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1	Construction and Characterization of Gene Regulatory Networks in Yeast Jedrysiak, Daniel K. 05 April 2013 (has links) Two major roadblocks in synthetic biology are the difficulties associated with the physical assembly of gene regulatory networks (GRNs) and the lack of characterized biological parts. In this work we aimed to address both of these issues. We developed a novel method for the assembly of GRNs called Brick- Mason assembly. We have shown that the method can assemble a 6 part network in a single day and provides significant advancements over traditional cloning methods. We used BrickMason to assemble GRNs that would allow us to compare natural yeast mechanisms of repression to the steric hindrance based mechanisms that are commonly used in synthetic GRNs in yeast. Our results show that the two mechansisms of repression are not equivalent. This finding opens possibilities for using a new class of repressor in a synthetic context in yeast. gene regulatory network synthetic biology yeast DNA cloning BrickMason GRN CYC8 TUP1 SSN6
2	Construction and Characterization of Gene Regulatory Networks in Yeast Jedrysiak, Daniel K. 05 April 2013 (has links) Two major roadblocks in synthetic biology are the difficulties associated with the physical assembly of gene regulatory networks (GRNs) and the lack of characterized biological parts. In this work we aimed to address both of these issues. We developed a novel method for the assembly of GRNs called Brick- Mason assembly. We have shown that the method can assemble a 6 part network in a single day and provides significant advancements over traditional cloning methods. We used BrickMason to assemble GRNs that would allow us to compare natural yeast mechanisms of repression to the steric hindrance based mechanisms that are commonly used in synthetic GRNs in yeast. Our results show that the two mechansisms of repression are not equivalent. This finding opens possibilities for using a new class of repressor in a synthetic context in yeast. gene regulatory network synthetic biology yeast DNA cloning BrickMason GRN CYC8 TUP1 SSN6
3	Construction and Characterization of Gene Regulatory Networks in Yeast Jedrysiak, Daniel K. January 2013 (has links) Two major roadblocks in synthetic biology are the difficulties associated with the physical assembly of gene regulatory networks (GRNs) and the lack of characterized biological parts. In this work we aimed to address both of these issues. We developed a novel method for the assembly of GRNs called Brick- Mason assembly. We have shown that the method can assemble a 6 part network in a single day and provides significant advancements over traditional cloning methods. We used BrickMason to assemble GRNs that would allow us to compare natural yeast mechanisms of repression to the steric hindrance based mechanisms that are commonly used in synthetic GRNs in yeast. Our results show that the two mechansisms of repression are not equivalent. This finding opens possibilities for using a new class of repressor in a synthetic context in yeast. gene regulatory network synthetic biology yeast DNA cloning BrickMason GRN CYC8 TUP1 SSN6
4	The Regulation of NAP4 in Saccharomyces cerevisiae Capps, Denise 20 May 2011 (has links) The CCAAT binding-factor (CBF) is a transcriptional activator conserved in eukaryotes. The CBF in Saccharomyces cerevisiae is a multimeric heteromer termed the Hap2/3/4/5 complex. Hap4, which contains the activation domain of the complex, is also the regulatory subunit and is known to be transcriptionally controlled by carbon sources. However, little is known about Hap4 regulation. In this report, I identify mechanisms by which Hap4 is regulated, including: (1) transcriptional regulation via two short upstream open reading frames (uORFs) in the 5' leader sequence of HAP4 mRNA; (2) proteasome-dependent degradation of Hap4; and (3) identification of two negative regulators of HAP4 expression, CYC8 and SIN4. I also report differential patterns of Hap4 cellular localization which depends on (1) carbon sources, (2) abundance of Hap4 protein, and (3) presence or absence of mitochondrial DNA (mtDNA). Hap2 Hap3 Hap4 Hap5 Hap2-5 CCAAT-binding factor CBF cerevisiae SSN6 CYC8 SIN4 upstream open reading frames uORF glucose repression carbon catabolite repression

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