iTHEMS Biology Seminar

Parameter Fitting for Glucose Homeostasis - Searching for Methods to Predict and Diagnose

September 12 (Tue) at 16:00 - 17:00, 2023

Gabriel Gress (Specially Appointed Research Fellow, Mathematical Science Group, Advanced Institute for Materials Research (AIMR), Tohoku University)

The human body regulates glucose through a complex web of biological interactions, for which state-of-the-art models require dozens of variables and parameters to even emulate. But while we've had devices to measure glucose levels as far back as the 1980's, nearly all of the remaining variables and parameters cannot be measured directly to this day. While continuous glucose monitors have greatly improved the health of diabetic patients, there are still many barriers in the diagnosis of at-risk patients as well as accurately dispersing insulin to counteract future trends in glucose levels. While glucose readings are only a small window into one of many factors of how the human body maintains glucose homeostasis, we search for ways to leverage the high-frequency and high-volume data to improve the state of diagnosis and prediction in diabetic patients.

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

Event Official Language: English

Landscape structure drives eco-evolution in host parasite systems

August 24 (Thu) at 16:00 - 17:00, 2023

Jhelam Deshpande (Ph.D. Student, Biodiversity: dynamics, interactions and conservation team, Institute of Evolutionary Science of Montpellier, France)

As all biological and many artificial systems, hosts and their parasites are most often spatially structured. Besides this highly relevant spatial context, parasites may change through time due to to evolutionary processes, including mutation and selection. These facts imply that we must study host-parasite systems taking into account space and evolution. Past work has mainly focused on simple spatial structures, but how parasites evolve in realistically complex landscapes remains unclear, hampering the translation of theoretical predictions to real ecological systems.Therefore, we here develop an eco-evolutionary metapopulation model of host-parasite interactions in which hosts and parasites disperse through realistically complex spatial graphs. Parasite virulence, a parasite life-history trait of central importance that here impacts host reproduction, is able to evolve. Our model therefore captures the eco-evolutionary feedback loop between host demography and parasite evolution in space. In order to gain a general understanding of parasite eco-evolution in space, we analyse our model for spatial networks that represent terrestrial (represented by random-geometric graphs; RGG) and riverine aquatic (represented by optimal channel networks; OCN) landscapes. We find that evolved virulence is generally a function of host dispersal, with a unimodal relationship in aquatic and a saturating relationship in terrestrial landscape, and this is driven by higher order network properies. Consistent with previous work, we show that our results are driven by kin selection, because dispersal and landscape structure impact both patterns of relatedness and availability of susceptible hosts. Our model yields readily testable predictions, including that terrestrial parasites should be more virulent than aquatic parasites are low dispersal rates and vice versa as dispersal increases. These differences in evolved virulence directly lead to differences in system stability, with more virulent parasites more often leading to host extinction. Thus, in this study we highlight the role of landscape structure in driving eco-evolutionary dynamics of parasites.

Venue: via Zoom

Event Official Language: English

Mating system of buckwheat

August 17 (Thu) at 16:00 - 17:00, 2023

Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

Buckwheat (soba in Japanese) has a slightly unusual mating system called heterostylous self-incompatibility where two types of individuals coexist, one that produces flowers with a long style (female part of the flower) and short stamen (male part of the flower), and the other that produces flowers with a short style and long stamen. Mating is only successful when it occurs between the different types of individuals. It is a bit similar to sexual dimorphism where males and females coexists but in this case all individuals have both male and female organs. In this talk, I will introduce the basics of this mating system in buckwheat and some work we have been doing. In particular, I will talk about its genetic architecture and some parallels observed with other plants in which a similar mating system evolved independently. The talk will be aimed at non-experts so non-biologists are also welcome to attend.

