Matching Items (82)
Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
Description
The study of bacterial resistance to antimicrobial peptides (AMPs) is a significant area of interest as these peptides have the potential to be developed into alternative drug therapies to combat microbial pathogens. AMPs represent a class of host-mediated factors that function to prevent microbial infection of their host and serve as a first line of defense. To date, over 1,000 AMPs of various natures have been predicted or experimentally characterized. Their potent bactericidal activities and broad-based target repertoire make them a promising next-generation pharmaceutical therapy to combat bacterial pathogens. It is important to understand the molecular mechanisms, both genetic and physiological, that bacteria employ to circumvent the bactericidal activities of AMPs. These understandings will allow researchers to overcome challenges posed with the development of new drug therapies; as well as identify, at a fundamental level, how bacteria are able to adapt and survive within varied host environments. Here, results are presented from the first reported large scale, systematic screen in which the Keio collection of ~4,000 Escherichia coli deletion mutants were challenged against physiologically significant AMPs to identify genes required for resistance. Less than 3% of the total number of genes on the E. coli chromosome was determined to contribute to bacterial resistance to at least one AMP analyzed in the screen. Further, the screen implicated a single cellular component (enterobacterial common antigen, ECA) and a single transporter system (twin-arginine transporter, Tat) as being required for resistance to each AMP class. Using antimicrobial resistance as a tool to identify novel genetic mechanisms, subsequent analyses were able to identify a two-component system, CpxR/CpxA, as a global regulator in bacterial resistance to AMPs. Multiple previously characterized CpxR/A members, as well as members found in this study, were identified in the screen. Notably, CpxR/A was found to transcriptionally regulate the gene cluster responsible for the biosynthesis of the ECA. Thus, a novel genetic mechanism was uncovered that directly correlates with a physiologically significant cellular component that appears to globally contribute to bacterial resistance to AMPs.
ContributorsWeatherspoon-Griffin, Natasha (Author) / Shi, Yixin (Thesis advisor) / Clark-Curtiss, Josephine (Committee member) / Misra, Rajeev (Committee member) / Nickerson, Cheryl (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Nowadays product reliability becomes the top concern of the manufacturers and customers always prefer the products with good performances under long period. In order to estimate the lifetime of the product, accelerated life testing (ALT) is introduced because most of the products can last years even decades. Much research has been done in the ALT area and optimal design for ALT is a major topic. This dissertation consists of three main studies. First, a methodology of finding optimal design for ALT with right censoring and interval censoring have been developed and it employs the proportional hazard (PH) model and generalized linear model (GLM) to simplify the computational process. A sensitivity study is also given to show the effects brought by parameters to the designs. Second, an extended version of I-optimal design for ALT is discussed and then a dual-objective design criterion is defined and showed with several examples. Also in order to evaluate different candidate designs, several graphical tools are developed. Finally, when there are more than one models available, different model checking designs are discussed.
ContributorsYang, Tao (Author) / Pan, Rong (Thesis advisor) / Montgomery, Douglas C. (Committee member) / Borror, Connie (Committee member) / Rigdon, Steve (Committee member) / Arizona State University (Publisher)
Created2013
Description
During the initial stages of experimentation, there are usually a large number of factors to be investigated. Fractional factorial (2^(k-p)) designs are particularly useful during this initial phase of experimental work. These experiments often referred to as screening experiments help reduce the large number of factors to a smaller set. The 16 run regular fractional factorial designs for six, seven and eight factors are in common usage. These designs allow clear estimation of all main effects when the three-factor and higher order interactions are negligible, but all two-factor interactions are aliased with each other making estimation of these effects problematic without additional runs. Alternatively, certain nonregular designs called no-confounding (NC) designs by Jones and Montgomery (Jones & Montgomery, Alternatives to resolution IV screening designs in 16 runs, 2010) partially confound the main effects with the two-factor interactions but do not completely confound any two-factor interactions with each other. The NC designs are useful for independently estimating main effects and two-factor interactions without additional runs. While several methods have been suggested for the analysis of data from nonregular designs, stepwise regression is familiar to practitioners, available in commercial software, and is widely used in practice. Given that an NC design has been run, the performance of stepwise regression for model selection is unknown. In this dissertation I present a comprehensive simulation study evaluating stepwise regression for analyzing both regular fractional factorial and NC designs. Next, the projection properties of the six, seven and eight factor NC designs are studied. Studying the projection properties of these designs allows the development of analysis methods to analyze these designs. Lastly the designs and projection properties of 9 to 14 factor NC designs onto three and four factors are presented. Certain recommendations are made on analysis methods for these designs as well.
