Papers by Kenichi Yoshikawa
The Journal of Chemical Physics, 1995
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Chaos: An Interdisciplinary Journal of Nonlinear Science, 2010
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<p>Panel A): First row- frequency distribution (bin size = 0.1) of mRNAs (<i>n</i&... more <p>Panel A): First row- frequency distribution (bin size = 0.1) of mRNAs (<i>n</i> = 440 mRNAs) at 10 min shows a unimodal to bimodal change around critical point (0.090 <<i>nrmsf</i>< 0.092). The <i>x</i>-axis represents the natural log of mRNA expression, <i>ln</i>(<i>ε</i>(10min)) for a specific range of <i>nrmsf</i>: unimodal (left panel: 0.105 <<i>nrmsf</i>< 0.109), flattened unimodal (middle panel: 0.090 <<i>nrmsf</i>< 0.092), and bimodal (right panel: 0.084 <<i>nrmsf</i>< 0.086). The y-axis represents frequency of expression. Second row- the corresponding probability density profile in the regulatory space—expression vs. expression change in log scale with probability density (color bars) confirms the unimodal to bimodal transition through flattened unimodality, where a black arrow points to the bifurcation of low-expression state (LES). Panel B): First row—the frequency distribution of barcode genes (<i>n</i> = 182 barcodes) shows a unimodal to bimodal change around a critical point (0.108 <<i>nrmsf</i>< 0.112) for unimodal (left), flattened (middle) and bimodal (right) distributions. Second row—this is confirmed by probability density profile in the regulatory space. Both mRNAs and barcode genes on chromosomes reveal the existence of self-similar power law (scaling) behavior around CP analogous to that of the whole mRNA expression (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128565#pone.0128565.g001" target="_blank">Fig 1</a>), which is an essential characteristic of SOC.</p
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International Journal of Molecular Sciences, 2021
Polyamines are involved in various biological functions, including cell proliferation, differenti... more Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers on the activity of gene expression by adapting a cell-free luciferase assay. Interestingly, the potency of their effects on the DNA conformation and also on the inhibition of gene expression activity indicates the highest...
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Physical Review Letters, 2007
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Background A fundamental issue in bioscience is to understand the mechanism that underlies the dy... more Background A fundamental issue in bioscience is to understand the mechanism that underlies the dynamic control of genome-wide expression through the complex temporal-spatial self-organization of the genome to regulate the change in cell fate. We address this issue by elucidating a physically motivated mechanism of self-organization. Principal Findings Building upon transcriptome experimental data for seven distinct cell fates, including early embryonic development, we demonstrate that self-organized criticality (SOC) plays an essential role in the dynamic control of global gene expression regulation at both the population and single-cell levels. The novel findings are as follows: i) Mechanism of cell-fate changes: A sandpile-type critical transition self-organizes overall expression into a few transcription response domains (critical states). A cell-fate change occurs by means of a dissipative pulse-like global perturbation in self-organization through the erasure of initial-state c...
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Journal of Physical Chemistry C, 2008
ABSTRACT We report the vectorial transport of a material object to a desired location by chemical... more ABSTRACT We report the vectorial transport of a material object to a desired location by chemical waves generated in an excitable medium (Belousov-Zhabotinsky reaction). The transportation route is determined by the excitable waves induced at a certain point on the excitable medium. This study realized direct coupling between a chemical reaction and vectorial motion; such transduction of energy is generally found in biological motility but has been difficult to achieve in artificial model systems. We discuss the future possible application of these findings to the fabrication of a chemical machine that works under the self-management of motion in response to external stimuli.
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Physical Review E, 2008
We report the dynamical behavior of microm-sized phase separation for a homogeneous mixture of D2... more We report the dynamical behavior of microm-sized phase separation for a homogeneous mixture of D2O and 3-methylpyridine (3MP) induced under continuous photon-flux by a focused YAG laser. At a water-rich composition, stable rhythmic oscillation of the emergence-growth escape of a 3MP-rich droplet is generated. In contrast, at a near-critical composition, an emergent droplet exhibits significant nonequilibrium fluctuation. Such dynamic phenomena are interpreted in terms of the effect of a local dielectric field and a dissipative system generated by a focused laser on the binary mixture.
