iTHEMS Biology Seminar

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

Exploring the impact of environments on flower color differentiation: A meta-analytical approach

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

Masaru Bamba (Assistant Professor, Graduate School of Science, Tohoku University)

Flower color is one of the most diverse phenotypes in angiosperms, yet the initial processes of its differentiation remain unclear. Flower color is primarily expressed through the accumulation of pigment compounds in the petals, which are also associated with various stress responses. While it is conceivable that the environmental conditions during plant evolution could contribute to the differentiation of flower color, few studies have examined this hypothesis. Therefore, I conducted a meta-analysis using plant flower color information and growth environment data to elucidate the relationship between flower color differentiation and growth environments. Flower color data was extracted using LLM from botanical descriptions, and growth environment data was acquired by aligning GBIF occurrence information with WorldClim and ISRIC databases. Integrating approximately 30,000 flower color data points and 35 million occurrence records revealed trends such as a predominance of red flowers at higher altitudes and white flowers in arid areas. This study is still preliminary, so I would welcome discussions on more suitable analytical methods and models.

Venue: via Zoom

Event Official Language: English

Deep Learning for Estimating Two-Body Interactions in Mixed-Species Collective Motion

May 9 (Thu) at 16:00 - 17:00, 2024

Masahito Uwamichi (Project Researcher, Graduate School of Arts and Sciences, The University of Tokyo)

(This is a joint seminar with the Information Theory Study Group.) Collective motion is a fundamental phenomenon observed in various biological systems, characterized by the coordinated movement of individual entities. Such dynamics are especially crucial in understanding cellular behaviors, which can now be observed at an individual level in complex tissue formations involving multiple types of cells, thanks to recent advancements in imaging technology. To harness this rich data and uncover the hidden mechanisms of such dynamics, we developed a deep learning framework that estimates equations of motion from observed trajectories. By integrating graph neural networks with neural differential equations, our framework effectively predicts the two-body interactions as a function of the states of the interacting entities. In this seminar, I will first introduce the structure and hyperparameters of our framework. Subsequently, I will detail two numerical experiments. The first is a simple toy model that was employed to generate data for testing our framework to refine the hyperparameters. The second explores a more complex scenario mimicking the collective motion of cellular slime molds, highlighting our model's ability to adapt to mixed-species interactions.

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

Event Official Language: English

Tracing link of cell ageing and disease progression: Joining factors and facilitators

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

Rajkumar Singh Kalra (Staff Scientist, Immune Signal Unit, Okinawa Institute of Science and Technology Graduate University (OIST))

Cell ageing is an inevitable biological process. It marks declined homeostatic processes in a cell, the impact of which is reflected in the organism’s function/physiology. Ageing, thus, raises risks of disease progression in elderly people and compromises their immunity. Progression of cancer and neurodegenerative diseases and weak immune response against a pathogen(s) represent cases of ageing-related diseases. What molecular factors/signaling could be associated with disease progression or take part in governing such decisions in aging? – remained a key focus of my research so far. In my talk, I shall shed light on the part characterizing key proteins and their signalling in ageing-related diseases with an emphasis on cancer, neurodegenerative disease, and immunity. Taking advantage of wet lab and system biology studying gene networks, and genomic, proteomic, and metabolomic readouts, I investigated the molecular expression and processes impacted and compromised by ageing. I shall be discussing new knowledge from my work on the linkage of cell ageing and disease progression and therein role of key factors and facilitators I studied.

Venue: via Zoom

Event Official Language: English

Zooming into the ancient world by reconstructing the joint genealogies of modern and ancient humans

April 18 (Thu) at 16:00 - 18:00, 2024

Leo Speidel (Senior Research Fellow, Genetics Institute, University College London, UK)

In recent years, we have gone from databases that store the genetic differences observed between hundreds of thousands of sequenced people to using this information to build the actual genetic trees that relate individuals through their shared ancestors back in time. These genetic trees describe how our genomes have evolved up to millions of years into the past. Additionally, sequencing of DNA from ancient human bone has enabled the direct observation of genomic change over past millennia and has unlocked numerous previously hidden genetic histories. In this talk, I will illustrate how we can unearth the human past from these data, ranging from ancient migrations out of Africa and subsequent mixtures with now extinct Neanderthals to waves of ancestry transformations in a nation’s recent past.

Venue: via Zoom

Event Official Language: English

A socio-ecological and genomic approach to mixed-species formation of African forest guenons

April 4 (Thu) at 16:00 - 17:00, 2024

Haruka Kitayama (Ph.D. Student, Graduate School of Environmental Science, Hokkaido University)

While many animal groups consist of a single species, some species have been observed forming mixed-species groups (MSGs). It is thought that by forming groups with different species, animals may reduce predation risk, improve foraging efficiency, and even gain social and reproductive benefits. Red-tailed monkeys and blue monkeys, African forest guenons (Tribe Cercopithecini), are known to form MSGs in several regions in Africa, despite the large niche overlap. The underlying mechanisms driving the formation of MSGs in red-tailed monkeys and blue monkeys are still unclear. One reason is that previous studies have been limited to behavioral ecological approaches. By combining field observations with genomic analyses in the laboratory, we seek to shed light on the role of genetic factors in mediating interspecies interactions within MSGs. In this talk, I will introduce our studies on genomic introgression and gut microbiome sharing within the mixed-species population of red-tailed monkeys and blue monkeys in the Kalinzu Forest Reserve, Uganda.

Venue: via Zoom

Event Official Language: English