iTHEMS生物学セミナー

iTHEMS Biology welcomes 2 new members!

2025年5月15日(木) 13:00 - 14:15

イザク・プラナス シッジャ (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 特別研究員)
アントワーヌ・ディエズ (理化学研究所 数理創造研究センター (iTHEMS) 数理展開部門 数学応用研究チーム 研究員)

This meeting will be used to welcome 2 new members to the iTHEMS Biology Study Group; Postdoc Isaac Planas-Sitjà and Senior Researcher Antoine Diez. They will each give us a 15-20 min talk to introduce their research. If time permits, let's also use this time to catch up on each other's current research. I hope that many people will join us to welcome these new members and come meet them and hear about their research.

会場: 研究本館 4階 共有スペースとZoomのハイブリッド開催

イベント公式言語: 英語

The role of the visual information of fish schooling via selective decision-making

2025年5月8日(木) 16:00 - 17:00

伊藤 将 (東北大学 大学院理学研究科 物理学専攻 博士課程)

Visual cues play crucial roles in the collective motion of animals, birds, fish, and insects. Recently, experiments have revealed that organisms such as fish selectively utilize a portion, rather than the entirety, of visual information. This method of the visual interaction avoids heavy load for small brain of the organisms. However, the previous models using visual interaction implicitly assume that an agent interacts with all visible neighbors. Therefore, we study the effect of the selective decision-making on the collective motion via the agent-based model and the coarse grained continuous model. In the former study, we have constructed a visual model which takes into account the motion of visual attention of agents induced by the visual stimuli, and our model can simultaneously show the spontaneous appearance of various collective patterns and the bifurcation process of the tracking of a neighbor. The later study, the agents corresponds to the density field by the coarse graining, and the visual occlusion is treated in a self-consistent manner via a coarse-grained density field, which renders the interaction effectively pairwise. The model exhibits a discontinuous transition as in the conventional models by the local collision, and but the discontinuity is weakened by the non-locality of visual interaction. Our studies clarify the comprehensive coincidence with experimental results via selective decision-making and the essential role of non-locality in the visual interactions.

会場: via Zoom

イベント公式言語: 英語

iTHEMS Biology Study Group April Launch Meeting (Part 2)

2025年4月10日(木) 13:00 - 14:00

Let's launch our Biology Study Group activities for the new year (Part 2 of 2). This meeting will be used to (1) say welcome to new member (SPDR Kenji Okubo, and Postdoc Lucas Sort); (2) discuss Biology seminar management in light of the new iTHEMS Centre; and (3) catch up on each other's current research. Since this will probably take us 2h, this will be Part 2 of 2 (Part 1 was on 4/3). On 4/10 (Part 2) we will get a 15 min introduction talk by Postdoc Lucas Sort. This meeting is open to all RIKEN and guests. You do not need to be a member of the iTHEMS Biology Study Group.

会場: via Zoom / 研究本館 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

iTHEMS Biology Study Group April Launch Meeting (Part 1)

2025年4月3日(木) 14:00 - 15:00

Let's launch our Biology Study Group activities for the new year (Part 1 of 2). This meeting will be used to (1) say welcome to new member (SPDR Kenji Okubo, and Postdoc Lucas Sort); (2) discuss Biology seminar management in light of the new iTHEMS Centre; and (3) catch up on each other's current research. Since this will probably take us 2h, this will be Part 1 of 2 (Part 2 on 4/10). On 4/3 (Part 1) we will get a 15 min introduction talk by SPDR Kenji Okubo. This meeting is open to all RIKEN and guests. You do not need to be a member of the iTHEMS Biology Study Group.

会場: via Zoom / 研究本館 4階 共有スペース

イベント公式言語: 英語

The rarer-sex effect

2025年3月27日(木) 16:00 - 17:00

Andy Gardner (Professor, School of Biology, University of St Andrews, UK)

The study of sex allocation—that is, the investment of resources into male versus female reproductive effort—yields among the best quantitative evidence for Darwinian adaptation, and has long enjoyed a tight and productive interplay of theoretical and empirical research. The fitness consequences of an individual's sex allocation decisions depend crucially upon the sex allocation behaviour of others and, accordingly, sex allocation is readily conceptualized in terms of an evolutionary game. I will discuss the historical development of understanding of a fundamental driver of the evolution of sex allocation—the rarer-sex effect—from its inception in the writing of Charles Darwin in 1871 through to its explicit framing in terms of consanguinity and reproductive value by William D. Hamilton in 1972. I will show that step-wise development of theory proceeded through refinements in the conceptualization of the strategy set, the payoff function and the unbeatable strategy.

