iTHEMS Biology Seminar
113 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 Tomorrow
Asymmetric enzyme kinetics of F1-ATPase resulted from asymmetric allosterism
March 30 (Thu) at 16:00 - 17:00, 2023
Dr. 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
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Seminar
Warming reduces the density-dependent divergence in emergence time for two competing parasitoid species
March 23 (Thu) at 16:00 - 17:00, 2023
Dr. 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
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Seminar
Reproductive interference can affect trait diversity of closely related animal species
March 9 (Thu) at 16:00 - 17:00, 2023
Mr. Keiichi Morita (Ph.D. Student, School of Advanced Sciences Department of Evolutionary Studies of Biosystems, SOKENDAI, the Graduate University for Advanced Studies)
Previous theoretical studies have considered that evolution driven by resource competition is important for the creation and maintenance of biodiversity. Recently, reproductive interference caused by misrecognition of sexual traits such as calling between closely related species has been increasingly important for the creation and maintenance of diversity, but the impact of reproductive interference on trait diversity between closely related species remains unresolved. In this study, we combined population dynamics model with reproductive interference in two closely related species with an evolutionary model of traits related to reproduction to examine the impact of reproductive interference on the evolutionary consequences of reproductive traits in the two closely related species. The model assumed a trade-off in which reproductive interference weakens as reproductive traits diverge between the two species, but predation pressure increases as the reproductive traits diverge from their optimum traits in their habitat. For simplicity, we assumed that only one species evolves. Our model analysis revealed that convergence and divergence of traits of two closely related species occurs depending on initial trait divergence. Also, under the parameter condition where trait convergence occurs, large mutation makes trait divergence possible. Our model will provide a new framework for understanding evolutionary dynamics in ecological communities containing closely related species.
Venue: via Zoom
Event Official Language: English
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Seminar
Elasticities of population growth and their significance to evolutionary biology
February 9 (Thu) at 16:00 - 17:00, 2023
Dr. Stefano Giaimo (Postdoc, Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Germany)
The elasticity of population growth to a demographic parameter quantifies the proportional sensitivity of population growth to such parameter. In this talk, I will illustrate some cases where elasticities of population growth to demographic parameters acquire a special importance to evolutionary biology. In particular, I will discuss the relevance of these elasticities in studying the evolution of aging, their role in the computation of the generation time and their relationship to some trade-offs organisms may face as they optimise their fitness.
Venue: via Zoom
Event Official Language: English
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Seminar
Universal Biology in Adaptation and Evolution: Dimensional Reduction and Fluctuation-Response Relationship
February 2 (Thu) at 16:00 - 17:00, 2023
Prof. Kunihiko Kaneko (Professor, Niels Bohr Institute, University of Copenhagen, Denmark)
A macroscopic theory for adaptive changes of cells is presented, based on consistency between cellular growth and molecular replication, as well as robustness of fitted phenotypes against perturbations. Adaptive changes in high-dimensional phenotypes are shown to be restricted within a low-dimensional slow manifold, from which a macroscopic law for cellular states is derived, as is confirmed by adaptation experiments of bacteria under stress. The theory is extended to phenotypic evolution, leading to proportionality between phenotypic responses against genetic evolution and by environmental adaptation, which also explains the evolutionary fluctuation-response relationship previously uncovered. Relevance of statistical-physics and dynamical-systems approach is discussed.
Venue: via Zoom
Event Official Language: English
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Seminar
Mathematical models inspired by the Lenski experiment
January 19 (Thu) at 10:00 - 11:00, 2023
Dr. Adrian Gonzalez-Casanova (Neyman Visiting Assistant Professor, The University of California, Berkeley, USA / Associate Professor, National Autonomous University of Mexico, Mexico)
We will discuss the basic models of mathematical population genetics and see how to apply them to the study of the Lenski experiment. Furthermore, we will describe novel models that are capable of providing a parsimonious explanation of the deceleration of the relative fitness and can be used to attack questions such as, is it advantageous to be efficient? If time permits, we will also discuss examples of mathematical modelling beyond the Lenski experiment, including the study of populations of bacteria carrying plasmids.
