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  1. Article ; Online: Voltage sensors of a Na

    Sumino, Ayumi / Sumikama, Takashi / Shibata, Mikihiro / Irie, Katsumasa

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7835

    Abstract: Understanding voltage-gated sodium ( ... ...

    Abstract Understanding voltage-gated sodium (Na
    MeSH term(s) Ion Channel Gating ; Action Potentials ; Membranes ; Sodium
    Chemical Substances Sodium (9NEZ333N27)
    Language English
    Publishing date 2023-12-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-43347-3
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  2. Article ; Online: High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes.

    Morioka, Shin / Oishi, Takumi / Hatazawa, Suguru / Kakuta, Takahiro / Ogoshi, Tomoki / Umeda, Kenichi / Kodera, Noriyuki / Kurumizaka, Hitoshi / Shibata, Mikihiro

    Nano letters

    2024  

    Abstract: Each nucleosome contains four types of histone proteins, each with a histone tail. These tails are essential for the epigenetic regulation of gene expression through post-translational modifications (PTMs). However, their influence on nucleosome dynamics ...

    Abstract Each nucleosome contains four types of histone proteins, each with a histone tail. These tails are essential for the epigenetic regulation of gene expression through post-translational modifications (PTMs). However, their influence on nucleosome dynamics at the single-molecule level remains undetermined. Here, we employed high-speed atomic force microscopy to visualize nucleosome dynamics in the absence of the N-terminal tail of each histone or all of the N-terminal tails. Loss of all tails stripped 6.7 base pairs of the nucleosome from the histone core, and the DNA entry-exit angle expanded by 18° from that of wild-type nucleosomes. Tail-less nucleosomes, particularly those without H2B and H3 tails, showed a 10-fold increase in dynamics, such as nucleosome sliding and DNA unwrapping/wrapping, within 0.3 s, emphasizing their role in histone-DNA interactions. Our findings illustrate that N-terminal histone tails stabilize the nucleosome structure, suggesting that histone tail PTMs modulate nucleosome dynamics.
    Language English
    Publishing date 2024-04-11
    Publishing country United States
    Document type Journal Article
    ISSN 1530-6992
    ISSN (online) 1530-6992
    DOI 10.1021/acs.nanolett.4c00801
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  3. Article ; Online: Antithetic effects of agonists and antagonists on the structural fluctuations of TRPV1 channel.

    Sumino, Ayumi / Zhao, Yimeng / Mukai, Daichi / Sumikama, Takashi / Puppulin, Leonardo / Hattori, Motoyuki / Shibata, Mikihiro

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 20, Page(s) e2301013120

    Abstract: Transient receptor potential vanilloid member 1 (TRPV1) is a heat and capsaicin receptor that allows cations to permeate and cause pain. As the molecular basis for temperature sensing, the heat capacity ( ... ...

    Abstract Transient receptor potential vanilloid member 1 (TRPV1) is a heat and capsaicin receptor that allows cations to permeate and cause pain. As the molecular basis for temperature sensing, the heat capacity (Δ
    MeSH term(s) Transient Receptor Potential Channels ; Capsaicin/pharmacology ; Capsaicin/metabolism ; TRPV Cation Channels/metabolism ; Hot Temperature ; Cations/metabolism ; Diterpenes/metabolism
    Chemical Substances Transient Receptor Potential Channels ; Capsaicin (S07O44R1ZM) ; TRPV Cation Channels ; Cations ; Diterpenes
    Language English
    Publishing date 2023-05-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2301013120
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  4. Article ; Online: Deciphering load attenuation mechanisms of the dentin-enamel junction: Insights from a viscoelastic constitutive model.

    Hasegawa, Masataka / Tanaka, Reina / Zhong, Jingxiao / Kobayashi, Mikihiro / Manabe, Atsufumi / Shibata, Yo

    Acta biomaterialia

    2023  Volume 171, Page(s) 193–201

    Abstract: A considerable material discontinuity between the enamel and dentin might jeopardize the tooth's mechanical durability over time without the attenuation of the dentin-enamel junction (DEJ). However, the critical loading transmission mechanism at the DEJ ... ...

