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Title: Environmental Microbial Surveillance : From Source Tracking in Watersheds to Pathogen Monitoring in Sewersheds
Creator: Flood, Matthew Thomas
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Understanding of the connections between water and health, through the use of water quality monitoring, surveys and surveillance, can help to address the impacts of anthropomorphic changes on the environment. This study sought to understand these connections through the water quality monitoring within watershed basins as well as pathogen surveillance within sewersheds. Specifically, this dissertation sought to 1) understand the sources of pollution and their connections with land use in the...
Show moreUnderstanding of the connections between water and health, through the use of water quality monitoring, surveys and surveillance, can help to address the impacts of anthropomorphic changes on the environment. This study sought to understand these connections through the water quality monitoring within watershed basins as well as pathogen surveillance within sewersheds. Specifically, this dissertation sought to 1) understand the sources of pollution and their connections with land use in the various subsections of watersheds; 2) to find a cost-effective way to surveil the spread of SARS-CoV-2 using wastewater surveillance; and 3) to understand the differences in wastewater surveillance between communities. Water quality monitoring using microbial source tracking (MST) was performed with a survey of five mixed-use watersheds in Michigan. Through the use of spatial clustering, it was found that temporal contamination was primarily driven by precipitation and its associated variables (e.g., streamflow, turbidity, overland flow), while spatial contamination is driven by land uses (e.g., septic tank density, tile drain proportions, and tillage). Additionally, porcine fecal contamination was more often correlated with nutrients in streams than either bovine or human contamination. The development of a cost-effective workflow for the detection and quantification of SARS-COV-2 in wastewater was undertaken. Wastewater from communities around Michigan were collected and analyzed along with viral surrogates for SARS-CoV-2 to investigate different workflow options. The Pseudomonas phage Phi6 was seeded in different wastewater matrices to test concentration and recovery by ultrafiltration-based method and polyethylene glycol (PEG) precipitation. The PEG method provided better virus recovery than the ultrafiltration-based methods as measured using RT-ddPCR. The comparison of two communities (A and B) wastewater results for SARS-CoV-2 analyzed against case data was undertaken. These results were significantly correlated with cases in both communites, but the level of correlation differed based on spatial (e.g., zipcode vs county level cases) and temporal (e.g., date of symptom(s) onset vs. the referral date for cases) resolution. Wastewater surveillance was more representative of higher spatial resolution (zipcode data) of cases in both communities. When examining the temporal resolution of the communities, community B’s wastewater results were more closely tied to the onset of symptoms and not the case referral date. The ability to monitor indicators of pollution in watersheds and surveil etiological agents of disease in sewersheds provide non-intrusive methods for evaluating the potential risks and current burdens to community health. The first part of the work could be considered “downstream” monitoring identifying sources and potential exposures with the goal of reducing waterborne disease. While “upstream” monitoring was used for identifying the disease trends in the community and was focused on public health measures to prevent transmission. This project contributed novel methods, results and analysis providing valuable knowledge ultimately addressing the role of monitoring strategies to protect public health.
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Title: ECOPHYSIOLOGY OF (PERI)ORAL BACTERIA AND IMPACT OF OTIC COLONIZATION
Creator: Jacob, Kristin Marie
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The middle ear is typically assumed to be sterile in health due to its secluded location, closed off from external forces by the tympanic membrane (ear drum) and from the naso/oropharynx by a collapsed Eustachian tube. However, the periodic opening of the Eustachian tube to the naso/oropharyngeal space, which releases pressure across the eardrum and drains otic fluids, could introduce bacteria. Previous studies have tested for the presence of bacteria in the uninfected otic cavity using...
Show moreThe middle ear is typically assumed to be sterile in health due to its secluded location, closed off from external forces by the tympanic membrane (ear drum) and from the naso/oropharynx by a collapsed Eustachian tube. However, the periodic opening of the Eustachian tube to the naso/oropharyngeal space, which releases pressure across the eardrum and drains otic fluids, could introduce bacteria. Previous studies have tested for the presence of bacteria in the uninfected otic cavity using samples collected via invasive surgeries (through or around the eardrum). Findings from these studies are controversial due to contradictory results between studies, lack of critical experimental controls, and sampling of participants with underlying ailments (i.e., cochlear implant surgery) that could impact the microbiology of the otic mucosa. The studies reported herein bypass these limitations by using samples of otic secretions collectively non-invasively (through the mouth) in a cohort of healthy young adults. This dissertation describes cultivation-dependent methods to investigate the microbiology of the middle ear in health. The study used an IRB-approved protocol (#17-502) to collect otic secretions in order to 1) sequence their microbiome (contribution by Dr. Joo-Young Lee) and 2) recover in pure culture otic bacteria for further characterization (my contribution). As controls, we also collected buccal (top palate and inside of cheeks) and oropharyngeal swabs from each participant. Of the collected secretions, samples from 19 individuals were used for culture independent studies, while samples from the remaining 3 participants were subjected to culture dependent studies. 16S rRNA-V4 sequencing detected a diverse and distinct microbiome in otic secretions comprised primarily of strictly anaerobic bacteria belonging to the phyla Bacteroidetes, Firmicutes and Fusobacteria, and to a lesser extent facultative anaerobes (Streptococcus). I recovered from the otic, oropharyngeal, and buccal secretions 39 isolates of predominantly facultative anaerobes belonging to Firmicutes (Streptococcus and Staphylococcus), Actinobacteria (Micrococcus and Corynebacterium), and Proteobacteria (Neisseria) phyla, and used partial 16S rRNA amplicon sequences to demonstrate the distinct phylogenetic placement of otic streptococci compared to the oral ancestors (Chapter 2). This finding is consistent with the ecological diversification of oral streptococci once in the middle ear microenvironment. The recovery of streptococci and transient migrants (Staphylococcus, Neisseria, Micrococcus and Corynebacterium) from otic secretions prompted us to study the adaptive responses that give the streptococcal migrants a competitive advantage during the colonization of the middle ear (Chapter 3). For these studies, I sequenced and partially assembled the genomes of the otic isolates and used the full length 16S rRNA sequences for taxonomic demarcation at the species levels. Phylogenetic analyses demonstrated the oral ancestry of the otic streptococci, which retained from the otic adaptive traits critical for growth and reproduction in the middle ear mucosa (biofilm formation, mucolytic and proteolytic activity, robust growth under redox fluctuations, and fermentative production of lactate, a key metabolic intermediate in the otic trophic webs). These adaptive traits give oral streptococci a colonization advantage over competing (peri)oral migrants such as Staphylococcus. Furthermore, the otic streptococci inhibited the growth of otopathogens, including Staphylococcus aureus. These antagonistic interactions give streptococci a competitive advantage during the colonization of the middle ear and suggest a role for these commensals in promoting mucosal health. The ability of staphylococcal migrants to breach the middle ear mucosal barrier and cause infections prompted us to study the environmental factors that facilitate the spreading of staphylococci from the nasal to the middle ear mucosa. Allergies, respiratory maladies (cold, flu), or (peri)oral bacterial infections (sinus, adenoids, tonsils, etc.) lead to inflammation of the Eustachian tube and changes in the rheological properties of the otic mucus that increase the risk of infections. Thus, we examined the spreading of staphylococci on mucus-like viscous surfaces (semisolid agar plates). In Chapter 4, I show that mucins, the mucosal glycoproteins that control the viscosity and wettability of the mucus layer, induce the rapid spreading and dendritic expansion of clinical isolates closely related to S. aureus and Staphylococcus epidermidis but not of Staphylococcus hominis. Mucin glycosylation controlled the hydration of the mucoid surface and the ability of the cells to spread rapidly, in a process that was dependent on the secretion of surfactant-active, phenol-soluble modulins via the agr-quorum sensing two-component system. These results provide a plausible explanation for the rapid spreading of staphylococcal otopathogens from the nasopharynx to the middle ear through a swollen, and mucin-rich Eustachian tube. The work described in this dissertation provides much needed understanding of the adaptive responses that allow (peri)oral bacteria to colonize the middle ear. The studies add to the accumulating evidence that the middle ear mucosa is not sterile but rather harbors a commensal microbiota in health. These commensal community shares many metabolic similarities with ancestors in oral biofilms and retain adaptive traits critical for growth in the otic mucosa and inhibition of otopathogens. Additionally, this work identifies environmental factors that could contribute to staphylococcal virulence, broadening the understanding of newly identified motility phenotypes in the genus that could provide novel pharmaceutical targets.
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Title: UNDERSTANDING DRIVERS OF PLANT MICROBIOME IN MICHIGAN AGRICULTURE : STUDIES OF THE APPLE ROOT ZONE AND COMMON BEAN SEEDS
Creator: Bintarti, Ari Fina
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Plant-associated microbial communities are crucial for plant health and fitness, and may enhance plant tolerance to various environmental stresses. As global climate change threatens crop production and increases demands on sustainable agriculture, harnessing the plant microbiome has become one potential strategy to address these issues. Thus, it is fundamental to understand the relative contributions of both the host plant as well as the environment in shaping the plant microbiome. Moreover,...
