iTHEMS Biology Seminar

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.

Seminar

iTHEMS Biology Seminar

Modeling Membrane Morphological Change during Autophagosome Formation

May 14 at 10:00 - 11:00, 2021

Prof. Yuji Sakai (Visiting Scientist, iTHEMS / Assistant Professor, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Kullback-Leibler divergence and stochastic dynamics

May 6 at 10:00 - 11:00, 2021

Dr. Ryosuke Iritani (Research Scientist, iTHEMS)

*Detailed information about the seminar refer to the email.

Event Official Language: English

Seminar

iTHEMS Biology Seminar

The rheotaxis mechanism of swimming ciliates

April 22 at 10:00 - 11:00, 2021

Dr. Yukinori Nishigami (Research Institute for Electronic Science, Hokkaido University)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Liquid condensates in cell nucleus

April 15 at 10:00 - 11:00, 2021

Dr. 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))

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Simple models of cancer growth, MCMC parameter estimation and identifiability

April 8 at 10:00 - 11:00, 2021

Prof. Catherine Beauchemin (Deputy Program Director, iTHEMS / 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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Structural reduction of chemical reaction networks based on topology

April 1 at 10:00 - 11:00, 2021

Dr. Yuji Hirono (Junior Research Group Leader/Assistant Professor, Research Division, 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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

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

March 25 at 10:00 - 11:00, 2021

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Microeconomics of metabolism

March 10 at 10:00 - 11:00, 2021

Mr. Jumpei Yamagishi (Kaneko Laboratory, 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

Seminar

iTHEMS Biology Seminar

Origin of non-linearity of large deformation on DNA stretched

February 25 at 10:00 - 11:00, 2021

Dr. 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

Seminar

iTHEMS Biology Seminar

High-throughput laboratory evolution with machine learning reveals constraints for drug resistance evolution

February 18 at 10:00 - 11:00, 2021

Mr. 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

Seminar

iTHEMS Biology Seminar

A machine learning approach for prediction of mitochondrial proteins in non-model organisms

February 12 at 10:00 - 11:00, 2021

Dr. 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

Seminar

iTHEMS Biology Seminar

System identification of mechano-chemical epithelial sheet dynamics

February 4 at 10:00 - 11:00, 2021

Mr. 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

Seminar

iTHEMS Biology Seminar

Numerical inference of the molecular origin of the cyanobacterial circadian rhythm

January 28 at 10:00 - 11:00, 2021

Dr. 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

Seminar

iTHEMS Biology Seminar

Introduction to Boolean modeling and Boolean networks as information processing units

January 21 at 10:00 - 11:00, 2021

Dr. 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

Seminar

iTHEMS Biology Seminar

What are genes and how can we find them?

January 14 at 10:00 - 11:00, 2021

Dr. 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

Seminar

iTHEMS Biology Seminar

From local resynchronization to global pattern recovery in the zebrafish segmentation clock

January 7 at 10:00 - 11:00, 2021

Dr. 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

Seminar

iTHEMS Biology Seminar

Mathematical model-based quantitative data analysis for COVID-19

December 22 at 10:00 - 11:00, 2020

Prof. 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

Seminar

iTHEMS Biology Seminar

Autoimmune diseases initiated by pathogen infection: mathematical modeling

December 17 at 10:00 - 11:00, 2020

Ms. 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

Seminar

iTHEMS Biology Seminar

How to obtain the large amount of sequence data from the eukaryote

December 10 at 10:00 - 11:00, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Rotifer can be a good model organism for theoretical biology

November 27 at 10:00 - 11:00, 2020

Dr. 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