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Title: Environmental regulation of cyclic di-GMP turnover in vibrio cholerae
Creator: Koestler, Benjamin J.
Date: 2014
Collection: Electronic Theses & Dissertations
Description: 3', 5'-cyclic diguanylic acid (c-di-GMP) is an intracellular bacterial second messenger that mediates the transition between a sessile, biofilm forming lifestyle to a motile, virulent lifestyle. Diguanylate cyclase (DGC) enzymes synthesize c-di-GMP, whereas c-di-GMP specific phosphodiesterase (PDE) enzymes hydrolyze the second messenger. Although numerous bacterial behaviors are regulated by c-di-GMP, the regulatory inputs of this system remain mostly undefined. Here, I examine how the marine...
Show more3', 5'-cyclic diguanylic acid (c-di-GMP) is an intracellular bacterial second messenger that mediates the transition between a sessile, biofilm forming lifestyle to a motile, virulent lifestyle. Diguanylate cyclase (DGC) enzymes synthesize c-di-GMP, whereas c-di-GMP specific phosphodiesterase (PDE) enzymes hydrolyze the second messenger. Although numerous bacterial behaviors are regulated by c-di-GMP, the regulatory inputs of this system remain mostly undefined. Here, I examine how the marine bacterium and human pathogen Vibrio cholerae utilizes c-di-GMP signaling to interpret and respond to environmental cues. The central hypothesis that underpins my research is that V. cholerae senses environmental signals with DGCs and PDEs to modulate c-di-GMP concentrations in different environments. As c-di-GMP is a widely conserved second messenger utilized by many different bacteria, the mechanisms by which V. cholerae utilizes c-di-GMP in different environments can be applied to other bacterial systems to further comprehend how they behave in and adapt to various surroundings. To examine the influence of environmental factors on c-di-GMP synthesis and hydrolysis, I have developed a novel method named The Ex vivo Lysate c-di-GMP Assay (TELCA) that systematically measures total DGC and PDE cellular activity. I have shown that V. cholerae grown in different environments exhibits distinct intracellular levels of c-di-GMP, and using TELCA have determined that these differences correspond to changes in both c-di-GMP synthesis and hydrolysis. These findings highlight that modulation of both total DGC and PDE activity alters the intracellular concentration c-di-GMP.While searching for specific environmental cues that regulate c-di-GMP, I have found that bile acids, a prevalent constituent of the human proximal small intestine, increase intracellular c-di-GMP in V. cholerae. This bile-mediated increase in c-di-GMP is quenched by bicarbonate, the intestinal pH buffer secreted by intestinal epithelial cells. These findings lead me to propose that V. cholerae senses distinct microenvironments within the small intestine, using bile and bicarbonate as chemical cues, and responds by modulating intracellular c-di-GMP.In addition to its function as a bacterial second messenger, c-di-GMP has potent immunostimulatory properties in eukaryotes; these properties make c-di-GMP a prime candidate for use as a vaccine adjuvant. Here, I present a novel method of delivering c-di-GMP into eukaryotic cells using adenovirus. I have demonstrated that c-di-GMP can be synthesized in vivo by delivering DGC DNA into the cell, and that this c-di-GMP increases the secretion of numerous cytokines and chemokines. This novel adenovirus c-di-GMP delivery system offers a more efficient and cost-effective method to administer c-di-GMP as an adjuvant to stimulate innate immunity.
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Title: Effects of dietary fiber sources on the gastro-intestinal microbiota, fermentation metabolites, and listeria monocytogenes in vivo and in vitro
Creator: Walker, Ryan (Ryan Adam)
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Dietary fiber consumption influences the gastro-intestinal microbiota, gastro-intestinal function, and health. This research investigated the effects of dietary fiber sources on bacterial composition, short-chain fatty acid (SCFA) production, gastro-intestinal barrier function, and Listeria monocytogenes challenge in mice and human colon cells. L. monocytogenes causes life-threatening illness in humans and animals. Some dietary fibers protect animals against illness in models of infection,...
Show moreDietary fiber consumption influences the gastro-intestinal microbiota, gastro-intestinal function, and health. This research investigated the effects of dietary fiber sources on bacterial composition, short-chain fatty acid (SCFA) production, gastro-intestinal barrier function, and Listeria monocytogenes challenge in mice and human colon cells. L. monocytogenes causes life-threatening illness in humans and animals. Some dietary fibers protect animals against illness in models of infection, while others enhance infection. Therefore, it is unclear if consuming certain dietary fiber sources confers protection against foodborne illnesses. The objectives of this research were: 1) describe how dietary fiber sources affect bacterial composition in vivo and in vitro; 2) quantify SCFAs produced by bacterial fermentation; 3) determine if fiber sources differentially affect L. monocytogenes infection in vivo; and 4) determine if bacterial metabolites promote or inhibit L. monocytogenes infection by affecting in vitro epithelial barrier function.In this project, dietary fiber sources differentially affected gastro-intestinal bacterial composition in vivo and in vitro, L. monocytogenes infection in mice, and enhanced barrier integrity in vitro. The overall results of this project demonstrate that dietary fiber sources differentially influence certain gastro-intestinal bacterial populations, measures of diversity, and that resulting compositional changes are important in the pathogenicity of L. monocytogenes. Additionally, fermentation end products enhance gastro-intestinal barrier function in this in vitro model, which may be an important factor in the prevention of enteric infection in humans. In summary, both the gastro-intestinal microbiota and its metabolites are important factors for maintaining gastro-intestinal health.
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Title: Identifying the underlying mechanisms of Marek's disease vaccine synergy
Creator: Umthong, Supawadee
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Marek’s disease virus (MDV; Gallid herpesvirus 2, aka, serotype 1) is a ubiquitous and highly oncogenic α-herpesvirus that causes Marek’s disease (MD), a lymphoproliferative disorder affecting chickens with estimated annual costs to the poultry industry of ~$2 billion worldwide. Since 1970, MD has been largely controlled through widespread vaccination. While MD vaccines are very successful in preventing tumors, they do not prevent viral replication and spread. As a consequence, new and more...
