dc.rights.license | CC-BY-NC-ND | |
dc.contributor.advisor | Boer, Rob de | |
dc.contributor.author | During, Vince | |
dc.date.accessioned | 2025-05-12T23:01:27Z | |
dc.date.available | 2025-05-12T23:01:27Z | |
dc.date.issued | 2025 | |
dc.identifier.uri | https://studenttheses.uu.nl/handle/20.500.12932/48924 | |
dc.description.abstract | DNA deuterium labeling provides a minimally invasive technique for studying cell population dynamics over prolonged periods. However, interpreting labeling data is sometimes complicated by the persistent high labeling fractions at late time points, here called the ”fat-tail” phenomenon. In this study, we systematically evaluated three kinetic models aimed at addressing this phenomenon: the Gamma-Distributed Death Rate (GDDR) model, the Gamma-Distributed Lifespan (GDLS) model, and the Non-Exponential Death Model. Through comparative analyses, we found that the general 2-dimensional kinetic heterogeneity model that is often used to fit deuterium labeling data effectively reproduced curves predicted by the more complex GDDR model, indicating that gamma distributed death rates do not resolve the problem. Additionally, while kinetically distinct, the GDLS model showed no significant practical advantage over the GDDR model when fitting artificially generated realistic noisy datasets. The Non-Exponential Death Model approached a fit of the one population model by making the transition rate of the first subpopulation very fast, and was unable to to describe experimental data that were well described with the 2-dimensional kinetic heterogeneity model. We propose future modeling directions, including time-dependent death rates, maturation delays, and stochastic models, emphasizing that increased complexity does not inherently resolve the fat-tail issue. Our findings underscore the importance of selecting biologically realistic model refinements to improve the interpretation of DNA deuterium labeling studies of immune cell turnover. | |
dc.description.sponsorship | Utrecht University | |
dc.language.iso | EN | |
dc.subject | DNA deuterium labeling is a method in which DNA is tagged with ”heavy water” to track how long cells live and how they renew over time. In previous studies, we observed that when immune cells are labeled, the amount of label sometimes remains detectable much longer than expected based on current models. We refer to this as the “fat-tail” problem. In this study, we tested three different mathematical models to see if they could explain this issue. | |
dc.title | The Fat Tail Problem | |
dc.type.content | Master Thesis | |
dc.rights.accessrights | Open Access | |
dc.subject.keywords | DNA deuterium labeling; fat-tail problem; immune cell dynamics; T-cell turnover; kinetic heterogeneity; Gamma-Distributed Death Rate model; Gamma-Distributed Lifespan model; Non-Exponential Death Model; labeling curves; cell proliferation; exponential death rate; mathematical modeling; stochastic modeling; maturation delay; time-dependent death rate; deuterated water; kinetic models; model comparison; fitting accuracy; immune system; modeling limitations; average death rate; immune cell kinetics; measurement noise; model complexity. | |
dc.subject.courseuu | Bioinformatics and Biocomplexity | |
dc.thesis.id | 45675 | |