QUADRAT DTP: Multi-omics characterization of metabolic and signaling pathways involved in Harmful algal bloom toxin production - applicable for the development of diagnostic kits


   School of Biological Sciences

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  Prof K Campbell, Prof F Kuepper  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

This fully funded, 42-month PhD project is part of the QUADRAT Doctoral Training Partnership.

Dinoflagellates and diatoms such as Alexandrium spp., Dinophysis spp. and Pseudonitzschia spp are widely distributed bloom-forming marine micro-algae. These organisms can produce potent toxins which cause different shellfish poisoning syndromes. Human exposure to these toxins is potentially deadly and occurs via the consumption of toxin-exposed filter-feeding shellfish. Understanding the factors which contribute to the formation of algal blooms and toxin production and identification of the genetic and environmental key drivers is of environmental, economic, and clinical importance. For example the dinoflagellate Alexandrium spp. contains a number of toxic as well as non-toxic species. The genetic and environmental factors inducing toxin production are not well understood. Due to the unusual complexity and size of dinoflagellate genomes, there are limited genome sequencing projects for these organisms, and transcriptome sequencing has become the major focus in this field.

However, a serious limitation is our incomplete understanding of genetic and metabolic network regulation in harmful algae species. Dinoflagellates have a well-developed metabolism to survive even under extreme stress conditions in which gene silencing mechanisms have been reported to be involved in modulating metabolic responses to environmental stress. In particular, microRNAs (miRNAs), a class of endogenous non‐coding RNAs, play an essential role in post‐transcriptional gene regulation in plants, animals and dinoflagellates. These are key factors in stress response molecular pathways triggering cellular responses and metabolic adjustments to stress conditions that affect toxin production. The project proposes to identify and characterize marine algal blooms for example Alexandrium spp. RNAs and proteins and metabolite‐mediated responses to different stress conditions on the toxin production procedures. Both toxin-producing and non-toxin-producing species will be compared. The data will be analyzed to detect the major cascades triggered when the organism faces toxin-inducing environmental conditions.

The project will involve the information transfer from these procedures for the design and production of a prototype diagnostic kit for the detection of the toxin genes specific to the species. Molecular probes are being applied to distinguish species-specific RNA and DNA sequences for the rapid identification of toxins produced by organisms. The direction of this new technology is to develop rapid reliable screening methods for phycotoxins and the causative organisms to protect public health, aquaculture, and natural resources. An innovative sample preparation for toxin detection will be designed so that the device can be used in field. To date a novel method that can be applied on-site and by non-educated farm owners is needed to accurately detect the harmful algae and toxin as an early warning monitoring device. Such a kit must be financially affordable so that it can be used by farm owners.

This can be undertaken using a two-fold approach: Developing a sample preparation method away from the device but where no laboratory equipment is required and secondly the utilization of specific reagents particular for metabolite or nucleic acid amplification that can be built into a cartridge to provide a significant level of detection for both species and toxin analysis.  The system will be evaluated for culture analysis using cultures and real samples.

Candidate Background:

Applicants should have a primary degree (1st or 2.1) in an appropriate discipline (e.g., Genetics, Molecular biology, Biochemistry, Environmental Science). Some experience of PCR – bioinformatics – metabolomics – Transcriptomics -

M.Sc. in an appropriate discipline is desirable e.g., Molecular biology, Biochemistry, Environmental Science, Biotechnology. Some practical experience in bioanalytical analysis

Candidates should have, or expect to achieve, a minimum of a 2.1 Honours degree (or equivalent) in a relevant subject. Applicants with a minimum of a 2.2 Honours degree may be considered providing they have a Distinction at Masters level.

We encourage applications from all backgrounds and communities, and are committed to having a diverse, inclusive team.

Informal enquiries are encouraged, please contact Prof Katrina Campbell ([Email Address Removed]) for further information.

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APPLICATION PROCEDURE:

  • Please visit this page for full application information: How To Apply – QUADRAT
  • Please send your completed application form, along with academic transcripts to [Email Address Removed]
  • Please ensure that two written references from your referees are submitted. It is your responsibility to ensure these are provided, as we will not request references on your behalf.
  • Unfortunately, due to workload constraints, we cannot consider incomplete applications.
  • CV's submitted directly through a FindAPhD enquiry WILL NOT be considered.
  • If you require any additional assistance in submitting your application or have any queries about the application process, please don't hesitate to contact us at [Email Address Removed]

Biological Sciences (4) Chemistry (6) Computer Science (8) Environmental Sciences (13)

Funding Notes

This opportunity is open to UK and International students (The proportion of international students appointed through the QUADRAT DTP is capped at 30% by UKRI NERC).
Funding covers:
• A monthly stipend for accommodation and living costs, based on UKRI rates (£18,622 for the 23/24 academic year. Stipend rates for the 24/25 academic year have not been set yet)
• Tuition Fees
• Research and training costs
QUADRAT DTP does not provide funding to cover visa and associated healthcare surcharges for international students.

References

• Ho KC, Lee TCH, Kwok OT and Lee FWF. (2012). Phylogenetic analysis on a strain of Alexandrium tamarense collected from Antarctic Ocean. Harmful Algae, 15: 100-108.
• Cusick K and Sayler G S. (2013). An overview on the marine neurotoxin, saxitoxin: Genetics, molecular targets, methods of detection and ecological functions. Marine drugs, 11(4): 991-1018.
• McLean TI. (2013). “Eco-omics”: A Review of the Application of Genomics, Transcriptomics, and Proteomics for the Study of the Ecology of Harmful Algae. Microbial ecology, 65: 901-915.
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