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Title: Adaptation and divergence in experimental populations of the bacterium escherichia coli : the roles of environment, phylogeny and chance
Creator: Travisano, Michael
Date: 1993
Collection: Electronic Theses & Dissertations

Title: Adhesion of K99-positive enteropathogenic Escherichia coli to pig intestinal brush borders
Creator: Grimes, Sheila D., 1958-
Date: 1984
Collection: Electronic Theses & Dissertations

Title: Alterations in the membrane proteins of FLA, CHE, MOT and HAG mutants of Escherichia coli
Creator: Liao, Chwen Lin
Date: 1976
Collection: Electronic Theses & Dissertations

Title: An analysis of fitness in long-term asexual evolution experiments
Creator: Wiser, Michael J.
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Evolution is the central unifying concept of modern biology. Yet it can be hard to study in natural system, as it unfolds across generations. Experimental evolution allows us to ask questions about the process of evolution itself: How repeatable is the evolutionary process? How predictable is it? How general are the results? To address these questions, my collaborators and I carried out experiments both within the Long-Term Evolution Experiment (LTEE) in the bacteria Escherichia coli, and the...
Show moreEvolution is the central unifying concept of modern biology. Yet it can be hard to study in natural system, as it unfolds across generations. Experimental evolution allows us to ask questions about the process of evolution itself: How repeatable is the evolutionary process? How predictable is it? How general are the results? To address these questions, my collaborators and I carried out experiments both within the Long-Term Evolution Experiment (LTEE) in the bacteria Escherichia coli, and the digital evolution software platform Avida. In Chapter 1, I focused on methods. Previous research in the LTEE has relied on one particular way of measuring fitness, which we know becomes less precise as fitness differentials increase. I therefore decided to test whether two alternate ways of measuring fitness would improve precision, using one focal population. I found that all three methods yielded similar results in both fitness and coefficient of variation, and thus we should retain the traditional method.In Chapter 2, I turned to measuring fitness in each of the populations. Previous work had considered fitness to change as a hyperbola. A hyperbolic function is bounded, and predicts that fitness will asymptotically approach a defined upper bound; however, we knew that fitness in these populations routinely exceeded the asymptotic limit calculated from a hyperbola fit to the earlier data. I instead used to a power law, a mathematical function that does not have an upper bound. I found that this function substantially better describes fitness in this system, both among the whole set of populations, and in most of the individual populations. I also found that the power law models fit on just early subsets of the data accurately predict fitness far into the future. This implies that populations, even after 50,000 generations of evolution in consistent environment, are so far from the tops of fitness peaks that we cannot detect evidence of those peaks.In Chapter 3, I examined to how variance in fitness changes over long time scales. The among-population variance over time provides us information about the adaptive landscape on which the populations have been evolving. I found that among-population variance remains significant. Further, competitions between evolved pairs of populations reveal additional details about fitness trajectories than can be seen from competitions against the ancestor. These results demonstrate that our populations have been evolving on a complex adaptive landscape.In Chapter 4, I examined whether the patterns found in Chapter 2 apply to a very different evolutionary system, Avida. This system incorporates many similar evolutionary pressures as the LTEE, but without the details of cellular biology that underlie nearly all organic life. I find that in both the most complex and simplest environments in Avida, fitness also follows the same power law dynamics as seen in the LTEE. This implies that power law dynamics may be a general feature of evolving systems, and not dependent on the specific details of the system being studied.
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Title: An investigation of the structural components involved in the mechanism of the pH induced switch in the channel size of OmpF porin from E. coli K-12
Creator: Roundtree, John D. (John Dale)
Date: 1998
Collection: Electronic Theses & Dissertations

Title: Anti-late RNA and transcriptional control in T4 bacteriophage infected Escherichia coli
Creator: Frederick, Robert John, 1944-
Date: 1976
Collection: Electronic Theses & Dissertations

