Structural Analysis of Collecting Ducts and Chromatin in Mouse Kidney

Abstract

The kidney is an essential organ whose functions include regulating electrolyte concentration, blood pH, and removing waste from the blood. It is composed of thousands of functional units called nephrons, where blood filtration begins in the glomerulus, a dense ball-like structure of capillaries, and is collected in the collecting ducts for final waste concentration. As the kidney ages, the ability of the renal tubule system to filter and concentrate waste becomes severely hampered. In this thesis, two main topics will be discussed. The first will explore the process of aging in the mouse kidney by studying the DNA organization of single cells and an aged cell state known as senescence. Preliminary results indicate that the reorganization of DNA throughout the aging process is gradual and significant. However, due to various challenges in the sample preparation pipeline, throughput, and quantitative analysis of the senescent state, this work was placed on hold. The second topic explored here is the structure of entire collecting duct systems within the mouse kidney. Until recently, it has been difficult to study large, complex tissues and retain all of the spatial information. The Vaughan lab utilized tissue clearing and light sheet microscopy to obtain a large data set of a 1 mm thick mouse kidney section. This sample was used to reconstruct over 1000 nephrons within the spatial context of the kidney,176 leaving the collecting duct system unknown. This analysis focuses on the reconstruction of multiple collecting duct networks, including branch generations, connected nephrons, and volumetric analysis of the tubule lumen, none of which have been studied on this scale before.