Show moreMarek’s disease virus (MDV; Gallid herpesvirus 2, aka, serotype 1) is a ubiquitous and highly oncogenic α-herpesvirus that causes Marek’s disease (MD), a lymphoproliferative disorder affecting chickens with estimated annual costs to the poultry industry of ~$2 billion worldwide. Since 1970, MD has been largely controlled through widespread vaccination. While MD vaccines are very successful in preventing tumors, they do not prevent viral replication and spread. As a consequence, new and more virulent MDV strains have repeatedly emerged in vaccinated flocks. Thus, there is a need to understand how MD vaccines work in order to design future vaccines that are more protective, especially against more virulent MDVs. One promising insight for vaccine development is based upon protective synergism, a phenomenon where two vaccines when combined provide greater protection compared to either original vaccine when administered alone as a monovalent vaccine. The mechanism that underlines the synergistic effect between SB-1 (a Gallid herpesvirus 3, aka, serotype 2 strain) and HVT (herpesvirus of turkey, aka, Meleagrid herpesvirus 1 or serotype 3), two of the most widely used MD vaccines, has never been investigated, and thus, provides a highly relevant and useful model to explore. To investigate the mechanisms of protective synergy of SB-1 and HVT, we used three approaches. First, we investigated how monovalent SB-1 or HVT replicates when they were alone in the host or together as a bivalent vaccine. We observed that the replication patterns of SB-1 and HVT were different with respect to time after administration into the bird and the organs that they were found to replicate in regardless if the other vaccine were present. Based on the observation that HVT replicated primarily early in the bursa, we found that this organ was necessary for protection using both HVT and bivalent HVT + SB-1 vaccines. Second, we measured the effects of CD8 T cells in monovalent SB-1, HVT, and bivalent SB-1+HVT vaccine treatment. Specifically, we reduced CD8 T cells to see their effect of CD8 T cells on MD incidence and vaccinal protection by injecting the chickens with a monoclonal antibody directed against chicken CD8 T cells. In this study, we found that CD8 T cells were necessary for protection induced by vaccines. Third, we identified the cytokine profiles induced by SB-1, HVT, and the bivalent vaccine to see if cytokine synergy could be one of the mechanisms to explain protective synergy. We found that SB-1 induced an innate anti-viral response typified by IFN-α, IFN-β, IL-1β, T-cell proliferation cytokine IL-21, and Th2 cytokine IL-5, while HVT suppressed TGF-β3 and TGF-β4. The early stimulation of IL-1β and IL-21 (IFN-γ-promoting cytokines) at 4 days post vaccination (DPV) by SB-1 combined with the suppression of TGF-β (IFN-γ- suppressing cytokine) at 1 day post challenge (DPC) by HVT could result in the strong induction of IFN-γ found in the bivalent vaccine at 10 DPC. The induction of IFN-γ supports the synergistic effect of cytokines by a cooperative action mechanism where multiple cytokines work together to enhance the signal. Based on these findings, we propose a model to explain bivalent SB-1 and HVT vaccine synergy, which combines the replication of vaccines, T cell response to vaccinations, and cytokine synergy between SB-1 and HVT vaccine. Our proposed mechanism provides insights on how to generate rationally designed MD vaccines.
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Title: Combination of physical and chemical interventions for reduction of loosely and tightly associated bacteria on broiler carcass skin
Creator: Singh, Pranjal
Date: 2016
Collection: Electronic Theses & Dissertations
Description: The study was conducted to develop processing interventions to reduce pathogen load on broiler carcasses and to understand patterns of bacterial association to broiler skin with the following purposes: 1) assess the effect of hot water spray (HWS, 71oC, 1 min) on broiler carcasses for reduction of loosely, intermediately, and tightly associated bacteria, 2) quantify loosely and tightly associated bacteria on broiler skin using different sampling protocols, 3) assess the effect of trisodium...
Show moreThe study was conducted to develop processing interventions to reduce pathogen load on broiler carcasses and to understand patterns of bacterial association to broiler skin with the following purposes: 1) assess the effect of hot water spray (HWS, 71oC, 1 min) on broiler carcasses for reduction of loosely, intermediately, and tightly associated bacteria, 2) quantify loosely and tightly associated bacteria on broiler skin using different sampling protocols, 3) assess the effect of trisodium phosphate dip, hot water dip, and their combinations with/without brushing on reduction of loosely- and tightly-associated bacteria on broiler carcasses and related structural changes in the skin, and 4) assess the characteristics of Salmonella association and penetration to broiler skin with and without stomaching. In study 1, broiler skin was quantitatively assessed for loosely, intermediately, and tightly associated bacteria by rinsing, stomaching, and grinding the same skin. Hot water spraying (71oC, 1 min) of broiler carcasses followed by water immersion chilling reduced mesophilic aerobic bacteria (MAB) populations by 2.07, 1.84, and 2.04 log CFU/g and Salmonella prevalence by 65, 65, and 73% at loose, intermediate and tight association levels, respectively. Hot water spraying and chilling reduced loosely associated Campylobacter prevalence by 45% but no reduction was observed at intermediate and tight association levels. Broiler carcasses suffered from an undesirable partially cooked appearance after the hot water spray treatment. In study 2, the left and right side skin (10 X 7 cm) of broiler carcasses were sampled by 10 swabings and 10 stomachings, and finally ground. Sixty five and 83 % of MAB populations on broiler skin could not be recovered after 10 consecutive stomachings and swabbings, respectively, but were recovered after grinding. The first stomaching or swabbing recovered most of the loosely associated bacteria but not tightly associated bacteria, which were recovered by grinding. In general, stomaching was more effective than swabbing for bacteria recovery from broiler skin. In study 3, microbial reductions and structural changes in broiler skin were evaluated after trisodium phosphate dip (TWD/TSP), hot water dip (TWD/HWD), and their combination (TSP/HWD) with (TSP/HWD/B)/without brushing. Microbial analysis, scanning electron microscopy and histological staining showed that TSP/HWD caused greater reduction in MAB, E. coli, total coliforms, and Salmonella with deeper penetration into the stratum compactum layer of the skin dermis than single application of TSP or hot water dip. TSP/HWD/B yielded lowest skin population of MAB whereas penetration into the dermis was similar to TSP/HWD but with sloughing off of part of stratum compactum in some areas. Both TSP/HWD and TSP/HWD/B changed skin color, with an increase in yellowness being the most prominent. In study 4, loose and tight associated GFP tagged Salmonella were quantified and imaged after refrigerated incubation of inoculated broiler skins for up to 48 h. GFP tagged Salmonella were not able to associate tightly with broiler skin during exposure for up to 48 h at 4oC as application of two stomachings (1 min each) removed almost 88% of the Salmonella cells from the inoculated skin. Confocal imaging of broiler skins, either dipped (2 min) or stomached (2 min) in inoculated buffer, revealed that Salmonellae were present on the surface and inside crevices at average depths of 10 and 68 μm, respectively, after dipping, with some cells pushed to average depths of 62 and 132 μm, respectively, after stomaching. Trapped water seemed to hold Salmonellae deep inside the crevices.
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Title: Characterization of the development of the tonsillar microbiome in pigs
Creator: Peña Cortes, Luis Carlos
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Pig tonsils are identified as a potential reservoir for many bacterial and viral pathogens that can survive asymptomatically in this location and may have a high potential of being zoonotic. It has been suggested that the microbiome plays a significant/ substantial role in host colonization by pathogenic microorganisms and also exerts regulatory roles in the resistance to infection. Despite the important role that the tonsillar microbiome could play in the colonization and persistence of...
Show more"Pig tonsils are identified as a potential reservoir for many bacterial and viral pathogens that can survive asymptomatically in this location and may have a high potential of being zoonotic. It has been suggested that the microbiome plays a significant/ substantial role in host colonization by pathogenic microorganisms and also exerts regulatory roles in the resistance to infection. Despite the important role that the tonsillar microbiome could play in the colonization and persistence of pathogens in the host, there are no in-depth studies characterizing the development of tonsillar microbiome in pigs or how this microbiome is structured over time. Surprisingly a similar study is also absent in humans. There was a clear need to investigate the development of the tonsillar microbiome in pigs to lay the basis for future studies focused on more complex subjects such as the relationship between the normal tonsillar microbiome and pathogens in the tonsils. Understanding the development of the pig tonsillar microbiome over time and the role of the tonsillar microbiome in the acquisition and persistence of a pathogenic microorganism will lay the basis for the design of novel intervention strategies to control the presence of the pathogen and reduce the risk of transmission to other animals or humans. Moreover, these studies are expected to provide an animal model to test hypotheses generated by microbiome data that cannot be tested in humans. The goal of this study was to characterize tonsillar microbiome development in pigs, and how this microbiome is structured and how the structure changes through different times in the life of pigs. The chapters in this thesis will present pertinent data related with the composition of the pig tonsillar microbiome and how it alters through the life of pigs, possible maternal sources for some of the identified members of this microbiome, as well as the microbiome structure and progressive change through their life. Furthermore, the results will show that challenges associated with management procedures typically present in swine farms generate prominent changes in the microbiome composition and abundance of diverse bacterial families. Finally, the study will show the microscopic structure of the tonsillar epithelium and crypts and the presence of diverse bacterial communities on the surface of pig tonsils throughout different time points of their life. The final chapter will also describe the morphological changes of the tonsillar surface in pigs that are seen and are associated with changes in the microbial communities observed through different time points in their life. Taken together, the results presented here demonstrate that there is a temporal succession in the development of the pig tonsillar microbiome through the life of pigs."--Pages ii-iii.
