Supervisors:
Dr Julie Robidart (NOC), Prof Matt Mowlem (NOC), Dr Tom Bibby (UoS)
Ocean microbes are essential to processes that sustain Earth’s habitability, yet we are only beginning to understand the complexity of their interactions with each other and with the environment. This is, in part, due to two challenges: 1) linking specific functions to the marine organisms responsible and 2) a lack of regular high-resolution sampling and data collection in the marine environment. To address this, scientists and engineers at the National Oceanography Centre (NOC) are developing a new generation of miniaturised and robust sampling and analysis (sensing) technology that can be deployed directly in the ocean and provide samples and data at high temporal and spatial resolution. Aptamers represent a promising, new sensor technology for the sensitive and specific recognition of marine biology, from whole cells to proteins and even small molecule metabolites. They are short sequences of nucleic acid (DNA or RNA), selected in vitro to bind with potentially any target molecule, making them one of the most versatile biosensor formats to date. Lab on a Chip (LOC) technology uses miniature fluidic channels and integrated pumps, valves and optics typically in a plastic “chip” to automate complex laboratory based analytical techniques in a compact device. This project will combine these state of the art technologies to create new, autonomous sensors and datasets for the study of microbial ecology, allowing rapid in situ analysis of the microbial processes that are central to governing global climate.
Aptamers will be made available from an existing library (available at the NOC), purchased from suppliers. In addition, new Aptamers for new targets and improved performance will be selected from a pool of random DNA and RNA sequences using SELEX (Systematic Evolution of Ligands by Exponential Enrichment). The Aptamers will be developed into biosensors using a range of state of the art, and fully optimised protocols resulting in colourimetric, fluorometric and electrochemical detection of Aptamer-target interactions. These biosensors will serve as a test-bed for integration with, and development of, existing LOC systems to support Aptamer-based sensing applications in the environment; specifically marine and estuarine waters. The student will develop and test Aptamers and detection schemes and will optimise strategies for preserving aptamer based reagent longevity (we currently use dehydration (lyophilisation) and gelification). Further the student will fully optimise assay conditions in different environments and will work with a team of engineers, and extensive existing LOC technology to apply, trouble shoot and optimise Aptamer enabled LOC systems for integration with Autonomy. This project will culminate in the deployment of one or more LOC Aptamer-based biosensors for a full field test followed by iterative rounds of performance optimisation and development as required.
The NEXUSS CDT provides state-of-the-art, highly experiential training in the application and development of cutting-edge Smart and Autonomous Observing Systems for the environmental sciences, alongside comprehensive personal and professional development. There will be extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial / government / policy partners. The student will be registered at the University of Southampton and hosted by the Ocean Technology and Engineering Group at the National Oceanography Centre Southampton (NOCS). Specific training will include: (i) advanced training in state of the art molecular biological and chemical methods including but not limited to the selection and engineering of Aptamers, synthesis and manipulation of nucleic acids and the use of reagent preservation methods; (ii) the generation of biosensors from aptamers including using optical, electrochemical and enzymatic methods; and (iii) the design, fabrication and optimisation of autonomous sensors including chip assembly, decontamination, sensor electronics and software; (iv) the integration and operation of sensors on autonomous systems. Because of the multidisciplinary field, we expect to train students in some or all of the core skills required. Experience in molecular biology, chemistry, engineering, or applied technical disciplines relevant to the specific research would be an advantage.
To apply for this project, use the: apply for a NEXUSS CDT studentship