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Full-Text Articles in Life Sciences
Antimicrobial Peptide Development: From Massively Parallel Peptide Sequencing To Bioinformatic Motif Identification, Alexander K. Erikson
Antimicrobial Peptide Development: From Massively Parallel Peptide Sequencing To Bioinformatic Motif Identification, Alexander K. Erikson
Theses and Dissertations
The isolation, purification, and clinical deployment of antibiotics is one of the major drivers of decrease in morbidity and mortality from infectious bacteria in the 20th century. The rapid, ubiquitous deployment of antibiotics encouraged swift development and distribution of antibiotic resistance. New, novel techniques, technologies, and ultimately therapeutic antimicrobial compounds will be required to counter the rise of antibiotic resistant microbes. Historically, mimicking naturally occurring compounds has been the most fruitful method for discovering new antibiotics; unsurprisingly, many recent efforts have focused on expanding the cultivation and detection of previously unknown microbes and compounds, respectively. Other techniques explore developing compounds …
Genomewide Evaluation Of Cis-Elements And Cognate Transcription Factors In Nicotiana Attenuata Predicts 27 Unique Transcription Factor-Binding Site Pairs, Ashton Omdahl
Undergraduate Honors Theses
Nicotiana attenuata has been widely studied for its ecological plant-herbivore relationships and response to environmental stress. The jasmonate signaling pathway regulated by jasmonate ZIM-domiain (JAZ) repressor proteins that modulate defense response levels has been of particular focus in this research. While our understanding of the genes associated with defense response and their regulation continues to expand, the transcriptional regulation of these genes is largely uncharacterized. In an effort to provide insight into these relationships, we performed genomewide analysis of transcript level data in order to predict transcription factors (TFs), their respective binding sites (TFBS), and the genes they regulate. We …
Bioinformatics For The Comparative Genomic Analysis Of The Cotton (Gossypium) Polyploid Complex, Justin Thomas Page
Bioinformatics For The Comparative Genomic Analysis Of The Cotton (Gossypium) Polyploid Complex, Justin Thomas Page
Theses and Dissertations
Understanding the composition, evolution, and function of the cotton (Gossypium) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). Specifically, read-mapping (a fundamental part of next-generation sequence analysis) cannot adequately differentiate reads as belonging to one genome or the other. These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we developed PolyCat to categorize reads according to their genome of origin based on homoeo-SNPs that differentiate the two genomes. We re-sequenced the genomes of extant diploid relatives of tetraploid cotton …
Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor
Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor
Theses and Dissertations
Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. The complexity and volume of data produced by modern MS-omic instrumentation challenges biological interpretation, while the complexity of the instrumentation, sample noise, and complexity of data analysis present difficulties in maintaining and ensuring data quality, validity, and relevance. We present a corpus of tools which improves …