Matching Items (6)
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- All Subjects: Biology
- Genre: Masters Thesis
- Creators: Hall, Sharon J
Description
The Multiple Antibiotic Resistance Regulator Family (MarR) are transcriptional regulators, many of which forms a dimer. Transcriptional regulation provides bacteria a stabilized responding system to ensure the bacteria is able to efficiently adapt to different environmental conditions. The main function of the MarR family is to create multiple antibiotic resistance from a mutated protein; this process occurs when the MarR regulates an operon. We hypothesized that different transcriptional regulator genes have interactions with each other. It is known that Salmonella pagC transcription is activated by three regulators, i.e., SlyA, MprA, and PhoP. Bacterial Adenylate Cyclase-based Two-Hybrid (BACTH) system was used to research the protein-protein interactions in SlyA, MprA, and PhoP as heterodimers and homodimers in vivo. Two fragments, T25 and T18, that lack endogenous adenylate cyclase activity, were used for construction of chimeric proteins and reconstruction of adenylate cyclase activity was tested. The significant adenylate cyclase activities has proved that SlyA is able to form homodimers. However, weak adenylate cyclase activities in this study has proved that MprA and PhoP are not likely to form homodimers, and no protein-protein interactions were detected in between SlyA, MprA and PhoP, which no heterodimers have formed in between three transcriptional regulators.
ContributorsTao, Zenan (Author) / Shi, Yixin (Thesis advisor) / Wang, Xuan (Committee member) / Bean, Heather (Committee member) / Arizona State University (Publisher)
Created2018
Description
Emergence of multidrug resistant (MDR) bacteria is a major concern to global health. One of the major MDR mechanisms bacteria employ is efflux pumps for the expulsion of drugs from the cell. In Escherichia coli, AcrAB-TolC proteins constitute the major chromosomally-encoded drug efflux system. AcrB, a trimeric membrane protein is well-known for its substrate promiscuity. It has the ability to efflux a broad spectrum of substrates alongside compounds such as dyes, detergent, bile salts and metabolites. Newly identified AcrB residues were shown to be functionally relevant in the drug binding and translocation pathway using a positive genetic selection strategy. These residues—Y49, V127, D153, G288, F453, and L486—were identified as the sites of suppressors of an alteration, F610A, that confers a drug hypersensitivity phenotype. Using site-directed mutagenesis (SDM) along with the real-time efflux and the classical minimum inhibitory concentration (MIC) assays, I was able to characterize the mechanism of suppression.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
ContributorsBlake, Mellecha (Author) / Misra, Rajeev (Thesis advisor) / Stout, Valerie (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
The spread of dengue worldwide currently places half of the world’s population at risk. In the absence of a dengue vaccine, control of the disease requires control of the mosquito species that transmit the virus. The most important of these is. Advances in research detailing the responsiveness of Aedes aegypti to small changes in climate enable the production of more sophisticated remote sensing and surveillance techniques for monitoring these populations. Close monitoring of global dengue activity and outbreaks likewise enables a greater specificity when determining to which human populations the virus is most likely to spread. There have been no locally acquired cases in Arizona to date, but the high abundance of Aedes aegypti in the Phoenix Metropolitan area raises concern within the Arizona Department of Health Services over the potential transmission of dengue in the city. This study develops a model that combines mosquito abundance, micro-climatic and demographic information to delineate regions in Phoenix that are most support transmission of dengue. The first chapter focuses on the impact that daytime high and low temperatures have on Aedes aegypti’s ability to become infectious with dengue. It argues that NDVI (normal difference vegetative index) imaging of the Phoenix area can be used to plot areas where mosquitoes are most likely to become competent vectors. The second chapter focuses on the areas in the city where mosquitoes are most likely to be exposed to the virus. Based on proximity to Phoenix and the high volume of traffic across the Arizona-Mexico border, I treat the Mexican state of Sonora as the source of infection. I combine these two analyses, micro-climatic and demographic, to produce maps of Phoenix that show the locations with the highest likelihood of transmission overall.
