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Analysis of the Interaction of H-NOX with DGC using in vivo methods and Analytical Ultracentrifugation

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dc.contributor.advisor Boon, Elizabeth M. en_US
dc.contributor.author Zielinski, Patryk en_US
dc.contributor.other Department of Chemistry. en_US
dc.date.accessioned 2017-09-20T16:52:09Z
dc.date.available 2017-09-20T16:52:09Z
dc.date.issued 2013-12-01 en_US
dc.identifier.uri http://hdl.handle.net/11401/77174 en_US
dc.description 62 pg. en_US
dc.description.abstract Biofilms are a naturally occurring phenomenon and are known to be a significant problem in various fields including both the industrial and health environments. Bacterial biofilms are defined as the attachment and aggregation of a community of bacteria to solid surfaces. This behavior can lead to infections via medical transplants and compromise the functionality and durability of industrial equipment. Two proteins, Heme-Nitric oxide/Oxygen (H-NOX) and di-guanylate cyclase (DGC), are known to play an important role in the regulation of biofilm formation in bacteria. These two proteins down regulate the concentration of c-di-GMP, a second messenger molecule, in a cell. Since c-di-GMP has been shown to directly affect a cell's motile state, further studies on the H-NOX and DGC proteins may bring about an understanding of possible ways to artificially manipulate their biological roles. <italic>Shewanella woodyi</italic> (<italic>S.woodyi</italic>) is a marine bacterium which contains the genes encoding for H-NOX and DGC and, additionally, has been observed to participate in biofilm formation. Recent <italic>in vitro</italic> studies have shown that H-NOX directly interacts with DGC to regulate its cyclase and phosphodiesterase activities. In one study we aim to show this direct interaction using <italic>in vivo</italic> methods involving the re-introduction of tagged equivalents of these two genes, via a broad host range vector, into a mutant strain of <italic>S.woodyi</italic> lacking these two proteins. The experimental design is centered on using the native ribosome binding site of the genes encoding for H-NOX and DGC for the <italic>in vivo</italic> expression of these two proteins in the mutant <italic>S.woodyi</italic> organism. Multiple tests for the detection of these two proteins from the <italic>S.woodyi</italic> complements were performed with an observed absence of the presence of either of the two proteins. These results indicate that either the lack of efficiency of plasmid replication and/or the occurrence of random mutations is possible. Since DGC is a complex protein containing three domains, two of which are enzymatically active, we decided to perform another study involving the isolation and purification of each of these domains to examine their behavior in the absence of the other two proteins. We also wanted to observe which domains were capable of interacting with the H-NOX protein. Currently we have successfully analyzed the oligometric state of the EAL, EAL with H-NOX, and PAS proteins and assessed the lack of activity for the isolated EAL and GGDEF proteins. Future tests will be performed to study the oligomeric state of the GGDEF protein (in the presence and in the absence of H-NOX) and PAS in the presence of H-NOX. en_US
dc.description.sponsorship This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree. en_US
dc.format Monograph en_US
dc.format.medium Electronic Resource en_US
dc.language.iso en_US en_US
dc.publisher The Graduate School, Stony Brook University: Stony Brook, NY. en_US
dc.subject.lcsh Biochemistry en_US
dc.subject.other biofilms, DGC, H-NOX, in vivo, Nitric Oxide, Shewanella woodyi en_US
dc.title Analysis of the Interaction of H-NOX with DGC using in vivo methods and Analytical Ultracentrifugation en_US
dc.type Thesis en_US
dc.mimetype Application/PDF en_US
dc.contributor.committeemember Koch, Stephen en_US
dc.contributor.committeemember Drueckhammer, Dale. en_US

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