iTHEMS Biology Seminar
176 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
Conditions for maintaining pseudo-overdominance
May 11 (Thu) at 16:00 - 17:00, 2023
Diala Abu Awad (Associate Professor, Génétique Quantitative et Évolution - Le Moulon, Université Paris-Saclay, France)
Deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. However, arrays of deleterious recessives linked in repulsion could generate appreciable pseudo-overdominance, mimicking overdominant selection that would sustain segregating load. We use analytical approches and simulations to explore whether and for how long pseudo-overdominant (POD) zones can persist once created (e.g., by hybridization between populations fixed for alternative mildly deleterious mutations). Balanced haplotype loads, tight linkage, and moderate to strong cumulative selective effects all serve to maintain POD zones. Tight linkage is key, suggesting that such regions are most likely to arise and persist in low recombination regions (like inversions). Selection and drift unbalance the load, eventually eliminating POD zones, but this process is quite slow, and could influence short term evolution of populations.
Venue: via Zoom
Event Official Language: English
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Seminar
Introduction to Genomics
April 27 (Thu) at 16:00 - 17:00, 2023
Jeffrey Fawcett (Senior Research Scientist, iTHEMS)
A 'genome' is a single set of genetic information of a given individual, which is encoded by the nucleotide sequence of the DNA. For instance, the human genome consists of around 3 billion nucleotide base pairs, although the size and content of the genome differs greatly across species and individuals. Some species such as the budding yeast has a genome as small as 12 million base pairs, whereas other species such as Paris japonica, a flowering plant native to the sub-alpine regions of Japan, is said to have a genome as large as 150 billion base pairs. In this talk, I will give a introduction of what kind of information is contained within a genome, and how that differs across species and individuals. This talk will be introductory and aimed at non-experts including non-biologists.
Venue: via Zoom
Event Official Language: English
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Seminar
Machine learning predicts biological system evolution by gene gains and losses
April 20 (Thu) at 16:00 - 17:00, 2023
Naoki Konno (Ph.D. Student, Department of Biological Sciences, Graduate School of Science, The University of Tokyo)
Prediction of evolution is a fundamental goal of biology with a potential impact on strategic pathogen control and genome engineering. While predictability of short-term and sequence-level evolution has been investigated, that of long-term and system-level evolution has not been systematically examined. Here, we show that evolution of metabolic systems by gene gains and losses is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss events at the branches of the reference phylogenetic tree, suggesting universally shared evolutionary pressures and constraints on metabolic systems. I herein present the mathematical model of Evodictor and our findings on evolutionary rules from physiological and ecological aspects. I will further discuss potential versatility of Evodictor approach to analyze various diversification processes along branching lineage trees, not only evolution, but also developmental processes.
Venue: via Zoom
Event Official Language: English
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Seminar
Why are cell populations maintained via multiple compartments?
April 13 (Thu) at 10:00 - 11:00, 2023
Carmen Molina-París (Researcher, Theoretical Biology and Biophysics, Los Alamos National Laboratory, USA)
We consider the maintenance of “product” cell populations from “progenitor” cells via a sequence of one or more cell types, or compartments, where each cell’s fate is chosen stochastically. If there is only one compartment then large amplification, that is, a large ratio of product cells to progenitors comes with disadvantages. The product cell population is dominated by large families (cells descended from the same progenitor) and many generations separate, on average, product cells from progenitors. These disadvantages are avoided using suitably-constructed sequences of compartments: the amplification factor of a sequence is the product of the amplification factors of each compartment, while the average number of generations is a sum over contributions from each compartment. Passing through multiple compartments is, in fact, an efficient way to maintain a product cell population from a small flux of progenitors, avoiding excessive clonality and minimising the number of rounds of division en route. We analyse the possible descendants of one progenitor cell, families of cells that journey through the sequence of compartments. We find that the ability of product cells to perform their function may be negatively affected by the number of rounds of cell division that separates them from their progenitor, because every round of division brings with it a risk of mutation.
