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

On Flow and Form at Low Reynolds Number

January 27 at 10:00 - 11:00, 2022

Prof. Kenta Ishimoto (Associate Professor, Research Institute for Mathematical Sciences (RIMS), Kyoto University)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

A study of biological systems from topological point of view

January 20 at 10:00 - 11:00, 2022

Dr. Hiroyasu Miyazaki (Senior Research Scientist, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

A comprehensive view of the SARS-CoV-2 infection process

January 13 at 10:00 - 11:00, 2022

Dr. Wataru Nishima (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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Physics of nuclear bodies

January 6 at 10:00 - 11:00, 2022

Prof. Tetsuya Yamamoto (Specially Appointed Associate Professor, Institute for Chemical Reaction Design and Discovery, Hokkaido University)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Hidden Markov Models and their applications

December 23 at 10:00 - 11:00, 2021

Dr. Takashi Okada (Senior Research Scientist, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Revisiting Standard Methods for Phylogenetic Tree Inference

December 16 at 10:00 - 11:00, 2021

Dr. Motomu Matsui (Research Associate, Graduate School of Science, The University of Tokyo)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Selective inference for testing trees and edges in hierarchical clustering and phylogeny

December 9 at 10:00 - 11:00, 2021

Prof. Hidetoshi Shimodaira (Professor, Graduate School of Informatics, Kyoto University / Team Leader, Mathematical Statistics Team, RIKEN Center for Advanced Intelligence Project (AIP))

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Spatial structure in ecology: the effects of dispersal network structure on biodiversity pattern and stability in metacommunities

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

Dr. Yuka Suzuki (Okinawa Institute of Science and Technology Graduate University (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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Toward mathematical medicine: development of a new drug and digital medicine for sleep disorders

November 11 at 12:30 - 13:30, 2021

Dr. 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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Protein structure modeling from cryo-electron microscopy data

November 4 at 13:30 - 14:30, 2021

Dr. Takaharu Mori (Senior research scientist, Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research (CPR))

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Nonlinear dynamics in frog choruses

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

Prof. Ikkyu Aihara (Associate Professor, Faculty of Engineering, Information and Systems, University of Tsukuba)

Male frogs produce sounds to attract conspecific females as well as advertise their own territories to other males. Subsequently male frogs acoustically interact with each other, which induces various types of synchronized behavior. In this seminar, I will introduce the synchronized calling behavior of actual male frogs as well as theoretical studies using a phase oscillator model [1, 2]. Next, I will introduce our recent projects on the identification of the phase oscillator model from empirical data [3] and the extension of the model to a hybrid dynamical system in which male frogs intermittently switch their behavioral mode based on internal condition and also the interaction with other males [4].

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Evaluation of origin of driving force for loop formation in a chromatin fiber

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

Dr. Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Understanding the effect of defective, interfering influenza virus

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

Prof. Catherine Beauchemin (Deputy Program Director, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Evolutionary dynamics of seasonal influenza viruses

September 30 at 10:00 - 11:00, 2021

Dr. Takashi Okada (Senior Research Scientist, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

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

September 9 at 10:00 - 11:00, 2021

Dr. Euki Yazaki (Postdoctoral Researcher, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

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

September 2 at 10:00 - 11:00, 2021

Dr. Yingying Xu (Special Postdoctoral Researcher, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Mathematical analysis of body temperature fluctuation during hibernation

August 26 at 10:00 - 11:00, 2021

Dr. Gen Kurosawa (Senior Research Scientist, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

The damped circadian oscillator in cyanobacterium: kaiA-less oscillator

August 19 at 10:00 - 11:00, 2021

Dr. Naohiro Kawamoto (Researcher, Research Center for Solar Energy Chemistry, Osaka University)

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Rational design of autonomous, peptide-based ion channels

August 5 at 10:00 - 11:00, 2021

Dr. Ai Niitsu (Postdoctoral Researcher, Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research (CPR))

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.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Application of bioenergetics to microbial modeling

July 29 at 10:00 - 11:00, 2021

Prof. Mayumi Seto (Assistant Professor, Department of Chmistry, Biology, and Environmental Science, Faculty of Science, Nara Women's University)

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.

Venue: via Zoom

Event Official Language: English