Venue: via Zoom

Event Official Language: English

Evolution of dormant egg production and their hatching rate in Aedes albopictus

July 13 (Thu) at 16:00 - 17:00, 2023

Yusuke Kuwano (Ph.D. Student, The Graduate University for Advanced Studies (SOKENDAI))

Mosquitoes are important insect vectors of infectious diseases in humans, and knowledge of their population dynamics is pivotal in disease control. Some mosquito species have dormancy in their life history to survive harsh environments. However, the population dynamics of mosquitoes have not yet been well understood due to the lack of field and experimental data on dormancy. For that reason, I modeled the population dynamics of mosquitoes that face environmental fluctuations and examine the evolution of egg dormancy strategy to survive harsh periods. I found that the ESS dormancy fraction monotonically increases with the period of environmental fluctuation. Next, I analyzed evolutionary traits of the dependence of the dormancy rate and the hatching rate from dormant egg on soil moisture content and conducted evolutionary simulations using actual weather measurement in Tokyo. The results of the hatching rate from dormant egg showed that two mosquito phenotypes having distinctly different responses to soil moisture were selected.

Venue: via Zoom

Event Official Language: English

Journal Club: Inference of hydrodynamic equations for active matter

June 29 (Thu) at 16:00 - 17:00, 2023

Kyosuke Adachi (Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research (BDR))

Event Official Language: English

The role of fluid dynamics in microbial ecology

June 22 (Thu) at 14:00 - 15:00, 2023

Douglas R. Brumley (Senior Lecturer, Applied Mathematics, University of Melbourne, Australia)

Bacterial motility, symbioses, and marine nutrient cycling unfold at the scale of individual microbes, and are inherently dynamic. In this talk, I will discuss the role that fluid flows play in shaping the ecology of microbes, both in the open ocean as well as around coral surfaces. In each case, I will demonstrate how iteratively combining video-microscopy, image processing and mathematical modelling can resolve features of microbial lifestyles that are difficult or impossible to see otherwise, and show how single-cell measurements can be connected to bulk processes at the population-level.

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

Event Official Language: English

Phase reduction beyond the Kuramoto model

June 15 (Thu) at 14:00 - 15:00, 2023

Iván León (Research Scientist, Department of Systems and Control Engineering, Tokyo Institute of Technology)

Many biological, engineering and natural systems can be modeled as populations of coupled oscillators where each oscillator behaves periodically. When these units are coupled to each other, emergent phenomena, as synchronization, appears. However, dealing with those systems is usually difficult due to the large number of degrees of freedom. Conditionality reduction techniques to obtain simple tractable models are usually considered. The most common method is "phase reduction" that allows to capture the dynamics of each oscillator with just one variable, the phase. The succeed of the method was clear when the Kuramoto model, derived through phase reduction, gave a simple explanation to collective synchronization. Despite this success, phase reduction is often limited to the Kuramoto model because of the challenge to obtain analytical expressions. The porpoise of this talk is to make clear that phase reduction beyond Kuramoto model is possible. On the first part of the talk we introduce phase reduction and its limitations. Then we show how it is possible to obtain analytical phase reduced model for weakly nonlinear oscillators. Finally, we talk about second order phase reduction where higher order corrections are included to capture the qualitative dynamics and improve accuracy.

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

Event Official Language: English

Deciphering speciation processes: a mathematical modelling approach to biodiversity patterns

June 8 (Thu) at 10:00 - 11:00, 2023

Ryo Yamaguchi (Assistant Professor, Department of Advanced Transdisciplinary Sciences, Faculty of Advanced Life Science, Hokkaido University / Postdoctoral Research Fellow, Biodiversity Research Centre, University of British Columbia, Canada)

The grandeur and complexity of Earth’s biodiversity present a challenge to comprehend the intricate mechanisms underlying speciation. Once dubbed by Darwin as the “mystery of mysteries,” speciation remains a frontier in biology, with much still cloaked in obscurity. Applying mathematical models inspired by population genetics and individual-based simulations, I aim to shed light on the complex mechanisms underlying speciation. In this talk, I focus on the concept of a “speciation cycle,” a recurring pattern integral to the formation of biodiversity. In contrast to traditional views that focus solely on a single speciation event, our approach argues for the necessity of multiple intertwined processes. These include the coexistence of closely related species, ongoing diversification, and the accumulation of new species, all while avoiding extinction. By overviewing mathematical models of each evolutionary and ecological process, I will introduce their basic ideas, and examine under what conditions the formation and coexistence of new species are promoted. Then we further explore the temporal and spatial dimensions of speciation, looking closely at the intervals between speciation events and the steady buildup of biodiversity over geological timescales. By bridging the gap between microevolutionary processes and macroevolutionary patterns, I hope to enable the prediction of biodiversity patterns based on a deeper understanding of speciation mechanisms.

