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Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e.,

Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
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Description
The study of bacterial resistance to antimicrobial peptides (AMPs) is a significant area of interest as these peptides have the potential to be developed into alternative drug therapies to combat microbial pathogens. AMPs represent a class of host-mediated factors that function to prevent microbial infection of their host and serve

The study of bacterial resistance to antimicrobial peptides (AMPs) is a significant area of interest as these peptides have the potential to be developed into alternative drug therapies to combat microbial pathogens. AMPs represent a class of host-mediated factors that function to prevent microbial infection of their host and serve as a first line of defense. To date, over 1,000 AMPs of various natures have been predicted or experimentally characterized. Their potent bactericidal activities and broad-based target repertoire make them a promising next-generation pharmaceutical therapy to combat bacterial pathogens. It is important to understand the molecular mechanisms, both genetic and physiological, that bacteria employ to circumvent the bactericidal activities of AMPs. These understandings will allow researchers to overcome challenges posed with the development of new drug therapies; as well as identify, at a fundamental level, how bacteria are able to adapt and survive within varied host environments. Here, results are presented from the first reported large scale, systematic screen in which the Keio collection of ~4,000 Escherichia coli deletion mutants were challenged against physiologically significant AMPs to identify genes required for resistance. Less than 3% of the total number of genes on the E. coli chromosome was determined to contribute to bacterial resistance to at least one AMP analyzed in the screen. Further, the screen implicated a single cellular component (enterobacterial common antigen, ECA) and a single transporter system (twin-arginine transporter, Tat) as being required for resistance to each AMP class. Using antimicrobial resistance as a tool to identify novel genetic mechanisms, subsequent analyses were able to identify a two-component system, CpxR/CpxA, as a global regulator in bacterial resistance to AMPs. Multiple previously characterized CpxR/A members, as well as members found in this study, were identified in the screen. Notably, CpxR/A was found to transcriptionally regulate the gene cluster responsible for the biosynthesis of the ECA. Thus, a novel genetic mechanism was uncovered that directly correlates with a physiologically significant cellular component that appears to globally contribute to bacterial resistance to AMPs.
ContributorsWeatherspoon-Griffin, Natasha (Author) / Shi, Yixin (Thesis advisor) / Clark-Curtiss, Josephine (Committee member) / Misra, Rajeev (Committee member) / Nickerson, Cheryl (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Hepatitis C virus (HCV) is a globally prevalent infection which is a main contributor to the global burden of liver disease. Due to its ability to establish a chronic infection, and the lack of usefulness of traditional neutralizing antibody vaccine design in producing a protective immune response, a preventative vaccine

Hepatitis C virus (HCV) is a globally prevalent infection which is a main contributor to the global burden of liver disease. Due to its ability to establish a chronic infection, and the lack of usefulness of traditional neutralizing antibody vaccine design in producing a protective immune response, a preventative vaccine has been notoriously difficult to produce. To overcome this, a vaccine using non-structural protein 3 (NS3) as a target to elicit a T cell specific immune response is thought to be a possible strategy for eliciting a protective immune response against hepatitis C infection. In this paper, a recombinant strain of measles virus (MV) that expresses HCV NS3 protein was analyzed. The replication fitness of this recombinant virus also indicates that this construct replicates at a higher rate than parental measles strain. It is also demonstrated through western blot analysis of protein expression and immunofluorescence that this recombinant virus expresses both the inserted HCV NS3 protein, as well as native measles proteins.
ContributorsWoell, Dana Marie (Author) / Reyes del Valle, Jorge (Thesis director) / Nickerson, Cheryl (Committee member) / Julik, Emily (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05
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Description
Clean water for drinking, food preparation, and bathing is essential for astronaut health and safety during long duration habitation of the International Space Station (ISS), including future missions to Mars. Despite stringent water treatment and recycling efforts on the ISS, it is impossible to completely prevent microbial contamination of onboard

