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Principles Of Aaa+ Proteases, Samar Mahmoud
Principles Of Aaa+ Proteases, Samar Mahmoud
Doctoral Dissertations
ATPases associated with diverse cellular activities (AAA+) proteases in bacteria help maintain protein homeostasis by degrading misfolded and regulatory proteins. While a handful of protein targets for these proteases have been identified in Caulobacter crescentus and other organisms, more research is needed to elucidate mechanisms that govern substrate specificity. In the second chapter of this thesis, I will elaborate on how AAA+ substrate specificity is less rigid than previous work has suggested and how limiting ATP or mutations can alter substrate preferences of the ClpXP protease. In the third chapter, I will highlight our efforts to use a quantitative proteomics …
The Spatial, Temporal, And Ecological Constraints Of Plant-Host Associated Microbial Communities, Jonathan Dickey
The Spatial, Temporal, And Ecological Constraints Of Plant-Host Associated Microbial Communities, Jonathan Dickey
Doctoral Dissertations
With the development of next generation sequencing technology, ecologists have recently been able to describe microbial communities across a wide array of niches at an accelerated pace. De-novo-based patterns in richness and relative abundance have been described for bacterial and fungal communities in terrestrial, aquatic, and host-associated microhabitats. A recent synthesis has shown that these communities exhibit similar geographical patterns that have been traditionally described for plant and animals. Yet, there is a lack of hypothesis-based research for host-associated microbial communities. Throughout this dissertation, I will address how spatial scale, sequencing resolution, and manipulative rainfall exclusion govern host-associated microbial communities …
Antibiotic Sensitivity Testing Of Foodborne Bacteria Using Surface-Enhanced Raman Spectroscopy, Joshua Gukowsky
Antibiotic Sensitivity Testing Of Foodborne Bacteria Using Surface-Enhanced Raman Spectroscopy, Joshua Gukowsky
Doctoral Dissertations
The spread of antibiotic resistant bacteria around the world has become a major public health issue, and it is essential that effective detection methods exist for identifying these organisms and preventing them from spreading throughout our food systems and into the environment. The goal of this research is to develop a novel analytical procedure that is capable of easily identifying antibiotic resistance in bacterial samples, and also provides more information about the biochemical characteristics of the bacteria and their responses to antibiotic exposure. Surface-enhanced Raman Spectroscopy (SERS), an analytical technique that uses light scattering to produce a spectrum based on …
The Effects Of Urbanization On The Avian Gut Microbiome, Mae Berlow
The Effects Of Urbanization On The Avian Gut Microbiome, Mae Berlow
Doctoral Dissertations
The gut microbiome influences and is influenced by the host, and can affect the host organism by contributing to health, development and immunity. Similarly, the host can influence this community; it’s makeup can vary with host species, locality, diet, social stressors, and environmental stressors. Some of these environmental stressors have arisen due to human-induced rapid environmental change, like urbanization. The physiology and behaviors of organisms that are able to persist in urban environments are often different from their non-urban congeners. Nutrition, development, and immunity—all of which are affected by the gut microbiome—are important factors that can determine survival in urban …
Engineered Nanoparticles For Site-Specific Bioorthogonal Catalysis: Imaging And Therapy, Riddha Das
Engineered Nanoparticles For Site-Specific Bioorthogonal Catalysis: Imaging And Therapy, Riddha Das
Doctoral Dissertations
Bioorthogonal catalysis offers a strategy for chemical transformations complementary to bioprocesses and has proven to be a powerful tool in biochemistry and medical sciences. Transition metal catalysts (TMCs) have emerged as a powerful tool to execute selective chemical transformations, however, lack of biocompatibility and stability limits their use in biological applications. Incorporation of TMCs into nanoparticle monolayers provides a versatile strategy for the generation of bioorthogonal nanocatalysts known as “nanozymes”. We have fabricated a family of nanozymes using gold nanoparticles (AuNPs) as scaffolds featuring diverse chemical functional groups for controlled localization of nanozymes in biological environments, providing unique strategies for …