Venue: via Zoom
Event Official Language: English
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Seminar
Organizational meeting
April 6 (Thu) at 16:00 - 17:00, 2023
Catherine Beauchemin (Deputy Program Director, iTHEMS)
The purpose of the organizational meetings is to discuss various topics of interest to the members of iTHEMS in the field of Biology, but also to participants of the iTHEMS BIology Seminar, irrespective of their field. The primary objective of this meeting will be to discuss recruitment of JRAs, SPDRs, and female researchers from Biology into iTHEMS. I hope we can identify the main obstacles and consider together possible solutions. As usual, any additional topic can be brought up spontaneously by participants. Anyone with thoughts about iTHEMS Biology is welcome to join us, no matter their field.
Venue: via Zoom
Event Official Language: English
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Seminar
Asymmetric enzyme kinetics of F1-ATPase resulted from asymmetric allosterism
March 30 (Thu) at 16:00 - 17:00, 2023
Yohei Nakayama (Assistant Professor, Department of Applied Physics, Graduate School of Engineering, Tohoku University)
Bio-molecular machines play various roles in cells where thermal fluctuation is dominant. Since artificial molecular machines are far behind bio-molecular machines for the present, we should begin with understanding how bio-molecular machines are designed to play their roles. We examine the motion of a bio-molecular machine, F1-ATPase, in single molecule experiments. In particular, we focus on the operation of F1-ATPase as ATP synthase in addition to as molecular motor. In this seminar, I talk about the enzyme kinetics, dependence of reaction rate on substrate concentration, of F1-ATPase in ATP synthesis. The experimental result shows that the enzyme kinetics of F1-ATPase in ATP synthesis exhibits weaker dependence on substrate concentration than the ordinary Michaelis-Menten kinetics, whereas that in ATP hydrolysis follows Michaelis-Menten kinetics. Therefore, the enzyme kinetics of F1-ATPase turned out to be asymmetric between ATP synthesis and hydrolysis. We analyzed this asymmetry based on a potential switching model, totally asymmetric allosteric model, whose characteristic is asymmetry in angular dependence of binding rates of substrates. It was shown that the totally asymmetric allosteric model may reproduce the experimental results, where the asymmetry of binding rates is essential. We also discuss physiological roles that the asymmetry of enzyme kinetics may play.
Venue: via Zoom
Event Official Language: English
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Seminar
Warming reduces the density-dependent divergence in emergence time for two competing parasitoid species
March 23 (Thu) at 16:00 - 17:00, 2023
Midori Tuda (Associate Professor, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University)
Climate change is expected to directly affect ectothermic species through their sensitivity to temperature, with cascading effects on populations and communities. Here we experimentally tested predictions from two non-exclusive hypotheses concerning the impacts of elevated temperature (+2°C) on interactions between a single host species (the azuki bean beetle) and two species of parasitoid wasps. We hypothesized that increasing temperature shortens the time that the host is vulnerable to parasitoid attack. This change in available resource should heighten intra- and interspecific competition among parasitoids, which could induce divergence in emergence times. We found that intraspecific competition of both parasitoid species was more intense than interspecific competition irrespective of temperature. The difference (d) in the emergence times of the two parasitoid species increased with the density of each parasitoid but decreased at the elevated temperature. Both parasitoids emerged sooner at the elevated temperature and experienced a reduction in body size. Thus, high levels of intraspecific competition (along with the consequent reduction in body size) may have attenuated the intensity of interspecific competition at the elevated temperature despite a reduction in the differentiation of emergence times.
Venue: via Zoom
Event Official Language: English
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Seminar
Reproductive interference can affect trait diversity of closely related animal species
March 9 (Thu) at 16:00 - 17:00, 2023
Keiichi Morita (Ph.D. Student, School of Advanced Sciences Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI))
Previous theoretical studies have considered that evolution driven by resource competition is important for the creation and maintenance of biodiversity. Recently, reproductive interference caused by misrecognition of sexual traits such as calling between closely related species has been increasingly important for the creation and maintenance of diversity, but the impact of reproductive interference on trait diversity between closely related species remains unresolved. In this study, we combined population dynamics model with reproductive interference in two closely related species with an evolutionary model of traits related to reproduction to examine the impact of reproductive interference on the evolutionary consequences of reproductive traits in the two closely related species. The model assumed a trade-off in which reproductive interference weakens as reproductive traits diverge between the two species, but predation pressure increases as the reproductive traits diverge from their optimum traits in their habitat. For simplicity, we assumed that only one species evolves. Our model analysis revealed that convergence and divergence of traits of two closely related species occurs depending on initial trait divergence. Also, under the parameter condition where trait convergence occurs, large mutation makes trait divergence possible. Our model will provide a new framework for understanding evolutionary dynamics in ecological communities containing closely related species.