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Title: Modeling the movement of water, bacteria and nutrients across heterogeneous landscapes in the Great Lakes region using a process-based hydrologic model
Creator: Niu, Jie
Date: 2013
Collection: Electronic Theses & Dissertations
Description: The development and application of process-based hydrologic models (PBHMs) continues to be a topic of significant interest to the hydrologic community. Although numerous studies have applied PBHMs at small scales ranging from plot and field scales to small-watershed scales, the application of PBHMs to understand large-scale hydrology remains a topic that is relatively unexplored. Understanding controls on large-scale hydrology is key to climate change assessments and effective water resources...
Show moreThe development and application of process-based hydrologic models (PBHMs) continues to be a topic of significant interest to the hydrologic community. Although numerous studies have applied PBHMs at small scales ranging from plot and field scales to small-watershed scales, the application of PBHMs to understand large-scale hydrology remains a topic that is relatively unexplored. Understanding controls on large-scale hydrology is key to climate change assessments and effective water resources management; therefore, to quantify the nature and magnitude of fluxes in regional Great Lakes watersheds, we use a new distributed hydrologic model (PAWS+CLM). Here we describe the application of the model to several large watersheds in the State of Michigan including the Grand River, Saginaw Bay, Kalamazoo and Red Cedar River watersheds and evaluate model performance by comparing model results with different types of data including point measurements of streamflows, groundwater heads, soil moisture, soil temperature as well as remotely-sensed datasets for evapotranspiration (ET) and land water thickness equivalent (GRACE). We then report a budget analysis of major hydrologic fluxes and compute annual-average fluxes due to infiltration, ET, surface runoff, sublimation, recharge, and groundwater contributions to streams etc. as percentage of precipitation and use this information to understand the inter-annual variability of these fluxes and to quantify storage in these large watersheds. After testing the model for its ability to describe hydrologic fluxes and states, we describe the development of solute transport models at the watershed scale by using a mechanistic, reactive transport modeling framework in which the advection, dispersion and reaction steps are solved using an operator-splitting strategy. The solute transport models are tested extensively using available analytical solutions for different hydrologic domains and then applied to describe transport with surface - subsurface interactions and to describe the fate and transport of fecal indicator bacteria such as Escherichia coli in the Red Cedar River watershed in Michigan. Following the successful application of the bacterial fate and transport model, we describe detailed reactive transport modules for predicting the levels of nutrients (N and P). The models are tested using available field observations for the Kalamazoo River watershed in Michigan. The watershed-scale fate and transport modules are expected to aid management by quantifying the impacts of upstream watershed influences on water quality in downstream receiving water bodies such as lakes and oceans. Together with the flow modules they represent a comprehensive suite of process-based models to describe the terrestrial hydrologic cycle coupled with vegetation/land surface and biogeochemical processes.
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Title: New insights in the urease activation process obtained by characterization of apourease complexes and the UreG accessory protein of Klebsiella aerogenes
Creator: Quiroz Valenzuela, Soledad De Los Ángeles
Date: 2008
Collection: Electronic Theses & Dissertations

Title: EPIDEMIOLOGY OF ANTIBIOTIC RESISTANT SHIGA TOXIN-PRODUCING ESCHERICHIA COLI (STEC) AND NON-TYPHOIDAL SALMONELLA (NTS) IN MICHIGAN
Creator: Mukherjee, Sanjana
Date: 2018
Collection: Electronic Theses & Dissertations
Description: The enteric pathogens, Shiga toxin-producing E. coli (STEC) and non-typhoidal Salmonella (NTS), are leading causes of foodborne infections in the US, resulting in 265,000 and 1.2 million illnesses every year, respectively. The emergence of antibiotic resistance in these pathogens has been documented and is of great concern due to negative patient health outcomes and the possibility of transfer of resistance genes to other clinically relevant pathogens. However, there is a scarcity in...
Show moreThe enteric pathogens, Shiga toxin-producing E. coli (STEC) and non-typhoidal Salmonella (NTS), are leading causes of foodborne infections in the US, resulting in 265,000 and 1.2 million illnesses every year, respectively. The emergence of antibiotic resistance in these pathogens has been documented and is of great concern due to negative patient health outcomes and the possibility of transfer of resistance genes to other clinically relevant pathogens. However, there is a scarcity in information about frequencies of antibiotic resistant and factors associated with resistant STEC and NTS infections in Michigan. It is necessary to have a complete understanding about the of emerging antibiotic resistance and factors driving the rise of resistance in STEC and NTS to help develop effective control strategies. In this dissertation, 980 STEC isolates collected from patients in Michigan between 2001 and 2014 were examined for resistance to clinically relevant antibiotics. The examination of STEC strains for resistance, revealed high frequencies of resistance to ampicillin and trimethoprim-sulfamethoxazole, with significant increases in antibiotic resistance rates observed over this 14-year period. Multivariate logistic regression analysis identified non-O157 serotypes to be independently associated with antibiotic resistance. The recent increase in incidence of non-O157 serotypes observed in the US, coupled with the high frequencies of antibiotic resistance observed in this study, suggest the emergence of antibiotic resistant non-O157s as important human pathogens. Additionally, antibiotic resistant STEC isolates from patients in recent years (2010-2014) were more likely to cause hospitalizations than pansusceptible STEC isolates, suggesting that resistant STEC infections may result in adverse patient outcomes. Using whole genome sequencing, we also identified chromosomal mutations and 33 horizontally acquired genes present in the genomes of non-O157 STEC, likely conferring resistance. Importantly, by creating a co-occurrence network of these genes, we identified the co-occurrence of certain resistance genes, which are possibly present on the same mobile genetic element, thus resulting in multi-drug resistance. In addition to examining resistance in STEC, a total of 198 clinical NTS isolates collected between 2011 and 2014 were also examined for antibiotic resistance in this dissertation. Resistance to tetracycline, trimethoprim-sulfamethoxazole and ampicillin were commonly observed. Concerningly, high frequencies of multidrug resistant NTS were also observed with significant increases in their prevalence observed between 2011 and 2014. These high multidrug resistant rates have important implications on patient care as the efficacy of multiple antibiotics is reduced. Antibiotic resistant NTS isolates were also found to result in significantly longer mean hospital stays compared to pansusceptible NTS. Serovar specific differences in frequencies of antibiotic resistance were observed; S. Enteritidis were observed to have lower resistance frequencies than other serovars. Lastly, to better understand the role that cattle reservoirs play in harbouring antibiotic resistant STEC strains, we examined 121 STEC isolates collected in 2012 from six cattle farms in Michigan for antibiotic resistance. While high resistance frequencies to tetracycline and trimethoprim-sulfamethoxazole were observed in certain herds, no resistance to ampicillin was observed, unlike what was observed in STEC isolates collected from patients. While different populations of resistant STEC may be circulating in the clinical and agricultural environments, continuous monitoring of resistance in the cattle reservoir is warranted to determine if animal reservoirs can serve as potential sources of resistant infections in humans.