Surface-Enhanced Raman Spectroscopic Imaging Of Bacteria Within Fresh Produce In Situ, Michael Hickey
Surface-Enhanced Raman Spectroscopic Imaging Of Bacteria Within Fresh Produce In Situ, Michael Hickey
Doctoral Dissertations
The growth curves for E. coli O157:H7 (#043888) are reported. We make the case that the onset of stationary growth is the optimal point at which a bacteria culture is considered suitable for quantitative Raman analyses. The optimal conditions for 3-mercaptophenylboronic acid coating of bacteria cells is also reported. Fundamental drawbacks of the status-quo approach have been elucidated and overcome, based on measurable improvements to the experimental methodology. This approach is shown to be suitable for the evaluation of bacterial rinse-washing efficacy by means of Raman light-scattering. The data were compared to label-free applications and the measurable differences between each …
Structure-Property Relationships Of Polymer Films And Hydrogels To Control Bacterial Adhesion, Kristopher W. Kolewe
Structure-Property Relationships Of Polymer Films And Hydrogels To Control Bacterial Adhesion, Kristopher W. Kolewe
Doctoral Dissertations
The emergence and spread of antibiotic resistance across microbial species necessitates the need for alternative approaches to mitigate the risk of infection without relying on commercial antibiotics. Biofilm-related infections are a class of notoriously difficult to treat healthcare-associated infections that frequently develop on the surface of implanted medical devices. As biofilm formation is a surface-associated phenomenon, understanding how the intrinsic properties of materials affect bacterial adhesion enables the development of structure-property relationships that can guide the future design of infection-resistant materials. Despite lacking visual, auditory, and olfactory perception, bacteria still manage to sense and attach to surfaces. Previously, it has …
Pore Forming Protein Assembly And The Use In Nanopore Sensing: A Study On E. Coli Proteins Clya And Ompg, Monifa Fahie
Pore Forming Protein Assembly And The Use In Nanopore Sensing: A Study On E. Coli Proteins Clya And Ompg, Monifa Fahie
Doctoral Dissertations
Pore forming proteins are typically the proteins that form channels in membranes. They have several roles ranging from molecule transport to triggering the death of a cell. This work focuses on two E. coli pore forming proteins that have vastly differing roles in nature. Outer membrane protein G (OmpG) is an innocuous β-barrel porin while Cytolysin A (ClyA) is an α-helical pore forming toxin. For OmpG we probed its potential to be a nanopore sensor for protein detection and quantification. A small high affinity ligand, biotin, was covalently attached to loop 6 of OmpG and used to capture biotin-binding proteins. …
The Effect Of Management Practices On Bacterial, Fungal, And Nematode Communities On Cool Season Turfgrass, Elisha Allan-Perkins
The Effect Of Management Practices On Bacterial, Fungal, And Nematode Communities On Cool Season Turfgrass, Elisha Allan-Perkins
Doctoral Dissertations
Golf courses comprise 50 million acres in the United States of highly managed turf susceptible to abiotic and biotic stressors. A growing area of interest is utilizing microbes to improve plant growth, increase disease and stress tolerance, and reduce pathogens. In order to develop these new practices, we must gain an understanding of turfgrass microbial communities and how they are affected by management practices. We characterized bacteria, fungi, and nematodes on three golf courses: one organic, one with reduced inputs, and one conventional. We took samples from three management areas on each course representing different management intensities (roughs, fairways, and …
Bacterial Diversity And Function Within An Epigenic Cave System And Implications For Other Limestone Cave Systems, Kathleen Merritt Brannen-Donnelly
Bacterial Diversity And Function Within An Epigenic Cave System And Implications For Other Limestone Cave Systems, Kathleen Merritt Brannen-Donnelly
Doctoral Dissertations