Venue: via Zoom

Event Official Language: English

Modelling radiation cancer treatment with ordinary and fractional differential equations

June 1 (Thu) at 10:00 - 11:00, 2023

Kathleen Wilkie (Associate Professor, Department of Mathematics, Toronto Metropolitan University, Canada)

Fractional calculus has recently been applied to mathematical modelling of tumour growth, but its use introduces complexities that may not be warranted. Mathematical modelling with differential equations is a standard approach to study and predict treatment outcomes for population-level and patient-specific responses. Here we use patient data of radiation-treated tumours to discuss the benefits and limitations of introducing fractional derivatives into three standard models of tumour growth. The fractional derivative introduces a history-dependence into the growth function, which requires a continuous death-rate term for radiation treatment. This newly proposed radiation-induced death-rate term improves computational efficiency in both ordinary and fractional derivative models. This computational speed-up will benefit common simulation tasks such as model parameterization and the construction and running of virtual clinical trials.

Venue: via Zoom

Event Official Language: English

Molecular and evolutionary bases of Pieris butterflies for overcoming diverse chemical defenses in their host plants

May 25 (Thu) at 16:00 - 17:00, 2023

Yu Okamura (JSPS Research Fellow PD, Department of Biological Sciences, Graduate School of Science, The University of Tokyo)

In terrestrial ecosystems, plants and herbivorous insects account for more than half of the described species and play quite important ecological roles. Plants and herbivorous insects have strong chemical interaction as plants defend themselves with various defense compounds such as secondary metabolites and herbivores adapt to it by evolving detoxification mechanisms. Larvae of Pieris butterflies feed on Brassicaceae plants as the main host. Brassicaceae plants contain diverse glucosinolates (GLS) as a main chemical defense, which can be rapidly hydrolyzed into toxic isothiocyanates by a plant enzyme called myrosinase upon tissue damage. Larvae of Pieris butterflies are known to express nitrile-specifier protein in their gut and this can redirect toxic breakdown products of GLSs to less toxic metabolites. Although NSP is considered an evolutionary key innovation for Pieridae that enabled these butterflies to colonize GLS-containing plants, it has been largely unclear whether NSP is enough for Pieris butterfly larvae to overcome the diverse types of GLS they encounter in their host plants. In this seminar, I would like to introduce our recent findings showing that Pieris butterfly larvae not only use NSP but also use its ortholog major allergen (MA) to overcome the diverse types of GLS in their Brassicaceae host plants. We found that Pieris larvae show fine-tuned regulation of those two adaptive genes depending on the chemical profiles of their host plants. Furthermore, those two adaptive genes have different evolutionary trajectories in macro- and micro-evolutionary scales among Pieris species or populations associated with their pattern of host plant usage. Moreover, with an approach using CRISPR/Cas9 genome editing, we showed that both NSP and MA have different but complementary roles in disarming GLS-based defenses in their host plants and that both genes are crucial for Pieris in overcoming their host plant’s major chemical defense. Those highlight that having both NSP and MA is a key for Pieris butterflies to overcome the diverse types and GLS and, consequently, adapt to a wider range of Brassicaceae hosts. Our results illuminate that gene duplication, functional differentiation, and the evolution of gene regulation mechanisms are all crucial for herbivorous insects to overcome co-evolving chemical defenses in their host plants.