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Title: Transfer and inactivation of Salmonella during post-harvest processing of tomatoes
Creator: Wang, Haiqiang
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Salmonella outbreaks have been historically linked to tomatoes, with cross-contamination during post-harvest processing having become a major public health concern. In response, a series of studies were developed to assess the extent to which dump tanks, conveyors, slicers, and dicers can spread Salmonella and other microorganisms. An evaluation of the microbiological quality of tomatoes and dump tank water was conducted during three visits to a local tomato packinghouse. At the beginning of...
Show moreSalmonella outbreaks have been historically linked to tomatoes, with cross-contamination during post-harvest processing having become a major public health concern. In response, a series of studies were developed to assess the extent to which dump tanks, conveyors, slicers, and dicers can spread Salmonella and other microorganisms. An evaluation of the microbiological quality of tomatoes and dump tank water was conducted during three visits to a local tomato packinghouse. At the beginning of whole-day processing and after 3 h of operation, bacteria and yeast/mold populations decreased < 2 logs on tomatoes, with these microbial counts greatly impacted by changes in organic load and sanitizer concentration during washing. When the spread of Salmonella was assessed during washing of tomatoes with various sanitizers and subsequent conveying in a pilot-scale packing line, ~ 90% of the original Salmonella inoculum transferred to sanitizer-free water. Acidified chlorine yielded the greatest Salmonella reduction on tomatoes (3.1 log CFU/g). After processing with sanitizers, Salmonella populations decreased to non-detectable levels (< 0.2 log CFU/100 cm2) on the equipment surfaces. Thereafter, Salmonella transfer was assessed during conveying of tomatoes with plastic, foam, or brush rollers. Overall, cross-contamination was greatest using foam, followed by plastic and brush rollers (P < 0.05). After 5 inoculated tomatoes were roller conveyed, 24 and 76% of all uninoculated subsequently conveyed tomatoes were cross-contaminated with Salmonella of 10 - 100 and 1 - 10 CFU/tomato, respectively, compared to 8% of 25 tomatoes using brush rollers.The next two studies focused on Salmonella transfer during slicing and dicing of tomatoes. For tomato slicing, one red round tomato was inoculated with Salmonella Typhimurium LT2 (~ 5 log CFU/g) and sliced using a manual or electric slicer, followed by 20 uninoculated tomatoes, all of which yielded quantifiable numbers of Salmonella after slicing. The quantitative data was fitted to a two-parameter exponential model (Y = A  e(B  X)). While significantly higher (P ≤ 0.05) percentages of Salmonella were transferred to wet (12.2%) as opposed to dry tomatoes (1.1%), with the variety of tomato also impacting transfer, post-contamination hold time, processing temperature and tomato slice thickness did not significantly impact the overall percentage of cells transferred. When one 0.9 kg batch of inoculated Roma tomatoes (~5 log CFU/g) was mechanically diced, followed by ten batches of uninoculated tomatoes, all uninoculated tomatoes yielded Salmonella, with populations exponentially decreasing from 3.3 to 1.1 log CFU/g. Flume tank washing in sanitizer-free water or water containing 80 ppm peroxyacetic acid, 80 ppm mixed peracid, or 80 ppm total chlorine decreased the Salmonella populations on diced tomatoes 1.3 ± 0.2, 2.3 ± 0.3, 2.4 ± 0.4, and 2.4 ± 0.1 log CFU/g, respectively. Spray sanitation on conveyor belts proved to be an effective way to enhance safety of diced tomatoes, with electrolyzed water being especially attractive due to its relatively low cost and ease of preparation.Finally, the impact of temperature, pH, and wash water organic load on Salmonella morphology and early-biofilm formation was assessed on different surfaces encountered in tomato packing houses. Both pH and temperature significantly affected the surface hydrophobicity of Salmonella. Early-biofilm formation on tomatoes was significantly affected by both time (P = 0.0004) and temperature (P < 0.0001). After 6 d, early-biofilms consistently developed on stainless steel and HDPE surface, with the former being more evenly distributed.
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Title: Genetic diversity of clinical and bovine non-o157 shiga toxin-producing escherichia coli (stec
Creator: Blankenship, Heather Marie
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Shiga toxin-producing Escherichia coli (STEC) is a leading cause of foodborne infection resulting in 265,000 illnesses and more than 3,600 hospitalizations annually. Since its identification in 1982 associated with an outbreak of haemorrhagic colitis, serotype O157:H7 has been the primary focus of research and surveillance. However, the increasing incidence of other serogroups, or non-O157 STEC, that are associated with clinical illness has since surpassed the incidence of O157 and has raised...
Show moreShiga toxin-producing Escherichia coli (STEC) is a leading cause of foodborne infection resulting in 265,000 illnesses and more than 3,600 hospitalizations annually. Since its identification in 1982 associated with an outbreak of haemorrhagic colitis, serotype O157:H7 has been the primary focus of research and surveillance. However, the increasing incidence of other serogroups, or non-O157 STEC, that are associated with clinical illness has since surpassed the incidence of O157 and has raised questions about the genetic diversity of this pathogen population. Six serogroups, O26, O45, O103, O111, O121, and O145, have been denoted as "big six" non-O157 STEC serogroups since they are frequently associated with clinical outcomes.In this dissertation, 895 non-O157 STEC isolates recovered from patients in Michigan between 2001-2018 were analyzed using whole genome sequencing (WGS) to identify virulence gene profiles and apply new typing methods to better discriminate closely related strains. The recovery of a wide range of serogroups from cases presenting with symptoms ranging from mild diarrhea to hemorrhagic colitis, indicates that genetic diversity and variation may have an impact on disease outcomes. The number and richness of serogroups identified over the past 18 years has been steadily increasing and serogroup alone lacks the discriminatory capabilities to classify related isolates. Indeed, strains representing the same sequence types (ST) were often found to be unrelated by serogroup. Notably, some serogroups, STs, virulence gene profiles and alleles were associated with clinical outcomes and patient demographics. Contrast to national surveillance, cases between 11 and 29 years of age had the highest frequency of STEC infections in Michigan.Additionally, a subset of 44 non-O157 STEC recovered from Michigan patients between 2000 and 2006 were examined more comprehensively while making comparisons to 114 clinical STEC isolates from Connecticut to examine the impact of geographic location on risk factors for non-O157 STEC infections. Lastly, a subset of STEC isolates associated with outbreaks in Michigan were examined to identify the impact of WGS on identification of strain relatedness for surveillance compared to pulsed-field gel electrophoresis.While most of the work outlined in this dissertation focused on characterizing clinical non-O157 STEC isolates, a comparative analysis of cattle isolates was also performed since cattle are an important reservoir of STEC. Indeed, numerous outbreaks and illnesses have been traced back to contaminated cattle-based food products or fecal contamination of water and crops. The ability of STEC to persist in the cattle reservoir and farm environment may give rise to more pathogenic strains due to the accumulation of horizontally acquired genes. 66 STEC isolates recovered from a beef herd over four samplings were examined to identify the genetic diversity within the cattle population and longitudinal persistence. The ability of a strain to form a strong biofilm was associated with the ability to persist and be recovered at multiple sampling phases from the same animal. Further, to better understand the genetic diversity of STEC recovered from the cattle reservoir, an additional 12 STEC isolates from three bovine herds (n = 78) and 241 clinical O157 STEC isolates (n = 1,135) were included to identify shared profiles. The similarity in serogroups and virulence gene profiles warrant a continued surveillance of the cattle environment to better understand crossover events and the ability of strains to evolve into new virulent STEC lineages. The work described in this dissertation helped to elucidate the genetic characteristics important for clinical outcomes and identified targets for future surveillance to better understand lineages that may be important for disease.