Show morePlant-associated microbial communities are crucial for plant health and fitness, and may enhance plant tolerance to various environmental stresses. As global climate change threatens crop production and increases demands on sustainable agriculture, harnessing the plant microbiome has become one potential strategy to address these issues. Thus, it is fundamental to understand the relative contributions of both the host plant as well as the environment in shaping the plant microbiome. Moreover, the response of plant microbiomes to stress and any consequences of microbiome stress responses for the host plants are poorly understood, though this information is critical to achieve a basis of knowledge for plant microbiome engineering. My research aimed to contribute to this knowledge by investigating the factors that structure root- and seed-associated microbial communities of two valuable crops for Michigan’s agricultural economy: apple and common bean. The first chapter of my dissertation aimed to assess the biogeography of bacterial, archaeal, fungal, and nematode communities in the root zone of apple trees, and to determine their relationships with each other and their changes over natural abiotic gradients across orchards. I also assessed the influence of plant cultivar on microbiome structure in the root zone. I found that root zone microbiome community structure was strongly affected by geographic location and edaphic properties of soil. The next chapter of my dissertation investigated the variability of seed endophyte community of common bean (Phaseolus vulgaris L.). My results showed that plant-to-plant variability under controlled growth conditions exceeded within-plant variability among seeds from different pods. My study developed protocols and added insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems. The last chapter assessed the responses of common bean seed endophytes to drought stress in the field across two growing locations and four genotypes of common bean. To summarize, this work advances foundational knowledge of the seed microbiome as a critical component of the plant microbiome, and in the context of two key crops for Michigan agriculture.
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Title: Molecular epidemiology, pangenomic diversity, and comparative genomics of Campylobacter jejuni
Creator: Rodrigues, Jose Alexandre
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the United States, is often resistant to commonly used antibiotics and has been classified as a serious threat to public health. Through this work, we sought to evaluate infection trends, quantify resistance frequencies, identify epidemiological factors associated with infection, and use whole-genome sequencing (WGS) as well as comparative phylogenomic and pangenomic approaches to understand circulating C. jejuni...
Show moreCampylobacter jejuni, the leading cause of bacterial gastroenteritis in the United States, is often resistant to commonly used antibiotics and has been classified as a serious threat to public health. Through this work, we sought to evaluate infection trends, quantify resistance frequencies, identify epidemiological factors associated with infection, and use whole-genome sequencing (WGS) as well as comparative phylogenomic and pangenomic approaches to understand circulating C. jejuni populations in Michigan. C. jejuni isolates (n=214) were collected from patients via an active surveillance system at four metropolitan hospitals in Michigan between 2011 and 2014. Among the 214 C. jejuni isolates, 135 (63.1%) were resistant to at least one antibiotic. Resistance was observed for all nine antibiotics tested yielding 11 distinct resistance phenotypes. Tetracycline resistance predominated (n=120; 56.1%) followed by resistance to ciprofloxacin (n= 49; 22.9%), which increased from 15.6% in 2011 to 25.0% in 2014. Notably, patients with ciprofloxacin resistant infections were more likely to report traveling in the past month (Odds Ratio (OR): 3.0; 95% confidence interval (CI): 1.37, 6.68) and international travel (OR: 9.8; 95% CI: 3.69, 26.09). To further characterize these strains, we used WGS to examine the pangenome and investigate the genomic epidemiology of this set of C. jejuni strains recovered from Michigan patients. Among the 214 strains evaluated, 83 unique multilocus sequence types (STs) were identified that were classified as belonging to 19 previously defined clonal complexes (CCs). Core-gene phylogenetic reconstruction based on 615 genes identified three clades, with Clade I comprising six subclades (IA-IF) and predominating (83.2%) among the strains. Because specific cattle-associated STs, such as ST-982, predominated among strains from Michigan patients, we also examined a collection of 72 C. jejuni strains from cattle recovered during an overlapping time period by WGS. Several phylogenetic analyses demonstrated that most cattle strains clustered separately within the phylogeny, but a subset clustered together with human strains. Hence, we used high quality single nucleotide polymorphism (hqSNP) profiling to more comprehensively examine those cattle and human strains that clustered together to evaluate the likelihood of interspecies transmission. Notably, this method distinguished highly related strains and identified clusters comprising strains from both humans and cattle. For instance, 88 SNPs separated a cattle and human strain that were previously classified as ST-8, while the human and cattle derived ST-982 strains differed by >200 SNP differences. These findings demonstrate that highly similar strains were circulating among Michigan patients and cattle during the same time period and highlight the potential for interspecies transmission and diversification within each host. In all, the data presented illustrate that WGS and pangenomic analyses are important tools for enhancing our understanding of the distribution, dissemination, and evolution of specific pathogen populations. Combined with more traditional phenotypic and genotypic approaches, these tools can guide the development of public health prevention and mitigation strategies for C. jejuni and other foodborne pathogens.
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Title: Characterization of Broadly Conserved AvcID Toxin-Antitoxin System and Its Mechanism to Inhibit Phage by Disrupting Nucleotide Metabolism
Creator: Hsueh, Brian Yifei
Date: 2022
Collection: Electronic Theses & Dissertations
Description: ABSTRACTCHARACTERIZATION OF BROADLY CONSERVED AVCID TOXIN-ANTITOXIN SYSTEM AND ITS MECHANISM TO INHIBIT PHAGE BY DISRUPTING NUCLEOTIDE METABOLISMByBrian Yifei HsuehThe prevalence of antiphage defense systems, which have recently been shown to be located on mobile genetic elements in bacteria, have sparked interest to understand the coevolutionary arms race of bacteria and bacteriophage (phage). Bacteria and phages have coexisted for billions of years, and phages are widely distributed in...
Show moreABSTRACTCHARACTERIZATION OF BROADLY CONSERVED AVCID TOXIN-ANTITOXIN SYSTEM AND ITS MECHANISM TO INHIBIT PHAGE BY DISRUPTING NUCLEOTIDE METABOLISMByBrian Yifei HsuehThe prevalence of antiphage defense systems, which have recently been shown to be located on mobile genetic elements in bacteria, have sparked interest to understand the coevolutionary arms race of bacteria and bacteriophage (phage). Bacteria and phages have coexisted for billions of years, and phages are widely distributed in different environmental niches populated by their bacterial hosts, including the human intestine and marine environment. The evolutionary pressure imposed by phages have led bacteria to evolve diverse strategic systems to protect themselves from phage predation, including CRISPR-Cas, restriction-modification, and abortive infection. Recent studies have begun to reveal that toxin-antitoxin (TA) system are associated with antiphage defense systems. Vibrio cholerae El Tor, the causative agent of current cholera pandemics, has acquired two unique genomic islands of unknown origins, known as Vibrio Seventh Pandemic Islands 1 & 2 (VSP-1 & 2). It is hypothesized that the acquisition of VSP islands increase environmental fitness of El Tor. While both islands encode approximately 36 open reading frames, yet many remain largely uncharacterized. In this work, I characterize a novel TA antiphage system encoded on VSP-1 of V. cholerae, here named AvcID. Chapter 2 describes the biological function of AvcD toxin by which it possesses deoxycytidylate deaminase (DCD) activity and produces dUMP as the final product. Further experiments identify the AvcI antitoxin as a small RNA and determine that it post-translationally inhibits the activity of AvcD. Moreover, AvcD consists of two domains—a N-terminal P-loop NTPase and a C-terminal DCD—and mutations in conserved features of each domain abrogate its activity. AvcD is widely conserved across kingdoms, and virtually all bacteria that encode AvcD also have AvcI homologs. Notably, chromosomal AvcID can solely be activated by transcriptional shutoff in V. cholerae, demonstrating that AvcID is a type III TA system. Unlike canonical type III TA systems, in which the toxin is an endoribonuclease, the AvcD toxin is a deaminase. Importantly, the AvcID system provides antiphage defense in Escherichia coli that lacks this system by corrupting nucleotides for phages to utilize to reduce coliphage replication efficiency. In Chapter 3, I explore the activation mechanism of the AvcID system as well as the consequences to phages after encountering AvcID. During infection, virtually all lytic phages induce transcription shutoff of the host by hijacking host transcription machinery to make virion progeny. I uncover that phage-induced transcriptional shutoff leads to turnover of labile AvcI antitoxin and concomitantly activates the deaminase activity of AvcD, leading to a disruption of nucleotide levels. This disruption of nucleotide levels is shown in both susceptible phages (ex. T5) and resistant phages (ex. T7). Through an unknown mechanism, AvcID also increases the abundance of defective phages that are susceptible to AvcID. In summary, this work has made contributions in the field of TA systems and its association with the antiphage defense paradigm by uncovering the biological function and mechanism in response to phage infection.
