Profiling gene expression in early vertebrate embryos

This is a summer student position supervised by Arsham Nejad Kourki in James DiFrisco's lab.

Introduction to the science

Our lab investigates the conserved principles that shape early embryonic development across vertebrates. We focus on diverse embryos, and how, despite major differences in geometry, yolk, and extraembryonic tissues, they deploy shared regulatory systems during gastrulation to establish the body axis and germ layers. By combining comparative embryology with modern single-cell, spatial, and chromatin accessibility approaches, we aim to uncover the gene regulatory networks and cell behaviours that define evolutionarily conserved structures during early development. Ultimately, our work seeks to clarify how homologous developmental mechanisms are maintained or transformed across evolution.

About the project

This project will explore how early embryos from frog, fish, and chicken use similar genes during gastrulation. Although these species look very different, many of the key developmental genes are shared. The student will help identify where these genes are active by imaging their expression patterns in whole embryos.

The work will involve three main steps. First, the student will perform HCR-FISH to label specific genes in fixed embryos. This technique uses fluorescent probes to show exactly where a gene is expressed. Next, the student will prepare thin sections of these embryos to examine tissue layers. Finally, they will image the samples using spinning-disk or laser-scanning confocal microscopy, allowing high-resolution visualisation of gene expression patterns.

By comparing frog, fish, and chicken embryos, the student will help us understand whether conserved developmental structures show similar molecular signatures across species. Their work will contribute to our broader research on how early body axes and germ layers form during gastrulation.

Techniques the student will learn :

1. HCR-FISH probe hybridisation and amplification

2. Fluorescent imaging of whole mounts

3. Cryosectioning or vibratome sectioning

4. Confocal microscopy (spinning disk or laser scanning)

This project provides hands-on experience with modern molecular imaging techniques and promises a valuable introduction to comparative developmental biology.

Candidate background