Project Description

A full project description can be found on Find a PhD. Please see below for additional information about this project.

The PhD will be hosted by QUB and training will be provided in novel binder production, molecular and (bio)analytical methods and implementation for environmental contaminants. The candidate will also receive training in the additional areas of experimental design, data analysis, literature review, meta-analysis and science communication, data management with support from both the supervisors and the Graduate School at QUB. Together, the skillset developed during this project opens a range of opportunities in academia and industry especially in environmental monitoring. The knowledge gained will also broaden employability skills since diagnostics are widely applied in many sectors including the pharmaceutical industry, public and private food security agencies, and clinical settings. The partner institute at ABDN will provide skills in risk analysis and exposure as well as in application approaches in the field. In addition in working with colleagues at AFBI the student will have the opportunity to gain an understanding of the science policy interface and legislation. The student will also gain skills in statistics, computer modelling and field based research for environmental monitoring in support with AFBI. In line with the NERC report on skills the application of new and emerging technologies in the field in particular sensing technologies for remote sensing and communicating with the end users in plain language are also important skills for the student. As a postgraduate at QUB, the applicant will develop attributes of thinker, communicator, innovator, leader and be future ready through the unique combination of specialist disciplinary study and high-level, transdisciplinary and leadership skills training offered by the Graduate School at QUB.

Essential skills

  • Applicants should have a primary degree (2.1 or 1st) in an appropriate discipline (e.g., Molecular biology, Biochemistry, Environmental Science, Toxicology, Immunology )

Desirable skills

  • M.Sc. in an appropriate discipline e.g., Molecular biology, Biochemistry, Environmental Science, Toxicology, Immunology
  • Some practical experience in bioanalytical method development and understanding of validation requirements for method development.

 

Photo by FLY:D on Unsplash.

Supervisors

Katrina Campbell

Primary Supervisor:

Profile: Katrina Campbell
Email: katrina.campbell@qub.ac.uk
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

Lenka Mbadugha

Secondary Supervisor:

Profile: Lenka Mbadugha
Email: lenka.mbadugha@abdn.ac.uk
Institution: University of Aberdeen
Department/School: School of Biological Sciences

Sarah Helyar

Additional Supervisor:

Profile: Sarah Helyar
Email: s.helyar@qub.ac.uk
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

References

Dillon, M, Zaczek-Moczydlowska, MA, Edwards, C, Turner, AD, Miller, PI, Moore, H, McKinney, A, Lawton, L & Campbell, K 2021, ‘Current trends and challenges for rapid smart diagnostics at point-of-site testing for marine toxins’, Sensors, vol. 21, no. 7, 2499. https://doi.org/10.3390/s21072499

Nolan, P, Auer, S, Spehar, A, Oplatowska-Stachowiak, M & Campbell, K 2021, ‘Evaluation of Mass Sensitive Micro-Array biosensors for their feasibility in multiplex detection of low molecular weight toxins using mycotoxins as model compounds’, Talanta, vol. 222, 121521. https://doi.org/10.1016/j.talanta.2020.121521

Zaczek-Moczydłowska, MA, Mohamed-Smith, L, Toldrà, A, Hooper, C, Campàs, M, Furones, MD, Bean, TP & Campbell, K 2020, ‘A Single-Tube HNB-Based Loop-Mediated Isothermal Amplification for the Robust Detection of the Ostreid herpesvirus 1’, International Journal of Molecular Sciences, vol. 21, no. 18. https://doi.org/10.3390/ijms21186605

Expected Training Provision

The student will have access to the state of the art labs in IGFS. This will include state of the art biosensing equipment and mass spectrometry and core technology facilities in genomics. In addition to the traditional enzyme and luminescence based immunoassay design capabilities (e.g. ELISA and LFDs) the ASSET centre hosts a suite of optical (e.g. SPR, planar waveguide, Luminex XMap) and electrochemical (e.g. Palmsens) biosensor platforms with full capabilities in printing technology for developing nanosensing lab on a chip nucleic acid or proteins multiplex arrays. To complement these platforms are the molecular and protein tools for characterisation eg PCR, RT-PCR, 2D gel electrophoresis and imager, Western blots, nanodrop and bioanalyser. The Institute has top class Category 2 and 3 mammalian and bacterial cell culturing facilities for phage protein and monoclonal antibody production and for the utilisation of cultures for developing and validating biosensor methods of analysis for toxin and pathogen detection.

