iTHEMS Biology Seminar

Application of genetics and genomics to breeding

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

Jeffrey Fawcett (Chief Scientist, Regional Fish Institute, Ltd.)

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

Theoretical analysis of High-dose/Refuge strategy for durability of pest control

November 21 (Thu) at 16:00 - 17:00, 2024

Sayaki Suzuki (Postdoctoral Researcher, Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies)

When using chemicals to control pathogens or pests, a problem that always arises is that parasites develop resistance to the chemicals. In many cases, the amount of chemical used must be reduced for using the chemicals sustainably. However, if certain conditions are met, a method is known that can suppress the development of resistance in diploid organisms such as pest insects. This is the high-dose/refuge strategy (HD/R) proposed by Comins (1977). This unique method combines high doses of pesticide spraying with ‘Refuge’ that are completely pesticide-free, and is a rare example of a successful method that actually fields. In this presentation, I will provide an overview of the HD/R strategy, a formulation that incorporates the entire life cycle of the insect, which was an issue that Comins had not yet resolved. And show the life cycle of the insect and the conditions under which the HD/R strategy is effective, based on the results of an approximation using a source-think model.

Venue: via Zoom

Event Official Language: English

Finding Rules for Condensation of Disordered Protein Sequences

November 14 (Thu) at 16:00 - 17:00, 2024

Kyosuke Adachi (Research Scientist, iTHEMS)

Event Official Language: English

Mathematical modeling of circadian rhythm: temperature compensation and after effect

November 7 (Thu) at 16:00 - 17:00, 2024

Yuta Kitaguchi (Ph.D. Student, Graduate School of Natural Science & Technology, Kanazawa University)

Almost all organisms have a circadian clock. This circadian clock consists of negative transcriptional-translational feedback loops (TTFLs) between various circadian clock genes in cells. Collective gene expression rhythms in the central circadian pacemaker tissue regulate nearly 24-hour behavioral rhythms of organisms. The circadian clock has three characteristics: (1) autonomous oscillation, (2) temperature compensation of the period, and (3) entrainment to external cycles such as a light-dark cycle. In this presentation, I will talk about theoretical studies on temperature compensation, and the entrainment to light-dark cycles. For temperature compensation, I will show that only a few temperature-insensitive reactions in the complex TTFLs of the circadian clock are sufficient to maintain the circadian period under increasing temperature. For entrainment to the light-dark cycle, I will show the mechanism for after-effect where the period of the circadian clock in constant darkness correlates with that of a previously entrained light-dark cycle for several months.

Venue: via Zoom

Event Official Language: English

Heterostyly and the evolution of mating system in plants

October 31 (Thu) at 16:00 - 17:00, 2024

Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

Many organisms exhibit various strategies to avoid self-fertilization and promote outcrossing (mating with different individuals). Such strategies have repeatedly evolved and been disrupted throughout evolution, resulting in a remarkable diversity of mating systems. The most well-known strategy is sexual dimorphism, in which mating is only successful between opposite sexes (e.g. male and female) which exhibit different morphology (e.g. males and females look different). However, some plants, including buckwheat that I have been studying, have evolved a strategy where all individuals either have flowers with long or short styles (female organ), referred to as heterostyly or distyly, and mating is typically only successful between individuals with long-styled flowers and those with short-styled flowers, i.e., outcrossing is promoted by floral dimorphism that is not associated with sexes. While how such a system evolves and its genetic basis are still largely unknown, the genomic region responsible for heterostyly has been identified in many different species within the past year or two, revealing some interesting parallels between independently evolved systems. In this seminar, I will introduce these recent findings and discuss how heterostyly may be linked to the diverse mating systems observed in plants. I will also introduce what we have been doing and are planning/hoping to do in buckwheat and its related species.

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

Event Official Language: English

The hidden language of light: Polarization signals in cuttlefish courtship

October 24 (Thu) at 16:00 - 17:00, 2024

Arata Nakayama (Postdoctoral Fellow, Atmosphere and Ocean Research Institute, The University of Tokyo)

The most conspicuous signals are generally the most attractive; this principle underlies the evolution of sexual signal. While the sexual signal design and its exceptional diversity have primarily explored on the color (wavelength) of light, various animals utilize a different property of light for signaling: polarization. In short, polarization is a third physical property of light, alongside color and intensity, and refers to the orientation of light waves' vibrations. While most vertebrate species, including humans, cannot perceive polarized light, some invertebrate species, such as crustaceans and cephalopods (e.g., octopus, squid, and cuttlefish), can detect the polarization of light and reflect polarized light from their body surfaces, suggesting that the polarization of light might function as a communication signal. In our study, by focusing on the sexually ornamented trait and the courtship behavior of specific cephalopod species, we found an polarization courtship signal, which is extremely conspicuous from the perspective of cephalopod polarization vision. Additionally, we conducted morphological observations and optical analyses of their polarization-reflective body surfaces, uncovering a novel mechanism for generating complex polarization patterns. In this gethering, I will provide a general introduction to the role of polarization as a visual cue and signal, followed by an overview of our study on the unique courtship behavior involving polarization signaling in the cuttlefish Sepia andreana.

