Probing biology on its home turf: Tools for ethology and protein dynamics

Biological systems exist out of equilibrium by constantly exchanging information and energy with their environment. This exchange is characterized by complex interactions at multiple length and time scales. Top-down approaches seeking a mechanistic understanding of biological processes require quantitative observations in the full context of these interactions. This requirement motivates the need to engineer tools that enable probing biological systems closer to their native environment. This work includes efforts in developing two such tools that allow probing the larval zebrafish system in the context of biophysical questions. The thesis is broadly divided into three parts, one part for the introduction, and one part each focusing on one of the techniques. In Chapter 1, I will motivate the need to probe biological systems close to their native environment. Chapter 1 forms the first part of the thesis. Chapter 2-3, I will discuss a novel technique to perform behavioral experiments and pose estimation of larval zebrafish in a 3-D cubic tank. A convolutional neural network model predicts larval poses across various experiments rapidly using a digitally generated and broadly applicable training dataset. In Chapter 4, I will perform objective behavioral analysis of 3-D larval behaviors and compare them with behaviors observed in classical 2-D locomotion assays. The 3-D behavioral analysis reveals the ability of the larva to feint when startled. Chapters 2-4 form the second part of the thesis. In Chapter 5, using the larval zebrafish system, I will broadly describe a technique to perform temperature-dependent FRET measurements of proteins in single cells of live zebrafish on an epifluorescence microscope, allowing observations of protein-protein interactions and changes in protein stability.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics & Quant Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2023

Author dc:creator

• Ravan, Aniket S.

Contributors dc:contributor

• Gruebele, Martin
• Chemla, Yann
• Shukla, Diwakar
• Nelson, Mark

• Animal Behavior
• Protein Dynamics
• Computer Vision
• Machine Learning
• Microscopy

Statement dc:rights

• Copyright 2023 Aniket Ravan

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/122143

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F122143