Clean water for drinking, food preparation, and bathing is essential for astronaut health and safety during long duration habitation of the International Space Station (ISS), including future missions to Mars. Despite stringent water treatment and recycling efforts on the ISS, it is impossible to completely prevent microbial contamination of onboard water supplies. In this work, we used a spaceflight analogue culture system to better understand how the microgravity environment can influence the pathogenesis-related characteristics of Burkholderia cepacia complex (Bcc), an opportunistic pathogen previously recovered from the ISS water system. The results of the present study suggest that there may be important differences in how this pathogen can respond and adapt to spaceflight and other low fluid shear environments encountered during their natural life cycles. Future studies are aimed at understanding the underlying mechanisms responsible for these phenotypes.
ContributorsKang, Bianca Younseon (Author) / Nickerson, Cheryl (Thesis director) / Barrila, Jennifer (Committee member) / Ott, Mark (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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Description

Objectives: We estimated neighborhood effects of population characteristics and built and natural environments on deaths due to heat exposure in Maricopa County, Arizona (2000–2008).

Methods: We used 2000 U.S. Census data and remotely sensed vegetation and land surface temperature to construct indicators of neighborhood vulnerability and a geographic information system to

Objectives: We estimated neighborhood effects of population characteristics and built and natural environments on deaths due to heat exposure in Maricopa County, Arizona (2000–2008).

Methods: We used 2000 U.S. Census data and remotely sensed vegetation and land surface temperature to construct indicators of neighborhood vulnerability and a geographic information system to map vulnerability and residential addresses of persons who died from heat exposure in 2,081 census block groups. Binary logistic regression and spatial analysis were used to associate deaths with neighborhoods.

Results: Neighborhood scores on three factors—socioeconomic vulnerability, elderly/isolation, and unvegetated area—varied widely throughout the study area. The preferred model (based on fit and parsimony) for predicting the odds of one or more deaths from heat exposure within a census block group included the first two factors and surface temperature in residential neighborhoods, holding population size constant. Spatial analysis identified clusters of neighborhoods with the highest heat vulnerability scores. A large proportion of deaths occurred among people, including homeless persons, who lived in the inner cores of the largest cities and along an industrial corridor.

Conclusions: Place-based indicators of vulnerability complement analyses of person-level heat risk factors. Surface temperature might be used in Maricopa County to identify the most heat-vulnerable neighborhoods, but more attention to the socioecological complexities of climate adaptation is needed.

ContributorsHarlan, Sharon L. (Author) / Declet-Barreto, Juan H. (Author) / Stefanov, William L. (Author) / Petitti, Diana B. (Author)
Created2013-02-01
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Description

In this study we characterized the relationship between temperature and mortality in central Arizona desert cities that have an extremely hot climate. Relationships between daily maximum apparent temperature (ATmax) and mortality for eight condition-specific causes and all-cause deaths were modeled for all residents and separately for males and females ages

In this study we characterized the relationship between temperature and mortality in central Arizona desert cities that have an extremely hot climate. Relationships between daily maximum apparent temperature (ATmax) and mortality for eight condition-specific causes and all-cause deaths were modeled for all residents and separately for males and females ages <65 and ≥65 during the months May–October for years 2000–2008. The most robust relationship was between ATmax on day of death and mortality from direct exposure to high environmental heat. For this condition-specific cause of death, the heat thresholds in all gender and age groups (ATmax = 90–97 °F; 32.2‒36.1 °C) were below local median seasonal temperatures in the study period (ATmax = 99.5 °F; 37.5 °C). Heat threshold was defined as ATmax at which the mortality ratio begins an exponential upward trend. Thresholds were identified in younger and older females for cardiac disease/stroke mortality (ATmax = 106 and 108 °F; 41.1 and 42.2 °C) with a one-day lag. Thresholds were also identified for mortality from respiratory diseases in older people (ATmax = 109 °F; 42.8 °C) and for all-cause mortality in females (ATmax = 107 °F; 41.7 °C) and males <65 years (ATmax = 102 °F; 38.9 °C). Heat-related mortality in a region that has already made some adaptations to predictable periods of extremely high temperatures suggests that more extensive and targeted heat-adaptation plans for climate change are needed in cities worldwide.

