| Flechsig H (2016), "Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.", Frontiers in Physics. Vol. 4(3) |
| Abstract: ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter. Possible explanations are discussed in the light of currently debated transport scenarios of ABC transporters. |
BibTeX:
@article{10.3389/fphy.2016.00003,
author = {Flechsig, Holger},
title = {Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.},
journal = {Frontiers in Physics},
year = {2016},
volume = {4},
number = {3},
url = {http://www.frontiersin.org/biophysics/10.3389/fphy.2016.00003/abstract},
doi = {10.3389/fphy.2016.00003}
}
|
| Lee SS (2016), "Positioning of polarity formation by extracellular signaling during asymmetric cell division ", Journal of Theoretical Biology . Vol. 400, pp. 52 - 64. |
| Abstract: Abstract Anterior–posterior (AP) polarity formation of cell membrane proteins plays a crucial role in determining cell asymmetry, which ultimately generates cell diversity. In Caenorhabditis elegans, a single fertilized egg cell (P0), its daughter cell (P1), and the germline precursors (P2 and P3 cells) form two exclusive domains of different PAR proteins on the membrane along the anterior–posterior axis. However, the phenomenon of polarity reversal has been observed in which the axis of asymmetric cell division of the P2 and P3 cells is formed in an opposite manner to that of the P0 and P1 cells. The extracellular signal MES-1/SRC-1 has been shown to induce polarity reversal, but the detailed mechanism remains elusive. Here, using a mathematical model, I explore the mechanism by which MES-1/SRC-1 signaling can induce polarity reversal and ultimately affect the process of polarity formation. I show that a positive correlation between SRC-1 and the on-rate of PAR-2 is the essential mechanism underlying polarity reversal, providing a mathematical basis for the orientation of cell polarity patterns. |
BibTeX:
@article{Lee2016,
author = {Sungrim Seirin Lee},
title = {Positioning of polarity formation by extracellular signaling during asymmetric cell division },
journal = {Journal of Theoretical Biology },
year = {2016},
volume = {400},
pages = {52 - 64},
url = {http://www.sciencedirect.com/science/article/pii/S0022519316300236},
doi = {10.1016/j.jtbi.2016.04.004}
}
|
| Lee SS (2016), "Lateral inhibition-induced pattern formation controlled by the size and geometry of the cell ", Journal of Theoretical Biology . Vol. 404, pp. 51 - 65. |
| Abstract: Abstract Pattern formation in development biology is one of the fundamental processes by which cells change their functions. It is based on the communication of cells via intra- and intercellular dynamics of biochemicals. Thus, the cell is directly involved in biochemical interactions. However, many theoretical approaches describing biochemical pattern formation have usually neglected the cell's role or have simplified the subcellular process without considering cellular aspects despite the cell being the environment where biochemicals interact. On the other hand, recent experimental observations suggest that a change in the physical conditions of cell-to-cell contact can result in a change in cell fate and tissue patterning in a lateral inhibition system. Here we develop a mathematical model by which biochemical dynamics can be directly observed with explicitly expressed cell structure and geometry in higher dimensions, and reconsider pattern formation by lateral inhibition of the Notch–Delta signaling pathway. We explore how the physical characteristic of cell, such as cell geometry or size, influences the biochemical pattern formation in a multi-cellular system. Our results suggest that a property based on cell geometry can be a novel mechanism for symmetry breaking inducing cell asymmetry. We show that cell volume can critically influence cell fate determination and pattern formation at the tissue level, and the surface area of the cell-to-cell contact can directly affect the spatial range of patterning. |
BibTeX:
@article{Lee2016b,
author = {Sungrim Seirin Lee},
title = {Lateral inhibition-induced pattern formation controlled by the size and geometry of the cell },
journal = {Journal of Theoretical Biology },
year = {2016},
volume = {404},
pages = {51 - 65},
url = {http://www.sciencedirect.com/science/article/pii/S0022519316301175},
doi = {10.1016/j.jtbi.2016.05.025}
}
|
| Lee SS, Tashiro S, Awazu A and Kobayashi R (2016), "A new application of the phase-field method for understanding the mechanisms of nuclear architecture reorganization", Journal of Mathematical Biology. , pp. 1-22. |
| Abstract: Specific features of nuclear architecture are important for the functional organization of the nucleus, and chromatin consists of two forms, heterochromatin and euchromatin. Conventional nuclear architecture is observed when heterochromatin is enriched at nuclear periphery, and it represents the primary structure in the majority of eukaryotic cells, including the rod cells of diurnal mammals. In contrast to this, inverted nuclear architecture is observed when the heterochromatin is distributed at the center of the nucleus, which occurs in the rod cells of nocturnal mammals. The inverted architecture found in the rod cells of the adult mouse is formed through the reorganization of conventional architecture during terminal differentiation. Although a previous experimental approach has demonstrated the relationship between these two nuclear architecture types at the molecular level, the mechanisms underlying long-range reorganization processes remain unknown. The details of nuclear structures and their spatial and temporal dynamics remain to be elucidated. Therefore, a comprehensive approach, using mathematical modeling, is required, in order to address these questions. Here, we propose a new mathematical approach to the understanding of nuclear architecture dynamics using the phase-field method. We successfully recreated the process of nuclear architecture reorganization, and showed that it is robustly induced by physical features, independent of a specific genotype. Our study demonstrates the potential of phase-field method application in the life science fields. |
BibTeX:
@article{Lee2016a,
author = {Lee, S. Seirin |
| Akimoto T, Nakagawa M, Shinkai S and Aizawa Y (2015), "Generalized Lyapunov exponent as a unified characterization of dynamical instabilities", Phys. Rev. E., Jan, 2015. Vol. 91, pp. 012926. American Physical Society. |
| Abstract: The Lyapunov exponent characterizes an exponential growth rate of the difference of nearby orbits. A positive Lyapunov exponent (exponential dynamical instability) is a manifestation of chaos. Here, we propose the Lyapunov pair, which is based on the generalized Lyapunov exponent, as a unified characterization of nonexponential and exponential dynamical instabilities in one-dimensional maps. Chaos is classified into three different types, i.e., superexponential, exponential, and subexponential chaos. Using one-dimensional maps, we demonstrate superexponential and subexponential chaos and quantify the dynamical instabilities by the Lyapunov pair. In subexponential chaos, we show superweak chaos, which means that the growth of the difference of nearby orbits is slower than a stretched exponential growth. The scaling of the growth is analytically studied by a recently developed theory of a continuous accumulation process, which is related to infinite ergodic theory. |
BibTeX:
@article{Akimoto2015a,
author = {Akimoto, Takuma and Nakagawa, Masaki and Shinkai, Soya and Aizawa, Yoji},
title = {Generalized Lyapunov exponent as a unified characterization of dynamical instabilities},
journal = {Phys. Rev. E},
publisher = {American Physical Society},
year = {2015},
volume = {91},
pages = {012926},
url = {http://link.aps.org/doi/10.1103/PhysRevE.91.012926},
doi = {10.1103/PhysRevE.91.012926}
}
|
| Akimoto T, Shinkai S and Aizawa Y (2015), "Distributional Behavior of Time Averages of Non-L^1 Observables in One-dimensional Intermittent Maps with Infinite Invariant Measures", Journal of Statistical Physics. Vol. 158(2), pp. 476-493. Springer US. |
| Abstract: In infinite ergodic theory, two distributional limit theorems are well-known. One is characterized by the Mittag-Leffler distribution for time averages of $L^1(m)$ functions, i.e., integrable functions with respect to an infinite invariant measure. The other is characterized by the generalized arc-sine distribution for time averages of non-$L^1(m)$ functions. Here, we provide another distributional behavior of time averages of non-$L^1(m)$ functions in one-dimensional intermittent maps where each has an indifferent fixed point and an infinite invariant measure. Observation functions considered here are non-$L^1(m)$ functions which vanish at the indifferent fixed point. We call this class of observation functions weak non-$L^1(m)$ function. Our main result represents a first step toward a third distributional limit theorem, i.e., a distributional limit theorem for this class of observables, in infinite ergodic theory. To prove our proposition, we propose a stochastic process induced by a renewal process to mimic a Birkoff sum of a weak non-$L^1(m)$ function in the one-dimensional intermittent maps. |
BibTeX:
@article{Akimoto2015,
author = {Akimoto, Takuma and Shinkai, Soya and Aizawa, Yoji},
title = {Distributional Behavior of Time Averages of Non-L^1 Observables in One-dimensional Intermittent Maps with Infinite Invariant Measures},
journal = {Journal of Statistical Physics},
publisher = {Springer US},
year = {2015},
volume = {158},
number = {2},
pages = {476-493},
url = {http://dx.doi.org/10.1007/s10955-014-1138-0},
doi = {10.1007/s10955-014-1138-0}
}
|
| Awazu A (2015), "Nuclear dynamical deformation induced hetero- and euchromatin positioning", Phys. Rev. E., Sep, 2015. Vol. 92, pp. 032709. American Physical Society. |
BibTeX:
@article{PhysRevE.92.032709,
author = {Awazu, Akinori},
title = {Nuclear dynamical deformation induced hetero- and euchromatin positioning},
journal = {Phys. Rev. E},
publisher = {American Physical Society},
year = {2015},
volume = {92},
pages = {032709},
url = {http://link.aps.org/doi/10.1103/PhysRevE.92.032709},
doi = {10.1103/PhysRevE.92.032709}
}
|
| Erban R. FAHMKTJTKTY (2015), "DNA Structural Dynamics (Team 5)(in Gilbert, D., et al. eds., Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481))", Dagstuhl Reports. Dagstuhl, Germany Vol. 4(11), pp. 191-194. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik. |
BibTeX:
@article{Erban2015,
author = {Erban, R., Funahashi, A., Herajy, M., Kobayashi, T. J., Takahashi, K., Togashi, Y.},
editor = {David Gilbert and Monika Heiner and Koichi Takahashi and Adelinde M. Uhrmacher},
title = {DNA Structural Dynamics (Team 5)(in Gilbert, D., et al. eds., Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481))},
journal = {Dagstuhl Reports},
publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
year = {2015},
volume = {4},
number = {11},
pages = {191-194},
url = {http://drops.dagstuhl.de/opus/volltexte/2015/4972},
doi = {10.4230/DagRep.4.11.138}
}
|
| Hirao K, Nagano AJ and Awazu A (2015), "Noise–plasticity correlations of gene expression in the multicellular organism Arabidopsis thaliana ", Journal of Theoretical Biology . Vol. 387, pp. 13 - 22. |
| Abstract: Abstract Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions (called gene expression “noise” or phenotype “fluctuation”). In yeast and Escherichia coli, positive correlations have been found between such gene expression noise and “plasticity” with environmental variations. To determine the universality of such correlations in both unicellular and multicellular organisms, we focused on the relationships between gene expression “noise” and “plasticity” in Arabidopsis thaliana, a multicellular model organism. In recent studies on yeast and E. coli, only some gene groups with specific properties of promoter architecture, average expression levels, and functions exhibited strong noise–plasticity correlations. However, we found strong noise–plasticity correlations for most gene groups in Arabidopsis; additionally, promoter architecture, functional essentiality of genes, and circadian rhythm appeared to have only a weak influence on the correlation strength. The differences in the characteristics of noise–plasticity correlations may result from three-dimensional chromosomal structures and/or circadian rhythm. |
BibTeX:
@article{Hirao201513,
author = {Koudai Hirao and Atsushi J. Nagano and Akinori Awazu},
title = {Noise–plasticity correlations of gene expression in the multicellular organism Arabidopsis thaliana },
journal = {Journal of Theoretical Biology },
year = {2015},
volume = {387},
pages = {13 - 22},
url = {http://www.sciencedirect.com/science/article/pii/S0022519315004609},
doi = {10.1016/j.jtbi.2015.09.017}
}
|
| Isami S, Sakamoto N, Nishimori H and Awazu A (2015), "Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence", PLoS ONE., 12, 2015. Vol. 10(12), pp. 1-22. Public Library of Science. |
| Abstract: Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ?150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences. |
BibTeX:
@article{10.1371/journal.pone.0143760,
author = {Isami, Shuhei AND Sakamoto, Naoaki AND Nishimori, Hiraku AND Awazu, Akinori},
title = {Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence},
journal = {PLoS ONE},
publisher = {Public Library of Science},
year = {2015},
volume = {10},
number = {12},
pages = {1-22},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0143760},
doi = {10.1371/journal.pone.0143760}
}
|
| Lee SS and Shibata T (2015), "Self-organization and advective transport in the cell polarity formation for asymmetric cell division ", Journal of Theoretical Biology . Vol. 382, pp. 1 - 14. |
| Abstract: Abstract Anterior–Posterior (AP) polarity formation of cell membrane proteins plays a crucial role in determining cell asymmetry, which depends not only on the several genetic process but also biochemical and biophysical interactions. The mechanism of AP formation of Caenorhabditis elegans embryo is characterized into the three processes: (i) membrane association and dissociation of posterior and anterior proteins, (ii) diffusion into the membrane and cytosol, and (iii) active cortical and cytoplasmic flows induced by the contraction of the acto-myosin cortex. We explored the mechanism of symmetry breaking and AP polarity formation using self-recruitment model of posterior proteins. We found that the AP polarity pattern is established over wide range in the total mass of polarity proteins and the diffusion ratio in the cytosol to the membrane. We also showed that the advective transport in both membrane and cytosol during the establishment phase affects optimal time interval of establishment and positioning of the posterior domain, and plays a role to increase the robustness in the AP polarity formation by reducing the number of posterior domains for the sensitivity of initial conditions. We also demonstrated that a proper ratio of the total mass to cell size robustly regulate the length scale of the posterior domain. |
BibTeX:
@article{Lee2015,
author = {Sungrim Seirin Lee and Tatsuo Shibata},
title = {Self-organization and advective transport in the cell polarity formation for asymmetric cell division },
journal = {Journal of Theoretical Biology },
year = {2015},
volume = {382},
pages = {1 - 14},
url = {http://www.sciencedirect.com/science/article/pii/S0022519315003112},
doi = {10.1016/j.jtbi.2015.06.032}
}
|
| Miyamoto T, Hosoba K, Ochiai H, Royba E, Izumi H, Sakuma T, Yamamoto T, Dynlacht B and Matsuura S (2015), "The Microtubule-Depolymerizing Activity of a Mitotic Kinesin Protein KIF2A Drives Primary Cilia Disassembly Coupled with Cell Proliferation ", Cell Reports . Vol. 10(5), pp. 664 - 673. |
| Abstract: Summary The primary cilium is an antenna-like, microtubule-based organelle on the surface of most vertebrate cells for receiving extracellular information. Although primary cilia form in the quiescent phase, ciliary disassembly occurs when quiescent cells re-enter the proliferative phase. It was shown that a mitotic kinase, Polo-like kinase 1 (PLK1), is required for cell-proliferation-coupled primary cilia disassembly. Here, we report that kinesin superfamily protein 2A (KIF2A), phosphorylated at T554 by PLK1, exhibits microtubule-depolymerizing activity at the mother centriole to disassemble the primary cilium in a growth-signal-dependent manner. KIF2A-deficient hTERT-RPE1 cells showed the impairment of primary cilia disassembly following growth stimulation. It was also found that the PLK1-KIF2A pathway is constitutively active in cells from patients with premature chromatid separation (PCS) syndrome and is responsible for defective ciliogenesis in this syndrome. These findings provide insights into the roles of the PLK1-KIF2A pathway in physiological cilia disassembly and cilia-associated disorders. |
BibTeX:
@article{Miyamoto2015,
author = {Tatsuo Miyamoto and Kosuke Hosoba and Hiroshi Ochiai and Ekaterina Royba and Hideki Izumi and Tetsushi Sakuma and Takashi Yamamoto and Brian David Dynlacht and Shinya Matsuura},
title = {The Microtubule-Depolymerizing Activity of a Mitotic Kinesin Protein KIF2A Drives Primary Cilia Disassembly Coupled with Cell Proliferation },
journal = {Cell Reports },
year = {2015},
volume = {10},
number = {5},
pages = {664 - 673},
url = {http://www.sciencedirect.com/science/article/pii/S2211124715000042},
doi = {10.1016/j.celrep.2015.01.003}
}
|
| Nanbu T, Nguy?n LC, Habib AGK, Hirata N, Ukimori S, Tanaka D, Masuda K, Takahashi K, Yukawa M, Tsuchiya E and Ueno M (2015), "Fission Yeast Exo1 and Rqh1-Dna2 Redundantly Contribute to Resection of Uncapped Telomeres", PLoS ONE., 10, 2015. Vol. 10(10), pp. 1-16. Public Library of Science. |
| Abstract: The uncapping of telomeres induces a DNA damage response. In |
BibTeX:
@article{10.1371/journal.pone.0140456,
author = {Nanbu, Tomoko AND Nguy?n, Lu穗 C. AND Habib, Ahmed G. K. AND Hirata, Naoya AND Ukimori, Shinobu AND Tanaka, Daiki AND Masuda, Kenta AND Takahashi, Katsunori AND Yukawa, Masashi AND Tsuchiya, Eiko AND Ueno, Masaru},
title = {Fission Yeast Exo1 and Rqh1-Dna2 Redundantly Contribute to Resection of Uncapped Telomeres},
journal = {PLoS ONE},
publisher = {Public Library of Science},
year = {2015},
volume = {10},
number = {10},
pages = {1-16},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0140456},
doi = {10.1371/journal.pone.0140456}
}
|
| Ochiai H, Sugawara T and Yamamoto T (2015), "Simultaneous live imaging of the transcription and nuclear position of specific genes", Nucleic Acids Research. |
| Abstract: The relationship between genome organization and gene expression has recently been established. However, the relationships between spatial organization, dynamics, and transcriptional regulation of the genome remain unknown. In this study, we developed a live-imaging method for simultaneous measurements of the transcriptional activity and nuclear position of endogenous genes, which we termed the ‘Real-time Observation of Localization and EXpression (ROLEX)’ system. We demonstrated that ROLEX is highly specific and does not affect the expression level of the target gene. ROLEX enabled detection of sub-genome-wide mobility changes that depended on the state of Nanog transactivation in embryonic stem cells. We believe that the ROLEX system will become a powerful tool for exploring the relationship between transcription and nuclear dynamics in living cells. |
BibTeX:
@article{Ochiai2015a,
author = {Ochiai, Hiroshi and Sugawara, Takeshi and Yamamoto, Takashi},
title = {Simultaneous live imaging of the transcription and nuclear position of specific genes},
journal = {Nucleic Acids Research},
year = {2015},
url = {http://nar.oxfordjournals.org/content/early/2015/06/19/nar.gkv624.abstract},
doi = {10.1093/nar/gkv624}
}
|
| Ochiai H and Yamamoto T (2015), "Genome Editing Using Zinc-Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs)", In Targeted Genome Editing Using Site-Specific Nucleases. , pp. 3-24. Springer Japan. |
BibTeX:
@incollection{Ochiai2015b,
author = {Ochiai, Hiroshi and Yamamoto, Takashi},
editor = {Yamamoto, Takashi},
title = {Genome Editing Using Zinc-Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs)},
booktitle = {Targeted Genome Editing Using Site-Specific Nucleases},
publisher = {Springer Japan},
year = {2015},
pages = {3-24},
url = {http://dx.doi.org/10.1007/978-4-431-55227-7_1},
doi = {10.1007/978-4-431-55227-7_1}
}
|
| Shinkai S (2015), "Dissipative Heat Decomposition in Stochastic Energetics: Implication of the Instantaneous Diffusion Coefficient in Nonequilibrium Steady States", Journal of the Physical Society of Japan. Vol. 84(1), pp. 015001. |
| Abstract: We give a decomposition expression for dissipative heat using the instantaneous diffusion coefficient in a nonequilibrium steady state. The dissipative heat can be expressed using three diffusion coefficients: instantaneous, equilibrium, and drift. An experimental application of the decomposition expression permits us to evaluate the heat dissipation rate from single-trajectory data only. We also numerically demonstrate this method. |
BibTeX:
@article{Shinkai2015,
author = {Shinkai, Soya},
title = {Dissipative Heat Decomposition in Stochastic Energetics: Implication of the Instantaneous Diffusion Coefficient in Nonequilibrium Steady States},
journal = {Journal of the Physical Society of Japan},
year = {2015},
volume = {84},
number = {1},
pages = {015001},
url = {http://dx.doi.org/10.7566/JPSJ.84.015001},
doi = {10.7566/JPSJ.84.015001}
}
|
| Shinkai S (2015), "Analytical theory of individual diffusion trajectories in living cells", Advances in Science, Technology and Environmentology. Vol. B11, pp. 167-169.
