Doctor of Philosophy

dissertationSepsis is a life-threatening systemic inflammatory condition that is characterized by a high degree of patient heterogeneity, making it notoriously difficult to diagnose and treat. Among the most common and lethal causes of sepsis are strains of Extraintestinal Pathogenic Escherichia coli (ExPEC). These genetically diverse pathogens are becoming increasingly problematic due to the rise of multidrug resistant strains. During sepsis, the infecting microbes are commonly viewed as generic inducers of inflammation, while the host background is considered the primary variable affecting disease progression and outcome. My doctoral research challenges this assumption and establishes a novel zebrafish embryo infection model to study the effects of ExPEC strain differences on the maladaptive immune responses that are induced during sepsis. Zebrafish embryos infected with ExPEC isolates display many of the key pathophysiological features seen in human septic patients, including dysregulated inflammatory responses (cytokine storms), tachycardia, and endothelial leakage. Mirroring what is seen in human patients, antibiotic therapy reduces bacterial titers in infected embryos and improves host survival rates, but is only effective within limited time frames, and surviving animals often develop lasting edema and other defects. Intriguingly, genetically distant ExPEC isolates stimulate markedly different host responses, including disparate levels of inflammatory (e.g., IL-1 β, TNF-α) and immunomodulatory (e.g., IL-10) mediators. These variances are attributable to differential activation of TLR5 by these strains, which vary in the levels and the serotypes of flagellin that they express. To examine the specific effects of IL-10 on disease progression, I created and begun to characterize engineered gene knockout and inducible transgenic zebrafish lines for this cytokine. Altogether, my graduate research establishes zebrafish as a relevant model for studying sepsis and highlights the ability of genetically distinct ExPEC isolates to induce divergent host responses independent of baseline host attributes and implicates bacterial flagellin as a key mediator of inflammation during sepsis

Dynamin2- and endothelial nitric oxide synthase–regulated invasion of bladder epithelial cells by uropathogenic Escherichia coli

eNOS-mediated S-nitrosylation of dynamin2 promotes infection of epithelial cells by E. coli

Doctor of Philosophy

dissertationUropathogenic Escherichia coli (UPEC) cause the overwhelming majority of community-acquired urinary tract infections (UTI) worldwide. A particularly problematic aspect of UPEC-associated UTI is the rate of recurrent infections- one in four UTIs will recur within six months of the initial infection. In the majority of cases, the strain responsible for the primary infection is identical to the strain causing the recurrent infection. Usually, the urinary tract is maintained as a sterile environment by an array of host defenses. Some of the genetic mechanisms by which UPEC cope with or subvert host defenses in order to colonize and persist within the urinary tract is the primary focus of this thesis. I start by exploring the effects of global metabolic and stress response transcriptional regulation on the virulence potential of UPEC within the murine urinary tract. Therein, I better define the metabolic and stress response limitations affecting UPEC colonization of this niche. I then address the advantages of chromosomally encoded toxin-antitoxin systems in allowing for niche-specific colonization of the urinary tract and explore how these small genetic elements can specifically affect the stress resistance and antibiotic persistence of UPEC. This work, specifically, identifies a novel target for chemotherapeutic agents that would theoretically home in on and hinder only uropathogenic subsets of E. coli, combating UTI while leaving commensal E. coli iv unphazed. Lastly, I attempt to better understand the generation of UPEC stress resistance by studying the evolutionarily conserved genomic rearrangement of chromosomally encoded toxin-antitoxin hicAB within these pathogens. I found that constructing this evolutionarily conserved hicAB truncation within the ancestral E. coli MG1655 promotes serum resistance and survival of this characteristically nonpathogenic strain of E. coli within the blood of a murine host. Furthermore, ancestral strains carrying this truncated allele are, in general, more resistant to stress than their unevolved counterparts. In total, this body of work better defines the stress resistance and persistence capacities of UPEC

Reordering for Improved Constrained Reconstruction from Undersampled k-Space Data

Recently, there has been a significant interest in applying reconstruction techniques, like constrained reconstruction or compressed sampling methods, to undersampled k-space data in MRI. Here, we propose a novel reordering technique to improve these types of reconstruction methods. In this technique, the intensities of the signal estimate are reordered according to a preprocessing step when applying the constraints on the estimated solution within the iterative reconstruction. The ordering of the intensities is such that it makes the original artifact-free signal monotonic and thus minimizes the finite differences norm if the correct image is estimated; this ordering can be estimated based on the undersampled measured data. Theory and example applications of the method for accelerating myocardial perfusion imaging with respiratory motion and brain diffusion tensor imaging are presented

Foetal echocardiographic segmentation

Congenital heart disease affects just under one percentage of all live births [1]. Those defects that manifest themselves as changes to the cardiac chamber volumes are the motivation for the research presented in this thesis. Blood volume measurements in vivo require delineation of the cardiac chambers and manual tracing of foetal cardiac chambers is very time consuming and operator dependent. This thesis presents a multi region based level set snake deformable model applied in both 2D and 3D which can automatically adapt to some extent towards ultrasound noise such as attenuation, speckle and partial occlusion artefacts. The algorithm presented is named Mumford Shah Sarti Collision Detection (MSSCD). The level set methods presented in this thesis have an optional shape prior term for constraining the segmentation by a template registered to the image in the presence of shadowing and heavy noise. When applied to real data in the absence of the template the MSSCD algorithm is initialised from seed primitives placed at the centre of each cardiac chamber. The voxel statistics inside the chamber is determined before evolution. The MSSCD stops at open boundaries between two chambers as the two approaching level set fronts meet. This has significance when determining volumes for all cardiac compartments since cardiac indices assume that each chamber is treated in isolation. Comparison of the segmentation results from the implemented snakes including a previous level set method in the foetal cardiac literature show that in both 2D and 3D on both real and synthetic data, the MSSCD formulation is better suited to these types of data. All the algorithms tested in this thesis are within 2mm error to manually traced segmentation of the foetal cardiac datasets. This corresponds to less than 10% of the length of a foetal heart. In addition to comparison with manual tracings all the amorphous deformable model segmentations in this thesis are validated using a physical phantom. The volume estimation of the phantom by the MSSCD segmentation is to within 13% of the physically determined volume

Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics

This book is a collection of original research articles in the field of computer-aided drug design. It reports the use of current and validated computational approaches applied to drug discovery as well as the development of new computational tools to identify new and more potent drugs

First Security Corporation v. Belle Ranch, LLC Clerk\u27s Record v. 1 Dckt. 46144

https://digitalcommons.law.uidaho.edu/idaho_supreme_court_record_briefs/8539/thumbnail.jp

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.

Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20th-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6]