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- All Subjects: Biology
- All Subjects: Ecology
- Genre: Masters Thesis
- Creators: Hall, Sharon J
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
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
More people live in cities or metropolitan areas than ever before, which encompass many types of urbanization. These areas are culturally diverse and densely populated heterogeneous landscapes that are shaped by socio-ecological patterns. Cities support human and wildlife populations that are influenced indirectly and directly by human decisions. This process can result in unequal access to environmental services and accessible green spaces. Additionally, biodiversity distribution is influenced by human decisions. Although neighborhood income can drive biodiversity in metropolitan areas (i.e., the ‘luxury effect’), other socio-cultural factors may also influence the presence and abundance of wildlife beyond simple measures of wealth. To understand how additional social factors shape distributions of wildlife, I ask, are patterns of wildlife distribution associated with neighborhood ethnicity, in addition to income and ecological landscape characteristics within metropolitan areas? Utilizing data from 38 wildlife cameras deployed in neighborhood public parks and non-built spaces in metro Phoenix, AZ (USA), I estimated occupancy and activity patterns of coyotes (Canis latrans), desert cottontail rabbits (Sylvilagus audubonii), and domestic cats (Felis catus) across gradients of median household income and neighborhood ethnicity, estimated by the proportion of Latinx residents. Neighborhood ethnicity appeared in the top models for all species, and neighborhood % of Latinx residents was inversely associated with presence of native Sonoran Desert animals (coyotes and cottontail rabbits). Furthermore, daily activity patterns of coyotes differed in neighborhoods with higher vs. lower proportion of Latinx residents. My results suggest that socio-cultural variables beyond income are associated with wildlife distributions, and that factors associated with neighborhood ethnicity may be an informative correlate of city-wide ecological patterns. In this research, I unraveled predictive social variables and differentiated wildlife distribution across neighborhood gradients of income and ethnic composition, bringing attention to the potentially unequal distribution of mammals in cities.
ContributorsCocroft, Alexandreana (Author) / Hall, Sharon J (Thesis advisor) / Lerman, Susannah B (Committee member) / Lewis, Jesse (Committee member) / Arizona State University (Publisher)
Created2022
Description
Reactive oxygen species (ROS) including superoxide, hydrogen peroxide, and hydroxyl radicals occur naturally as a byproduct of aerobic respiration. To mitigate damages caused by ROS, Escherichia coli employs defenses including two cytosolic superoxide dismutases (SODs), which convert superoxide to hydrogen peroxide. Deletion of both sodA and sodB, the genes coding for the cytosolic SOD enzymes, results in a strain that is unable to grow on minimal medium without amino acid supplementation. Additionally, deletion of both cytosolic SOD enzymes in a background containing the relA1 allele, an inactive version of the relA gene that contributes to activation of stringent response by amino acid starvation, results in a strain that is unable to grow aerobically, even on rich medium. These observations point to a relationship between the stringent response and oxidative stress. To gain insight into this relationship, suppressors were isolated by growing the ∆sodAB relA1 cells aerobically on rich medium, and seven suppressors were further examined to characterize distinct colony sizes and temperature sensitivity phenotypes. In three of these suppressor-containing strains, the relA1 allele was successfully replaced by the wild type relA allele to allow further study in aerobic conditions. None of those three suppressors were found to increase tolerance to exogenous superoxides produced by paraquat, which shows that these mutations only overcome the superoxide buildup that naturally occurs from deletion of SODs. Because each of these suppressors had unique phenotypes, it is likely that they confer tolerance to SOD-dependent superoxide buildup by different mechanisms. Two of these three suppressors have been sent for whole-genome sequencing to identify the location of the suppressor mutation and determine the mechanism by which they confer superoxide tolerance.
ContributorsFlake, Melissa (Author) / Misra, Rajeev (Thesis advisor) / Shah, Dhara (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2024
Description
As a result of growing populations and uncertain resource availability, urban areas are facing pressure from federal and state agencies, as well as residents, to promote conservation programs that provide services for people and mitigate environmental harm. Current strategies in US cities aim to reduce the impact of municipal and household resource use, including programs to promote water conservation. One common conservation program incentivizes the replacement of water-intensive turfgrass lawns with landscapes that use less water consisting of interspersed drought-tolerant shrubs and trees with rock or mulch groundcover (e.g. xeriscapes, rain gardens, water-wise landscapes). A handful of previous studies in experimental landscapes have shown that converting a turfgrass yard to a shrub-dominated landscape has the potential to increase rates of nitrate (NO3-) leaching. However, no studies have examined the drivers or patterns across diverse management practices. In this research, I compared soil nutrient retention and cycling in turfgrass and lawn-alternative xeriscaped yards along a chronosequence of time since land cover change in Tempe, Arizona, in the semi-arid US Southwest. Soil inorganic extractable nitrogen (N) pools were greater in xeriscapes compared to turfgrass lawns. On average xeriscapes contained 2.5±0.4 g NO3--N/m2 in the first 45 cm of soil, compared to 0.6±0.7 g NO3--N/m2 in lawns. Soil NO3--N pools in xeriscaped yards also varied significantly with time: pools were largest 9-13 years after cover change and declined to levels comparable to turfgrass at 18-21 years. Variation in soil extractable NO3--N with landscape age was strongly influenced by management practices that control soil water availability, including shrub cover, the presence of sub-surface plastic sheeting, and the frequency of irrigation. This research is the first to explore the ecological outcomes and temporal dynamics of an increasingly common, ‘sustainable’ land use practice that is universally promoted in US cities. Our findings show that transitioning from turfgrass to water-efficient residential landscaping can lead to an accumulation of NO3--N that may be lost from the soil rooting zone over time, through leaching following irrigation or rainfall. These results have implications for best management practices to optimize the benefits of water-conserving residential yards.
