Guanosine tetraphosphate (ppGpp) is a bacterial signaling molecule involved in activating the stringent response, a cellular reaction to environmental stress that downregulates cell division and metabolism processes to conserve nutrients. The stringent response is implicated in some instances of antibiotic persistence, so broadening the current understanding of ppGpp signaling is useful. This thesis seeks to generate a ppGpp biosensor that will bind ppGpp and emit fluorescent light in its presence, which will allow for improved research into the pathways and functions of the signaling molecule. To generate a novel ppGpp biosensor, I converted a biosensor previously used to detect cyclic di-GMP (a different signaling molecule) to contain a binding site transformed to now bind specifically with ppGpp. The genetic sequence for the cyclic di-GMP binding site was replaced with the ppGpp hydrolase domain which has a specific affinity for ppGpp; however, hydrolase activity would provide unwanted breakdown of the ppGpp, so it is mutated further to neutralize hydrolase activity. The desired outcome of this thesis results in a biosensor with a binding site that has a specific and sufficient binding affinity for the ppGpp molecule. Using this, we can determine how ppGpp levels are regulated in bacteria under conditions of stress, and how this signaling molecule is related to the survival of bacteria in response to antibiotic treatment.

Background: The incidence of Pseudomonas aeruginosa bacteremia has not been defined in a population-based investigation. Methods: We performed a retrospective, population-based incidence study using resources of the Rochester Epidemiology Project of Olmsted County, Minnesota. We identified all Olmsted County residents with P. aeruginosa bacteremia between January 1, 1997, and December 31, 2006, by microbiology records in the only 2 laboratories in the county. Medical records were reviewed to confirm diagnosis, residency status, and clinical characteristics. Results: Age-adjusted incidence per 100,000 person-years was 10.8 (95% confidence interval [CI], 7.5-14.0) in men and 3.7 (95% CI, 2.2-5.2) in women for total P. aeruginosa bacteremia, and 8.4 (95% CI, 5.5-11.2) in men and 2.5 (95% CI, 1.3-3.8) in women for monomicrobial P. aeruginosa bacteremia. There was no significant change in incidence of total P. aeruginosa bacteremia during the past decade (P = .418). Incidence increased exponentially with age, with a greater magnitude of increase in men compared with women for total and monomicrobial P. aeruginosa bacteremia (P = .007 and P = .015, respectively). In patients with monomicrobial P. aeruginosa bacteremia, the median age was 69 years, and 78.4% of cases were either nosocomial or health care associated. Most patients had multiple comorbid conditions. The urinary tract was the most common primary source of infection. The 28-day all-cause mortality of monomicrobial P. aeruginosa bacteremia was 25.5%. In vitro susceptibility to ciprofloxacin was 95.3%. Conclusion: To our knowledge, this is the first population-based incidence study of P. aeruginosa bacteremia. The incidence of P. aeruginosa bacteremia has remained stable during the past decade. Fluoroquinolone susceptibility is high among local P. aeruginosa bacteremia isolates.

Indiana University-Purdue University Indianapolis (IUPUI) / For regenerative endodontic procedures (REPs) to be successful an elimination of bacteria from the root canal system must be accomplished. Many different medicaments with antibacterial properties have been used to obtain complete disinfection. Double antibiotic paste (DAP) containing a mixture of ciprofloxacin and metronidazole has been shown to be a promising intracanal medicament. The addition of a radiopaque filler such as zirconium oxide to DAP may affect the antibacterial properties of DAP as well as allow precise placement and radiographic visualization of its position in the canal system. The aim of the proposed study was to evaluate the direct antibacterial properties of zirconium oxide radiopacifier combined with DAP (RoDAP) against a multispecies biofilm from a bacterial isolate from an infected immature tooth with a necrotic pulp and a known single species biofilm. 4x4 mm radicular dentin specimens (n = 112) obtained from human extracted teeth were used prepared and sterilized prior to use. A multispecies clinical bacterial isolate from an immature tooth with a necrotic pulp and a single species Enterococcus faecalis isolate were obtained. These bacterial isolates were used to inoculate dentin slabs and grown for 3 weeks. The dentin slabs were treated for 1 week with 1.0-mg/mL and 10- mg/mL RoDAP, 1.0-mg/mL DAP, and two placebo pastes consisting of methyl cellulose (MC) and methyl cellulose combined with zirconium oxide (RoMC), respectively, as well as two no-treatment controls. Following treatment, the grown biofilm was detached and spiral plated. The plated biofilm cells were cultured for 24 hours and each group examined using a colony counter to determine bacterial numbers (CFUs/mL). Data analysis, using a 5.0-percent significance level was conducted using one-way ANOVA followed by pair-wise group comparisons. Both 1.0-mg/mL and 10 mg/mL RoDAP demonstrated significant antibacterial effects against bacterial isolates from an immature tooth with a necrotic pulp as well as an E. faecalis isolate. The precise application of RoDAP confirmed radiographically with its direct antibacterial properties may be beneficial for intracanal disinfection during REPs.