ContributorsHarlan, Sharon L. (Author) / Chowell, Gerardo (Author) / Yang, Shuo (Author) / Petitti, Diana B. (Author) / Morales Butler, Emmanuel J. (Author) / Ruddell, Benjamin L. (Author) / Ruddell, Darren M. (Author)
Created2014-05-20
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Description

Human exposure to excessively warm weather, especially in cities, is an increasingly important public health problem. This study examined heat-related health inequalities within one city in order to understand the relationships between the microclimates of urban neighborhoods, population characteristics, thermal environments that regulate microclimates, and the resources people possess to

Human exposure to excessively warm weather, especially in cities, is an increasingly important public health problem. This study examined heat-related health inequalities within one city in order to understand the relationships between the microclimates of urban neighborhoods, population characteristics, thermal environments that regulate microclimates, and the resources people possess to cope with climatic conditions. A simulation model was used to estimate an outdoor human thermal comfort index (HTCI) as a function of local climate variables collected in 8 diverse city neighborhoods during the summer of 2003 in Phoenix, USA. HTCI is an indicator of heat stress, a condition that can cause illness and death. There were statistically significant differences in temperatures and HTCI between the neighborhoods during the entire summer, which increased during a heat wave period. Lower socioeconomic and ethnic minority groups were more likely to live in warmer neighborhoods with greater exposure to heat stress. High settlement density, sparse vegetation, and having no open space in the neighborhood were significantly correlated with higher temperatures and HTCI. People in warmer neighborhoods were more vulnerable to heat exposure because they had fewer social and material resources to cope with extreme heat. Urban heat island reduction policies should specifically target vulnerable residential areas and take into account equitable distribution and preservation of environmental resources.

ContributorsHarlan, Sharon L. (Author) / Brazel, Anthony J. (Author) / Prashad, Lela (Author) / Stefanov, William L. (Author) / Larsen, Larissa (Author)
Created2006-09-25
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Description

We conducted microclimate simulations in ENVI-Met 3.1 to evaluate the impact of vegetation in lowering temperatures during an extreme heat event in an urban core neighborhood park in Phoenix, Arizona. We predicted air and surface temperatures under two different vegetation regimes: existing conditions representative of Phoenix urban core neighborhoods, and

We conducted microclimate simulations in ENVI-Met 3.1 to evaluate the impact of vegetation in lowering temperatures during an extreme heat event in an urban core neighborhood park in Phoenix, Arizona. We predicted air and surface temperatures under two different vegetation regimes: existing conditions representative of Phoenix urban core neighborhoods, and a proposed scenario informed by principles of landscape design and architecture and Urban Heat Island mitigation strategies. We found significant potential air and surface temperature reductions between representative and proposed vegetation scenarios:

1. A Park Cool Island effect that extended to non-vegetated surfaces.
2. A net cooling of air underneath or around canopied vegetation ranging from 0.9 °C to 1.9 °C during the warmest time of the day.
3. Potential reductions in surface temperatures from 0.8 °C to 8.4 °C in areas underneath or around vegetation.

ContributorsDeclet-Barreto, Juan (Author) / Brazel, Anthony J. (Author) / Martin, Chris A. (Author) / Chow, Winston, 1951- (Author) / Harlan, Sharon L. (Author)
Created2012-12-21
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Description

Urban ecosystems are subjected to high temperatures—extreme heat events, chronically hot weather, or both—through interactions between local and global climate processes. Urban vegetation may provide a cooling ecosystem service, although many knowledge gaps exist in the biophysical and social dynamics of using this service to reduce climate extremes. To better