Venue: via Zoom
Event Official Language: English
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Seminar
Basic of microbial ecology and applicability of your life and research
January 12 (Thu) at 16:00 - 17:00, 2023
Mr. Daiki Kumakura (Ph.D. Student, Graduate School of Life Science, Hokkaido University)
Microbial ecology is a fascinating field that examines the various environments in which microbes can thrive and their potential applications to human life. In this seminar, I will delve into four main topics:
Venue: via Zoom
Event Official Language: English
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Seminar
A cell membrane model that reproduces cortical flow-driven cell migration and collective movement
January 5 (Thu) at 16:00 - 17:00, 2023
Dr. Katsuhiko Sato (Associate Professor, Research Institute for Electronic Science, Hokkaido University)
Cellular migration is a key component of numerous biological processes, including the morphogenesis of multicellular organisms, wound healing, and cancer metastasis, where cells adhere to each other to form a cluster and collectively migrate. Although the mechanisms controlling single-cell migration are relatively well understood, those underlying multiple-cell migration still remain unclear. A key reason for this knowledge gap is the so-called many-body problem. That is, many forces—including contraction forces from actomyosin networks, hydrostatic pressure from the cytosol, frictional forces from the substrate, and forces from adjacent cells—contribute to cell cluster movement, making it challenging to model, and ultimately elucidate, the final result of these forces. In this talk, I provide a two-dimensional cell membrane model that represents cells on a substrate with polygons and expresses various mechanical forces on the cell surface, keeping these forces balanced at all times by neglecting cell inertia. The model is discrete but equivalent to a continuous model if appropriate replacement rules for cell surface segments are chosen. When cells are given a polarity, expressed by a direction-dependent surface tension reflecting the location dependence of contraction and adhesion on a cell boundary, the cell surface begins to flow from front to rear as a result of force balance. This flow produces unidirectional cell movement, not only for a single cell but also for multiple cells in a cluster, with migration speeds that coincide with analytical results from a continuous model. Further, if the direction of cell polarity is tilted with respect to the cluster center, surface flow induces cell cluster rotation. The reason why this model moves while keeping force balance on cell surface (i.e., under no net forces from outside) is because of the implicit inflow and outflow of cell surface components through the inside of the cell. I provide an analytical formula connecting cell migration speed and turnover rate of cell surface components.
Venue: via Zoom
Event Official Language: English
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Seminar
How to infer evolutionary history
December 22 (Thu) at 16:00 - 17:00, 2022
Dr. Jeffrey Fawcett (Senior Research Scientist, iTHEMS)
One main goal of evolutionary studies is to infer the evolutionary that explains the current diversity. We want to infer the ancestral state and what kind of changes occurred from the previous ancestral state to the current state. In other words, we want to infer the phylogenetic relationship that explains the branching pattern that leads to the current diversity and infer the state at each node and the changes that occurred in each branch of the phylogeny. In this talk, I will introduce some basic concepts that are used in evolutionary biology to tackle these questions, especially how molecular data, i.e., DNA and protein sequence data, can be utilized. This talk will be introductory and aimed at non-experts including non-biologists.
Venue: via Zoom
Event Official Language: English
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Seminar
Chemophoresis Engine: Theory of ATPase-driven Cargo Transport
December 15 (Thu) at 16:00 - 17:00, 2022
Dr. Takeshi Sugawara (Project Researcher, Universal Biology Institute, The University of Tokyo)
The formation of macromolecule patterns depending on chemical concentration under non-equilibrium conditions, first observed during morphogenesis, has recently been observed at the intracellular level, and its relevance as intracellular morphogen has been demonstrated in the case of bacterial cell division. These studies have discussed how cargos maintain positional information provided by chemical gradients. However, how cargo transports are directly mediated by chemical gradients remains unknown. Based on the previously proposed mechanism of chemotaxis-like behavior of cargos (referred to as chemophoresis), we introduce the chemophoresis engine as a physicochemical mechanism of cargo motion, which transforms chemical free energy to directed motion through the catalytic ATP hydrolysis [1]. We propose its possible role as a universal principle of hydrolysis-driven intracellular transport.
