iTHEMS Biology Seminar
174 events
We are holding regular seminars and other activities on topics related to biology. Our aim is to lower the boundaries between biology and mathematics/physics, to identify common grounds between biology and mathematics/physics, and to develop ideas for new research topics at the intersection of biology and mathematics or physics.
For further details see iTHEMS Biology Seminar Study Group page.
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Seminar
Evolutionary conservativeness and diversification of cycads: Understanding the evolution of living fossils
March 25 (Thu) at 10:00 - 11:00, 2021
José 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.
Venue: via Zoom
Event Official Language: English
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Seminar
Microeconomics of metabolism
March 10 (Wed) at 10:00 - 11:00, 2021
Jumpei Yamagishi (Ph.D. Student, Kaneko Laboratory, The University of Tokyo)
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.
Venue: via Zoom
Event Official Language: English
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Seminar
Origin of non-linearity of large deformation on DNA stretched
February 25 (Thu) at 10:00 - 11:00, 2021
Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)
Since DNA in a cell is mechanically stretched or rotated by many proteins, the mechanical response of DNA in vitro is expected to be basic point for understanding its behavior. When DNA is stretched by relatively high force, the length of DNA shows the nonlinear response. In this talk, I introduce the theoretical treatment of DNA stretching in high force region based on polymer physics.
Venue: via Zoom
Event Official Language: English
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Seminar
High-throughput laboratory evolution with machine learning reveals constraints for drug resistance evolution
February 18 (Thu) at 10:00 - 11:00, 2021
Junichiro Iwasawa (Ph.D. Student, Department of Physics, Graduate School of Science, The University of Tokyo)
The understanding of evolution is crucial to tackle the problem of antibiotic resistance which is a growing health concern. Although the lack of sufficient data has long hindered the mechanism of evolution, laboratory evolution experiments equipped with high-throughput sequencing/phenotyping are now gradually changing this situation. The emerging data from recent laboratory evolution experiments have revealed repeatable features in evolutionary processes, suggesting the existence of constraints on evolutionary outcomes [1,2]. Despite its importance for understanding evolution, however, we still lack a systematic investigation for evolutionary constraints. In this seminar, I would like to talk about two projects on the investigation of evolutionary constraints using data acquired from laboratory evolution of Escherichia coli. In the first half, I will explain how to extract an effective latent space for probing constraints in resistance evolution using gene expression data. We will further discuss what kind of structure exists in this space [3]. In the latter half, I will talk about our recent study on how to construct a predictive model for evolution using the information of evolutionary constraints.
Venue: via Zoom
Event Official Language: English
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Seminar
A machine learning approach for prediction of mitochondrial proteins in non-model organisms
February 12 (Fri) at 10:00 - 11:00, 2021
Keitaro Kume (Assistant Professor, Faculty of Medicine, University of Tsukuba)
The evolution of the repertoire of proteins localized to organelles is important for understanding the evolutionary process of organelles. However, experimental methods for identifying organelle-localized proteins have been established only for model organisms and some organisms. Therefore, prediction methods using sequence data obtained from genome and transcriptome analyses, which are relatively easy to obtain, are useful. However, such prediction methods had also been established only for model organisms. In this talk, I will introduce our study in which a machine learning method was used to obtain protein candidates localized to mitochondrion-related organelles in non-model organisms.
Venue: via Zoom
Event Official Language: English
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Seminar
System identification of mechano-chemical epithelial sheet dynamics
February 4 (Thu) at 10:00 - 11:00, 2021
Yoshifumi Asakura (Ph.D. Student, Graduate School of Biostudies, Kyoto University)
Collective migration of epithelial cells is a fundamental process of multi-cellular organisms. Our recent study using live imaging with FRET-based biosensor discovered that cell migration within an epithelial sheet is oriented by traveling waves of ERK activation. However, it is still elusive how the cells make a decision on migration direction by integrating mechano-chemical signals. Here, we performed reverse-engineering approach to extract a hidden control mechanism in the epithelial sheet dynamics in a data-driven manner. Our model has an ability to forecast cell migration quantified in time-lapse images. Therefore, our approach would be powerful to understand mechano-chemical epithelial sheet dynamics.