Title: Assessment of E. coli and total coliforms in surface irrigation water sources in Michigan blueberry farms
Creator: Alraqibah, Sultan Ali
Date: 2016
Collection: Electronic Theses & Dissertations
Description: Fresh produce that is consumed raw can be a source of pathogens that cause human illness. This is particularly true for produce that is irrigated with untreated surface water at times close to harvest. Michigan has many blueberry farms, and these farms often irrigate their crops using untreated water drawn from irrigation ponds. This research was conducted to quantify E. coli levels in irrigation water sources at six blueberry farms in Michigan, and associate these levels with factors such as...
Show moreFresh produce that is consumed raw can be a source of pathogens that cause human illness. This is particularly true for produce that is irrigated with untreated surface water at times close to harvest. Michigan has many blueberry farms, and these farms often irrigate their crops using untreated water drawn from irrigation ponds. This research was conducted to quantify E. coli levels in irrigation water sources at six blueberry farms in Michigan, and associate these levels with factors such as, rainfall, pH and conductivity of the water, and susceptibility of the water sources to runoff. Samples of water and blueberries were collected during summer 2015. Water samples were obtained twice weekly and blueberry samples once weekly. The Colilert Quanti-Tray/2000 method was used to quantify E. coli. Among the water samples (n=111), 95% contained detectable E. coli, and 17% of samples had E. coli levels greater than 126 MPN/100 ml, - the maximum geometric mean (GM) of E. coli level allowed in agricultural water under the FDA Produce Safety Regulation. The maximum detected level of E. coli was 4,611 MPN. Among the blueberry samples assayed (n=68), only 4.4% tested positive for E. coli, with the maximum level detected being 12 MPN E. coli per 100 grams of blueberries. These results indicate a high likelihood of detecting E. coli in surface irrigation water sources used on selected Michigan blueberry farms, and will be useful in establishing initial water quality profiles for these farms as required under the new FDA Produce Safety Regulation.
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Title: Bioactivities of bovine anti-coliform antibodies elicited by J5 vaccinations
Creator: Chaiyotwittayakun, Anatachai
Date: 2003
Collection: Electronic Theses & Dissertations

Title: Bioavailability of tetracycline in water and soil to Escherichia coli for expression of antibiotic resistance
Creator: Zhang, Yingjie
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Tetracyclines are a class of antimicrobials extensively used as human and veterinary medicine, and in livestock production since they were discovered in the 1940s. A large portion of tetracyclines administered to humans and animals are excreted and subsequently released into the environment, where they pose potential risks to ecosystem and human health. There is a growing concern that the presence of antibiotics such as tetracycline at trace levels in the environment is related to the...
Show moreTetracyclines are a class of antimicrobials extensively used as human and veterinary medicine, and in livestock production since they were discovered in the 1940s. A large portion of tetracyclines administered to humans and animals are excreted and subsequently released into the environment, where they pose potential risks to ecosystem and human health. There is a growing concern that the presence of antibiotics such as tetracycline at trace levels in the environment is related to the emergence and ever-increasing abundance of antibiotic resistance genes in natural and engineered microbial populations. However, basic knowledge at the molecular scale of bacterial access to tetracyclines present in environmental matrices and expression of antibiotic resistance genes remain nearly unknown. In this study, we used the E. coli MC4100/pTGM whole-cell bioreporter as an effective tool to investigate bioavailability of tetracycline in water and soil to bacteria for expression of antibiotic resistance genes. Our hypothesis was that the speciation of tetracycline dissolved in water and sorption by soil minerals controls the bioavailabilities for bacterial uptake and subsequent activation of antibiotic resistance genes. The results revealed that activation of antibiotic resistance in the E. coli bioreporter responded linearly to intracellular tetracycline concentration. The extent of tetracycline uptake by E. coli was modulated by tetracycline speciation. We have identified that zwitterionic tetracycline as the primary species favorable for bacterial uptake. Geochemical factors such as pH, salt composition and concentration influenced the fractional distributions of tetracycline species in aqueous solution and hence altered uptake by E. coli. In addition, the presence of organic ligands could also alter tetracycline speciation by releasing tetracycline from its metal complexes in aqueous solution. For tetracycline associated with Mg-smectite, desorption of tetracycline from clay to solution was the major exposure pathway for bacterial uptake and subsequent activation of antibiotic resistance in the diluted clay suspensions. In clay film cultivation, clay-sorbed tetracycline was still bioaccessible to E. coli evoking strong expression of antibiotic resistance. Direct contact of the E. coli bioreporters with clay surfaces and further formation of biofilms plausibly facilitated tetracycline transfer to bacteria. Overall, this study greatly advances the fundamental understanding of bioavailability of tetracycline in the environment to bacteria for expression of antibiotic resistance genes.
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Title: Biological activity of the lipids from Escherichia coli and Shigella dysenteriae and their characterization by means of infrared spectrophotometry
Creator: Neblett, Thomas Randolph, 1928-
Date: 1957
Collection: Electronic Theses & Dissertations

