Morris, Ann C

Introduction

Our research focuses on understanding neural development and regeneration in the vertebrate retina. We principally use zebrafish as a model genetic organism because the anatomical organization and development of the zebrafish retina are well conserved with mammals, and they are particularly suitable for developmental and genetic studies. Furthermore, in contrast to humans, the zebrafish retina exhibits persistent neurogenesis and the capacity for injury-induced regeneration, providing a much-needed in vivo vertebrate model for regenerative neurobiology. Overall, our goal is to understand the genetic pathways that regulate cellular differentiation during retinogenesis and retinal regeneration, with the hope that this will aid in the development of therapies for diseases affecting the human visual system, such as retinitis pigmentosa and macular degeneration. Some projects in our lab involve investigations of the role of a single gene in retinal development, whereas others are exploring how dysregulation of signaling pathways or cell metabolism impact retinal development, photoreceptor homeostasis, and/or regeneration.

Project:

Single cell RNA-Seq of the eye field, optic vesicle, and retinal neuroepithelium

This project seeks to determine the extent of cellular heterogeneity in the zebrafish eye field and it’s later derivatives, the optic vesicle and retina. Eventually, we also plan to perform scRNA-Seq on a zebrafish line that carries a mutation in the transcription factor sox4, and to compare those data with the wild type condition to determine whether loss of Sox4 alters cell type composition in the developing eye. The DLX cluster will be used to map RNAseq reads.

Students:

Rebecca Petersen, Grad, Added 12/2/2020

Jessica D Bills, Grad, Added on MCC cluster, 02/08/2023 

Collaborators:

UKY, Douglas A Harrison, Faculty

UKY, Jinze Liu, Faculty

Computational Methods:

The sequencing data will be analyzed using the commercially available Cell Ranger program developed by 10X Genomics.  Cell Ranger is already currently available at UK.

Software:

CellRanger from 10X Genomics (commercially available)

Project:

CUT&RUN analysis of wild type and mutant zebrafish retina

This project seeks to identify the molecular targets of various transcription factors in the developing retina using the technique of CUT&RUN followed by sequencing. The DLX cluster will be used to map sequencing reads.

Students:

Zun Yi Lim, Technician, Added on 

Tasha M Swenney, Graduate Student, Added on MCC cluster, 12/06/2022 

Computational Methods:

CUT&RUN: the sequencing data will be aligned using BowTie2, which is available at UK.

Software:

CUT&RUN: BowTie2, MACS2, Picard, diffReps, and Integrated Genome Viewer 2 (IGV2)

Collaborators:

Doug Harrison, UK

Grants:

Publications: