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Hokkaido University Collection of Scholarly and Academic Papers (135.521 recursos)

HUSCAP (Hokkaido University Collection of Scholarly and Academic Papers) contains peer-reviewed journal articles, proceedings, educational resources and any kind of scholarly works of Hokkaido University.

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Mostrando recursos 1 - 20 de 170

  1. Different aggregation states of a nuclear localization signal-tagged 25-kDa C-terminal fragment of TAR RNA/DNA-binding protein 43 kDa

    Kitamura, A; Yuno, S; Muto, H
    The mechanism and cause of motor neuronal cell death in amyotrophic lateral sclerosis (ALS),a devastating neurodegenerative disorder, are unknown; gain of function of oligomers andaggregation of misfolded proteins, including carboxyl-terminal fragments (CTFs) of TARRNA/DNA-binding protein 43 kDa (TDP-43), have been proposed as important causative fac-tors in the onset of ALS. We recently reported that a nuclear localization signal (NLS)-tagged25-kDa CTF of TDP-43 (TDP25) could dec rease the cell-death proportion compared with thatpromoted by TDP25 . Here, we show oligomeric states of NLS-TDP25 and its detailed local-ization prope rty using super-resolution fluorescence microscopy, FR ET, fluorescence recoveryafter photobleaching, and fluorescence correlation...

  2. Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus

    Komoda, Keisuke; Narita, Masanori; Yamashita, Keitaro; Tanaka, Isao; Yao, Min
    Tomato spotted wilt virus (TSWV), belonging to the genus Tospovirus of the family Bunyaviridae, causes significant economic damage to several vegetables and ornamental plants worldwide. Similar to those of all other negative-strand RNA viruses, the nucleocapsid (N) protein plays very important roles in its viral life cycle. N proteins protect genomic RNAs by encapsidation and form a viral ribonucleoprotein complex (vRNP) with some RNA-dependent RNA polymerases. Here we show the crystal structure of the N protein from TSWV. Protomers of TSWV N proteins consist of three parts: the N arm, C arm, and core domain. Unlike N proteins of other...

  3. Bulk Energy Dissipation Mechanism for the Fracture of Tough and Self-Healing Hydrogels

    Sun, Tao Lin; Luo, Feng; Hong, Wei; Cui, Kunpeng; Huang, Yiwan; Zhang, Hui Jie; King, Daniel R.; Kurokawa, Takayuki; Nakajima, Tasuku; Gong, Jian Ping
    Recently, many tough and self-healing hydrogels have been developed based on physical bonds as reversible sacrificial bonds. As breaking and re-forming of physical bonds are time-dependent, these hydrogels are viscoelastic and the deformation rate and temperature pronouncedly influence their fracture behavior. Using a polyampholyte hydrogel as a model system, we observed that the time–temperature superposition principle is obeyed not only for the small strain rheology but also for the large strain hysteresis energy dissipation and the fracture energy below a certain temperature. The three processes possess the same shift factors that obey the equation of Williams, Landel, and Ferry (WLF)...

  4. Defect in dermatan sulfate in urine of patients with Ehlers-Danlos syndrome caused by a CHST14/D4ST1 deficiency

    Mizumoto, Shuji; Kosho, Tomoki; Hatamochi, Atsushi; Honda, Tomoko; Yamaguchi, Tomomi; Okamoto, Nobuhiko; Miyake, Noriko; Yamada, Shuhei; Sugahara, Kazuyuki
    Purpose: Dermatan sulfate (DS) plays a number of roles in a wide range of biological activities such as cell signaling and tissue morphogenesis through interactions with various extracellular matrix proteins including collagen. Mutations in the carbohydrate sulfotransferase 14 gene (CHST14) encoding CHST14/dermatan 4-O-sulfotransferase-1 (D4ST1), which is responsible for the biosynthesis of DS, cause a recently delineated form of Ehlers-Danlos syndrome (EDS, musculocontractural type 1), an autosomal recessive connective tissue disorder characterized by congenital malformations (specific craniofacial features, and congenital multiple contractures) and progressive fragility-related complications (skin hyperextensibility, bruisability, and fragility with atrophic scars; recurrent dislocations; progressive talipes or spinal deformities;...

