Life Sciences Commons^™

Investigating The Role Of Brachypodium Distachyon Cellulose Synthase 8 In Gluconacetobacter Diazotrophicus Colonization, Xuan Yang

Electronic Thesis and Dissertation Repository

Nitrogen is an essential nutrient for plant growth. Significant amount of nitrogen fertilizer is applied to crop field to maintain high yield. Alternatives to chemical nitrogen fertilizer are needed to reduce the costs of crop production and offset environmental damage. Gluconacetobacter diazotrophicus is a nitrogen fixing bacterium that was originally isolated from sugarcane and has been proposed as a possible biofertilizer for monocot crop production. However, the colonization of G. diazotrophicus in most monocot crops is limited and deep understanding of the response of the host plants to G. diazotrophicus colonization is still lacking. In this study, research was conducted …

Spatial And Temporal Patterns Of Neutral And Adaptive Genetic Variation In The Alpine Butterfly, Parnassius Smintheus, Maryam Jangjoo

Electronic Thesis and Dissertation Repository

Understanding how much genetic diversity exists in populations, and the processes that maintain that diversity, has been a central focus of population genetics. The evolutionary processes that determine patterns of genetic diversity depend on underlying ecological processes such as dispersal and changes in population size. In this thesis, I examine the influence of dispersal and population dynamics on neutral and adaptive genetic variation in a naturally occurring network of populations of the alpine butterfly, Parnassius smintheus.

My first objective was to determine the combined consequences of demographic bottlenecks and dispersal on neutral genetic variation within and among populations. Using …

Dna Sequence Classification: It’S Easier Than You Think: An Open-Source K-Mer Based Machine Learning Tool For Fast And Accurate Classification Of A Variety Of Genomic Datasets, Stephen Solis-Reyes

Electronic Thesis and Dissertation Repository

Supervised classification of genomic sequences is a challenging, well-studied problem with a variety of important applications. We propose an open-source, supervised, alignment-free, highly general method for sequence classification that operates on k-mer proportions of DNA sequences. This method was implemented in a fully standalone general-purpose software package called Kameris, publicly available under a permissive open-source license. Compared to competing software, ours provides key advantages in terms of data security and privacy, transparency, and reproducibility. We perform a detailed study of its accuracy and performance on a wide variety of classification tasks, including virus subtyping, taxonomic classification, and human haplogroup assignment. …

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 …

The Role Of Thymine-Dna Glycosylase In Transcriptional Regulation, Bart Kolendowski

Electronic Thesis and Dissertation Repository

Precise control over transcriptional regulation is required for normal cell function. Errors in transcriptional regulation underpin many diseases including cancer. Thymine DNA Glycosylase (TDG) is a base excision repair protein and a coregulator that has been implicated in a diverse set of fundamental biological processes including embryonic development, nuclear receptor signaling and Wnt signaling. Importantly, TDG has been shown to play an important role in transcriptional regulation in a wide variety of systems. Details surrounding the mechanism through which TDG acts remain unclear. In this thesis we explore the role of TDG in Estrogen Receptor (ER)-dependent signaling and in cellular …

Characterization Of Urinary Microbiome And Their Association With Health And Disease, Yige Bao

Electronic Thesis and Dissertation Repository

There has been a growing interest in human microbiome studies in the past decade, with the development of high-throughput sequencing techniques. These microorganisms interact and respond to the host as an entity, and are involved in various homeostatic functions including nutrition digestion, immune response, metabolism and endocrine regulation. The urinary microbiome, however, remains relatively under-investigated.

One of the technical challenges of urinary microbiome studies is the samples usually contain a large number of host cells and low microbial biomass. These samples with the high host, low microbial abundance (“high-low” samples) are associated with increased risk of compromised quality of …

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 …

Characterizing The Role Of Thymine Dna Glycosylase In Transcriptional Regulation And Cancer In Vivo, Mohammad Haider Hassan

Electronic Thesis and Dissertation Repository

Cytosine methylation (5mC) is essential for transcriptional control and genomic stability and is often used as a prognostic marker in cancer. Although 5mC has long been considered a relatively stable epigenetic mark, recent studies have demonstrated that it can be reversed enzymatically by TET proteins which oxidize 5mC into 5-hydroxymethylcytosine (5-hmC), and then to 5-formylcytosine (5-fC) and 5-carboxylcytosine (5caC). This mechanism is known as active DNA demethylation and the base excision repair enzyme Thymine DNA Glycosylase (TDG) plays an essential role in this process by removing 5-fC and 5-caC which are subsequently replaced by the unmethylated cytosine. Importantly, homozygous loss …