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

Event Official Language: English

Digital Twinning of Plant Internal Clocks for Robotics and Virtual Reality Enhancements in Agriculture

October 17 (Thu) at 16:00 - 17:00, 2024

Hirokazu Fukuda (Professor, Graduate School of Engineering, Osaka Metropolitan University)

Digital twinning, widely used in fields like industrial and agricultural engineering, creates digital replicas of physical systems. When applied to plant circadian clocks, these digital twins simulate physiological processes governed by circadian rhythms. This technology aids in predicting and optimizing plant growth and productivity in controlled environments, such as greenhouses and plant factories (vertical farms). By understanding key processes like photosynthesis and nutrient uptake, researchers can more effectively manage environmental factors, boosting crop yields and reducing waste. The integration of robotics and virtual reality further enhances these systems, enabling precise automation and real-time optimization. This presentation will explore these advancements, with a focus on mathematical models for controlling circadian clocks.

Venue: via Zoom

Event Official Language: English

The laser light shed on Darwin’s ‘Abominable mystery’

October 10 (Thu) at 16:00 - 17:00, 2024

Chiharu Kato (Ph.D. Student, Department of Biological Sciences, Graduate School of Science, The University of Tokyo)

Reproductive isolation is the inability of a species to breed with related species and thus is a key to evolution of new species in flowering plants. In interspecific crosses between closely related species, a stage of pollen tube reception by female tissues of the pistil act as a pivotal hybridization barrier. Within the genus Arabidopsis, pistils of Arabidopsis thaliana can be fertilized by pollen from its relative species, but about half of the ovules reject the release of sperm from heterospecific pollen tubes and these rejected pollen tubes continue growing inside the embryo sacs (referred to as pollen tube overgrowth). A loss-of function mutant line of ARTUMES gene, encoding a subunit of the oligosaccharyltransferase complex, pollinated with heterospecific pollen shows a higher overgrowth rate than the wild type, suggesting that ARTUMES is involved in interspecific pollen tube reception. However, its molecular mechanism is largely unknown. Here, we report that some knockout lines of receptor kinases show ARTUMES mutant-like impairment in interspecific pollen tube reception, indicating that these receptor kinases might be potentially the target proteins of ARTUMES. We anticipate these receptors recognize the ligands from conspecific (self) pollen and heterospecific pollen either in the presence of ARTUMES, thus they can lead successful interspecific fertilization. We also identified ARTUMES mutant shows abnormal calcium dynamics in their female tissue during pollen tube reception. In this talk, I would like to briefly mention about how mathematical modeling can be promoting to pursue the questions regarding calcium dynamics reflecting male-female communication during fertilization. We anticipate these mechanisms that enable interspecific fertilization contribute to rapid development and diversification of flowering plants in recent geological time.

Venue: via Zoom

Event Official Language: English

Clinical trials and standards of care: How doctors decide your medical treatment

October 2 (Wed) at 16:00 - 17:00, 2024

Catherine Beauchemin (Deputy Program Director, iTHEMS)

Ever wondered what data is considered sufficient for approval of a new drug or vaccine? In this talk, I will talk about some of the errors and shortcomings with how clinical trials are run and regulated. I will also show how the data and analyses behind clinical trials can be very poorly done. I will show one example of very bad data and analysis, but I will also show an example of the valuable information that can come out of doing a good job in presenting, interpreting, and following the data. I will highlight how the over-reliance on summarizing measures like averages and the Gaussian assumption can lead to overlooking therapies that could otherwise have been extremely effective. This talk should be of critical importance to those working in the fields of health, medical and clinical research. But this talk is about data and its analysis, and as such is also very relevant to physicists and other scientists who generate, present or analyse data as part of their research.

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

Event Official Language: English

Organizational meeting 4

September 26 (Thu) at 16:00 - 17:00, 2024

This the semi-regular opportunity for iTHEMS Biology members to discuss their current research progress and/or difficulties and/or research questions. Anyone is welcome to join. It will be held in hybrid form.

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

Event Official Language: English