Genetics and Genomics Commons^™

Defective Aba-Mediated Sugar Signalling Pathway In An Established Arabidopsis Thaliana Cell Suspension Culture Explains Its Stay-Green Phenotype At High Sugar Concentrations, Avery Mccarthy

Electronic Thesis and Dissertation Repository

An unusual sugar insensitive phenotype was identified in an established cell suspension culture of Arabidopsis thaliana. We characterized the physiology, biochemistry and genetics of the sugar insensitive cell culture, in order to identify factors contributing to the phenotype. Chlorophyll levels of the cell suspension culture were insensitive to high sucrose (6-15% w/v) and maintained a green phenotype. Immunoblotting indicated that levels of key photosynthetic proteins (PsaA, Lhcb2 and Rubisco) increased as a function of external sucrose concentration. The green cell culture was photosynthetically competent based on light-dependent, CO₂-saturated rates of O₂ evolution as well as Fv/Fm …

Computational Modelling Of Human Transcriptional Regulation By An Information Theory-Based Approach, Ruipeng Lu

Electronic Thesis and Dissertation Repository

ChIP-seq experiments can identify the genome-wide binding site motifs of a transcription factor (TF) and determine its sequence specificity. Multiple algorithms were developed to derive TF binding site (TFBS) motifs from ChIP-seq data, including the entropy minimization-based Bipad that can derive both contiguous and bipartite motifs. Prior studies applying these algorithms to ChIP-seq data only analyzed a small number of top peaks with the highest signal strengths, biasing their resultant position weight matrices (PWMs) towards consensus-like, strong binding sites; nor did they derive bipartite motifs, disabling the accurate modelling of binding behavior of dimeric TFs.

This thesis presents a novel …

A Genetic Screen To Identify Fission Yeast Genes With Roles In Protecting Against Perturbation Of The Actin Cytoskeleton, Dorota Michalski

Electronic Thesis and Dissertation Repository

In the fission yeast, Schizosaccharomyces pombe, stress upon the cell division machinery leads to the activation of a cytokinesis checkpoint. This checkpoint results in a delay in cell cycle progression and the prolonged maintenance of a cytokinesis competent cellular state. In this state the cell is able to continuously reform/repair the actomyosin ring until cell division is achieved. To uncover genes that play a role in enforcing this checkpoint, the actin depolymerizing drug Latrunculin A (LatA) was used to perturb the cytokinetic machinery in a set of 3400 viable haploid S. pombe gene deletion mutants. Thirty-eight gene deletion mutants hypersensitive …

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 …