There are approximately 48,000 known cave systems in the United States of America, with caves formed in carbonate karst terrains being the most common. Epigenic systems develop from the downward flow of meteoric water through carbonate bedrock and the solutional enlargement of interconnected subsurface conduits. Despite carbonate karst aquifers being globally extensive and important drinking water sources, microbial diversity and function are poorly understood compared to other Earth environments. After several decades of research, studies have shown that microorganisms in caves affect water quality, rates of carbonate dissolution and precipitation, and ecosystem nutrition through organic matter cycling. However, limited prior …
Engineering Novel Detection And Treatment Strategies For Bacterial Therapy Of Cancer, Jan T. Panteli
Engineering Novel Detection And Treatment Strategies For Bacterial Therapy Of Cancer, Jan T. Panteli
Doctoral Dissertations
Finding and treating cancer is difficult due to limited sensitivity and specificity of current detection and treatment strategies. Many chemotherapeutic drugs are small molecules that are limited by diffusion, making it difficult to reach cancer sites requiring high doses that lead to systemic toxicity and off-target effects. Tomographic detection techniques, like PET, MRI and CT, are good at identifying macroscopic lesions in the body but are limited in their ability to detect microscopic lesions. Biomarker detection strategies are extremely sensitive and able to identify ng/ml concentrations of protein, but are poor at discriminating between healthy and disease state levels due …
Genetic And Ecological Characterization Of Indigoidine Production By Phaeobacter Sp. Strain Y4i, William Nathan Cude
Genetic And Ecological Characterization Of Indigoidine Production By Phaeobacter Sp. Strain Y4i, William Nathan Cude
Doctoral Dissertations
The Roseobacter clade is a widely distributed, abundant, and biogeochemically active lineage of marine alpha-proteobacteria. Members of the Roseobacter lineage are prolific surface colonizers in marine coastal environments, and antimicrobial secondary metabolite production has been hypothesized to provide a competitive advantage in colonization. In this work, Phaeobacter sp. strain Y4I was found to produce the water soluble, blue pigment indigoidine via a nonribosomal peptide synthase-based biosynthetic pathway encoded by a novel series of genetically linked genes, termed igiBCDFE. Comparison of wildtype, non-pigmented, and hyper-pigmented Y4I insertional mutants demonstrated a perfect correlation between indigoidine production and the inhibition of Vibrio …
Validating Approaches For Studying Microbial Diversity To Characterize Communities From Roots Of Populus Deltoides, Migun Shakya
Validating Approaches For Studying Microbial Diversity To Characterize Communities From Roots Of Populus Deltoides, Migun Shakya
Doctoral Dissertations
Microbial (archaeal, bacterial, and fungal) communities associated with plant roots are central to its health, survival, and growth. However, a robust understanding of root microbiota and the factors that govern their community structure and dynamics have remained elusive, especially in mature perennial plants from natural settings. Although the advent of Next Generation Sequencing (NGS) technologies have changed the scale of microbial ecological studies by enabling exhaustive characterization of microbial communities, the accuracy of taxonomic and quantitative inferences are affected by multiple experimental and computational steps and lack of knowledge of the true ecological diversity. To test for inaccuracies and biases, …
Microbial Community Structure And Ecosystem Function In A Changing World, Melissa Ann Cregger
Microbial Community Structure And Ecosystem Function In A Changing World, Melissa Ann Cregger
Doctoral Dissertations
Understanding the effects climate change will have on the structure and function of global ecosystems is a pressing ecological and social issue. Global change driven changes in atmospheric warming and precipitation régimes have begun to alter the distribution of plants and animals in, as well as the function of, ecosystems. Using two large-scale climate change manipulations, I assessed the effect of changing precipitation and temperature regimes on soil microbial community structure and function. Soil microbial communities regulate decomposition and nutrient cycling rates in ecosystems, thus understanding their response to climatic changes will enable scientists to better predict carbon feedbacks to …