[BibTeX] |
BibTeX:
@article{Shinkai2015a,
author = {Soya Shinkai},
title = {Analytical theory of individual diffusion trajectories in living cells},
journal = {Advances in Science, Technology and Environmentology},
year = {2015},
volume = {B11},
pages = {167-169}
}
|
| Takami T, Ojiro Y, Ogawa S, Takakuwa Y, Ogawa Y, Saito M, Matsuoka H and ichi Tate S (2015), "Coating the Outer Surface of Glass Nanopipette with Chlorobenzene-Terminated Polysiloxane", e-Journal of Surface Science and Nanotechnology. Vol. 13( ), pp. 79-84. |
BibTeX:
@article{Takami2015,
author = {Tomohide Takami and Yoshihiro Ojiro and Shuichi Ogawa and Yuji Takakuwa and Yoshihide Ogawa and Mikako Saito and Hideaki Matsuoka and Shin-ichi Tate},
title = {Coating the Outer Surface of Glass Nanopipette with Chlorobenzene-Terminated Polysiloxane},
journal = {e-Journal of Surface Science and Nanotechnology},
year = {2015},
volume = {13},
number = { },
pages = {79-84},
doi = {10.1380/ejssnt.2015.79}
}
|
| Tamiya Y and Aizawa SSY (2015), "Log-Weibull law in Fermi-Pasta-Ulam oscillator chain: Induction time as Nekhoroshev stable time", Advances in Science, Technology and Environmentology. Vol. B11, pp. 181-183.
[BibTeX] |
BibTeX:
@article{Tamiya2015,
author = {Yuji Tamiya and Soya Shinkai Yoji Aizawa},
title = {Log-Weibull law in Fermi-Pasta-Ulam oscillator chain: Induction time as Nekhoroshev stable time},
journal = {Advances in Science, Technology and Environmentology},
year = {2015},
volume = {B11},
pages = {181-183}
}
|
| Togashi Y (2015), "Spying “Minorities” in the Cell(in Gilbert, D., et al. eds., Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481))", Dagstuhl Reports. Dagstuhl, Germany Vol. 4(11), pp. 165-166. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik. |
BibTeX:
@article{Togashi2015a,
author = {Togashi, Y},
editor = {David Gilbert and Monika Heiner and Koichi Takahashi and Adelinde M. Uhrmacher},
title = {Spying “Minorities” in the Cell(in Gilbert, D., et al. eds., Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481))},
journal = {Dagstuhl Reports},
publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
year = {2015},
volume = {4},
number = {11},
pages = {165-166},
url = {http://drops.dagstuhl.de/opus/volltexte/2015/4972},
doi = {10.4230/DagRep.4.11.138}
}
|
| Togashi Y and Casagrande V (2015), "Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes", New Journal of Physics. Vol. 17(3), pp. 033024. |
| Abstract: Enzymatic reactions often involve slow conformational changes, with reaction cycles that sometimes require milliseconds or seconds to complete. The dynamics are strongly affected by fluctuations at the nanoscale. However, such enzymes often occur in small numbers in a cell; hence, the fluctuations caused by finite numbers of molecules should also be substantial. Because of these factors, the behavior of the system is likely to deviate from that of classical reaction–diffusion equations, in which immediate reaction events are assumed to occur without memory and between a huge number of molecules. In this work, we model each enzyme as a unit represented by a phase variable to investigate the effects of fluctuations in arrays of enzymes. Using an analysis based on partial differential equations and stochastic simulations, we show that fluctuations arising from internal states of enzymes (intramolecular fluctuations) and those arising from the stochastic nature of interactions between molecules (intermolecular fluctuations) have distinctive effects on spatiotemporal patterns; the former generally disturb synchronization at high frequencies, whereas the latter can enhance synchronization. The balance of the two types of fluctuations may determine the spatiotemporal behavior of biochemical processes. |
BibTeX:
@article{Togashi2015,
author = {Yuichi Togashi and Vanessa Casagrande},
title = {Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes},
journal = {New Journal of Physics},
year = {2015},
volume = {17},
number = {3},
pages = {033024},
url = {http://stacks.iop.org/1367-2630/17/i=3/a=033024}
}
|
| 落合 博 and 松浦 伸也 (2015), "新規一塩基置換導入法による高発癌性遺伝病の原因変異の同定 (AYUMI ゲノム編集 : 基礎から応用へ)", 医学のあゆみ., jan, 2015. Vol. 252(2), pp. 153-158. 医歯薬出版. |
BibTeX:
@article{Ochiai2015,
author = {落合 博 and 松浦 伸也},
title = {新規一塩基置換導入法による高発癌性遺伝病の原因変異の同定 (AYUMI ゲノム編集 : 基礎から応用へ)},
journal = {医学のあゆみ},
publisher = {医歯薬出版},
year = {2015},
volume = {252},
number = {2},
pages = {153-158},
url = {http://ci.nii.ac.jp/naid/40020320271/}
}
|
| Flechsig H (2014), "TALEs from a Spring – Superelasticity of Tal Effector Protein Structures", PLoS ONE., 10, 2014. Vol. 9(10), pp. e109919. Public Library of Science. |
| Abstract: Transcription activator-like effectors (TALEs) are DNA-related proteins that recognise and bind specific target sequences to manipulate gene expression. Recently determined crystal structures show that their common architecture reveals a superhelical overall structure that may undergo drastic conformational changes. To establish a link between structure and dynamics in TALE proteins we have employed coarse-grained elastic-network modelling of currently available structural data and implemented a force-probe setup that allowed us to investigate their mechanical behaviour in computer experiments. Based on the measured force-extension curves we conclude that TALEs exhibit superelastic dynamical properties allowing for large-scale global conformational changes along their helical axis, which represents the |
BibTeX:
@article{Flechsig2014,
author = {Flechsig, , Holger},
title = {TALEs from a Spring – Superelasticity of Tal Effector Protein Structures},
journal = {PLoS ONE},
publisher = {Public Library of Science},
year = {2014},
volume = {9},
number = {10},
pages = {e109919},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0109919},
doi = {10.1371/journal.pone.0109919}
}
|
| Hayashi T, Sakamoto K, Sakuma T, Yokotani N, Inoue T, Kawaguchi E, Agata K, Yamamoto T and Takeuchi T (2014), "Transcription activator-like effector nucleases efficiently disrupt the target gene in Iberian ribbed newts (Pleurodeles waltl), an experimental model animal for regeneration", Development, Growth & Differentiation. Vol. 56(1), pp. 115-121. |
| Abstract: Regeneration of a lost tissue in an animal is an important issue. Although regenerative studies have a history of research spanning more than a century, the gene functions underlying regulation of the regeneration are mostly unclear. Analysis of knockout animals is a very powerful tool with which to elucidate gene function. Recently, transcription activator-like effector nucleases (TALENs) have been developed as an effective technique for genome editing. This technique enables gene targeting in amphibians such as newts that were previously impossible. Here we show that newts microinjected with TALEN mRNAs designed for targeting the tyrosinase gene in single-cell stage embryos revealed an albino phenotype. Sequence analysis revealed that the tyrosinase genes were effectively disrupted in these albino newts. Moreover, precise genome alteration was achieved using TALENs and single strand oligodeoxyribonucleotides. Our results suggest that TALENs are powerful tools for genome editing for regenerative research in newts. |
BibTeX:
@article{Hayashi2014,
author = {Hayashi, Toshinori and Sakamoto, Kousuke and Sakuma, Tetsushi and Yokotani, Naoki and Inoue, Takeshi and Kawaguchi, Eri and Agata, Kiyokazu and Yamamoto, Takashi and Takeuchi, Takashi},
title = {Transcription activator-like effector nucleases efficiently disrupt the target gene in Iberian ribbed newts (Pleurodeles waltl), an experimental model animal for regeneration},
journal = {Development, Growth & Differentiation},
year = {2014},
volume = {56},
number = {1},
pages = {115--121},
url = {http://dx.doi.org/10.1111/dgd.12103},
doi = {10.1111/dgd.12103}
}
|
| Hiraishi N, Tochio N, Kigawa T, Otsuki M and Tagami J (2014), "Role of 2-hydroxyethyl methacrylate in the interaction of dental monomers with collagen studied by saturation transfer difference NMR ", Journal of Dentistry . Vol. 42(4), pp. 484 - 489. |
| Abstract: AbstractObjections Functional adhesive monomers are formulated with solvents and hydrophilic resin monomers, such as 2-hydroxyethyl methacrylate (HEMA). In theory, exposed collagen fibrils should be covered and protected by the resin matrix. We examined if the atomic- and molecular-level interaction of monomers with collagen would be affected when the monomers are blended with HEMA. Methods We performed saturation transfer difference (STD) NMR spectroscopy to investigate the binding interaction of two functional monomers, 4-methacryloyloxyethyl trimellitic acid (4-MET) and 10-methacryloyloxydecyl dihydrogen phosphate (MDP), with atelocollagen as a triple-helical peptide model. The STD NMR measurement was performed by adding 4-MET or MDP to the atelocollagen solution. Results When the atelocollagen was saturated, the STD signals were detected in the MDP spectrum for the protons in the aliphatic chain when MDP was dissolved in DMSO. However, the STD signals disappeared when MDP was mixed with HEMA. No STD signal was visible for the 4-MET ligand samples in either DMSO or for the HEMA blend sample. Discussion The interaction of MDP with atelocollagen is hydrophobic; however, the MDP-HEMA blend may form an aggregate in the atelocollagen solution, which would suppress the hydrophobicity of MDP. The formation of the MDP-HEMA aggregate may compromise the MDP–collagen interaction, and leave the collagen fibrils unprotected by MDP and HEMA. Unstable chemical interaction of the monomers with the exposed collagen may deteriorate hybrid layer integrity and strong dentine bonding. |
BibTeX:
@article{Hiraishi2014,
author = {Noriko Hiraishi and Naoya Tochio and Takanori Kigawa and Masayuki Otsuki and Junji Tagami},
title = {Role of 2-hydroxyethyl methacrylate in the interaction of dental monomers with collagen studied by saturation transfer difference NMR },
journal = {Journal of Dentistry },
year = {2014},
volume = {42},
number = {4},
pages = {484 - 489},
url = {http://www.sciencedirect.com/science/article/pii/S0300571214000153},
doi = {10.1016/j.jdent.2013.12.016}
}
|
| Hosoi S, Sakuma T, Sakamoto N and Yamamoto T (2014), "Targeted mutagenesis in sea urchin embryos using TALENs", Development, Growth & Differentiation. Vol. 56(1), pp. 92-97. |
| Abstract: Genome editing with engineered nucleases such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) has been reported in various animals. We previously described ZFN-mediated targeted mutagenesis and insertion of reporter genes in sea urchin embryos. In this study, we demonstrate that TALENs can induce mutagenesis at specific genomic loci of sea urchin embryos. Injection of TALEN mRNAs targeting the HpEts transcription factor into fertilized eggs resulted in the impairment of skeletogenesis. Sequence analyses of the mutations showed that deletions and/or insertions occurred at the HpEts target site in the TALEN mRNAs-injected embryos. The results suggest that targeted gene disruption using TALENs is feasible in sea urchin embryos. |
BibTeX:
@article{Hosoi2014,
author = {Hosoi, Sayaka and Sakuma, Tetsushi and Sakamoto, Naoaki and Yamamoto, Takashi},
title = {Targeted mutagenesis in sea urchin embryos using TALENs},
journal = {Development, Growth & Differentiation},
year = {2014},
volume = {56},
number = {1},
pages = {92--97},
url = {http://dx.doi.org/10.1111/dgd.12099},
doi = {10.1111/dgd.12099}
}
|
| Kondo T, Sakuma T, Wada H, Akimoto-Kato A, Yamamoto T and Hayashi S (2014), "TALEN-induced gene knock out in Drosophila", Development, Growth & Differentiation. Vol. 56(1), pp. 86-91. |
| Abstract: We report here a case study of TALEN-induced gene knock out of the trachealess gene of Drosophila. Two pairs of TALEN constructs caused targeted mutation in the germ line of 39% and 17% of injected animals, respectively. In the extreme case 100% of the progeny of TALEN-injected fly was mutated, suggesting that highly efficient biallelic germ line mutagenesis was achieved. The mutagenic efficiency of the TALEN pairs paralleled their activity of single strand annealing (SSA) assay in cultured cells. All mutations were deletion of 1 to 20 base pairs. Merit and demerit of TALEN-based gene knockout approach compared to other genome editing technologies is discussed. |
BibTeX:
@article{Kondo2014,
author = {Kondo, Takefumi and Sakuma, Tetsushi and Wada, Housei and Akimoto-Kato, Ai and Yamamoto, Takashi and Hayashi, Shigeo},
title = {TALEN-induced gene knock out in Drosophila},
journal = {Development, Growth & Differentiation},
year = {2014},
volume = {56},
number = {1},
pages = {86--91},
url = {http://dx.doi.org/10.1111/dgd.12097},
doi = {10.1111/dgd.12097}
}
|
| Nakagawa Y, Yamamoto T, Suzuki K-I, Araki K, Takeda N, Ohmuraya M and Sakuma T (2014), "Screening Methods to Identify TALEN-Mediated Knockout Mice", Experimental Animals. Vol. 63(1), pp. 79-84. |
BibTeX:
@article{Nakagawa2014,
author = {Yoshiko Nakagawa and Takashi Yamamoto and Ken-Ichi Suzuki and Kimi Araki and Naoki Takeda and Masaki Ohmuraya and Tetsushi Sakuma},
title = {Screening Methods to Identify TALEN-Mediated Knockout Mice},
journal = {Experimental Animals},
year = {2014},
volume = {63},
number = {1},
pages = {79-84},
doi = {10.1538/expanim.63.79}
}
|
| Nakano A, Masuda K, Hiromoto T, Takahashi K, Matsumoto Y, Habib AGK, Darwish AGG, Yukawa M, Tsuchiya E and Ueno M (2014), "Rad51-Dependent Aberrant Chromosome Structures at Telomeres and Ribosomal DNA Activate the Spindle Assembly Checkpoint", Molecular and Cellular Biology. Vol. 34(8), pp. 1389-1397. |
| Abstract: The spindle assembly checkpoint (SAC) monitors defects in kinetochore-microtubule attachment or lack of tension at kinetochores and arrests cells at prometaphase. In fission yeast, the double mutant between pot1Δ and the helicase-dead point mutant of the RecQ helicase Rqh1 gene (rqh1-hd) accumulates Rad51-dependent recombination intermediates at telomeres and enters mitosis with those intermediates. Here, we found that SAC-dependent prometaphase arrest occurred more frequently in pot1Δ rqh1-hd double mutants than in rqh1-hd single mutants. SAC-dependent prometaphase arrest also occurred more frequently in rqh1-hd single mutants after cells were released from DNA replication block compared to the rqh1-hd single mutant in the absence of exogenous insult to the DNA. In both cases, Mad2 foci persisted longer than usual at kinetochores, suggesting a defect in kinetochore-microtubule attachment. In pot1Δ rqh1-hd double mutants and rqh1-hd single mutants released from DNA replication block, SAC-dependent prometaphase arrest was suppressed by the removal of the recombination or replication intermediates. Our results indicate that the accumulation of recombination or replication intermediates induces SAC-dependent prometaphase arrest, possibly by affecting kinetochore-microtubule attachment. |
BibTeX:
@article{Nakano2014,
author = {Nakano, Akemi and Masuda, Kenta and Hiromoto, Taisuke and Takahashi, Katsunori and Matsumoto, Yoshitake and Habib, Ahmed G. K. and Darwish, Ahmed G. G. and Yukawa, Masashi and Tsuchiya, Eiko and Ueno, Masaru},
title = {Rad51-Dependent Aberrant Chromosome Structures at Telomeres and Ribosomal DNA Activate the Spindle Assembly Checkpoint},
journal = {Molecular and Cellular Biology},
year = {2014},
volume = {34},
number = {8},
pages = {1389-1397},
url = {http://mcb.asm.org/content/34/8/1389.abstract},
doi = {10.1128/MCB.01704-13}
}
|
| Ochiai H, Miyamoto T, Kanai A, Hosoba K, Sakuma T, Kudo Y, Asami K, Ogawa A, Watanabe A, Kajii T, Yamamoto T and Matsuura S (2014), "TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS (MVA) syndrome", Proceedings of the National Academy of Sciences. Vol. 111(4), pp. 1461-1466. |
