PhD Dissertations - DO NOT EDIT
http://hdl.handle.net/10106/24842
2024-03-29T09:44:14ZMolecular Mechanisms That Regulate the Stress Response In A. baumannii
http://hdl.handle.net/10106/31785
Molecular Mechanisms That Regulate the Stress Response In A. baumannii
**Please note that the full text is embargoed until 08/01/2025** Acinetobacter baumannii is particularly problematic in hospital settings, where infections can occur in a range of tissues. This bacterium can endure extreme stress from various antimicrobial agents, biocides, host immune response etc. Not much is known about how these bacteria react to such high stress. A. baumannii also possesses a unique ability to inactivate lipooligosaccharide (LOS) biosynthesis, which is an essential molecule in most Gram-negative bacteria. LOS is enriched in the outer membrane and is the targeted by the last-resort antibiotic, colistin. LOS-deficient A. baumannii is highly resistant to the list-line antimicrobial. Previously, our lab discovered that a two-component system, called BaeSR, showed increased transcription in LOS-deficient cells relative to wild type. Furthermore, baeSR was required for LOS-deficient A. baumannii viability, suggesting that it regulated expression of some essential product. To determine BaeSR-dependent regulatory products we performed transcriptomics analysis on wild type and baeR mutants. Several pathways were downregulated in the mutant, including putative lipoproteins, lipoprotein transport genes, efflux pump genes, genes that regulate biofilm formation and phenylacetic acid catabolism. The paa operon acts on phenylacetic acid (PAA), an intermediary in the breakdown of phenylalanine, and is differently regulated in stress-induced conditions. Previous work showed that the GacSA two-component system also regulates the paa operon, but it was unknown if this regulation was direct or indirect. Notably, the sensor kinase, GacS, and response regulator, GacA, are not co-transcribed, which raises the possibility that the sensor kinase, GacS, may signal through other response regulators. We found that BaeR complementation not only restored wild type paa expression levels in ΔbaeR and ΔgacS, but IPTG-dependent overexpression further induced paa overexpression. Electrophoretic mobility shift assay showed that the paa promoter bound recombinant BaeR6X-his, suggesting a direct interaction. We also found that BaeR regulates expression of csu operon genes that controls biofilm formation. Biofilm formation is considered a stress response which relies on production of extracellular polymeric substances (EPS) to provide structural support so bacterial pathogens can withstand adverse conditions. This data presented here in suggest the BaeSR TCS contributes to A. baumannii survival in stress.
2023-08-14T00:00:00ZBiodiversity in the Anthropocene, understanding the impacts of land-use change, and species interactions.
http://hdl.handle.net/10106/31776
Biodiversity in the Anthropocene, understanding the impacts of land-use change, and species interactions.
**Please note that the full text is embargoed until 8/1/2024** ABSTRACT: The extent of human influences on the environment and biodiversity has led to naming our current time period the Anthropocene. A primary way in which humans impact biodiversity is through habitat modification. Despite the knowledge that habitat modification is negative for many species, we still don’t understand why some species are able to persist despite habitat modification while others do not. In my first chapter I used a trait-based approach to understand what determines species’ sensitivity to habitat modification. Trait-based approaches from different regions often disagree on the importance of the same traits, and I thought climate and land use change severity may account for some of these discrepancies. I set out to test the role of microhabitat use, climate and land use change severity in determining how species respond to habitat modifications. I used anuran abundance data from 18 studies across tropical forests, in conjunction with trait data (microhabitat use and reproductive mode). I found that microhabitat use greatly impacts species’ sensitivity to habitat modification, particularly that species vertical niche is important as species’ abundance tends to track the availability of their preferred vegetative strata. Arboreal anurans are most sensitive to conversion to land uses which lack vegetative strata, however the extent to which arboreal anurans are sensitive varies with climate. In warmer regions arboreal species are not as sensitive to habitat modification as terrestrial species, as their arboreal nature may have pre-adapted them to the warmer conditions associated with habitat loss. The finding that climate influences trait-based responses to habitat modification is novel and shows that conservation efforts need to incorporate climate context into planning. In my next chapter (chapter 3) I assess what accounts for variation between communities in sensitivity to habitat modification. Previous research has demonstrated that populations and communities vary in their sensitivity to habitat modification, and contemporary factors such as climate account for some of this variation. Here I focus on how historical factors
ii
