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Ugent Faculteit Diergeneeskunde, departement virologie, parasitologie en immunologie

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Proposal item traineeship banaba 2017-2018:

Our research group is focusing on the validation of novel sequencing technologies as a diagnostic tool for viral infections, mainly in pigs. A bioinformatics pipeline is being developed and needs to process raw nanopore sequencing reads into an understandable report. 

This involves different computational steps which needs to be validated, including quality control, viral database assembly, finding the best and most sensitive tool to identify viral sequences, de novo assembly of viral genomes, mapping of viral genomes, visualisation… A high performant in house computing system is available, but also HPC of Ghent University can be used for data analysis.

Abstract Bachelor Project FBT 2018-2019Development and optimization of ddPCR for detection and qualification of a SNP linked to anthelmintic resistance in Trichuris trichiura

Soil-transmitted helminths (Ascaris lumbricoides, Trichuris trichiura and the hookworms Ancylostoma duodenale and Necator americanus) are a group of intestinal parasitic nematodes that infect one fifth of the world’s population and cause significant morbidity. Preventive chemotherapy with benzimidazoles (BZ, i.e. albendazole or mebendazole) is implemented as the main strategy for controlling Soil-transmitted helminthiasis. However, there is grounded fear that drug resistance may develop as a result of (1) the high degree of drug pressure, (2) the suboptimal doses and (3) the reliance on only two drugs that have a common mode of action.

Experience from the veterinary field has further ratified these concerns. In veterinary nematodes, BZ-resistance is caused by single nucleotide polymorphisms (SNPs) located in the β-tubulin isotype 1 gene at codon position 167, 198 and/or 200. Therefore, the development of a system to monitor the emergence and spread of anthelmintic resistance is crucial. In this study, a novel competitive digital droplet PCR (ddPCR) assay was designed for the detection of both the wildtype and the SNP 200 in the β-tubulin isotype 1 gene of T. trichiura. This species was chosen based on data that indicate that BZ efficacy against T. trichiura is unsatisfactory, hence likely the biggest chance of finding resistance. The newly developed ddPCR assays were first optimized using quantitative Polymerase Chain Reaction (qPCR). The results indicate that the final assay allows specific detection and quantification of mutant and wild-type targets.

Further optimization is necessary to make the assay even more efficient, as it may be valuable for the detection and monitoring of anthelminthic resistance in the future.

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Salisburylaan 133
9820 Merelbeke
Belgium

Contacts

Traineeship supervisor
Dr. Sebastiaan Theuns
+32 9 264 73 87
Sebastiaan.Theuns@UGent.be
Traineeship supervisor
Piet Cools
piet.cools@ugent.be
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