iTHEMS Biology Seminar
174 events
We are holding regular seminars and other activities on topics related to biology. Our aim is to lower the boundaries between biology and mathematics/physics, to identify common grounds between biology and mathematics/physics, and to develop ideas for new research topics at the intersection of biology and mathematics or physics.
For further details see iTHEMS Biology Seminar Study Group page.
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Seminar
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
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Seminar
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
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Seminar
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
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Seminar
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
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Seminar
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
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Seminar
Arrhythmic activity rhythms in ants
March 26 (Tue) at 16:00 - 17:00, 2024
Haruna Fujioka (Assistant Professor, Faculty of Environmental, Life, Natural Science and Technology, Okayama University)
Most organisms exhibit a periodic activity of about 24 h. This circadian rhythm is considered to be an adaptation to the fluctuations of the environment. In social insects such as honeybees and ants, individual behavior, including activity-rest rhythms, is influenced by interactions within the colony. However, it is challenging to monitor individual activity-rest rhythms in an ant colony due to their large group size and small body size. To address this, we developed an image-based tracking system using 2D barcodes a monomorphic ant and measured the locomotor activities of all colony members under laboratory conditions. Activity-rest rhythms appeared only in isolated ants, not under colony conditions. This suggests that a mixture of social interactions, not light and temperature, induces the loss of activity-rest rhythms. These findings contribute to our understanding of the diverse patterns of circadian activity rhythms in social insects.
Venue: via Zoom
Event Official Language: English
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Seminar
The evolution of unusual inheritance and chromosome behaviour in flies and other critters
March 14 (Thu) at 16:00 - 17:00, 2024
Laura Ross (Senior Lecturer, Institute of Evolutionary Biology, University of Edinburgh, UK)
Under Mendelian inheritance, individuals receive one set of chromosomes from each of their parents, and transmit one set of these chromosomes at random to their offspring. Yet, in thousands of animals Mendel's laws are broken and the transmission of maternal and paternal alleles becomes unequal. Why such non-Mendelian reproductive systems have evolved repeatedly across the tree of life remains unclear. My lab studies a variety of arthropod species to understand why, when and how the transmission of genes from one generation to the next deviate from Mendel’s laws. We mainly focus on species with Paternal Genome Elimination: Males transmit only those chromosomes they inherited from their mother to their offspring, while paternal chromosomes are excluded from sperm through meiotic drive. I will present recent work aimed at understanding the evolution of this unusual reproductive strategy in a clade of flies. These flies arguably have one of the most bizarre and complex chromosome systems of any insect and we use this complexity to study a range of topics including the evolution of sex chromosomes, germline-restricted chromosomes and sexual conflict.
Venue: Seminar Room #359 / via Zoom
Event Official Language: English
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Seminar
Plant hackers: galling insects extend their phenotypes on the trees by novel plant organogenesis
February 27 (Tue) at 16:00 - 17:00, 2024
Xin Tong (Special Postdoctoral Researcher, Cell Function Research Team, RIKEN Center for Sustainable Resource Science (CSRS))
When it comes to plant-insect interactions, insects are generally seen as pests like caterpillars eating vegetables or fruits. However, one group of insects, the galling insects can induce de novo organogenesis on the host plants which are often woody plants. Each galling insect species ‘designs’ its own gall as the extended phenotype which are so-called species-specific gall formation. Different from leaves and roots, galls represent unique plant organs swiftly formed in response to parasitic organisms, observed across diverse plant species. Yet, the precise mechanisms by which normal plant development is interrupted and redirected to form galls by galling organisms remain elusive. During the talk, I will share some discoveries and views related to aphid gall formation on the elm tree, which is the super host plant for more than 30 galling species, and further discussion about why an insect gall is not simple cell mass but well-organized structure, and how we could systematically understand insect gall formation.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Cellular-level left-right asymmetry, cell chirality, induces the chiral collective rotation of multicellular colony
February 15 (Thu) at 16:00 - 17:00, 2024
Tomoki Ishibashi (Special Postdoctoral Researcher, Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research (BDR))
