Matching Items (876)
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Description
In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different

In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different illumination intensities or different local environments); and (3) inferring the camera gain. My general theoretical framework utilizes the Bayesian nonparametric Gaussian and beta-Bernoulli processes with a Markov chain Monte Carlo sampling scheme, which I further specify and implement for Total Internal Reflection Fluorescence (TIRF) microscopy data, benchmarking the method on synthetic data. These three frameworks are self-contained, and can be used concurrently so that the fluorescence profile and emitter locations are both considered unknown and, under some conditions, learned simultaneously. The framework I present is flexible and may be adapted to accommodate the inference of other parameters, such as emission photophysical kinetics and the trajectories of moving molecules. My TIRF-specific implementation may find use in the study of structures on cell membranes, or in studying local sample properties that affect fluorescent molecule photon emission rates.
ContributorsWallgren, Ross (Author) / Presse, Steve (Thesis advisor) / Armbruster, Hans (Thesis advisor) / McCulloch, Robert (Committee member) / Arizona State University (Publisher)
Created2019
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Description
Bdellovibrio bacteriovorus is a predatory bacterium that may serve as a living antibiotic by destroying biofilms and invading gram-negative bacteria. Swimming at over 100μm s-1, these predators collide into their prey and invade them to complete their life cycle. While previous experiments have investigated B. bacteriovorus’ motility, no study has

Bdellovibrio bacteriovorus is a predatory bacterium that may serve as a living antibiotic by destroying biofilms and invading gram-negative bacteria. Swimming at over 100μm s-1, these predators collide into their prey and invade them to complete their life cycle. While previous experiments have investigated B. bacteriovorus’ motility, no study has yet collected swim speed variations over the lifespan of B. bacteriovorus. In this study, we used state-of-the-art bacterial tracking methods to record the speed of tens of thousands of bacteria. These results were used to describe their metabolic state under starvation conditions in which they lose energy in a dissipative manner by propelling themselves at high speeds through solution. In particular, we investigated the metabolic response of starved predators to the addition of prey-lysate.
ContributorsCarlson, Mikayla Lynn (Co-author) / David, Rowland (Co-author) / Presse, Steve (Thesis director) / Gile, Gillian (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description

Single molecule FRET experiments are important for studying processes that happen on the molecular scale. By using pulsed illumination and collecting single photons, it is possible to use information gained from the fluorescence lifetime of the chromophores in the FRET pair to gain more accurate estimates of the underlying FRET

Single molecule FRET experiments are important for studying processes that happen on the molecular scale. By using pulsed illumination and collecting single photons, it is possible to use information gained from the fluorescence lifetime of the chromophores in the FRET pair to gain more accurate estimates of the underlying FRET rate which is used to determine information about the distance between the chromophores of the FRET pair. In this paper, we outline a method that utilizes Bayesian inference to learn parameter values for a model informed by the physics of a immobilized single-molecule FRET experiment. This method is unique in that it combines a rigorous look at the photophysics of the FRET pair and a nonparametric treatment of the molecular conformational statespace, allowing the method to learn not just relevant photophysical rates (such as relaxation rates and FRET rates), but also the number of molecular conformational states.

ContributorsSafar, Matthew Matej (Author) / Presse, Steve (Thesis director) / Sgouralis, Ioannis (Committee member) / Department of Physics (Contributor) / School of Mathematical and Statistical Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

A statistical method is proposed to learn what the diffusion coefficient is at any point in space of a cell membrane. The method used bayesian non-parametrics to learn this value. Learning the diffusion coefficient might be useful for understanding more about cellular dynamics.

ContributorsGallimore, Austin Lee (Author) / Presse, Steve (Thesis director) / Armbruster, Dieter (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05