PhD Advisor: Prof. Magdy Mahfouz

Abstract:
CRISPR-Cas systems have transformed molecular biology by enabling programmable manipulation of nucleic acids. However, two technical bottlenecks continue to constrain the scope of CRISPR-based applications in plants: the site-specific integration of large DNA cargos at predetermined genomic loci, and the rapid, instrument-free detection of defined nucleic acid variants outside specialized laboratories.
In this thesis, I describe two complementary CRISPR-based platforms developed to address these limitations. The first, PrimeStack, combines twin prime editing and Bxb1 recombinase-mediated integration to enable site-specific insertion of large DNA payloads into genomic safe harbors. Using the PE6c editor and engineered pegRNAs (epegRNAs), PrimeStack achieved integration frequencies exceeding 40% in rice and enabled the delivery of multikilobase cassettes.
The second platform, Bio-SCAN, combines biotinylated nuclease-dead Cas9 (dCas9), FAM-labeled amplicons, and lateral flow strips for rapid, sequence-specific nucleic acid detection without specialized instrumentation. Bio-SCAN enabled the detection of resistance alleles, transgenic elements, and diverse plant pathogens.
Together, PrimeStack and Bio-SCAN expand the CRISPR toolkit for precise genome engineering and field-deployable molecular diagnostics in plants.

Bio:
Edith is a PhD candidate in Bioengineering at King Abdullah University of Science and Technology, where she conducts research in genome engineering and synthetic biology in the laboratory of Prof. Magdy Mahfouz. Her work focuses on developing CRISPR-based technologies for precise plant genome engineering and molecular diagnostics. During her PhD, she developed PrimeStack, a platform for site-specific large DNA integration in plants, and co-developed Bio-SCAN, a CRISPR-based lateral flow diagnostic system for rapid nucleic acid detection. Her research interests include plant biotechnology, synthetic biology, genome editing, and next-generation delivery technologies for agricultural applications.