iTHEMS生物学セミナー
140 イベント
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。
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セミナー
Do the mechanisms of speciation vary with latitude? Empirical case study 1: evolution of the plant cycad genus Ceratozamia from Mexico
2022年6月2日(木) 16:00 - 17:00
ホセ サイード・グティエレス オルテガ (数理創造プログラム 基礎科学特別研究員)
“Species” form biodiversity, and “speciation” is the evolutionary process that originate them. Speciation can occur by stochastic processes —neutral theory— or through the influence of ecological factors —selection theory—. They are not competing theories, but rather explain different facets of speciation. But the mechanisms of speciation seem quite to depend on the group of study and its underlying spatial and temporal factors. Why do in some groups species are more prone to evolve via selection or stochastically than others? It does not exist a unified theory that can explain and predict events of speciation at the global level. However, I hypothesize that there is a latitude-association between two main mechanisms of speciation: 1) “allopatric speciation by means of niche conservatism” and 2) “ecological speciation by means of niche divergence”. The first is hypothetically more common at low latitudes, and the second is more common at high latitudes. In this context, I will use the recent results of my own empirical research on the plant cycad genus Ceratozamia from Mexico as an example to show how mechanisms of speciation seem to covariate with latitude. Hopefully, you can help me to formulate a theory that can explain where and under what factors speciation can occur.
会場: via Zoom
イベント公式言語: 英語
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セミナー
More Data, More Problems: Big Data in Correlative Ecology
2022年5月19日(木) 16:00 - 17:00
Dan Warren (沖縄科学技術大学院大学 (OIST) 生物多様性・複雑性研究ユニット 研究員)
The rapidly expanding pool of large data sets on species distributions, community composition, and environmental factors has been accompanied by an increasing number of methodological approaches to analyze this data. If done correctly, this represents an unprecedented opportunity for understanding ecological processes at large scales. However, it also represents an opportunity to be wrong about those same processes at a scale that was previously not possible. In this talk, I will use examples from ecology and other fields to discuss some of the issues that arise when we take big data approaches to ecological questions.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Classical and Quantum Chaos
2022年5月12日(木) 16:00 - 17:00
首藤 啓 (東京都立大学 大学院理学研究科 物理学専攻 教授)
Classical and quantum mechanics in multi-dimensions are qualitatively different from those in one-dimension since they are no more integrable in general and chaos appears in the dynamics. This brings a great deal of complexity or even richness both in classical and quantum dynamics. Especially in generic nonintegrable systems which are neither completely integrable nor fully chaotic, phase space becomes a mixture of regular and chaotic components. Such an aspect is a source of inexhaustible questions not only in the past but in the future. We here overview classical and quantum chaos in Hamiltonian systems.
会場: via Zoom
イベント公式言語: 英語
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Diversity of Asgardarchaota and Theoretical verification of the endosymbiotic theory
2022年4月28日(木) 10:00 - 11:00
熊倉 大騎 (北海道大学 大学院生命科学院 生命科学専攻 博士課程)
How did intracellular symbiosis occur and give rise to eukaryotic ancestor? This question has been considered to the two theories as three-domain theory and eocyte theory. Here I present asgard archaea, the archaeon closest to eukaryotes. Asgard archaea is an archaeon found at a deep-sea sampling site called Loki's castle at between Greenland and Norway. So all the closely related species are named after Norse mythology (Loki-, Thor-, Odin-, Heimdall-, etc.). Unlike other archaea, asgard archaea has many eukaryotic-specific proteins and is considered to be the closest to eukaryotes. In 2020, one of the asgard archaea species was finally successfully cultured. This archaeon was cultured and found to take on a branch-like structure. It is then hypothesized that intracellular symbiosis between this archaeon and the ancestor of mitochondria resulted in the ancestor of today's eukaryotic cells. In this talk, I would like to discuss with you the explanation of how we arrived at this hypothesis and how to construct a mathematical model.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Neurons are potential statisticians
2022年4月21日(木) 10:00 - 11:00
磯村 拓哉 (理化学研究所 脳神経科学研究センター (CBS) 脳型知能理論研究ユニット ユニットリーダー)
Humans and animals can predict what will happen in the future and act appropriately by inferring how the sensory inputs were generated from underlying hidden causes. The free-energy principle is a theory of the brain that can explain how these processes occur in a unified way. However, how the fundamental units of the brain, such as the neurons and synapses, implement this principle has yet to be fully established. Here, we have mathematically shown that neural networks that minimise a cost function implicitly follow the free-energy principle and actively perform statistical inference. We have reconstructed a biologically plausible cost function for neural networks based on the equation of neural activity and shown that the reconstructed cost function is identical to variational free energy, which is the cost function of the free-energy principle. This equivalence speaks to the free-energy principle as a universal characterisation of neural networks, implying that even at the level of the neurons and synapses, the neural networks can autonomously infer the underlying causes from the observed data, just as a statistician would. The proposed theory will advance our understanding of the neuronal basis of the free-energy principle, leading to future applications in the early diagnosis and treatment of psychiatric disorders, and in the development of brain-inspired artificial intelligence that can learn like humans.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Coarse-grained molecular dynamics simulation via Langevin simulation
2022年4月14日(木) 10:00 - 11:00
横田 宏 (数理創造プログラム 特別研究員)
In the cell biology or biophysics, many mechanical properties of proteins or DNA are discussed. In order to consider the dynamics, coarse-grained molecular dynamics simulation (Langevin simulation) is useful. In this seminar, I will give you the introductory and methodology talk about the Langevin simulation.
