iTHEMS生物学セミナー

生物学に関連する様々なトピックを扱ったセミナーを定期的に開催しています。生物学と数学・物理学との境界を低くし、接点を見つけ出すことで、新しい学際的な研究のアイデアが生まれることを期待しています。

詳細はiTHEMS生物学セミナースタディーグループのページをご覧下さい。

セミナー

iTHEMS生物学セミナー

How to make a dataset for phylogeny and the background of mathematical theory

2021年9月9日10:00 - 11:00

矢﨑 裕規 (数理創造プログラム 特別研究員)

Molecular phylogenetic analysis is a very important method of analysis for understanding the evolution of organisms and so on. The method of molecular phylogenetic analysis itself is often discussed, and you are probably familiar with the background of the analysis. The dataset to be analyzed is just as important as the analysis method. However, it is not well known how the data set is made and what the methodology behind it is. Therefore, I will outline the background to the creation of data sets.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Journal Club: A quantitative quasispecies theory-based model of virus escape mutation under immune selection

2021年9月2日10:00 - 11:00

許 インイン (数理創造プログラム 基礎科学特別研究員)

I would like to introduce the paper "a quantitative quasispecies theory-based model of virus escape mutation under immune selection", written by Hyung-June Woo and Jaques Reifman [1]. Paper abstract: Viral infections involve a complex interplay of the immune response and escape mutation of the virus quasispecies inside a single host. Although fundamental aspects of such a balance of mutation and selection pressure have been established by the quasispecies theory decades ago, its implications have largely remained qualitative. Here, we present a quantitative approach to model the virus evolution under cytotoxic T-lymphocyte immune response. The virus quasispecies dynamics are explicitly represented by mutations in the combined sequence space of a set of epitopes within the viral genome. We stochastically simulated the growth of a viral population originating from a single wild-type founder virus and its recognition and clearance by the immune response, as well as the expansion of its genetic diversity. Applied to the immune escape of a simian immunodeficiency virus epitope, model predictions were quantitatively comparable to the experimental data. Within the model parameter space, we found two qualitatively different regimes of infectious disease pathogenesis, each representing alternative fates of the immune response: It can clear the infection in finite time or eventually be overwhelmed by viral growth and escape mutation. The latter regime exhibits the characteristic disease progression pattern of human immunodeficiency virus, while the former is bounded by maximum mutation rates that can be suppressed by the immune response. Our results demonstrate that, by explicitly representing epitope mutations and thus providing a genotype–phenotype map, the quasispecies theory can form the basis of a detailed sequence-specific model of real-world viral pathogens evolving under immune selection. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Mathematical analysis of body temperature fluctuation during hibernation

2021年8月26日10:00 - 11:00

黒澤 元 (数理創造プログラム 専任研究員)

Hibernation (tomin in Japanese) is a strategy for the organisms to survive in a severe season with limited food and water availability. During hibernation, the organisms drastically decrease their basal metabolisms, drop their body temperature (Tb) more than 10 degree, and become immobile. Interestingly, body temperature during hibernation does not remain constant at very low value, but greatly fluctuates with inconstant period of several days. Although there have been many studies about hibernation since the era of Aristotle, fundamental problems of hibernation remain elusive. Recently, we started to investigate Tb data during hibernation by using a method in acoustic engineering for the analysis of irregular time-series such as music. We succeeded in quantifying many individual data, and found that a simple model can reproduce well and forecast Tb data during hibernation. This is the collaboration with Yoshifumi Yamaguchi at Institute of Low Temperature Science, Hokkaido University and Shingo Gibo at iTHEMS.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

The damped circadian oscillator in cyanobacterium: kaiA-less oscillator

2021年8月19日10:00 - 11:00

河本 尚大 (大阪大学 太陽エネルギー化学研究センター 特任研究員)

Circadian clocks are conserved in almost all organisms and provide fitness advantages to their owners through scheduling biological processes at appropriate time of diurnal cycles. Cyanobacteria possess circadian clock genes named kaiA, kaiB and kaiC. The phosphorylation cycle of KaiC, driven by KaiA and KaiB, is assumed to be a core oscillator in the cyanobacterial clock, and it has been believed that all of the three genes are essential for circadian oscillations since their finding in 1998. However, we found that the kaiA-disrupted strains exhibited a faint damped oscillation. Measuring the bioluminescence rhythms of mutants revealed that the damped oscillation is generated by transcriptional-translational feedback of kaiBC, but not by the phosphorylation cycle of KaiC. In this talk, in addition to the mechanism of the kaiA-less oscillator, I will propose how it can be beneficial for the total circadian system in the cyanobacterium by analyzing the simple model of the two coupled oscillators.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Rational design of autonomous, peptide-based ion channels