Urban ecosystems are subjected to high temperatures—extreme heat events, chronically hot weather, or both—through interactions between local and global climate processes. Urban vegetation may provide a cooling ecosystem service, although many knowledge gaps exist in the biophysical and social dynamics of using this service to reduce climate extremes. To better understand patterns of urban vegetated cooling, the potential water requirements to supply these services, and differential access to these services between residential neighborhoods, we evaluated three decades (1970–2000) of land surface characteristics and residential segregation by income in the Phoenix, Arizona, USA metropolitan region. We developed an ecosystem service trade‐offs approach to assess the urban heat riskscape, defined as the spatial variation in risk exposure and potential human vulnerability to extreme heat. In this region, vegetation provided nearly a 25°C surface cooling compared to bare soil on low‐humidity summer days; the magnitude of this service was strongly coupled to air temperature and vapor pressure deficits.

To estimate the water loss associated with land‐surface cooling, we applied a surface energy balance model. Our initial estimates suggest 2.7 mm/d of water may be used in supplying cooling ecosystem services in the Phoenix region on a summer day. The availability and corresponding resource use requirements of these ecosystem services had a strongly positive relationship with neighborhood income in the year 2000. However, economic stratification in access to services is a recent development: no vegetation–income relationship was observed in 1970, and a clear trend of increasing correlation was evident through 2000. To alleviate neighborhood inequality in risks from extreme heat through increased vegetation and evaporative cooling, large increases in regional water use would be required. Together, these results suggest the need for a systems evaluation of the benefits, costs, spatial structure, and temporal trajectory for the use of ecosystem services to moderate climate extremes. Increasing vegetation is one strategy for moderating regional climate changes in urban areas and simultaneously providing multiple ecosystem services. However, vegetation has economic, water, and social equity implications that vary dramatically across neighborhoods and need to be managed through informed environmental policies.

ContributorsJenerette, G. Darrel (Author) / Harlan, Sharon L. (Author) / Stefanov, William L. (Author) / Martin, Chris A. (Author)
Created2011-10-01
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Description

Context:
With rapidly expanding urban regions, the effects of land cover changes on urban surface temperatures and the consequences of these changes for human health are becoming progressively larger problems.

Objectives:
We investigated residential parcel and neighborhood scale variations in urban land surface temperature, land cover, and residents’ perceptions of landscapes and heat

Context:
With rapidly expanding urban regions, the effects of land cover changes on urban surface temperatures and the consequences of these changes for human health are becoming progressively larger problems.

Objectives:
We investigated residential parcel and neighborhood scale variations in urban land surface temperature, land cover, and residents’ perceptions of landscapes and heat illnesses in the subtropical desert city of Phoenix, AZ USA.

Methods:
We conducted an airborne imaging campaign that acquired high resolution urban land surface temperature data (7 m/pixel) during the day and night. We performed a geographic overlay of these data with high resolution land cover maps, parcel boundaries, neighborhood boundaries, and a household survey.

Results:
Land cover composition, including percentages of vegetated, building, and road areas, and values for NDVI, and albedo, was correlated with residential parcel surface temperatures and the effects differed between day and night. Vegetation was more effective at cooling hotter neighborhoods. We found consistencies between heat risk factors in neighborhood environments and residents’ perceptions of these factors. Symptoms of heat-related illness were correlated with parcel scale surface temperature patterns during the daytime but no corresponding relationship was observed with nighttime surface temperatures.

Conclusions:
Residents’ experiences of heat vulnerability were related to the daytime land surface thermal environment, which is influenced by micro-scale variation in land cover composition. These results provide a first look at parcel-scale causes and consequences of urban surface temperature variation and provide a critically needed perspective on heat vulnerability assessment studies conducted at much coarser scales.

ContributorsJenerette, Darrel G. (Author) / Harlan, Sharon L. (Author) / Buyantuev, Alexander (Author) / Stefanov, William L. (Author) / Declet-Barreto, Juan (Author) / Ruddel, Benjamin L. (Author) / Myint, Soe Win (Author) / Kaplan, Shari (Author) / Li, XiaiXiao (Author)
Created2015-10-19