Ian Swinburne, Professor

Closed (1) How does the zebrafish eye develop the ability to manage pressure?

Applications for fall 2021 are now closed for this project.

Day-to-day health of the eye relies on the accumulation of the eye’s internal fluid being balanced by release of excess fluid or pressure. The fluid’s flow and pressure help keep the eye’s tissues healthy and the correct size and shape. Glaucoma, a leading cause of blindness, is usually characterized by elevated fluid pressure within the eye. Elevated pressure within the eye’s chambers harms the optic nerve by transmitting excess force to its cells. The physical pinching of the optic nerve damages its cells thus deteriorating the transmission of signals from the eye to the brain. As the underlying mechanisms of disease progression are incompletely understood, there is an urgent need to determine how the relevant physiologies develop and function.

A goal of our group is to determine how genes associated with various forms of glaucoma alter the development or function of the cells and tissues that manage pressure within the eye. The work of many researchers indicates that tissues called Schlemm’s canal and the trabecular meshwork, located in the front of the eye, are the primary site of fluid release within the eye. We hypothesize that a subset of mutations that are associated with glaucoma in human patients alter the mechanism by which Schlemm’s canal and the trabecular meshwork promote release of excess fluid.



We identified 110 zebrafish orthologs and paralogs of genes implicated or associated with glaucoma in humans. Together, we will harness the great power of Cas9 to knock-out these genes in zebrafish. We will apply embryology, live imaging, and molecular and cellular analyses to determine how loss of these genes might alter pressure management within the zebrafish eye. The apprentice will be trained in zebrafish developmental genetics, molecular biology, live imaging, and data analysis.

After the team’s initial screen, a more independent project may be developed to dissect the activities of proteins in the context of the eye’s development and homeostasis.

Day-to-day supervisor for this project: Samara Williams, Staff Researcher

Qualifications: We are looking for a curious, organized, and self-motivated apprentice that has good communications skills and enjoys working with a team.

Weekly Hours: 12 or more hours

Related website: http://www.swinburnelab.org

Closed (2) Using live-organism imaging and genome-editing to discover how cells in developing organs eat

Applications for fall 2021 are now closed for this project.

We are beginning an exciting moment in cell biology. The movements of molecules within tissues of a whole vertebrate can now be visualized with light microscopy. These feats of microscopy bridge an important gap in cell biology: how the dynamics of proteins and organelles govern the development of tissues and organs. We aim to establish zebrafish lines where a protein of interest is fluorescently tagged in order to track its dynamics as cells differentiate. These lines will be used for live-organism imaging where we will investigate how pluripotent cells take in molecules from their tissue’s neighborhood to promote the development and function of organs such as the skin, brain, eye, and ear. In particular, we will focus on clathrin-mediated endocytosis (CME) that serves as a major entryway into cells.

Studies of CME have pushed the boundaries of microscopy to dissect the timing, order, and abundance of proteins at sites of CME, which involves the coordination of dozens of unique proteins over the time scale of a minute. Studies of CME have primarily focused on individual cells, however, there is a considerable gap in knowledge which can be addressed with modern microscopy to reveal how CME operates between cells, inside tissues, and within organs.

By using gene-editing to fuse fluorescent proteins to genes-of-interest in the host cells’ genome, protein dynamics can be studied without altering physiological expression levels. We are now interested in exploring the adaptability of CME in vivo using gene-edited zebrafish as a model organism. Zebrafish offer unique advantages for live-cell imaging since they are transparent in early development and there are robust genetic tools available. This project proposal calls for students who are interested in working at the intersection of developmental biology, live-cell microscopy, and image-analysis. Together we will generate zebrafish lines for various proteins-of-interest, image the specimens, and use computational science approaches to mine our data.


Day-to-day supervisor for this project: Cyna Shirazinejad, Ph.D. candidate

Qualifications: This project will provide training in several areas. First, we will use bioinformatics tools to assess the feasibility of our desired gene-editing targets. Next, we will use molecular biology techniques to generate reagents for gene-editing. Along the way, we will practice zebrafish husbandry to produce embryos that will be used as subjects for your gene-editing experiments. After generating successfully edited zebrafish lines, we will raise fish for future imaging experiments. Imaging of the zebrafish will take place in collaboration with the Advanced Bioimaging Center (ABC, UC Berkeley), where we will use cutting-edge microscopes and algorithms dedicated to study your movies of CME dynamics.

Weekly Hours: 12 or more hours

Related website: http://www.swinburnelab.org