iTHEMS Biology Seminar

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

A model to unify the theory of speciation

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

José Said Gutiérrez-Ortega (Special Postdoctoral Researcher, iTHEMS)

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.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Chromatophore patterns, packing, and scaling on a growing squid

August 20 (Tue) at 16:00 - 17:00, 2024

Robert Ross (Interdisciplinary Postdoctoral Researcher, Biological Complexity Unit / Computational Neuroethology Unit, Okinawa Institute of Science and Technology Graduate University (OIST))

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.

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

Event Official Language: English

Social behavior and social engineering in bacteria

August 1 (Thu) at 16:00 - 17:00, 2024

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.

Venue: Seminar Room #359 / via Zoom

Event Official Language: English

Multi-Agent Reinforcement Learning for Exploring Collective Behavior

July 25 (Thu) at 16:00 - 17:00, 2024

Kazushi Tsutsui (Assistant Professor, Graduate School of Arts and Sciences, The University of Tokyo)

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.

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

Event Official Language: English

Optimal control of stochastic reaction networks

July 18 (Thu) at 16:00 - 17:00, 2024

Shuhei Horiguchi (JSPS Postdoctoral Research Fellow, Nano Life Science Institute, Kanazawa University)

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.

Venue: via Zoom

Event Official Language: English

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

July 9 (Tue) at 16:00 - 17:00, 2024

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.

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

Event Official Language: English

Y-chromosome turnover in Drosophila – Escaping from an evolutionary dead-end?

June 28 (Fri) at 14:00 - 16:00, 2024

Masafumi Nozawa (Associate Professor, Tokyo Metropolitan University)

The Y chromosome (Y, hereafter) is degenerated in many organisms but cannot be lost due to their important functions in sex determination and/or male fertility. This is true for Drosophila and an individual without Y become a sterile male. Therefore, the Y has been considered as indispensable in Drosophila as in the case of mammals. However, we recently discovered that Drosophila lacteicornis, endemic to Ryukyu islands, is polymorphic in terms of the presence or absence of the Y; i.e., XY and XO males coexist within species. Unlike other Drosophila species, the XO males of this species are fertile. In this seminar, I will introduce how the Y becomes dispensable in this species. To our surprise, our genome and transcriptome analyses revealed that a novel Y is likely emerging in this species rather than an old Y is being lost. In other words, a turnover of the Y is ongoing in this species. Our results indicate that the Y is not necessarily a static entity in an evolutionary dead-end but can be a dynamic entity, sometimes going back to an autosome or even disappearing. Therefore, I would like to emphasize that we should understand the evolution of sex chromosomes not by a one-way path to dead-end but by a circular process, i.e., “sex-chromosome cycle.”

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

Event Official Language: English

Finding and understanding disease-causing genetic mutations

June 20 (Thu) at 16:00 - 17:00, 2024

Kojima Shohei (Special Postdoctoral Researcher, Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences (IMS))

Disease is caused by genetic factors and environmental factors. Genome-wide association study (GWAS) is a powerful method to find genetic factors associated with disease and human complex traits. One conceptual finding GWAS revealed is that many common diseases are caused by a combination of multiple genetic factors (polygenic), rather than a single causal mutation (monogenic). I have been working on finding genetic factors causing polygenic diseases by developing software that accurately finds sequence insertions and deletions from human population-scale sequencing datasets. In this talk, first, I will introduce some examples of disease-causing variants we recently discovered. Next I will also introduce my current research theme aiming to untangle how multiple genetic factors coordinately change cellular homeostasis, which I would like to have a collaboration with mathematical scientists.