ContributorsHeavenrich, Hannah (Author) / Hall, Sharon J (Thesis advisor) / Larson, Kelli L (Committee member) / Potaki, Diane E (Committee member) / Arizona State University (Publisher)
Created2015
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
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
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
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
Land use change driven by human population expansion continues to influence
the integrity and configuration of riparian corridors worldwide. Wildlife viability in semi-arid regions depend heavily on the connectivity of riparian corridors, since water is the primary limiting resource. The Madrean Archipelago in northern Mexico and southwestern United States (US) is a biodiversity hotspot that supports imperiled wildlife like jaguar (Panthera onca) and ocelot (Leopardus pardalis). Recent and ongoing infrastructure developments in the historically understudied US-México borderlands region, such as the border wall and expansion of Federal Highway 2, are altering wildlife movement and disconnecting essential habitat.
I used wildlife cameras to assess species occupancy, abundance, and related habitat variables affecting the use of washes as corridors for mammals in semi-arid Los Ojos (LO), a private ranch within a 530 km2 priority conservation area in Sonora, México located south of the border and Federal Highway 2. From October 2018 to April 2019, I deployed 21 wildlife cameras in five different riparian corridors within LO. I used single- season occupancy models and Royal Nichols abundance models to explore the relationship between habitat variables and use of riparian corridors by mammal communities of conservation concern within this region.
Twenty-one mammal species were recorded in the study area, including American black bear (Ursus americanus), white-tailed deer (Odocoileus virginianus) and the first sighting of jaguar (Panthera onca) in this region in 25 years. For the 11 medium- and large-bodied mammals recorded, habitat variables related to perennial river characteristics (distance to river, weekly water, and site width) and remoteness (distance from highway, elevation, and NDVI) were important for occupancy, but the direction of the relationship varied by species. For commonly observed species such as mountain lion (Puma concolor) and white-nosed coati (Nasua narica), topographic variety was highly informative for species abundance. These results highlight the importance of habitat diversity when identifying corridors for future protection to conserve wildlife communities in semi-arid regions. Additionally, this study provides robust evidence in support of mitigation measures (e.g. funnel fencing, over- or under- passes) along Federal Highway 2, and other barriers such as the border wall, to facilitate wildlife connectivity.
the integrity and configuration of riparian corridors worldwide. Wildlife viability in semi-arid regions depend heavily on the connectivity of riparian corridors, since water is the primary limiting resource. The Madrean Archipelago in northern Mexico and southwestern United States (US) is a biodiversity hotspot that supports imperiled wildlife like jaguar (Panthera onca) and ocelot (Leopardus pardalis). Recent and ongoing infrastructure developments in the historically understudied US-México borderlands region, such as the border wall and expansion of Federal Highway 2, are altering wildlife movement and disconnecting essential habitat.
I used wildlife cameras to assess species occupancy, abundance, and related habitat variables affecting the use of washes as corridors for mammals in semi-arid Los Ojos (LO), a private ranch within a 530 km2 priority conservation area in Sonora, México located south of the border and Federal Highway 2. From October 2018 to April 2019, I deployed 21 wildlife cameras in five different riparian corridors within LO. I used single- season occupancy models and Royal Nichols abundance models to explore the relationship between habitat variables and use of riparian corridors by mammal communities of conservation concern within this region.
Twenty-one mammal species were recorded in the study area, including American black bear (Ursus americanus), white-tailed deer (Odocoileus virginianus) and the first sighting of jaguar (Panthera onca) in this region in 25 years. For the 11 medium- and large-bodied mammals recorded, habitat variables related to perennial river characteristics (distance to river, weekly water, and site width) and remoteness (distance from highway, elevation, and NDVI) were important for occupancy, but the direction of the relationship varied by species. For commonly observed species such as mountain lion (Puma concolor) and white-nosed coati (Nasua narica), topographic variety was highly informative for species abundance. These results highlight the importance of habitat diversity when identifying corridors for future protection to conserve wildlife communities in semi-arid regions. Additionally, this study provides robust evidence in support of mitigation measures (e.g. funnel fencing, over- or under- passes) along Federal Highway 2, and other barriers such as the border wall, to facilitate wildlife connectivity.
ContributorsRagan, Kinley (Author) / Hall, Sharon J (Thesis advisor) / Schipper, Jan (Thesis advisor) / Bateman, Heather L (Committee member) / Arizona State University (Publisher)
Created2020