Life Sciences Commons^™

Molecular Identification And Characterization Of Viral Pathogens Infecting Sweet Cherry, Aaron J. Simkovich

Electronic Thesis and Dissertation Repository

Stone fruits are a valuable crop grown worldwide, however pathogens such as viruses threaten fruit production by reducing tree health and fruit yield. In an orchard within the Niagara region of Ontario, symptoms typical of viral infection such as chlorosis and leaf deformation were seen on sweet cherry (Prunus avium L.) trees. Next generation sequencing was performed on symptomatic and asymptomatic leaves and four viruses were identified. On the tree displaying the most severe symptoms, Prune dwarf virus (PDV), was the only virus detected. A survey conducted during this work showed 42% of cherry trees on a single …

Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste

Electronic Thesis and Dissertation Repository

The DNA Next Generation Sequencing (NGS) technologies produce data at a low cost, enabling their application to many ambitious fields such as cancer research, disease control, personalized medicine etc. However, even after a decade of research, the modern aligners and assemblers are far from providing efficient and error free genome alignments and assemblies respectively. This is due to the inherent nature of the genome alignment and assembly problem, which involves many complexities. Many algorithms to address this problem have been proposed over the years, but there still is a huge scope for improvement in this research space.

Many new genome …

Epigenetics Of Stress Adaptation In Arabidopsis: The Case Of Histone Modifications, Behnaz Najafi Majdabadi Farahani

Electronic Thesis and Dissertation Repository

Changes in the epigenetic status of plants, which contribute to changes in gene expression, in response to abiotic stress are well documented. However, their stability and transmission to subsequent generations, and their incorporation into plant stress adaptation are still a matter for debate. Using chromatin immuno-precipitation and Next Generation Sequencing (ChIP-seq), we compared genome wide enrichment of two histone marks, H3K9ac and H3K4me2, in the progeny of salt stressed and control Arabidopsis plants. Data showed less enrichment of the H3K9ac in the chromatin of the progeny of salt stressed plants, but no changes were detected in the enrichment of the …