Venue: via Zoom
Event Official Language: English
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Seminar
Community assembly and species coexistence in the heterogeneous world
November 28 (Mon) at 16:00 - 17:00, 2022
Dr. Naoto Shinohara (Assistant Professor, Graduate School of Life Sciences, Tohoku University)
How ecological communities are assembled and maintained is a fundamental question in community ecology. To tackle this challenge in the heterogeneous world, we need to understand how community assembly patterns change with environmental gradients and how species coexist in temporally fluctuating environments. In the first of my talk, I introduce our study on how plant community assembly patterns change along with the largest global environmental gradient, the latitudinal gradient. Then, I will present how the seasonal variability of environments contributes to the coexistence of phytoplankton species in a lake. These results altogether uncover how spatiotemporal heterogeneity of environments forms ecological communities in nature.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
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Seminar
RNA-Puzzles - the evaluation and automation of RNA 3D structure
November 24 (Thu) at 16:00 - 17:00, 2022
Prof. Zhichao (Chichau) Miao (Principal Investigator, Guangzhou Laboratory, China / Guangzhou Medical University, China)
RNA-Puzzles is a collective endeavour dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. Systematic protocols for comparing models and crystal structures are described and analyzed. In RNA-Puzzles, we discuss a) the capabilities and limitations of current methods of 3D RNA structure based on sequences; b) the progress in RNA structure prediction; c) the possible bottlenecks that hold back the field; d) the comparison between the automated web server and human experts; e) the prediction rules, such as coaxial stacking; f) the prediction of structural details and ligand binding; g) the development of novel prediction methods; and h) the potential improvements to be made. Till now, 37 RNAs with crystal structures have been predicted, while many of them have achieved high accuracy in comparison with the crystal structures. We have summarized part of our results in three papers and two community-wide meetings. With the results in RNA-Puzzles, we illustrate that the current bottlenecks in the field may lie in the prediction of non-Watson-Crick interactions and the reconstruction of the global topology. Correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution. For the model evaluation, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods, (ii) 3D structure normalization, analysis, manipulation, visualization tools and (iii) 3D structure comparison metric tools. With the increasing number of RNA structures being solved as well as the high-throughput biochemical experiments, RNA 3D structure prediction is becoming routine and accurate. Structure modelling may effectively help in understanding the viral RNA structures, including the SARS-CoV-2.
Venue: via Zoom
Event Official Language: English
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Seminar
Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism
November 17 (Thu) at 18:00 - 19:00, 2022
Dr. Yusuke Himeoka (Assistant Professor, Universal Biology Institute, The University of Tokyo)
Physiological states of bacterial cells exhibit a wide spectrum of timescale. Under nutrient-rich conditions, most of the cells in an isogenic bacterial population grow at certain rates, while a small subpopulation sometimes stays in a dormant state where the growth rates slow down by orders of magnitude. For revealing the origins of such heterogeneity of timescales, we studied the kinetic model of Escherichia coli central carbon metabolism. We found that the model robustly exhibits both the growing- and the dormant state. Performing the model reduction, we have revealed the necessary conditions for the distinct behaviour, namely, the depletion of energy due to the futile cycle and its non-uniform impact on the kinetics because of the coexistence of the energy currency-coupled and uncoupled reactions as well as branching of the network.
Venue: via Zoom
Event Official Language: English
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Seminar
Sociogenesis: motivations and first steps
November 10 (Thu) at 16:00 - 17:00, 2022
Dr. Cédric Ho Thanh (Postdoctoral Researcher, Prediction Science Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Sociogenesis is a project that aims to study emergent social behaviors of multi-agent systems. In its simplest form, and agent simply seeks to survive by consuming food and maximizing some happiness score. In this presentation, I will discuss some motivations and inspirations of this project, as well as the challenges to get an agent to survive on its own. I will then showcase some methods to evaluate the quality of agents and their underlying architecture beyond simply looking at their lifespan. I will then conclude with some potential applications. No prior knowledge in reinforcement/deep learning is required to attend this presentation. This work is still mostly at an exploratory stage, so discussions and inputs from the audience are more than welcome!