会場: 研究本館 4階 445-447号室 (Hybrid) / via Zoom

イベント公式言語: 英語

It’s about time! Daily rhythms in malaria infections matter for parasite survival and transmission

2025年3月13日(木) 17:00 - 18:00

Reece Sarah (Professor, University of Edinburgh, UK)

The Reece lab provides a unique perspective on parasites, examining their world within hosts and vectors (insects that transmit parasites). Working at the intersection of parasitology, chronobiology, and evolutionary ecology, our research asks: “what makes a successful parasite” and “what are their evolutionary limits”? Unlike most infection research, that focuses solely on genetics and molecular aspects, our approach considers parasites in their ecological and evolutionary contexts. This has enabled us to uncover the sophisticated strategies that malaria parasites possess, such as optimizing the balance between transmission and replication, strategic investment in each sex of transmission stages, and scheduling activities according to the time of day. By understanding how parasites navigate their challenging lifestyles and seize opportunities, we contribute to interventions that can outsmart parasites and reduce the risk of resistance evolution. Our findings extend beyond the laboratory, showcasing the potential of environmental research to curb the impact of parasitic infections, whether in humans, wildlife, livestock, or agriculture, and helping to protect ecosystems.

会場: via Zoom

イベント公式言語: 英語

From the Andes to the Lab Bench: Genomic, Evolutionary, and Functional Insights into Amylase Gene Variation and Metabolic Adaptation

2025年3月6日(木) 16:00 - 17:00

Gokcumen Omer (Professor, Department of Biological Sciences, University at Buffalo, USA)

Our laboratory investigates how genomic structural variations (SVs) uniquely drive biological diversity and evolution, surpassing smaller-scale variations like single nucleotide polymorphisms. This talk highlights our work on the amylase locus, a rapidly evolving genomic region shaped by dietary adaptations, frequent duplications, and high mutation rates. I will discuss its convergent evolution across mammals, driven by natural selection linked to starch-rich diets, and describe how long-read sequencing uncovered the mutational mechanisms behind its rapid evolution. We also examine local positive selection in indigenous Andean populations with historically starch-rich diets and how these adaptations impact metabolic health. Finally, I will summarize functional experiments in transgenic mice and diabetic-prone Western Nile rats, relevant models for human metabolism, to investigate the broader metabolic roles of amylase gene duplications. This research provides a roadmap for studying complex SVs in evolution, offering insights into human adaptation and health.

会場: via Zoom / セミナー室 (359号室)

イベント公式言語: 英語

Density-dependent dispersal promotes female-biased sex allocation in viscous populations: From theory to experiment

2025年3月4日(火) 16:00 - 17:00

Chedhawat Chokechaipaisarn (Ph.D Student, School of Biology, University of St Andrews, UK)

A key prediction in sex allocation theory is that the optimal sex ratio is completely independent to the rate of dispersal. This result challenges the notion of any relationship between dispersal and sex ratio evolution. However, the invariant result is based on the assumption that an individual's dispersal behaviour is not modulated by population density. In this talk, I will explore how density-dependent dispersal impact upon the evolution of sex allocation in a viscous-population setting. Additionally, I will discuss the process of testing this prediction through experimental evolution in spider mites.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Genome and Sex Chromosome Analyses of Japanese Frogs Carrying Both XY and ZW Chromosomes Within the Same Species

2025年2月27日(木) 16:00 - 17:00

桂 有加子 (京都大学 京都大学ヒト行動進化研究センター 助教)