ContributorsHughes, Tyler (Author) / Perrings, Charles (Thesis advisor) / Kinzig, Ann (Committee member) / Hall, Sharon J (Committee member) / Arizona State University (Publisher)
Created2016
Description
As an industrial society, humans have increasingly separated agricultural processes from natural ecosystems. Many areas of the Southwestern US, however, maintain traditional practices that link agricultural systems to the natural environment. One such practice, diverting river water into fields via earthen irrigation canals, allows ditch water to recharge groundwater and riparian vegetation to prosper along canal banks. As there is growing interest in managing landscapes for multiple ecosystem services, this study was undertaken to determine if irrigation canals function as an extension of the riparian corridor. I was specifically interested in determining if the processes within semi-arid streams that drive riparian plant community structure are manifested in earthen irrigation ditches. I examined herbaceous and woody vegetation along the middle Verde River, AZ, USA and three adjacent irrigation ditches across six months. I also collected sieved hydrochores--seeds dispersing through water--within ditches and the river twelve times. Results indicate that ditch vegetation was similar to streamside river vegetation in abundance (cover and basal area) due to surface water availability but more diverse than river streamside vegetation due to high heterogeneity. Compositionally, herbaceous vegetation along the ditch was most similar to the river banks, while low disturbance fostered woody vegetation along the ditches similar to high floodplain and river terrace vegetation. Hydrochore richness and abundance within the river was dependent on seasonality and stream discharge, but these relationships were dampened in the ditches. Species-specific strategies of hydrochory, however, did emerge in both systems. Strategies include pulse species, which disperse via hydrochory in strict accordance with their restricted dispersal windows, constant species, which are year round hydrochores, and combination species, which show characteristics of both. There was high overlap in the composition of hydrochores in the two systems, with obligate wetland species abundant in both. Upland species were more seasonally constant and abundant in the ditch water than the river. The consistency of river processes and similarity of vegetation suggest that earthen irrigation ditches do function as an extension of the riparian corridor. Thus, these man-made irrigation ditches should be considered by stakeholders for their multiple ecosystem services.
ContributorsBetsch, Jacqueline Michelle (Author) / Stromberg, Juliet C. (Thesis advisor) / Hall, Sharon J (Committee member) / Merritt, David M. (Committee member) / Arizona State University (Publisher)
Created2010
Description
This thesis explores the independent effects of the manipulation of rocks into alignments, prehistoric farming, and season on soil properties in two areas with a history of prehistoric agriculture in central Arizona, Pueblo la Plata within the Agua Fria National Monument (AFNM), and an archaeological site north of the Phoenix basin along Cave Creek (CC). Soil properties, annual herbaceous biomass and the physical properties of alignments and surface soils were measured and compared across the landscape, specifically on: 1) agricultural rock alignments that were near the archaeological site 2) geologically formed rock alignments that were located 0.5-1 km away from settlements; and 3) areas both near and far from settlements where rock alignments were absent. At AFNM, relatively well-built rock alignments have altered soil properties and processes while less-intact alignments at CC have left few legacies.
ContributorsTrujillo, Jolene Eve (Author) / Hall, Sharon J (Thesis advisor) / Collins, Scott L. (Committee member) / Spielmann, Katherine A. (Committee member) / Arizona State University (Publisher)
Created2011
Description
Biomass synthesis is a competing factor in biological systems geared towards generation of commodity and specialty chemicals, ultimately limiting maximum titer and yield; in this thesis, a widely generalizable, modular approach focused on decoupling biomass synthesis from the production of the phenylalanine in a genetically modified strain of E. coli BW25113 was explored with the use of synthetic trans-encoded small RNA (sRNA) to achieve greater efficiency. The naturally occurring sRNA MicC was used as a scaffold, and combined on a plasmid with a promoter for anhydrous tetracycline (aTc) and a T1/TE terminator. The coding sequence corresponding to the target binding site for fourteen potentially growth-essential gene targets as well as non-essential lacZ was placed in the seed region of the of the sRNA scaffold and transformed into BW25113, effectively generating a unique strain for each gene target. The BW25113 strain corresponding to each gene target was screened in M9 minimal media; decreased optical density and elongated cell morphology changes were observed and quantified in all induced sRNA cases where growth-essential genes were targeted. Six of the strains targeting different aspects of cell division that effectively suppressed growth and resulted in increased cell size were then screened for viability and metabolic activity in a scaled-up shaker flask experiment; all six strains were shown to be viable during stationary phase, and a metabolite analysis showed increased specific glucose consumption rates in induced strains, with unaffected specific glucose consumption rates in uninduced strains. The growth suppression, morphology and metabolic activity of the induced strains in BW25113 was compared to the bacteriostatic additives chloramphenicol, tetracycline, and streptomycin. At this same scale, the sRNA plasmid targeting the gene murA was transformed into BW25113 pINT-GA, a phenylalanine overproducer with the feedback resistant genes aroG and pheA overexpressed. Two induction times were explored during exponential phase, and while the optimal induction time was found to increase titer and yield amongst the BW25113 pINT-GA murA sRNA variant, overall this did not have as great a titer or yield as the BW25113 pINT-GA strain without the sRNA plasmid; this may be a result of the cell filamentation.
ContributorsHerschel, Daniel Jordan (Author) / Nielsen, David R (Thesis advisor) / Torres, César I (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016