iTHEMS生物学セミナー

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

Mechanism for Converting Temporal Rhythms into Spatial Patterns of Body Segment

2024年12月12日(木) 13:00 - 14:00

瓜生 耕一郎 (東京科学大学 生命理工学院 准教授)

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.

会場: セミナー室 (359号室) / via Zoom

イベント公式言語: 英語

Bacterial ecospecies and ecoclines

2024年12月5日(木) 16:00 - 17:00

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.

会場: via Zoom / セミナー室 (359号室)

イベント公式言語: 英語

Analysing and Visualising Single Cell Omits Data

2024年11月28日(木) 15:30 - 16:30

Dorothy Ellis (理化学研究所 生命医科学研究センター (IMS) 統合ゲノミクス研究チーム 特別研究員)

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.

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

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

2024年11月21日(木) 16:00 - 17:00

鈴木 清樹 (総合研究大学院大学 統合進化科学研究センター 博士研究員)

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.

会場: via Zoom

イベント公式言語: 英語

Finding Rules for Condensation of Disordered Protein Sequences

2024年11月14日(木) 16:00 - 17:00

足立 景亮 (数理創造プログラム 研究員)

イベント公式言語: 英語

Mathematical modeling of circadian rhythm: temperature compensation and after effect

2024年11月7日(木) 16:00 - 17:00

北口 裕太 (金沢大学 大学院自然科学研究科 博士課程)

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.

会場: via Zoom

イベント公式言語: 英語

Heterostyly and the evolution of mating system in plants

2024年10月31日(木) 16:00 - 17:00

ジェフリ・フォーセット (数理創造プログラム 上級研究員)

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.

会場: via Zoom / 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

The hidden language of light: Polarization signals in cuttlefish courtship

2024年10月24日(木) 16:00 - 17:00

中山 新 (東京大学 大気海洋研究所 博士研究員)

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.

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

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

2024年10月17日(木) 16:00 - 17:00

福田 弘和 (大阪公立大学 大学院工学研究科)

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.

会場: via Zoom

イベント公式言語: 英語

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

2024年10月10日(木) 16:00 - 17:00

加藤 千遥 (東京大学 大学院理学系研究科 生物科学専攻 博士課程)

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.

会場: via Zoom

イベント公式言語: 英語

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

2024年10月2日(水) 16:00 - 17:00

カトゥリン・ボシゥメン (数理創造プログラム 副プログラムディレクター)

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.

会場: via Zoom / 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

Organizational meeting 4

2024年9月26日(木) 16:00 - 17:00

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.

会場: via Zoom / 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 model to unify the theory of speciation

2024年9月5日(木) 16:00 - 17:00

ホセ サイード・グティエレス オルテガ (数理創造プログラム 基礎科学特別研究員)

Speciation, the process by which new species originate, occurs due to geographic (physical distance), ecological (different background environments), and historical (divergence time) factors that promote reproductive isolation among lineages. However, we don’t know how these factors interplay; therefore, our empirical and theoretical knowledge about speciation is limited, fragmented, and lacks unification. To fill this knowledge gap, I propose a model and an experiment that treats speciation as a continuum of the interplay between geographic and ecological factors. Empirical evidence has shown that the extremes of this continuum produce high evolutionary rate (faster speciation), while I expect that intermediate values in the interplay continuum would produce reduced evolutionary rates. I expect this seminar can open opportunities for collaboration.

会場: via Zoom / セミナー室 (359号室)

イベント公式言語: 英語

Chromatophore patterns, packing, and scaling on a growing squid

2024年8月20日(火) 16:00 - 17:00

ロバート・ロス (沖縄科学技術大学院大学 (OIST) 生物複雑性ユニット / 計算行動神経科学ユニット 学際研究員)

