Analysis of the Brownian Motion by Elementary School Students

To stimulate the intellectual curiosity of elementary school students, we conducted a workshop in distance education aimed at exploring the microscopic world inside a cell. In this workshop, elementary school students motivated to learn more on the subject of science analyzed movies of the Brownian motion of micrometer-sized particles suspended in water, using an open-source software, Tracker. These students then performed two-dimensional(2D)-random walk experiments using a dice game sheet to examine the physical mechanism of Brownian motion. After the workshop, we conducted a questionnaire-based survey. Many participants answered that the contents were difficult but interesting, suggesting that our workshop was very efficient to stimulate the curiosity of motivated students.Comment: 16 pages, 10 figures, the following article has been submitted to The Physics Teache

Geometric trade-off between contractile force and viscous drag determines the actomyosin-based motility of a cell-sized droplet

動きまわる人工細胞、その鍵は摩擦にあり --細胞が狭い空間を利用して運動する仕組みを解明--. 京都大学プレスリリース. 2022-07-21.Cell migration in confined environments is fundamental for diverse biological processes from cancer invasion to leukocyte trafficking. The cell body is propelled by the contractile force of actomyosin networks transmitted from the cell membrane to the external substrates. However, physical determinants of actomyosin-based migration capacity in confined environments are not fully understood. Here, we develop an in vitro migratory cell model, where cytoplasmic actomyosin networks are encapsulated into droplets surrounded by a lipid monolayer membrane. We find that the droplet can move when the actomyosin networks are bound to the membrane, in which the physical interaction between the contracting actomyosin networks and the membrane generates a propulsive force. The droplet moves faster when it has a larger contact area with the substrates, while narrower confinement reduces the migration speed. By combining experimental observations and active gel theory, we propose a mechanism where the balance between sliding friction force, which is a reaction force of the contractile force, and viscous drag determines the migration speed, providing a physical basis of actomyosin-based motility in confined environments

Microscopic Temperature Control Reveals Cooperative Regulation of Actin–Myosin Interaction by Drebrin E

胎児の神経を形作る仕組みは精密な温度センサー --母体の体温維持が神経の成熟に重要であることを示唆--. 京都大学プレスリリース. 2021-11-10.Drebrin E is a regulatory protein of intracellular force produced by actomyosin complexes, that is, myosin molecular motors interacting with actin filaments. The expression level of drebrin E in nerve cells decreases as the animal grows, suggesting its pivotal but unclarified role in neuronal development. Here, by applying the microscopic heat pulse method to actomyosin motility assay, the regulatory mechanism is examined from the room temperature up to 37 °C without a thermal denaturing of proteins. We show that the inhibition of actomyosin motility by drebrin E is eliminated immediately and reversibly during heating and depends on drebrin E concentration. The direct observation of quantum dot-labeled drebrin E implies its stable binding to actin filaments during the heat-induced sliding. Our results suggest that drebrin E allosterically modifies the actin filament structure to regulate cooperatively the actomyosin activity at the maintained in vivo body temperature

Bayesian estimation of the internal structure of proteins from single-molecule measurements

In single-molecule protein experiments, the observable variables are restricted within a small fraction of the entire degrees of freedom. Therefore, to investigate the physical nature of proteins in detail, we always need to estimate the hidden internal structure referring only to the accessible degrees of freedom. We formulate this problem on the basis of Bayesian inference, which can be applied to various complex systems. In the ideal case, we find that in general the framework actually works. Although careful numerical studies confirm that our method outperforms the conventional method by up to two orders of magnitude, we find a striking phenomenon: a loss-of-precision transition occurs abruptly when the design of the observation system is inappropriate. The basic features of the proposed method are illustrated using a simple but nontrivial model

ランジュバン系に対するベイズ推定 : タンパク質の粗視化モデルを一分子時系列から構築する

京都大学0048新制・課程博士博士(理学)甲第15855号理博第3596号新制||理||1524(附属図書館)28434京都大学大学院理学研究科物理学・宇宙物理学専攻(主査)教授 吉川 研一, 教授 太田 隆夫, 教授 小貫 明学位規則第4条第1項該当Doctor of ScienceKyoto UniversityDA

Go-and-Back method: effective estimation of the hidden motion of proteins from single-molecule time series.

We present an effective method for estimating the motion of proteins from the motion of attached probe particles in single-molecule experiments. The framework naturally incorporates Langevin dynamics to compute the most probable trajectory of the protein. By using a perturbation expansion technique, we achieve computational costs more than 3 orders of magnitude smaller than the conventional gradient descent method without loss of simplicity in the computation algorithm. We present illustrative applications of the method using simple models of single-molecule experiments and confirm that the proposed method yields reasonable and stable estimates of the hidden motion in a highly efficient manner

Tug-of-war between actomyosin-driven antagonistic forces determines the positioning symmetry in cell-sized confinement

細胞内構造の配置対称性が決まる仕組みを解明 --人工細胞と物理学からメカニズムに迫る--. 京都大学プレスリリース. 2020-06-15.The tug-of-war at the heart of cellular symmetry. 京都大学プレスリリース. 2020-06-26.Symmetric or asymmetric positioning of intracellular structures including the nucleus and mitotic spindle steers various biological processes such as cell migration, division, and embryogenesis. In typical animal cells, both a sparse actomyosin meshwork in the cytoplasm and a dense actomyosin cortex underneath the cell membrane participate in the intracellular positioning. However, it remains unclear how these coexisting actomyosin structures regulate the positioning symmetry. To reveal the potential mechanism, we construct an in vitro model composed of cytoplasmic extracts and nucleus-like clusters confined in droplets. Here we find that periodic centripetal actomyosin waves contract from the droplet boundary push clusters to the center in large droplets, while network percolation of bulk actomyosin pulls clusters to the edge in small droplets. An active gel model quantitatively reproduces molecular perturbation experiments, which reveals that the tug-of-war between two distinct actomyosin networks with different maturation time-scales determines the positioning symmetry

Interleukin-17A and Neutrophils in a Murine Model of Bird-Related Hypersensitivity Pneumonitis.

Hypersensitivity pneumonitis (HP) is an immune mediated lung disease induced by the repeated inhalation of a wide variety of antigens. Bird-related hypersensitivity pneumonitis (BRHP) is one of the most common forms of HP in human and results from the inhalation of avian antigens. The findings of a recent clinical analysis suggest that in addition to Th1 factors, the levels of interleukin(IL)-17 and IL-17-associated transcripts are increased in the setting of HP, and that both IL-17A and neutrophils are crucial for the development of pulmonary inflammation in murine models of HP. Our objectives were to investigate the roles of IL-17A and neutrophils in granuloma-forming inflammation in an acute HP model. We developed a mouse model of acute BRHP using pigeon dropping extract. We evaluated the process of granuloma formation and the roles of both IL-17A and neutrophils in a model. We found that the neutralization of IL-17A by the antibody attenuated granuloma formation and the recruitment of neutrophils, and also decreased the expression level of chemokine(C-X-C motif) ligand 5 (CXCL5) in the acute HP model. We confirmed that most of the neutrophils in the acute HP model exhibited immunoreactivity to the anti-IL-17 antibody. We have identified the central roles of both IL-17A and neutrophils in the pathogenesis of granuloma formation in acute HP. We have also assumed that neutrophils are an important source of IL-17A in an acute HP model, and that the IL-17A-CXCL5 pathway may be responsible for the recruitment of neutrophils