iTHEMS Biology Seminar

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

October 21 (Thu) 10:00 - 11:00, 2021

Hiroshi Yokota (Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

Understanding the effect of defective, interfering influenza virus

October 14 (Thu) 10:00 - 11:00, 2021

Catherine Beauchemin (Deputy Program Director, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

Speed limit for population dynamics

October 7 (Thu) 10:00 - 11:00, 2021

Kyosuke Adachi (Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research (BDR))

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.

Venue: via Zoom

Event Official Language: English

Evolutionary dynamics of seasonal influenza viruses

September 30 (Thu) 10:00 - 11:00, 2021

Takashi Okada (Senior Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

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

September 9 (Thu) 10:00 - 11:00, 2021

Euki Yazaki (Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

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

September 2 (Thu) 10:00 - 11:00, 2021

Yingying Xu (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

Mathematical analysis of body temperature fluctuation during hibernation

August 26 (Thu) 10:00 - 11:00, 2021

Gen Kurosawa (Senior Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

The damped circadian oscillator in cyanobacterium: kaiA-less oscillator

August 19 (Thu) 10:00 - 11:00, 2021

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

Rational design of autonomous, peptide-based ion channels

August 5 (Thu) 10:00 - 11:00, 2021

Ai Niitsu (Special 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

Application of bioenergetics to microbial modeling

July 29 (Thu) 10:00 - 11:00, 2021

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

How nucleus size affects chromatin motion? - Experimental measurements and a polymer physics theory

July 1 (Thu) 10:00 - 11:00, 2021

Takahiro Sakaue (Associate Professor, Department of Physics and Mathematics, College of Science and Engineering, Aoyama Gakuin University)

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.

Venue: via Zoom

Event Official Language: English

Period variability can provide valuable information in oscillatory systems

June 24 (Thu) 10:00 - 11:00, 2021

Fumito Mori (Assistant Professor, Department of Human Science, Faculty of Design, Kyushu University)

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.

Venue: via Zoom

Event Official Language: English

The origin and dispersal of buckwheat

June 10 (Thu) 10:00 - 11:00, 2021

Jeffrey Fawcett (Senior Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))

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.

Venue: via Zoom

Event Official Language: English

An overview of genome-wide epistasis and co-selection analysis

June 3 (Thu) 10:00 - 11:00, 2021

Yingying Xu (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))

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.

Venue: via Zoom

Event Official Language: English

A Mathematical Model for Stem Cell Competition to Maintain a Cell Pool Injured by Radiation Exposure

May 27 (Thu) 10:00 - 11:00, 2021

Kouki Uchinomiya (Central Research Institute of Electric Power Industry)

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.

Venue: via Zoom

Event Official Language: English

Organ-to-organ two-way coupling contributes to the stabilization of circadian clock in Arabidopsis.

May 20 (Thu) 10:00 - 11:00, 2021

Kyohei Uemoto (Kyoto University / NARA Institute of Science and Technology)

Circadian clocks increase plant fitness by anticipating periodic environmental changes using unstable temporal information perceived in each tissue/organ. However, little is known about how such local and noisy temporal information regulates global and coordinated plant growth. Here, we show that nutrient-mediated two-way communication between shoots and roots stabilizes circadian rhythms and aids plant growth. The photosynthetic product, sucrose, is transported from the shoot to the root, where it regulates the expression of a clock gene and nutrients uptake rhythms. A lack of nutrient rhythms destabilizes the shoot circadian rhythms and reduces the growth rate. Our mathematical model supports that two-way communication between organs reduces the heterogeneity of the circadian rhythm, thereby maintaining the robustness of the circadian clock in a noisy environment. As with feedback loops in other hierarchies, nutrient-mediated shoot-root interorgan communication of the circadian clock is advantageous for proper growth under fluctuating environmental conditions. *Please refer to the email to get access to the Zoom meeting room.

Venue: via Zoom

Event Official Language: English

Modeling Membrane Morphological Change during Autophagosome Formation

May 14 (Fri) 10:00 - 11:00, 2021

Yuji Sakai (Visiting Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

Kullback-Leibler divergence and stochastic dynamics

May 6 (Thu) 10:00 - 11:00, 2021

Ryosuke Iritani (Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))

*Detailed information about the seminar refer to the email.

Event Official Language: English

The rheotaxis mechanism of swimming ciliates

April 22 (Thu) 10:00 - 11:00, 2021

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

Liquid condensates in cell nucleus

April 15 (Thu) 10:00 - 11:00, 2021

Kyosuke Adachi (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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