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Pages
- Title
- Strategies for improving synthesis of quinic acid and shikimic acid from D-glucose
- Creator
- Jancauskas, Justas
- Date
- 2008
- 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
- Selected studies on the somatic antigens of Escherichia coli 0111 and B₄ and 055 B₅ Isolated as the Impure Polysaccharides
- Creator
- Ellis, Edwin Marshall, 1914-
- Date
- 1954
- Collection
- Electronic Theses & Dissertations
- Title
- Piliated Escherichia coli and porcine enteric disease in Michigan
- Creator
- Evans, Mark G.
- Date
- 1983
- Collection
- Electronic Theses & Dissertations
- Title
- Enteric colibacillosis in gnotobiotic swine : fluorescence and electron microscopic studies
- Creator
- Drees, David T., 1933-
- Date
- 1969
- Collection
- Electronic Theses & Dissertations
- Title
- Membrane structural transitions modulate growth limits of Escherichia coli
- Creator
- Janoff, Andrew Stuart
- Date
- 1980
- Collection
- Electronic Theses & Dissertations
- Title
- Evidence for the formation of Pyridoximine-5-phosphate by the biodegradative L-threonine dehydrase of E̲s̲c̲h̲e̲r̲i̲c̲h̲i̲a̲ c̲o̲l̲i̲
- Creator
- Riebow, John Frank
- Date
- 1978
- Collection
- Electronic Theses & Dissertations
- Title
- X-ray crystallographic studies of Escherichia coli branching enzyme in complex with maltooctaose and rice branching enzyme I in complex with dodecaose
- Creator
- Fawaz, Remie
- Date
- 2016
- Collection
- Electronic Theses & Dissertations
- Description
-
ABSTRACTX-RAY CRYSTALLOGRAPHIC STUDIES OF ESCHERICHIA COLI BRANCHING ENZYME IN COMPLEX WITH MALTOOCTAOSE AND RICE BRANCHING ENZYME I IN COMPLEX WITH DODECAOSEByRemie FawazBranching enzyme plays a key role in determining the final structure of glycogen or starch; this outcome structure is unique to every species, therefore the diversity of branching enzymes structures. While the biosynthesis of the polymers constitutes of three major steps, the last reaction of the pathway catalyzed by...
Show moreABSTRACTX-RAY CRYSTALLOGRAPHIC STUDIES OF ESCHERICHIA COLI BRANCHING ENZYME IN COMPLEX WITH MALTOOCTAOSE AND RICE BRANCHING ENZYME I IN COMPLEX WITH DODECAOSEByRemie FawazBranching enzyme plays a key role in determining the final structure of glycogen or starch; this outcome structure is unique to every species, therefore the diversity of branching enzymes structures. While the biosynthesis of the polymers constitutes of three major steps, the last reaction of the pathway catalyzed by branching enzyme embodies the cleavage of the α-1,4 glycosidic bond and the transfer of the produced oligosaccharide to the specific α-1,6 position creating an α-1,6 branch point. This process results in highly branched polymeric structures, which represent major carbon sources and carbohydrate storage compounds in living organisms, and are essential both in nature and industry. The structure of Escherichia coli glycogen branching enzyme has been solved both in the apo and holo forms. Binding to linear and cyclic oligosaccharides has been studied and showed seven external binding sites, but binding in the active site was not seen. Oligomers longer than previously used were investigated in an attempt to see binding in the catalytic center, only to discover more peripheral binding sites seemingly independent of each other. Examining the binding sites’ locations and sugars’ orientations indicates that these sites probably cooperate together in order to hold the long sugar polymer on the surface of the protein during the branching reaction. Hypotheses regarding the mode of binding between E. coli branching enzyme and the sugar during the reaction, and the roles for key binding sites and residues in the mechanism are proposed.Rice branching enzyme I, a starch branching enzyme, was also previously crystallized and the structure of the truncated version was solved. Binding attempts on this protein showed surface binding sites as well. In an effort to better understand the mechanism of action of this enzyme, we crystallized the protein and soaked it in a 12-unit oligomer, which bound to the enzyme hanging over the active site without reaching into the groove. Two new binding sites were discovered for this protein and the residues involved were identified. There are several hydrogen bonds and aromatic stacking interactions within the binding sties. Hypotheses for the binding mode and reaction mechanism are proposed.In addition, we have worked on ADP-glucose pyrophosphorylases that catalyze the first step in the biosynthesis pathway. The small subunit of the protein expresses as a homotetramer that is highly active. Although the potato tuber form was previously expressed in a collaborating laboratory at extremely small levels, and the protein was crystallized in the inactive form in the Geiger lab, our intensive attempts only succeeded in purifying the protein of interest, but the enzyme would precipitate instead of concentrating.