Venue: via Zoom
Event Official Language: English
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Seminar
Elasticities of population growth and their significance to evolutionary biology
February 9 (Thu) at 16:00 - 17:00, 2023
Stefano Giaimo (Postdoc, Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Germany)
The elasticity of population growth to a demographic parameter quantifies the proportional sensitivity of population growth to such parameter. In this talk, I will illustrate some cases where elasticities of population growth to demographic parameters acquire a special importance to evolutionary biology. In particular, I will discuss the relevance of these elasticities in studying the evolution of aging, their role in the computation of the generation time and their relationship to some trade-offs organisms may face as they optimise their fitness.
Venue: via Zoom
Event Official Language: English
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Seminar
Universal Biology in Adaptation and Evolution: Dimensional Reduction and Fluctuation-Response Relationship
February 2 (Thu) at 16:00 - 17:00, 2023
Kunihiko Kaneko (Professor, Niels Bohr Institute, University of Copenhagen, Denmark)
A macroscopic theory for adaptive changes of cells is presented, based on consistency between cellular growth and molecular replication, as well as robustness of fitted phenotypes against perturbations. Adaptive changes in high-dimensional phenotypes are shown to be restricted within a low-dimensional slow manifold, from which a macroscopic law for cellular states is derived, as is confirmed by adaptation experiments of bacteria under stress. The theory is extended to phenotypic evolution, leading to proportionality between phenotypic responses against genetic evolution and by environmental adaptation, which also explains the evolutionary fluctuation-response relationship previously uncovered. Relevance of statistical-physics and dynamical-systems approach is discussed.
Venue: via Zoom
Event Official Language: English
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Seminar
Mathematical models inspired by the Lenski experiment
January 19 (Thu) at 10:00 - 11:00, 2023
Adrian Gonzalez-Casanova (Neyman Visiting Assistant Professor, University of California, Berkeley, USA / Associate Professor, National Autonomous University of Mexico, Mexico)
We will discuss the basic models of mathematical population genetics and see how to apply them to the study of the Lenski experiment. Furthermore, we will describe novel models that are capable of providing a parsimonious explanation of the deceleration of the relative fitness and can be used to attack questions such as, is it advantageous to be efficient? If time permits, we will also discuss examples of mathematical modelling beyond the Lenski experiment, including the study of populations of bacteria carrying plasmids.
Venue: via Zoom
Event Official Language: English
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Seminar
Basic of microbial ecology and applicability of your life and research
January 12 (Thu) at 16:00 - 17:00, 2023
Daiki Kumakura (Ph.D. Student, Graduate School of Life Science, Hokkaido University)
Microbial ecology is a fascinating field that examines the various environments in which microbes can thrive and their potential applications to human life. In this seminar, I will delve into four main topics:
Venue: via Zoom
Event Official Language: English
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Seminar
A cell membrane model that reproduces cortical flow-driven cell migration and collective movement
January 5 (Thu) at 16:00 - 17:00, 2023
Katsuhiko Sato (Associate Professor, Research Institute for Electronic Science, Hokkaido University)
Cellular migration is a key component of numerous biological processes, including the morphogenesis of multicellular organisms, wound healing, and cancer metastasis, where cells adhere to each other to form a cluster and collectively migrate. Although the mechanisms controlling single-cell migration are relatively well understood, those underlying multiple-cell migration still remain unclear. A key reason for this knowledge gap is the so-called many-body problem. That is, many forces—including contraction forces from actomyosin networks, hydrostatic pressure from the cytosol, frictional forces from the substrate, and forces from adjacent cells—contribute to cell cluster movement, making it challenging to model, and ultimately elucidate, the final result of these forces. In this talk, I provide a two-dimensional cell membrane model that represents cells on a substrate with polygons and expresses various mechanical forces on the cell surface, keeping these forces balanced at all times by neglecting cell inertia. The model is discrete but equivalent to a continuous model if appropriate replacement rules for cell surface segments are chosen. When cells are given a polarity, expressed by a direction-dependent surface tension reflecting the location dependence of contraction and adhesion on a cell boundary, the cell surface begins to flow from front to rear as a result of force balance. This flow produces unidirectional cell movement, not only for a single cell but also for multiple cells in a cluster, with migration speeds that coincide with analytical results from a continuous model. Further, if the direction of cell polarity is tilted with respect to the cluster center, surface flow induces cell cluster rotation. The reason why this model moves while keeping force balance on cell surface (i.e., under no net forces from outside) is because of the implicit inflow and outflow of cell surface components through the inside of the cell. I provide an analytical formula connecting cell migration speed and turnover rate of cell surface components.