Venue: via Zoom
Event Official Language: English
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Seminar
Migration dynamics and model of cells crawling on a matrix with cell-scale stiffness heterogeneity
October 27 (Thu) at 16:00 - 17:00, 2022
Dr. Hiroyuki Ebata (Assistant Professor, Graduate School of Science, Kyushu University)
In living tissues where cells migrate, spatial distribution of mechanical properties, especially matrix stiffness, are generally heterogenous with cell-scales ranging from 10 to 1000 μm. Since the cell migration in our body plays critical role in morphogenesis, wound healing, and cancer metastasis, it is essential to understand the migratory dynamics on the matrix with cell-scale stiffness heterogeneity. However, while cellular responses to homogeneous matrix have been extensively explored, studies of the cell motility with stiffness heterogeneity have been limited to the directional movement (durotaxis) driven by a simple stiffness gradient. Thus, we need to elucidate how cell migration is determined through the interaction among cell-scale stiffness heterogeneity and cellular responses such as dynamics of the cell-matrix adhesion site, the intracellular prestress, and cell shape. In this talk, we introduce our experiments on cell motility, shaping, adhesion, and traction forces at long time scales using microelastically patterned hydrogels that enable us to systematically control the cell-scale heterogeneity of the matrix-stiffness. Using microelastically patterned hydrogels, we showed that the cell exhibited a general mode of durotaxis depending on the shape and size of the stiff domains, which was coincided with the extraordinarily large fluctuation of the traction force. We proposed a cell migration model based on equations of a deformable self-propelled particle adopting an amoeboid swimmer-like velocity-shape relationship. By considering the cellular response to stiffness gradients, the model can reproduce general durotaxis driven by cell-scale heterogeneity of the matrix-stiffness.
Venue: via Zoom
Event Official Language: English
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Seminar
How can interspecific pollen transfer affect coexistence and evolution of sex ratio of two closely related plant species?
October 20 (Thu) at 16:00 - 17:00, 2022
Mr. Keiichi Morita (Ph.D. Student, School of Advanced Sciences Department of Evolutionary Studies of Biosystems, SOKENDAI, the Graduate University for Advanced Studies)
In co-flowering species with shared pollinators, interspecific pollen transfer (IPT) may occur, in which pollen grains are transferred between different species. Yet, it is unclear how the costs of IPT in reduced pollen grains (i.e., costs for males) and seed set (i.e., costs for females) can affect coexistence and evolution of sex ratio. We investigated the conditions for which two closely related plants can coexist and of evolution in sex ratio, by constructing a theoretical model that incorporates the dynamics of population, pollen export, pollen reception on an ovule, and seed production in two closely related plants with resource competition and IPT. The model analysis revealed that coexistence is likely with infrequent IPT, α, and weak interspecific resource competition, β, and high production rates of pollen, Am, and ovules, Af. Also, we found a trade-off where too low value of either Am or Af makes both species go extinct. Furthermore, even when α and β were small enough, too low Am and Af made extinction of both species likely, because of the Allee effect due to resource competition and interspecific pollen competition for a small number of ovules. Adaptive dynamics, analysis of evolutionary dynamics showed that sex ratio evolve to 1:1 as the optimum allocation of resource to produce pollen grains and ovules.
Venue: via Zoom
Event Official Language: English
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Seminar
Introduction to cepstrum analysis and its applications
October 13 (Thu) at 16:00 - 17:00, 2022
Dr. Shingo Gibo (Postdoctoral Researcher, iTHEMS)
Recent advances in experimental technique enable us to obtain many time-series data of biological oscillatory systems. These time-series are of various shapes, which means that the envelop of spectrum are also various. Cepstrum analysis is well-known method for evaluating the spectrum shapes in acoustic engineering. In this talk, I will introduce cepstrum analysis and its applications for analyzing biological oscillations.
