Background: Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated...
N-ary relationships, which relate N entities where N is not necessarily two, are omnipresent in real life. In this thesis, we develop a visualization technique for N-ary relationships.
First, we propose a visual metaphor that utilizes vertices and polygons to represent entities and N-ary relationships. Based on this visual metaphor,...
Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement...
Understanding the mechanisms through which stem cells self-renew is important for the development of new therapies to repair and restore damaged tissue. This research explores possible mechanisms of telomere mimic action and seeks to validate a new assay for evaluating telomere binding antagonists and studying the effects of telomere binding...
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possible mechanisms of telomere mimic action and seeks to validate a new
assay for evaluating telomere
Gene expression is largely regulated by the binding of transcription factors to short sequences of DNA (transcription factor binding sites) to drive or repress transcription of an adjacent gene. Identifying the key transcription factor binding sites associated with a particular biological outcome provides an avenue for tailored transcriptional regulation in...
Strawberry is economically the most important berry crop grown worldwide and breeders are continuously striving to develop improved cultivars. So far, marker assisted breeding (MAB) in strawberry has been limited to the private sector. However, loci controlling some traits of economic importance such as perpetual flowering (PF) and soluble solids...
Background: Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions...
Some positive-strand RNA plant viruses possess a transfer RNA-like structure (TLS) at the 3'-terminus of their genomic RNAs. The closest mimicry to tRNA is exhibited by the valylatable TLSs from tymoviruses and furo-like viruses, which are able to interact with key cellular tRNA enzymes: [CTP, ATP]:tRNA nucleotidyltransferase (CCA NTase), valyl-tRNA...
Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental...
Advancements in molecular biology and computer science have enabled researchers the ability to investigate the transcriptome – the quantification of an organism’s RNA transcripts in response to its environment on a system wide scale. The collective chapters of this thesis utilize high-throughput RNA sequencing, which produces hundreds of millions of...