| Abstract: Cancer-prone syndrome of premature chromatid separation with mosaic variegated aneuploidy [PCS (MVA) syndrome] is a rare autosomal recessive disorder characterized by constitutional aneuploidy and a high risk of childhood cancer. We previously reported monoallelic mutations in the BUB1B gene (encoding BUBR1) in seven Japanese families with the syndrome. No second mutation was found in the opposite allele of any of the families studied, although a conserved BUB1B haplotype and a decreased transcript were identified. To clarify the molecular pathology of the second allele, we extended our mutational search to a candidate region surrounding BUB1B. A unique single nucleotide substitution, G > A at ss802470619, was identified in an intergenic region 44 kb upstream of a BUB1B transcription start site, which cosegregated with the disorder. To examine whether this is the causal mutation, we designed a transcription activator-like effector nuclease–mediated two-step single-base pair editing strategy and biallelically introduced this substitution into cultured human cells. The cell clones showed reduced BUB1B transcripts, increased PCS frequency, and MVA, which are the hallmarks of the syndrome. We also encountered a case of a Japanese infant with PCS (MVA) syndrome carrying a homozygous single nucleotide substitution at ss802470619. These results suggested that the nucleotide substitution identified was the causal mutation of PCS (MVA) syndrome. |
BibTeX:
@article{Ochiai2014a,
author = {Ochiai, Hiroshi and Miyamoto, Tatsuo and Kanai, Akinori and Hosoba, Kosuke and Sakuma, Tetsushi and Kudo, Yoshiki and Asami, Keiko and Ogawa, Atsushi and Watanabe, Akihiro and Kajii, Tadashi and Yamamoto, Takashi and Matsuura, Shinya},
title = {TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS (MVA) syndrome},
journal = {Proceedings of the National Academy of Sciences},
year = {2014},
volume = {111},
number = {4},
pages = {1461-1466},
url = {http://www.pnas.org/content/111/4/1461.abstract},
doi = {10.1073/pnas.1317008111}
}
|
| Ochiai H, Sugawara T, Sakuma T and Yamamoto T (2014), "Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells", Scientific Reports. Vol. 4(7125) |
| Abstract: Mouse embryonic stem cells (mESCs) are self-renewing and capable of differentiating into any of the three germ layers. An interesting feature of mESCs is the presence of cell-to-cell heterogeneity in gene expression that may be responsible for cell fate decisions. Nanog, a key transcription factor for pluripotency, displays heterogeneous expression in mESCs, via mechanisms that are not fully understood. To understand this variability, we quantitatively analyzed it Nanog transcription and found that it Nanog was both infrequently transcribed, and transcribed in a pulsatile and stochastic manner. It is possible that such stochastic transcriptional activation could contribute to the heterogeneity observed in it Nanog expression as “intrinsic noise.” To discriminate the effects of both intrinsic noise from other (extrinsic) noise on the expression variability of it Nanog mRNA, we performed allele-specific single-molecule RNA fluorescent in situ hybridization in a reporter cell line and found that intrinsic noise contributed to approximately 45% of the total variability in it Nanog expression. Furthermore, we found that it Nanog mRNA and protein levels were well correlated in individual cells. These results suggest that stochastic promoter activation significantly affects the Nanog expression variability in mESCs. |
BibTeX:
@article{Ochiai2014b,
author = {Hiroshi Ochiai and Takeshi Sugawara and Tetsushi Sakuma and Takashi Yamamoto},
title = {Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells},
journal = {Scientific Reports},
year = {2014},
volume = {4},
number = {7125},
url = {http://www.nature.com/srep/2014/141120/srep07125/full/srep07125.html},
doi = {10.1038/srep07125}
}
|
| Ohori Y, Okazaki H, Watanabe S, Tochio N, Arai M, Kigawa T and Nishimura C (2014), "Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange with NMR ", Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics . Vol. 1844(3), pp. 520 - 526. |
| Abstract: Abstract The HIV-1 p17 matrix protein is a multifunctional protein that interacts with other molecules including proteins and membranes. The dynamic structure between its folded and partially unfolded states can be critical for the recognition of interacting molecules. One of the most important roles of the p17 matrix protein is its localization to the plasma membrane with the Gag polyprotein. The myristyl group attached to the N-terminus on the p17 matrix protein functions as an anchor for binding to the plasma membrane. Biochemical studies revealed that two regions are important for its function: D14–L31 and V84–V88. Here, the dynamic structures of the p17 matrix protein were studied using NMR for relaxation and amide proton exchange experiments at the physiological pH of 7.0. The results revealed that the α12-loop, which includes the 14–31 region, was relatively flexible, and that helix 4, including the 84–88 region, was the most protected helix in this protein. However, the residues in the α34-loop near helix 4 had a low order parameter and high exchange rate of amide protons, indicating high flexibility. This region is probably flexible because this loop functions as a hinge for optimizing the interactions between helices 3 and 4. The C-terminal long region of K113-Y132 adopted a disordered structure. Furthermore, the C-terminal helix 5 appeared to be slightly destabilized due to the flexible C-terminal tail based on the order parameters. Thus, the dynamic structure of the p17 matrix protein may be related to its multiple functions. |
BibTeX:
@article{Ohori2014,
author = {Yuka Ohori and Honoka Okazaki and Satoru Watanabe and Naoya Tochio and Munehito Arai and Takanori Kigawa and Chiaki Nishimura},
title = {Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange with NMR },
journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics },
year = {2014},
volume = {1844},
number = {3},
pages = {520 - 526},
url = {http://www.sciencedirect.com/science/article/pii/S1570963913004330},
doi = {10.1016/j.bbapap.2013.12.010}
}
|
| Sakane Y, Sakuma T, Kashiwagi K, Kashiwagi A, Yamamoto T and Suzuki K-IT (2014), "Targeted mutagenesis of multiple and paralogous genes in Xenopus laevis using two pairs of transcription activator-like effector nucleases", Development, Growth & Differentiation. Vol. 56(1), pp. 108-114. |
| Abstract: Transcription activator-like effector nucleases (TALENs) have been extensively used in genome editing in various organisms. In some cases, however, it is difficult to efficiently disrupt both paralogous genes using a single pair of TALENs in Xenopus laevis because of its polyploidy. Here, we report targeted mutagenesis of multiple and paralogous genes using two pairs of TALENs in X. laevis. First, we show simultaneous targeted mutagenesis of three genes, tyrosinase paralogues (tyra and tyrb) and enhanced green fluorescent protein (egfp) by injection of two TALENs pairs in transgenic embryos carrying egfp. Consistent with the high frequency of both severe phenotypic traits, albinism and loss of GFP fluorescence, frameshift mutation rates of tyr paralogues and egfp reached 40–80%. Next, we show early introduction of TALEN-mediated mutagenesis of these target loci during embryogenesis. Finally, we also demonstrate that two different pairs of TALENs can simultaneously introduce mutations to both paralogues encoding histone chaperone with high efficiency. Our results suggest that targeted mutagenesis of multiple genes using TALENs can be applied to analyze the functions of paralogous genes with redundancy in X. laevis. |
BibTeX:
@article{Sakane2014,
author = {Sakane, Yuto and Sakuma, Tetsushi and Kashiwagi, Keiko and Kashiwagi, Akihiko and Yamamoto, Takashi and Suzuki, Ken-Ichi T.},
title = {Targeted mutagenesis of multiple and paralogous genes in Xenopus laevis using two pairs of transcription activator-like effector nucleases},
journal = {Development, Growth & Differentiation},
year = {2014},
volume = {56},
number = {1},
pages = {108--114},
url = {http://dx.doi.org/10.1111/dgd.12105},
doi = {10.1111/dgd.12105}
}
|
| Shinkai S and Togashi Y (2014), "Energetics of single active diffusion trajectories", EPL (Europhysics Letters). Vol. 105(3), pp. 30002. |
| Abstract: The fundamental insight into Brownian motion by Einstein is that all substances exhibit continual fluctuations due to thermal agitation balancing with the frictional resistance. However, even at thermal equilibrium, biological activity can give rise to non-equilibrium fluctuations that cause “active diffusion” in living cells. Because of the non-stationary and non-equilibrium nature of such fluctuations, mean square displacement analysis, relevant only to a steady-state ensemble, may not be the most suitable choice as it depends on the choice of the ensemble; hence, a new analytical method for describing active diffusion is desired. Here we discuss the stochastic energetics of a thermally fluctuating single active diffusion trajectory driven by non-thermal random forces. Heat dissipation, usually difficult to measure, can be estimated from the active diffusion trajectory; guidelines on the analysis such as criteria for the time resolution and driving force intensity are shown by a statistical test. This leads to the concept of an “instantaneous diffusion coefficient” connected to heat dissipation that may be used to analyse the activity and molecular transport mechanisms of living systems. |
BibTeX:
@article{Shinkai2014,
author = {S. Shinkai and Y. Togashi},
title = {Energetics of single active diffusion trajectories},
journal = {EPL (Europhysics Letters)},
year = {2014},
volume = {105},
number = {3},
pages = {30002},
url = {http://stacks.iop.org/0295-5075/105/i=3/a=30002}
}
|
| Sugi T, Sakuma T, Ohtani Y and Yamamoto T (2014), "Versatile strategy for isolating transcription activator-like effector nuclease-mediated knockout mutants in Caenorhabditis elegans", Development, Growth & Differentiation. Vol. 56(1), pp. 78-85. |
| Abstract: Targeted genome editing using transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems has recently emerged as a potentially powerful method for creating locus-specific mutations in Caenorhabditis elegans. Due to the low mutation frequencies, one of the crucial steps in using these technologies is screening animals that harbor a targeted mutation. In previous studies, identifying targeted mutations in C. elegans usually depended on observations of fluorescent markers such as a green fluorescent protein or visible phenotypes such as dumpy and uncoordinated phenotypes. However, this strategy is limited in practice because the phenotypes caused by targeted mutations such as defects in sensory behaviors are often apparently invisible. Here, we describe a versatile strategy for isolating C. elegans knockout mutants by TALEN-mediated genome editing and a heteroduplex mobility assay. We applied TALENs to engineer the locus of the neural gene glr-1, which is a C. elegans AMPA-type receptor orthologue that is known to have crucial roles in various sensory behaviors. Knockout mutations in the glr-1 locus, which caused defective mechanosensory behaviors, were efficiently identified by the heteroduplex mobility assay. Thus, we demonstrated the utility of a TALEN-based knockout strategy for creating C. elegans with mutations that cause invisible phenotypes. |
BibTeX:
@article{Sugi2014,
author = {Sugi, Takuma and Sakuma, Tetsushi and Ohtani, Yasuko and Yamamoto, Takashi},
title = {Versatile strategy for isolating transcription activator-like effector nuclease-mediated knockout mutants in Caenorhabditis elegans},
journal = {Development, Growth & Differentiation},
year = {2014},
volume = {56},
number = {1},
pages = {78--85},
url = {http://dx.doi.org/10.1111/dgd.12108},
doi = {10.1111/dgd.12108}
}
|
| Tokumasu D, Sakuma T, Hayashi Y, Hosoi S, Hiyama E and Yamamoto T (2014), "FAST-id system for enrichment of cells with TALEN-induced mutations and large deletions", Genes to Cells. Vol. 19(5), pp. 419-431. |
| Abstract: Transcription activator-like effector nuclease (TALEN)-mediated genome editing is a powerful technique for analyzing gene functions in various cells and organisms. At target loci, TALENs can not only introduce short insertions and deletions, but also yield large deletions through the use of two TALEN pairs. Here, we report easy and efficient methods for enrichment of cells with TALEN-induced mutations and large deletions. First, we established the fluorescence-activated sorting of TALEN-induced deletions (FAST-id) system that enabled fluorescence-activated cell sorting-mediated enrichment of cells with TALEN-induced mutations. In the FAST-id system, either EGFP or mCherry and TALENs were co-expressed. Using dual fluorescence selection, both left and right TALEN-expressing cells were easily concentrated, resulting in enrichment of TALEN-mediated mutated cells. Next, to apply the FAST-id system to enrichment of cells with large deletions, we developed the fast unification of separate endonucleases (FUSE) method for assembly of two TALENs into a single expression vector. Using the FUSE method, we easily obtained a TALEN pair-expressing plasmid driven by a single promoter. By combining the FAST-id system and FUSE method, cells with large deletions were efficiently enriched. To the best of our knowledge, this is the first report of enrichment of cells with TALEN-induced large deletions. |
BibTeX:
@article{Tokumasu2014,
author = {Tokumasu, Daisuke and Sakuma, Tetsushi and Hayashi, Yoko and Hosoi, Sayaka and Hiyama, Eiso and Yamamoto, Takashi},
title = {FAST-id system for enrichment of cells with TALEN-induced mutations and large deletions},
journal = {Genes to Cells},
year = {2014},
volume = {19},
number = {5},
pages = {419--431},
url = {http://dx.doi.org/10.1111/gtc.12142},
doi = {10.1111/gtc.12142}
}
|
| Tokuyama T, Nakano Y, Awazu A, Uchimura-Makita Y, Fujiwra M, Watanabe Y, Sairaku A, Kajihara K, Motoda C, Oda N and Kihara Y (2014), "Deterioration of the circadian variation of heart rate variability in Brugada syndrome may contribute to the pathogenesis of ventricular fibrillation ", Journal of Cardiology . Vol. 64(2), pp. 133 - 138. |
| Abstract: AbstractAims Abnormal sympathetic innervation triggers ventricular fibrillation (VF). We examined the circadian variation of autonomic nervous system and its relevance to risk stratification of VF in patients with Brugada syndrome (Brs). Methods We enrolled 12 male Brs patients with documented VF (Brs-S; mean age, 42 ± 4 years), 17 without documented VF (Brs-N; mean age 48 ± 4 years), and 16 age- and gender-matched controls. The clinical data, 12-lead electrocardiography (ECG), signal-averaged ECG, electrophysiological study (EPS), and heart rate variability from 24 h Holter ECG were compared between the groups. Results The low frequency components (LF) in Brs-S and Brs-N and high frequency components (HF) in Brs-S patients were significantly lower than in the controls (409.8 ± 128.6 ms2, 329.5 ± 108 ms2 vs. 945.3 ± 111.3 ms2; 135.1 ± 73.8 ms2 vs. 391.8 ± 63.9 ms2, respectively). The circadian variation of the LF and LF/HF decreased in the Brs patients, the standard deviation (SD) of LF/HF (<2.5) and SD of LF (<400 ms2) had sufficiently high sensitivity (96.6%) and specificity (92.9%) for the diagnosis of Brs. Most of the Brs-S patients (83.3%) were located under the line formed by the SD/mean of HF = SD/mean of LF in the scatter plots. Conclusion Lack of the circadian variation of autonomic function occurs in Brs, and this may contribute to the pathogenesis of VF. |
BibTeX:
@article{Tokuyama2014,
author = {Takehito Tokuyama and Yukiko Nakano and Akinori Awazu and Yuko Uchimura-Makita and Mai Fujiwra and Yoshikazu Watanabe and Akinori Sairaku and Kenta Kajihara and Chikaaki Motoda and Noboru Oda and Yasuki Kihara},
title = {Deterioration of the circadian variation of heart rate variability in Brugada syndrome may contribute to the pathogenesis of ventricular fibrillation },
journal = {Journal of Cardiology },
year = {2014},
volume = {64},
number = {2},
pages = {133 - 138},
url = {http://www.sciencedirect.com/science/article/pii/S0914508713003857},