会場: via Zoom
イベント公式言語: 英語
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Journal Club: Phase separation in a many-component system with random interactions
2022年3月31日(木) 10:00 - 11:00
足立 景亮 (理化学研究所 生命機能科学研究センター (BDR) 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)
Several kinds of protein condensates have been observed in living cells, and the liquid-liquid phase separation is regarded as a basic mechanism of the condensate formation. However, given that there are thousands of protein species in a cell, it is not clear how the number and the composition of distinct condensates are controlled. One of the physics approaches to this problem is considering a model of many components with random interactions. In this Journal Club, I will introduce a recent paper [1] that applies random-matrix theory to the phase separation dynamics.
会場: via Zoom
イベント公式言語: 英語
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Criticality in stochastic SIR model for infectious diseases based on path-integral approach
2022年3月24日(木) 10:00 - 11:00
安井 繁宏 (高知大学医学部 医療情報科学センター 助教)
The susceptible-infected-removed (SIR) model provides us with a basic scheme for the analysis of the epidemic infectious diseases such as the COVID-19. In this presentation, we focus on the stochastic SIR model which describes the stochastic time-evolutions of the population sizes for the susceptible, infected, and removed individuals. We consider the master equation (Kolmogorov forward equation) for the infection transmission and recovery processes (SI->II and I->R), and transform it into the Hamiltonian formalism with the Fock space a la quantum physics. According to the Doi-Peliti prescription, furthermore, we introduce the path-integral formalism similar to the quantum field theory, and perform the perturbative and non-perturbative calculations for the time-evolution of the susceptible, infected, and removed populations. We find that the critical value Rc of the basic reproduction number, which determines the spreading or the convergence of the infectious diseases, can be modified by the stochastic effects in comparison to the Rc in the conventional deterministic SIR model.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Phylogenomics revealed one of the problems for phylogeny –The monophyly of Archaeplastida including land plant-
2022年3月17日(木) 10:00 - 11:00
矢﨑 裕規 (数理創造プログラム 特別研究員)
There are many problems between large eukaryotic lineages. One of these is the monophyly of Archaeplastida to which land plants and other photosynthetic organisms belong. Although it has been believed that the Archaeplastida are monophyletic because they share common chloroplast structures, several large-scale molecular phylogenetic analyses have failed to reproduce this phylogenetic relationship. In this study, by enhancing the taxon sampling of the data set, the monophyly of Archaeplastida was successfully reconstructed, showing that the taxa critical for the reconstruction are present. Through detailed molecular phylogenetic and statistical analyses, it was estimated that the lack of monophyly ofArchaeplastida is due to the specific evolutionary signals of certain taxa.