Many biological patterns are formed during growth, and various modeling approaches have repeatedly shown that growth can substantially impact pattern formation. However, experimental testing of these ideas has been limited, largely due to the difficulty in precisely measuring organism growth while simultaneously tracking the dynamics of pattern formation. To address this, we turned to the skin of the oval squid. The oval squid grows rapidly, hatching with a length of approximately 16mm and reaching 90mm within 3 months. Throughout development, its skin is populated by pigment-filled cells called chromatophores. Following insertion into the skin, chromatophores do not move. This means that squid chromatophores, besides being the constitutive elements of a point pattern, can also function as reference points to precisely determine skin growth. For the more biologically-minded, I will explain how the chromatophore pattern emerges through the interplay of growth and decreasing chromatophore growth rates. For those who lean physics, I will talk about how due to the combination of volume exclusion and growth, chromatophores exhibit a scaling in which relative density fluctuations grow with spatial scale, akin to a critical 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

Social behavior and social engineering in bacteria

2024年8月1日(木) 16:00 - 17:00

Ashleigh Griffin (Professor, Department of Biology, University of Oxford, UK)

This year is the 60th anniversary of WD Hamilton’s seminal paper in which he outlined his theory of inclusive fitness and showed how it could be used to understand altruism in the social insects. In this talk, I will describe efforts made to use his theory to understand social behavior in bacteria. And I’ll go on to explore the potential of using these insights to tackle problems of antibiotic resistance in infections.

会場: セミナー室 (359号室) / via Zoom

イベント公式言語: 英語

Multi-Agent Reinforcement Learning for Exploring Collective Behavior

2024年7月25日(木) 16:00 - 17:00

筒井 和詩 (東京大学 大学院総合文化研究科 助教)

Humans and other organisms develop collective behaviors through interactions with diverse environments and various species. These behaviors are significant topics across multiple research fields, including evolutionary biology, behavioral ecology, and animal sociology. Unraveling the decision-making mechanisms of individuals in groups within cooperative and competitive contexts has captured the attention of many researchers but remains a complex challenge. This seminar will present research cases that employ multi-agent reinforcement learning, a machine learning technique, to investigate the decision-making processes underlying collective behavior. Through this approach, we aim to provide deeper insights into the dynamics and mechanisms that drive group behaviors in various biological systems.

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

Optimal control of stochastic reaction networks

2024年7月18日(木) 16:00 - 17:00

堀口 修平 (金沢大学 ナノ生命科学研究所 特任研究員)

Optimal control problems for the population of interacting particles arise in various fields, including pandemic management, species conservation, cancer therapy, and chemical engineering. When the population size is small, the time evolution of the particle numbers is inherently noisy and modeled by stochastic reaction networks, a class of jump processes on the space of particle number distributions. However, compared to deterministic and other stochastic models, optimal control problems for stochastic reaction networks have not been extensively studied. In this talk, I will review a formulation of stochastic reaction networks and present a new class of optimal control problems that are efficiently solvable and widely applicable. The optimal solution can be efficiently obtained using the Kullback–Leibler divergence as a control cost. We apply this framework to the control of interacting random walkers, birth-death processes, and stochastic SIR models. Both numerical and analytical solutions will be presented, highlighting the practical applications and theoretical significance of this approach.

会場: via Zoom

イベント公式言語: 英語

The role of demographic stochasticity in the evolution of spite and altruism

2024年7月9日(火) 16:00 - 17:00

Troy Day (Professor, Head of Department, Department of Mathematics and Statistics, Queen's University, Canada)

The evolution of spiteful and altruistic behaviour remains a fascinating and somewhat puzzling phenomenon. In recent years there has been interest in examining how stochasticity arising from a finite population size might affect the evolution of these traits. Some results suggest that such stochasticity can reverse the direction of selection and promote the evolution of traits like altruism and spitefulness that are selected against in very large (deterministic) populations. However, other results seem to call this finding into question. In this talk I will consider a simple but quite general model of spite and of altruistic behaviour and examine how demographic stochasticity affects the evolution of these traits. I will show that stochasticity can indeed affect the direction of evolution but not in the way that previous studies have suggested. The results also help to clarify the broader issue of how and why stochasticity can sometimes reverse the direction of evolution.

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