Ryohei Nishizawa (Ph.D. Student, Graduate School of Frontier Biosciences, Osaka University)The left-right (LR) asymmetric morphology of organs is essential for the development and maintenance of their functions in various species. In recent years, it has become clear that the LR asymmetry of organs originates from cell chirality, the LR asymmetric nature at the cellular level [1]. However, it is unclear how the cell chirality generates the LR asymmetry at the multicellular level. Here we show a mechanism of LR asymmetry formation at the multicellular level based on cell chirality. We previously found that Caco-2 cells, a typical cultured epithelial cell line derived from human colon cancer, exhibit stereotypical and directional cell chirality; when Caco-2 cells are cultured as single cells, their nuclei and cytoplasm rotate in the clockwise direction at a rate of 50°/h [2]. Interestingly, when Caco-2 forms multicellular colonies, the colonies also undergo a collective clockwise rotation at 10º/h. We revealed that the actomyosin cytoskeleton is essential for the formation of the collective rotation [2]. We also found that Caco-2 cells formed lamellipodia and focal adhesions LR asymmetrically during the collective colony rotation, which may be responsible for the chiral collective motion. Interestingly, the disruption of microtubules reversed the direction of collective rotation. The LR asymmetric formation of lamellipodia and focal adhesions was also reversed by inhibition of microtubule polymerization. We will discuss the possible mechanism and the mathematical model where cell chirality induces multicellular chiral rotation depending on microtubules.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Chemical reaction network theory and the problem of reaction rate
February 8 (Thu) at 16:00 - 17:00, 2024
Tomoharu Suda (Postdoctoral Researcher, Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS))
A chemical system can be described at different levels. When we focus on the population of chemical species, it is convenient to consider the system as consisting of a number of chemical reactions, which assumes the structure of a (hyper)graph together with the species. The chemical reaction network theory studies chemical systems described in such a way. It aims to elucidate the dynamics of overall chemical composition in terms of the associated graph structure. Notably, it applies not only to chemical systems but also to more general systems as long as the mathematical structure is compatible. In the first part of this talk, we will review the basic concepts and results of the theory, which mainly concern the existence and stability of the equilibrium. From the viewpoint of chemical kinetics, it is interesting to consider the rate of the overall reaction, which may be obtained by the total balance of chemical species. The second part of the talk will be devoted to this topic. Formulation of the problem and some results will be presented. In particular, chemical reaction networks with first-order reactions will be considered in detail.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Competition across scales in biology
January 31 (Wed) at 11:00 - 12:00, 2024
Sidhartha Goyal (Associate Professor, Department of Physics, University of Toronto, Canada)
Many biological phenomena emerge from interaction and competition between its parts. I will share some examples across biological scales where data-driven theory can reveal new rules of biological competition. At the molecular scale competition between mitochondrial genomes within budding yeast depends on genome architecture; dynamics of adaptive immunity in microbes reveal different modalities of competition and coexistence of bacteria and its phages; in mammals cellular reprogramming may be driven by elite clones, and tumor response to drugs is driven by "epigenetic" switching. Going beyond, I will present some ideas on understanding dynamical systems that govern cell fate dynamics and if competition may play a role in it. Short bio: Sidhartha Goyal got his PhD in Physics at Princeton in 2009 and then moved to Kavli Institute for Theoretical Physics, Santa Barbara for a postdoc. He got his first degree in Electrical Engineering from IIT Bombay. He is now an Associate Professor in the Physics Department at University of Toronto interested in collective phenomena in biology across scales.
Venue: via Zoom
Event Official Language: English
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Seminar
Does horizontal gene transfer stabilize cooperation in bacteria?
January 16 (Tue) at 16:00 - 17:00, 2024
Anna Dewar (Postdoctoral Researcher, Department of Biology, University of Oxford, UK)
Bacteria are highly social. Much of this sociality occurs through the production of cooperative ‘public goods’. Unlike in animals, bacterial genes are able to transfer horizontally between individuals, in addition to vertically via descendants. This widespread horizontal gene transfer has implications for the concept of relatedness and how cooperation is maintained in bacteria. It has been suggested that horizontal gene transfer, particularly via small segments of DNA called plasmids, could stabilize cooperation in bacteria. Transfer of a cooperative gene could turn non-cooperative ‘cheats’ into cooperators, preventing cheats from invading and destabilizing cooperation. We tested this with a comparative analysis across bacterial species. In contrast to the predictions of the hypothesis, we found that genes for cooperative traits were not more likely to be carried on either: (1) plasmids compared to chromosomes; or (2) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that, while horizontal gene transfer can help cooperative genes initially invade a population, it has less influence on the longer-term maintenance of cooperation.
Venue: via Zoom
Event Official Language: English
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Seminar
Oscillatory data analysis using the extended Hilbert transform method
December 26 (Tue) at 16:00 - 17:00, 2023
Akari Matsuki (Postdoctoral Researcher, Department of Advanced Transdisciplinary Sciences, Hokkaido University)
Oscillatory phenomena are observed in various biological systems, such as spinal nervous systems and circadian rhythms. These macroscopic oscillatory phenomena appear as a result of synchronization of microscopic oscillators, such as pacemaker cells. The first step in the analysis of synchronization is to reconstruct the "phase" from the observed signal. The Hilbert transform method is one of the popular methods for phase reconstruction, but it is known that it can only accurately reconstruct the phase from a limited class of signals such as narrowband signals. In this study, we show that the Hilbert transform method has a low-pass filter-like effect on the phase modulation and propose an "extended Hilbert transform method" that can be applied to a wider class of signals. In this talk, I will introduce the extended Hilbert transform method, and its application to phase shift detection and coupling network inference.
