PhD Studentship in Microlaser Barcoding for In Vivo Sensing – Understanding Gene Expression Patterns in 3D Space

Prof Frank Vollmer, Prof Steffen Scholpp, University of Exeter

Project Overview:

This exciting PhD opportunity focuses on developing a novel 3D in vivo sensing approach using microlaser barcodes to profile gene expression in a three-dimensional context. Understanding gene expression patterns (GEPs) within 3D space is essential for developmental biology, tissue homeostasis, and the study of diseases such as cancer. This research will provide deeper insights into gene expression across entire embryos, improve our understanding of tumor heterogeneity, and contribute to engineering biology for biotechnological solutions.

Research Context:

Emerging techniques like spatial transcriptomics and RNA sequencing offer valuable insights into gene expression by mapping RNA distribution within tissues. However, current methods face limitations such as the disruption of 3D tissue structures during sectioning and challenges in accurately reconstructing gene expression in thicker tissues. This PhD project will address these challenges by developing a new technique that maintains the 3D integrity of biological samples and allows for high-resolution, spatially resolved RNA profiling in zebrafish embryos.

Research Proposal:

The project will focus on the development and application of microlaser barcodes for RNA profiling in the model organism, Danio rerio (zebrafish). By microinjecting biocompatible microbeads containing RNA-capture DNA into the zebrafish embryos, these microlasers will capture high-resolution 3D gene expression data. This novel “RNAlaser” technology, combining microlaser barcoding with whispering-gallery mode (WGM) sensing, will be developed and tested in Prof. Vollmer’s lab in Exeter.

Timeliness and Innovation:

While microlaser barcoding is emerging in various fields, its application to in vivo sensing is still in its infancy. This project will be among the first to apply this innovative technology to 3D gene expression analysis, pushing the boundaries of what is possible in in vivo sensing. The project’s interdisciplinary nature brings together expertise in optics, material science, and developmental biology, offering significant opportunities for technological advancement in biological research.

Research Objectives:

• Develop biocompatible carbon dot microlasers for large-scale barcoding in 3D in vivo sensing.
• Apply microlaser barcoding to study gene expression in complex tissues, particularly the developing zebrafish embryo.
• Investigate and optimise fluorescence/microlaser beads for biomolecular sensing and RNA sequencing.

Collaborative Research:

This PhD project will bring together experts in optical sensing (Prof. Vollmer), material science and microlaser fabrication (Prof. Vollmer’s lab), and zebrafish developmental biology and transcriptomics (Prof. Scholpp, Dr. Jeffries). The collaboration will foster an international research network to develop a cutting-edge tool for 3D in vivo sensing, with applications in engineering biology and beyond.

Skills and Training:

The successful candidate will receive interdisciplinary training in:

• Microlaser fabrication and WGM-based sensing technologies.
• RNA sequencing and transcriptomics techniques.
• Zebrafish embryo handling and developmental biology.
• Scientific communication through publications and presentations at international conferences.

Impact and Broader Applications:

The new 3D in vivo sensing method developed in this project has the potential to revolutionise the study of gene expression in biological systems. This platform will also contribute to the development of more efficient and robust biotechnological solutions, such as organ-on-chips, and enhance our understanding of disease mechanisms, including cancer. The research will result in high-impact publications and provide the candidate with unique opportunities for collaboration in the rapidly evolving field of biotechnological sensing.

How to Apply:

Interested candidates should have a background in biology, biophysics, or a related field. Experience in molecular biology techniques or optical sensing is desirable. To apply, please submit your application through the official funding portal: PhD Studentship Application.

Please include:

• A cover letter detailing your interest in this specific project and your motivation for working under the supervision of Prof. Frank Vollmer.
• Your CV, including relevant academic qualifications and research experience.

Application Deadline:

The deadline for applications is 10 January 2025.

Award details Funding and scholarships for students University of Exeter

Make sure to reference this project and supervisor in your application cover letter.

Contact for questions about the project: f.vollmer@exeter.ac.uk