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To identify the optimum conditions for the optical trapping of a droplet under microgravity, we t... more To identify the optimum conditions for the optical trapping of a droplet under microgravity, we theoretically analyzed the eciency of trapping with counter laser beams. We found that the distance between the two foci is an important parameter for obtaining stable trapping conditions. We also performed an optical trapping experiment with counter laser beams under microgravity. The experimental results correspond well to the theoretical prediction. 1
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Department of Physics, Graduate School of Science,Kyoto University, Kyoto 606-8502, Japan(Dated: ... more Department of Physics, Graduate School of Science,Kyoto University, Kyoto 606-8502, Japan(Dated: February 2, 2008)Ten µm -sized droplets in an aqueous-two-phase system (water/ polyethylene-glycol (PEG)/ dex-tran) dissapear upon irradiation with a focused YAG laser. The interface of the dextran-rich dropletbroadens, indicating smoothing of the concentration profile, whereas, the PEG-rich droplet shrinksand disappears. These phenomena can be described in terms of the Ginzburg-Landau free energy,by considering the laser-induced dielectric potential.
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Phase separation of a mixture of charged and neutral lipids on a giant vesicle induced by small c... more Phase separation of a mixture of charged and neutral lipids on a giant vesicle induced by small cations
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The Journal of Physical Chemistry C
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DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and th... more DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus there have been many quantitative studies of DSBs both in vivo and in vitro [1–7]. Despite this fact, the processes that lead to their production have not yet been clearly understood, and there is no established theory that can account for the statistics of their production, in particular, the number of DSBs per base pair per unit Gy, here denoted by P1, which is the most important parameter for evaluating the degree of risk posed by DSBs. Here, using the single-molecule observation method with giant DNA molecules (166 kbp), we evaluate the number of DSBs caused by γ-ray irradiation. We find that P1 is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. A simple model that accounts for the marked decrease of P1 shows that it is necessary to consider the characteristics of giant DNA molecules as semiflexible polymers to interpret the intr...
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PLoS ONE, 2020
Background Polyamines are involved in a wide variety of biological processes including a marked e... more Background Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K+ enhanced in vitro gene expression in the presence of polyamine more strongly than Na+. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K+ and Na+. Principal findings It was found that K+ enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na+, through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na+ prevents the folding transition of DNA into a compact state more strongly than K+. 1H NMR measurement revealed that Na+ inhibits the binding of SPD to DNA more strongly than K+. Thus, SPD binds to DNA more favorably in K+-rich medium than in Na+-rich medium, which leads to favorable conditions...
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Polyamines are involved in various biological functions, including cell proliferation, differenti... more Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers on the activity of gene expression by adapting a cell-free luciferase assay. Interestingly, the potency of their effects on the DNA conformation and also on the inhibition of gene expression activity indicates the highest...
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Chemical Physics Letters, 2015
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arXiv: Biological Physics, 2006
We report that a cell-sized water droplet (CWD) with a diameter of several tens of microns can se... more We report that a cell-sized water droplet (CWD) with a diameter of several tens of microns can serve as a micro-biochemical reactor. Since the droplet inner surface is covered by a phospholipid layer, it provides an environment similar to that in living cells. The CWD is manipulated with laser tweezers and we monitor the time-development of biochemical reactions in a single CWD by fusing two droplets which contain a substrate and an enzyme, respectively. As actual examples of enzymatic reactions, we present results on the reaction of calcein with esterase and on the expression reaction of green fluorescent protein.
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Life (Basel, Switzerland), Jan 9, 2015
We report the spontaneous generation of a cell-like morphology in an environment crowded with the... more We report the spontaneous generation of a cell-like morphology in an environment crowded with the polymers dextran and polyethylene glycol (PEG) in the presence of DNA. DNA molecules were selectively located in the interior of dextran-rich micro-droplets, when the composition of an aqueous two-phase system (ATPS) was near the critical condition of phase-segregation. The resulting micro-droplets could be controlled by the use of optical tweezers. As an example of laser manipulation, the dynamic fusion of two droplets is reported, which resembles the process of cell division in time-reverse. A hypothetical scenario for the emergence of a primitive cell with DNA is briefly discussed.
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Polymers
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In general, bio-macromolecules are composed of hydrophilic and hydrophobic moieties and are confi... more In general, bio-macromolecules are composed of hydrophilic and hydrophobic moieties and are confined within small cavities, such as cell membranes and intracellular organelles. Here, we studied the self-organization of macromolecules having groups with different affinities to solvents under spherical nano-scale confinement by means of computer modeling. It is shown that depending on the interaction parameters of monomer units composed of side- and main-chain monomer groups along a single linear macromolecule and on cavity size, such amphiphilic polymers undergo the conformational transitions between hollow nanospheres, rod-like and folded cylindrical structures, and a necklace conformation with and without a particular ordering of beads. The diagram of the conformations in the variables the incompatibility parameter of monomer units and the cavity radius is constructed.
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Papers by Kenichi Yoshikawa