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Articles 1 - 5 of 5
Full-Text Articles in Life Sciences
Adaptation Reshapes The Distribution Of Fitness Effects, Diego Tenoch Morales Lopez
Adaptation Reshapes The Distribution Of Fitness Effects, Diego Tenoch Morales Lopez
Electronic Thesis and Dissertation Repository
The process of adaptation has been of interest since the XIX century, when Darwin first proposed the idea of natural selection. Since then, there has been a myriad of theoretical and empirical works that have expanded the field. From the many evolutionary insights these works have produced, a foundational idea is that spontaneous mutations in the genome of organisms can produce changes to their reproductive success that might confer an advantage for the mutant organisms with respect to their peers. Therefore, mutations drive adaptive evolution by virtue of their heritable effects on fitness. Empirical measures of the distribution of these …
Rna Sequence To Structure Analysis From Comprehensive Pairwise Mutagenesis Of Multiple Self-Cleaving Ribozymes, Jessica M. Roberts, James D. Beck, Tanner B. Pollock, Devin P. Bendixsen, Eric J. Hayden
Rna Sequence To Structure Analysis From Comprehensive Pairwise Mutagenesis Of Multiple Self-Cleaving Ribozymes, Jessica M. Roberts, James D. Beck, Tanner B. Pollock, Devin P. Bendixsen, Eric J. Hayden
Biology Faculty Publications and Presentations
Self-cleaving ribozymes are RNA molecules that catalyze the cleavage of their own phosphodiester backbones. These ribozymes are found in all domains of life and are also a tool for biotechnical and synthetic biology applications. Self-cleaving ribozymes are also an important model of sequence-to-function relationships for RNA because their small size simplifies synthesis of genetic variants and self-cleaving activity is an accessible readout of the functional consequence of the mutation. Here, we used a high-throughput experimental approach to determine the relative activity for every possible single and double mutant of five self-cleaving ribozymes. From this data, we comprehensively identified non-additive effects …
Improved Computational Prediction Of Function And Structural Representation Of Self-Cleaving Ribozymes With Enhanced Parameter Selection And Library Design, James D. Beck
Boise State University Theses and Dissertations
Biomolecules could be engineered to solve many societal challenges, including disease diagnosis and treatment, environmental sustainability, and food security. However, our limited understanding of how mutational variants alter molecular structures and functional performance has constrained the potential of important technological advances, such as high-throughput sequencing and gene editing. Ribonuleic Acid (RNA) sequences are thought to play a central role within many of these challenges. Their continual discovery throughout all domains of life is evidence of their significant biological importance (Weinreb et al., 2016). The self-cleaving ribozyme is a class of noncoding Ribonuleic Acid (ncRNA) that has been useful for …
Developing Ultra-High Throughput Sequencing Based Assay For Ligase Ribozymes For The Study Of Evolutionary Innovations, James Collet
Developing Ultra-High Throughput Sequencing Based Assay For Ligase Ribozymes For The Study Of Evolutionary Innovations, James Collet
Boise State University Theses and Dissertations
The study of evolutionary innovations, or novel traits, is integral to understanding evolution yet is poorly understood. By studying the regions between genotype networks that produce the same phenotype, we can better characterize the process by which innovation occurs. The overarching goal of this study is to assign fitness values to the overlapping genotype network of two catalytic RNA molecules, or ribozymes. Properly characterizing this region requires the study of thousands of individual sequences, which is achievable through the use of high-throughput sequencing analysis. This thesis focuses on developing assays for one of the ribozymes, the ligase ribozyme. Due to …
Empirical Investigations Of Rna Fitness Landscapes: Harnessing The Power Of High-Throughput Sequencing And Evolutionary Simulations, Devin Pratt Bendixsen
Empirical Investigations Of Rna Fitness Landscapes: Harnessing The Power Of High-Throughput Sequencing And Evolutionary Simulations, Devin Pratt Bendixsen
Boise State University Theses and Dissertations
Fitness landscapes or adaptive landscapes represent the mapping of genotype (sequence) to phenotype (function or fitness). Originally proposed as a metaphor to envision evolutionary processes and mutational interactions, the fitness landscape has recently transitioned from theoretical to empirical. This is due in part to advances in DNA synthesis and high-throughput sequencing. This allows for the construction and analysis of empirical fitness landscapes that encompass thousands of genotypes. These landscapes provide tractable insight into mutational pathways, the predictability of evolution or even the evolution of life. RNA enzymes (ribozymes) are an attractive model system for the construction of empirical fitness landscapes. …