Ocean Diagnostics: Development of a detection system for ocean biology monitoring using integrated silicon nitride fluorescence spectroscopy

Supervisory Team:  Thalia Dominguez Bucio, Frederic Gardes, Rand Ismaeel, Matthew Mowlem 

Project description

This project sheds light on ocean biology and ecosystems by developing a robust, deployable, and fully submersible photonics detector for in situ detection and quantification of bio-reporter constructs, enabling state-of-the-art bio-analytical assays at the point of the sample.

The novel sensor will provide high-performance fluorescence detection to support the detection of DNA, RNA and eDNA, enabling the study of several key biological essential ocean variables (EOVs) including ecosystem structure and function, and the identification of harmful and invasive species. Almost all nucleic acid assays require some form of optics for signal detection. These are fluorescently labelled reporters, which emit light upon specific recognition of a target gene sequence. The measurement of this signal over the duration of an assay is necessary to achieve quantification of a target sequence, and this can be utilized to enumerate a target cell type. The aim of the project is to exploit an integrated silicon nitride platform to measure fluorescence enabling biological sensing in the ocean.

The suitability of photonic-based sensors for biological oceanography has already been demonstrated in our preliminary, proof of concept work. The novelty of this technique relies on light immunity at harsh temperatures and high pressure, which usually requires bulky and expensive pressure shielding.

Unlike conventional free space optics sensors, the proposed integrated silicon nitride sensor is composed of robust low-loss waveguides. In such geometry, the light path is formed by the different refractive index of the material and therefore no air gaps exist between the optical elements. This feature makes this type of photonics detector particularly suitable for ocean sensing, where systems may remain submerged and at high pressure for an extended duration.

You will be based at both the optoelectronics research centre for designing and fabricating the chip, you will have full access to the ORC world-class cleanroom and the ORC state-of-the-art photonics labs.

 You will also spend significant time at the National Oceanography Centre to test the fabricated chips with different assays. At the NOC, you will also be able to compare the sensitivity of the developed sensor with the current gold-standard biological equipment.

If you wish to discuss any details of the project informally, please contact Dr Rand Ismaeel, Marine Photonics, Email: [Email Address Removed], Tel: +44 7401472027.

Entry Requirements

A very good undergraduate degree (at least a UK 2:1 honours degree, or its international equivalent).

Closing date: 31 August 2024. Applications will be considered in the order that they are received, the position will be considered filled when a suitable candidate has been identified.

Funding: We offer a range of funding opportunities for both UK and international students, including Bursaries and Scholarships. For more information please visit PhD Scholarships | Doctoral College | University of Southampton Funding will be awarded on a rolling basis, so apply early for the best opportunity to be considered.

How To Apply

Apply online: Search for a Postgraduate Programme of Study (soton.ac.uk). Select programme type (Research), Faculty of Engineering and Physical Sciences, next page select “PhD Zepler”. In Section 2 of the application form you should insert the name of the supervisor.

Applications should include:

Curriculum Vitae

Two reference letters

Degree Transcripts/Certificates to date

For further information please contact: [Email Address Removed]