2021年8月5日10:00 - 11:00

新津 藍 (理化学研究所 杉田理論分子科学研究室 基礎科学特別研究員)

Designing artificial ion channel proteins has been a major challenge since rational design of membrane proteins is still in its infancy. To address this challenge, we aim to understand the most fundamental interaction in membrane proteins, helix-helix packing, using artificial peptides. Here, we rationally design, synthesise and characterise transmembrane peptides which self-assemble into stable channels. In this talk, I will present our computational de novo peptide design, structure modelling and molecular dynamics simulations, followed by biophysical experiments indicating structure and function of the designed channels. These works shed light on a sequence-to-structure/stoichiometry of membrane alpha-helices, which will aid more accurate membrane protein designs in future. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Application of bioenergetics to microbial modeling

2021年7月29日10:00 - 11:00

瀬戸 繭美 (奈良女子大学 理学部 化学生物環境科学科 助教)

Bioenergetics, the study of thermodynamics as applied to biological systems, aims to understand how energy flows through a living system. Since thermodynamics provides a framework for predicting the progress of a spontaneous reaction and for harnessing the energy released, bioenergetics can help us to understand the ecological processes of chemotrophic microorganisms that harvest metabolic energy from various chemical reactions. In this talk, I will introduce a theoretical model as an attempt to describe the growth of chemotrophic microorganisms in terms of the interrelationships between microbial activities and the change in Gibbs energy of a system. Based on our findings and previous literature in the field, I will discuss ecological insights into microbial ecosystems thriving in low-energy environment.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

How nucleus size affects chromatin motion? - Experimental measurements and a polymer physics theory

2021年7月1日10:00 - 11:00

坂上 貴洋 (青山学院大学 理工学部物理・数理学科 准教授)

Chromatin moves dynamically inside the cell nucleus, and its motion is often correlated with gene functions such as DNA recombination and transcription. A recent study has shown that during early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases with the cell stage. However, the underlying mechanism for this transition has yet to be elucidated. Here we systematically investigate the impact of nuclear size to demonstrate that it is indeed a decisive factor in chromatin mobility. We show that a simple theoretical description, which takes into account the length and time scales of chromatin polymer solution, can quantitatively describe the relationship between the nucleus size and the chromatin motion in vivo. Our results emphasize a regulatory role of nuclear size in restricting chromatin motion, and a generic polymer physics model plays a guiding role in capturing this essential feature. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Period variability can provide valuable information in oscillatory systems

2021年6月24日10:00 - 11:00

森 史 (九州大学 芸術工学研究院 デザイン人間科学部門 助教)

Biological clocks generate temporally precise oscillations although they are subjected to various types of noise. In other words, oscillations with only a small variability in the period are observed under action of noise. In this talk, I focus on period variability in coupled phase oscillators and complex oscillatory dynamical systems, and present the following topics:(i) A phase oscillator subjected to noise can become to generate more precise oscillations not only when it is synchronized with periodic signal but also when it is mutually synchronized with another phase oscillator with stronger noise. (ii) In complex oscillatory dynamical systems, period variability is sensitive to the choice of an output variable and output checkpoint; it can be reduced by an appropriate selection of them. (iii) Noise intensity and coupling strength in synchronized phase oscillators can be inferred from data about period variability. This talk is based on joint researches with Dr. Hiroshi Kori (Tokyo Univ) and Dr. Alexander Mikhailov (Kanazawa Univ). *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

The origin and dispersal of buckwheat

2021年6月10日10:00 - 11:00

ジェフリ・フォーセット (数理創造プログラム 上級研究員)

Buckwheat, which soba noodles is made from, originated from a wild species that is distributed in southwest China, around Yunnan, Sichuan, and Tibet. We are trying to understand when, where, and how it originated and then spread across the world and came to Japan. To do so, we are using genomic data of wild samples from China and cultivated samples from various parts of the world. I will give a brief introduction about buckwheat, explain what we already know about its origin and dispersal, and show a bit of our results. I will also explain the significance of studying "domestication", that is, the process that plants/animals that humans currently use originated from their ancestral wild species. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

An overview of genome-wide epistasis and co-selection analysis

2021年6月3日10:00 - 11:00

許 インイン (数理創造プログラム 基礎科学特別研究員)