The evolution of sex chromosomes, particularly sex chromosome turnover, is a complex and fascinating topic in genetics and evolutionary biology. Sex chromosome turnover refers to the process in which the sex chromosome system changes from XY to ZW (or vice versa), or in which sex chromosomes with different evolutionary origins emerge within the same system (e.g., from one XY system to another XY system). To study sex chromosome turnover, we focus on the Japanese frog (Glandirana rugosa), which possesses both XY and ZW sex chromosomes within the same species, and investigate the molecular mechanisms behind the turnover in the frog (Review: Hayashi et al. JB 2024). Previously, we sequenced the nuclear genome of the ZZ frog (Katsura et al. LSA 2021) and identified sex-linked genes in two populations of the XY and ZW frogs (Miura et al. Mol Ecol 2022). It has been suggested that sex chromosomes originating from at least three different chromosomal lineages have independently emerged within this species. The frogs have a total of 13 chromosomes, and in two populations (Tokai/Eastern Central Japan and Hokuriku-Tohoku/North-Western Japan), chromosome 7 has morphologically differentiated into both ZW and XY chromosomes. However, in other populations, sex chromosomes do not show any morphological differentiation. In this seminar, I introduce the background of our sex chromosome study and present the results of sequence comparisons of morphologically differentiated XY and ZW chromosomes, as well as findings from our analyses of populations, genome, and transcriptome.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Exploring the evolutionary fate of a mutualistic community using automated microbial culture system

2025年2月20日(木) 16:00 - 17:00

砂川 純也 (北海道大学 大学院生命科学院 生命科学専攻 博士課程)

Microbes are ubiquitous around the world, forming systems where they interact through competition or cooperation. Especially in the form of cooperation, exchange of essential metabolites, known as metabolic cross-feeding, plays a fundamental role in the assembly of microbial communities. An extreme case of metabolic cross-feeding is an obligate mutualism, where one organism can only grow with the help of a partner supplying metabolites (e.g., amino acid). When they face environmental stresses such as antibiotics, it is unclear whether the benefit that causes the formation of obligate ecological mutualism may benefit (or cost) the members to increases (inhibits) resistance through interactions at the evolutionary scale. Another fascinating question is whether an additional benefit (e.g., an enzyme that helps the community persistence against environmental change) will select the community to increase the resistance. Here, I will report my ongoing research progress of obligate cross-feedings involving β-lactamase and discuss the conditions where the benefit can overcome the cost of the obligate interaction. I have started to address this issue by conducting laboratory evolution experiments with an automated culture system which can automatically adjust the strength of the stress (i.e., concentration of the antibiotics), so that the focal microbes have to get evolved. I will also share my story about building this automated culture system.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Application of genetics and genomics to breeding

2025年2月13日(木) 16:00 - 17:30

ジェフリ・フォーセット (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)

Humans have domesticated and modified several plants and animals over the course of history to achieve food security. However, drastic changes are required in order to meet the needs of a growing population while facing global warming. In particular, utilizing and improving the productivity of unutilized or underutilized resources such as minor crops, aquatic species, and insects are thought to be essential. Here, I will provide an overview of how humans have been modifying organisms by selective breeding, the role of genetics and genomics in modern selective breeding, and the challenges we are currently facing. This talk will be aimed at non-experts/non-biologists and will cover the basics of genetics.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

A coarse-grained model of disordered RNA for simulations of biomolecular condensates

2025年2月6日(木) 16:00 - 17:00

安田 一希 (慶應義塾大学 大学院理工学研究科 博士課程)

Protein-RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models of intrinsically disordered proteins have been developed to shed light on and predict single-chain properties and phase separation. An RNA model compatible with such models for disordered proteins would enable the study of complex biomolecular mixtures involving RNA. Here, we present a sequence-independent coarse-grained, two-bead-per-nucleotide model of disordered, flexible RNA based on a hydropathy scale. We parameterize the model, which we term CALVADOS-RNA, using a combination of bottom-up and top-down approaches to reproduce local RNA geometry and intramolecular interactions based on atomistic simulations and in vitro experiments. The model semi-quantitatively captures several aspects of RNA-RNA and RNA-protein interactions. We examined RNA-RNA interactions by comparing calculated and experimental virial coefficients, and non-specific RNA-protein interaction by studying reentrant phase behavior of protein-RNA mixtures. We demonstrate the utility of the model by simulating the formation of mixed condensates consisting of the disordered region of MED1 and RNA chains, and the selective partitioning of disordered regions from transcription factors into these, and compare the results to experiments. Despite the simplicity of our model we show that it captures several key aspects of protein-RNA interactions and may therefore be used as a baseline model to study several aspects of the biophysics and biology of protein-RNA condensates.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Effective size and dimension, in biology and beyond

