iTHEMS Biology Seminar

iTHEMS Biology Study Group April Launch Meeting (Part 2)

April 10 (Thu) at 13:00 - 14:00, 2025

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.

Venue: via Zoom / Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

iTHEMS Biology Study Group April Launch Meeting (Part 1)

April 3 (Thu) at 14:00 - 15:00, 2025

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.

Venue: via Zoom / 4th floor public space, Main Research Building

Event Official Language: English

The rarer-sex effect

March 27 (Thu) at 16:00 - 17:00, 2025

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.

Venue: #445-447, 4F (Hybrid), Main Research Building / via Zoom

Event Official Language: English

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

March 13 (Thu) at 17:00 - 18:00, 2025

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.

Venue: via Zoom

Event Official Language: English

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

March 6 (Thu) at 16:00 - 17:00, 2025

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.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

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

March 4 (Tue) at 16:00 - 17:00, 2025

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.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

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

February 27 (Thu) at 16:00 - 17:00, 2025

Yukako Katsura (Assistant Professor, Center for the Evolutionary Origins of Human Behavior, Kyoto University)

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.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

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

February 20 (Thu) at 16:00 - 17:00, 2025

Junya Sunagawa (Ph.D. Student, Graduate School of Life Science, Hokkaido University)

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.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Application of genetics and genomics to breeding

February 13 (Thu) at 16:00 - 17:30, 2025

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

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.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

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

February 6 (Thu) at 16:00 - 17:00, 2025

Ikki Yasuda (Ph.D. Student, Graduate School of Science and Technology, Keio University)

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.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Effective size and dimension, in biology and beyond

January 30 (Thu) at 16:00 - 17:00, 2025

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

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

Venue: via Zoom

Event Official Language: English

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

January 23 (Thu) at 16:00 - 17:00, 2025

Takahisa Matsuzaki (TechnoArena Associate Professor, Center for Future Innovation, Graduate School of Engineering, Osaka University / Assistant Professor, Department of Applied Physics, Graduate School of Engineering, Osaka University)

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.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

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

January 16 (Thu) at 16:00 - 17:15, 2025

Kenji Itao (Special Postdoctoral Researcher, Computational Group Dynamics Collaboration Unit, RIKEN Center for Brain Science (CBS))

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.

Venue: via Zoom / Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

Applied plant genomics for evolutionary history, agriculture, and conservation

December 19 (Thu) at 16:00 - 17:00, 2024

Antonio Hernández-López (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.

Venue: via Zoom

Event Official Language: English

Mechanism for Converting Temporal Rhythms into Spatial Patterns of Body Segment

December 12 (Thu) at 13:00 - 14:00, 2024

Koichiro Uriu (Associate Professor, School of Life Science and Technology, Institute of Science Tokyo)

In development, spatially periodic structures are spontaneously formed in various tissues. These developmental structures are also formed in a proper temporal order. How is such spatial and temporal coordination achieved in morphogenesis? In this presentation, we discuss the mechanism that translates temporal rhythms of gene expression into spatially periodic patterns in vertebrate body segment formation. Mechanisms for converting oscillatory signals into vertebrate body segments have been proposed previously. Cooke and Zeeman 1976 proposed the Clock and Wavefront model based on the concept of the catastrophe theory. Still, it remains unclear how this conceptual model actually works in embryos. Here we develop a mathematical model aided by recent imaging and molecular genetics data and reveal a spatiotemporal bifurcation structure for vertebrate segment formation by using the dynamical systems theory.

Venue: Seminar Room #359 / via Zoom

Event Official Language: English

Bacterial ecospecies and ecoclines

December 5 (Thu) at 16:00 - 17:00, 2024

Daniel Falush (Professor, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, China)

All bacteria reproduce clonally but some species exchange DNA frequently enough that they have well mixed geographic gene pools, similar to those found in outbreeding animals and plants. Using data from multiple species we show that these “recombinogenic” bacteria also have genome-wide genetic structures generated by natural selection, including discrete “ecospecies” and continuous “ecoclines”. These structures reflect evolutionary strategies employed within natural populations, which can be dissected using the powerful techniques of molecular microbiology, providing a unique new view into the private lives of bacteria.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Analysing and Visualising Single Cell Omits Data

November 28 (Thu) at 15:30 - 16:30, 2024

Dorothy Ellis (Postdoctoral Researcher, Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS))

Single cell multimodal omics data are characterized by sparsity, noise, and high dimension. Incorporating information across modalities is challenging. We developed a non-negative matrix factorization based algorithm to identify latent factors that can facilitate improved cell-type clustering and visualizations for multimodal single cell omics count data. We then extend this algorithm to larger datasets and for different distributions of data in different modalities.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English