Title: Breaking biofilms : regulation of Type II secretion system in V. cholerae and the formation of the hyper-pseudopilus
Creator: Sloup, Rudolph E.
Date: 2016
Collection: Electronic Theses & Dissertations
Description: Vibrio cholerae is the causative agent of the human disease cholera, it resides in aquatic resevoirs and forms biofilms, which are closely associated communities of bacteria embedded in polysaccharides, DNA, and proteins. In V. cholerae biofilm formation is regulated by the second messenger molecule cyclic di-GMP (c-di-GMP). A genetic screen for promoters regulated by the c-di-GMP revealed a novel promoter (PepsG) in the eps operon encoding the V. cholerae Type 2 secretion system (T2SS). The...
Show moreVibrio cholerae is the causative agent of the human disease cholera, it resides in aquatic resevoirs and forms biofilms, which are closely associated communities of bacteria embedded in polysaccharides, DNA, and proteins. In V. cholerae biofilm formation is regulated by the second messenger molecule cyclic di-GMP (c-di-GMP). A genetic screen for promoters regulated by the c-di-GMP revealed a novel promoter (PepsG) in the eps operon encoding the V. cholerae Type 2 secretion system (T2SS). The T2SS, which exports proteins from the periplasm to the extracellular space, is phylogenetically related to Type 4 pili. The major pseudopilin is encoded by epsG which forms a short piston like structure necessary for secretion. I hypothesized that differential regulation of the eps operon extends the pseudopilin forming a structure called a hyper-pseudopilus outside the cell where it promotes biofilm development. In Chapter 2, I determined that the promoter upstream of the operon (PepsC1) is induced four fold by c-di-GMP and this induction is mediated by the c-di-GMP binding transcription factor VpsR directly. High levels of c-di-GMP were found to decrease the activity of extra cellular proteases secreted by the T2SS, however this effect was not a direct result of regulation of the T2SS as determined by mutation of the VpsR binding site in PepsC1. I was unable to establish a phenotype for the transcriptional control of the eps operon. This work establishes T2S as a new phenotype which is transcriptionally controlled by c-di-GMP and the biofilm associated transcription factor VpsR. In Chapter 3, I show that overexpression of epsG in a continuous flow cell system increased V. cholerae biofilms while a ΔepsG strain showed no biofilm formation. However, there was no change in activity of T2S dependent serine proteases while epsG was over expressed indicating increased biofilms is not likely due to increased secretion. Polyclonal antibody stained EpsG was also detectable on the surface of WT cells and long pseudopili were visualized with over expression of epsG. This evidence suggests the T2SS forms a hyper-pseudopilus important for biofilm formation. In Chapter 4, I present my work identifying novel anti-biofilm compounds. In 2011 Escherichia coli O104:H4 caused the deadliest E. coli outbreak in modern times resulting in 54 deaths and the highest rate of hemolytic uremic syndrome ever recorded. Subsequently, we showed a correlation between biofilm gene expression and virulence factor expression. I sought to identify small molecule compounds effective at inhibiting O104:H4 biofilms. I discovered at a concentration of 0.01% the nonionic surfactants polysorbate 80 (PS80) and polysorbate 20 (PS20) were found to inhibit biofilm formation by 90% and 91% respectively. These compounds were able to disperse preformed biofilms. Treatment of mice infected with E. coli O104:H4 resulted in high bacterial loads and inflammation. While addition of PS80 in the drinking water of the mice did not reduce bacterial loads, it completely abolished inflammation symptoms. PS80 is an FDA approved compound, well studied and effective at low nanomolar concentrations that reduces symptoms of infection in mice. which establishes it as an excellent candidate for further study as an anti-infective agent with anti-biofilm capabilities
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Title: Cell division in cis-platinum(II)diamminodichloride-induced filaments of Escherichia coli : dependence upon completion of deoxyribonucleic acid repair and a protease activity
Creator: Markham, Bruce Edward
Date: 1980
Collection: Electronic Theses & Dissertations

Title: Characterization of E. coli Aid B : a component of the adaptive response to alkylating agents
Creator: Rohankhedkar, Mukta S.
Date: 2005
Collection: Electronic Theses & Dissertations

Title: Characterization of OmpC and OmpF porins from Escherichia coli K-12
Creator: Rocque, Warren J.
Date: 1990
Collection: Electronic Theses & Dissertations

Title: Characterization of ion exchange resins for the immobilization of Escherichia Coli
Creator: Czupski, Leonard Matthew
Date: 1989
Collection: Electronic Theses & Dissertations

Title: Cloning of the polysaccharide depolymerase gene of bacteriophage pea1 (h) and its expression in Erwinia amylovora
Creator: Hartung, John Stephen
Date: 1985
Collection: Electronic Theses & Dissertations