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Title: BIOSENSING TOTAL BACTERIAL LOAD IN LIQUID MATRICES TO IMPROVE FOOD SUPPLY CHAIN SAFETY USING CARBOHYDRATE-FUNCTIONALIZED MAGNETIC NANOPARTICLES FOR CELL CAPTURE AND GOLD NANOPARTICLES FOR SIGNALING
Creator: Matta, Leann Lerie
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Economical rapid nano-biosensing methods with expedited electrochemical signaling, were developed using carbohydrate-functionalized magnetic nanoparticles (MNP) and gold-nanoparticles (AuNP) to detect pathogenic bacteria in liquid or homogenized food samples. MNP functionalized with glycan- and amino/glycan ligands were able to rapidly extract bacteria, while concentrated dextrin-coated AuNP labeling improved detection sensitivity. Carbohydrate ligands are more stable than antibodies,...
Show moreEconomical rapid nano-biosensing methods with expedited electrochemical signaling, were developed using carbohydrate-functionalized magnetic nanoparticles (MNP) and gold-nanoparticles (AuNP) to detect pathogenic bacteria in liquid or homogenized food samples. MNP functionalized with glycan- and amino/glycan ligands were able to rapidly extract bacteria, while concentrated dextrin-coated AuNP labeling improved detection sensitivity. Carbohydrate ligands are more stable than antibodies, permitting long shelf life of MNP at room temperature and minimized AuNP aggregation during simple refrigeration. Transmission electron microscopy (TEM) imaged the electrostatic binding between MNP and Salmonella Enteritidis, E. coli O157:H7, Bacillus cereus, Listeria monocytogenes and E. coli C3000, which mimics electrostatic binding by antibodies, although with lower specificity. Capture index (CI) is defined as the parts-per-thousand (ppt) of bacteria extracted per initial bacterial presence. TEM mages showed that attached milk matrix components did not interfere with microbial. capture. Salmonella, E. coli, and Bacillus (3 to 5 log CFU/mL) capture in three milks was 2 ppt to 120 ppt CI. Capture in beef juice and apple cider was 0.002 ppt to 0.011 ppt for E. coli and Listeria, respectively, at 10 log cfu/mL due to accelerated microbial growth immediately following the spike. Viscous homogenized eggs, though, impeded MNP-Salmonella migration to the magnet during separation. This phenomenon was a motivating factor in creating “dip-sticks”: plastic strips coated in MNP (MNP-strip). Rapid nano-biosensing of MNP-cell complexes in under 30 min from either suspended or strip capture was possible using electrochemical technology of spectrometry or a simple handheld potentiostat. Capture concentrates bacteria as MNP-cell from large volumes allowing strong cyclic voltammetric (CV) signaling. Normalized peak current responses (NPCR) for microbial detection from simple matrices (PBS and beef juices) showed sample (S) NPCR lower than negative controls (N) (S/N < 1.0). Whereas in complex matrices (milk, apple cider, and homogenized eggs), S/N were significantly greater than 1.0. NPCR for negative controls were found to be linearly related to matrix components fats, proteins, and sodium (R2 = 0.92). Except for E. coli in beef juices, all S/N were significant (p < 0.05) for contamination levels ranging between 6.2 to 12.3 log CFU/mL.Enhanced signaling of low pathogen presence in food was achieved using electrically active AuNP labeling. Electrochemical detection of MNP-cell-AuNP complexes with spectrophotometry or differential pulse voltammetry (DPV) was significantly more sensitive, detecting 3 log CFU/mL and 5 log CFU/mL E. coli contamination in milk (p < 0.20), respectively. Food component attachment to the complexes altered, but did not interfere, with distinguishing samples from negative controls . MNP carbohydrate ligands exposed to refrigerated milk matrix components (fats, lipids, sugars, protein and sodium) for up to 9-days still extracted bacteria. This makes possible future biocompatible tag-on nano-biosensors inside individual food packaging. Pathogen presence could be monitored over the lifetime of the product, reducing consumption of contaminated foods. Reliable frequent testing along the food supply chain would facilitate reduced human disease, while reducing industry financial losses due to foodborne outbreaks. Flexible carbohydrate-based MNP-cell/(CV) and MNP-cell-AuNP/(DPV or spectrometry) nano-biosensing with electrochemical detection can provide a truly rapid, economical test.
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Title: Crop microbiomes and the search for effective biocontrol of Fusarium graminearum on wheat
Creator: MacCready, Kristi Gdanetz
Date: 2018
Collection: Electronic Theses & Dissertations
Description: "Manipulation of naturally occurring microbial communities to reduce plant diseases or increase crop yields requires a thorough understanding of interactions within the phytobiome, in particular, how microbial communities change as plants age, across plant species and organs, and under different land management regimes. Plants were sampled from a wheat-maize-soybean crop rotation site that implements four different land management strategies (conventional, no-till, reduced inputs, and organic...
Show more"Manipulation of naturally occurring microbial communities to reduce plant diseases or increase crop yields requires a thorough understanding of interactions within the phytobiome, in particular, how microbial communities change as plants age, across plant species and organs, and under different land management regimes. Plants were sampled from a wheat-maize-soybean crop rotation site that implements four different land management strategies (conventional, no-till, reduced inputs, and organic). The fungal and bacterial communities of leaves, stems, and roots of wheat, maize, and soybean throughout the growing season were analyzed using fungal internal transcribed spacer and bacterial 16S rRNA gene amplicon sequencing. Analysis of sequence-based fungal communities has some limitations due to the unreliable phylogenetic resolution of DNA sequence alignments. To improve this deficiency, a tool that improved phylogenetic resolution was developed. This tool increases the number of operational taxonomic units which are identified at genus and species levels. Endophytes were isolated from the wheat plants used for microbial community analysis and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum during wheat seedling and head infection. Endophytes on crops can be developed to manage disease, and endophyte-based biocontrols could solve current limitations in F. graminearum disease control. Additionally, functional analysis of F. graminearum secondary metabolite genes provides insight into the function of their gene products for this fungal pathogen. Microbial community structure is affected by various genetic factors of the host plant, environmental factors, and interactions with other organisms. Understanding community responses to these factors is necessary for targeted manipulation of communities to reduce plant disease."--Pages ii-iii.
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Title: Fate and detection of Bacillus anthracis spores in pasteurized milk, juice and eggs
Creator: Shah, Sandip H.
Date: 2009
Collection: Electronic Theses & Dissertations

Title: THE IDENTIFICATION OF NOVEL AMINOGLYCOSIDE ADJUVANTS FOR THE ERADICATION OF PSEUDOMONAS AERUGINOSA BIOFILMS
Creator: Maiden, Michael M.
Date: 2018
Collection: Electronic Theses & Dissertations
Description: The Infectious Disease Society of America has named antimicrobial resistance the greatest global threat to human health. More than half of all infections are due to bacteria growing as biofilms, which are a community of cells enmeshed in a self-made matrix that can be up to 1000x more resistant conventional antimicrobials. Pseudomonas aeruginosa in particular, due to its numerous resistance mechanisms is a formable threat that often forms biofilms. Few new therapies have been developed to...