Venue: via Zoom
Event Official Language: English
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Seminar
How to infer evolutionary history
December 22 (Thu) at 16:00 - 17:00, 2022
Jeffrey Fawcett (Senior Research Scientist, iTHEMS)
One main goal of evolutionary studies is to infer the evolutionary that explains the current diversity. We want to infer the ancestral state and what kind of changes occurred from the previous ancestral state to the current state. In other words, we want to infer the phylogenetic relationship that explains the branching pattern that leads to the current diversity and infer the state at each node and the changes that occurred in each branch of the phylogeny. In this talk, I will introduce some basic concepts that are used in evolutionary biology to tackle these questions, especially how molecular data, i.e., DNA and protein sequence data, can be utilized. This talk will be introductory and aimed at non-experts including non-biologists.
Venue: via Zoom
Event Official Language: English
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Seminar
Chemophoresis Engine: Theory of ATPase-driven Cargo Transport
December 15 (Thu) at 16:00 - 17:00, 2022
Takeshi Sugawara (Project Researcher, Universal Biology Institute, The University of Tokyo)
The formation of macromolecule patterns depending on chemical concentration under non-equilibrium conditions, first observed during morphogenesis, has recently been observed at the intracellular level, and its relevance as intracellular morphogen has been demonstrated in the case of bacterial cell division. These studies have discussed how cargos maintain positional information provided by chemical gradients. However, how cargo transports are directly mediated by chemical gradients remains unknown. Based on the previously proposed mechanism of chemotaxis-like behavior of cargos (referred to as chemophoresis), we introduce the chemophoresis engine as a physicochemical mechanism of cargo motion, which transforms chemical free energy to directed motion through the catalytic ATP hydrolysis [1]. We propose its possible role as a universal principle of hydrolysis-driven intracellular transport.
Venue: via Zoom
Event Official Language: English
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Seminar
Community assembly and species coexistence in the heterogeneous world
November 28 (Mon) at 16:00 - 17:00, 2022
Naoto Shinohara (Assistant Professor, Graduate School of Life Sciences, Tohoku University)
How ecological communities are assembled and maintained is a fundamental question in community ecology. To tackle this challenge in the heterogeneous world, we need to understand how community assembly patterns change with environmental gradients and how species coexist in temporally fluctuating environments. In the first of my talk, I introduce our study on how plant community assembly patterns change along with the largest global environmental gradient, the latitudinal gradient. Then, I will present how the seasonal variability of environments contributes to the coexistence of phytoplankton species in a lake. These results altogether uncover how spatiotemporal heterogeneity of environments forms ecological communities in nature.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
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Seminar
RNA-Puzzles - the evaluation and automation of RNA 3D structure
November 24 (Thu) at 16:00 - 17:00, 2022
Zhichao (Chichau) Miao (Principal Investigator, Guangzhou Laboratory, China / Guangzhou Medical University, China)
RNA-Puzzles is a collective endeavour dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. Systematic protocols for comparing models and crystal structures are described and analyzed. In RNA-Puzzles, we discuss a) the capabilities and limitations of current methods of 3D RNA structure based on sequences; b) the progress in RNA structure prediction; c) the possible bottlenecks that hold back the field; d) the comparison between the automated web server and human experts; e) the prediction rules, such as coaxial stacking; f) the prediction of structural details and ligand binding; g) the development of novel prediction methods; and h) the potential improvements to be made. Till now, 37 RNAs with crystal structures have been predicted, while many of them have achieved high accuracy in comparison with the crystal structures. We have summarized part of our results in three papers and two community-wide meetings. With the results in RNA-Puzzles, we illustrate that the current bottlenecks in the field may lie in the prediction of non-Watson-Crick interactions and the reconstruction of the global topology. Correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution. For the model evaluation, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods, (ii) 3D structure normalization, analysis, manipulation, visualization tools and (iii) 3D structure comparison metric tools. With the increasing number of RNA structures being solved as well as the high-throughput biochemical experiments, RNA 3D structure prediction is becoming routine and accurate. Structure modelling may effectively help in understanding the viral RNA structures, including the SARS-CoV-2.