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Title: DISRUPTIONS IN HEPATIC ONE CARBON METABOLISM AND THE GUT MICROBIOME DURING THE PROGRESSION OF NON-ALCOHOLIC FATTY LIVER DISEASE
Creator: Fling, Russell Ryan
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The etiology of non-alcoholic fatty liver disease is complex, with multiple contributing factors including dietary, environmental, gut microbiome and genetic mechanisms. Accumulating evidence suggests exposure to polychlorinated dibenzo-p-dioxins and similar compounds may increases risk for NAFLD development. These environmentally persistent dioxin-like compounds bind and activate the aryl hydrocarbon receptor, a transcription factor that regulates intestinal homeostasis, xenobiotic and...
Show moreThe etiology of non-alcoholic fatty liver disease is complex, with multiple contributing factors including dietary, environmental, gut microbiome and genetic mechanisms. Accumulating evidence suggests exposure to polychlorinated dibenzo-p-dioxins and similar compounds may increases risk for NAFLD development. These environmentally persistent dioxin-like compounds bind and activate the aryl hydrocarbon receptor, a transcription factor that regulates intestinal homeostasis, xenobiotic and central metabolism. In a AhR-dependent manner, mice orally gavaged with 2,3,7,8-tetracholordibenzo-p-dioxin (TCDD) exhibit steatosis progressing to steatohepatitis with fibrosis akin to NAFLD progression. NAFLD and hepatocellular carcinoma (HCC) is also closely correlated with dysregulation of central metabolism e.g., hepatic one carbon metabolism (OCM), and gut dysbiosis contributing to NAFLD progression and worsening prognosis. This report investigates mechanisms involved in the dysregulation of the gut microbiome and OCM associated pathways relevant to NAFLD progression through comparisons of molecular analyses of TCDD-treated mice to human NAFLD and HCC. OCM describes the biosynthesis, homeostasis, and utilization of the cell’s main methyl donor, S-adenosylmethionine (SAM) including high flux anabolic biosynthesis of polyamines, phosphatidylcholine and creatine. In later stages of NAFLD, OCM is dysregulated with altered OCM gene expression as well as SAM and s-adenosylhomocysteine (SAH) levels. To assess TCDD-elicited effects on OCM, mice were orally gavaged with TCDD every 4 days for 28 days. Serum and livers collected at early (8 days) and late (28 days) time points were subjected to metabolomic analyses with integration of chromatin immunoprecipitation sequencing, transcriptomics and protein levels. Results from these studies suggest AhR-mediated repression of OCM required prolonged repeated TCDD-treatment and indirect effects elicited by AhR activation e.g., oxidative stress. Gut dysbiosis with disrupted enterohepatic bile acid metabolism is commonly associated with NAFLD and recapitulated in TCDD-treated mice. Similar to NAFLD, TCDD also increases systematic levels of secondary bile acids. These microbial transformed secondary bile acids are involved in modulation of host bile acid signaling pathways relevant to NAFLD. To investigate the effects of TCDD on the gut microbiota, the cecum contents of TCDD-treated mice were subjected to shotgun metagenomic sequencing. Taxonomic analysis identified dose-dependent increases in Lactobacillus species, notably Lactobacillus reuteri. Top enriched species were also associated with increased abundances of bile salt hydrolase sequences, responsible for the initial deconjugation reaction in secondary bile acid metabolism. L. reuteri levels were also attributed to enrichment of mevalonate-dependent isopentenyl diphosphate (IPP) biosynthesis genes, a pathway that was also elevated in cirrhosis patients. These results extend the role of Lactobacilli in the AhR/intestinal axis and NAFLD progression as well as highlight the similarities between TCDD-elicited phenotypes in mice to human NAFLD. Collectively, these studies evaluated TCDD-elicited mechanisms involved in disruptions in host and microbial metabolism, highlighting the AhR’s role in NAFLD progression.
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Title: Interactions Between Plasma and Material Surfaces for Sterilization and Impurity Adsorption
Creator: Mackinder, Madeline Ann
Date: 2022
Collection: Electronic Theses & Dissertations
Description: As the worldwide population increases, maintaining a standard of public health becomes more critical. Two major concerns in this area are nosocomial infections (NI) and water contamination. Current processes in sterilization and water treatment have limitations that could be overcome using plasma techniques. The unique characteristics of plasma make it a promising alternative for energy-intensive processes. This work investigated the characteristics of plasma that have the greatest impact on...
Show moreAs the worldwide population increases, maintaining a standard of public health becomes more critical. Two major concerns in this area are nosocomial infections (NI) and water contamination. Current processes in sterilization and water treatment have limitations that could be overcome using plasma techniques. The unique characteristics of plasma make it a promising alternative for energy-intensive processes. This work investigated the characteristics of plasma that have the greatest impact on sterilization and the reactivation of activated carbon. Previous studies have researched the physical and chemical surface properties of biochar but have not been able to establish an efficient process to activate biochar with desired characteristics. Plasma treatment would offer a way to etch the surface of biochar and specifically functionalize the surface. Successfully activating biochar would increase its adsorption ability and enable its use for water treatment. This project aims to harness these plasma properties and use plasmas to address three important topics related to public health: sterilization of surfaces, modulating commercial activated carbon (AC), and activations of biochar.Cold plasma sterilization offers an efficient way to sterilize medical components and instruments without the risk of deformation to heat-sensitive materials. This paper reports the use of magnetized plasma to realize low-temperature sterilization. A radio frequency dielectric barrier discharge was created in a quartz tube using a mixture of argon and oxygen gas. Glass slides inoculated with a uniform amount of Escherichia coli were exposed to the plasma afterglow at different pressures with and without a magnetic field. A global model was developed to evaluate the magnetically enhanced dielectric barrier discharges and predict species densities. Optical emission spectroscopy identified the plasma species present and validated the model. The magnetic field significantly promoted the intensity of the plasma and the sterilization efficiency. A process gas pressure of 100 mTorr presented the most effective treatment with a sterilization time less than one minute and sample temperature below 32 °C. The effects of O2 plasma on the adsorption capacity of activated carbon (AC) was investigated by varying treatment times. Transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and Zeta potential were used to characterize the surface properties of the AC. The carbon was then applied to remove methylene blue (MB) from an aqueous solution. The adsorption kinetics and isotherm were also studied. Results showed that pseudo-second-order kinetics was the most suitable model for describing the adsorption of MB onto AC. Equilibrium data were well fitted to the Freundlich and Langmuir isotherm models. The highest adsorption capacity resulted from 4 minutes of O2 plasma treatment. This work shows that activation of AC by plasma can open the micropore and increase the effectiveness of chemical removal.Biochar was activated using a combination of O2 plasma and KOH. The adsorption capacity was investigated for different O2 plasma treatment times, KOH concentrations, and treatment temperatures. The adsorption capacity of methylene blue (MB) by the plasma activated biochar was evaluated. The adsorption kinetics and isotherm were also investigated. Results showed that pseudo-second-order kinetics was the most suitable model for describing the adsorption of MB onto biochar. Both the Freundlich and Langmuir isotherm models fit the equilibrium data. The highest adsorption capacity resulted from 10\% KOH + 300 °C for 5 minutes. This work shows that activation of biochar by plasma can improve adsorption capacity. The plasma treated AC and the plasma activated biochar were applied to the removal of PFOA. It was demonstrated that plasma treatment can improve PFOA adsorption. The negative surface charge was shown to negatively impact PFOA adsorption which aligns with the hypothesis that PFOA would preferentially adsorb onto more positive surfaces due to its anionic state in water.
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Title: MEMBRANE-LOCALIZED TRANSCRIPTION REGULATORS : UNDERSTANDING POST-TRANSLATIONAL REGULATION AND SINGLE-MOLECULE DYNAMICS OF TCPP IN VIBRIO CHOLERAE
Creator: Demey, Lucas Maurice
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Vibrio cholerae is a Gram-negative gastrointestinal pathogen that has evolved an elegant regulatory system to precisely time production of essential virulence factors. A key step in this regulatory system is the transcription of a soluble AraC-like transcription factor, ToxT. ToxR and TcpP, two membrane-localized transcription regulators (MLTRs), positively regulate toxT. Much work has contributed to our understanding of TcpP and ToxR regulation, yet major gaps remain in our knowledge of...
