Shaira Jane Acosta
PhD Programme: Nanoscience, Materials and Chemical Engineering
Research group: INTERFIBIO – Grup de recerca de la Interficie físico/biològica
Supervisor: Ciara Kathleen O'sullivan
Bio
Shaira Jane Acosta obtained her Bachelor's degree in Biology, with an Outstanding Student Award, from Miriam College - Quezon City, Philippines, and her Master's degree in Microbiology from the University of the Philippines (UP) Diliman with a Department of Science and Technology scholarship. Her graduate research focused on the isothermal DNA detection of Trichomonas vaginalis, a human parasitic pathogen, based on enzyme-linked oligonucleotide assay. During her graduate studies, she also received a research travel grant from UP to do mobility research in 2019 with the Interfibio Research Group at Universitat Rovira i Virgili (URV), where she deepened her interests and understanding on various nano- and bio-technological developments that she then applied in her master's thesis. Prior to joining URV as a doctoral student, she served as a Science Research Specialist II at UP Manila, where she worked on a project on the detection of RNA of Flaviviruses that cause several illnesses in humans. She was also involved in volunteering activities such as in joining the task force that responded to the detection of SARSCoV-2 in March 2020 in Manila, Philippines. Driven into broadening her knowledge and skills to other systems, her research interests encompass interdisciplinary fields in molecular diagnostics and biosensors to develop innovative, yet accessible, detection tools and produce impactful researches that will help in addressing the spread and evolution of diseases.
Project: Rapid detection of Mycobacterium tuberculosis antibiotic resistance
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.
Outreach activities
- European Researchers' Night 2023: "H2O Heroes: Kids' Demonstration on Water Conservation, Pollution, and Treatment".