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- 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
- The relationship between substrate concentration, respiration rate, and growth rate of Escherichia coli in continuous flow culture
- Creator
- Lipe, Robert Sterling
- Date
- 1961
- Collection
- Electronic Theses & Dissertations
- 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
- 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
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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
- Investigation of bacterial fecal indicators and coliphage virus in sediment and surface water of parks and beaches along the Grand River (MI) and Lake Michigan (MI)
- Creator
- Singh, Shikha
- Date
- 2007
- Collection
- Electronic Theses & Dissertations
- Title
- Microfiltration process for enhanced production of rDNA receptor cells of Escherichia coli
- Creator
- Anderson, Kevin Warren
- Date
- 1983
- Collection
- Electronic Theses & Dissertations
- Title
- Enzymatic characteristics of a-galactosidases from Aspergillus niger, coffee beans and Escherichia coli
- Creator
- Gavriel, Penelope
- Date
- 1984
- Collection
- Electronic Theses & Dissertations
- Title
- Rapid concentration/detection of Escherichia coli O157:H7 and Listeria monocytogenes from lettuce wash water
- Creator
- Gustafson, Ryann Elizabeth
- Date
- 2017
- Collection
- Electronic Theses & Dissertations
- Description
-
"Dead-end ultrafiltration concentration (DEUF-C) prior to qPCR or standard enrichment was used to determine presence/absence of Escherichia coli O157:H7 (Ec) and Listeria monocytogenes (Lm) in various lettuce wash waters generated using both a pilot- and commercial scale processing line. After inoculating and pilot-scale processing of the ice berg lettuce, 8 of 24 (33%) of Ec and Lm samples were positive by DEUF-C, but negative by commercial FDA BAM. In addition, populations of both pathogens...
Show more"Dead-end ultrafiltration concentration (DEUF-C) prior to qPCR or standard enrichment was used to determine presence/absence of Escherichia coli O157:H7 (Ec) and Listeria monocytogenes (Lm) in various lettuce wash waters generated using both a pilot- and commercial scale processing line. After inoculating and pilot-scale processing of the ice berg lettuce, 8 of 24 (33%) of Ec and Lm samples were positive by DEUF-C, but negative by commercial FDA BAM. In addition, populations of both pathogens were significantly higher in DEUF-C samples compared to unconcentrated samples after 7 h of enrichment (P < 0.05). Using the commercial-scale processing line, 14 of 14 (100%) samples yielded Ec and Lm using DEUF-C compared to 1 of 15 (6.7%) and 3 of 15 (20%) wash water grab samples, respectively. Higher total filterable volumes were achieved for flume (30.6 + 9.9 L) compared to centrifugation water (9.9 + 2.0 L) (P < 0.05). Ec and Lm were also detected in 16 of 16 (100%) DEUF-C samples compared to 2 of 18 (11.1%) and 3 of 18 (16.7%) grab samples, respectively, from a commercial-scale test facility. These studies indicate that DEUF-C can detect lower levels of Ec and Lm in lettuce wash water compared to standard culture methods. However, the filtration times and total filterable volumes will need to be further improved for commercial produce wash and centrifugation water containing high organic loads."--Page ii.