Venue: via Zoom
Event Official Language: English
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Seminar
Numerical inference of the molecular origin of the cyanobacterial circadian rhythm
January 28 (Thu) at 10:00 - 11:00, 2021
Shin-ichi Koda (Assistant Professor, Institute for Molecular Science)
The cyanobacterial clock proteins, KaiA, KaiB, and KaiC, are known as the simplest biological clock; Just by mixing them with ATP in a test tube, self-sustaining oscillation with a nearly 24h temperature-compensated period is reconstituted. To elucidate the molecular mechanisms of this oscillator, experimental studies have revealed and investigated in detail various elementary reactions/processes, ranging from local chemical reactions of ligands to global (dis)assembly of the proteins. Yet, proposing molecularly detailed mechanisms of the clock functions is still difficult because almost all experimentally measurable quantities are the results of complicated interplays between many elementary processes, i.e. independent measurement of an elementary process is difficult. In this talk, I will present a numerical approach to obtain the rate constants of the elementary processes from experimental data [1, 2]. First, a reaction model consisting of rate equations of the elementary processes is built. Then, their rate constants and temperature dependence are inferred by simultaneously fitting model outputs to multiple types of experimental data (such as phosphorylation reactions and ATPase activity) at various temperatures. On the basis of the inferred parameter values, we can quantitatively discuss how the clock functions arise from the interplays between elementary processes. As an example, I will present a potential molecular mechanism of the temperature compensation of period.
Venue: via Zoom
Event Official Language: English
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Seminar
Introduction to Boolean modeling and Boolean networks as information processing units
January 21 (Thu) at 10:00 - 11:00, 2021
Takashi Okada (Senior Research Scientist, iTHEMS)
Boolean networks are widely used in physics, biology, social science, and computer science. In this talk, I will introduce the basics of Boolean networks and give an overview of Biological applications. Then, I will discuss information transfer in Boolean networks and discuss optimal design principles. The latter part of the talk is based on joint work with Fumito Mori (Kyushu Univ).
Venue: via Zoom
Event Official Language: English
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Seminar
What are genes and how can we find them?
January 14 (Thu) at 10:00 - 11:00, 2021
Jeffrey Fawcett (Senior Research Scientist, iTHEMS)
Although 'gene' is a word that is used frequently in the society, most people probably do not know what genes actually are. In fact, its definition is not so straightforward. In this talk, I will first give a historical perspective and our current understanding of what genes are and what they look like. Then, I will talk about 'gene prediction'. Once we obtain the DNA (genome) sequence data of a given species, we must 'find' the genes within the genome. This involves computational prediction utilizing probabilistic models and various sources of external evidence. I will briefly explain how this is done.
Venue: via Zoom
Event Official Language: English
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Seminar
From local resynchronization to global pattern recovery in the zebrafish segmentation clock
January 7 (Thu) at 10:00 - 11:00, 2021
Koichiro Uriu (Assistant Professor, College of Science and Engineering, Kanazawa University)
Tissue-scale developmental patterns are often generated by local cellular interactions and global tissue deformation. An example is gene expression rhythms in vertebrate, termed the segmentation clock. The oscillatory spatial pattern of the segmentation clock across a tissue determines the timing of body segment formation. In this seminar, we discuss pattern recovery in the zebrafish segmentation clock after perturbation in oscillator coupling. To predict pattern recovery in embryos, we develop a physical model that describes both cell mechanics and genetic oscillations. We show that the physical model explains experimentally observed intermingled segmental defects, and their axial distributions in different embryonic developmental stages. Our analysis suggests that pattern recovery in developing tissues occurs at two scales; local pattern formation and transport of these patterns through tissue morphogenesis.
Venue: via Zoom
Event Official Language: English
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Seminar
Mathematical model-based quantitative data analysis for COVID-19
December 22 (Tue) at 10:00 - 11:00, 2020
Shingo Iwami (Associate Professor, Mathematical Biology Laboratory, Department of Biology, Faculty of Science, Kyushu University)
The recent spread of corona threatens the health of people around the world. We urgently need strategies to reduce COVID-19 spread and to enhance antiviral drug development for individual patients. Mathematics could contribute to control of COVID-19 pandemic by informing decisions about pandemic planning, resource allocation, and implementation of social distancing measures and other interventions. My group is conducting interdisciplinary research to elucidate "Quantitative Population Dynamics" with original mathematical theory and computational simulation, which are both our CORE approach. Our mathematical model-based approach has quantitatively improved a current gold-standard approach essentially relying on the statistical analysis of "snapshot data" during dynamic interaction processes in virus infection. In my talk, I would like to discuss how our approach improves our current understanding of COVID-19 research, and help an establishment of a "standard antiviral treatment" for COVID-19 as well.