    Abstract A considerable material discontinuity between the enamel and dentin might jeopardize the tooth's mechanical durability over time without the attenuation of the dentin-enamel junction (DEJ). However, the critical loading transmission mechanism at the DEJ remains understudied. This study aimed to define the extent and effective width of the DEJ, along with its mechanical competence. The presence of DEJ interphase layer was identified using a motif analysis based on the ion beam-transmission electron microscopy coupled with nanoindentation modulus mapping. For each region, nanoindentation load-displacement curves were recorded and mathematically analyzed using an appropriate viscoelastic constitutive model. The time-course of indenter penetration (creep) behavior of the tooth tissues can be mathematically approximated by the Kelvin-Voigt model in series, which determined the visco-contribution to the overall mechanical responses. Therefore, the elastic-plastic contribution can be distinguished from the overall mechanical responses of the tooth after subtracting the visco-contributions. During the loading period, the enamel behavior was dominated by elastic-plastic responses, while both the dentin and DEJ showed pronounced viscoelastic responses. The instantaneous modulus of the DEJ, which was measured by eliminating viscoelastic behavior from the raw load-displacement curve, was almost double that of the dentin. The DEJ was stiffer than the dentin, but it exhibited large viscoelastic motion even at the initial loading stage. This study revealed that the load attenuation competence of the DEJ, which involves extra energy expenditure, is mainly associated with its viscoelasticity. The mathematical analysis proposed here, performed on the nanoindentation creep behavior, could potentially augment the existing knowledge on hard-tissue biomechanics. STATEMENT OF SIGNIFICANCE: In this study, we undertake a rigorous mechanical characterization of the dentin-enamel junction (DEJ) using an advanced nanoindentation technique coupled with a pertinent viscoelastic constitutive model. Our approach unveils the substantial viscoelastic contribution of the DEJ during the initial indentation loading phase and offers an elaborate delineation of the DEJ interphase layer through sophisticated image analysis. These insights significantly augment our understanding of tooth durability. Importantly, our innovative mathematical analysis of creep behavior introduces a novel approach with profound implications for future research in the expansive field of hard-tissue biomechanics. The pioneering methodologies and findings presented in this work hold substantial potential to invigorate progress in biomaterials research and fuel further explorations into the functionality of biological tissues.
    MeSH term(s) Dentin/physiology ; Stress, Mechanical ; Tooth ; Biomechanical Phenomena ; Dental Enamel
    Language English
    Publishing date 2023-09-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2173841-5
    ISSN 1878-7568 ; 1742-7061
    ISSN (online) 1878-7568
    ISSN 1742-7061
    DOI 10.1016/j.actbio.2023.08.050
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  5. Article ; Online: Dynamics of Target DNA Binding and Cleavage by

    Puppulin, Leonardo / Ishikawa, Junichiro / Sumino, Ayumi / Marchesi, Arin / Flechsig, Holger / Umeda, Kenichi / Kodera, Noriyuki / Nishimasu, Hiroshi / Shibata, Mikihiro

    ACS nano

    2023  Volume 17, Issue 5, Page(s) 4629–4641

    Abstract: Programmable DNA binding and cleavage by CRISPR-Cas9 has revolutionized the life sciences. However, the off-target cleavage observed in DNA sequences with some homology to the target still represents a major limitation for a more widespread use of Cas9 ... ...

    Abstract Programmable DNA binding and cleavage by CRISPR-Cas9 has revolutionized the life sciences. However, the off-target cleavage observed in DNA sequences with some homology to the target still represents a major limitation for a more widespread use of Cas9 in biology and medicine. For this reason, complete understanding of the dynamics of DNA binding, interrogation and cleavage by Cas9 is crucial to improve the efficiency of genome editing. Here, we use high-speed atomic force microscopy (HS-AFM) to investigate
    MeSH term(s) CRISPR-Cas Systems ; Staphylococcus aureus/metabolism ; Microscopy, Atomic Force ; Gene Editing/methods ; DNA/chemistry
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-02-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.2c10709
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  6. Article ; Online: Imaging single CaMKII holoenzymes at work by high-speed atomic force microscopy.