Venue: via Zoom
Event Official Language: English
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Seminar
Extremely low-coverage whole genome sequencing (XLC-WGS) as a cost-effective tool for pharmacogenomic profiling: Advantages and Challenges
October 6 (Thu) at 10:00 - 11:00, 2022
Dr. Lazaro-Guevara Jose Miguel (Postdoctoral Researcher, Department of Botany, The University of British Columbia, Canada)
Despite more than 10 years have passed since the first FDA labeling for pharmacogenomics (PGx), factors like the continuous updates on PGx related SNVs and the high cost for PGx testing have challenged its clinical implementation. However, next generation sequencing technologies like extremely low coverage whole genome sequencing (XLC-WGS) could overcome these difficulties. Our purpose is to explore the potential use of XLC-WGS as a cost-effective way for generate reliable PGx profiles that can be applied in preemptive and clinical scenarios. We sequenced 195 patients enrolled to the Utah Diabetes and Diabetic Complications Study using XLC-WGS, for further PGx Profiles generation. Additionally, we sequenced a subset of 190 individuals using Illumina CoreExome-24 v1.3 microarray and 50 individuals using Deep Coverage Whole Genome Sequencing (DC-WGS) for cross-platform comparisons. We built the Pharmacogenomic profiles extracting the genetic information from XLC-WGS in accordance to the extended manifest of the commercially available PGx microarray PharmacoScan. Once the PGx profiles were generated we perform a preemptive analysis using the Clinical Pharmacogenetics Implementation Consortium (CPIC®) Gene-Drugs interaction with “A” level. The cross-platform comparison revealed that genetic concordance between XLC-WGS, DC-WGS and Microarray platforms ranged from 98.25% to 99.7%. The preemptive PGx profiles identified patients at risk of potential adverse effects for intake of commonly prescribed medications, including 4 homozygote carriers of rs4149056 (in SLCO1B1) which has previously been associated with statin-related myopathy. As well as 25 homozygote carriers of rs9923231 (in VKORC1) that increased risk of Hemorrhage when starting Warfarin intake without dose adjustment/reduction.
Venue: via Zoom
Event Official Language: English
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Seminar
Discrete Stochastic Model for the Co-infection Dynamics with Defective Interfering Particles
September 26 (Mon) at 16:00 - 17:00, 2022
Dr. Jizhou Li (Postdoctoral Researcher, iTHEMS)
Defective interfering particle (DIP) in the context of influenza A virus is a virion with a significantly shortened RNA segment substituting one of its eight full-length parent RNA segments, such that it is preferentially amplified during replications. Therefore, a cell co-infected by standard viruses (STVs) and DIPs will produce mainly DIPs, suppressing the STV yield and displaying nontrivial co-infection dynamics. An important approach to quantifying the co-infection dynamics is mathematical modeling with ordinary differential equations (ODEs), which treat relevant quantities (such as numbers of target cells, STVs, and DIPs) as continuous numbers evolving with prescribed physical laws. However, the ODE models are mean-field in nature that is only valid for scenarios with large numbers of STVs and DIPs. For small-number scenarios, the infection outcomes can be dominated by random fluctuations and stochasticity, which cannot be captured by ODE models. In this week’s biology seminar, we introduce a new Discrete Stochastic Model (DSM) aimed to rectify the shortcomings of the ODEs by treating the co-infection dynamics as stochastic processes. As we will show, the new DSM is consistent with the ODE model in the large number regime. In the low number regime, the DSM yields bi-modal distributions for the infection outcomes (extinct vs established infections) that are otherwise unattainable by ODE models.
Venue: via Zoom
Event Official Language: English
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Seminar
Genetic Drift and Gnatural Selection
September 22 (Thu) at 16:00 - 17:00, 2022
Dr. Thomas Hitchcock (Special Postdoctoral Researcher, iTHEMS)
Understanding how the various evolutionary forces of mutation, selection, and drift collectively shape the genetic composition of populations is a key goal of population genetics research. One classic method of study has been to compare different inheritance systems, and particularly popular has been the within genome comparison of autosomes and sex chromosomes. However, inferences from such comparisons can be limited by the fact that multiple factors differ between sex chromosomes and autosomes (e.g. ploidy and transmission genetics). Here, we study a group of black winged fungus gnats with a peculiar type of reproduction “digenic PGE” in which X and autosomes are inherited equally from females and males, but the X remains expressed in a haploid state in males compared to a diploid state in females. I first explain what is known about their inheritance system, and then show how we can extend classic theory to the various inheritance systems that coexists within the fungus gnats.
Venue: via Zoom
Event Official Language: English
113 events