this ability has been of...
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...
Tumors Widely Express Hundreds of Embryonic Germline Genes.
Jan Willem Bruggeman, Naoko Irie, Paul Lodder, Ans MM van Pelt, Jan Koster, Geert Hamer
Dec 22, 2020
We have recently described a class of 756 genes that are widely expressed in cancers, but are normally restricted to adult germ cells, referred to as germ cell cancer genes (GC genes). We hypothesized that carcinogenesis...
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...
Shaping the growth behaviour of biofilms initiated from bacterial aggregates
Gavin Melaugh, Jaime Hutchison, Kasper Nørskov Kragh, Yasuhiko Irie, Aled Roberts, Thomas Bjarnsholt, Stephen P. Diggle, Vernita D. Gordon, Rosalind J. Allen
Mar 02, 2016
Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and...
Shaping the growth behaviour of biofilms initiated from bacterial aggregates
Gavin Melaugh, Jaime Hutchison, Kasper Nørskov Kragh, Yasuhiko Irie, Aled Roberts, Thomas Bjarnsholt, Stephen P. Diggle, Vernita D. Gordon, Rosalind J. Allen
Mar 02, 2016
Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and...
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
A PAX5-OCT4-PRDM1 developmental switch specifies human primordial germ cells.
Fang Fang, Benjamin Angulo, Ninuo Xia, Meena Sukhwani, Zhengyuan Wang, Charles C Carey, Aurélien Mazurie, Jun Cui, Royce Wilkinson, Blake Wiedenheft, Naoko Irie, M Azim Surani, Kyle E Orwig, Renee A Reijo Pera
Sep 11, 2018
Dysregulation of genetic pathways during human germ cell development leads to infertility. Here, we analysed bona fide human primordial germ cells (hPGCs) to probe the developmental genetics of human germ cell specification and...
Animals Cell Differentiation Cell Line Gene Editing Gene Expression Regulation Developmental Human Embryonic Stem Cells Humans Male Mice Nude Octamer Transcription Factor-3 PAX5 Transcription Factor Positive Regulatory Domain I-Binding Factor 1 Protein Binding SOXB1 Transcription Factors Signal Transduction Spermatozoa Testis Time Factors Transcription Genetic
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...
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
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...
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...
|
|< |
< |
1 |