The Bloomsbury Colleges | PhD Studentships | Studentships 2018 | A multi-omics approach to improve Eimeria functional genome annotation
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A multi-omics approach to improve Eimeria functional genome annotation

Principal Supervisor: Dr Dong Xia (Royal Veterinary College)
Email: dxia@rvc.ac.uk

Co-Supervisor: Dr Ozan Gundogdu (London School of Hygiene & Tropical Medicine)
Email: Ozan.Gundogdu@lshtm.ac.uk

Co-Supervisor: Professor Fiona Tomley (Royal Veterinary College)
Email: ftomley@rvc.ac.uk

Co-Supervisor: Professor Damer Blake (Royal Veterinary College)
Email: dblake@rvc.ac.uk

Project description

Eimeria is a genus of apicomplexan parasites that cause serious veterinary and human infectious diseases, including Plasmodium, the malaria agent and Toxoplasma, a zoonotic opportunistic pathogen in immunocompromised hosts such as AIDS patients. Coccidiosis, an enteric disease caused by Eimeria parasites, is a major threat to food security in poultry production, where it costs ~3 billion USD per year. A group of specialized secretory organelles including the micronemes and rhoptries drive the invasion and intracellular survival of these parasites. Parasite life cycle stages that contain these organelles induce strong protective immunity in the chicken host, so they are of considerable interest for the development of novel vaccines against coccidiosis. However, despite extensive community efforts, there are still 68% of proteins annotated as hypothetical in Eimeria tenella, one of the best-curated Eimeria species, with limited information on function and subcellular localisation. This lack of annotation has restricted the search for additional valid recombinant vaccine candidates.
Harnessing the recent advancement in instrument resolution of mass spectrometers and analytical power provided by machine learning algorithms, this project aims to characterise the localisation of organelle proteins using advanced spatial proteomics approaches followed by machine learning based classification solutions. A number of novel protein candidates will be fused with fluorescent reporters to validate localisation and feedback to a bioinformatics pipeline to iteratively improve the prediction and classification accuracy. Data generated will be subsequently integrated with a multi-omics proteogenomic pipeline to further refine gene model predictions in collaboration with EuPathDB team. Functional annotation and domain structure of novel organelle proteins identified will be examined to identify new targets for disease intervention.

This is an exciting opportunity for an individual interested in parasitology and systems biology to join a multi-disciplinary project based at the UK's oldest and largest veterinary school and the London School of Hygiene and Tropical Medicine. The successful candidate will receive extensive training and support to develop laboratory techniques and data analysis skills in microbiology, molecular biology and cutting edge systems biology technologies in a high impact scientific field, where the novelty of the approach can be applied to other pathogens of medical and veterinary importance.
A candidate should have a good first degree in a relevant subject. An MSc would be an advantage, as would experience of practical parasitology, and molecular biology.

Eimeria is a genus of apicomplexan parasites that cause serious veterinary and human infectious diseases, including Plasmodium, the malaria agent and Toxoplasma, a zoonotic opportunistic pathogen in immunocompromised hosts such as AIDS patients. Coccidiosis, an enteric disease caused by Eimeria parasites, is a major threat to food security in poultry production, where it costs ~3 billion USD per year. A group of specialized secretory organelles including the micronemes and rhoptries drive the invasion and intracellular survival of these parasites. Parasite life cycle stages that contain these organelles induce strong protective immunity in the chicken host, so they are of considerable interest for the development of novel vaccines against coccidiosis. However, despite extensive community efforts, there are still 68% of proteins annotated as hypothetical in Eimeria tenella, one of the best-curated Eimeria species, with limited information on function and subcellular localisation. This lack of annotation has restricted the search for additional valid recombinant vaccine candidates.

Harnessing the recent advancement in instrument resolution of mass spectrometers and analytical power provided by machine learning algorithms, this project aims to characterise the localisation of organelle proteins using advanced spatial proteomics approaches followed by machine learning based classification solutions. A number of novel protein candidates will be fused with fluorescent reporters to validate localisation and feedback to a bioinformatics pipeline to iteratively improve the prediction and classification accuracy. Data generated will be subsequently integrated with a multi-omics proteogenomic pipeline to further refine gene model predictions in collaboration with EuPathDB team. Functional annotation and domain structure of novel organelle proteins identified will be examined to identify new targets for disease intervention.

This is an exciting opportunity for an individual interested in parasitology and systems biology to join a multi-disciplinary project based at the UK's oldest and largest veterinary school and the London School of Hygiene and Tropical Medicine. The successful candidate will receive extensive training and support to develop laboratory techniques and data analysis skills in microbiology, molecular biology and cutting edge systems biology technologies in a high impact scientific field, where the novelty of the approach can be applied to other pathogens of medical and veterinary importance.

Subject areas/ keywords

Microbiology, Molecular parasitology, Coccidian parasites, Systems biology, Spatial proteomics, Genome annotation, Machine learning

Candidate requirements

Essential requirements

  • You should have a good first degree in a relevant subject.

Desirable requirements

  • An MSc in a relevant subject
  • Experience of practical parasitology, and molecular biology.
  • Understanding of basic bioinformatic principles

Key References

  • Tomley F. Methods. 1997;13(2):171-6.
  • Thul P.J., Åkesson L., Wiking M., et al., Science. 2017; 26(356) 6340.
  • Xia, D., Sanderson, S.J., Jones, A.R., et al., Genome Biol, 2008. 9(7): p. R116.
  • Krishna, R., Xia, D., Sanderson, S., et al., Proteomics, 2015. 15(15): p. 2618-28.

Further information

Further information about PhDs at Royal Veterinary College is available here.

The successful student will be registered at: The Royal Veterinary College

How to apply

Instructions for applicants

Applications should be made to the RVC via UKPASS – information on how to apply can be found here.

Queries about the application process should be sent to: researchdegrees@rvc.ac.uk

The closing date for applications is: 22nd April 2018