    Tsujioka, Shotaro / Sumino, Ayumi / Nagasawa, Yutaro / Sumikama, Takashi / Flechsig, Holger / Puppulin, Leonardo / Tomita, Takuya / Baba, Yudai / Kakuta, Takahiro / Ogoshi, Tomoki / Umeda, Kenichi / Kodera, Noriyuki / Murakoshi, Hideji / Shibata, Mikihiro

    Science advances

    2023  Volume 9, Issue 26, Page(s) eadh1069

    Abstract: ... ...

    Abstract Ca
    MeSH term(s) Animals ; Rats ; Calcium-Calmodulin-Dependent Protein Kinase Type 2 ; Caenorhabditis elegans ; Microscopy, Atomic Force ; Holoenzymes ; Hydra ; Mammals
    Chemical Substances Calcium-Calmodulin-Dependent Protein Kinase Type 2 (EC 2.7.11.17) ; Holoenzymes
    Language English
    Publishing date 2023-06-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adh1069
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  7. Article ; Online: High-Speed Atomic Force Microscopy Reveals Spontaneous Nucleosome Sliding of H2A.Z at the Subsecond Time Scale.

    Morioka, Shin / Sato, Shoko / Horikoshi, Naoki / Kujirai, Tomoya / Tomita, Takuya / Baba, Yudai / Kakuta, Takahiro / Ogoshi, Tomoki / Puppulin, Leonardo / Sumino, Ayumi / Umeda, Kenichi / Kodera, Noriyuki / Kurumizaka, Hitoshi / Shibata, Mikihiro

    Nano letters

    2023  Volume 23, Issue 5, Page(s) 1696–1704

    Abstract: Nucleosome dynamics, such as nucleosome sliding and DNA unwrapping, are important for gene regulation in eukaryotic chromatin. H2A.Z, a variant of histone H2A that is highly evolutionarily conserved, participates in gene regulation by forming unstable ... ...

    Abstract Nucleosome dynamics, such as nucleosome sliding and DNA unwrapping, are important for gene regulation in eukaryotic chromatin. H2A.Z, a variant of histone H2A that is highly evolutionarily conserved, participates in gene regulation by forming unstable multipositioned nucleosomes
    MeSH term(s) Humans ; Nucleosomes ; Histones/chemistry ; Microscopy, Atomic Force ; Chromatin ; DNA/chemistry
    Chemical Substances Nucleosomes ; Histones ; Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2023-02-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1530-6992
    ISSN (online) 1530-6992
    DOI 10.1021/acs.nanolett.2c04346
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  8. Article: Surgical resection of a tuberculoma in the diaphragm: a case report.

    Hashinokuchi, Asato / Kohno, Mikihiro / Kosai, Keisuke / Ono, Yuki / Haratake, Naoki / Shibata, Daiki / Yamamoto, Hidetaka / Takenaka, Tomoyoshi / Yoshizumi, Tomoharu

    Surgical case reports

    2022  Volume 8, Issue 1, Page(s) 198

    Abstract: Background: Extrapulmonary tuberculosis commonly affects the lymphatic system, nervous system, and gastrointestinal system. Tuberculous infection in the muscle is very rare. Moreover, tuberculous infection in the diaphragm is extremely rare. We herein ... ...

