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Comparison Of The Regulatory Dynamics Of Related Small Gene Regulatory Networks That Control The Response To Cold Shock In Saccharomyces Cerevisiae, Natalie Williams
Comparison Of The Regulatory Dynamics Of Related Small Gene Regulatory Networks That Control The Response To Cold Shock In Saccharomyces Cerevisiae, Natalie Williams
Honors Thesis
The Dahlquist Lab investigates the global, transcriptional response of Sacchromyces cerevisiae, baker’s yeast, to the environmental stress of cold shock, using DNA microarrays for the wild type strain and strains deleted for a particular regulatory transcription factor. Gene regulatory networks (GRNs) consist of transcription factors (TF), genes, and the regulatory connections between them that control the resulting mRNA and protein expression levels. We use mathematical modeling to determine the dynamics of the GRN controlling the cold shock response to determine the relative influence of each transcription factor in the network. A family of GRNs has been derived from the …
Investigation Of A Mycobacteriophage Transcription Repressor, Kathryn Orban
Investigation Of A Mycobacteriophage Transcription Repressor, Kathryn Orban
Honors Thesis
Mycobacteriophage HelDan is a lysogenic, or temperate, phage (virus) of the bacterium Mycobacterium smegmatis, which is a fast-growing, close relative of Mycobacterium tuberculosis, the causative agent of tuberculosis. The phage replication cycle is dependent on time-coordinated gene expression events. In order to study the regulation of gene expression during phage replication, HelDan protein gp73, a putative transcriptional repressor, was studied. Characterization of gp73 structure and function, such as DNA binding activity and affinity, was done using both bioinformatics and biochemical analyses. To this end, the gene encoding gp73 was cloned and the ability of the recombinant gp73 protein …
Improving The Computer Science In Bioinformatics Through Open Source Pedagogy, John David N. Dionisio, Kam D. Dahlquist
Improving The Computer Science In Bioinformatics Through Open Source Pedagogy, John David N. Dionisio, Kam D. Dahlquist
Biology Faculty Works
Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total "incubation time" of six months.