ProfessorJan Slapeta

Project Opportunities

Title: Emerging parasitic disease: epidemiological, diagnostic and experimental approach

Summary of opportunity:

The project Emerging parasitic diseases: epidemiological, diagnostic and experimental approach will focus on development and elucidation of the epidemiology of newly or neglected disease in veterinary parasitology including (i) haemo- / tissue- parasites (Atoxoplasma, Babesia) and (ii) gastrointestinal parasites (Giardia, Cryptosporidium, Tritrichomonas).

Opportunity synopsis:

The project Emerging parasitic disease: epidemiological, diagnostic and experimental approach will focus on development and elucidation of the epidemiology of newly or neglected disease in veterinary parasitology including (i) haemo- / tissue- parasites (Atoxoplasma, Babesia) and (ii) gastrointestinal parasites (Giardia, Cryptosporidium, Tritrichomonas). This project aims to elucidate the molecular identity and relationships between different isolates using PCR diagnostic techniques using rDNA and protein coding genes. On the other hand, this study will deliver and validate the PCR diagnostic protocol for epidemiological studies and elucidating the biology of these organisms. This investigation will develop a collection of diagnostic procedures accurately and rapidly identifying the causative parasite. The investigation will be developed with close relationship with clinicians to deliver clinically meaningful applications. The study will further investigate the impact of the diagnosed agents onto the host population to reconstruct the epidemiology of the disease. To elucidate the causality of these agents an experimental studies will be conducted to provide direct evidence of the pathogen impact on the host. This presents opportunities for PhD topic projects: (1) Development of diagnostic procedures and DNA based techniques; (2) Epidemiological, clinical and host interaction issues and (3) Experimental study on laboratory animals to elucidate the hosts specificity.

Project Opportunities

Title: Bioinformatics approach to Cryptosporidium identity: database prospects

Summary of opportunity:

The Bioinformatics approach to Cryptosporidium identity: database prospects study will examine (i) the applicability of web based platform to clinical and field data and (ii) develop an automated approach to identification and annotation to sequences.

Opportunity synopsis:

Intracellular single-cell parasites of the genus Cryptosporidium infect vertebrates, including humans, worldwide. Cryptosporidiosis is self-limiting disease in healthy hosts but represents a life-threatening problem in immunocompromised individuals for which there is no effective treatment. The diversity of the genus Cryptosporidium is mystifying for many biologists and even more so for non-specialists nevertheless is critical for understanding the epidemiology of the disease. A DNA approach to identity stands on the implicit assumption that the reference databases used for comparison are sufficiently complete and feature rich with annotated entries. However, the uncertain taxonomic reliability and annotations in public DNA repositories (GenBank) form a major obstacle to sequence-based species identification. Finally yet importantly, a huge gap exists between the number of described names and number of identified genotypes. The closure of this gap represents a prime challenge for the decades to come. The Bioinformatics approach to Cryptosporidium identity: database prospects study will examine (i) the applicability of web based platform to clinical and field data and (ii) develop an automated approach to identification and annotation to sequences. The web portal will aim to provide a common gateway for analysing Cryptosporidium species and to standardize the terminology of individual isolates. Alignments of the reference sequences from the named species are provided with further detailed annotation of individual species. Furthermore, currently under development is a web based analysis (BLAST, multiple sequence alignment, tree building etc.) as well as an in-house annotation database of sequences to streamline and standardise the process for identification of Cryptosporidium isolates. This presents opportunities for PhD topic projects: (1) Development and implication of bioinformatics algorithms; (2) Database development and application and (3) Research based end-user web based applications.