Venue: via Zoom
Event Official Language: English
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Seminar
Application of mathematical models to the COVID-19 cohort study
December 19 (Tue) at 16:00 - 17:00, 2023
Takara Nishiyama (Ph.D. Student, Graduate School of Science, Nagoya University)
The COVID-19 pandemic, which began in 2019, has caused widespread morbidity and mortality across the globe. In response, a multitude of studies focusing on SARS-CoV-2 have been undertaken. Among these, cohort studies have been particularly significant. These studies, as a key observational research method, play a crucial role in exploring the links between various factors and the onset of diseases, offering valuable insights for disease control. Mathematical model, applied within these studies, provide essential quantitative data. In my talk, I will introduce how mathematical models are instrumental in cohort studies, drawing on two of my own COVID-19 cohort studies as examples.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Plasticity in the endogenous rhythms and the adaptation to the tidal environment in a freshwater snail
December 14 (Thu) at 16:00 - 17:00, 2023
Takumi Yokomizo (JSPS Research Fellow PD, Graduate School of Science, Chiba University)
Organisms have diverse biological clocks synchronized with environmental cycles depending on their habitats. The change in endogenous rhythms could contribute to range expansion in a novel rhythmic environment. For example, the Anticipation of tidal changes has driven the evolution of circatidal rhythms in some marine species. I am interested in the genetic and non-genetic changes in the biological rhythms and adaptation to tidal environments in the freshwater snail, Semisulcospira reiniana. Chronobiological analyses of behavior and gene expression revealed that snails had habitat-specific endogenous rhythms: individuals in a nontidal population showed the circadian rhythm while those in a tidal population showed the circadian and circatidal rhythms. The entrainment to the simulated tidal cycles increased the strength of circatidal activity only in snails in a tidal population. Although the circatidal rhythms in the transcriptome were clearer in individuals entrained to tidal cycles, the number of circatidal rhythmic transcripts was greater in a tidal population than in a nontidal population. These results suggest biological rhythms in the snails plastically change at the molecular level, but the strength of circatidal rhythm is different between populations. Finally, transcriptome-wide population genetic analysis revealed that these two populations can be clearly distinguished genetically, though the genetic distance was very small. Thus, genetic differentiation in biological rhythms could result from the evolution of a small number of genes. These findings suggest that adaptive plasticity and genetic changes in the biological rhythms play an important role in coping with tidal environments.
Venue: via Zoom
Event Official Language: English
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Seminar
Translating between evolutionary game theory and theoretical ecology
December 5 (Tue) at 16:30 - 17:30, 2023
Arne Traulsen (Director, Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, Germany)
Both theoretical ecology and evolutionary game theory describe the dynamics of interacting populations. More than 40 years ago, Hofbauer and Sigmund established a mathematical equivalence between the Lotka-Volterra equations and the replicator dynamics from evolutionary game theory. However, this equivalence has not been exploited by empiricists so far. One of the issues is dimensionality: An ecological interaction of two species corresponds to an evolutionary game between three types. Only when we focus on a special case with identical growth rates, it is possible to translate without this trick, leading to a more direct equivalence between the frameworks. Consequently, one has to be particularly careful how to classify interactions and how to assess dynamical outcomes. For example, a ‘Prisoner's Dilemma’ interaction where the `cooperators' have a higher intrinsic growth rate than `defectors' can result in stable coexistence of the two types and may ultimately not represent a social dilemma at all.
Venue: via Zoom
Event Official Language: English
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Seminar
Evolution by gene and genome duplications
November 28 (Tue) at 16:00 - 17:00, 2023
Jeffrey Fawcett (Senior Research Scientist, iTHEMS)
Each organism typically has (tens of) thousands of genes in its genome that perform various molecular and cellular functions, but how did these genes originate? The answer for most genes is by the duplication of another gene. In fact, all the genes (the entire genome) can get duplicated simultaneously on some instances. Thus, gene and genome duplications are considered key driving forces of evolution and are one of the most important topics in molecular evolutionary biology. In this talk, I will introduce the background and basic concepts related to gene and genome duplications. The talk will be aimed at non-experts so non-biologists are also welcome to attend.
