Kairi Raime defends her PhD thesis

Kairi Raime will defend her doctoral thesis in Gene Technology entitled "The identification of plant DNA in metagenomic samples" on August 25 at 11:15.

Kairi Raime has completed the curriculum of Doctoral Studies in Gene Technology and her thesis is available in DSpace.

The location of the event is Riia 23b/2 auditorium 105 and the event can also be followed online in Zoom.

Meeting ID: 964 1000 1692
Passcode: 632577

The supervisor of the thesis is Professor of Bioinformatics Maido Remm.

The opponent is Filipe Pereira, PhD (University of Coimbra, Portugal).

Thesis summary:

Food contains traces of DNA from plants, animals, and micro-organisms that have been used in its preparation or with which it has been in contact. DNA analysis makes it possible to reliably identify the components in food and their biological origin, which in turn makes it possible to identify counterfeits and food ingredients that are important for human health. The dissertation focuses on the development of DNA-based detection methods for the identification of plant allergens in food using modern DNA sequencing technology. DNA analysis of plant components in food requires consideration of the specifics of plant genomes and the identification of unique genomic regions in the laboratory. PCR-based methods for food DNA analysis use pre-designed specific PCR primers to identify the selected species or group of organisms. However, plant genomes may contain a large number of repetitive genomic regions that are not suitable for primer design. In the doctoral thesis, the primer3_masker program was applied to the analysis of the extent of repeated regions in the plant genome to identify more precisely the genome regions suitable for plant differentiation. Detection of many different plants in processed foods is more cost-effective using second-generation DNA sequencing technology and more efficient data analysis methods. In the doctoral thesis, a unique bioinformatics methodology for plant identification was developed, during which all the DNA in food is analyzed. Hundreds of short and specific DNA sequences, or k-mers, from the plastid genome, are used to identify plants of interest. The use of short k-mers also allows the detection of plants in processed foods in which DNA has been broken down into short fragments.