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- Title
- Mechanism of forelimb skin and skeletal muscle glucose uptake during Escherichia coli endotoxin shock in the dog
- Creator
- Karlstad, Michael Donald
- Date
- 1982
- Collection
- Electronic Theses & Dissertations
- Title
- The effects of genetic background on the evolution of antibiotic resistance and its fitness costs
- Creator
- Card, Kyle Joseph
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
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Antibiotic resistance is a growing public-health concern. Efforts to control the emergence and spread of resistance would benefit from an improved ability to forecast when and how it will evolve. To predict the evolution of resistance with accuracy, we must understand and integrate information about many factors, including a bacterium's evolutionary history. This dissertation centers on the effects of genetic background on the evolution of phenotypic resistance, its genetic basis, and its...
Show moreAntibiotic resistance is a growing public-health concern. Efforts to control the emergence and spread of resistance would benefit from an improved ability to forecast when and how it will evolve. To predict the evolution of resistance with accuracy, we must understand and integrate information about many factors, including a bacterium's evolutionary history. This dissertation centers on the effects of genetic background on the evolution of phenotypic resistance, its genetic basis, and its fitness costs. To address these issues, I used Escherichia coli strains from the long-term evolution experiment (LTEE) that independently evolved for multiple decades in an environment without antibiotics.First, I examined how readily these LTEE strains could overcome prior losses of intrinsic resistance through subsequent evolution when challenged with antibiotics. Second, I investigated whether lineages founded from different genotypes take parallel or divergent mutational paths to achieve increased resistance. Third, I tested whether fitness costs of resistance mutations are constant across different genetic backgrounds. In these studies, I focused attention on the interplay between repeatability and contingency in the evolutionary process. My findings demonstrate that genetic background can influence both the phenotypic and genotypic evolution of resistance and its associated fitness costs. I conclude this dissertation with a broader discussion about these and other factors that can influence the evolution of antibiotic resistance, and their clinical and public-health implications.
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- Title
- Deconstructing the correlated nature of ancient and emergent traits : an evolutionary investigation of metabolism, morphology, and mortality
- Creator
- Grant, Nkrumah Alions
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
-
Phenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have...
Show morePhenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have maintained - and even improved - the capacity of E. coli to grow in an anoxic environment despite 50,000 generations of relaxed selection for anaerobic growth. I present genomic evidence illustrating substantially more mutations have accumulated in anaerobic-specific genes and show parallel evolution at two genetic loci whose protein products regulate the aerobic-to-anaerobic metabolic switch. My findings reject the "if you don't use it, you lose it" notion underpinning relaxed selection and show modules with deep evolutionary roots can overlap more, hence making them harder to break. In chapter 2, I revisit previous work in the LTEE showing that the fitness increases measured for the 12 populations positively correlated with an increase in cell size. This finding was contrary to theory predicting smaller cells should have evolved. Sixty thousand generations have surpassed since that initial study, and new fitness data collected for the 12 populations show fitness has continued to increase over this period. Here, I asked whether cell size also continued to increase. To this end, I measured the size of cells for each of the 12 populations spanning 50,000 generations of evolution using a particle counter, microscopy, and machine learning. I show cell size has continued to increase and that it remains positively correlated with fitness. I also present several other observations including heterogeneity in cell shape and size, parallel mutations in cell-shape determining genes, and elevated cell death in the single LTEE population that evolved a novel metabolism - namely the ability to grow aerobically on citrate. This last observation formed the basis of my chapter 3 research where my collaborators and I fully examine the cell death finding and the associated genotypic and phenotypic consequences of the citrate metabolic innovation.
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- Title
- Reductive dechlorination of P, Pʹ-DDT by escherichia coli and pseudomonas aeruginosa
- Creator
- French, Allen Lee, 1939-
- Date
- 1968
- Collection
- Electronic Theses & Dissertations