This talk is a summary of research that have done by me and my team during 2016~2019. I was a postdoc researcher in Aalto university/Helsinki university in Finland. In the team, a worldwide active collaboration has happened between many fields including statistical physics, biology, computer science and statistics. The target is to analyze ultra-high dimensional large population genomic datasets of two major human pathogens, Streptococcus pneumoniae and Neisseria meningitidis, without phenotypic data. Interacting networks of resistance, virulence and core machinery genes are identified. Many different approaches have been invented and they can be generally applied to other datasets with similar mathematical setting. I will explain methods based on statistical model [1,2], mutual information [3], and theoretical performance analysis for statistical model [4]. In the end, I will briefly introduce a new phenomenon of random matrix which is discovered during the research process for statistical significance filtering [5]. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

A Mathematical Model for Stem Cell Competition to Maintain a Cell Pool Injured by Radiation Exposure

2021年5月27日10:00 - 11:00

内之宮 光紀 (電力中央研究所)

Cancer risk of low-dose-rate ionizing radiation exposure is one of the most important issues in radiation protection. Tissue stem cells have been considered one of the targets of radiation-induced carcinogenesis. There has been a hypothesis that the carcinogenic effects of radiation can be reduced if damaged stem cells are eliminated via stem cell competition between damaged and intact stem cells. This would be particularly effective under very low-dose-rate conditions, where only a few stem cells in a stem cell pool are affected by radiation. In this presentation, I will introduce a simple mathematical model to discuss the influence of stem cell competition on the accumulation of radiation damage and show that the character of damaged cells and the size of the stem cell pool may affect the accumulation of radiation damage. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Organ-to-organ two-way coupling contributes to the stabilization of circadian clock in Arabidopsis.

2021年5月20日10:00 - 11:00

上本 恭平 (京都大学 / 奈良先端科学技術大学院大学)

Circadian clocks increase plant fitness by anticipating periodic environmental changes using unstable temporal information perceived in each tissue/organ. However, little is known about how such local and noisy temporal information regulates global and coordinated plant growth. Here, we show that nutrient-mediated two-way communication between shoots and roots stabilizes circadian rhythms and aids plant growth. The photosynthetic product, sucrose, is transported from the shoot to the root, where it regulates the expression of a clock gene and nutrients uptake rhythms. A lack of nutrient rhythms destabilizes the shoot circadian rhythms and reduces the growth rate. Our mathematical model supports that two-way communication between organs reduces the heterogeneity of the circadian rhythm, thereby maintaining the robustness of the circadian clock in a noisy environment. As with feedback loops in other hierarchies, nutrient-mediated shoot-root interorgan communication of the circadian clock is advantageous for proper growth under fluctuating environmental conditions. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Modeling Membrane Morphological Change during Autophagosome Formation

2021年5月14日10:00 - 11:00

境 祐二 (数理創造プログラム 客員研究員 / 東京大学大学院 医学系研究科 助教)

Membrane-bound organelles compartmentalize eukaryotic cells and adopt various characteristic shapes such as disk-shaped, tubules, spherical vesicles, and their intermediate structures. Organellar morphology is regulated by protein and lipid compositions. Because organellar shape directly relates to organellar function, it is important to understand the mechanisms regulating organelle morphology. In autophagy, the morphologies of the isolation membrane change from disk- to cup-shaped, closed spherical double-membrane structure. Eventually the membrane engulfs the cytoplasmic materials. In this study [1], we investigate the dynamics of the continuous membrane morphological transition in autophagy, which is governed by the spatiotemporal regulation of curvature generators. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Kullback-Leibler divergence and stochastic dynamics

2021年5月6日10:00 - 11:00

入谷 亮介 (数理創造プログラム 研究員)

*Detailed information about the seminar refer to the email.

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

The rheotaxis mechanism of swimming ciliates

2021年4月22日10:00 - 11:00

西上 幸範 (北海道大学 電子科学研究所)

The swimming unicellular organisms, which live in freshwater, need to resist currents in the environment. Without this ability, their habitat changes with the flow, and they cannot survive in nature for a long time. It is reported that a kind of swimming microorganism, Paramecium, exhibits upstream swimming in 1904. However, the mechanism of the behavior has been still unclear. To elucidate the mechanism, we observed the behavior of a ciliate in a flow field and performed numerical fluid calculations. My results suggest that the rheotaxis is realized by cell shape and inhibition of ciliary beating near the wall. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Liquid condensates in cell nucleus

2021年4月15日10:00 - 11:00

足立 景亮 (数理創造プログラム 基礎科学特別研究員 / 理化学研究所 生命機能科学研究センター 生体非平衡物理学理研白眉研究チーム 基礎科学特別研究員)

I will give a talk in a journal club style. I will introduce recent papers regarding liquid-liquid phase separation in cells. In cell biology, several types of liquid condensates of proteins/RNAs have been found recently. The functions of such condensates and the physical mechanism of controlling the liquid state are intensely discussed. In this talk, I will focus on liquid condensates in the cell nucleus and review recent experimental results. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Simple models of cancer growth, MCMC parameter estimation and identifiability