Show moreThe Infectious Disease Society of America has named antimicrobial resistance the greatest global threat to human health. More than half of all infections are due to bacteria growing as biofilms, which are a community of cells enmeshed in a self-made matrix that can be up to 1000x more resistant conventional antimicrobials. Pseudomonas aeruginosa in particular, due to its numerous resistance mechanisms is a formable threat that often forms biofilms. Few new therapies have been developed to combat P. aeruginosa, and our antibacterial arsenal continues to decline. One solution to this daunting problem are anti-resistance compounds or adjuvants, which enhance conventional antimicrobials, extending and improving their utility. Here, we describe three adjuvants, triclosan, oxyclozanide and melittin. We demonstrate that each synergizes with tobramycin against mature P. aeruginosa biofilms. We also define the mechanism of action of triclosan and oxyclozanide, as protonophores that inhibit efflux pump activity, rendering cells susceptible to tobramycin killing. These adjuvants could be used in conjunction with current therapies to both improve their effectiveness, extend their lifespan, and target cells in biofilms
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Title: The impact of lactobacillus and bacteriophage on group b streptococcus and the placental membranes
Creator: Shiroda, Megan
Date: 2019
Collection: Electronic Theses & Dissertations
Description: The human microbiota encompasses the microbes that live on and in the human body. While some body sites including the vaginal and intestinal tracts have been studied extensively for their role in human health, other body sites have been historically considered sterile and are less studied. One such site is the placental membranes that surround the fetus during pregnancy and serve as an important protective barrier during pregnancy. Several studies have established which bacteria are found in...
Show moreThe human microbiota encompasses the microbes that live on and in the human body. While some body sites including the vaginal and intestinal tracts have been studied extensively for their role in human health, other body sites have been historically considered sterile and are less studied. One such site is the placental membranes that surround the fetus during pregnancy and serve as an important protective barrier during pregnancy. Several studies have established which bacteria are found in this site, but few studies have been conducted to characterize their interactions in vitro or to understand their impact on the placental membranes. Further, our knowledge of the viral component of the microbiome in human health remains incomplete.In this dissertation, Lactobacillus, a well-studied probiotic in other body sites, was evaluated for its effect in the placental membranes. As these membranes were previously considered sterile, we sought to assess the ability of Lactobacillus to colonize these cells and evaluate its impact on them. A cell line model of the outermost layer of these membranes, the decidual cells, was used to establish that Lactobacillus can associate and impact a known cell signaling pathway, the Mitogen Activated Protein Kinase (MAPK) pathway, which is associated with inflammation and host cell death. Total protein level of p38, an important upstream protein in this pathway, was found to be significantly lower with Lactobacillus than in mock infection. These data suggest that Lactobacillus could maintain a commensal interaction in the placental membranes as described in other body sites. Lactobacillus is also known to inhibit pathogen invasion. Group B Streptococcus (GBS) can ascend from the vaginal tract to infect placental membranes, triggering premature birth or neonatal infection. Four Lactobacillus strains representing three species were characterized to assess their impact on two GBS strains (colonizing and invasive). We found live Lactobacillus does not affect GBS growth or biofilm production. L. gasseri increased association of both strains of GBS to the decidual cells but did not result in increased invasion of the cells. Instead, co-culture with Lactobacillus reduced host cell death. Secreted products of Lactobacillus drastically reduced growth in 35 GBS strains that broadly represent GBS diversity and could prevent biofilm formation; this inhibition was strain dependent. Unfortunately, increased GBS-induced host cell death with Lactobacillus supernatants was observed. Collectively, these data suggest that both live Lactobacillus and its supernatant could impact GBS interactions with the placental membranes.Bacteriophage are one of the most abundant members of the microbiome but their impact on opportunistic pathogens such as GBS remains unknown. As GBS can be isolated from gastrointestinal tract, we hypothesized fecal phage communities would inhibit the growth of GBS in vitro. Approximately 6% of the tested communities inhibited the growth of 35 GBS strains. To better understand differences in GBS strain inhibition, we examined capsule, sequence and clinical types of the strains. As no significant differences were found with these traits, we next examined Clustered Regularly Interspaced Palindromic Repeats (CRISPR), which serve as an adaptive immune system against invading foreign DNA by the acquisition of spacer sequences. GBS strains with fewer than nine spacer sequences were less likely to be lysed by a phage community than strains with more than sixteen spacers. We further hypothesized that presence of GBS in the corresponding bacterial component of each phage community would correlate to its ability to inhibit GBS growth. While this correlation did not exist across all GBS strains tested, sensitive strains of GBS were significantly more likely to be inhibited by phage communities with a lower abundance of GBS. Collectively, these data suggest that the phage component of the intestinal microbiome could impact GBS colonization. To further characterize these interactions, an individual bacteriophage should be isolated from these communities.
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Title: SYNTHESIS AND CHARACTERIZATION OF BIOACTIVE GLASS-CERAMIC PARTICLES WITH ADVANCED ANTIBACTERIAL PROPERTIES FOR APPLICATIONS IN BONE REGENERATION
Creator: Pajares Chamorro, Natalia
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Bacterial infections are major surgical complications, which have worsened due to the continued evolution of drug-resistance. In coping with the decay of the antibiotic era, scientists eagerly search for alternative treatments. Multi-functional biomaterials capable of combating infections while triggering tissue regeneration are of great interest. For example, bioactive glasses have been regularly used to deliver drugs and regenerate tissue owed to their unique bone-bonding ability. Doping...
Show moreBacterial infections are major surgical complications, which have worsened due to the continued evolution of drug-resistance. In coping with the decay of the antibiotic era, scientists eagerly search for alternative treatments. Multi-functional biomaterials capable of combating infections while triggering tissue regeneration are of great interest. For example, bioactive glasses have been regularly used to deliver drugs and regenerate tissue owed to their unique bone-bonding ability. Doping the bioactive glass structure with broad-spectrum biocide ions such as Ag+ confers advanced antibacterial properties. The release of Ag+ is controlled by the degradation process of the glass network, maintaining the dose within a therapeutic window that is not cytotoxic to eukaryotic cells. Despite the extensive research performed on Ag-doped bioactive glasses, their regenerative properties in bone tissues have been rarely investigated. This thesis presents promising interactions between Ag-doped bioactive glass (Ag-BG) microparticles and osteoprogenitor cells, providing evidence of the ability to support bone regeneration. Ag-BG’s degradation provoked cell proliferation and cell differentiation in vitro and demonstrated healing of critical calvaria defects in mice after one month of implantation, thanks to the release of Si and Ca ions. Additionally, Ag-BG was antibacterial against Staphylococcus aureus (S. aureus), the most common cause of bone-degenerative diseases like osteomyelitis, and demonstrated low proclivity to induce resistance. The antibacterial potential originated from the degradation by-products of the structure. The mechanism of inhibition was built upon four main sources from higher to lower contribution: Ag+ release, oxidative stress, mechanical damage by nano-sized debris, and osmotic effect. In addition, Ag-BG was capable of restoring ineffective antibiotics with cell-wall-related inhibitory mechanisms by simple combinatorial therapies, rendering them effective in clearing infections. This unprecedented functionality of Ag-BG was expanded with antibiotic depots, where Ag-BG served as a carrier for an ineffective drug. Bioactive glass nanoparticles (BGNs) have been proposed to advance biological and antibacterial properties compared to their micro-sized counterparts. However, the challenges of producing BGNs with multifold metallic ions in a reproducible manner have limited their use. Here, the Stöber method was comprehensively studied to understand the effect of process variables on BGNs’ composition, structure, and morphology. The use of methanol as solvent and the early addition of metallic ion reagents before catalysis helped improved their cation incorporation within the glass network. Extended stirring was key to achieving the targeted composition and controlling the particle size. Monodispersed 10 nm Ag-doped BGNs (Ag-BGNs) were achieved. These Ag-BGNs were stronger antimicrobial weapons, providing bacterial inhibition within hours of treatment. The biological properties were not significantly advanced in the Ag-BGNs compared to Ag-BG; however, cell proliferation, differentiation, and bone re-growth were still provoked. These Ag-BGNs were used as fillers in hydrogel nanocomposites with natural matrices consisting of collagen type I or extracellular matrix. Ag-BGNs distributed homogeneously along the polymer fibrils and allowed polymerization within hours at physiological conditions. These materials hold potential for injectable devices, designing minimally invasive single-step treatment for debilitating bone infections while promoting tissue recovery.