会場: via Zoom
イベント公式言語: 英語
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Independent regulation of multiple checkpoints in cell-cycle network system -Biological function originated in the law of localization-
2022年3月10日(木) 10:00 - 11:00
望月 敦史 (京都大学 ウイルス･再⽣医学研究所 教授)
In cell cycle, G1-S and G2-M checkpoints are regulated by different protein complexes, Cdc2-Cdc13 and Cdc2-Cig2, respectively. For a normal mitosis, activity of two complexes should rise specifically at different timing. However, the complex formations share common species of proteins and activation reactions conform a complicated network. We study how independent regulation of two checkpoints is realized in the network system by “structural sensitivity analysis”, which was previously established by us. The analyses clarified that activities of two complexes are regulated by disjoint sets of reaction parameters in the system. A series of non-trivial behaviors are generated by “buffering structures with an intersection”, which can generally appear in chemical reaction network including complex formation.
会場: via Zoom
イベント公式言語: 英語
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Stator dynamics of the bacterial flagellar motor
2022年2月24日(木) 17:00 - 18:00
Ashley Nord (Researcher, Centre de Biologie Structurale, CNRS, France)
Rubén Pérez-Carrasco (Lecturer in Theoretical Systems Biology, Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, UK)The bacterial flagellar motor is the membrane-embedded rotary molecular motor which turns the flagellum that provides thrust to many bacteria for swimming, swarming, and chemotaxis. This large multimeric complex, composed of a few dozen constituent proteins, is a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels which dynamically bind to the cell wall and convert electrochemical energy into torque which is applied to the rotor. The dynamic exchange of stator units is a function of the viscous load on the flagellum, allowing the bacterium to adapt to its local environment, though the molecular mechanisms of this mechanosensitivity remain unknown. Previously, we have shown that stator units behave as a catch bond, a counterintuitive bond which becomes stronger under applied tension. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models which recapitulate the asymmetry, finding assembly dynamics to be particularly well described by a two-state catch-bond mechanism.
会場: via Zoom
イベント公式言語: 英語
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Hilbert transform and its applications to biology
2022年2月17日(木) 10:00 - 11:00
儀保 伸吾 (数理創造プログラム 特別研究員)
In chronobiology, the estimation of phase dynamics is important for measuring period and phase shift. However, it is difficult to precisely estimate the phase from time-series data when the frequency and the amplitude are nonstationary. Hilbert transform has been known as a signal processing method for decomposing time-series into the phase and the amplitude dynamics. This method allows us to analyze the phase from nonstationary time-series data. In this talk, I would like to introduce the basic concept of Hilbert transform and a few examples of its applications.
会場: via Zoom
イベント公式言語: 英語
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Stochastic operators: properties and applications
2022年2月10日(木) 10:00 - 11:00
ジルベルト・ナカムラ (数理創造プログラム 特別研究員)
Stochastic processes are widely used to model systems in which one or more variables fluctuate randomly. Problems arise when large sets of random variables are allowed to interact with each other, as is often the case with physical and biological systems. Stochastic operators provide a convenient framework for describing the interactions and evolution of the random variables. In this talk, I will discuss techniques and methods typically used in spin systems to deal with stochastic operators and their spectral analysis in the context of random processes. I will briefly review their properties and applications to biological systems. As practical examples, I will present some results of my research in infectious diseases and migration of glioma cells.
会場: via Zoom
イベント公式言語: 英語
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On Flow and Form at Low Reynolds Number
2022年1月27日(木) 10:00 - 11:00
石本 健太 (京都大学 数理解析研究所 (RIMS) 准教授)
Cell locomotion is mechanically restricted by surrounding viscous fluids. With a focus on swimming cells in a low-Reynolds-number flow, I will give a brief introduction to microbiological fluid dynamics and present a 'hydrodynamic shape' theory at the cellular scale.
会場: via Zoom
イベント公式言語: 英語
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A study of biological systems from topological point of view
2022年1月20日(木) 10:00 - 11:00
宮﨑 弘安 (数理創造プログラム 上級研究員)
A biological body can be regarded as a complicated network of chemical reactions. The chemical reaction network (CRN) is a (hyper)graph-theoretic model of such biological networks. Recently, in the joint work with Yuji Hirono, Takashi Okada and Yoshimasa Hidaka, we applied a topological method to the study of CRNs, and found a suitable way to simplify the networks. Since Professor Hirono has already explained our work in this seminar, I will try to explain it from a slightly different point of view. In the first half of the talk, I will review the entire work. In the second half, I will try to give a rough sketch of the mathematical method we used in the work.