Show moreVibrio cholerae is a Gram-negative gastrointestinal pathogen that has evolved an elegant regulatory system to precisely time production of essential virulence factors. A key step in this regulatory system is the transcription of a soluble AraC-like transcription factor, ToxT. ToxR and TcpP, two membrane-localized transcription regulators (MLTRs), positively regulate toxT. Much work has contributed to our understanding of TcpP and ToxR regulation, yet major gaps remain in our knowledge of these MLTRs. MLTRs are unique one-component signal transduction systems because they respond to extracellular stimuli by influencing gene transcription from their location in the cytoplasmic membrane. In Chapter 2, I explore the prevalence and diversity of MLTRs within prokaryotes to enhance our understanding of TcpP and ToxR. I show that MLTRs are far more common among prokaryotes than previously anticipated and that MLTRs are an understudied class of transcription regulators. In Chapter 3, I describe the use of super-resolution single-molecule tracking to investigate how TcpP, a model MLTR, identifies the toxT promoter. I provide evidence that TcpP binds to the toxT promoter independent of ToxR, and TcpP transitions to a specific diffusion state. The data support the first biophysical model for how TcpP-like MLTRs locate their target promoters. TcpP is subject to a form of post-translational regulation known as regulated intramembrane proteolysis (RIP). RIP of TcpP results in its complete inactivation, resulting in loss of virulence factor production. TcpH inhibits RIP of TcpP under certain pH and temperature conditions. In Chapter 4, I describe the mechanism TcpH employs to inhibit TcpP RIP while V. cholerae is present in the mouse gastrointestinal tract. I demonstrate that the dietary fatty acid α-linolenic acid enhances inhibition. I also show that α-linolenic acid promotes TcpH-mediated inhibition of TcpP RIP by increasing association of both proteins with detergent-resistant membrane (DRM) domains. My work provides the first evidence that DRMs influence virulence factor transcription in V. cholerae and that a dietary fatty acid promotes V. cholerae pathogenesis.
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Title: DEVELOPMENT OF 3D BIOACTIVE AND ANTIBACTERIAL SILICATE-BASED SCAFFOLDS FOR BONE TISSUE REGENERATION IN LOAD-BEARING APPLICATIONS
Creator: Marsh, Adam Christoph
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Current gold-standard approaches to addressing the needs of bone defects in load-bearing applications entail the use of either autographs or allographs. Both solutions, however, are imperfect as both autographs and allographs carry the risk of additional trauma, threat of disease transmission, and potential donor rejection respectively. Porous 3D scaffolds are attractive alternatives, illuminating a potential path towards achieving the ideal scaffold for targeting bone tissue regeneration in...
Show moreCurrent gold-standard approaches to addressing the needs of bone defects in load-bearing applications entail the use of either autographs or allographs. Both solutions, however, are imperfect as both autographs and allographs carry the risk of additional trauma, threat of disease transmission, and potential donor rejection respectively. Porous 3D scaffolds are attractive alternatives, illuminating a potential path towards achieving the ideal scaffold for targeting bone tissue regeneration in load-bearing applications, usurping autographs to become the new gold-standard. To unlock the full healing potential of 3D scaffolds, such scaffolds must be multifunctional such that (1) their mechanical performance meets the requisite requirements as dictated by the mechanical performance characteristics of interest for native bone tissue, (2) they stimulate the necessary biological responses for bone tissue regeneration, and (3) they exhibit antibacterial characteristics to combat the threat of infection. To date, no reports document 3D scaffolds exhibiting all three performance characteristics. The aim of this dissertation, therefore, is to deliver 3D scaffolds that are mechanically competent, possess and exhibit inherent and advanced antibacterial characteristics, and are successful at providing the needed biological characteristics for bone tissue regeneration. To achieve this, this dissertation implements a multidisciplinary approach, utilizing comprehensive structural characterization across a wide range of scales to elucidate process – performance relationships to execute scientifically driven modifications to engineer and deliver a 3D scaffold to successfully target bone tissue regeneration in load-bearing applications. A silver-doped bioactive glass-ceramic (Ag-BG) composition was selected as the material for scaffold synthesis due to its inherent and attractive antibacterial and biological performance characteristics. Two fundamentally different processing approaches were utilized for synthesizing Ag-BG scaffolds: the polymer foam replication technique and fused filament fabrication (FFF). The Ag-BG scaffolds studied herein were found to exhibit advanced antibacterial performance characteristics against methicillin-resistant Staphylococcus aureus (MRSA), a common pathogen implicated in osteomyelitis development, able to combat MRSA both in planktonic and biofilm forms. Ag-BG scaffolds demonstrated the ability to form an apatite-like layer when immersed in simulated body fluid (SBF), an indicator that Ag-BG scaffolds will induce the necessary mineralization for bone tissue regeneration, in addition to exhibiting attractive cell viability, proliferation, and differentiation characteristics when studied in vitro. The mechanical performance of Ag-BG scaffolds reported herein saw progressive improvements in each iteration of Ag-BG scaffold synthesis, achieving desirable mechanical competency and reliability as a result of the multidisciplinary approach formulated. In addition to the exploration of developing 3D antibacterial and biological silicate-based scaffolds capable of targeting bone tissue regeneration in load-bearing applications, foundational work towards the development of class II hybrid scaffolds comprised of gelatin methacryloyl (GelMA) and Ag-BG for targeting softer tissue regeneration. The novel syntheses applied to the successful molecular coupling of GelMA and Ag-BG presents an attractive class II hydrogel showing great promise as a compatible ink for 3D bioprinting cell-laden scaffolds capable of targeting tissue regeneration of more sophisticated systems.
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Title: CARBON-MEDIATED ECOLOGICAL AND PHYSIOLOGICAL CONTROLS ON NITROGEN CYCLING ACROSS AGRICULTURAL LANDSCAPES
Creator: Curtright, Andrew James
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The sustainable intensification of agriculture relies on the efficient use of ecosystem services, particularly those provided by the microbial community. Managing for these ecosystem services can improve plant yields and reduce off-site impacts. For instance, increasing plant diversity is linked to positive effects on yield, and these beneficial effects are often mediated by the microbial community and the nutrient transformations it carries out. My dissertation has aimed to elucidate the...
Show moreThe sustainable intensification of agriculture relies on the efficient use of ecosystem services, particularly those provided by the microbial community. Managing for these ecosystem services can improve plant yields and reduce off-site impacts. For instance, increasing plant diversity is linked to positive effects on yield, and these beneficial effects are often mediated by the microbial community and the nutrient transformations it carries out. My dissertation has aimed to elucidate the mechanisms by which plant diversity improves agricultural production. In particular, I have focused on how changes to the amount and diversity of carbon (C) inputs affects soil microorganisms involved in the nitrogen (N) cycle. My work spans multiple scales of observation: from a global meta-analysis to mechanistic studies utilizing denitrification as a model system.In a global meta-analysis, I found that increasing plant diversity through intercropping yields a net increase in extracellular enzyme activity. This effect varied by plant species and soil type suggesting that increases in the quality of nutrient inputs mediates these positive effects on microbial activity. Then, I looked at how intercropping cover crops into corn affects soil nutrient pools and microbial activities in a field experiment. No effect of interseeding cover crops into corn was found on soil nutrient pools or microbial activities. However, by analyzing differences in relationships between nutrient pools and microbial activities at two locations throughout Michigan, I was able to describe how the availability of dissolved organic C (DOC) drives differences in microbial N-cycling processes. I then investigated how C availability drives activity in microbial hotspots within the soil by comparing differences in denitrification potential in bulk soil versus the rhizospheres of corn and interseeded cover crops. Here, I found that denitrification rates were increased in the rhizospheres of all plant types, and this effect varied depending on the species of plant. I was able to further differentiate the impact of DOC and microbial biomass C on the rhizosphere effect and found that C availability was the primary driver of differences in denitrification rates between rhizospheres. Since plants provide many different forms of C to soil microbes, it is important to understand how the chemistry of C inputs affects microbial activity. I used a series of C-substrate additions to determine how C chemistry affects denitrifiers. I found that amino acids and organic acids tended to stimulate the most nitrous oxide (N2O) production and reduction. Although management and site affected overall rates of denitrification, C-utilization patterns of microbes were mostly similar between locations. To identify the mechanisms responsible for these effects, I performed a final experiment to track how denitrifiers utilized different C compounds. The C substrates that stimulated the most complete reduce of N2O also were utilized with the lowest C-use efficiency (CUE). This suggests possible trade-offs between N2O reduction and CUE, with important implications for how to manage microbial communities. Overall, my work demonstrates that land management can impact microbial community activity by influencing the identity of soil C inputs. While the importance of increasing soil C inputs has been known, this dissertation supports the notion that the chemical identity of C inputs can exert significant controls on microbial activity. Moreover, by comparing microbial traits I highlight the importance of trade-offs in how microbially mediated C- and N cycling are coupled.