doi = {10.1016/j.jjcc.2013.12.001}
}
|
| Treen N, Yoshida K, Sakuma T, Sasaki H, Kawai N, Yamamoto T and Sasakura Y (2014), "Tissue-specific and ubiquitous gene knockouts by TALEN electroporation provide new approaches to investigating gene function in Ciona", Development. Vol. 141(2), pp. 481-487. |
| Abstract: Custom designed nucleases can simplify gene targeting experiments and have the potential to allow these techniques to be performed in a wide range of organisms. Transcriptional activator-like effector nucleases (TALENs) are starting to fulfill this potential with the advantages of low cost and fast construction times. Here, we report that TALENs are highly effective at inducing mutations in specific genomic loci in the ascidian chordate Ciona intestinalis. In Ciona there are well-established methods to introduce exogenous DNA by electroporation, and we show that this method can be used to introduce constructs that can express TALENs ubiquitously or in specific tissues. Our current protocols enable the rapid analysis of hundreds of TALEN-induced mutants. TALEN electroporations result in a high rate of mutations. These mutations can result in gene knockouts that recapitulate previously described functions of Fgf3 and Hox12. We show that TALENs can work efficiently to cause tissue-specific knockouts and demonstrate this by knocking out Hox12 in the epidermis and Fgf3 in neural tissues. We also use tissue-specific knockouts to reveal a new function of Fgf3 during ascidian larval metamorphosis. |
BibTeX:
@article{Treen2014,
author = {Treen, Nicholas and Yoshida, Keita and Sakuma, Tetsushi and Sasaki, Haruka and Kawai, Narudo and Yamamoto, Takashi and Sasakura, Yasunori},
title = {Tissue-specific and ubiquitous gene knockouts by TALEN electroporation provide new approaches to investigating gene function in Ciona},
journal = {Development},
year = {2014},
volume = {141},
number = {2},
pages = {481-487},
url = {http://dev.biologists.org/content/141/2/481.abstract},
doi = {10.1242/dev.099572}
}
|
| Wang W, Uzawa T, Tochio N, Hamatsu J, Hirano Y, Tada S, Saneyoshi H, Kigawa T, Hayashi N, Ito Y, Taiji M, Aigaki T and Ito Y (2014), "A fluorogenic peptide probe developed by in vitro selection using tRNA carrying a fluorogenic amino acid", Chem. Commun.. Vol. 50, pp. 2962-2964. The Royal Society of Chemistry. |
| Abstract: A peptide that binds and emits fluorescence in response to conformational change in a target protein was developed by in vitro selection using tRNA carrying a fluorogenic amino acid. This technology could prove to be useful for the development of separation-free immunoassays and bio-imaging analyses. |
BibTeX:
@article{Wang2014,
author = {Wang, Wei and Uzawa, Takanori and Tochio, Naoya and Hamatsu, Jumpei and Hirano, Yoshinori and Tada, Seiichi and Saneyoshi, Hisao and Kigawa, Takanori and Hayashi, Nobuhiro and Ito, Yutaka and Taiji, Makoto and Aigaki, Toshiro and Ito, Yoshihiro},
title = {A fluorogenic peptide probe developed by in vitro selection using tRNA carrying a fluorogenic amino acid},
journal = {Chem. Commun.},
publisher = {The Royal Society of Chemistry},
year = {2014},
volume = {50},
pages = {2962-2964},
url = {http://dx.doi.org/10.1039/C3CC47624C},
doi = {10.1039/C3CC47624C}
}
|
| Yamamoto T and Nakamura H (2014), "Targeted genome editing", Development, Growth & Differentiation. Vol. 56(1), pp. 1-1. |
BibTeX:
@article{Yamamoto2014,
author = {Yamamoto, Takashi and Nakamura, Harukazu},
title = {Targeted genome editing},
journal = {Development, Growth & Differentiation},
year = {2014},
volume = {56},
number = {1},
pages = {1--1},
url = {http://dx.doi.org/10.1111/dgd.12120},
doi = {10.1111/dgd.12120}
}
|
| 西森 拓 (2014), "風紋と砂丘", In キリンの斑論争と寺田寅彦. 岩波出版.
[BibTeX] |
BibTeX:
@incollection{Nishimori2014,
author = {西森 拓},
title = {風紋と砂丘},
booktitle = {キリンの斑論争と寺田寅彦},
publisher = {岩波出版},
year = {2014}
}
|
| 冨樫 祐一 (2014), "（3）少数分子反応系理論・少数性生物学", 生体の科学. Vol. 65(5), pp. 450-451. |
BibTeX:
@article{Togashi2014,
author = {冨樫 祐一},
title = {（3）少数分子反応系理論・少数性生物学},
journal = {生体の科学},
year = {2014},
volume = {65},
number = {5},
pages = {450-451},
url = { http://medicalfinder.jp/doi/abs/10.11477/mf.2425200034 |
| Ansai S, Sakuma T, Yamamoto T, Ariga H, Uemura N, Takahashi R and Kinoshita M (2013), "Efficient Targeted Mutagenesis in Medaka Using Custom-Designed Transcription Activator-Like Effector Nucleases", Genetics. Vol. 193(3), pp. 739-749. |
| Abstract: Transcription activator-like effector nucleases (TALENs) have become powerful tools for targeted genome editing. Here we demonstrate efficient targeted mutagenesis in medaka (Oryzias latipes), which serves as an excellent vertebrate model for genetics and genomics. We designed and constructed a pair of TALENs targeting the medaka DJ-1 gene, a homolog of human DJ-1 (PARK7). These TALENs induced a number of insertions and deletions in the injected embryos with extremely high efficiency. This induction of mutations occurred in a dose-dependent manner. All screened G0 fish injected with the TALENs transmitted the TALEN-induced mutations to the next generation with high efficiency (44–100%). We also confirmed that these TALENs induced site-specific mutations because none of the mutations were found at potential off-target sites. In addition, the DJ-1 protein was lost in DJ-1Δ7/Δ7 fish that carried a TALEN-induced frameshift mutation in both alleles. We also investigated the effect of the N- and C-terminal regions of the transcription activator-like (TAL) effector domain on the gene-disrupting activity of DJ1-TALENs and found that 287 amino acids at the N terminus and 63 amino acids at the C terminus of the TAL domain exhibited the highest disrupting activity in the injected embryos. Our results suggest that TALENs enable us to rapidly and efficiently establish knockout medaka strains. This is the first report of targeted mutagenesis in medaka using TALENs. The TALEN technology will expand the potential of medaka as a model system for genetics and genomics. |
BibTeX:
@article{Ansai2013,
author = {Ansai, Satoshi and Sakuma, Tetsushi and Yamamoto, Takashi and Ariga, Hiroyoshi and Uemura, Norihito and Takahashi, Ryosuke and Kinoshita, Masato},
title = {Efficient Targeted Mutagenesis in Medaka Using Custom-Designed Transcription Activator-Like Effector Nucleases},
journal = {Genetics},
year = {2013},
volume = {193},
number = {3},
pages = {739-749},
url = {http://www.genetics.org/content/193/3/739.abstract},
doi = {10.1534/genetics.112.147645}
}
|
| Aoki Y, Sakogawa K, Hihara J, Emi M, Hamai Y, Kono K, Shi L, Sun J, Kitao H, Ikura T, Niida H, Nakanishi M, Okada M and Tashiro S (2013), "Involvement of ribonucleotide reductase-M1 in 5-fluorouracil‑induced DNA damage in esophageal cancer cell lines", Int. J. Oncol.., Apr, 2013. , pp. 1951-1960. Spandidos Publications. |
| Abstract: 5-Fluorouracil (5-FU) is one of the most well established chemotherapeutic agents in the treatment of esophageal cancer. Ribonucleotide reductase M1 (RRM-1) is the rate‑limiting enzyme in de novo DNA synthesis, and has been considered to play an important role in the 5-FU metabolic pathway. However, the means by which RRM-1 participates in the anticancer effects of 5-FU and cisplatin (CDDP) have not been well studied. Here, we show that RRM-1 significantly contributes to the induction of DNA damage by 5-FU in esophageal cancer cell lines. An assay of γ-H2AX focus formation, a marker of DNA damage, after 5-FU treatment revealed good correlation with the levels of RRM-1 protein expression. Moreover, the increased sensitivity and RAD51 focus formation induced by the combination treatment of 5-FU and CDDP were significantly repressed by RRM-1 depletion. These results suggest that RRM-1 is involved not only in the induction of DNA damage by 5-FU but also in the synergistic cytotoxic effect in the combination therapy of 5-FU and CDDP. |
BibTeX:
@article{Aoki2013,
author = {Yoshiro Aoki and Kenji Sakogawa and Jun Hihara and Manabu Emi and Yoichi Hamai and Kazuteru Kono and Lin Shi and Jiying Sun and Hiroyuki Kitao and Tsuyoshi Ikura and Hiroyuki Niida and Makoto Nakanishi and Morihito Okada and Satoshi Tashiro},
title = {Involvement of ribonucleotide reductase-M1 in 5-fluorouracil‑induced DNA damage in esophageal cancer cell lines},
journal = {Int. J. Oncol.},
publisher = {Spandidos Publications},
year = {2013},
pages = {1951-1960},
url = {http://dx.doi.org/10.3892/ijo.2013.1899},
doi = {10.3892/ijo.2013.1899}
}
|
| Fujii M, Nishimori H and Awazu A (2013), "Influences of Excluded Volume of Molecules on Signaling Processes on the Biomembrane", PLoS ONE., 05, 2013. Vol. 8(5), pp. e62218. Public Library of Science. |
| Abstract: We investigate the influences of the excluded volume of molecules on biochemical reaction processes on 2-dimensional surfaces using a model of signal transduction processes on biomembranes. We perform simulations of the 2-dimensional cell-based model, which describes the reactions and diffusion of the receptors, signaling proteins, target proteins, and crowders on the cell membrane. The signaling proteins are activated by receptors, and these activated signaling proteins activate target proteins that bind autonomously from the cytoplasm to the membrane, and unbind from the membrane if activated. If the target proteins bind frequently, the volume fraction of molecules on the membrane becomes so large that the excluded volume of the molecules for the reaction and diffusion dynamics cannot be negligible. We find that such excluded volume effects of the molecules induce non-trivial variations of the signal flow, defined as the activation frequency of target proteins, as follows. With an increase in the binding rate of target proteins, the signal flow varies by monotonically increasing; increasing then decreasing in a bell-shaped curve; or increasing, decreasing, then increasing in an S-shaped curve. We further demonstrate that the excluded volume of molecules influences the hierarchical molecular distributions throughout the reaction processes. In particular, when the system exhibits a large signal flow, the signaling proteins tend to surround the receptors to form receptor-signaling protein clusters, and the target proteins tend to become distributed around such clusters. To explain these phenomena, we analyze the stochastic model of the local motions of molecules around the receptor. |
BibTeX:
@article{Fujii2013,
author = {Fujii, Masashi AND Nishimori, Hiraku AND Awazu, Akinori},
title = {Influences of Excluded Volume of Molecules on Signaling Processes on the Biomembrane},
journal = {PLoS ONE},
publisher = {Public Library of Science},
year = {2013},
volume = {8},
number = {5},
pages = {e62218},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0062218},
doi = {10.1371/journal.pone.0062218}
}
|
| Fujita K, Nakamura Y, Oka T, Ito H, Tamura T, Tagawa K, Sasabe T, Katsuta A, Motoki K, Shiwaku H, Sone M, Yoshida C, Katsuno M, Eishi Y, Murata M, Taylor JP, Wanker EE, Kono K, Tashiro S, Sobue G, Spada ARL and Okazawa H (2013), "A functional deficiency of TERA/VCP/p97 contributes to impaired DNA repair in multiple polyglutamine diseases", Nature Communications. Vol. 4, pp. 1816-. |
| Abstract: It is hypothesized that a common underlying mechanism links multiple neurodegenerative disorders. Here we show that transitional endoplasmic reticulum ATPase (TERA)/valosin-containing protein (VCP)/p97 directly binds to multiple polyglutamine disease proteins (huntingtin, ataxin-1, ataxin-7 and androgen receptor) via polyglutamine sequence. Although normal and mutant polyglutamine proteins interact with TERA/VCP/p97, only mutant proteins affect dynamism of TERA/VCP/p97. Among multiple functions of TERA/VCP/p97, we reveal that functional defect of TERA/VCP/p97 in DNA double-stranded break repair is critical for the pathology of neurons in which TERA/VCP/p97 is located dominantly in the nucleus in vivo. Mutant polyglutamine proteins impair accumulation of TERA/VCP/p97 and interaction of related double-stranded break repair proteins, finally causing the increase of unrepaired double-stranded break. Consistently, the recovery of lifespan in polyglutamine disease fly models by TERA/VCP/p97 corresponds well to the improvement of double-stranded break in neurons. Taken together, our results provide a novel common pathomechanism in multiple polyglutamine diseases that is mediated by DNA repair function of TERA/VCP/p97. |
BibTeX:
@article{Fujita2013,
author = {Kyota Fujita and Yoko Nakamura and Tsutomu Oka and Hikaru Ito and Takuya Tamura and Kazuhiko Tagawa and Toshikazu Sasabe and Asuka Katsuta and Kazumi Motoki and Hiroki Shiwaku and Masaki Sone and Chisato Yoshida and Masahisa Katsuno and Yoshinobu Eishi and Miho Murata and J. Paul Taylor and Erich E. Wanker and Kazuteru Kono and Satoshi Tashiro and Gen Sobue and Albert R. La Spada and Hitoshi Okazawa},
title = {A functional deficiency of TERA/VCP/p97 contributes to impaired DNA repair in multiple polyglutamine diseases},
journal = {Nature Communications},
year = {2013},
volume = {4},
pages = {1816-},
url = {http://dx.doi.org/10.1038/ncomms2828},
doi = {10.1038/ncomms2828}
}
|
| Gaffney EA and Lee SS (2013), "The sensitivity of Turing self-organization to biological feedback delays: 2D models of fish pigmentation", Mathematical Medicine and Biology. |
| Abstract: Turing morphogen models have been extensively explored in the context of large-scale self-organization in multicellular biological systems. However, reconciling the detailed biology of morphogen dynamics, while accounting for time delays associated with gene expression, reveals aberrant behaviours that are not consistent with early developmental self-organization, especially the requirement for exquisite temporal control. Attempts to reconcile the interpretation of Turing's ideas with an increasing understanding of the mechanisms driving zebrafish pigmentation suggests that one should reconsider Turing's model in terms of pigment cells rather than morphogens (Nakamasu et al., 2009, PNAS, 106, 8429–8434; Yamaguchi et al., 2007, PNAS, 104, 4790–4793). Here the dynamics of pigment cells is subject to response delays implicit in the cell cycle and apoptosis. Hence we explore simulations of fish skin patterning, focussing on the dynamical influence of gene expression delays in morphogen-based Turing models and response delays for cell-based Turing models. We find that reconciling the mechanisms driving the behaviour of Turing systems with observations of fish skin patterning remains a fundamental challenge. |
BibTeX:
@article{Gaffney2013,
author = {Gaffney, E. A. and Lee, S. Seirin},
title = {The sensitivity of Turing self-organization to biological feedback delays: 2D models of fish pigmentation},
journal = {Mathematical Medicine and Biology},
year = {2013},
url = {http://imammb.oxfordjournals.org/content/early/2013/09/30/imammb.dqt017.abstract},
doi = {10.1093/imammb/dqt017}
}
|
| Guignier L, Niiya H, Nishimori H, Lague D and Valance A (2013), "Sand dunes as migrating strings", Phys. Rev. E., May, 2013. Vol. 87, pp. 052206. American Physical Society. |
| Abstract: We develop a reduced complexity model for three-dimensional sand dunes, based on a simplified description of the longitudinal and lateral sand transport. The spatiotemporal evolution of a dune migrating over a nonerodible bed under unidirectional wind is reduced to the dynamics of its crest line, providing a simple framework for the investigation of three-dimensional dunes, such as barchan and transverse dunes. Within this model, we derive analytical solutions for barchan dunes and investigate the stability of a rectilinear transverse dune against lateral fluctuations. We show, in particular, that the latter is unstable only if the lateral transport on the dune slip face prevails over that on the upwind face. We also predict the wavelength and the characteristic time that control the subsequent evolution of an unstable transverse dune into a wavy ridge and the ultimate fragmentation into barchan dunes. |