Impact

Currently chemical contaminants and pathogens found in the environment are monitored and tested for separately using multiple methodologies and approaches that can be expensive and time consuming requiring high skilled operators in often multiple laboratory settings. Often the data obtained for each contaminant or pathogen from the same environmental site is monitored and reviewed in isolation whereby synergistic and / or antagonistic effects in the natural environment can be overlooked. Therefore, the design and implementation of a bioanalytical tool that can be used to determine multiple chemical contaminants and pathogens by a novice end user and the data collated and compared could provide a wider understanding of the natural ecosystem for improved management decisions. In addition the construction of the roadmap to identify the gaps in knowledge of the current to required future monitoring and surveillance data will be performed in NI to provide a better understanding of the aquaculture ecosystem and effects of climate change To date the compilation of all current historical data has never been performed. This combined collation of data of monitored changes in climate or physical parameters and other environmental factors to identify and link the gaps in knowledge can be used to support local aquaculture in NI. This project has the opportunity to apply to a number of the UN sustainability goals in 3. Good health and well being 6. Clean water and sanitation, 12. Responsible consumption and production 13. Climate action, 14. Life under water and 15 life on land by offering a rapid in situ monitoring tool that can be altered in design and applied to different scenarios to help improve sustainability in both aquaculture and agriculture environments.

Proposed Timetable

  1. . Literature review (months 1 – 3)
  2. Collation of existing physical, chemical and biological data (months 4-5)
  3. Identification of key chemical contaminants / pathogens to design model multiplex assay (months 5 – 6)
  4. Development and production of antibodies / novel binders / DNA to important/novel identified targets (months 6 – 15)
  5. Evaluation of different biosensors for suitability in multiplex detection and suitability to couple to smartphone apps (months 9 – 12)
  6. Selection and characterisation of biosensor and assay design and evaluation in biological buffers for selected targets (months 12 – 16)
  7. Design of rapid sample preparation / concentration methods for key contaminants (months 16 – 18)
  8. Evaluation of the validity of the model biosensor with current state of the art approaches (months 19 – 24)
  9. Full validation of the biosensor to accredited standards with environmental / food samples (months 24 – 26)
  10. Evaluate model biological system lab on a chip biosensor against collated data (months 27 – 30)
  11. Construction of a roadmap of historical monitoring data to current gaps in the knowledge that need to be addressed to understand the environment holistically for enhanced aquaculture production (30-34).
  12. Completion of PhD thesis and manuscripts for publication (months 3 -36).

QUADRAT Themes

  • environmental-management

Partners

This is a CASE sponsored project in partnership with The Agri-Food and Biosciences Institute (AFBI).

 

The Agri-Food and Biosciences Institute (AFBI) is a multi-disciplinary organisation involved in high technology research and development, diagnostic and analytical testing for DAERA and other Government departments, public bodies and commercial companies in Northern Ireland, and further afield.

Its 3 main areas of work are:

  • Natural and marine environment
  • Animal, plant and human health and welfare
  • Sustainable livestock production

Under the natural and marine environment the fisheries and aquatic ecosystems programme provides research, monitoring and technology transfer in support of evidence based sustainable management of freshwater fisheries and marine resources in Northern Ireland. The key areas include:

  • Marine fisheries stock assessment, with the aid of the institute’s research vessel, the RV Corystes
  • Biological oceanography and marine environmental monitoring
  • Coastal zone science
  • Freshwater fisheries stock assessment and catchment management

This project aligns to biological oceanography and marine environmental monitoring whereby marine, phytoplankton data environmental and climatic data, chemical contaminant and toxin data collated by AFBI will be utilised in the project. The overall aim is to improve environmental monitoring and collate data for enhanced management practices. In addition, samples (water, sediments and shellfish) will be collected and used for both development and validation of the systems biology sensor chip.

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