Thesis advisor: Tim van Opijnen / Each year, the opportunistic pathogen Streptococcus pneumoniae causes millions of illnesses and nearly 300,000 deaths worldwide. Despite widespread vaccination campaigns, S. pneumoniae persists as a public health risk in large part to its high genomic diversity. In previous work, our group has shown that functional pathways, including stress response to antibiotics, are not necessarily conserved between pneumococcal strains. Thus, a holistic pangenome view of S. pneumoniae is a promising avenue to gain understanding of the species and to inform clinical treatment methods. Our group has selected 36 strains, covering 78% of known pneumococcal genetic diversity, for S. pneumoniae pangenome studies. We have previously constructed transposon libraries and performed Tn-seq for 22 of these strains in both in vitro and in vivo conditions. From these studies, our group has constructed pangenome profiles of genes essential for reproduction in culture conditions, infection in a mouse model, and attachment in a human nasopharyngeal epithelial cell line. In this study, we develop and execute a pipeline to construct iSP20, a set of in silico metabolic models for 34 S. pneumoniae strains. We employ these models to predict nutrient and metabolic gene essentiality on both the strain and pangenome level, demonstrating that key patterns in the strains’ essentialomes translate to a metabolic context. Additionally, we perform a functional analysis of the metabolic models, revealing a highly connected metabolic genome and essentialome. We uncover differences in the in vitro and in silico core essentialomes and identify potential sources of discrepancy between the two datasets. Overall, this work demonstrates the utility of strain-specific metabolic models in pangenome essentiality studies and provides enhanced understanding of metabolism in S. pneumoniae. / Thesis (BS) — Boston College, 2020. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Departmental Honors. / Discipline: Biology.

No description available.

The effects of dietary antimicrobial removal and Bacillus subtilis supplementation on the growth and intestinal health of male broilers were investigated. Birds were fed either a control, antimicrobial, or a B. subtilis probiotic diet at different feeding phases. Birds were challenged with a 10 × dose of a coccidiosis vaccine. Supplementation of B. subtilis in for antimicrobials in the late grower and early finisher phases improved growth similar to birds fed antimicrobials until withdrawal, while antimicrobial removal without B. subtilis supplementation in those periods hindered growth. The improved growth suggests that the probiotic was able to alleviate the stress of the challenge compared to antimicrobial removal. Processing yields were improved with antimicrobial removal and B. subtilis supplementation in late grower and early finisher phase. Intestinal health was improved with lower intestinal lesions when antimicrobial were removed and B. subtilis supplemented suggesting the reduction of Eimeria species from colonizing the intestine.

Salmonella enterica serovar Typhimurium (Salmonella) is a Gram-negative bacterial pathogen capable of causing both gastroenteritis and bacteraemia in human hosts. During infection, Salmonella invokes a complex network of virulence factors, regulatory systems, and metabolic pathways to promote immune evasion, sometimes demanding antibiotic treatment for resolution. Unfortunately, antibiotic resistance has reached critical levels in this and other pathogens, necessitating the discovery of new anti-infective targets and treatment options. Herein, we have sought to exploit the dynamic interactions between Salmonella and the host immune system to identify new, conditionally active anti-Salmonella therapies. In chapter 2, we aim to identify chemical compounds that are selectively antimicrobial against intracellular Salmonella, and discover that the anxiolytic drug metergoline inhibits Salmonella survival in cultured macrophages and systemically infected mice. In chapter 3, we screen for anti-virulence compounds that target regulatory signaling in Salmonella, and characterize the inhibitory activity of methyl-3,4-dephostatin, which perturbs SsrA/B and PmrB/A signaling and enhances sensitivity to colistin in vitro and in vivo. In chapter 4, we identify several host-directed compounds that modulate macrophage immunity and investigate their ability to attenuate a multidrug resistant Salmonella infection. Together, the work presented in this thesis demonstrates the potential for drug screening in infection-relevant conditions to identify new anti-infectives with non-traditional targets. / Thesis / Doctor of Philosophy (PhD)

No description available.