Venue: via Zoom
Event Official Language: English
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Seminar
X's Fast and Slow
November 21 (Tue) at 16:00 - 17:00, 2023
Thomas Hitchcock (Special Postdoctoral Researcher, iTHEMS)
Sex chromosomes have long been suggested to undergo distinct evolutionary dynamics to the rest of the genome. Their distinct ploidy and transmission genetics may result in differing strengths of selection, magnitude of drift, and mutation rates to the autosomes, particularly if there are sex differences. Consequently, a body of theory and empirical work has developed investigating such differences, and how they might manifest in the rates of change between populations, and the diversity observed within populations. I will briefly review the theoretical basis of these comparisons, how we can infer rates of evolutionary change from genetic data, and what we can learn from non-model systems, particularly focusing on fungus gnats and pea aphids.
Venue: via Zoom
Event Official Language: English
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Seminar
Patterns of fern community assembly throughout the American continent: Do the mechanisms of species diversification also vary with latitude?
November 7 (Tue) at 16:00 - 17:00, 2023
José Said Gutiérrez-Ortega (Special Postdoctoral Researcher, iTHEMS)
The global latitudinal gradient of biodiversity, a pattern suggesting that the low-latitude (tropical) areas have more species than the high-latitude (temperate) areas, represents the most conspicuous pattern of correlation between the environmental/geographic variation and biodiversity distribution. Yet, the relative roles of all ecological, geographic, and historical variables that can explain the gradient are unclear. Specifically, it is because we do not have a clear link between latitude and the underlying mechanisms that originate and extinct species throughout the gradient. In other words, we lack a connection between the “macroevolutionary patterns" and “microevolutionary processes”. I am researching the community assembly of ferns from the American continent, as it seems to be a group that can give some answers to what causes the latitudinal gradient of biodiversity and how the gradient is related to the processes of speciation and extinction. Regarding the community assembly, as expected, I found that the fern community clearly follows the latitudinal gradient: the number of species and localities colonized by ferns decrease with latitude. Also, this pattern is associated to a strong phylogenetic structure: the community at each latitudinal area is dependent of the previously colonizing genera (in other words, genera tend to diversify within specific latitudinal spans; most of them are restricted to the tropics). These results suggest that the fern community from the American continent follows the latitudinal gradient, and that it is a good representer of this pattern. Then, using linear regressions, I tested some classical hypotheses that have been proposed to explain the latitudinal gradient (e.g., that tropical environments, being more thermodynamically active, promote higher speciation rates). However, my results so far, suggest that none of the previously proposed hypotheses give a satisfactory explanation: there is no a single factor that can link the gradient with the processes of speciation or extinction. Rather, my data suggest that to promote speciation, the relative roles of environmental differentiation, geographic isolation, niche divergence, and time since divergence between sister species pairs vary with latitude. For example, to become new species, species near the equator did not need much geographic isolation or niche divergence from their sister counterparts (i.e., near the equator, species pairs tend to be more sympatric and present higher niche overlap). I hope my talk can stimulate some discussion about how to approach and treat the data that I have compiled, and that we can create opportunities for further collaboration.
Venue: via Zoom
Event Official Language: English
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Seminar
Mathematical modelling of the host response to inhalational anthrax across different scales
October 31 (Tue) at 16:00 - 17:00, 2023
Bevelynn Williams (Postdoctoral Fellow, School of Mathematics, University of Leeds, UK)
Inhalational anthrax, caused by the bacterium Bacillus anthracis, is a disease with very high fatality rates. Due to the significant risk posed if the bacterium was to be intentionally used as a bioweapon, it is important to be able to defend against such an attack and to make optimal decisions about treatment strategies. Mechanistic mathematical models can help to quantify and improve understanding of the underlying mechanisms of the infection. In this talk, I will present a multi-scale mathematical model for the infection dynamics of inhalational anthrax. This approach involves constructing individual models for the intracellular, within-host, and population-level infection dynamics, to define key quantities characterising infection at each level, which can be used to link dynamics across scales. I will begin by introducing a model for the intracellular infection dynamics of B. anthracis, which describes the interaction between B. anthracis spores and host cells. The model can be used to predict the distribution of outcomes from this host-pathogen interaction. For example, it can be used to estimate the number of bacteria released upon rupture of an infected phagocyte, as well as the timing of phagocyte rupture and bacterial release. Next, I will show how these key outputs can be used to connect the intracellular model to a model of the infection at the within-host scale. The within-host model aims to provide an overall understanding of the early progression of the infection, and is parametrised with infection data from studies of rabbits and guinea pigs. Furthermore, this model allows the probability of infection and the time to infection to be calculated. Building a model that offers a realistic mechanistic description of these different animal responses to the inhalation of B. anthracis spores is an important step towards eventually extrapolating the model to describe the dynamics of human infection. This would enable predictions of how many individuals would become infected in different exposure scenarios and also on what timescale this would occur.
Venue: via Zoom / Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
174 events