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

Event Official Language: English

The speciation-latitude relationship in ferns

June 6 (Thu) at 16:00 - 17:00, 2024

José Said Gutiérrez-Ortega (Special Postdoctoral Researcher, iTHEMS)

The latitudinal gradient of diversity (LGD), the pattern that shows that the highest numbers of species in major taxa are at low latitudes and that they decrease towards high latitudes, is the most conspicuous trend on the relationship between geography, environment, and biodiversity. But there is not a concrete answer of why it exists. Three hypotheses have been proposed so far: 1) tropics contain more species because communities have been climatically stable for longer time than the temperate areas; 2) the tropics receives more energy, which allows groups to diversify at higher rates; 3) the tropics provide a higher diversity of ecological opportunities for new species to specialize. By analyzing the fern community from the American continent, I tested the three hypotheses, and found that the first hypothesis is the most likely. The tropics contain more species not because they produce more species than the temperate areas, but because extinction has been lower historically. These results suggest that the climatic instability (cycles of interglaciation-glaciation) at high latitudes have shaped this curious pattern. I am using this seminar to show you some of my research progress, and to briefly mention some of the problems that I have encounter while trying to test my hypotheses. Maybe we can make some ideas to improve the methodological aspects of this kind of macro-ecological research

Venue: via Zoom

Event Official Language: English

Lipid Peroxidation Structure Selectivity: A Clue to Coal Workers' Pneumoconiosis

May 30 (Thu) at 16:00 - 17:00, 2024

Cai Tie (Associate Professor, China University of Mining and Technology, China)

Coal workers' pneumoconiosis (CWP), resulting from the inhalation of coal dust mixtures, is one of the leading occupational diseases globally. Despite its seriousness, there is still no effective curative method available for CWP. Therefore, a systemic understanding of CWP's pathogenesis is urgently needed. Peroxidation is an oxidation chain reaction in which lipids (glycerophospholipids and other membrane lipids) are degraded into excretory forms, such as fatty aldehydes. This process involves a series of enzymes that catalyze the reactions leading to lipid degradation. Our previous work identified specific regulatory mechanisms in lipid peroxidation processes triggered by diseases or various interventions. To gain a comprehensive understanding of lipid peroxidation, we developed a systematic profiling strategy that allows for the detailed observation of these oxidative processes. Additionally, we adapted this profiling strategy to investigate risk factors associated with coal workers' pneumoconiosis (CWP). By applying our methods to the study of CWP, we aimed to uncover the metabolic and molecular changes induced by coal dust inhalation, providing insights that could contribute to better prevention and treatment strategies for this occupational disease. To comprehensively investigate the lung alterations associated with CWP, both a cohort of coal miners and a CWP rat model were studied. Through the analysis of lipid peroxidation alterations associated with CWP occurrence, several CYP subtype-specific metabolic processes were identified. These findings suggest that coal-derived polycyclic aromatic hydrocarbons (PAHs) are major risk factors for CWP due to the specific activation of the Aryl Hydrocarbon Receptor (AhR) pathway. Further evidence at the gene level and morphological changes supports the role of coal-derived PAHs as key factors in the development of CWP. Hence, it is crucial to consider the toxicity induced by PAHs in the prevention and treatment of CWP.

Venue: via Zoom

Event Official Language: English

The collective order of human corneal endothelial cells as a unified biomarker for in vitro cultured cells and in vivo regenerated tissue

May 23 (Thu) at 16:00 - 17:00, 2024

Akihisa Yamamoto (Research Scientist, iTHEMS)

Approximately 200,000 corneal transplantations are performed worldwide yearly, and more than half of them are applied to patients with corneal endothelial dysfunction. Recently, the restoration of functional corneas by injecting culture-expanded cells has developed in contrast to the conventional transplantation which relies on a limited number of donors’ corneas. This novel treatment opens up the potential to cure more patients with less surgical invasion and allows the utilization of cells with consistent and controlled quality. In this talk, I will introduce a unified physical biomarker for the quality assessment of corneal endothelial cells in in vitro culture and the predictive diagnosis of in vivo tissues using a single equation based on the collective order of cells. Taking an analogy to the two-dimensional colloidal assembly, the spatial arrangement of cells is generalized in terms of many-body interactions, and the “spring constant” of the underlying interaction potential is calculated from microscopy images. I also would like to discuss our recent approach to characterize the local structure of the arrangement of cells based on the topological data analysis.

Venue: via Zoom

Event Official Language: English