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Title: IMPACT OF AGRICULTURAL MANAGEMENT AND MICROBIAL INOCULATION ON SOYBEAN (GLYCINE MAX) AND ITS ASSOCIATED MICROBIOME
Creator: Longley, Reid
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Soybean (Glycine max) is a globally important crop with uses as food, cooking oil livestock feed, and biodiesel. Soybean can be considered holobionts because they host diverse microbiomes which extend plant genotypes and phenotypes through various microbial functions such as nitrogen fixation and increased disease resistance. My research focused on assessing the impact of three agricultural management strategies on the soybean holobiont. Soybean cropping systems can be managed using various...
Show moreSoybean (Glycine max) is a globally important crop with uses as food, cooking oil livestock feed, and biodiesel. Soybean can be considered holobionts because they host diverse microbiomes which extend plant genotypes and phenotypes through various microbial functions such as nitrogen fixation and increased disease resistance. My research focused on assessing the impact of three agricultural management strategies on the soybean holobiont. Soybean cropping systems can be managed using various strategies, including conventional tillage, no-till, and organic management regimes. These management systems have been shown to impact the microbiomes of soybean-associated soils, however, their impacts on plant-associated microbiomes are still not well understood. In this study, I assessed the impact of conventional, no-till, and organic management treatments on soybean microbiomes at Michigan State’s Kellogg Biological Station Long-Term Ecological Research site (KBS LTER). I found that management impacted microbiome composition and diversity in soil, roots, stems, and leaves and that this impact persisted throughout the season. Additionally, when comparing the same soybean genotype grown in conventional and no-till management systems, tillage regime impacted the microbiome throughout the plant and the growing season. This effect impacted microbial taxa which are likely to be plant beneficial, including nitrogen fixing Bradyrhizobium. Another important management tool that is expected to impact plant-associated microbial communities is the application of foliar fungicides. While fungicides are known to protect plants from particular fungal pathogens, non-target impacts of fungicides on crop microbiomes, and the impact of management on microbiome recovery are not well understood. To address this knowledge gap, I assessed the impact of foliar fungicide application on the maize (Headline® fungicide, 2017) and soybean (Delaro® fungicide, 2018) microbiomes in conventional and no-till plots at the KBS LTER. I found that fungicide applications have a non-target impact on Tremellomycete yeasts in the phyllosphere and this impact was greater in soybean than maize. Co-occurrence network analysis and random forest modelling indicated that changes in fungal communities may lead to indirect impacts on prokaryotic communities in the phyllosphere. Importantly, this work demonstrated that phyllosphere communities of soybeans under no-till management had greater recovery from fungicide disturbance. This novel finding exemplifies how tillage regime can impact phyllosphere microbiomes and their responses to disturbance. Microbial inoculants in agriculture have long been used for biocontrol of pathogens, but there is also interest in their use to dampen the impacts of abiotic stress including drought. In this study, I tested whether inoculating soybeans with hub taxa identified through network analysis from no-till soybean root microbiome data from the KBS LTER could provide protection against water limitation. Soybean seedlings were enriched in consortia of hub bacteria and fungi and were grown in no-till field soil. Seedlings were then exposed to low-moisture stress, and plant phenotypes, plant gene expression, and amplicon sequencing of microbial DNA and cDNA were assessed throughout the stress period. Inoculation increased plant growth, nodule numbers, and led to increased expression of nodulation-associated genes. 16S sequencing of cDNA revealed higher levels Bradyrhizobium in inoculated samples. These results indicate that inoculation with hub microbes can benefit soybean plants, possibly through interaction with other microbes, interaction with the plant, or both. In summary, fungicide, tillage, and inoculation all impact the soybean microbiome, indicating that management choices impact the entire holobiont.
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Title: LISTERIA MONOCYTOGENES PLACENTAL COLONZATION AND CONSEQUENCES FOR PREGNANCY OUTCOME
Creator: Conner, Kayla Nicole
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Listeria monocytogenes (Lm) is a Gram-positive bacterium that causes the severe food-borne disease listeriosis. Listeriosis is particularly problematic in pregnant women as Lm colonizes the placenta, resulting in adverse pregnancy outcomes including stillbirth, miscarriage, and preterm labor. Despite numerous studies of placental listeriosis (PL) in various animal models, the mechanisms driving adverse outcomes following PL are largely uncharacterized. This dissertation addresses some of the...
Show moreListeria monocytogenes (Lm) is a Gram-positive bacterium that causes the severe food-borne disease listeriosis. Listeriosis is particularly problematic in pregnant women as Lm colonizes the placenta, resulting in adverse pregnancy outcomes including stillbirth, miscarriage, and preterm labor. Despite numerous studies of placental listeriosis (PL) in various animal models, the mechanisms driving adverse outcomes following PL are largely uncharacterized. This dissertation addresses some of the field’s knowledge gaps by analyzing the changes in placental gene expression and metabolism following infection with Lm and by characterizing a key Lm virulence factor, Internalin P (InlP), which plays a significant role in Lm placental colonization. Chapter 1 gives pertinent background information on the placenta, Lm, and PL and broadly addresses the knowledge gaps to be addressed by the rest of the dissertation. Chapter 2 describes an in vivo study of PL in mice. Infected and control placentas were analyzed for differences in gene expression profiles between the two groups. We identified an enrichment of genes associated with eicosanoid biosynthesis, suggesting perturbations in eicosanoid metabolism in infected tissues. By quantifying placental eicosanoid concentrations through mass spectrometry, we found a significant increase in the concentrations of several eicosanoids with known roles in inflammation and/or labor. This study provides a likely explanation for temporal disruptions of labor following placental infection. Chapters 3 and 4 discuss two studies of the Lm virulence factor InlP, a key player in placental colonization. InlP contributes to Lm’s placental pathogenesis likely by conferring the ability of Lm to transcytose through placental layers. Prior studies reported that no homologs of InlP exist in Listeria species other than Lm. Chapter 3 describes our discovery that at least two other Listeria species, L. ivanovii and L. seeligeri, encode InlP homologs. We characterized the domain architectures and genomic neighborhoods of these homologs and speculated on their implications for Listeria evolution. In chapter 4, I continue discussion of InlP and describe our identification and preliminary characterization of naturally occurring InlP variants. In this study, we used a bioinformatics approach to analyze Lm whole genome sequences (WGS) and identify InlP variants. We uncovered two InlP variants of interest in the Lm population. The first results from a start codon point mutation in the inlP gene, likely resulting in a truncated and potentially nonfunctional InlP protein product. The second is an InlP variant with a PRO to SER substitution in the InlP calcium binding loop, which is hypothesized to play a role in InlP activation or stabilization. These results provide two avenues for further investigation of InlP regulation and function and suggest the potential for InlP-dependent variation in placental colonization potential across Lm isolates. In chapter 5, I summarize this dissertation. This chapter reflects on the results, implications, and challenges of each study outlined in the prior chapters. I discuss the unique challenges faced due to the ongoing COVID-19 pandemic and its effects on my graduate training. Finally, I share concluding remarks and propose future directions for this project and the field of PL. Together, the chapters of this dissertation describe novel findings that contribute to the field by assessing genetic and metabolic changes to the placenta due to listeriosis and further characterizing a known key placental virulence factor.
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Title: COMPOSITION AND FUNCTION : UNRAVELING THE ROLE OF GROUP B STREPTOCOCCAL MEMBRANE VESICLES
Creator: McCutcheon, Cole Ross
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Group B Streptococcus (GBS) is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of approximately 30% of women. In individuals with an altered immune state such as the elderly, pregnant women, and neonates, GBS can cause invasive infections. During pregnancy, GBS frequently contributes to infections in utero that can result in chorioamnionitis, preterm birth, or miscarriage. The bacterial factors that promote these adverse outcomes, however, are under studied. For...
Show moreGroup B Streptococcus (GBS) is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of approximately 30% of women. In individuals with an altered immune state such as the elderly, pregnant women, and neonates, GBS can cause invasive infections. During pregnancy, GBS frequently contributes to infections in utero that can result in chorioamnionitis, preterm birth, or miscarriage. The bacterial factors that promote these adverse outcomes, however, are under studied. For instance, previous reports have demonstrated that GBS produces membrane vesicles (MVs), which have been linked to adverse pregnancy outcomes in a murine model. Nonetheless, little is known about the composition of GBS MVs and their role in pathogenesis and impact on the immune response. Therefore, using genotypically diverse strains of GBS, I sought to examine MV production and composition, as well as their impact on ascending infection in vivo to better understand their role in GBS disease. While MVs contain a variety of immunomodulatory virulence factors, including hyaluronidase, C5a peptidase, and sialidase, the relative abundance of these virulence factors varies in a lineage dependent manner. With this information in hand, I then assessed the host response to GBS derived MVs using human THP-1 derived macrophages. I found that regardless of strain, MVs induce a potent proinflammatory immune response characterized by the production of proinflammatory cytokines and chemokines. Notably, many neutrophil chemokines were highly upregulated in response to MVs, which is consistent with observations seen during murine challenge with MVs. I went on to demonstrate that MVs, in the absence of t, induce a potent IL-1ß response, which is dependent on caspase-1 and NLRP3, suggesting that the NLRP3 inflammasome is a sensor of GBS derived MVs. Previous data had suggested that MVs induce inflammation at the maternal-fetal interface. We have confirmed these findings and identified a potential mechanism for this inflammatory response. Furthermore, others utilized models of intra-amniotic injection that bypasses many immune defenses such as the extraplacental membranes and the cervix, which may prevent this response, while we assessed the role of MVs during vaginal challenge with GBS. However, we found that the addition of exogenous MVs does not promote ascending infection in vivo. While bacteria were able to ascend from the vaginal tract into gestational tissues, similar levels of bacteria were found regardless of the addition of exogenous MVs. Consistent with this observation, using flow cytometry we showed that neither exogenous MVs supplemented at the time of infection nor vaginal supplementation of MVs alone alter inflammatory responses at the maternal-fetal interface, suggesting that these innate barriers are capable of blocking MV mediated effects. The work presented here dramatically alters our understanding of the composition and host-pathogen interactions of GBS MVs, by substantially increasing our knowledge of both their composition and function during infection.