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Title: ENVIRONMENTAL DRIVERS AND EVOLUTIONARY CONSEQUENCES OF HORIZONTAL GENE TRANSFER IN SOIL BACTERIA
Creator: Kittredge, Heather
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Horizontal gene transfer (HGT) is a driving force in bacterial evolution and could drive rapid adaptation in bacterial communities. Natural transformation is one mechanism of HGT that allows bacteria to pick up extracellular DNA (eDNA) from the environment and integrate it into their genome. But the rate of HGT in natural environments, and the role this process plays in facilitating rapid adaptation remains unknown. As climate change threatens the stability of environments worldwide,...
Show moreHorizontal gene transfer (HGT) is a driving force in bacterial evolution and could drive rapid adaptation in bacterial communities. Natural transformation is one mechanism of HGT that allows bacteria to pick up extracellular DNA (eDNA) from the environment and integrate it into their genome. But the rate of HGT in natural environments, and the role this process plays in facilitating rapid adaptation remains unknown. As climate change threatens the stability of environments worldwide, understanding how quickly bacteria can adapt to novel environments is essential. My dissertation research characterizes the environmental drivers and evolutionary consequences of natural transformation in a highly transformable model soil bacterium Pseudomonas stutzeri.Despite decades of research on understanding HGT at the molecular level, less is known about the ecological drivers of HGT. To understand the soil conditions relevant for transformation, I first measured eDNA in the field over a short-term drying rewetting disturbance (Ch. 2). I found that eDNA increased in response to the rewetting disturbance but quickly disappeared from soil, suggesting a small portion of this eDNA could be transformed by bacterial cells recovering from the disturbance. To test the efficiency of transformation under the conditions in which eDNA disappeared, I created a novel microcosm system for quantifying transformation in soil (Ch. 3). Here, I inoculated soil with live antibiotic-susceptible, and dead antibiotic-resistant P. stutzeri. I then tracked the evolution of antibiotic resistance over a range of soil conditions and eDNA concentrations. Transformation drove the evolution of antibiotic resistance across a wide range of soil moistures and increased in response to larger inputs of dead cells (eDNA source), with antibiotic resistance repeatedly appearing in antibiotic free soil. Despite the prevalence of transformation across bacterial species, the evolutionary origins and consequences of transformation are still largely unknown. Transformation presumably provides a fitness benefit in stressful or continuously changing environments, but few studies have quantified changes in transformation in response to adaptive evolution. Here, I evolved P. stutzeri at different salinities and tested how the growth rate and transformation efficiency changed in response to salt adaptation (Ch. 4). Overall, the growth rate increased in response to adaptation, but the transformation efficiency declined, with only ~50% of the evolved populations transforming eDNA at the end of experiment – as opposed to 100% of ancestral populations transforming eDNA. Overall, my dissertation research elucidates the factors driving transformation in soil, setting the stage for future experiments to scale up estimates of transformation to the whole community level. I find that transformation occurs under most soil conditions and allows genetic variants to arise at low frequencies in the absence of selection. I also report novel experimental evidence that transformation efficiency can change dramatically, and in a highly variable manner, over just ~330 generations. Taken together, this body of research highlights a role for transformation in many natural systems of ecological significance, and points to dead cells as an important but often overlooked source of genetic diversity.
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Title: CHEMICAL BIOLOGY AND GENETIC STUDIES TARGETING THE MYCOBACTERIAL CELL ENVELOPE
Creator: Williams, John Tison
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Mycobacterium tuberculosis is one of the leading causes of death due to a single infectious pathogen. The evolution and spread of drug resistant strains requires new antibiotics to control the TB pandemic. Over the last decade, the lipid flippase MmpL3 has been identified as a potential drug candidate based on its essential nature for cell viability and repeated identification as the lead target of small molecule inhibitors of Mtb growth. Using a combined untargeted and targeted whole cell...
Show moreMycobacterium tuberculosis is one of the leading causes of death due to a single infectious pathogen. The evolution and spread of drug resistant strains requires new antibiotics to control the TB pandemic. Over the last decade, the lipid flippase MmpL3 has been identified as a potential drug candidate based on its essential nature for cell viability and repeated identification as the lead target of small molecule inhibitors of Mtb growth. Using a combined untargeted and targeted whole cell phenotypic screen I identified novel inhibitors of this valued target. A combination of lipid profiling and an innovative competitive binding assay supported MmpL3 as the target of these inhibitors. Cross resistance profiling of MmpL3 inhibitors against twenty-four unique mmpL3 Mtb mutants demonstrated that the level of resistance is associated with the proximity of resistant mutants to essential residues for protein function. Further, these resistance profiles suggested that MmpL3 inhibitors fall into separate clades depending on their chemical scaffolds. The results of this screen led to the development of novel potent analogs for one of the identified MmpL3 inhibitors, HC2099. These analogs were active against clinically relevant drug resistant Mtb strains that cause treatment failure in patients. Active analogs were able to kill Mtb inside of infected macrophages, an infectious niche of Mtb, without inducing cytotoxicity against these important immune cells. One of these analogs, MSU-43085, was orally bioavailable and successfully inhibited Mtb growth in infected mice, supporting further development and highlighting the therapeutic potential of this series. High throughput screens are often used to identify new inhibitors of Mtb growth. However, prioritized hits form these screens often identify similar targets such as MmpL3, lipid synthesis enzymes, redox cyclers, as well as inhibitors of the electron transport chain. Follow up studies of these inhibitors are often time consuming, costly and result in the rediscovery of previously identified targets. While this is not necessarily detrimental to Mtb drug discovery, as these reoccurring targets have therapeutic potential. The continued prioritization of inhibitors for these common metabolic pathways potentially limits the identification of inhibitors for novel targets. Therefore, additional steps that identify inhibitors of these common pathways could reshape how high throughput screen hits are prioritized. By applying the targeted mutant screen used to identify MmpL3 inhibitors to a non-prioritized library of hits from a high throughput screen, we identified more than fifty new potential MmpL3 inhibitors. Using an iterative strategy of applying additional mutants of commonly identified targets, this strategy promises to lead to parallel follow-up studies of inhibitors with known and unknown mechanisms of action. The ability of Mtb to enter into quiescent states in response to host stresses is one of the leading causes for the extended time to cure and evolution of drug resistance. These states can be induced by several environmental stresses including acidic pH, hypoxia, and others. In an effort to study this adaptation in the rapidly growing mycobacterial species M. smegmatis, we identified a lethal sodium citrate phenotype. Transcriptional profiling and genetic screening of mutants tolerant to sodium citrate indicated that this phenotype was due to the combined action of both chelation and osmotic stresses. Cell viability could be reduced from sodium citrate killing by cation and osmoprotectant supplementation. From these experiments we propose a model that can be applied to study carbon source uptake and probe the role of genes identified from the forward genetic screen with unknown function
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Title: SOCIOECOLOGICAL PREDICTORS OF MICROBIOME VARIATION IN WILD POPULATIONS OF AFRICAN MAMMALS
Creator: Rojas, Connie A.