    Abstract Background: Extrapulmonary tuberculosis commonly affects the lymphatic system, nervous system, and gastrointestinal system. Tuberculous infection in the muscle is very rare. Moreover, tuberculous infection in the diaphragm is extremely rare. We herein report a case of tuberculomas in the diaphragm and posterior mediastinum that were successfully diagnosed and treated.
    Case presentation: We encountered a 62-year-old woman with a tuberculoma in the diaphragm. The patient presented with mild dyspnea. Computed tomography showed a mass in the left diaphragm, focal thickening of the posterior mediastinum, and multiple nodules in the lungs. Positron emission tomography-computed tomography showed increased uptake in the left diaphragm mass and thickening of the posterior mediastinum; therefore, we considered the masses to be malignant and planned surgical resection. However, the patient was diagnosed with tuberculosis from a sputum culture, and she was treated with anti-tuberculous therapy. The masses in the diaphragm and posterior mediastinum had become enlarged after 6 months of anti-tuberculous therapy; therefore, the patient underwent resection of both masses. Tuberculous infection was histologically confirmed in each lesion. She was pathologically diagnosed with tuberculous abscesses in the diaphragm and posterior mediastinum and began treatment with anti-tuberculosis drugs.
    Conclusions: Preoperative diagnosis of a tuberculoma in the diaphragm is usually difficult, and surgical intervention is important for both diagnosis and treatment.
    Language English
    Publishing date 2022-10-14
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2809613-7
    ISSN 2198-7793
    ISSN 2198-7793
    DOI 10.1186/s40792-022-01554-y
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  9. Article ; Online: Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome

    Rina Hirano / Yasuhiro Arimura / Tomoya Kujirai / Mikihiro Shibata / Aya Okuda / Ken Morishima / Rintaro Inoue / Masaaki Sugiyama / Hitoshi Kurumizaka

    Communications Biology, Vol 4, Iss 1, Pp 1-

    2021  Volume 11

    Abstract: Hirano et al. show that the H2A.B-H2B histone dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from histone chaperones or nucleosome remodelers. This study provides insights into how the H2A.B ... ...

    Abstract Hirano et al. show that the H2A.B-H2B histone dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from histone chaperones or nucleosome remodelers. This study provides insights into how the H2A.B nucleosome exchanges its histones.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Applicability of Styrene-Maleic Acid Copolymer for Two Microbial Rhodopsins, RxR and HsSRI.

    Ueta, Tetsuya / Kojima, Keiichi / Hino, Tomoya / Shibata, Mikihiro / Nagano, Shingo / Sudo, Yuki

    Biophysical journal

    2020  Volume 119, Issue 9, Page(s) 1760–1770

    Abstract: The membrane-embedded protein rhodopsin is widely produced in organisms as a photoreceptor showing a variety of light-dependent biological functions. To investigate its molecular features, rhodopsin is often extracted from cellular membrane lipids by a ... ...

    Abstract The membrane-embedded protein rhodopsin is widely produced in organisms as a photoreceptor showing a variety of light-dependent biological functions. To investigate its molecular features, rhodopsin is often extracted from cellular membrane lipids by a suitable detergent as "micelles." The extracted protein is purified by column chromatography and then is often reconstituted into "liposomes" by removal of the detergent. The styrene-maleic acid ("SMA") copolymer spontaneously forms nanostructures containing lipids without detergent. In this study, we applied SMA to characterize two microbial rhodopsins, a thermally stable rhodopsin, Rubrobacter xylanophilus rhodopsin (RxR), and an unstable one, Halobacterium salinarum sensory rhodopsin I (HsSRI), and evaluated their physicochemical properties in SMA lipid particles compared with rhodopsins in micelles and in liposomes. Those two rhodopsins were produced in Escherichia coli cells and were successfully extracted from the membrane by the addition of SMA (5 w/v %) without losing their visible color. Analysis by dynamic light scattering revealed that RxR in SMA lipid particles (RxR-SMA) formed a discoidal structure with a diameter of 54 nm, which was 10 times smaller than RxR in phosphatidylcholine liposomes. The small particle size of RxR-SMA allowed us to obtain scattering-less visible spectra with a high signal-to-noise ratio similar to RxR in detergent micelles composed of n-dodecyl-β-D-maltoside. High-speed atomic force microscopy revealed that a single particle contained an average of 4.1 trimers of RxR (12.3 monomers). In addition, RxR-SMA showed a fast cyclic photoreaction (k = 13 s
    MeSH term(s) Actinobacteria ; Halobacterium salinarum ; Maleates ; Rhodopsins, Microbial ; Styrene
    Chemical Substances Maleates ; Rhodopsins, Microbial ; Styrene (44LJ2U959V) ; maleic acid (91XW058U2C)
    Language English
    Publishing date 2020-09-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2020.09.026
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    Zs.MO 2: Show issues

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