iTHEMS生物学セミナー
181 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
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
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セミナー
Spatial structure in ecology: the effects of dispersal network structure on biodiversity pattern and stability in metacommunities
2021年11月18日(木) 10:00 - 11:00
鈴木 裕香 (沖縄科学技術大学院大学 (OIST))
Ecological dynamics typically take place at a large spatial scale. However, it has been challenging to study them at a scale as large as a country, continent, or ocean. In particular, while there are many studies that consider systems with multiple local patches (known as "metacommunities"), spatial structures assumed in these studies are mostly simple or focused on a particular structure, despite the diverse landscape structures seen in nature. Thus, to understand how spatial structures affect metacommunities in nature, we need to expand our understanding of the role of spatial structure in regulating biodiversity patterns and stability across diverse spatial structures. In my study, I addressed this issue by using computer simulation with theoretical and empirical spatial structures. In this talk, I will show how the use of computational tools and network theoretical concepts aided investigating unexplored aspects of spatial structure and dissecting the complex nature of spatial network structure. Results suggest that how dispersal pathways are distributed in the network space affects total diversity, and the number of patches in a metacommunity is the dominant spatial parameter that regulate stability. Such an improved understanding of the role of spatial structure could contribute to a better conservation planning as well.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Toward mathematical medicine: development of a new drug and digital medicine for sleep disorders
2021年11月11日(木) 12:30 - 13:30
Jae Kyoung Kim (Associate Professor, Department of Mathematical Sciences, KAIST, Republic of Korea)
In this talk, I will illustrate collaborative stories between our math group and medical researchers to treat disrupted circadian rhythms and sleep. First, I will illustrate the key molecular mechanism for robust circadian rhythms against spatio-temporal noise, which we identified by analyzing spatio-temporal timeseries data of clock molecules. This explains why Alzheimer's diseases, obesity, and aging cause unstable circadian rhythms and sleep-wake cycle: cytoplasmic traffic jam, which provides a new paradigm to treat sleep disorders. Next, I will talk about our collaboration story with Pfizer Inc: how we used mathematical modeling to help the development of a new drug modulating the circadian phase. Finally, I will introduce our collaboration with Samsung medical center: how we used mathematical modeling to analyze complex sleep patterns of shift workers measured with wearables to find optimal sleep patterns minimizing sleep disorders. This opens the chance for the development of an app providing a personalized sleep schedule for shift workers.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Protein structure modeling from cryo-electron microscopy data
2021年11月4日(木) 13:30 - 14:30
森 貴治 (理化学研究所 開拓研究本部 (CPR) 杉田理論分子科学研究室 専任研究員)
Recent advances in cryo-electron microscopy (cryo-EM) have enabled us to determine three-dimensional structures of biomolecules at near-atomic resolution. Protein structure modeling from experimental cryo-EM data can be achieved using a molecular dynamics (MD) simulation, called flexible fitting. We have developed MD-based flexible fitting algorithms for efficient and reliable protein structure modeling. In this seminar, I would like to talk about our recent contributions to this field, and propose perspectives towards next-generation structural biology.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Nonlinear dynamics in frog choruses
2021年10月28日(木) 10:00 - 11:00
合原 一究 (筑波大学 システム情報系 准教授)
カエルのオスは、同種のメスを惹き寄せたり同種のオスへの縄張りを主張すべく鳴きます。結果としてオスは互いに相互作用しますが、そのなかにはさまざまな同調現象があります。この講演では、演者はオスの実際の同調的な鳴き方を紹介しつつ、その位相振動子モデルを紹介します[1,2]。続いて、最近取り組んでいるプロジェクトである、実証データから位相振動子を同定する研究を紹介します[3]。そしてモデルをハイブリッド力学系に拡張し、内在的な条件や同種オスとのやりとりに応じて オスが断続的に鳴き方を変更する現象の研究を紹介します[4]。
会場: via Zoom
イベント公式言語: 英語
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セミナー
Evaluation of origin of driving force for loop formation in a chromatin fiber
2021年10月21日(木) 10:00 - 11:00
横田 宏 (数理創造プログラム 特別研究員)
During cell division, chromatin fiber is condensed into the rod-like shape which is called chromosome. The rod-like shape of the chromosome is constructed by consecutive chromatin loop structures which are formed by the protein complex named condensin. In this talk, by calculating the driving force for the loop formation, we discuss the mechanism of loop formation which is the one of the controversial issues on chromosome condensation. The driving force is evaluated based on the free energy of the chromatin loop formation by constructing the polymer model. Based on the free energy, the loop growth length in the unit time is also evaluated. These evaluations also lead to the time evolution of the loop length and the mechanism of the loop formation.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Understanding the effect of defective, interfering influenza virus
2021年10月14日(木) 10:00 - 11:00
カトゥリン・ボシゥメン (数理創造プログラム 副プログラムディレクター)
Defective interfering virus particles (DIPs) are viruses that are defective in a very specific way that allows them to out-compete standard, non-defective virus. It is difficult to count DIPs because they can look too similar to standard virus. So instead, people are counting them based on their effect on suppressing the standard virus population. In this talk, I will explain the basic biology of virus replication, what are DIPs, and how they compete with standard virus. I will present our mathematical model (ordinary differential equation) that describes co-infection competition with DIPs and standard virus. I will use the mathematical model to show how experiments to count DIPs can give incorrect results, and I will propose some solutions.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Speed limit for population dynamics
2021年10月7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)
In statistical and quantum physics, the speed limit, i.e., upper bound for change rate, of time-dependent quantities has been discussed. In this talk, I will extend the concept of speed limit to ecological and evolutionary processes by considering the competitive Lotka-Volterra model and the quasi-species model. As an application of the speed limit, I will also discuss the universal constraint for the relaxation at the bifurcation point of such models.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Evolutionary dynamics of seasonal influenza viruses
2021年9月30日(木) 10:00 - 11:00
岡田 崇 (数理創造プログラム 上級研究員)
Seasonal influenza viruses undergo rapid evolution, which allows them to escape from human-immune-system responses and infect humans repeatedly. In this talk, I present some counter-intuitive properties observed in time-series data of viral sequence variation and then discuss how these strange properties can be explained by extending the standard framework of population genetics.
会場: via Zoom
イベント公式言語: 英語
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セミナー
How to make a dataset for phylogeny and the background of mathematical theory
2021年9月9日(木) 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
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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(木) 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
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セミナー
Mathematical analysis of body temperature fluctuation during hibernation
2021年8月26日(木) 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
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セミナー
The damped circadian oscillator in cyanobacterium: kaiA-less oscillator
2021年8月19日(木) 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
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セミナー
Rational design of autonomous, peptide-based ion channels
2021年8月5日(木) 10:00 - 11:00
新津 藍 (理化学研究所 開拓研究本部 (CPR) 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
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セミナー
Application of bioenergetics to microbial modeling
2021年7月29日(木) 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
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セミナー
How nucleus size affects chromatin motion? - Experimental measurements and a polymer physics theory
2021年7月1日(木) 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
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セミナー
Period variability can provide valuable information in oscillatory systems
2021年6月24日(木) 10:00 - 11:00
森 史 (九州大学 大学院芸術工学研究院 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
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セミナー
The origin and dispersal of buckwheat
2021年6月10日(木) 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
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セミナー
An overview of genome-wide epistasis and co-selection analysis
2021年6月3日(木) 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
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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(木) 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
181 イベント