ContributorsShinde, Shilpa (Author) / Montgomery, Douglas C. (Thesis advisor) / Borror, Connie (Committee member) / Fowler, John (Committee member) / Jones, Bradley (Committee member) / Arizona State University (Publisher)
Created2012
Description
A P-value based method is proposed for statistical monitoring of various types of profiles in phase II. The performance of the proposed method is evaluated by the average run length criterion under various shifts in the intercept, slope and error standard deviation of the model. In our proposed approach, P-values are computed at each level within a sample. If at least one of the P-values is less than a pre-specified significance level, the chart signals out-of-control. The primary advantage of our approach is that only one control chart is required to monitor several parameters simultaneously: the intercept, slope(s), and the error standard deviation. A comprehensive comparison of the proposed method and the existing KMW-Shewhart method for monitoring linear profiles is conducted. In addition, the effect that the number of observations within a sample has on the performance of the proposed method is investigated. The proposed method was also compared to the T^2 method discussed in Kang and Albin (2000) for multivariate, polynomial, and nonlinear profiles. A simulation study shows that overall the proposed P-value method performs satisfactorily for different profile types.
ContributorsAdibi, Azadeh (Author) / Montgomery, Douglas C. (Thesis advisor) / Borror, Connie (Thesis advisor) / Li, Jing (Committee member) / Zhang, Muhong (Committee member) / Arizona State University (Publisher)
Created2013
Description
The ever-changing economic landscape has forced many companies to re-examine their supply chains. Global resourcing and outsourcing of processes has been a strategy many organizations have adopted to reduce cost and to increase their global footprint. This has, however, resulted in increased process complexity and reduced customer satisfaction. In order to meet and exceed customer expectations, many companies are forced to improve quality and on-time delivery, and have looked towards Lean Six Sigma as an approach to enable process improvement. The Lean Six Sigma literature is rich in deployment strategies; however, there is a general lack of a mathematical approach to deploy Lean Six Sigma in a global enterprise. This includes both project identification and prioritization. The research presented here is two-fold. Firstly, a process characterization framework is presented to evaluate processes based on eight characteristics. An unsupervised learning technique, using clustering algorithms, is then utilized to group processes that are Lean Six Sigma conducive. The approach helps Lean Six Sigma deployment champions to identify key areas within the business to focus a Lean Six Sigma deployment. A case study is presented and 33% of the processes were found to be Lean Six Sigma conducive. Secondly, having identified parts of the business that are lean Six Sigma conducive, the next steps are to formulate and prioritize a portfolio of projects. Very often the deployment champion is faced with the decision of selecting a portfolio of Lean Six Sigma projects that meet multiple objectives which could include: maximizing productivity, customer satisfaction or return on investment, while meeting certain budgetary constraints. A multi-period 0-1 knapsack problem is presented that maximizes the expected net savings of the Lean Six Sigma portfolio over the life cycle of the deployment. Finally, a case study is presented that demonstrates the application of the model in a large multinational company. Traditionally, Lean Six Sigma found its roots in manufacturing. The research presented in this dissertation also emphasizes the applicability of the methodology to the non-manufacturing space. Additionally, a comparison is conducted between manufacturing and non-manufacturing processes to highlight the challenges in deploying the methodology in both spaces.
