| Laboratory | Title | Category |
| Oates | Biochemical Characterization of the Her1 Interactome via ScFv Pull-down Her1 serves as a critical oscillator within the zebrafish segmentation clock. While the lab has developed three novel ScFv antibody clones that recognize Her1, their potential for biochemical isolation is yet to be realized. This project aims to develop a robust protocol to “pull down” Her1 proteins directly from zebrafish embryos using these new antibodies. The student will adapt and optimize biochemical workflows for embryo lysates, ideally progressing to mass spectrometry analysis once the protocol is validated. This work is essential for identifying the protein partners that interact with Her1, providing deeper insight into the molecular machinery of the segmentation clock. This project provides training in protein biochemistry, you will work alongside a laboratory technician and a PhD student to help bridge the gap between molecular interactions and embryonic patterning. Keywords: protein biochemistry, pull-down assay, zebrafish embryos, mass spectrometry Supervisor: Andrew Oates Co-supervisor: Virginie Braman Contact: [email protected], [email protected] Required: – Posted in February 2026 | Developmental biology Wet |
| Oates | Combining Expansion Microscopy and In-situ Reverse Transcription in Zebrafish Embryos This project aims to develop and optimize a hybrid protocol combining Expansion Microscopy (ExM) with in-situ reverse transcription (ISRT) in zebrafish embryos. Expansion microscopy physically enlarges biological samples to achieve super-resolution results on conventional microscopes. By integrating ISRT, we would like to obtain bulk sequencing data corresponding to high resolution microscopy samples. The student will also utilize these tissues to quantify protein distribution within the nucleus using fluorescence in situ hybridization (FISH). This project is ideal for students interested in the intersection of molecular biology and advanced imaging technology. You will gain hands-on experience in tissue engineering, imaging, and transcriptomics. By refining this combined workflow, you will provide the lab with a powerful tool to visualize the nuclear environment of the segmentation clock at unprecedented scales. Keywords: expansion microscopy, in-situ RT, molecular biology, zebrafish development Supervisor: Andrew Oates Co-supervisor: Emanuel Vasquez Contact: [email protected], [email protected] Required: Experience in molecular biology preferred Posted in February 2026 | Molecular biology Wet |
| Oates | Computational Analysis of Cell Morphology During Zebrafish Body Axis Segmentation This project aims to understand how changes in cell morphology relate to developmental progression during the segmentation stage of zebrafish embryogenesis. Using acquired microscopy data from fixed embryos, the student will work with segmentation-based image analysis pipelines to extract quantitative geometric and spatial descriptors at single-cell resolution. These measurements will be used in classification and regression models to predict developmental progression and cell types, and to test whether static images can reliably capture underlying dynamic processes, such as tissue elongation, segmentation, and stem cell differentiation. The project combines image processing, supervised machine learning, and statistical analyses, offering training in computational analysis of large biological datasets. Keywords: image analysis, machine learning, cell biology Supervisor: Andrew Oates Co-supervisor: Feyza Nur Arslan Contact: [email protected], [email protected] Required: Knowledge in machine learning and data science; image processing experience is a plus Posted in February 2026 | Computational biology Dry |
| Oates | Fabricating a Fiber Optic System for Localized Heat Shock in Light-Sheet Microscopy Heat shock disrupts the zebrafish segmentation clock, causing transient but repeating defects in somite formation. Currently, we lack models that explain how developing tissue retains a “memory” of such thermal perturbations. This project focuses on the engineering and integration of a fiber optic localized-heating system for our light-sheet microscope to investigate these dynamics. The student will design and fabricate a specialized setup, utilizing 3D printing and fiber optics to deliver localized thermal stimuli to specific regions of the developing embryo. This will allow for real-time observation of how localized stress affects the global timing of somitogenesis. This interdisciplinary project is perfect for students with an interest in instrumentation, fabrication, and live-cell imaging. You will work on a that bridges physics and developmental biology. Keywords: live-imaging, fabrication, light-sheet microscopy, thermal perturbation Supervisor: Andrew Oates Co-supervisor: Emanuel Vasquez Contact: [email protected], [email protected] Required: Experience in computer aided design is a plus Posted in February 2026 | Developmental biology Dry and wet |
| Oates | Morphogen Gradients and Oscillatory Signaling in Zebrafish Development This project aims to understand how morphogen gradients regulate oscillatory signaling and muscle cell differentiation during zebrafish embryogenesis. Using light-sheet microscopy of zebrafish embryos and primary stem cell cultures, the student will quantify signaling dynamics at single-cell resolution in both in vivo and in vitro systems. Complementary immunohistochemistry will be used to characterize signaling modules. These measurements will be analyzed using advanced image processing to investigate how extrinsic cues shape oscillation properties and cellular differentiation. The project combines cutting-edge imaging, experimental manipulation, and computational analysis, offering training in both experimental and quantitative approaches to study dynamic developmental processes in a well-defined model system Keywords: embryology, morphogens, signaling dynamics Supervisor: Andrew Oates Co-supervisor: Feyza Nur Arslan Contact: [email protected], [email protected] Required: Knowledge in cell biology, hands-on lab experience is a plus Posted in February 2026 | Developmental biology Dry and wet |
| Oates | Validation of Novel ScFv Antibodies for Her1 Immunostaining in Zebrafish Her1 is a core oscillatory protein in the segmentation clock driving zebrafish embryo somite formation. Despite its importance in development, there is currently no functional antibody for immunostaining Her1. The Oates lab has recently generated three ScFv antibody clones that successfully recognize denatured Her1 in Hek293 cells. This project focuses on translating these results to in situ applications. The student will test these antibodies using whole-mount zebrafish immunostaining, specifically troubleshooting and adapting in-situ hybridization protocols to ensure compatibility. If successful, these tools will be used to quantify and compare Her1 behavior in wild-type embryos versus our Her1-YFP reporter line using advanced light-sheet microscopy. This project offers hands-on experience in protocol optimization and developmental imaging. You will collaborate closely with a laboratory technician and a PhD student, contributing directly to our understanding of this molecular clock. Keywords: immunostaining, antibodies, somitogenesis, optimization Supervisor: Andrew Oates Co-supervisor: Virginie Braman Contact: [email protected], [email protected] Required: – Posted in February 2026 | Developmental biology Wet |