2021年4月8日10:00 - 11:00

カトゥリン・ボシュメン (数理創造プログラム 副プログラムディレクター / Professor, Department of Physics, Ryerson University, Canada)

I would like to introduce some basic concepts about (very simple) mathematical model of cancer growth, the basic math behind parameter estimation via Markov chain Monte Carlo (MCMC) based on Bayes' theorem, and the different diagnostics you can use to know if the parameters are correctly estimated. I will use a recent example with cancer data in mice. I think this seminar can be interesting to mathematicians (because of the models and the math behind the parameter estimation, but the math is very basic!), to physicists (especially those that have to do some parameter estimation), and to biologists (the cancer model/data and the parameter estimation). I think it will also be interesting to the information theory and prediction science people. MCMC parameter estimation based on physical models is more valuable in my field than machine learning, so I think those interested in machine learning but maybe are not so familiar with MCMC should join to consider them as an alternative approach in certain contexts. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Structural reduction of chemical reaction networks based on topology

2021年4月1日10:00 - 11:00

広野 雄士 (Assistant Professor, Asia Pacific Center for Theoretical Physics, Republic of Korea)

Chemical reactions form a complex network in living cells and they play vital roles for physiological functions. An amusing question is how the structure of a reaction network is linked to its chemical functionalities. I’ll talk about a method of the reduction of chemical reaction networks, which is convenient for extracting important substructures. Mathematical concepts such as homology and cohomology groups are found to be useful for characterizing the shapes of reaction networks and for tracking the changes of them under reductions. For a given chemical reaction network, we identify topological conditions on its subnetwork, reduction of which preserves the steady state of the remaining part of the network.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Evolutionary conservativeness and diversification of cycads: Understanding the evolution of living fossils

2021年3月25日10:00 - 11:00

Dr. Jose Said Gutiérrez-Ortega (Assistant Professor, Institute for Excellence in Educational Innovation, Chiba University)

The cycads are a lineage of gymnosperms that represent an example of biological stasis success. Despite their early origin in the seed plant evolution, they survived multiple events of mass extinction and could diversify in modern tropical ecosystems during the Cenozoic, especially in countries known for their great biodiversity such as Mexico. What factors have allowed their persistence and diversification despite their conservative nature? I have studied the cycad genus Dioon, a group of 17 species occurring in habitats ranging from tropical forests to arid zones in Mexico and Honduras. Phylogenetic and phylogeographic analyses revealed that the diversification of Dioon has been driven by the long-term process of aridification of Mexico since the Miocene. The lineages that shifted from mesic forests to arid zones show leaf trait variations beneficial against water stress; this feature can be also observed at the inter-population level when comparing mesic versus arid sister pairs. What mechanism allows this aridification-driven diversification? Using population genetics and ecological niche modeling on sister lineage pairs, I have revealed that lineages at arid zones might tolerate arid environments, but within the arid habitat, they retain the same ancestral niche also observed on their mesic sisters. The surrounding areas that are suboptimal for their niches serve as barriers against gene flow: this promotes allopatric speciation. This research has revealed that the mechanism that allows the diversification process in Dioon involves three factors: 1) a habitat shift due to aridification, 2) niche conservatism that facilitates geographic isolation, 3) gaining unique morphological and anatomical features that help to counteract water stress, probably through long-term stabilizing selection. This research highlights the importance of biological conservatism in evolution, and how “living fossils” can still diversify into modern ecosystems.

会場: via Zoom

イベント公式言語: 英語

セミナー

iTHEMS生物学セミナー

Microeconomics of metabolism

2021年3月10日10:00 - 11:00

山岸 純平 (東京大学 金子研究室)

Metabolic behaviors of proliferating cells are often explained as a rational choice to optimize cellular growth rate. In contrast, microeconomics formulates consumption behaviors as optimization problems of utilities. We pushed beyond this analogy to precisely map metabolism onto the theory of consumer choice. We thereby revealed the correspondence between and a general mechanism for mysteries in biology and economics: the Warburg effect, a seemingly-wasteful but ubiquitous phenomenon where cells favor aerobic glycolysis over more energetically-efficient respiration, and Giffen behavior, the unexpected consumer behavior where a good is demanded more as its price rises. The correspondence implies that respiration is counterintuitively stimulated when its efficiency is decreased by drug administration. This “microeconomics of metabolism” will serve as a macroscopic phenomenology to predict the metabolic responses against environmental operations. In particular, it offers a universal relationship between the metabolic responses against drug administrations and changes in nutrient availability.

会場: via Zoom

イベント公式言語: 英語