BibTeX:
@article{Guignier2013,
author = {Guignier, L. and Niiya, H. and Nishimori, H. and Lague, D. and Valance, A.},
title = {Sand dunes as migrating strings},
journal = {Phys. Rev. E},
publisher = {American Physical Society},
year = {2013},
volume = {87},
pages = {052206},
url = {http://link.aps.org/doi/10.1103/PhysRevE.87.052206},
doi = {10.1103/PhysRevE.87.052206}
}
|
| Haino T (2013), "Molecular-recognition-directed formation of supramolecular polymers", Polym. J.. Vol. 45, pp. 363-383. Nature Publishing Group. |
| Abstract: In recent years, significant research effort has focused on creating supramolecular polymers that can be attained by specific host–guest interactions of the repeating units. During the supramolecular polymerization process, molecular recognition events, which are predetermined by the molecular building blocks, are highly selective and directional for defining the size, direction and dimension of the resulting supramolecular polymers. The diversity of the supramolecular building blocks ranges from small aromatic units to macrocycles. Recently, the interplay of supramolecular and polymer chemistry has led to the creation of novel supramolecular materials, which display fascinating functions such as self-healing, stimuli-responsiveness and rubber-like elastomeric properties. Supramolecular cross-linking and supramolecular block copolymerization are the methods that have been used to install fascinating and functional moieties onto polymer backbones. Currently, the development of practical supramolecular polymeric materials is an ongoing challenge for supramolecular chemists. This review will focus on the recent developments in supramolecular polymers composed of discrete repeating units, as well as novel supramolecular materials produced by the interplay of supramolecular and polymer chemistry. |
BibTeX:
@article{Haino2013,
author = {Haino, Takeharu},
title = {Molecular-recognition-directed formation of supramolecular polymers},
journal = {Polym. J.},
publisher = {Nature Publishing Group},
year = {2013},
volume = {45},
pages = {363-383},
url = {http://dx.doi.org/10.1038/pj.2012.144},
doi = {10.1038/pj.2012.144}
}
|
| Haino T (2013), "Supramolecular Chemistry: From Host-guest Complexes to Supramolecular Polymers", Journal of Synthetic Organic Chemistry, Japan. Vol. 71(11), pp. 1172-1181. |
| Abstract: Combining the concepts of supramolecular chemistry with material science has led to the development of supramolecular polymer chemistry. Although a large number of host-guest motifs have been produced, only a limited number of recognition motifs have been utilized as supramolecular connections within polymeric assemblies. In this account, we describe the molecular recognition of host molecules based on a calix[5]arene and a bisporphyrin, demonstrating unique guest encapsulations; subsequently, these host-guest motifs were applied to the synthesis of supramolecular polymers that display polymer-like properties in both solution and solid states. In addition, we disclose that bisresorcinarenes form supramolecular polymers that are connected via a hydrogen-bonded rim-to-rim dimeric structure, which is composed of two resorcinarene moieties. |
BibTeX:
@article{Haino2013a,
author = {Takeharu Haino},
title = {Supramolecular Chemistry: From Host-guest Complexes to Supramolecular Polymers},
journal = {Journal of Synthetic Organic Chemistry, Japan},
year = {2013},
volume = {71},
number = {11},
pages = {1172-1181},
doi = {10.5059/yukigoseikyokaishi.71.1172}
}
|
| Haino T, Hirai Y, Ikeda T and Saito H (2013), "Photoresponsive two-component organogelators based on trisphenylisoxazolylbenzene", Org. Biomol. Chem.. Vol. 11, pp. 4164-4170. The Royal Society of Chemistry. |
| Abstract: Photochromic tris(phenylisoxazolyl)benzene 1 and bispyridine derivatives 2a-e were mixed in a certain ratio to generate stable gels in benzyl alcohol, 4-methoxybenzyl alcohol, and aniline. Supramolecular assembly of 1 in solution was confirmed by 1H NMR study. The Tgel value was saturated in a 2 : 3 ratio of 1 and 2c. The intermolecular hydrogen bonds OHN and salt bridge O-H-N+ between 1 and 2c coexisted evidently, and these hydrogen bonds contributed to the stabilization of the gel networks. The lengths of alkyl chains of 2a-e governed the stabilities of the gels. The gel formations were driven by the morphological transition of 1 before and after the addition of 2a-e. Mixtures of 1 and 2a-e led to the well developed fibrillar networks, generating a lot of voids that are responsible for immobilizing solvent molecules. When the benzyl alcohol gel was irradiated at 360 nm, the gel turned to the sol. The sol was reversed to the gel by warming. This gel-to-sol phase transition was completely reversible. |
BibTeX:
@article{Haino2013b,
author = {Haino, Takeharu and Hirai, Yuko and Ikeda, Toshiaki and Saito, Hiroshi},
title = {Photoresponsive two-component organogelators based on trisphenylisoxazolylbenzene},
journal = {Org. Biomol. Chem.},
publisher = {The Royal Society of Chemistry},
year = {2013},
volume = {11},
pages = {4164-4170},
url = {http://dx.doi.org/10.1039/C3OB00041A},
doi = {10.1039/C3OB00041A}
}
|
| Harada R, Tochio N, Kigawa T, Sugita Y and Feig M (2013), "Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions", Journal of the American Chemical Society. Vol. 135(9), pp. 3696-3701. |
| Abstract: The effect of cellular crowding environments on protein structure and stability is a key issue in molecular and cellular biology. The classical view of crowding emphasizes the volume exclusion effect that generally favors compact, native states. Here, results from molecular dynamics simulations and NMR experiments show that protein crowders may destabilize native states via protein–protein interactions. In the model system considered here, mixtures of villin head piece and protein G at high concentrations, villin structures become increasingly destabilized upon increasing crowder concentrations. The denatured states observed in the simulation involve partial unfolding as well as more subtle conformational shifts. The unfolded states remain overall compact and only partially overlap with unfolded ensembles at high temperature and in the presence of urea. NMR measurements on the same systems confirm structural changes upon crowding based on changes of chemical shifts relative to dilute conditions. An analysis of protein–protein interactions and energetic aspects suggests the importance of enthalpic and solvation contributions to the crowding free energies that challenge an entropic-centered view of crowding effects. |
BibTeX:
@article{Harada2013,
author = {Harada, Ryuhei and Tochio, Naoya and Kigawa, Takanori and Sugita, Yuji and Feig, Michael},
title = {Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions},
journal = {Journal of the American Chemical Society},
year = {2013},
volume = {135},
number = {9},
pages = {3696-3701},
url = {http://pubs.acs.org/doi/abs/10.1021/ja3126992},
doi = {10.1021/ja3126992}
}
|
| Hashimoto M, Kodera N, Tsunaka Y, Oda M, Tanimoto M, Ando T, Morikawa K and Tate S-I (2013), "Phosphorylation-Coupled Intramolecular Dynamics of Unstructured Regions in Chromatin Remodeler FACT", Biophysical Journal. Vol. 104(10), pp. 2222 - 2234. |
| Abstract: Abstract The intrinsically disordered region (IDR) of a protein is an important topic in molecular biology. The functional significance of IDRs typically involves gene-regulation processes and is closely related to posttranslational modifications such as phosphorylation. We previously reported that the Drosophila facilitates chromatin transcription (FACT) protein involved in chromatin remodeling contains an acidic ID fragment (AID) whose phosphorylation modulates FACT binding to nucleosomes. Here, we performed dynamic atomic force microscopy and NMR analyses to clarify how the densely phosphorylated AID masks the DNA binding interface of the high-mobility-group domain (HMG). Dynamic atomic force microscopy of the nearly intact FACT revealed that a small globule temporally appears but quickly vanishes within each mobile tail-like image, corresponding to the HMG-containing IDR. The lifespan of the globule increases upon phosphorylation. NMR analysis indicated that phosphorylation induces no ordered structure but increases the number of binding sites in AID to HMG with an adjacent basic segment, thereby retaining the robust electrostatic intramolecular interaction within FACT even in the presence of DNA. These data lead to the conclusion that the inhibitory effect of nucleosome binding is ascribed to the increase in the probability of encounter between HMG and the phosphorylated IDR. |
BibTeX:
@article{Hashimoto2013,
author = {Manami Hashimoto and Noriyuki Kodera and Yasuo Tsunaka and Masayuki Oda and Mitsuru Tanimoto and Toshio Ando and Kosuke Morikawa and Tate, Shin-Ichi},
title = {Phosphorylation-Coupled Intramolecular Dynamics of Unstructured Regions in Chromatin Remodeler FACT},
journal = {Biophysical Journal},
year = {2013},
volume = {104},
number = {10},
pages = {2222 - 2234},
url = {http://www.sciencedirect.com/science/article/pii/S0006349513004335},
doi = {10.1016/j.bpj.2013.04.007}
}
|
| Hisano Y, Ota S, Arakawa K, Muraki M, Kono N, Oshita K, Sakuma T, Tomita M, Yamamoto T, Okada Y and Kawahara A (2013), "Quantitative assay for TALEN activity at endogenous genomic loci", Biology Open. Vol. 2(4), pp. 363-367. |
| Abstract: Artificially designed nucleases such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) can induce a targeted DNA double-strand break at the specific target genomic locus, leading to the frameshift-mediated gene disruption. However, the assays for their activity on the endogenous genomic loci remain limited. Herein, we describe a versatile modified lacZ assay to detect frameshifts in the nuclease target site. Short fragments of the genome DNA at the target or putative off-target loci were amplified from the genomic DNA of TALEN-treated or control embryos, and were inserted into the lacZα sequence for the conventional blue–white selection. The frequency of the frameshifts in the fragment can be estimated from the numbers of blue and white colonies. Insertions and/or deletions were easily determined by sequencing the plasmid DNAs recovered from the positive colonies. Our technique should offer broad application to the artificial nucleases for genome editing in various types of model organisms. |
BibTeX:
@article{Hisano2013,
author = {Hisano, Yu and Ota, Satoshi and Arakawa, Kazuharu and Muraki, Michiko and Kono, Nobuaki and Oshita, Kazuki and Sakuma, Tetsushi and Tomita, Masaru and Yamamoto, Takashi and Okada, Yasushi and Kawahara, Atsuo},
title = {Quantitative assay for TALEN activity at endogenous genomic loci},
journal = {Biology Open},
year = {2013},
volume = {2},
number = {4},
pages = {363-367},
url = {http://bio.biologists.org/content/2/4/363.abstract},
doi = {10.1242/bio.20133871}
}
|
| Horikoshi Y, Habu T and Matsumoto T (2013), "An E2 enzyme Ubc11 is required for ubiquitination of Slp1/Cdc20 and spindle checkpoint silencing in fission yeast", Cell Cycle., Mar, 2013. Vol. 12, pp. 961 - 971. |
| Abstract: For ordered mitotic progression, various proteins have to be regulated by an ubiquitin ligase, the anaphase-promoting complex or cyclosome (APC/C) with appropriate timing. Recent studies have implied that the activity of APC/C also contributes to release of mitotic checkpoint complexes (MCCs) from its target Cdc20 in the process of silencing the spindle assembly checkpoint (SAC). Here we describe a temperature-sensitive mutant (ubc11-P93L) in which cell cycle progression is arrested at mitosis. The mutant grows normally at the restrictive temperature when SAC is inactivated, suggesting that the arrest is not due to abnormal spindle assembly, but rather due to prolonged activation of SAC. Supporting this notion, MCCs remain bound to APC/C even when SAC is satisfied. The ubc11+ gene encodes one of the two E2 enzymes required for progression through mitosis in fission yeast. Remarkably, Slp1 (a fission yeast homolog of Cdc20), which is degraded in an APC/C-dependent manner, stays stable throughout the cell cycle in the ubc11-P93L mutant lacking the functional SAC. Other APC/C substrates, in contrast, were degraded on schedule. We have also found that a loss of Ubc4, the other E2 required for progression through mitosis, does not affect the stability of Slp1. We propose that each of the two E2 enzymes is responsible for collaborating with APC/C for a specific set of substrates, and that Ubc11 is responsible for regulating Slp1 with APC/C for silencing the SAC. |
BibTeX:
@article{Horikoshi2013,
author = {Y. Horikoshi and T. Habu and T. Matsumoto},
title = {An E2 enzyme Ubc11 is required for ubiquitination of Slp1/Cdc20 and spindle checkpoint silencing in fission yeast},
journal = {Cell Cycle},
year = {2013},
volume = {12},
pages = {961 - 971},
url = {https://www.landesbioscience.com/journals/cc/article/23946/},
doi = {10.4161/cc.23946}
}
|
| Hozumi A, Yoshida R, Horie T, Sakuma T, Yamamoto T and Sasakura Y (2013), "Enhancer activity sensitive to the orientation of the gene it regulates in the chordategenome ", Developmental Biology . Vol. 375(1), pp. 79 - 91. |
| Abstract: Enhancers are flexible in terms of their location and orientation relative to the genes they regulate. However, little is known about whether the flexibility can be applied in every combination of enhancers and genes. Enhancer detection with transposable elements is a powerful method to identify enhancers in the genome and to create marker lines expressing fluorescent proteins in a tissue-specific manner. In the chordate Ciona intestinalis, this method has been established with a Tc1/mariner superfamily transposon Minos. Previously, we created the enhancer detection line E[MiTSAdTPOG]15 (E15) that specifically expresses green fluorescent protein (GFP) in the central nervous system (CNS) after metamorphosis. In this study, we identified the causal insertion site of the transgenic line. There are two genes flanking the causal insertion of the E15 line, and the genomic region around the insertion site contains the enhancers responsible for the expression in the endostyle and gut in addition to the CNS. We found that the endostyle and gut enhancers show sensitivity to the orientation of the GFP gene for their enhancer activity. Namely, the enhancers cannot enhance the expression of GFP which is inserted at the same orientation as the E15 line, while the enhancers can enhance GFP expression inserted at the opposite orientation. The CNS enhancer can enhance GFP expression in both orientations. The DNA element adjacent to the endostyle enhancer is responsible for the orientation sensitivity of the enhancer. The different sensitivity of the enhancers to the orientation of the transgene is a cause of CNS-specific GFP expression in the E15line. |
BibTeX:
@article{Hozumi2013,
author = {Akiko Hozumi and Reiko Yoshida and Takeo Horie and Tetsushi Sakuma and Takashi Yamamoto and Yasunori Sasakura},
title = {Enhancer activity sensitive to the orientation of the gene it regulates in the chordategenome },
journal = {Developmental Biology },
year = {2013},
volume = {375},
number = {1},
pages = {79 - 91},
url = {http://www.sciencedirect.com/science/article/pii/S0012160612006781},
doi = {10.1016/j.ydbio.2012.12.012}
}
|
| Ikura YS, Heisler E, Awazu A, Nishimori H and Nakata S (2013), "Collective motion of symmetric camphor papers in an annular water channel", Phys. Rev. E., Jul, 2013. Vol. 88, pp. 012911. American Physical Society. |
| Abstract: We investigate the collective motion of symmetric self-propelled objects that are driven by a difference in the surface tension. The objects move around an annular water channel spontaneously and interact through the camphor layer that develops on the water surface. We found that two collective motion modes, discrete and continuous density waves, are generated depending on the number of self-propelled objects. The two modes are characterized by examining the local and global dynamics, and the collective motion mechanism is discussed in relation to the distribution of camphor concentration in the annular water channel. We conclude that the difference between these two modes originates from that of the driving mechanism that pushes a camphor paper away from a cluster, through which mechanism density waves are generated and maintained. |