Venue: via Zoom

Event Official Language: English

Excursion Theory, Galton Watson Trees and their Scaling Limits

May 18 (Thu) at 16:00 - 17:00, 2023

Christy Koji Kelly (Special Postdoctoral Researcher, iTHEMS)

In this talk we aim to introduce a recent perspective in probability theory that views random trees as random excursions with additional data. This perspective is particular suited to the study of the scaling limit of tree-valued random processes. Excursion theory is a useful and relatively elementary tool allowing one to derive rather explicit information about the local and global geometry of the resultant continuum trees which in turn can be used to derive information about large random trees. We illustrate these ideas in the context of the Brownian continuum random tree, the scaling limit of critical Galton-Watson trees and a structure that arises naturally in various contexts in physics; in particular the Brownian continuum random tree is a pathological model of quantum spacetime. Despite the fundamentally mathematical nature of the talk, the aim is to keep the presentation essentially heuristic emphasising key intuitions over rigorous proof. The content itself should be relevant to biologists interested in the theory of branching processes or coalescent theory.

Venue: Seminar Room #359 / via Zoom

Event Official Language: English

Conditions for maintaining pseudo-overdominance

May 11 (Thu) at 16:00 - 17:00, 2023

Diala Abu Awad (Associate Professor, Génétique Quantitative et Évolution - Le Moulon, Université Paris-Saclay, France)

Deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. However, arrays of deleterious recessives linked in repulsion could generate appreciable pseudo-overdominance, mimicking overdominant selection that would sustain segregating load. We use analytical approches and simulations to explore whether and for how long pseudo-overdominant (POD) zones can persist once created (e.g., by hybridization between populations fixed for alternative mildly deleterious mutations). Balanced haplotype loads, tight linkage, and moderate to strong cumulative selective effects all serve to maintain POD zones. Tight linkage is key, suggesting that such regions are most likely to arise and persist in low recombination regions (like inversions). Selection and drift unbalance the load, eventually eliminating POD zones, but this process is quite slow, and could influence short term evolution of populations.

Venue: via Zoom

Event Official Language: English

Introduction to Genomics

April 27 (Thu) at 16:00 - 17:00, 2023

Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

A 'genome' is a single set of genetic information of a given individual, which is encoded by the nucleotide sequence of the DNA. For instance, the human genome consists of around 3 billion nucleotide base pairs, although the size and content of the genome differs greatly across species and individuals. Some species such as the budding yeast has a genome as small as 12 million base pairs, whereas other species such as Paris japonica, a flowering plant native to the sub-alpine regions of Japan, is said to have a genome as large as 150 billion base pairs. In this talk, I will give a introduction of what kind of information is contained within a genome, and how that differs across species and individuals. This talk will be introductory and aimed at non-experts including non-biologists.

Venue: via Zoom

Event Official Language: English

Machine learning predicts biological system evolution by gene gains and losses

April 20 (Thu) at 16:00 - 17:00, 2023

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

Prediction of evolution is a fundamental goal of biology with a potential impact on strategic pathogen control and genome engineering. While predictability of short-term and sequence-level evolution has been investigated, that of long-term and system-level evolution has not been systematically examined. Here, we show that evolution of metabolic systems by gene gains and losses is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss events at the branches of the reference phylogenetic tree, suggesting universally shared evolutionary pressures and constraints on metabolic systems. I herein present the mathematical model of Evodictor and our findings on evolutionary rules from physiological and ecological aspects. I will further discuss potential versatility of Evodictor approach to analyze various diversification processes along branching lineage trees, not only evolution, but also developmental processes.

Venue: via Zoom

Event Official Language: English

Why are cell populations maintained via multiple compartments?

April 13 (Thu) at 10:00 - 11:00, 2023

Carmen Molina-París (Researcher, Theoretical Biology and Biophysics, Los Alamos National Laboratory, USA)

We consider the maintenance of “product” cell populations from “progenitor” cells via a sequence of one or more cell types, or compartments, where each cell’s fate is chosen stochastically. If there is only one compartment then large amplification, that is, a large ratio of product cells to progenitors comes with disadvantages. The product cell population is dominated by large families (cells descended from the same progenitor) and many generations separate, on average, product cells from progenitors. These disadvantages are avoided using suitably-constructed sequences of compartments: the amplification factor of a sequence is the product of the amplification factors of each compartment, while the average number of generations is a sum over contributions from each compartment. Passing through multiple compartments is, in fact, an efficient way to maintain a product cell population from a small flux of progenitors, avoiding excessive clonality and minimising the number of rounds of division en route. We analyse the possible descendants of one progenitor cell, families of cells that journey through the sequence of compartments. We find that the ability of product cells to perform their function may be negatively affected by the number of rounds of cell division that separates them from their progenitor, because every round of division brings with it a risk of mutation.