Title: Coevolution of bacterial-phage interactions
Creator: Meyer, Justin R.
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Bacteria and their viruses, phage, are the most abundant and genetically diverse group of organisms on earth. Given their prevalence, it is no wonder that recent studies have found their interactions important for ecosystem function, as well as the health of humans. Unfortunately, because of technical challenges with studying microbes, some of the most basic questions on their interactions, such as who infects whom, and how their relationships evolved in the first place, remain unanswered....
Show moreBacteria and their viruses, phage, are the most abundant and genetically diverse group of organisms on earth. Given their prevalence, it is no wonder that recent studies have found their interactions important for ecosystem function, as well as the health of humans. Unfortunately, because of technical challenges with studying microbes, some of the most basic questions on their interactions, such as who infects whom, and how their relationships evolved in the first place, remain unanswered. Here I report six studies on bacterial-phage interactions, each focused on understanding their pattern and the underlying biophysical, ecological, and evolutionary processes that shape them. To do this, I tested a number of hypotheses using laboratory experiments and analyses of natural microbial diversity. First, I tested whether Esherichia coli cultured without phage would counter-intuitively evolve new interactions with phage. Typically bacterial traits responsible for phage resistance have pleiotropic consequences on growth, therefore as a side-effect of adapting to an abiotic environment, bacteria may also evolve to become more or less vulnerable to their parasites. After 45,000 generations of laboratory culturing without phage, E. coli gained resistance to lambda phage, gained sensitivity to a mutant T6 phage, and remained resistant to wild type T6. Each response was explained by understanding the pleiotropic costs or benefits of mutations that confer resistance. Because of pleiotropy, interactions may even evolve in the absence of one player.For the rest of my studies I examined how interactions evolve when host and parasite co-occur. First, I found that when E. coli and phage lambda are cocultured, E. coli evolves resistance by reducing the number of phage genotypes that can infect it, whereas, lambda evolves to increase the number of bacterial genotypes it can infect. This antagonism produces a interaction matrix with a nested form where less derived host-ranges fall one within another. To determine whether this nested pattern is an artifact of the labratory environment, or if the pattern is general to natural communities, I performed a metaanalysis on already published phage-bacterial interaction matrices. The majority of networks were significantly nested (28 of 38). Lastly, I examined the molecular basis of E. coli resistance to lambda and found that resistance often evolves through mutations in E. coli's lamB, the gene for the phage receptor. Also, the strength of resistance is correlated with how the mutation perturbs the orientation specific features of the protein structure, primarily loop four which extends out of the cell membrane. For the final two chapters, I studied whether lambda could evolve to target a novel receptor and the evolutionary consequences of such an innovation. Under particular laboratory conditions, E. coli evolves resistance by down-regulating LamB, which sets the stage for lambda to evolve the necessary mutations to exploit a new protein receptor. When allowed to coevolve under this condition, lambda evolved to exploit another outer-membrane protein, OmpF. This new function is the result of a particular combination of four mutations in J, the gene for the protein ligand lambda uses to bind to its host. Once lambda evolves this novel interaction, an evolutionary arms-race begins that drives rapid diversification of the bacteria and phage. Overall, my studies show that coevolution between bacteria and phage, whether it be in the lab or in nature, produces nested interactions matrices. Secondly, antagonistic coevolution is a creative process able to generate new genotypes of host and parasite and promote the evolution of novel function. Lastly, costs for resistance have many important effects, from determining whether resistance will evolve or be lost, to the generation of diversity.
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Title: Comparison of Escherichia coli and Streptococcus faecalis as a test organism to determine the sanitary quality of food
Creator: Allen, Clarence Henry
Date: 1951
Collection: Electronic Theses & Dissertations

Title: Constraining mechanistic models of indicator bacteria at recreational beaches in Lake Michigan using easily-measurable environmental variables
Creator: Wendzel, Aaron
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Beach closures have significant economic and human health implications. The ability to create and use near-real time hydrodynamic and transport models that simulate fecal indicator bacteria (FIB) levels at our nation's recreational beaches is important to effectively managing coastal resources. Described herein is the development and application of an unsteady, three- dimensional hydrodynamic fate and transport model constrained using easily measurable environmental variables such as...
Show moreBeach closures have significant economic and human health implications. The ability to create and use near-real time hydrodynamic and transport models that simulate fecal indicator bacteria (FIB) levels at our nation's recreational beaches is important to effectively managing coastal resources. Described herein is the development and application of an unsteady, three- dimensional hydrodynamic fate and transport model constrained using easily measurable environmental variables such as electrical conductivity (EC) and turbidity. The model was able to simulate observed Escherichi coli (E. coli) concentrations at three beaches in close proximity to the Burns Waterway along the Indiana Dunes National Lakeshore. This model utilized an unstructured grid that has the ability to accurately represent local features in the area, including the complex shoreline and breakwaters that influence hydrodynamics and mixing. This allows for the better prediction of FIB at local beaches, reducing human health risks and decreasing the number of unnecessary beach closures.
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Title: Conversion of the mitochondrial gene for mammalian cytochrome oxidase subunit II to a universal equivalent and expression in E. coli, in vitro, and in Xenopus oocytes
Creator: Cao, Jianli
Date: 1990
Collection: Electronic Theses & Dissertations

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