BibTeX:
@article{Ikura2013,
author = {Ikura, Yumihiko S. and Heisler, Eric and Awazu, Akinori and Nishimori, Hiraku and Nakata, Satoshi},
title = {Collective motion of symmetric camphor papers in an annular water channel},
journal = {Phys. Rev. E},
publisher = {American Physical Society},
year = {2013},
volume = {88},
pages = {012911},
url = {http://link.aps.org/doi/10.1103/PhysRevE.88.012911},
doi = {10.1103/PhysRevE.88.012911}
}
|
| Iwaki M, Marcucci L, Togashi Y and Yanagida T (2013), "Single Molecule and Collective Dynamics of Motor Protein Coupled with Mechano-Sensitive Chemical Reaction", In Engineering of Chemical Complexity. World Science Publishing. |
| Abstract: Motor proteins such as myosin and kinesin hydrolyze ATP into ADP and Pi to convert chemical energy into mechanical work. This resultsin various motile processes like muscle contraction, vesicle transport and cell division. Recent single molecule experiments have revealed that external load applied to these motor proteins perturb not only the mechanical motion, but the ATP hydrolysis cycle as well, making these molecules mechano-enzymes. Here, we describe our single molecule detection techniques to reveal the mechano-enzymatic properties of myosin and introduce recent progress from both experimental and theoretical approaches at the single- and multiple-molecule level. |
BibTeX:
@incollection{Iwaki2013,
author = {Mitsuhiro Iwaki and Lorenzo Marcucci and Yuichi Togashi and Toshio Yanagida},
title = {Single Molecule and Collective Dynamics of Motor Protein Coupled with Mechano-Sensitive Chemical Reaction},
booktitle = {Engineering of Chemical Complexity},
publisher = {World Science Publishing},
year = {2013},
doi = {10.1142/9789814390460_0004}
}
|
| Iwamoto H, Takizawa W, Itoh K, Hagiwara T, Tayama E, Hasegawa E and Haino T (2013), "Selective Synthesis of [2]- and [3]Catenane Tuned by Ring Size and Concentration", The Journal of Organic Chemistry. Vol. 78(11), pp. 5205-5217. |
| Abstract: The syntheses of [2]- and [3]catenanes by olefin metathesis and oxidative acetylide coupling have been studied in detail. Pseudorotaxanes that were obtained by mixing crown ether and ammonium salts containing two terminal reactive end-groups were converted to [2]- and [3]catenane. Their yields were influenced not only by the chain length of the ammonium salts but also by the concentration of the crown ether and the ammonium salts. The strain energies of [2]catenane were responsible for the formation of [2]catenane. |
BibTeX:
@article{Iwamoto2013a,
author = {Iwamoto, Hajime and Takizawa, Wataru and Itoh, Koji and Hagiwara, Tatsuya and Tayama, Eiji and Hasegawa, Eietsu and Haino, Takeharu},
title = {Selective Synthesis of [2]- and [3]Catenane Tuned by Ring Size and Concentration},
journal = {The Journal of Organic Chemistry},
year = {2013},
volume = {78},
number = {11},
pages = {5205-5217},
url = {http://pubs.acs.org/doi/abs/10.1021/jo400239h},
doi = {10.1021/jo400239h}
}
|
| Iwamoto T, Watanabe Y, Takaya H, Haino T, Yasuda N and Yamago S (2013), "Size- and Orientation-Selective Encapsulation of C70 by Cycloparaphenylenes", Chemistry – A European Journal. Vol. 19(42), pp. 14061-14068. WILEY-VCH Verlag. |
| Abstract: The size- and orientation-selective formation of the shortest-possible C70 peapod in solution and in the solid state by using the shortest structural unit of an “armchair” carbon nanotube (CNT), cycloparaphenylene (CPP), has been studied. [10]CPP and [11]CPP exothermically formed 1:1 complexes with C70, thereby giving the resulting peapods. A van′t Hoff plot analysis revealed that the formation of these complexes in 1,2-dichlorobenzene was mainly driven by entropy, whereas the theoretical calculations suggested that the formation of the complex in the gas phase was predominantly driven by enthalpy. C70 was found to exist in two distinct orientations inside the CPP cavity, namely “lying” and “standing”, depending on the specific size of the CPP. The theoretical calculations and the X-ray crystallographic analysis revealed that the interactions between [10]CPP and the short axis of C70 in its lying orientation were isotropic and similar to those observed between [10]CPP and C60. However, the interactions between [11]CPP and C70 in its standing orientation were anisotropic, thereby involving the radial deformation of [11]CPP into an ellipsoidal shape. This “induced fit” maximized the van der Waals interactions with the long axis of C70. Theoretical calculations revealed that the deformation occurred readily with low energy loss, thus suggesting that CPPs are highly radially elastic molecules. These results also indicate that the same type of radial deformation should occur in CNT peapods that encapsulate anisotropic fullerenes. |
BibTeX:
@article{Iwamoto2013b,
author = {Iwamoto, Takahiro and Watanabe, Yoshiki and Takaya, Hikaru and Haino, Takeharu and Yasuda, Nobuhiro and Yamago, Shigeru},
title = {Size- and Orientation-Selective Encapsulation of C70 by Cycloparaphenylenes},
journal = {Chemistry – A European Journal},
publisher = {WILEY-VCH Verlag},
year = {2013},
volume = {19},
number = {42},
pages = {14061--14068},
url = {http://dx.doi.org/10.1002/chem.201302694},
doi = {10.1002/chem.201302694}
}
|
| Kato T, Miyata K, Sonobe M, Yamashita S, Tamano M, Miura K, Kanai Y, Miyamoto S, Sakuma T, Yamamoto T and et al. (2013), "Production of Sry knockout mouse using TALEN via oocyte injection", Sci. Rep.., Nov, 2013. Vol. 3 Nature Publishing Group. |
| Abstract: Recently developed transcription activator-like effector nuclease (TALEN) technology has enabled the creation of knockout mice, even for genes on the Y chromosome. In this study, we generated a knockout mouse for Sry, a sex-determining gene on the Y chromosome, using microinjection of TALEN RNA into pronuclear stage oocytes. As expected, the knockout mouse had female external and internal genitalia, a female level of blood testosterone and a female sexually dimorphic nucleus in the brain. The knockout mouse exhibited an estrous cycle and performed copulatory behavior as females, although it was infertile or had reduced fertility. A histological analysis showed that the ovary of the knockout mouse displayed a reduced number of oocytes and luteinized unruptured follicles, implying that a reduced number of ovulated oocytes is a possible reason for infertility and/or reduced fertility in the KO mouse |
BibTeX:
@article{Kato2013,
author = {Kato, Tomoko and Miyata, Kohei and Sonobe, Miku and Yamashita, Satoshi and Tamano, Moe and Miura, Kento and Kanai, Yoshiakira and Miyamoto, Shingo and Sakuma, Tetsushi and Yamamoto, Takashi and et al.},
title = {Production of Sry knockout mouse using TALEN via oocyte injection},
journal = {Sci. Rep.},
publisher = {Nature Publishing Group},
year = {2013},
volume = {3},
url = {http://dx.doi.org/10.1038/srep03136},
doi = {10.1038/srep03136}
}
|
| Kazama T, Kuroiwa K, Umedachi T, Komatsu Y and Kobayashi R (2013), "Locomotion diversity in an underwater soft-robot inspired by the polyclad flatworm", In Intelligent Robots and Systems (IROS), 2013 IEEE/RSJ International Conference on., Nov, 2013. , pp. 2083-2083. |
| Abstract: The underwater soft-robot inspired by polyclad flatworms has been developed. The oval, flat, soft body of the flatworm was represented by a rubber sheet. The sheet was controlled by controls with three degrees of freedom to allow flapping of both the lateral sides and the body axis. Swimming patterns, such as swimming forward, hovering, and swimming backwards, were achieved by coordinated movement of the lateral side flaps and the body axis of the soft robot. |
BibTeX:
@inproceedings{Kazama2013,
author = {Kazama, T. and Kuroiwa, K. and Umedachi, T. and Komatsu, Y. and Kobayashi, R.},
title = {Locomotion diversity in an underwater soft-robot inspired by the polyclad flatworm},
booktitle = {Intelligent Robots and Systems (IROS), 2013 IEEE/RSJ International Conference on},
year = {2013},
pages = {2083-2083},
doi = {10.1109/IROS.2013.6696646}
}
|
| Lee S, Baker R, Gaffney E and White S (2013), "Optimal barrier zones for stopping the invasion of Aedes aegypti mosquitoes via transgenic or sterile insect techniques", Theoretical Ecology. Vol. 6(4), pp. 427-442. Springer Netherlands. |
| Abstract: Biological invasions have dramatically altered the natural world by threatening native species and their communities. Moreover, when the invading species is a vector for human disease, there are further substantive public health and economic impacts. The development of transgenic technologies is being explored in relation to new approaches for the biological control of insect pests. We investigate the use of two control strategies, classical sterile insect techniques and transgenic late-acting bisex lethality (Release of Insects carrying a Dominant Lethal), for controlling invasion of the mosquito Aedes aegypti using a spatial stage-structured mathematical model. In particular, we explore the use of a barrier zone of sterile/transgenic insects to prevent or impede the invasion of mosquitoes. We show that the level of control required is not only highly sensitive to the rate at which the sterile/transgenic males are released in the barrier zone but also to the spatial range of release. Our models characterise how the distribution of sterile/transgenic mosquitoes in the barrier zone can be controlled so as to minimise the number of mass-produced insects required for the arrest of species invasion. We predict that, given unknown rates of mosquito dispersal, management strategies should concentrate on larger release areas rather than more intense release rates for optimal control. |
BibTeX:
@article{Lee2013,
author = {Lee, S.Seirin and Baker, RuthE. and Gaffney, EamonnA. and White, StevenM.},
title = {Optimal barrier zones for stopping the invasion of Aedes aegypti mosquitoes via transgenic or sterile insect techniques},
journal = {Theoretical Ecology},
publisher = {Springer Netherlands},
year = {2013},
volume = {6},
number = {4},
pages = {427-442},
url = {http://dx.doi.org/10.1007/s12080-013-0178-4},
doi = {10.1007/s12080-013-0178-4}
}
|
| Mashimo T, Kaneko T, Sakuma T, Kobayashi J, Kunihiro Y, Voigt B, Yamamoto T and Serikawa T (2013), "Efficient gene targeting by TAL effector nucleases coinjected with exonucleases in zygotes", Sci. Rep.., Feb, 2013. Vol. 3 Nature Publishing Group. |
| Abstract: TAL Effector Nucleases (TALENs) are versatile tools for targeted gene editing in various species. However, their efficiency is still insufficient, especially in mammalian embryos. Here, we showed that combined expression of Exonuclease 1 (Exo1) with engineered site-specific TALENs provided highly efficient disruption of the endogenous gene in rat fibroblast cells. A similar increased efficiency of up to ,30% with Exo1 was also observed in fertilized rat eggs, and in the production of knockout rats for the albino (Tyr) gene. These findings demonstrate TALENs with Exo1 is an easy and efficient method of generating gene knockouts using zygotes, which increases the range of gene targeting technologies available to various species. |
BibTeX:
@article{Mashimo2013,
author = {Mashimo, Tomoji and Kaneko, Takehito and Sakuma, Tetsushi and Kobayashi, Junya and Kunihiro, Yayoi and Voigt, Birger and Yamamoto, Takashi and Serikawa, Tadao},
title = {Efficient gene targeting by TAL effector nucleases coinjected with exonucleases in zygotes},
journal = {Sci. Rep.},
publisher = {Nature Publishing Group},
year = {2013},
volume = {3},
url = {http://dx.doi.org/10.1038/srep01253},
doi = {10.1038/srep01253}
}
|
| Nakano Y, Chayama K, Ochi H, Toshishige M, Hayashida Y, Miki D, Hayes CN, Suzuki H, Tokuyama T, Oda N, Suenari K, Uchimura-Makita Y, Kajihara K, Sairaku A, Motoda C, Fujiwara M, Watanabe Y, Yoshida Y, Ohkubo K, Watanabe I, Nogami A, Hasegawa K, Watanabe H, Endo N, Aiba T, Shimizu W, Ohno S, Horie M, Arihiro K, Tashiro S, Makita N and Kihara Y (2013), "A Nonsynonymous Polymorphism in |
| Abstract: Unexplained cardiac arrest with documented ventricular fibrillation (UCA) is defined as spontaneous ventricular fibrillation (VF) that is not associated with known structural or electrical heart diseases and is one of the major causes of sudden cardiac death. Identification of the genes responsible for UCA may further increase our understanding of mechanisms of UCA and facilitate more accurate diagnosis and preventive treatment, especially in asymptomatic disease-carrying relatives of the patient. However, molecular mechanisms of UCA have not been fully clarified due to the high mortality rate and difficulty of diagnosis. In this study, UCA patients are shown to have a high incidence of a polymorphism in the Semaphorin 3A gene (rs138694505, |
BibTeX:
@article{Nakano2013,
author = {Nakano, , Yukiko AND Chayama, , Kazuaki AND Ochi, , Hidenori AND Toshishige, , Masaaki AND Hayashida, , Yasufumi AND Miki, , Daiki AND Hayes, , C. Nelson AND Suzuki, , Hidekazu AND Tokuyama, , Takehito AND Oda, , Noboru AND Suenari, , Kazuyoshi AND Uchimura-Makita, , Yuko AND Kajihara, , Kenta AND Sairaku, , Akinori AND Motoda, , Chikaaki AND Fujiwara, , Mai AND Watanabe, , Yoshikazu AND Yoshida, , Yukihiko AND Ohkubo, , Kimie AND Watanabe, , Ichiro AND Nogami, , Akihiko AND Hasegawa, , Kanae AND Watanabe, , Hiroshi AND Endo, , Naoto AND Aiba, , Takeshi AND Shimizu, , Wataru AND Ohno, , Seiko AND Horie, , Minoru AND Arihiro, , Koji AND Tashiro, , Satoshi AND Makita, , Naomasa AND Kihara, , Yasuki},
title = {A Nonsynonymous Polymorphism in |
| Nakata S, Hata M, Ikura YS, Heisler E, Awazu A, Kitahata H and Nishimori H (2013), "Motion with Memory of a Self-Propelled Object", The Journal of Physical Chemistry C. Vol. 117(46), pp. 24490-24495. |
| Abstract: The concept of self-propelled objects is important for the understanding of biological mobility, as well as for the development of autonomous devices in medicine and engineering. In this study, a simple self-propelled object, driven by a difference in surface tension, was found to exhibit intermittent self-motion (alternately in motion and at rest) in an annular water channel, with resting positions and features of motion in subsequent cycles remaining almost the same as those previously visited; that is, memories of the resting positions and features of motion were observed. The occurrence of the memory phenomenon was found to depend on the relationship between the resting time and the period for one lap of the annular channel. The mechanism of memory is discussed in terms of the distribution of surface-active molecules and local surface tension at the resting positions. |
BibTeX:
@article{Nakata2013,
author = {Nakata, Satoshi and Hata, Misato and Ikura, Yumihiko S. and Heisler, Eric and Awazu, Akinori and Kitahata, Hiroyuki and Nishimori, Hiraku},
title = {Motion with Memory of a Self-Propelled Object},
journal = {The Journal of Physical Chemistry C},
year = {2013},
volume = {117},
number = {46},
pages = {24490-24495},
url = {http://pubs.acs.org/doi/abs/10.1021/jp409172m},
doi = {10.1021/jp409172m}
}
|
| Nanbu T, Takahashi K, Murray JM, Hirata N, Ukimori S, Kanke M, Masukata H, Yukawa M, Tsuchiya E and Ueno M (2013), "Fission Yeast RecQ Helicase Rqh1 Is Required for the Maintenance of Circular Chromosomes", Molecular and Cellular Biology. Vol. 33(6), pp. 1175-1187. |