may also contribute to this variation, I test if early humans have contributed to the variation in community sensitivity to land use change. I test the extinction filter hypothesis, using early humans as a filter, which may have already removed sensitive species from communities. I used the PREDICTS database to obtain bird community in different land uses from 54 studies across the world. I found that early humans impact community sensitivity, areas with a greater history of human presence, tend to be less sensitive to habitat modification. This reduced sensitivity to habitat modification comes from a decrease in the number of species found in primary vegetation, rather than an increase in species able to tolerate habitat modification. These results suggest that it is important to consider human history when considering patterns of diversity and/or assessing which communities are most critical to protect, as sensitive species are more likely to occur in areas with low histories of human presence. In my last chapter (chapter 4), I focus on species interactions, as a potential factor which may be causing species to decline. I assessed the population trends of a common lizard, the prairie lizard (S. consobrinus), which appears to be in decline, and a closely related species, the Texas Spiny Lizard (S. olivaceus). Occurrence data from the last 100 years reveals that S. consobrinus is declining, while S. olivaceus is increasing in relative abundance. I grouped the data into pseudo-sites to assess the role of climate change, land-use change, and species interactions in the decline of S. consobrinus. I found that climate alone does a poor job of predicting the current distribution of S. consobrinus, and that presence of S. olivaceus and amount urbanization are much better predictors of S. consobrinus occurrence. S. olivaceus seems to be critical in contributing to the decline of S. consobrinus, and co-occurrence between the two species has become increasingly infrequent through time. To validate that these results in patterns of co-occurrence are representative of natural communities, I performed 176 surveys spread across the distribution of S. consobrinus in
iii
Texas. Community surveys mirrored occurrence data and suggest that presence of S. olivaceus leads to absence of S. consobrinus in habitat it would otherwise likely occupy. Observations of the two species in the field revealed major shifts in habitat use by S. consobrinus in the presence of S. olivaceus, occupying habitat three times as open in areas which also possess S. olivaceus when compared to alone. Finally, to confirm that competition is occurring I conducted competition trials between the two species and found that S. olivaceus is the superior competitor when compared to S. consobrinus. Aggressive behaviour by S. olivaceus leads to frequent retreats by S. consobrinus, and greatly increased frequency of S. consobrinus hiding compared to when S. consobrinus is not present. Across all data, results suggest that S. olivaceus is competing with S. consobrinus, and that this contributes to the decline S. consobrinus in central and south Texas.
2023-08-10T00:00:00ZDETERMINING HOW ANTHROPOGENIC CHANGE FILTERS BIOLOGICAL COMMUNITIES AND HOW SPECIES MODIFY THEIR TRAITS IN RESPONSE TO URBANIZATION
http://hdl.handle.net/10106/31730
DETERMINING HOW ANTHROPOGENIC CHANGE FILTERS BIOLOGICAL COMMUNITIES AND HOW SPECIES MODIFY THEIR TRAITS IN RESPONSE TO URBANIZATION
Humans are significantly altering the environment at an alarming pace, leading to a reduction in species diversity. This transformation has created modified habitats where some species struggle to survive, while a few others not only manage to survive but thrive. One of the most drastic forms of habitat modification is urbanization, which is spreading worldwide and contributing to the decline of biodiversity. Urbanization has given rise to urban-tolerant species that differ ecologically from species that avoid urban areas across various niche dimensions. These urban-tolerant species must adapt to changes in food sources, microhabitat conditions, and alterations in physical habitat structures. The focus of my dissertation is to investigate the impact of urbanization on morphological and dietary changes in lizard populations. First, I aim to identify and characterize specific morphological traits associated with urbanization by determining how ecological filters are shaping urban lizard communities. Secondly, I will determine if lizard species inhabiting urban environments are undergoing phenotypic changes and categorize these changes as convergent, divergent, or idiosyncratic. Lastly, I will assess whether dietary niche breadth is expanding or contracting in urban environments compared to natural ones.
2023-08-11T00:00:00ZUrban Ecology in North Texas: Native Plants and Nitrogen Deposition
http://hdl.handle.net/10106/31686
Urban Ecology in North Texas: Native Plants and Nitrogen Deposition
Globally, the human population continues to grow and move into urban areas causing a range of effects on local ecosystems. Elevated temperatures, altered hydrology, and higher concentrations of atmospheric pollutants in urban environments create novel conditions for resident organisms. My research focused on one particular aspect of human alteration to urban environments – nitrogen (N) deposition – and its effects on native plants across an urban to rural gradient in the southern Great Plains, North Texas (NTX), USA.
Nitrogen oxides (NOx) – the product of combustion and precursor to nitrate deposition in precipitation – were significantly positively correlated with impervious surface area, a measure of urban development, in NTX. Dissolved inorganic nitrogen deposition (composed of nitrate and ammonium) was also greater in the developed parts of NTX than in the surrounding rural area. Bulk N deposition in NTX was dominated by ammonium suggesting that fertilizers are likely an important source of N in rural and urban environments.
Native plant responses to these differences in N deposition were subtle. Naturally occurring native post oak trees (Quercus stellata) had similar tissue quality (carbon:nitrogen ratio) across the gradient. Little bluestem (Schizachryium scoparium) and Texas wintergrass (Nasella leucotricha), native perennial grasses, grew similarly when planted at six sites along the gradient. However, little bluestem plants taken from urban and rural remnant prairie sites and grown together in a common garden differed in some plant characteristics, suggesting genetic divergence among these populations.
Native plants provide ecosystem services including cooling, carbon sequestration, erosion control, flood mitigation, and human health benefits. Because NTX is one of the most rapidly expanding urban areas, understanding the impacts of anthropogenic N deposition on native plants is crucial to maintaining ecosystem integrity in the southern Great Plains.