  5. Synthetic Mucin-Like Glycopeptides as Versatile Tools to Measure Effects of Glycan Structure/Density/Position on the Interaction with Adhesion/Growth-Regulatory Galectins in Arrays

    Artigas, Gerard; Hinou, Hiroshi; Garcia-Martin, Fayna; Gabius, Hans-Joachim; Nishimura, Shin-Ichiro
    Functional pairing of cellular glycoconjugates with tissue lectins is a highly selective process, whose determinative factors have not yet been fully delineated. Glycan structure and modes of presentation, that is, its position and density, can contribute to binding, as different members of a lectin family can regulate degrees of responsiveness to these factors. Using a peptide repeat sequence motif of the glycoprotein mucin-1, the principle of introducing synthetic (glyco) peptides with distinct variations in these three parameters to an array-based screening of tissue lectins is illustrated. Interaction profiles of seven adhesion/growth-regulatory galectins cover the range from intense signals with core...

  6. U6 snRNA expression prevents toxicity in TDP-43-knockdown cells

    Yahara, Masao; Kitamura, Akira; Kinjo, Masataka
    Depletion of amyotrophic lateral sclerosis (ALS)-associated transactivation response (TAR) RNA/DNA-binding protein 43 kDa (TDP-43) alters splicing efficiency of multiple transcripts and results in neuronal cell death. TDP-43 depletion can also disturb expression levels of small nuclear RNAs (snRNAs) as spliceosomal components. Despite this knowledge, the relationship between cell death and alteration of snRNA expression during TDP-43 depletion remains unclear. Here, we knocked down TDP-43 in murine neuroblastoma Neuro2A cells and found a time lag between efficient TDP-43 depletion and appearance of cell death, suggesting that several mechanisms mediate between these two events. The amount of U6 snRNA was significantly decreased...

  7. U6 snRNA expression prevents toxicity in TDP-43-knockdown cells

    Yahara, Masao; Kitamura, Akira; Kinjo, Masataka
    Depletion of amyotrophic lateral sclerosis (ALS)-associated transactivation response (TAR) RNA/DNA-binding protein 43 kDa (TDP-43) alters splicing efficiency of multiple transcripts and results in neuronal cell death. TDP-43 depletion can also disturb expression levels of small nuclear RNAs (snRNAs) as spliceosomal components. Despite this knowledge, the relationship between cell death and alteration of snRNA expression during TDP-43 depletion remains unclear. Here, we knocked down TDP-43 in murine neuroblastoma Neuro2A cells and found a time lag between efficient TDP-43 depletion and appearance of cell death, suggesting that several mechanisms mediate between these two events. The amount of U6 snRNA was significantly decreased...

  8. Structural basis for tRNA-dependent cysteine biosynthesis

    Chen, Meirong; Kato, Koji; Kubo, Yume; Tanaka, Yoshikazu; Liu, Yuchen; Long, Feng; Whitman, William B.; Lill, Pascal; Gatsogiannis, Christos; Raunser, Stefan; Shimizu, Nobutaka; Shinoda, Akira; Nakamura, Akiyoshi; Tanaka, Isao; Yao, Min
    Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA(Cys) followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA(Cys), respectively, which mediates the dynamic architecture of the transsulfursome and thus enables...

  9. Structural basis for tRNA-dependent cysteine biosynthesis

    Chen, Meirong; Kato, Koji; Kubo, Yume; Tanaka, Yoshikazu; Liu, Yuchen; Long, Feng; Whitman, William B.; Lill, Pascal; Gatsogiannis, Christos; Raunser, Stefan; Shimizu, Nobutaka; Shinoda, Akira; Nakamura, Akiyoshi; Tanaka, Isao; Yao, Min
    Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA(Cys) followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA(Cys), respectively, which mediates the dynamic architecture of the transsulfursome and thus enables...

  10. Negative Correlation between the Diffusion Coefficient and Transcriptional Activity of the Glucocorticoid Receptor

    Mikuni, Shintaro; Yamamoto, Johtaro; Horio, Takashi; Kinjo, Masataka
    The glucocorticoid receptor (GR) is a transcription factor, which interacts with DNA and other cofactors to regulate gene transcription. Binding to other partners in the cell nucleus alters the diffusion properties of GR. Raster image correlation spectroscopy (RICS) was applied to quantitatively characterize the diffusion properties of EGFP labeled human GR (EGFP-hGR) and its mutants in the cell nucleus. RICS is an image correlation technique that evaluates the spatial distribution of the diffusion coefficient as a diffusion map. Interestingly, we observed that the averaged diffusion coefficient of EGFP-hGR strongly and negatively correlated with its transcriptional activities in comparison to that...

