Population Dynamics of Microorganisms in Spatially Structured Environments

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyMicrobial populations live and grow in spatially structured environments. These structures lead to spatial patterns in populations and alter the course of their natural evolution. Such phenomena are theoretically studied using spatially explicit models. However, these models are still poorly understood due to their analytical and numerical complexity. In this thesis, we study two systems of microorganisms living and proliferating in different spatially structured environments. The first system consists of populations of Escherichia coli growing in rectangular microchannels with two open ends. We study such populations with a lattice model in which cells shift each other along lanes as they reproduce. The model predicts rapid diversity loss along the lanes, with neutral mutations appearing in the middle of the channel being the most likely to fixate. These theoretical predictions are in agreement with our experimental observations. The second system is constituted by planktonic microorganisms that are transported by chaotic oceanic currents. To replicate their dynamics, we employ an individual-based coalescence model. The model predicts the effect of oceanic currents on the biodiversity of planktonic communities, as observed in metabarcoding data sampled from oceans and lakes around the world.doctoral thesi

Population genetics in microchannels

Spatial constraints such as rigid barriers affect the dynamics of cell populations, potentially altering the course of natural evolution. In this paper, we study the population genetics of Escherichia coli proliferating in microchannels with open ends. Our experiments reveal that competition among two fluorescently labeled E. coli strains growing in a microchannel generates a self-organized stripe pattern aligned with the axial direction of the channel. To account for this observation, we employ a lattice population model in which reproducing cells push entire lanes of cells towards the open ends of the channel. By combining mathematical theory, numerical simulations, and experiments, we find that the fixation dynamics is extremely fast along the axial direction, with a logarithmic dependence on the number of cells per lane. In contrast, competition among lanes is a much slower process. We also demonstrate that random mutations appearing in the middle of the channel and close to its walls are much more likely to reach fixation than mutations occurring elsewhere.Comment: 21 pages, 14 figure

Rapid task-dependent tuning of the mouse olfactory bulb

Adapting neural representation to rapidly changing behavioural demands is a key challenge for the nervous system. Here, we demonstrate that the output of the primary olfactory area of the mouse, the olfactory bulb, is already a target of dynamic and reproducible modulation. The modulation depends on the stimulus tuning of a given neuron, making olfactory responses more discriminable through selective amplification in a demand-specific way

Generation and Characterization of a Cell Type-Specific, Inducible Cre-Driver Line to Study Olfactory Processing

In sensory systems of the brain, mechanisms exist to extract distinct features from stimuli to generate a variety of behavioral repertoires. These often correspond to different cell types at various stages in sensory processing. In the mammalian olfactory system, complex information processing starts in the olfactory bulb, whose output is conveyed by mitral cells (MCs) and tufted cells (TCs). Despite many differences between them, and despite the crucial position they occupy in the information hierarchy, Cre-driver lines that distinguish them do not yet exist. Here, we sought to identify genes that are differentially expressed between MCs and TCs of the mouse, with an ultimate goal to generate a cell type-specific Cre-driver line, starting from a transcriptome analysis using a large and publicly available single-cell RNA-seq dataset (Zeisel et al., 2018). Many genes were differentially expressed, but only a few showed consistent expressions in MCs and at the specificity required. After further validating these putative markers using ISH, two genes (i.e., Pkib and Lbdh2) remained as promising candidates. Using CRISPR/Cas9-mediated gene editing, we generated Cre-driver lines and analyzed the resulting recombination patterns. This indicated that our new inducible Cre-driver line, Lbhd2-CreERT2, can be used to genetically label MCs in a tamoxifen dose-dependent manner, both in male and female mice, as assessed by soma locations, projection patterns, and sensory-evoked responses in vivo. Hence, this is a promising tool for investigating cell type-specific contributions to olfactory processing and demonstrates the power of publicly accessible data in accelerating science

Population Dynamics of Microorganisms in Spatially Structured Environments

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyMicrobial populations live and grow in spatially structured environments. These structures lead to spatial patterns in populations and alter the course of their natural evolution. Such phenomena are theoretically studied using spatially explicit models. However, these models are still poorly understood due to their analytical and numerical complexity. In this thesis, we study two systems of microorganisms living and proliferating in different spatially structured environments. The first system consists of populations of Escherichia coli growing in rectangular microchannels with two open ends. We study such populations with a lattice model in which cells shift each other along lanes as they reproduce. The model predicts rapid diversity loss along the lanes, with neutral mutations appearing in the middle of the channel being the most likely to fixate. These theoretical predictions are in agreement with our experimental observations. The second system is constituted by planktonic microorganisms that are transported by chaotic oceanic currents. To replicate their dynamics, we employ an individual-based coalescence model. The model predicts the effect of oceanic currents on the biodiversity of planktonic communities, as observed in metabarcoding data sampled from oceans and lakes around the world.doctoral thesi

空間的構造を有する環境中の微生物の個体群集ダイナミクス

Microbial populations live and grow in spatially structured environments. These structures lead to spatial patterns in populations and alter the course of their natural evolution. Such phenomena are theoretically studied using spatially explicit models. However, these models are still poorly understood due to their analytical and numerical complexity. In this thesis, we study two systems of microorganisms living and proliferating in different spatially structured environments. The first system consists of populations of Escherichia coli growing in rectangular microchannels with two open ends. We study such populations with a lattice model in which cells shift each other along lanes as they reproduce. The model predicts rapid diversity loss along the lanes, with neutral mutations appearing in the middle of the channel being the most likely to fixate. These theoretical predictions are in agreement with our experimental observations. The second system is constituted by planktonic microorganisms that are transported by chaotic oceanic currents. To replicate their dynamics, we employ an individual-based coalescence model. The model predicts the effect of oceanic currents on the biodiversity of planktonic communities, as observed in metabarcoding data sampled from oceans and lakes around the world

Coalescent dynamics of planktonic communities

Planktonic communities are extremely diverse and include a vast number of rare species. The dynamics of these rare species is best described by individual-based models. However, individual-based approaches to planktonic diversity face substantial difficulties, due to the large number of individuals required to make realistic predictions. In this paper, we study diversity of planktonic communities by means of a spatial coalescence model, that incorporates transport by oceanic currents. As a main advantage, our approach requires simulating a number of individuals equal to the size of the sample one is interested in, rather than the size of the entire community. By theoretical analysis and simulations, we explore the conditions upon which our coalescence model is equivalent to individual-based dynamics. As an application, we use our model to predict the impact of chaotic advection by oceanic currents on biodiversity. We conclude that the coalescent approach permits to simulate marine microbial communities much more efficiently than with individual-based models

Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion

Bacteria are unicellular organisms whose length is usually around a few micrometers. Advances in microfabrication techniques have enabled the design and implementation of microdevices to confine and observe bacterial colony growth. Microstructures hosting the bacteria and microchannels for nutrient perfusion usually require separate microfabrication procedures due to different feature size requirements. This fact increases the complexity of device integration and assembly process. Furthermore, long-term imaging of bacterial dynamics over tens of hours requires stability in the microscope focusing mechanism to ensure less than one-micron drift in the focal axis. In this work, we design and fabricate an integrated multi-level, hydrodynamically-optimized microfluidic chip to study long-term Escherichia coli population dynamics in confined microchannels. Reliable long-term microscopy imaging and analysis has been limited by focus drifting and ghost effect, probably caused by the shear viscosity changes of aging microscopy immersion oil. By selecting a microscopy immersion oil with the most stable viscosity, we demonstrate successful captures of focally stable time-lapse bacterial images for ≥72 h. Our fabrication and imaging methodology should be applicable to other single-cell studies requiring long-term imaging