Venue: via Zoom
Event Official Language: English
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Seminar
Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism
November 17 (Thu) at 18:00 - 19:00, 2022
Yusuke Himeoka (Assistant Professor, Universal Biology Institute, The University of Tokyo)
Physiological states of bacterial cells exhibit a wide spectrum of timescale. Under nutrient-rich conditions, most of the cells in an isogenic bacterial population grow at certain rates, while a small subpopulation sometimes stays in a dormant state where the growth rates slow down by orders of magnitude. For revealing the origins of such heterogeneity of timescales, we studied the kinetic model of Escherichia coli central carbon metabolism. We found that the model robustly exhibits both the growing- and the dormant state. Performing the model reduction, we have revealed the necessary conditions for the distinct behaviour, namely, the depletion of energy due to the futile cycle and its non-uniform impact on the kinetics because of the coexistence of the energy currency-coupled and uncoupled reactions as well as branching of the network.
Venue: via Zoom
Event Official Language: English
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Seminar
Sociogenesis: motivations and first steps
November 10 (Thu) at 16:00 - 17:00, 2022
Cédric Ho Thanh (Postdoctoral Researcher, Prediction Science Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Sociogenesis is a project that aims to study emergent social behaviors of multi-agent systems. In its simplest form, and agent simply seeks to survive by consuming food and maximizing some happiness score. In this presentation, I will discuss some motivations and inspirations of this project, as well as the challenges to get an agent to survive on its own. I will then showcase some methods to evaluate the quality of agents and their underlying architecture beyond simply looking at their lifespan. I will then conclude with some potential applications. No prior knowledge in reinforcement/deep learning is required to attend this presentation. This work is still mostly at an exploratory stage, so discussions and inputs from the audience are more than welcome!
Venue: via Zoom
Event Official Language: English
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Seminar
Migration dynamics and model of cells crawling on a matrix with cell-scale stiffness heterogeneity
October 27 (Thu) at 16:00 - 17:00, 2022
Hiroyuki Ebata (Assistant Professor, Graduate School of Science, Kyushu University)
In living tissues where cells migrate, spatial distribution of mechanical properties, especially matrix stiffness, are generally heterogenous with cell-scales ranging from 10 to 1000 μm. Since the cell migration in our body plays critical role in morphogenesis, wound healing, and cancer metastasis, it is essential to understand the migratory dynamics on the matrix with cell-scale stiffness heterogeneity. However, while cellular responses to homogeneous matrix have been extensively explored, studies of the cell motility with stiffness heterogeneity have been limited to the directional movement (durotaxis) driven by a simple stiffness gradient. Thus, we need to elucidate how cell migration is determined through the interaction among cell-scale stiffness heterogeneity and cellular responses such as dynamics of the cell-matrix adhesion site, the intracellular prestress, and cell shape. In this talk, we introduce our experiments on cell motility, shaping, adhesion, and traction forces at long time scales using microelastically patterned hydrogels that enable us to systematically control the cell-scale heterogeneity of the matrix-stiffness. Using microelastically patterned hydrogels, we showed that the cell exhibited a general mode of durotaxis depending on the shape and size of the stiff domains, which was coincided with the extraordinarily large fluctuation of the traction force. We proposed a cell migration model based on equations of a deformable self-propelled particle adopting an amoeboid swimmer-like velocity-shape relationship. By considering the cellular response to stiffness gradients, the model can reproduce general durotaxis driven by cell-scale heterogeneity of the matrix-stiffness.
Venue: via Zoom
Event Official Language: English
176 events