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Title: ELUCIDATING THE POTENTIAL ROLE OF ARYL HYDROCARBON RECEPTOR IN THE PATHOGENESIS OF CAMPYLOBACTER JEJUNI.
Creator: Ahmed, Husnain
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Campylobacter jejuni is a leading cause of human foodborne gastroenteritis in the US, with an incidence rate of 13.6 diagnosed cases per 100,000 individuals. The most frequent cause of C. jejuni infection in the US is the consumption of chicken contaminated during processing. Macrolide antibiotics such as azithromycin and ciprofloxacin are the drug of choice to treat C. jejuni infection in human populations. However, the over-use of antibiotics has led to the emergence of antimicrobial...
Show moreCampylobacter jejuni is a leading cause of human foodborne gastroenteritis in the US, with an incidence rate of 13.6 diagnosed cases per 100,000 individuals. The most frequent cause of C. jejuni infection in the US is the consumption of chicken contaminated during processing. Macrolide antibiotics such as azithromycin and ciprofloxacin are the drug of choice to treat C. jejuni infection in human populations. However, the over-use of antibiotics has led to the emergence of antimicrobial-resistant C. jejuni strains and reduced treatment efficacy. The development of antimicrobial resistance traits in C. jejuni isolates has augmented the need to develop innovative strategies to treat drug-resistant C. jejuni infections in human and animal populations.Members of the genus Lactobacillus are commonly used as probiotics, however the mechanisms by which they provide protective health effects remain elusive. In the first study, we described a novel mechanism by which L. murinus attenuates pro-inflammatory responses in the human intestinal epithelial cells. The results showed that L. murinus activates aryl hydrocarbon receptor (AHR) to decrease the secretion of IL-8 in response to exogenous stimulation by TNF-alpha in the human intestinal epithelial cells. Furthermore, activating the AHR with its defined ligand also reduced the secretion of IL-8 upon TNF-alpha stimulation. These results suggest that AHR can a novel target for inflammatory bowel disease (IBD) treatment. Furthermore, these results suggest that L. murinus can be a novel probiotic for treating IBD. In the 2nd study, we determined the effect of prophylactic inoculation of L. muirnus on the pathogenesis of C. jejuni in the BALB/c IL-10-/- mice. A total of 41 BALB/c IL-10-/- mice were used in this study. 11 mice were sham inoculated, 10 mice received only L. murinus, 10 mice received only C. jejuni, and 10 mice in the test group received both L. murinus and C. jejuni such that L. murinus was inoculated 32 days before C. jejuni infection. In addition, 30 days post-C. jejuni challenge mice were sacrificed and assessed for gut pathology. Fecal samples were also collected to access bacterial colonization levels in the gut through routine culture techniques and 16S sequence analysis. Both positive control group for C. jejuni and test groups mice developed severe colitis. 16S analysis of fecal DNA revealed that bacterial diversity in the test and positive control group for C. jejuni was significantly less (P<0.001) than in the Lactobacillus only and negative control group. These results suggest that prophylactic administration of L. murinus does not protect BALB/c IL-10-/- mice from developing disease following C. jejuni infection. Overall, this dissertation contains identification of a novel mechanism of action of L. murinus. The results provide insights for the identification of novel targets to treat C. jejuni disease without using antibiotics. This dissertation provides a basis for the future studies to further dissect the role of the AHR in the pathogenesis of C. jejuni.
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Title: ADVANCING ENGINEERED ENDOSYMBIONTS AS A PLATFORM TECHNOLOGY FOR THERAPEUTIC MACROPHAGE MODULATION
Creator: Madsen, Cody Scott
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation describes the construction of engineered endosymbionts (EES) as a platform technology for modulating macrophage function for therapeutic applications. Dr. Ashley Makela and I worked closely to advance the EES technology. Dr. Makela focused on the characterization of the EES ability to change macrophage function and I focused on developing the EES technology and working with Dr. Makela on characterization and using the EES in applications (Chapter 2 and 3). In Chapter 2,...
Show moreThis dissertation describes the construction of engineered endosymbionts (EES) as a platform technology for modulating macrophage function for therapeutic applications. Dr. Ashley Makela and I worked closely to advance the EES technology. Dr. Makela focused on the characterization of the EES ability to change macrophage function and I focused on developing the EES technology and working with Dr. Makela on characterization and using the EES in applications (Chapter 2 and 3). In Chapter 2, Bacillus subtilis was developed as a chassis organism for EES that escape phagosome destruction, reside in the cytoplasm of mammalian cells, and secrete proteins that are transported to the nucleus to impact host cell response and function. Two synthetic operons encoding either the mammalian transcription factors (TFs) Stat-1 and Klf6 or Klf4 and Gata-3 were recombined into the genome of B. subtilis expressing listeriolysin O (LLO) from Listeria monocytogenes and expressed from regulated promoters. Controlled expression of the mammalian proteins from B. subtilis LLO in the cytoplasm of J774A.1 macrophage/monocyte cells altered surface marker, cytokine and chemokine expression. Once the EES platform was developed and initially tested in vitro with a macrophage cell line, translating the EES to applications became the next step to understand the capacity of the new technology (Chapter 3). For increased translatability, the effect of the engineered B. subtilis LLO TF strains on murine bone marrow-derived macrophages (BMDMs) function was characterized. The TF strains shifted BMDM production of cytokines, chemokines and metabolic patterns. RNA-seq is still being analyzed to elucidate effects on gene expression. Furthermore, the ability of the B. subtilis LLO TF strains to alter the tumor microenvironment was characterized in a murine 4T1 orthotopic breast cancer model. The B. subtilis LLO strains altered the tumor microenvironment by promoting immune cell invasion, altering the functional metabolism of cells within the tumor, and causing tumor growth stabilization. Additionally, safety of this EES platform was observed as multiple doses at bacterial concentrations 100-fold more than other bacterial therapies were injected without affecting the health of mice. Yet, during the development and characterization of the EES, the sugar (D-mannose) that was used to induce transcription in the EES once inside the host cell was observed to significantly impact macrophage physiology which created additional complexity and was not ideal for in vivo applications. Accordingly, Emily Greeson and I worked on developing a mechanism for non-invasive localized control of gene expression in vivo. Emily Greeson engineered B. subtilis with temperature sensitive repressors (TSRs) and characterized this new genetic switch. I then coated B. subtilis with superparamagnetic iron oxide nanoparticles (SPIONs) which could be stimulated by an alternating magnetic field (AMF) to generate thermal energy. Chapter 4 discusses this new approach, and we investigated the ability of magnetic hyperthermia to regulate TSRs of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium, and used here for thermal control of reporter gene expression in Gram-positive B. subtilis. In vitro heating of B. subtilis with TlpA39 controlling bacterial luciferase expression, resulted in a 14.6-fold (12 hour; h) and 1.8-fold (1 h) increase in reporter transcripts with a 9-fold (12 h) and 11.1-fold (1 h) increase in bioluminescence. To develop magnetothermal control, B. subtilis cells were coated with three SPION variations which was confirmed by electron microscopy coupled with energy dispersive X-ray spectroscopy. Furthermore, using long duration AMF, we demonstrated magnetothermal induction of the TSRs in SPION-coated B. subtilis with a maximum of 4.6-fold increases in bioluminescence. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to improved EES transcriptional control. The research described in this dissertation demonstrates a multi-disciplinary approach towards developing a new modular technology to alter mammalian cell function with the specific focus on macrophages.