| Abstract: Protection of telomeres protein 1 (Pot1) binds to single-stranded telomere overhangs and protects chromosome ends. RecQ helicases regulate homologous recombination at multiple stages, including resection, strand displacement, and resolution. Fission yeast pot1 and RecQ helicase rqh1 double mutants are synthetically lethal, but the mechanism is not fully understood. Here, we show that the synthetic lethality of pot1Δ rqh1Δ double mutants is due to inappropriate homologous recombination, as it is suppressed by the deletion of rad51+. The expression of Rad51 in the pot1Δ rqh1Δ rad51Δ triple mutant, which has circular chromosomes, is lethal. Reduction of the expression of Rqh1 in a pot1 disruptant with circular chromosomes caused chromosome missegregation, and this defect was partially suppressed by the deletion of rad51+. Taken together, our results suggest that Rqh1 is required for the maintenance of circular chromosomes when homologous recombination is active. Crossovers between circular monomeric chromosomes generate dimers that cannot segregate properly in Escherichia coli. We propose that Rqh1 inhibits crossovers between circular monomeric chromosomes to suppress the generation of circular dimers. |
BibTeX:
@article{Nanbu2013,
author = {Nanbu, Tomoko and Takahashi, Katsunori and Murray, Johanne M. and Hirata, Naoya and Ukimori, Shinobu and Kanke, Mai and Masukata, Hisao and Yukawa, Masashi and Tsuchiya, Eiko and Ueno, Masaru},
title = {Fission Yeast RecQ Helicase Rqh1 Is Required for the Maintenance of Circular Chromosomes},
journal = {Molecular and Cellular Biology},
year = {2013},
volume = {33},
number = {6},
pages = {1175-1187},
url = {http://mcb.asm.org/content/33/6/1175.abstract},
doi = {10.1128/MCB.01713-12}
}
|
| Nishigami Y, Ichikawa M, Kazama T, Kobayashi R, Shimmen T, Yoshikawa K and Sonobe S (2013), "Reconstruction of Active Regular Motion in Amoeba Extract: Dynamic Cooperation between Sol and Gel States.", PloS ONE., aug, 2013. Vol. 8(8) |
| Abstract: Amoeboid locomotion is one of the typical modes of biological cell migration. Cytoplasmic sol–gel conversion of an actomyosin system is thought to play an important role in locomotion. However, the mechanisms underlying sol–gel conversion, including trigger, signal, and regulating factors, remain unclear. We developed a novel model system in which an actomyosin fraction moves like an amoeba in a cytoplasmic extract. Rheological study of this model system revealed that the actomyosin fraction exhibits shear banding: the sol–gel state of actomyosin can be regulated by shear rate or mechanical force. Furthermore, study of the living cell indicated that the shear-banding property also causes sol–gel conversion with the same order of magnitude as that of shear rate. Our results suggest that the inherent sol–gel transition property plays an essential role in the self-regulation of autonomous translational motion in amoeba. |
BibTeX:
@article{Nishigami2013,
author = {Nishigami, Yukinori and Ichikawa, Masatoshi and Kazama, Toshiya and Kobayashi, Ryo and Shimmen, Teruo and Yoshikawa, Kenichi and Sonobe, Seiji},
title = {Reconstruction of Active Regular Motion in Amoeba Extract: Dynamic Cooperation between Sol and Gel States.},
journal = {PloS ONE},
year = {2013},
volume = {8},
number = {8},
url = {http://ci.nii.ac.jp/naid/120005312151/},
doi = {10.1371/journal.pone.0070317}
}
|
| Ohmae E, Miyashita Y, Tate S-I, Gekko K, Kitazawa S, Kitahara R and Kuwajima K (2013), "Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: Comparison of wild-type protein and active-site mutant D27E ", Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. Vol. 1834(12), pp. 2782 - 2794. |
| Abstract: Abstract To investigate the contribution of solvent environments to the enzymatic function of Escherichia coli dihydrofolate reductase (DHFR), the salt-, pH-, and pressure-dependence of the enzymatic function of the wild-type protein were compared with those of the active-site mutant D27E in relation to their structure and stability. The salt concentration-dependence of enzymatic activity indicated that inorganic cations bound to and inhibited the activity of wild-type DHFR at neutral pH. The BaCl2 concentration-dependence of the 1H–15N HSQC spectra of the wild-type DHFR–folate binary complex showed that the cation-binding site was located adjacent to the Met20 loop. The insensitivity of the D27E mutant to univalent cations, the decreased optimal pH for its enzymatic activity, and the increased Km and Kd values for its substrate dihydrofolate suggested that the substrate-binding cleft of the mutant was slightly opened to expose the active-site side chain to the solvent. The marginally increased fluorescence intensity and decreased volume change due to unfolding of the mutant also supported this structural change or the modified cavity and hydration. Surprisingly, the enzymatic activity of the mutant increased with pressurization up to 250 MPa together with negative activation volumes of − 4.0 or − 4.8 mL/mol, depending on the solvent system, while that of the wild-type was decreased and had positive activation volumes of 6.1 or 7.7 mL/mol. These results clearly indicate that the insertion of a single methylene at the active site could substantially change the enzymatic reaction mechanism of DHFR, and solvent environments play important roles in the function of this enzyme. |
BibTeX:
@article{Ohmae2013,
author = {Eiji Ohmae and Yurina Miyashita and Shin-Ichi Tate and Kunihiko Gekko and Soichiro Kitazawa and Ryo Kitahara and Kunihiro Kuwajima},
title = {Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: Comparison of wild-type protein and active-site mutant D27E },
journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
year = {2013},
volume = {1834},
number = {12},
pages = {2782 - 2794},
url = {http://www.sciencedirect.com/science/article/pii/S1570963913003592},
doi = {10.1016/j.bbapap.2013.09.024}
}
|
| Okazaki H, Ohori Y, Komoto M, Lee Y-H, Goto Y, Tochio N and Nishimura C (2013), "Remaining structures at the N- and C-terminal regions of alpha-synuclein accurately elucidated by amide-proton exchange NMR with fitting ", FEBS Letters . Vol. 587(22), pp. 3709 - 3714. |
| Abstract: Abstract Alpha-synuclein is analyzed in physiological conditions by CLEANEX-PM methodology, in which the amide-proton exchange can be monitored at millisecond scale. The relationship between kex and [OH]− is confirmed as a linear correlation with slope 1, indicating EX2 regime. There are significant residual structures at the N- and C-terminal regions. The structure at the C-terminal region is more stable than that of the N-terminal region. The middle part including NAC region is not completely protected. The data acquired at various pH and mixing time conditions followed by linear fitting give accurate information about residual structures. |
BibTeX:
@article{Okazaki2013,
author = {Honoka Okazaki and Yuka Ohori and Masaya Komoto and Young-Ho Lee and Yuji Goto and Naoya Tochio and Chiaki Nishimura},
title = {Remaining structures at the N- and C-terminal regions of alpha-synuclein accurately elucidated by amide-proton exchange NMR with fitting },
journal = {FEBS Letters },
year = {2013},
volume = {587},
number = {22},
pages = {3709 - 3714},
url = {http://www.sciencedirect.com/science/article/pii/S0014579313007345},
doi = {10.1016/j.febslet.2013.09.039}
}
|
| Oulhen N, Yoshida T, Yajima M, Song JL, Sakuma T, Sakamoto N, Yamamoto T and Wessel GM (2013), "The 3′UTR of nanos2 directs enrichment in the germ cell lineage of the sea urchin ", Developmental Biology . Vol. 377(1), pp. 275 - 283. |
| Abstract: Nanos is a translational regulator required for the survival and maintenance of primordial germ cells during embryogenesis. Three nanos homologs are present in the genome of the sea urchin Strongylocentrotus purpuratus (Sp), and each nanos mRNA accumulates specifically in the small micromere (sMic) lineage. We found that a highly conserved element in the 3′ UTR of nanos2 is sufficient for reporter expression selectively in the sMic lineage: microinjection into a Sp fertilized egg of an RNA that contains the GFP open reading frame followed by Sp nanos2 3′UTR leads to selective reporter enrichment in the small micromeres in blastulae. The same result was seen with nanos2 from the sea urchin Hemicentrotus pulcherrimus (Hp). In both species, the 5′UTR alone is not sufficient for the sMic localization but it always increased the sMic reporter enrichment when present with the 3′UTR. We defined an element conserved between Hp and Sp in the nanos2 3′UTR which is necessary and sufficient for protein enrichment in the sMic, and refer to it as GNARLE (Global Nanos Associated RNA Lability Element). We also found that the nanos2 3′UTR is essential for the selective RNA retention in the small micromeres; GNARLE is required but not sufficient for this process. These results show that a combination of selective RNA retention and translational control mechanisms instills nanos accumulation uniquely in the sMic lineage. |
BibTeX:
@article{Oulhen2013,
author = {Nathalie Oulhen and Takaya Yoshida and Mamiko Yajima and Jia L. Song and Tetsushi Sakuma and Naoaki Sakamoto and Takashi Yamamoto and Gary M. Wessel},
title = {The 3′UTR of nanos2 directs enrichment in the germ cell lineage of the sea urchin },
journal = {Developmental Biology },
year = {2013},
volume = {377},
number = {1},
pages = {275 - 283},
url = {http://www.sciencedirect.com/science/article/pii/S0012160613000377},
doi = {10.1016/j.ydbio.2013.01.019}
}
|
| Sakogawa K, Aoki Y, Misumi K, Hamai Y, Emi M, Hihara J, Shi L, Kono K, Horikoshi Y, Sun J, Ikura T, Okada M and Tashiro S (2013), "Involvement of homologous recombination in the synergism between cisplatin and poly (ADP-ribose) polymerase inhibition", Cancer Science. Vol. 104(12), pp. 1593-1599. |
| Abstract: Poly (ADP-ribose) polymerase (PARP) plays a critical role in responding to DNA damage, by activating DNA repair pathways responsible for cellular survival. Inhibition of PARP is used to treat certain solid cancers, such as breast and ovarian cancers. However, its effectiveness with other solid cancers, such as esophageal squamous cell carcinoma (ESCC), has not been clarified. We evaluated the effects of PARP inhibition on the survival of human esophageal cancer cells, with a special focus on the induction and repair of DNA double-strand breaks. The effects were monitored by colony formation assays and DNA damage responses, with immunofluorescence staining of γH2AX and RAD51. We found that PARP inhibition synergized with cisplatin, and the cells were highly sensitive, in a similar manner to the combination of cisplatin and 5-fluorouracil (5-FU). Comparable increases in RAD51 foci formation were observed after each combined treatment with cisplatin and either 3-aminobenzamide (3-AB) or 5-FU in three human esophageal cancer cell lines, TE11, TE14, and TE15. In addition, decreasing the amount of RAD51 by RNA interference rendered the TE11 cells even more hypersensitive to these treatments. Our findings suggested that the homologous recombinational repair pathway may be involved in the synergism between cisplatin and either 3-AB or 5-FU, and that 3-AB and 5-FU may similarly modify the cisplatin-induced DNA damage to types requiring the recruitment of RAD51 proteins for their repair. Understanding these mechanisms could be useful for improving the clinical outcome of ESCC patients who suffer from aggressive disease that presently lacks effective treatment options. |
BibTeX:
@article{Sakogawa2013,
author = {Sakogawa, Kenji and Aoki, Yoshiro and Misumi, Keizo and Hamai, Yoichi and Emi, Manabu and Hihara, Jun and Shi, Lin and Kono, Kazuteru and Horikoshi, Yasunori and Sun, Jiying and Ikura, Tsuyoshi and Okada, Morihito and Tashiro, Satoshi},
title = {Involvement of homologous recombination in the synergism between cisplatin and poly (ADP-ribose) polymerase inhibition},
journal = {Cancer Science},
year = {2013},
volume = {104},
number = {12},
pages = {1593--1599},
url = {http://dx.doi.org/10.1111/cas.12281},
doi = {10.1111/cas.12281}
}
|
| Sakuma T, Hosoi S, Woltjen K, Suzuki K-I, Kashiwagi K, Wada H, Ochiai H, Miyamoto T, Kawai N, Sasakura Y, Matsuura S, Okada Y, Kawahara A, Hayashi S and Yamamoto T (2013), "Efficient TALEN construction and evaluation methods for human cell and animal applications", Genes to Cells. Vol. 18(4), pp. 315-326. |
| Abstract: Transcription activator–like effector nucleases (TALENs) have recently arisen as effective tools for targeted genome engineering. Here, we report streamlined methods for the construction and evaluation of TALENs based on the ‘Golden Gate TALEN and TAL Effector Kit’ (Addgene). We diminished array vector requirements and increased assembly rates using six-module concatemerization. We altered the architecture of the native TALEN protein to increase nuclease activity and replaced the final destination vector with a mammalian expression/in vitro transcription vector bearing both CMV and T7 promoters. Using our methods, the whole process, from initiating construction to completing evaluation directly in mammalian cells, requires only 1 week. Furthermore, TALENs constructed in this manner may be directly applied to transfection of cultured cells or mRNA synthesis for use in animals and embryos. In this article, we show genomic modification of HEK293T cells, human induced pluripotent stem cells, Drosophila melanogaster, Danio rerio and Xenopus laevis, using custom-made TALENs constructed and evaluated with our protocol. Our methods are more time efficient compared with conventional yeast-based evaluation methods and provide a more accessible and effective protocol for the application of TALENs in various model organisms. |
BibTeX:
@article{Sakuma2013a,
author = {Sakuma, Tetsushi and Hosoi, Sayaka and Woltjen, Knut and Suzuki, Ken-Ichi and Kashiwagi, Keiko and Wada, Housei and Ochiai, Hiroshi and Miyamoto, Tatsuo and Kawai, Narudo and Sasakura, Yasunori and Matsuura, Shinya and Okada, Yasushi and Kawahara, Atsuo and Hayashi, Shigeo and Yamamoto, Takashi},
title = {Efficient TALEN construction and evaluation methods for human cell and animal applications},
journal = {Genes to Cells},
year = {2013},
volume = {18},
number = {4},
pages = {315--326},
url = {http://dx.doi.org/10.1111/gtc.12037},
doi = {10.1111/gtc.12037}
}
|
| Sakuma T, Ochiai H, Kaneko T, Mashimo T, Tokumasu D, Sakane Y, Suzuki K-I, Miyamoto T, Sakamoto N, Matsuura S and Yamamoto T (2013), "Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity", Sci. Rep.., Nov, 2013. Vol. 3 Nature Publishing Group. |
| Abstract: Transcription activator-like effector (TALE) nuclease (TALEN) is a site-specific nuclease, which can be freely designed and easily constructed. Numerous methods of constructing TALENs harboring different TALE scaffolds and repeat variants have recently been reported. However, the functionalities of structurally different TALENs have not yet been compared. Here, we report on the functional differences among several types of TALENs targeting the same loci. Using HEK293T cell-based single-strand annealing and Cel-I nuclease assays, we found that TALENs with periodically-patterned repeat variants harboring non-repeat-variable di-residue (non-RVD) variations (Platinum TALENs) showed higher activities than TALENs without non-RVD variations. Furthermore, the efficiencies of gene disruption mediated by Platinum TALENs in frogs and rats were significantly higher than in previous reports. This study therefore demonstrated an efficient system for the construction of these highly active Platinum TALENs (Platinum Gate system), which could establish a new standard in TALEN engineering. |
BibTeX:
@article{Sakuma2013b,
author = {Sakuma, Tetsushi and Ochiai, Hiroshi and Kaneko, Takehito and Mashimo, Tomoji and Tokumasu, Daisuke and Sakane, Yuto and Suzuki, Ken-Ichi and Miyamoto, Tatsuo and Sakamoto, Naoaki and Matsuura, Shinya and Yamamoto, Takashi},
title = {Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity},
journal = {Sci. Rep.},
publisher = {Nature Publishing Group},
year = {2013},
volume = {3},
url = {http://dx.doi.org/10.1038/srep03379},
doi = {10.1038/srep03379}
}
|
| Sekiya R, Yamasaki Y, Katayama S, Shio H and Haino T (2013), "Head-to-tail polymeric columnar structure of calix[4]arene possessing catechol arms in the solid state", CrystEngComm. Vol. 15, pp. 8404-8407. The Royal Society of Chemistry. |
| Abstract: Calix[4]arene 1 cocrystallized with methanol (MeOH), ethanol (EtOH), isopropanol (iPrOH) and 1,4-butanediol (BDO) to afford clathrate compounds 1[middle dot](MeOH)4, 1[middle dot](EtOH)4, 1[middle dot](iPrOH)4, and 1[middle dot](BDO)2, respectively. The unique head-to-tail polymeric columnar structures of 1 were found in the solid state. |
BibTeX:
@article{Sekiya2013,
author = {Sekiya, Ryo and Yamasaki, Yutaro and Katayama, Susumu and Shio, Hidemi and Haino, Takeharu},
title = {Head-to-tail polymeric columnar structure of calix[4]arene possessing catechol arms in the solid state},
journal = {CrystEngComm},
publisher = {The Royal Society of Chemistry},
year = {2013},
volume = {15},
pages = {8404-8407},
url = {http://dx.doi.org/10.1039/C3CE41660G},
doi = {10.1039/C3CE41660G}
}
|
| Shima H, Suzuki H, Sun J, Kono K, Shi L, Kinomura A, Horikoshi Y, Ikura T, Ikura M, Kanaar R, Igarashi K, Saitoh H, Kurumizaka H and Tashiro S (2013), "Activation of the SUMO modification system is required for the accumulation of RAD51 at sites of DNA damage", Journal of Cell Science. Vol. 126(22), pp. 5284-5292. |
| Abstract: Genetic information encoded in chromosomal DNA is challenged by intrinsic and exogenous sources of DNA damage. DNA double-strand breaks (DSBs) are extremely dangerous DNA lesions. RAD51 plays a central role in homologous DSB repair, by facilitating the recombination of damaged DNA with intact DNA in eukaryotes. RAD51 accumulates at sites containing DNA damage to form nuclear foci. However, the mechanism of RAD51 accumulation at sites of DNA damage is still unclear. Post-translational modifications of proteins, such as phosphorylation, acetylation and ubiquitylation play a role in the regulation of protein localization and dynamics. Recently, the covalent binding of small ubiquitin-like modifier (SUMO) proteins to target proteins, termed SUMOylation, at sites containing DNA damage has been shown to play a role in the regulation of the DNA-damage response. Here, we show that the SUMOylation E2 ligase UBC9, and E3 ligases PIAS1 and PIAS4, are required for RAD51 accretion at sites containing DNA damage in human cells. Moreover, we identified a SUMO-interacting motif (SIM) in RAD51, which is necessary for accumulation of RAD51 at sites of DNA damage. These findings suggest that the SUMO–SIM system plays an important role in DNA repair, through the regulation of RAD51 dynamics. |
BibTeX:
@article{Shima2013,
author = {Shima, Hiroki and Suzuki, Hidekazu and Sun, Jiying and Kono, Kazuteru and Shi, Lin and Kinomura, Aiko and Horikoshi, Yasunori and Ikura, Tsuyoshi and Ikura, Masae and Kanaar, Roland and Igarashi, Kazuhiko and Saitoh, Hisato and Kurumizaka, Hitoshi and Tashiro, Satoshi},
title = {Activation of the SUMO modification system is required for the accumulation of RAD51 at sites of DNA damage},
journal = {Journal of Cell Science},
year = {2013},
volume = {126},
number = {22},
pages = {5284-5292},
url = {http://jcs.biologists.org/content/126/22/5284.abstract},
doi = {10.1242/jcs.133744}
}
|
| Shimahara H, Hirano T, Ohya K, Matsuta S, Seeram SS and Tate S-I (2013), "Nucleosome structural changes induced by binding of non-histone chromosomal proteins HMGN1 and HMGN2 ", FEBS Open Bio. Vol. 3(0), pp. 184 - 191. |
| Abstract: Abstract Interactions between the nucleosome and the non-histone chromosomal proteins (HMGN1 and HMGN2) were studied by circular dichroism (CD) spectroscopy to elucidate structural changes in the nucleosome induced by HMGN binding. Unlike previous studies that used a nucleosome extracted from living cells, in this study we utilized a nucleosome reconstituted from unmodified recombinant histones synthesized in Escherichia coli and a 189-bp synthetic DNA fragment harboring a nucleosome positioning sequence. This DNA fragment consists of 5′-TATAAACGCC-3′ repeats that has a high affinity to the histone octamer. A nucleosome containing a unique octamer-binding sequence at a specific location on the DNA was produced at sufficiently high yield for spectroscopic analysis. CD data have indicated that both HMGN1 and HMGN2 can increase the winding angle of the nucleosome DNA, but the extent of the structural changes induced by these proteins differs significantly. This suggests HMGN1 and HMGN2 would have different abilities to facilitate nucleosome remodeling. |
BibTeX:
@article{Shimahara2013,
author = {Hideto Shimahara and Takaaki Hirano and Kouichi Ohya and Shun Matsuta and Sailaja S. Seeram and Shin-Ichi Tate},
title = {Nucleosome structural changes induced by binding of non-histone chromosomal proteins HMGN1 and HMGN2 },
journal = {FEBS Open Bio},
year = {2013},
volume = {3},
number = {0},
pages = {184 - 191},
url = {http://www.sciencedirect.com/science/article/pii/S221154631300017X},
doi = {10.1016/j.fob.2013.03.002}
}
|
| Sogawa H, Shiotsuki M, Hirao T, Haino T and Sanda F (2013), "Synthesis of Optically Active Poly(m-phenyleneethynylene–aryleneethynylene)s Bearing Hydroxy Groups and Examination of the Higher Order Structures", Macromolecules. Vol. 46(20), pp. 8161-8170. |
| Abstract: Novel optically active poly(m-phenyleneethynylene–aryleneethynylene)s bearing hydroxy groups with various arylene units poly[(S)-/(R)-1–3a]–poly[(R)-1–3e] and poly[(S)-2–3a] were synthesized by the Sonogashira–Hagihara coupling polymerization of 3,5-diiodo-4-hydroxy-C6H4CONHCH(CH3)COXC12H25 [(S)-/(R)-1 (X = O), (S)-2 (X = NH)] with HC≡C–Ar–C≡CH [3a (Ar = 1,4-C6H4), 3b (Ar = 1,4-C6H4-1,4-C6H4−), 3c (Ar = 1,4-C6H4-1,4-C6H4-1,4-C6H4−), 3d (Ar = 2,5-dihexyl-1,4-C6H2), 3e (Ar = 2,5-didodecyl-1,4-C6H2)]. The yields and number-average molecular weights of the polymers were in the ranges 60–94% and 7,000–29,500 with no correlation between the yield and the Mn. Circular dichroism (CD), UV–vis, and fluorescence spectroscopic analyses indicated that poly[(S)-1–3a]–poly[(S)-1–3c] and poly[(S)-2–3a] formed predominantly one-handed helical structures in THF, while poly[(S)-1–3d] and poly[(S)-1–3e] showed no evidence for forming chirally ordered structures. All polymers emitted blue fluorescence. The solution state IR measurement revealed the presence of intramolecular hydrogen bonding between the amide groups at the side chains of poly[(S)-1–2a]. The helical structures and helix-forming abilities of the polymers were analyzed by the molecular mechanics (MM), semiempirical molecular orbital (MO) and density functional theory (DFT) methods. Tube-like structures, presumably formed by perpendicular aggregation of the helical polymers, were observed by atomic force microscopy (AFM). |
BibTeX:
@article{Sogawa2013,
author = {Sogawa, Hiromitsu and Shiotsuki, Masashi and Hirao, Takehiro and Haino, Takeharu and Sanda, Fumio},
title = {Synthesis of Optically Active Poly(m-phenyleneethynylene–aryleneethynylene)s Bearing Hydroxy Groups and Examination of the Higher Order Structures},
journal = {Macromolecules},
year = {2013},
volume = {46},
number = {20},
pages = {8161-8170},
url = {http://pubs.acs.org/doi/abs/10.1021/ma4017295},
doi = {10.1021/ma4017295}
}
|
| Suzuki K-IT, Isoyama Y, Kashiwagi K, Sakuma T, Ochiai H, Sakamoto N, Furuno N, Kashiwagi A and Yamamoto T (2013), "High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos", Biology Open. Vol. 2(5), pp. 448-452. |
| Abstract: Recently, gene editing with transcription activator-like effector nucleases (TALENs) has been used in the life sciences. TALENs can be easily customized to recognize a specific DNA sequence and efficiently introduce double-strand breaks at the targeted genomic locus. Subsequent non-homologous end-joining repair leads to targeted gene disruption by base insertion, deletion, or both. Here, to readily evaluate the efficacy of TALENs in Xenopus laevis embryos, we performed the targeted gene disruption of tyrosinase (tyr) and pax6 genes that are involved in pigmentation and eye formation, respectively. We constructed TALENs targeting tyr and pax6 and injected their mRNAs into fertilized eggs at the one-cell stage. Expectedly, introduction of tyr TALEN mRNA resulted in drastic loss of pigmentation with high efficiency. Similarly, for pax6, TALENs led to deformed eyes in the injected embryos. We confirmed mutations of the target alleles by restriction enzyme digestion and sequence analyses of genomic PCR products. Surprisingly, not only biallelic but also paralogous, gene disruption was observed. Our results demonstrate that targeted gene disruption by TALENs provides a method comparable to antisense morpholinos in analyzing gene function in Xenopus F0 embryos, but also applies beyond embryogenesis to any life stage. |
BibTeX:
@article{Suzuki2013,
author = {Suzuki, Ken-Ichi T. and Isoyama, Yukiko and Kashiwagi, Keiko and Sakuma, Tetsushi and Ochiai, Hiroshi and Sakamoto, Naoaki and Furuno, Nobuaki and Kashiwagi, Akihiko and Yamamoto, Takashi},
title = {High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos},
journal = {Biology Open},
year = {2013},
volume = {2},
number = {5},
pages = {448-452},
url = {http://bio.biologists.org/content/2/5/448.abstract},
doi = {10.1242/bio.20133855}
}
|
| Uewaki J-I, Kamikubo H, Kurita J-I, Hiroguchi N, Moriuchi H, Yoshida M, Kataoka M, Utsunomiya-Tate N and Tate S-I (2013), "Preferential domain orientation of HMGB2 determined by the weak intramolecular interactions mediated by the interdomain linker", Chemical Physics. Vol. 419, pp. 212 - 223. |
| Abstract: Abstract High mobility group box protein 2 (HMGB2) contains homologous tandem HMG box DNA-binding domains, boxes A and B. These two boxes are linked by a short basic linker having a sequence characteristic of an intrinsically disordered element. The combined use of NMR and small angle X-ray scattering (SAXS) showed that the two boxes assume a preferred orientation to make their DNA binding surface in opposite directions, although the linker does not keep any specific conformation. A series of site directed mutations to the residues in the linker showed that a network of CH-π interactions connects the N-terminal part of the linker to box A. The mutants having impaired intramolecular CH-π interactions changed the interdomain dynamics and their dynamic averaged orientation relative to the wild-type. This work demonstrates that the apparently unstructured linker plays a role in defining the preferential domain orientation through the intramolecular CH-π interactions, even though the interactions are weak and transient. |
BibTeX:
@article{Uewaki2013212,
author = {Uewaki, Jun-Ichi and Hironari Kamikubo and Kurita, Jun-Ichi and Noriteru Hiroguchi and Hiroshi Moriuchi and Michiteru Yoshida and Mikio Kataoka and Naoko Utsunomiya-Tate and Tate, Shin-Ichi},
title = {Preferential domain orientation of HMGB2 determined by the weak intramolecular interactions mediated by the interdomain linker},
journal = {Chemical Physics},
year = {2013},
volume = {419},
pages = {212 - 223},
note = {Supra Functional System},
url = {http://www.sciencedirect.com/science/article/pii/S0301010413000840},
doi = {10.1016/j.chemphys.2013.02.004}
}
|
| Wang J, Tochio N, Takeuchi A, Uewaki J-I, Kobayashi N and Tate S-I (2013), "Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA", Biochemical and Biophysical Research Communications. Vol. 441(4), pp. 701 - 706. |
| Abstract: Abstract HMGB1 (high-mobility group B1) is a ubiquitously expressed bifunctional protein that acts as a nuclear protein in cells and also as an inflammatory mediator in the extracellular space. HMGB1 changes its functions according to the redox states in both intra- and extra-cellular environments. Two cysteines, Cys23 and Cys45, in the A-domain of HMGB1 form a disulfide bond under oxidative conditions. The A-domain with the disulfide bond shows reduced affinity to cisplatin modified DNA. We have solved the oxidized A-domain structure by NMR. In the structure, Phe38 has a flipped ring orientation from that found in the reduced form; the phenyl ring in the reduced form intercalates into the platinated lesion in DNA. The phenyl ring orientation in the oxidized form is stabilized through intramolecular hydrophobic contacts. The reorientation of the Phe38 ring by the disulfide bond in the A-domain may explain the reduced HMGB1 binding affinity towards cisplatinated DNA. |
BibTeX:
@article{Wang2013,
author = {Jing Wang and Naoya Tochio and Aya Takeuchi and Jun-Ichi Uewaki and Naohiro Kobayashi and Shin-Ichi Tate},
title = {Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA},
journal = {Biochemical and Biophysical Research Communications},
year = {2013},
volume = {441},
number = {4},
pages = {701 - 706},
url = {http://www.sciencedirect.com/science/article/pii/S0006291X1301766X},
doi = {10.1016/j.bbrc.2013.10.085}
}
|
| 荻原 悠佑, 秋野 順治 and 西森 拓 (2013), "アリの集団採餌における方位情報の選択と切り替え", 計測と制御., mar, 2013. Vol. 52(3), pp. 201-206. 計測自動制御学会.
[BibTeX] |
BibTeX:
@article{Nishimori2013,
author = {荻原 悠佑 and 秋野 順治 and 西森 拓},
title = {アリの集団採餌における方位情報の選択と切り替え},
journal = {計測と制御},
publisher = {計測自動制御学会},
year = {2013},
volume = {52},
number = {3},
pages = {201-206}
}
|
| 佐久間 哲史, 鈴木 賢一 and 坂本 尚昭 (2013), "TALENの効率的な作製と動物個体への応用", In 細胞工学. Vol. 32(5), pp. 510-514. 学研メディカル秀潤社.
[BibTeX] |
BibTeX:
@incollection{Sakamoto2013,
author = {佐久間 哲史 and 鈴木 賢一 and 坂本 尚昭},
title = {TALENの効率的な作製と動物個体への応用},
booktitle = {細胞工学},
publisher = {学研メディカル秀潤社},
year = {2013},
volume = {32},
number = {5},
pages = {510-514}
}
|
| 坂本 尚昭 and 山本 卓 (2013), "棘皮動物のウニ", 生物工学会誌., aug, 2013. Vol. 91(8), pp. 473-476. 公益社団法人日本生物工学会.
[BibTeX] |
BibTeX:
@article{SakamotoYamamoto2013,
author = {坂本 尚昭 and 山本 卓},
title = {棘皮動物のウニ},
journal = {生物工学会誌},
publisher = {公益社団法人日本生物工学会},
year = {2013},
volume = {91},
number = {8},
pages = {473-476}
}
|
| 西森 拓 (2013), "生物系の自己組織化", In 応用数理ハンドブック.
[BibTeX] |
BibTeX:
@incollection{Nishimori2013a,
author = {西森 拓},
title = {生物系の自己組織化},
booktitle = {応用数理ハンドブック},
year = {2013}
}
|
| 西森 拓 (2013), "アリのＹ路実験", In 行動生物学辞典. 東京化学同人.
[BibTeX] |
BibTeX:
@incollection{Nishimori2013b,
author = {西森 拓},
title = {アリのＹ路実験},
booktitle = {行動生物学辞典},
publisher = {東京化学同人},
year = {2013}
}
|
| 西森 拓 (2013), "生物集団の現象数理", In 現象数理学入門. 東京大学出版会.
[BibTeX] |
BibTeX:
@incollection{Nishimori2013c,
author = {西森 拓},
title = {生物集団の現象数理},
booktitle = {現象数理学入門},
publisher = {東京大学出版会},
year = {2013}
}
|
| 落合 博, 柴田 達夫 and 山本 卓 (2013), "ゲノム編集技術を用いた遺伝子発現の定量的イメージング", In 細胞工学. Vol. 32(5), pp. 538-542. 学研メディカル秀潤社.
[BibTeX] |
BibTeX:
@incollection{OchiaiYamamoto2013,
author = {落合 博 and 柴田 達夫 and 山本 卓},
title = {ゲノム編集技術を用いた遺伝子発現の定量的イメージング},
booktitle = {細胞工学},
publisher = {学研メディカル秀潤社},
year = {2013},
volume = {32},
number = {5},
pages = {538-542}
}
|
研究成果公開
（1）数理モデルグループ 准教授 粟津 暁紀による、ヌクレオソーム形成・排他配列を推定するアルゴリズム論文で提案している方法を実装した、Excelシートを公開しています。
-> Excelシートダウンロード用ページ (predictors)
論文：Awazu A, Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition,
Bioinfomatics (2016) DOI 10.1093/bioinformatics/btw562.
謝辞の記載について
クロマチン動態数理研究拠点でサポートされた研究において、論文発表・学会発表・プレス発表・メディア対応等をされる際には、下記のとおり謝辞を掲載していただきますよう、よろしくお願いいたします。
日本語文
本研究は国立研究開発法人 日本医療研究開発機構 創薬等ライフサイエンス研究支援基盤事業（生命動態システム科学推進拠点事業）「核内クロマチン・ライブダイナミクスの数理研究拠点形成」の助成を受けたものです。
英語文
（1）〜H26年度（MEXT事業）までの成果については「MEXTのみ」
This research is (partially) supported
by the Platform Project for Supporting in Drug Discovery and Life Science Research
(Platform for Dynamic Approaches to Living System)
from the Ministry of Education, Culture, Sports, Science and Technology (MEXT).
（2）〜H26年度（MEXT事業）及びH27年度〜（AMED事業）にまたがる成果については「MEXT及びAMED」
This research is (partially) supported
by the Platform Project for Supporting in Drug Discovery and Life Science Research
(Platform for Dynamic Approaches to Living System)
from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
and Japan Agency for Medical Research and Development (AMED).
（3）H27年度〜（AMED事業）における成果については「AMEDのみ」
This research is (partially) supported by
the Platform Project for Supporting in Drug Discovery and Life Science Research
(Platform for Dynamic Approaches to Living System)
from Japan Agency for Medical Research and Development (AMED).