会場: via Zoom
イベント公式言語: 英語
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A comprehensive view of the SARS-CoV-2 infection process
2022年1月13日(木) 10:00 - 11:00
二島 渉 (Scientist, New Mexico Consortium, Mexico)
Nishima et al. recently published a paper about a computational model of SARS-CoV-2 Spike Protein [1]. Although it is still a hypothesis due to the lack of direct experimental evidence, the story comprehensively explains the initial infection process of SARS-CoV-2 consistent with most of the empirical evidence. In the presentation, I would like to explain the overview of the infection process for the non-expert audience and how the hypothesis influences the current COVID-19 situation. If time permits, I would like to briefly explain the current plan of the iTHEMS-NMC COVID project, which is going to be the first case of undergoing an interdisciplinary collaboration framework between Japan and the US.
会場: via Zoom
イベント公式言語: 英語
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Physics of nuclear bodies
2022年1月6日(木) 10:00 - 11:00
山本 哲也 (北海道大学 創成研究機構化学反応創成研究拠点 特任准教授)
Eukaryotic nucleus is not a uniform solution of DNA, but there are a number of nuclear bodies in the interchromatin spaces. There are growing number of experiments that suggest that nuclear bodies are assembled by liquid-liquid phase separation (LLPS). Condensates assembled by LLPS show coarsening or coalescence to decrease the surface energy. However, in some nuclear bodies, such as paraspeckles, nuclear stress bodies, and fibrillar centers in nucleoli, multiple condensates are stably dispersed and are not likely assembled by LLPS. The assembly mechanism of nuclear bodies is relevant to the regulation of the area of condensate surfaces, which are functional in some nuclear bodies, and the mobility of nuclear bodies. Hirose group (Osaka Univ.) has elucidated that nuclear bodies are scaffolded by a class of RNA, called architectural RNA (arcRNA), which forms complexes with RNA binding proteins. This implies that the assembly of nuclear bodies is governed RNA dynamics, such as transcription, degradation, and processing, and the sequence of bases of arcRNA. In the seminar, I will show how the base sequences and the dynamics of RNA are involved in the assembly of paraspeckles and fibrillar centers in nucleoli.
会場: via Zoom
イベント公式言語: 英語
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Hidden Markov Models and their applications
2021年12月23日(木) 10:00 - 11:00
岡田 崇 (数理創造プログラム 上級研究員)
The Hidden Markov models (HMM) have been used in a variety of fields for different purposes. I am going to review statistical inference methods associated with HMM & related biological problems. As an example of their applications, I'll also present my research on the SARS-CoV-2 evolution.
会場: via Zoom
イベント公式言語: 英語
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Revisiting Standard Methods for Phylogenetic Tree Inference
2021年12月16日(木) 10:00 - 11:00
松井 求 (東京大学 大学院理学系研究科 助教)
Phylogenetic tree inference is the foundation to answer any biological questions, for example, how the living systems were established. However, the existing methods show poor performance to infer the phylogenetic tree when constructing an informative multiple sequence alignment (MSA) is difficult. In this talk, I will first review the current problems in phylogenetics, then introduce the graph splitting (GS), and edge perturbation (EP) method. The GS method rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach; evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees when sequences substantially diverge. The EP method is the bootstrap-like method using pairwise sequence alignment (PSA) instead of MSA, which can provide reliable measurements on the estimated branches. In addition, we can rapidly and reliably reconstruct a phylogenetic tree with problematic MSA switching NJ+EP and GS+EP methods, because the EP method can be applied to the NJ method. These methods not only improve the accuracy of phylogenetic tree inference, but they also could open the door for revisiting phylogenetics.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Selective inference for testing trees and edges in hierarchical clustering and phylogeny
2021年12月9日(木) 10:00 - 11:00
下平 英寿 (京都大学 大学院情報学研究科 教授 / 理化学研究所 革新知能統合研究センター (AIP) 数理統計学チーム チームリーダー)
Bootstrap resampling is quite useful for computing “confidence values” or “p-values” of trees and edges. However, they are biased and may lead to false positives (too many wrong discoveries) or false negatives (too few correct discoveries) depending on the “curvature” of the boundary surface of a hypothesis region in the data space. In addition, we face the issue of selection bias because we tend to use the dataset twice for hypothesis selection and its evaluation. I will explain these two types of bias and show methods to adjust the confidence values.
会場: via Zoom
イベント公式言語: 英語
140 イベント