Venue: via Zoom
Event Official Language: English
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Seminar
Autoimmune diseases initiated by pathogen infection: mathematical modeling
December 17 (Thu) at 10:00 - 11:00, 2020
Akane Hara (Ph.D. Student, Graduate School of Systems Life Sciences, Kyushu University)
The pathogen with proteins similar to host’s proteins is likely to cause autoimmunity, which is called “molecular mimicry”. To understand the mechanism of autoimmunity development caused by pathogen infection, we considered the following scenario: the infection activates the immune system, which results in clearance of pathogens, and the enhanced immune responses to the host’s body may remain and attack the host’s cells after the pathogen clearance. We developed a mathematical model describing the dynamics of T helper (Th) cells, viruses, self-antigens, and memory T cells and identified the conditions necessary to realize the scenario. We considered the cross-immunity of three different modes of action: [1] virus elimination by Th cells reactive to the self-antigen, [2] activation of Th cells reactive to viruses by self-antigens and Th cells reactive to self-antigens by viruses, and [3] enhancement of immune responses to self-antigens by Th cells reactive to viruses after the infection. The cross-immunity of type [3] was found to be most important for autoimmunity development. In contrast, [1] and [2] suppressed autoimmunity by effectively decreasing the viral abundance.
Venue: via Zoom
Event Official Language: English
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Seminar
How to obtain the large amount of sequence data from the eukaryote
December 10 (Thu) at 10:00 - 11:00, 2020
Euki Yazaki (Postdoctoral Researcher, iTHEMS)
Most of the modern biology is supported by genetic sequence data. Recent advances in sequencing technology have made it possible to obtain comprehensive and large numbers of sequence data from a small amount of samples, which are deposited in public databases and are easily available. In this talk, I want to give an overview of how these large scale sequence data are obtained from samples and how they become available for us to use in our biological studies, through my eukaryotic sequence studies.
Venue: via Zoom
Event Official Language: English
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Seminar
Rotifer can be a good model organism for theoretical biology
November 27 (Fri) at 10:00 - 11:00, 2020
Yuri Kominami (Specially Appointed Assistant Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo)
Rotifers are cylindrical zooplankton which constitute the phylum Rotifera. They have organs and tissues including ganglia, muscles, digestive organs, ovaries, and sensory organs in their <1mm body. Rotifers are suitable for the study on the population dynamics and longevity due to their short generation time. Furthermore the most attractive characteristic of the rotifers is asexual propagation, makes it easy to obtain clonal cultures. The genomic and transcriptomic database are developed and molecular biological techniques such as RNAi for using rotifers have been established. In this seminar, other attractive characteristics of rotifer as a model organism for theoretical biology and great studies using rotifers will be introduced. Our recent results of investigating the effects of calorie condition on longevity will be discussed.
Venue: via Zoom
Event Official Language: English
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Seminar
Symmetry and conservation laws in neural networks
November 20 (Fri) at 10:00 - 11:00, 2020
Hidenori Tanaka (Group Leader & Senior Scientist, Physics & Informatics Laboratories, NTT Research, Inc., USA / Visiting Scholar, Stanford University, USA)
Symmetry is the central guiding principle in the exploration of the physical world but has been underutilized in understanding and engineering neural networks. We first identify simple yet powerful geometrical properties imposed by symmetry. Then, we apply the theory to answer a series of following important questions: (i) What, if anything, can we quantitatively predict about the complex learning dynamics of real-world deep learning models driven by real-world datasets? (ii) How can we make deep learning models more efficient by removing parameters without disconnecting information flow? (iii) How can we distill experimentally testable neuroscientific hypotheses by reducing the complexity of deep learning models mimicking the brain? Overall, our approach demonstrates how we can harness the principles of symmetry and conservation laws to reduce deep learning models' complexity and make advances in the science and engineering of biological and artificial neural networks.
Venue: via Zoom
Event Official Language: English
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Seminar
Evolution of a peak of genetic divergence driven by local adaptation
November 5 (Thu) at 10:00 - 11:00, 2020
Takahiro Sakamoto (Postdoctoral Researcher, School of Advanced Sciences, The Graduate University for Advanced Studies (SOKENDAI))
In species that are distributed in various environments, each subpopulation adapts to the local environment. In general, when there is migration between subpopulations, genetic divergence does not proceed because the genomes are exchanged between subpopulations. However, around the loci involved in local adaptation, genetic divergence proceeds. This is because different genotypes are favored between subpopulations, so that the alleles of migrants are purged by natural selection and the exchange of genomes is suppressed. It has not been theoretically known how the degree of genetic differentiation evolves over time, making the interpretation of population genomic data difficult. In this study, we constructed and analyzed a model of population genetics to clarify the dynamics of genetic divergence.