A novel approach to access N-Aryl nitrones via copper catalyzed coupling of benzyl alcohols with nitrosobenzenes is described. The results of mechanistic studies are conflicting but suggest this reaction proceeds through either redox process or a nucleophilic nitroso hydrate intermediate formed in situ, which was previously unprecedented. The unique electronics of this process allow access to nitrones with excellent step and atom economy, which are otherwise difficult to make using conventional methods. In this work, a total of 22 nitrones have been made. 15 of which from pure starting materials with yields ranging from 26 - 89 % and another 7 from two step, one pot reactions where the nitrosobenzenes were made in situ from commercially available anilines and reacted in a subsequent step to produce the nitrone in 8 - 46 % yield. In addition to the nitrone forming reaction occurring in the second step of a two-step sequence, we have also shown that subsequent reactions can be done on newly formed nitrones in one pot. This was demonstrated with a newly synthesized nitrone and a donor-acceptor cyclopropane in a [3+3] annulation reaction forming the cycloadduct in 90% yield. / Thesis / Master of Science (MSc) / With over 250 000 cases of resistant bacterial infections reported, and more than 5 400 directly causing Canadian deaths in 2018, we are currently facing an antibiotic crisis[67]. A particularly worrying class of resistance involves Gram-negative bacteria, as their highly impermeable outer membrane poses added complexity to their evolved resistance mechanisms[68]. The outer membrane restricts the chemical matter able to cross, making the bacteria intrinsically resistant to small molecule antibiotics and other compounds which may have intracellular targets[69],[70]. This barrier is therefore a major bottleneck for cellular mechanistic studies and compound mechanism of action, as these small molecules cannot gain entry to the cell. To circumvent this issue, outer membrane permeabilizing compounds must be discovered so that these systems can be more effectively studied. Commonly used membrane active compounds such as colistin and its derivatives, interact with both the outer and inner membranes of Gram-negative bacteria, and are toxic to cells[71]. Therefore, molecules that are outer membrane selective and nontoxic to Gram negative bacteria would be useful tools to expedite the study of biological systems.

With the rise of antibiotic resistance, there is ongoing need to find new antibiotics. As bacteria develop resistance to the current classes of antibiotics available, it is imperative to discover new ways to target bacteria. In this thesis, I focused on one of the basic components that all bacteria need to survive: a source of carbon. Here, I explore whether we can exploit this aspect for drug discovery. For bacteria to colonize a host and cause an infection, it must first be able to meet its nutritional needs for growth. Different host infection sites will have different carbon sources available. Some sites, like the gut, will have commensal bacteria which will compete with invading pathogens for carbon sources. While we still lack understanding of the specific growth environment bacteria experience during infection, it is important to understand how bacteria grow when given different nutrients. For the first part of my work, I systematically probed the gene essentiality patterns of E. coli grown in different carbon sources. I generated a large dataset of growth phenotypes that I compiled into a user-friendly web-application, Carbon Phenotype Explorer (CarPE). I identified many poorly annotated genes, and further characterized the gene ydhC as an adenosine transporter. After characterizing how the growth of E. coli and the genes essential for survival change depending on each carbon source, I looked at whether antibiotic efficacy changed depending on the carbon source used. I found that growth in oxaloacetate alters the proton motive force and potentiates macrolide antibiotics. I also found that linezolid, a compound that does not work on gram-negative bacteria due to efflux, is more effective when adenosine is the carbon source. Together, this work forms a foundation for future research into studying how carbon sources can be exploited in the field of antibiotic discovery. / Thesis / Candidate in Philosophy / There is an urgent need for new antibiotics. Previous antibiotic discovery has primarily been conducted on bacteria growing in nutrient rich laboratory conditions. This led to antibiotics that targeted the same few bacterial processes. However, since bacteria need to survive in a host to cause an infection, there are targets that may be viable during an infection that we miss by using standard laboratory media. Bacteria need a source of carbon to survive, and each infection site contains different chemicals that bacteria can use as a source of carbon. My work studies how bacteria grow in the presence of different carbon sources. First, I systematically tested which bacterial genes are required for E. coli to grow in 30 different carbon sources. I then examined the effectiveness of antibiotics on bacteria grown using these different carbon sources. Together, this work helps us understand how changing carbon sources in the growth media we use to cultivate bacteria can change which genes are required and how it may change how bacteria survive antibiotic stress. When we discover the specific compositions of host infection environments, we can leverage this knowledge to find antibiotics that target these carbon acquisition pathways in bacteria.