  11. Stretching-induced ion complexation in physical polyampholyte hydrogels

    Cui, Kunpeng; Sun, Tao Lin; Kurokawa, Takayuki; Nakajima, Tasuku; Nonoyama, Takayuki; Chen, Liang; Gong, Jian Ping
    Recently, we have developed a series of charge balanced polyampholyte (PA) physical hydrogels by random copolymerization in water, which show extraordinarily high toughness, self-healing ability and viscoelasticity. The excellent performance of PA hydrogels is ascribed to dynamic ionic bond formation through inter-and intra-chain interactions. The randomness results in ionic bonds of wide strength distribution, the strong bonds, which serve as permanent crosslinking, imparting the elasticity, while the weak bonds reversibly break and re-form, dissipating energy. In this work, we developed a simple physical method, called a pre-stretching method, to promote the performance of PA hydrogels. By imposing a pre-stretching on...

  12. Stretching-induced ion complexation in physical polyampholyte hydrogels

    Cui, Kunpeng; Sun, Tao Lin; Kurokawa, Takayuki; Nakajima, Tasuku; Nonoyama, Takayuki; Chen, Liang; Gong, Jian Ping
    Recently, we have developed a series of charge balanced polyampholyte (PA) physical hydrogels by random copolymerization in water, which show extraordinarily high toughness, self-healing ability and viscoelasticity. The excellent performance of PA hydrogels is ascribed to dynamic ionic bond formation through inter-and intra-chain interactions. The randomness results in ionic bonds of wide strength distribution, the strong bonds, which serve as permanent crosslinking, imparting the elasticity, while the weak bonds reversibly break and re-form, dissipating energy. In this work, we developed a simple physical method, called a pre-stretching method, to promote the performance of PA hydrogels. By imposing a pre-stretching on...

  13. Photochemical characterization of actinorhodopsin and its functional existence in the natural host

    Nakamura, Shintaro; Kikukawa, Takashi; Tamogami, Jun; Kamiya, Masakatsu; Aizawa, Tomoyasu; Hahn, Martin W.; Ihara, Kunio; Kamo, Naoki; Demura, Makoto
    Actinorhodopsin (ActR) is a light-driven outward H+ pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR phototrophy in the native actinobacterium. Genome analysis showed that Candidatus Rhodoluna planktonica, a freshwater actinobacterium, encodes one microbial rhodopsin (RpActR) belonging to the ActR family. Reflecting the functional expression of RpActR, illumination induced the acidification of the actinobacterial cell suspension and then elevated the ATP content inside the cells. The photochemistry of RpActR was also examined using heterologously expressed RpActR in Escherichia coli membranes....

  14. Photochemical characterization of actinorhodopsin and its functional existence in the natural host

    Nakamura, Shintaro; Kikukawa, Takashi; Tamogami, Jun; Kamiya, Masakatsu; Aizawa, Tomoyasu; Hahn, Martin W.; Ihara, Kunio; Kamo, Naoki; Demura, Makoto
    Actinorhodopsin (ActR) is a light-driven outward H+ pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR phototrophy in the native actinobacterium. Genome analysis showed that Candidatus Rhodoluna planktonica, a freshwater actinobacterium, encodes one microbial rhodopsin (RpActR) belonging to the ActR family. Reflecting the functional expression of RpActR, illumination induced the acidification of the actinobacterial cell suspension and then elevated the ATP content inside the cells. The photochemistry of RpActR was also examined using heterologously expressed RpActR in Escherichia coli membranes....

  15. Crystal structure of the flexible tandem repeat domain of bacterial cellulose synthesis subunit C

    Nojima, Shingo; Fujishima, Ayumi; Kato, Koji; Ohuchi, Kayoko; Shimizu, Nobutaka; Yonezawa, Kento; Tajima, Kenji; Yao, Min
    Bacterial cellulose (BC) is synthesized and exported through the cell membrane via a large protein complex (terminal complex) that consists of three or four subunits. BcsC is a little-studied subunit considered to export BC to the extracellular matrix. It is predicted to have two domains: a tetratrico peptide repeat (TPR) domain and a beta-barrelled outer membrane domain. Here we report the crystal structure of the N-terminal part of BcsC-TPR domain (Asp24-Arg272) derived from Enterobacter CJF-002. Unlike most TPR-containing proteins which have continuous TPR motifs, this structure has an extra a-helix between two clusters of TPR motifs. Five independent molecules in...