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Host-associated microbial communities (e.g. microbiomes) influence multiple aspects of their host’s phenotype. Over a decade of research shows that the microbiome can vary with both host factors and environmental factors. However, much of the existing literature has been limited to intestinal microbiomes and to laboratory and domesticated animals. Multi-body site and longitudinal analyses of the microbiomes of wild mammals are lacking. Here, I address these gaps in knowledge and use DNA...
Show moreHost-associated microbial communities (e.g. microbiomes) influence multiple aspects of their host’s phenotype. Over a decade of research shows that the microbiome can vary with both host factors and environmental factors. However, much of the existing literature has been limited to intestinal microbiomes and to laboratory and domesticated animals. Multi-body site and longitudinal analyses of the microbiomes of wild mammals are lacking. Here, I address these gaps in knowledge and use DNA sequencing to survey the microbiomes of a highly gregarious carnivore, the spotted hyena (Crocuta crocuta). Due to their complex societies, spotted hyenas offer an excellent model system for investigating how host physiology and ecology interact with the microbiome, and for elucidating the contributions of the microbiome to host function. In this dissertation, I leverage over three decades of data and samples collected by my adviser from wild hyenas residing in the Masai Mara National Reserve, Kenya (MMNR). Because this dissertation involved many collaborations with other scientists, I use the first person plural throughout this dissertation. In Chapter 1, I evaluate whether the microbiomes at six body-sites vary with host age, sex, and social rank in spotted hyenas, and find that the microbiome is distinct among body sites, and that this differentiation in microbiomes occurs early in life. For Chapter 2, I conduct a longitudinal analysis of the gut microbiome across 3 generations of spotted hyenas from 4 lineages, and elucidate the potential ways gut microbes may be contributing to their host’s digestion of animal carcasses. Findings show that the composition of the gut microbiome is highly variable across time, but its functional repertoire of genes is highly consistent. Furthermore, our analyses reveal that the abundances of bacterial taxa are associated with long-term ecological changes in livestock grazing, anthropogenic disturbance, and herbivore densities that occurred in the Masai Mara reserve. Chapter 3 inquires whether host social interactions and close associations between individuals shape gut microbiota similarity and diversity in a social group of spotted hyenas, which exhibit fission-fusion dynamics. Consistent with our hypothesis, close hyena affiliates share a greater number of bacterial types than hyena dyads that rarely encountered one another, but contrary to our hypothesis, more socially connected individuals do not harbor more diverse gut microbiotas than more isolated individuals. Chapter 4 compares the gut microbiomes of 11 species of sympatric African herbivores from the MMNR and Laikipia region in Kenya, and determines the relative influence of host diet and host phylogenetic relatedness in structuring the microbiome. My findings indicate that across distantly related hosts, herbivore gut microbiotas are strongly shaped by host phylogenetic relatedness and taxonomy, but among closely related hosts, host diet explains the most variation in the gut microbiota. Findings suggest that the gut microbiota is species-specific, but can be further modified by host ecology, including host diet and geography, especially among closely related host species. Overall, my dissertation provides novel insight regarding the factors shaping the gut microbiome in wild carnivores and herbivores, at individual, group-level, and ecosystem-wide scales.
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Title: WILDFIRE IMPACTS ON SOIL CARBON POOLS AND MICROBIAL COMMUNITIES IN MIXED-CONIFER FORESTS OF CALIFORNIA
Creator: Adkins, Jaron
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Forest ecosystems are important reservoirs for long term carbon (C) storage. Forests of the western United States account for 20-40% of total U.S. carbon C sequestration, and nearly half of the total C in these forests is stored in soil. However, many forests in the western U.S are experiencing wildfire conditions that diverge from historical fire regimes. Prior to Euro-American settlement, California’s mixed-conifer forests typically experienced frequent surface fires of low to moderate burn...
Show moreForest ecosystems are important reservoirs for long term carbon (C) storage. Forests of the western United States account for 20-40% of total U.S. carbon C sequestration, and nearly half of the total C in these forests is stored in soil. However, many forests in the western U.S are experiencing wildfire conditions that diverge from historical fire regimes. Prior to Euro-American settlement, California’s mixed-conifer forests typically experienced frequent surface fires of low to moderate burn severity, but, due to the combined effects of altered forest structure and climate change, now experience fires that are larger and more severe than historical conditions. Fires have numerous direct and indirect effects on the soil biological, chemical, and physical characteristics that influence the soil C cycle. Understanding how altered soil characteristics influence the cycling and persistence of soil C, and how they vary with severity, is important for managing forests for C storage and for predicting fire-climate feedbacks. My dissertation work incorporates observational and manipulative experiments to understand the direct and indirect effects of burn severity on soil C cycling and microbial communities over the short to intermediate term, with a particular focus on the distribution of soil C between active and slow cycling pools. Soil C can be conceptualized as discrete pools of variable persistence in soil. The active C pool is quickly decomposed, contributing to the return of CO2 to the atmosphere, whereas the non-active C pool is more stable and contributes to long term C storage. I leveraged a burn severity gradient resulting from a wildfire in a California mixed-conifer forest to determine the structure and kinetics of these C pools at an intermediate time point in post-fire recovery (i.e. three years). I found that the size of the non-active C pool was smaller in burned areas than unburned areas, and the kinetic rate of the non-active C pool was negatively related to burn severity. I also characterized the soil microbial communities across this severity gradient and identified the environmental characteristics responsible for differences. I found that fungal-to-bacterial ratio and oligotroph-to-copiotroph bacteria ratio decreased with burn severity, and these effects were driven by differences in live and dead tree basal area, soil nutrients, and pH. Leveraging another burn severity gradient, I then determined whether differences in microbial communities and soil C pools were related one-year post-fire in a mixed-conifer forest. I again found lower non-active C pool kinetic rates, and higher abundances of copiotrophic bacteria in burned compared to unburned areas. Differences in soil C pool kinetics were related to tree basal area, soil nutrients, and bacterial communities. I determined the short-term impacts of fire on soil C pools and cycling using lab experiments in which I manipulated soil heating intensity and pyrogenic organic matter (PyOM) additions. I found that high intensity soil heating can decrease microbial biomass C (MBC) accumulation, whereas PyOM had minimal effects on MBC in the short-term. Finally, I found that the size of the active C pool increased with soil heating intensity, while the kinetic rate of the non-active C pool decreased; PyOM primarily increased the size of the non-active C pool. Taken as a whole, my research suggests that fire induces short-term soil C losses by increasing the size of the active C pool, but, over the intermediate-term, residual soil C is more persistent. Fire severity is predicted to increase globally throughout the 21st century, and my research contributes to understanding how forest C storage will be affected by disrupted wildfire regimes.
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