Martí-Franquès COFUND Fellowship Programme


Details

Login to the application
Reference:

2021MFP-COFUND-19

Area:

Sciences

Supervisor name and surname:

Ciara O` Sullivan

Supervisor email:

ciara.osullivan@urv.cat

Supervisor short biography

PhD programme:

Nanoscience, Materials and Chemical Engineering

Title of the research project:

Rapid detection of Mycobacterium tuberculosis antibiotic resistance

Description of the research project:

The concept of the project is to develop an electrochemical platform for the detection of single nucleotide polymorphisms associated with antibiotic resistance. As a model system, rifampicin resistance in Mycobacterium tuberculosis will be used. The sequencing of the whole genome of Mycobacterium tuberculosis revealed that 95 to 98% of all rifampicin-resistant strains is related to single nucleotide polymorphisms (SNPs), located in the 81-bp RIF-resistance determining region (RRDR) of the beta subunit of the RNA polymerase (rpoB) gene There is a mature need for reliable, cost-effective and rapid tests for the detection of the clinically relevant mutations/SNPs conferring rifampicin resistance in Mycobacterium tuberculosis. The objective of the project is to develop an approach for the electrochemical detection of solid-phase primer elongation using ferrocene-labelled dNTPs, for the unequivocal identification of SNPs.

The motivation for this work is to develop a generic platform for the electrochemical detection of SNPs, which could be exploited in a portable device for the multiplexed identification of SNPs at the point of need. To date, many of the multiplexed SNP microarray platforms exploit fluorescence detection with CCDs, which inherently require cooling and complex optics. We are motivated to develop an alternative to fluorescence detection via the use of electrochemical detection, compatible with handheld potentiostats such as those used in glucometers, thus facilitating portability and cost-effectiveness. Exploiting our previous knowledge in the development of biosensors and in the use of redox-labelled nucleotides, we want to combine this know-how to demonstrate a proof-of-concept for the cost-effective, rapid and facile detection of SNPs, in a platform that could easily be expanded to multiplexed detection with a plethora of niche applications.

In a first proof-of-concept, we will focused on the detection of a single SNP associated with rifampicin resistance. Individual electrodes of an array will be functionalised with thiolated primers identical with the exception of their 3’ terminal base. Following hybridisation with the target DNA containing the SNP site to be interrogated, isothermal solid-phase primer elongation with ferrocene labelled oligonucleotides should result in an unequivocal identification of the SNP, even at low concentrations of target DNA. The work will then be extended to the parallelised, multiplexed detection of SNPs, and will detect all 11 SNPs in the 81-bp rpoB gene, and will then be further extended to the detection of SNPs associated with iosazanid resistance. The system will be validated using real samples from the London School of Hygiene and Tropical Medicine, which have already been genotyped using next generation sequencing. Once the platform has been demonstrated and validated, further application such as advanced forensics will be explored.

Highly desirable attributes of the ideal candidate

* Demonstrated previous experience in one or more of the following topics: Biology, Chemistry, Electrochemistry, Molecular Biology
* Hold a Master degree, or equivalent, in: Chemistry, Biology
* Language skills: English (essential), Spanish / Catalan (preferable)
* Specific Software skills: Excel, Word, Graphpad
* Other skills: Good oral and written presentation skills
* Personality traits: Team player, Independent thinking, Time management
---------------------------------------------------------------------------
Ethics: This project doesn’t involve ethical aspects

Workplace Location: Campus Sescelades, Tarragona

Gross anual salary:

27103.20 €

Dedication:

Full time

Working hours:

37.5 hours a week

Earliest expected start date:

14 February 2022

European union This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 945413