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Title: LISTERIA MONOCYTOGENES INFECTION ALTERS TROPHOBLAST EXTRACELLULAR VESICLES
Creator: Kaletka, Jonathan Matthew
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Listeria monocytogenes (Lm) is a bacterial pathogen that utilizes an intracellular lifecycle to spread throughout the body, including the placenta in pregnant individuals. Placental infection and disease can lead to negative fetal outcomes including spontaneous abortion, birth defects, and stillbirths. Extracellular vesicles (EVs) are tiny particles secreted by nearly every cell type in the body and serve as a cellular signaling mechanism. EVs have been implicated in many cellular functions...
Show moreListeria monocytogenes (Lm) is a bacterial pathogen that utilizes an intracellular lifecycle to spread throughout the body, including the placenta in pregnant individuals. Placental infection and disease can lead to negative fetal outcomes including spontaneous abortion, birth defects, and stillbirths. Extracellular vesicles (EVs) are tiny particles secreted by nearly every cell type in the body and serve as a cellular signaling mechanism. EVs have been implicated in many cellular functions and diseases throughout the body, including those involving the placenta. Placental EVs can have immunomodulatory effects, but during placental disease they can also act in a pro-inflammatory manner, leading to disease progression. EVs can also be proinflammatory during intracellular bacterial infection, where they can communicate the infection and coordinate an immune response. In this dissertation, I investigated how Lm infection of trophoblasts alters the EVs produced by the infected cells, and how they can activate an immune response. Chapter 1 of the dissertation details the current literature on the role that EVs play during bacterial infections and placental development and disease. Chapter 2 focuses on establishing a trophoblast stem cell model (TSC) to study placental infections. TSCs are the source of trophoblasts in the placenta, and cultivation of these cells allow for the continual study of placental disease. Here, I found that TSCs are susceptible to Lm infection, although it requires a higher bacterial load and longer time course compared to other cell types. This chapter details ways to model placenta-pathogen interactions in vitro, allowing for the study of these interactions in a laboratory setting. Chapter 3 investigated how Lm infection of TSCs altered the cargo of the tEVs produced. Previous studies into EVs from infected cells found components from the bacterial cells loaded into the EVs, including bacterial DNA, RNA, and proteins. We found many more unique proteins in the tEVs from infected cells. The infection tEVs had a substantial increase in the number of peptides identified of ribosomal, histone, and tubulin proteins, among others. Gene ontology (GO) analysis showed that the proteins seen in the tEVs from infected TSCs primarily belonged to RNA-binding pathways. This result piqued our curiosity as to if Lm infection also changed the RNA loaded into the tEVs. We performed RNA sequencing to determine the host RNA profiles found in the tEVs. We found different RNA profiles in the tEVs from uninfected and Lm-infected cells. GO analysis on the mRNAs overrepresented in the infection tEVs found that they represent genes from vasculogenesis and placental development pathways. Our results in this chapter show that Lm infection can alter the production and contents of tEVs from TSCs. Chapter 4 of this dissertation aimed to determine how tEVs from Lm-infected TSCs affect immune cells. We found that macrophages treated with infection tEVs produced TNF-α, a pro-inflammatory cytokine. Surprisingly, when we subsequently infected tEV treated cells with Lm, some of the cells became more susceptible to Lm infection. Similar results were seen with treatment with macrophage EVs, where infection EVs made the macrophages susceptible to Lm infection. The work in this chapter suggests that tEVs from Lm-infected TSCs can indeed induce a pro-inflammatory response in macrophages, although this makes the cells more susceptible to infection. Overall, the work presented here explores potential mechanisms as to how the placenta communicates bacterial infections.
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Title: Characterization of the human gut resistome, microbiome, and metabolome during enteric infection
Creator: Hansen, Zoe A.
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The human gut environment is replete with host-microbe and microbe-microbe interactions that shape human health. This system is also a known reservoir for antimicrobial resistance (AMR). The ubiquity of AMR is alarming, as greater than 2.8 million antibiotic-resistant infections and 35,000 deaths occur annually in the United States. Multiple human pathogens have demonstrated reduced susceptibility to various antibiotics, including enteric pathogens such as Campylobacter, Salmonella, Shigella,...
Show moreThe human gut environment is replete with host-microbe and microbe-microbe interactions that shape human health. This system is also a known reservoir for antimicrobial resistance (AMR). The ubiquity of AMR is alarming, as greater than 2.8 million antibiotic-resistant infections and 35,000 deaths occur annually in the United States. Multiple human pathogens have demonstrated reduced susceptibility to various antibiotics, including enteric pathogens such as Campylobacter, Salmonella, Shigella, and STEC, which cause millions of foodborne infections each year. The increasing incidence of antibiotic resistant enteric infections substantiates a need to further characterize these pathogens’ role in the curation and dissemination of AMR across environments. In this dissertation, a total of 223 human stools were assessed using shotgun metagenomics sequencing to investigate gut microbiome changes associated with enteric infection. Sixty-three stools were collected from patients suffering from enteric infection between 2011-2015 by the Michigan Department of Health and Human Services (MDHHS). Sixty-one of these patients submitted a follow-up sample between 1- and 29-weeks post-infection, and 99 healthy household members also submitted stools to serve as controls. In Chapter 2, a subset of patients infected with Campylobacter spp. and their related controls were investigated to assess the gut resistome, or collection of all antimicrobial resistance genes (ARGs) and their genetic precursors, related to infection. This examination revealed significantly higher ARG diversity in infected patients compared to healthy controls. Specifically, levels of multi-drug resistance (MDR) were greatly increased during infection. Three case clusters with distinct resistomes were identified; two of these clusters had unique ARG profiles that differed from those of healthy family members. In Chapter 3, a larger subset of 120 paired samples (60 infected vs. 60 recovered) were investigated to further characterize resistome and microbiome fluctuations related to infection and recovery. Again, infected patients harbored greater resistome diversity; however, recovered individuals displayed higher diversity in their microbiota composition. Despite their lower overall microbial diversity, patients with acute infections showed an increase in the abundance of members of Enterobacteriaceae, with specific expansion of the genus Escherichia. Host-tracking analysis revealed that many Enterobacteriaceae carried ARGs related to MDR and biocide resistance, a finding with broad implications for the ecology of resistance during infection. The fourth chapter explored metabolic capacity of gut microbial communities. In addition to metabolic pathway prediction, untargeted metabolomics was performed via LC/MS for 122 paired samples. Pathway annotation suggested that infected individuals contain greater microbial functional capacity, but metabolomics indicated greater overall metabolite diversity among recovered patients. Infection was associated with enhanced nitrogen and amino acid metabolism pathways. Although many metabolites remain uncharacterized, their presence or absence among individuals suggest their importance during and after infection. Altogether, the findings of this dissertation further characterize ecological consequences related to enteric infection in the human gut. Specifically, this research illustrates the importance of enteric infection in the dissemination and persistence of resistance determinants. Moreover, the expansion of Enterobacteriaceae and the evident increase in nitrogen- and amino acid-related metabolism during infection represent potential targets for future intervention practices.
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Title: ENGINEERING B. SUBTILIS TRANSCRIPTIONAL CONTROL AND PHYSIOLOGY FOR THE ADVANCEMENT OF BACTERIOTHERAPIES
Creator: Greeson, Emily Marilynn
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation explores to avenues of improvement for current bacteriotherapy approaches. Cody Madsen and I worked closely to advance engineered B. subtilis as a modular platform technology and Dr. Ashley Makela was instrumental in the in vivo studies (Chapter 2). In Chapter 2, transcriptional control of B. subtilis will demonstrate the ability to use magnetothermal energy generated by superparamagnetic iron oxide nanoparticles (SPIONs) and alternating magnetic fields (AMF) to induce...