Venue: via Zoom
Event Official Language: English
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Seminar
Basics of population genomic data analysis
October 29 (Thu) at 10:00 - 11:00, 2020
Jeffrey Fawcett (Senior Research Scientist, iTHEMS)
In recent years, it has become possible to obtain the DNA sequence data of a large number of individuals of the same species. This data set is basically a M (number of samples) x N (number of genomic positions) matrix where each data point is 0 or 1. Using this data set, we try to understand, for example, the relationship between each sample or group of samples, and the population process that has generated the data set. In this talk, I will introduce the basic concepts behind the approaches we use to analyze such data sets.
Venue: via Zoom
Event Official Language: English
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Seminar
Bayesian nonparametric estimation of Random Dynamical Systems
October 21 (Wed) at 14:00 - 15:00, 2020
Christos Merkatas (Postdoctoral Researcher, Aalto University, Finland)
In this talk, a Bayesian nonparametric framework for the estimation and prediction, from observed time series data, of discretized random dynamical systems is presented [1]. The size of the observed time series can be small and the additive noise may not be Gaussian distributed. We show that as the dynamical noise departs from normality, simple Markov Chain Monte Carlo method (MCMC) models are inefficient. The proposed models assume an unknown error process in the form of a countable mixture of zero mean normals, where a–priori the number of the countable normal components and their variances is unknown. Our method infers the number of unknown components and their variances, i.e., infers the density of the error process directly from the observed data. An extension for the joint estimation and prediction of multiple discrete time random dynamical systems based on multiple time-series observations contaminated by additive dynamical noise is presented [2]. In this case the model assumes an unknown joint error process with a pairwise dependence in the sense that to each pair of unknown dynamical error processes, we assign a– priori an independent Geometric Stick-Breaking process mixture of normals with zero mean. These mixtures a–posteriori will capture common characteristics, if there are any, among the pairs of noise processes. We show numerically that when the unknown error processes share common characteristics, it is possible under suitable prior specification to induce a borrowing of strength relationship among the dynamical error pairs. Then time-series with an inadequate sample size for an independent Bayesian reconstruction can benefit in terms of model estimation accuracy. Finally, possible directions for future research will be discussed.
Venue: via Zoom
Event Official Language: English
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Seminar
A PDE model for the localization and spread of flu in the human respiratory tract
October 14 (Wed) at 10:00 - 11:00, 2020
Christian Quirouette (Ph.D. Student, Department of Medical Physics, Ryerson University, Canada)
Within the human respiratory tract (HRT), virus diffuses through the periciliary fluid (PCF) bathing the epithelium. But it also undergoes advection: as the mucus layer sitting atop the PCF is pushed along by the ciliated cell's beating cilia, the PCF and its virus contents are also pushed along, upwards towards the nose and mouth. Our PDE model represents the HRT as a one-dimensional track extending from the nose down to the lower HRT, wherein stationary cells interact with virus which moves within (diffusion) and along with (advection) the PCF. In the PDE model, diffusion is negligible in the presence of advection which effectively sweeps away virus, preventing infection from spreading below the depth of deposition. Higher virus production rates (10-fold) are required at higher advection speeds (40 micron/s) to maintain equivalent infection severity and timing. Because virus is entrained upwards, upper parts of the HRT located downstream of the advection flow see more virus than lower parts, and so infection grows, peaks, and resolves later in the lower HRT. Clinically, the infection would appear to progress from the upper towards the lower HRT, as reported in mice. When the PDE model is expanded to include cellular regeneration and an immune response, it reproduces tissue damage levels reported in patients. This new PDE model offers a convenient and unique platform from which to study the localization and spread of respiratory viruses (flu, RSV, COVID-19) within the HRT during an infection.
Venue: via Zoom
Event Official Language: English
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Seminar
Phase Transitions in Biological Systems
September 23 (Wed) at 10:00 - 11:00, 2020
Kyosuke Adachi (Special Postdoctoral Researcher, iTHEMS / Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research (BDR))
Biological systems are built hierarchically by DNA, proteins, cells, tissues, organs, individuals, etc. Recent experiments have clarified the existence of interesting mesoscale phenomena inside cells, where the concept of condensed matter physics such as phase transition can be useful in its understanding. For example, interacting nucleosomes in a chromatin chain can cause the mega-base scale structural change, and sub-micron scale dense droplets of proteins/mRNAs can appear through phase separation. In this talk, I will discuss our recent topics: (i) structural transition of a chromatin with epigenetic marks, (ii) intracellular wetting of phase-separated droplets, and (iii) spontaneous aggregation of self-propelled individuals.
Venue: via Zoom
Event Official Language: English
174 events