  16. Pathophysiological Significance of Dermatan Sulfate Proteoglycans Revealed by Human Genetic Disorders

    Mizumoto, Shuji; Kosho, Tomoki; Yamada, Shuhei; Sugahara, Kazuyuki
    The indispensable roles of dermatan sulfate-proteoglycans (DS-PGs) have been demonstrated in various biological events including construction of the extracellular matrix and cell signaling through interactions with collagen and transforming growth factor- , respectively. Defects in the core proteins of DS-PGs such as decorin and biglycan cause congenital stromal dystrophy of the cornea, spondyloepimetaphyseal dysplasia, and Meester-Loeys syndrome. Furthermore, mutations in human genes encoding the glycosyltransferases, epimerases, and sulfotransferases responsible for the biosynthesis of DS chains cause connective tissue disorders including Ehlers-Danlos syndrome and spondyloepimetaphyseal dysplasia with joint laxity characterized by skin hyperextensibility, joint hypermobility, and tissue fragility, and by severe skeletal disorders such as kyphoscoliosis, short trunk, dislocation, and...

  17. A Quantitative Study of Internal and External Interactions of Homodimeric Glucocorticoid Receptor Using Fluorescence Cross-Correlation Spectroscopy in a Live Cell

    Tiwari, Manisha; Oasa, Sho; Yamamoto, Johtaro; Mikuni, Shintaro; Kinjo, Masataka
    Glucocorticoid receptor (GR alpha) is a well-known ligand-dependent transcription-regulatory protein. The classic view is that unliganded GRa resides in the cytoplasm, relocates to the nucleus after ligand binding, and then associates with a specific DNA sequence, namely a glucocorticoid response element (GRE), to activate a specific gene as a homodimer. It is still a puzzle, however, whether GRa forms the homodimer in the cytoplasm or in the nucleus before DNA binding or after that. To quantify the homodimerization of GR alpha, we constructed the spectrally different fluorescent protein tagged hGR alpha and applied fluorescence cross-correlation spectroscopy. First, the dissociation constant...

  18. Energy-Dissipative Matrices Enable Synergistic Toughening in Fiber Reinforced Soft Composites

    Huang, Yiwan; King, Daniel R.; Sun, Tao Lin; Nonoyama, Takayuki; Kurokawa, Takayuki; Nakajima, Tasuku; Gong, Jian Ping
    Tough hydrogels have shown strong potential as structural biomaterials. These hydrogels alone, however, possess limited mechanical properties (such as low modulus) when compared to some load-bearing tissues, e.g., ligaments and tendons. Developing both strong and tough soft materials is still a challenge. To overcome this obstacle, a new material design strategy has been recently introduced by combining tough hydrogels with woven fiber fabric to create fiber reinforced soft composites (FRSCs). The new FRSCs exhibit extremely high toughness and tensile properties, far superior to those of the neat components, indicating a synergistic effect. Here, focus is on understanding the role of...

  19. Phase-Separation-Induced Anomalous Stiffening, Toughening, and Self-Healing of Polyacrylamide Gels

    Sato, Koshiro; Nakajima, Tasuku; Hisamatsu, Toshiyuki; Nonoyama, Takayuki; Kurokawa, Takayuki; Gong, Jian Ping
    Novel, tough, strong, and self-healable polyacrylamide (PAAm) gels are fabricated by inducing an appropriate phase-separation structure using a poor solvent. The phase separation induces a gel-glass-like transition of the PAAm gels, providing the gels an anomalously high modulus (211 MPa), fracture stress (7.13 MPa), and fracture energy (4.16 x 10(4) J m(-2)), while keeping a high solvent content (approximate to 60 vol%).

  20. Concentration-dependent oligomerization of an alpha-helical antifreeze polypeptide makes it hyperactive

    Mahatabuddin, Sheikh; Hanada, Yuichi; Nishimiya, Yoshiyuki; Miura, Ai; Kondo, Hidemasa; Davies, Peter L.; Tsuda, Sakae
    A supersoluble 40-residue type I antifreeze protein (AFP) was discovered in a righteye flounder, the barfin plaice (bp). Unlike all other AFPs characterized to date, bpAFP transitions from moderately-active to hyperactive with increasing concentration. At sub-mM concentrations, bpAFP bound to pyramidal planes of ice to shape it into a bi-pyramidal hexagonal trapezohedron, similarly to the other moderately-active AFPs. At sub-mM concentrations, bpAFP uniquely underwent further binding to the whole ice crystal surface including the basal planes. The latter caused a bursting ice crystal growth normal to c-axis, 3 degrees C of high thermal hysteresis, and alteration of an ice crystal...

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