Venue: via Zoom

Event Official Language: English

Organizational meeting

April 6 (Thu) at 16:00 - 17:00, 2023

Catherine Beauchemin (Deputy Program Director, iTHEMS)

The purpose of the organizational meetings is to discuss various topics of interest to the members of iTHEMS in the field of Biology, but also to participants of the iTHEMS BIology Seminar, irrespective of their field. The primary objective of this meeting will be to discuss recruitment of JRAs, SPDRs, and female researchers from Biology into iTHEMS. I hope we can identify the main obstacles and consider together possible solutions. As usual, any additional topic can be brought up spontaneously by participants. Anyone with thoughts about iTHEMS Biology is welcome to join us, no matter their field.

Venue: via Zoom

Event Official Language: English

Asymmetric enzyme kinetics of F1-ATPase resulted from asymmetric allosterism

March 30 (Thu) at 16:00 - 17:00, 2023

Yohei Nakayama (Assistant Professor, Department of Applied Physics, Graduate School of Engineering, Tohoku University)

Bio-molecular machines play various roles in cells where thermal fluctuation is dominant. Since artificial molecular machines are far behind bio-molecular machines for the present, we should begin with understanding how bio-molecular machines are designed to play their roles. We examine the motion of a bio-molecular machine, F1-ATPase, in single molecule experiments. In particular, we focus on the operation of F1-ATPase as ATP synthase in addition to as molecular motor. In this seminar, I talk about the enzyme kinetics, dependence of reaction rate on substrate concentration, of F1-ATPase in ATP synthesis. The experimental result shows that the enzyme kinetics of F1-ATPase in ATP synthesis exhibits weaker dependence on substrate concentration than the ordinary Michaelis-Menten kinetics, whereas that in ATP hydrolysis follows Michaelis-Menten kinetics. Therefore, the enzyme kinetics of F1-ATPase turned out to be asymmetric between ATP synthesis and hydrolysis. We analyzed this asymmetry based on a potential switching model, totally asymmetric allosteric model, whose characteristic is asymmetry in angular dependence of binding rates of substrates. It was shown that the totally asymmetric allosteric model may reproduce the experimental results, where the asymmetry of binding rates is essential. We also discuss physiological roles that the asymmetry of enzyme kinetics may play.

Venue: via Zoom

Event Official Language: English

Warming reduces the density-dependent divergence in emergence time for two competing parasitoid species

March 23 (Thu) at 16:00 - 17:00, 2023

Midori Tuda (Associate Professor, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University)

Climate change is expected to directly affect ectothermic species through their sensitivity to temperature, with cascading effects on populations and communities. Here we experimentally tested predictions from two non-exclusive hypotheses concerning the impacts of elevated temperature (+2°C) on interactions between a single host species (the azuki bean beetle) and two species of parasitoid wasps. We hypothesized that increasing temperature shortens the time that the host is vulnerable to parasitoid attack. This change in available resource should heighten intra- and interspecific competition among parasitoids, which could induce divergence in emergence times. We found that intraspecific competition of both parasitoid species was more intense than interspecific competition irrespective of temperature. The difference (d) in the emergence times of the two parasitoid species increased with the density of each parasitoid but decreased at the elevated temperature. Both parasitoids emerged sooner at the elevated temperature and experienced a reduction in body size. Thus, high levels of intraspecific competition (along with the consequent reduction in body size) may have attenuated the intensity of interspecific competition at the elevated temperature despite a reduction in the differentiation of emergence times.

Venue: via Zoom

Event Official Language: English