Show moreThis dissertation explores to avenues of improvement for current bacteriotherapy approaches. Cody Madsen and I worked closely to advance engineered B. subtilis as a modular platform technology and Dr. Ashley Makela was instrumental in the in vivo studies (Chapter 2). In Chapter 2, transcriptional control of B. subtilis will demonstrate the ability to use magnetothermal energy generated by superparamagnetic iron oxide nanoparticles (SPIONs) and alternating magnetic fields (AMF) to induce temperature-sensitive repressors. Chapter 3 demonstrates how synthetic biology techniques can allow engineered B. subtilis to invade epithelial cells with the “zipper” mechanism. This was a collaborative effort as it was a multidisciplinary study and the contributions of Cody Madsen, Evran Ural, Dr. Ashley Makela, Dr. Bige Unluturk, and Victoria Toomajian were important and have been specifically noted in author contributions at the end of Chapter 3.Most patients on organ transplant waitlists will need alternative therapeutics due to a deficit of organ donations. Regenerative medicine approaches, including cellular reprogramming are being used to help address the deficit, but there are limitations. Bacteriotherapies aim to better deliver the therapeutics to a variety of targets, however, most approaches do so externally to the target cells. B. subtilis, a generally recognized as safe organism, engineered to express listeriolysin O (LLO) has been shown to replicate in the cytoplasm of macrophages and deliver transcription factors and modulate cell surface markers, cytokines, and chemokines. This mechanism of uptake only works with phagocytic cells creating an opportunity for the engineering of B. subtilis that targets internalization into non-phagocytic cells. When introducing known virulence factors into non-native organisms it is important to consider controlling the gene expression while trying to remain as minimally invasive as possible. Alternating magnetic fields (AMF) cause local temperature increases in regions with Superparamagnetic iron oxide nanoparticles (SPIONs), and we investigated the ability of this magnetic hyperthermia approach to regulate temperature-sensitive repressors (TSRs) in bacteria. Magnetic hyperthermia-based control of bacterial gene expression would advance development of bacteriotherapies and expand options of regulated bacterial transcription. TSRs block transcription in a temperature-dependent manner. B. subtilis was coated with three SPION variations, plain-dextran, amine- or carboxyl-coated and the interactions and AMF responses were characterized and induction of the TSRs was demonstrated using AMF. Murine intramuscular injections revealed continual association of SPIONs with B. subtilis. While there was no induction via AMF in vivo, pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to regional bacterial transcriptional control, a minimally invasive method that could be used with virulence factors and therapeutics. To delivery therapeutics to epithelial cells, B. subtilis llo was engineered to express internalin A (InlA), a protein native to Listeria monocytogenes. Internalin A is an adhesin that binds to the E-cadherin host cell receptor found in epithelial cells and mediates a “zipper” mechanism of invasion. B. subtilis llo inlA demonstrated cytosolic persistence and B. subtilis llo remained extracellular. Ultimately, the engineering of B. subtilis transcriptional control and physiology creates a new modular approach to regenerative medicine, cellular reprogramming, and cancer therapy that can be used in human health applications.
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Title: EFFECTS OF PLACENTAL LISTERIA MONOCYTOGENES INFECTION ON FETAL NEURODEVELOPMENT
Creator: Lee, Kun Ho
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Maternal infection can lead to adverse pregnancy outcomes. Numerous epidemiological studies have demonstrated an association between prenatal infection and neuropsychiatric disorders, including autism spectrum disorder (ASD). Different prenatal infections are associated with distinct neurological pathologies, necessitating studies of the diversity of prenatal pathogens and their consequences. Listeria monocytogenes (Lm) is a foodborne pathogen that causes listeriosis, which typically affects...
Show moreMaternal infection can lead to adverse pregnancy outcomes. Numerous epidemiological studies have demonstrated an association between prenatal infection and neuropsychiatric disorders, including autism spectrum disorder (ASD). Different prenatal infections are associated with distinct neurological pathologies, necessitating studies of the diversity of prenatal pathogens and their consequences. Listeria monocytogenes (Lm) is a foodborne pathogen that causes listeriosis, which typically affects immunocompromised individuals, including pregnant mothers. Prenatal infection with Lm can cause detrimental pregnancy outcomes, such as miscarriages, stillbirths, preterm labor, and death in newborns. However, neurological outcomes of maternal listeriosis have not been characterized. Here, I sought to investigate whether placental infection with Lm is associated with altered neurodevelopment by using a bioluminescence strain of Lm and a murine model of pregnancy-associated listeriosis. I show that placental infection affects neurodevelopment during pregnancy and behavior in the offspring.To investigate how placental infection with Lm dysregulates fetal brain development, I performed RNA-seq on fetal brains to quantify the enrichment of genes that were associated with the infection during gestation. The findings of RNA-seq analysis illustrated that placental infection with Lm altered fetal brain transcriptome and showed sexually dichotomous gene expression profiles. I further assessed the effects of different traits, including Lm exposure, the intensity of placental infection, and sex on the fetal transcriptome using systems biology. The genes were grouped into co-expression modules. Notably, maternal infection and its intensity measured by bioluminescence imaging signal were significantly associated with specific modules, suggesting these traits are the main factors driving these transcriptional changes. Lastly, I showed that placental Listeria infection enriched ASD-associated genes. These results demonstrate that maternal listeriosis dysregulates fetal brain transcriptome during gestation. Neurodevelopment is a complex process influenced by various environmental factors during pregnancy. To examine whether prenatal infection with Lm affects cortical lamination and neural activity, I performed hematoxylin and eosin staining and immunohistochemistry. Gross anatomy of the brain structure analysis showed that placental infection with Lm affected cortical lamination in a localized manner. Furthermore, increased neural activity was observed in Lm- exposed male offspring. These results illustrate that placental infection with Lm induces morphological changes in brain tissue during neurodevelopment. Behavioral symptoms of neuropsychiatric disorders are an important component of the diagnosis. Animal behavioral assays and tools have been developed to examine animal behavior such as social interactions, anxiety, and repetitive behaviors. I examined behavior tests that resembled ASD to determine if mouse offspring born following placental infection displayed abnormal behavior. Lm-exposed offspring exhibited altered behaviors and showed sex-dependent behavioral changes. Overall, my work highlights the impact of maternal listeriosis on brain development during pregnancy and its effects on offspring’s behavior and contributes to the understanding of the spectrum of fetal neurodevelopment.
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Title: Genetic and chemical biology studies of Mycobacterium tuberculosis pH-driven adaptation
Creator: Dechow, Shelby J.
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Mycobacterium tuberculosis (Mtb) endures robust immune responses by sensing and adapting to its host environment. One of the first cues the bacterium encounters during infection is acidic pH, a characteristic of its host niche – the macrophage. Targeting the ability of Mtb to sense and adapt to acidic pH has the potential to reduce survival of Mtb in macrophages. A high throughput screen of a >220,000 compound small molecule library was conducted to discover chemical probes that inhibit Mtb...
Show moreMycobacterium tuberculosis (Mtb) endures robust immune responses by sensing and adapting to its host environment. One of the first cues the bacterium encounters during infection is acidic pH, a characteristic of its host niche – the macrophage. Targeting the ability of Mtb to sense and adapt to acidic pH has the potential to reduce survival of Mtb in macrophages. A high throughput screen of a >220,000 compound small molecule library was conducted to discover chemical probes that inhibit Mtb growth at acidic pH. From this screen, AC2P20 was identified as a chemical probes that kills Mtb at pH 5.7 but is inactive at pH 7.0. Through a combination of transcriptional profiling, mass spectrometry, and free thiol abundance and redox assays, I show that AC2P20 likely functions by depleting intracellular thiol pools and dysregulating redox homeostasis. Findings from this study have helped define new pathways involved in Mtb’s response to acidic pH using a chemical genetic approach.Upon sensing acid stress, Mtb can adapt accordingly by entering a nonreplicating persistent state, resulting in increased tolerance to host immune pressures and antibiotics. During growth in vitro, when given glycerol as a sole carbon source, Mtb responds to acidic pH by arresting its growth and entering a metabolically active state of nonreplicating persistence, a physiology known as acid growth arrest. To answer how Mtb regulates and responds to acidic pH, I performed genetic selections to identify Mtb mutants defective in acid growth arrest. These selections identified enhanced acidic growth (eag) mutants which all mapped to the proline-proline-glutamate ppe51 gene and resulted in distinct amino acid substitutions: S211R, E215K, and A228D. I demonstrated that expression of the PPE51 variants in Mtb promotes significantly enhanced growth at acidic pH showing that the mutant alleles are sufficient to cause the dominant gain-of-function, eag phenotype. Furthermore, I performed single carbon source experiments and radiolabeling experiments showing that PPE51 variants preferentially uptake glycerol at an enhanced rate, suggesting a role in glycerol acquisition. Notably, the eag phenotype is deleterious for growth in macrophages, where the mutants have selectively faster replication but reduced virulence in activated macrophages as compared to resting macrophages. This supports that acid growth arrest is a genetically controlled, adaptive process that could act as a potential targetable physiology in future TB therapeutics. My work with the carbonic anhydrase inhibitor, ethoxzolamide, sought to combine genetic and chemical biology to better understand pH-adaptation in Mtb. Ethoxzolamide is a potent inhibitor of Mtb carbonic anhydrase activity and the PhoPR regulon, suggesting a previously unknown link between carbon dioxide and pH-sensing. We hypothesized that the production of protons from carbonic anhydrase activity could be modulating PhoPR signaling. Mtb has three carbonic anhydrases (CanA, CanB, and CanC), and by using CRISPRi and gene knockout, I show that CanB is required for pathogenesis in macrophages, but I did not observe a function in controlling PhoPR signaling. However, transcriptional profiling at different pH and CO2 concentrations show that PhoPR is induced by high CO2 and also revealed a core subset of CO2 responsive genes independent of PhoPR or acidic pH regulation. Overall, these studies defined new functions for thiol- and redox-homeostasis, glycerol uptake, and CO2-concentration in regulating Mtb adaptation to acidic environments and provide new targets for the development of acidic pH-dependent therapeutics.
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