2025年1月30日(木) 16:00 - 17:00

入谷 亮介 (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)

This talk will be a very short, introductory talk on some fundamental concepts of “effective size” from population-biological, statistical, and mathematical viewpoints.

会場: via Zoom

イベント公式言語: 英語

Quantitative Characterization of the Cellular Physical Properties to Understand the Organ Regeneration and Cancer Progression

2025年1月23日(木) 16:00 - 17:00

松﨑 賢寿 (大阪大学 大学院工学研究科附属フューチャーイノベーションセンター テクノアリーナ准教授 / 大阪大学 大学院工学研究科物理学系専攻応用物理学コース 助教)

Since the discovery of regulating the differentiation of "single" stem cells by extracellular mechanics, researchers have focused on the mechanobiology of single cells. Our collaborative studies provided the first breakthrough to identify optimal mechanics for multi-cellular, liver organogenesis (Takebe, .., Matsuzaki,.., Yoshikawa et al., Cell Stem Cell 2015, Stem Cell Reports 2018). My motivation is to be a pioneer internationally in understanding the role of heterogenic physical properties in multi-cellular related life-phenomena such as cancer cell adhesion (Matsuzaki et al., Phys Chem Chem Phys 2018, Bioconjugate Chem 2023, PNAS 2024, Osaka University Award 2024.), regeneration of colon/muscle (iScience 2022, Taniguchi,.., Matsuzaki et al., Mucosal Immunology 2023, J. Phys Chem Letter 2014, 2022, 2024.), and bone (Mizuno, .., Matsuzaki et al., Stem Cell Res. Ther. 2022, iScience 2024). In my presentation, I will overview the recent progress in developing fluorescence/interference microscopy combining atomic force microscopy (AFM), and its application to organ regeneration and cancer progression.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Principles of the evolution of human social structures: kinship and gift-giving

2025年1月16日(木) 16:00 - 17:15

板尾 健司 (理化学研究所 脳神経科学研究センター (CBS) 計算論的集団力学連携ユニット 基礎科学特別研究員)

Anthropologists have long noted structural similarities among geographically distant societies. To investigate the origins of these patterns, I develop simple models of human interactions based on field observations, simulating the emergence of social structures. This talk focuses on two key topics. The first examines the evolution of kinship structures in clan societies [1, 2, 3]. By modeling kin and in-law cooperation alongside mating competition, I show how cultural groups with specific marriage rules spontaneously emerge. The second explores the transition of social organizations through competitive gift-giving [4, 5]. By modeling how gifts deliver material goods to recipients and confer social reputation upon donors, I demonstrate transitions across four phases—band, tribe, chiefdom, and kingdom—each characterized by distinct social networks and distributions of wealth and reputation. In both cases, I highlight the alignment between theoretical predictions and empirical observations, offering quantitative criteria and empirically measurable explanatory parameters for classifying social structures.

会場: via Zoom / 研究本館 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Applied plant genomics for evolutionary history, agriculture, and conservation

2024年12月19日(木) 16:00 - 17:00

アントニオ・エルナンデズ ロペズ (Professor, National Autonomous University of Mexico, Mexico)

I will explore the transformative role of genomic tools in understanding biological diversity across a range of organisms. By delving into the genetic blueprints of various species, we can unravel evolutionary histories, identify key traits for conservation, and develop strategies to preserve endangered ecosystems. Additionally, I will discuss practical applications of genomic data, such as enhancing agricultural biodiversity, improve traditional uses, and fostering sustainable development. Through case studies and recent advancements, this presentation highlights the critical intersection of genomics, biodiversity preservation, and its multifaceted uses in addressing global challenges.

会場: via Zoom

イベント公式言語: 英語