ContributorsDuarte, Brett Marc (Author) / Fowler, John W (Thesis advisor) / Montgomery, Douglas C. (Thesis advisor) / Shunk, Dan (Committee member) / Borror, Connie (Committee member) / Konopka, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation presents methods for the evaluation of ocular surface protection during natural blink function. The evaluation of ocular surface protection is especially important in the diagnosis of dry eye and the evaluation of dry eye severity in clinical trials. Dry eye is a highly prevalent disease affecting vast numbers (between 11% and 22%) of an aging population. There is only one approved therapy with limited efficacy, which results in a huge unmet need. The reason so few drugs have reached approval is a lack of a recognized therapeutic pathway with reproducible endpoints. While the interplay between blink function and ocular surface protection has long been recognized, all currently used evaluation techniques have addressed blink function in isolation from tear film stability, the gold standard of which is Tear Film Break-Up Time (TFBUT). In the first part of this research a manual technique of calculating ocular surface protection during natural blink function through the use of video analysis is developed and evaluated for it's ability to differentiate between dry eye and normal subjects, the results are compared with that of TFBUT. In the second part of this research the technique is improved in precision and automated through the use of video analysis algorithms. This software, called the OPI 2.0 System, is evaluated for accuracy and precision, and comparisons are made between the OPI 2.0 System and other currently recognized dry eye diagnostic techniques (e.g. TFBUT). In the third part of this research the OPI 2.0 System is deployed for use in the evaluation of subjects before, immediately after and 30 minutes after exposure to a controlled adverse environment (CAE), once again the results are compared and contrasted against commonly used dry eye endpoints. The results demonstrate that the evaluation of ocular surface protection using the OPI 2.0 System offers superior accuracy to the current standard, TFBUT.
ContributorsAbelson, Richard (Author) / Montgomery, Douglas C. (Thesis advisor) / Borror, Connie (Committee member) / Shunk, Dan (Committee member) / Pan, Rong (Committee member) / Arizona State University (Publisher)
Created2012
Description
Hepatitis C virus (HCV) is a globally prevalent infection which is a main contributor to the global burden of liver disease. Due to its ability to establish a chronic infection, and the lack of usefulness of traditional neutralizing antibody vaccine design in producing a protective immune response, a preventative vaccine has been notoriously difficult to produce. To overcome this, a vaccine using non-structural protein 3 (NS3) as a target to elicit a T cell specific immune response is thought to be a possible strategy for eliciting a protective immune response against hepatitis C infection. In this paper, a recombinant strain of measles virus (MV) that expresses HCV NS3 protein was analyzed. The replication fitness of this recombinant virus also indicates that this construct replicates at a higher rate than parental measles strain. It is also demonstrated through western blot analysis of protein expression and immunofluorescence that this recombinant virus expresses both the inserted HCV NS3 protein, as well as native measles proteins.
ContributorsWoell, Dana Marie (Author) / Reyes del Valle, Jorge (Thesis director) / Nickerson, Cheryl (Committee member) / Julik, Emily (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05
Description
Clean water for drinking, food preparation, and bathing is essential for astronaut health and safety during long duration habitation of the International Space Station (ISS), including future missions to Mars. Despite stringent water treatment and recycling efforts on the ISS, it is impossible to completely prevent microbial contamination of onboard water supplies. In this work, we used a spaceflight analogue culture system to better understand how the microgravity environment can influence the pathogenesis-related characteristics of Burkholderia cepacia complex (Bcc), an opportunistic pathogen previously recovered from the ISS water system. The results of the present study suggest that there may be important differences in how this pathogen can respond and adapt to spaceflight and other low fluid shear environments encountered during their natural life cycles. Future studies are aimed at understanding the underlying mechanisms responsible for these phenotypes.
ContributorsKang, Bianca Younseon (Author) / Nickerson, Cheryl (Thesis director) / Barrila, Jennifer (Committee member) / Ott, Mark (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The widespread use of statistical analysis in sports-particularly Baseball- has made it increasingly necessary for small and mid-market teams to find ways to maintain their analytical advantages over large market clubs. In baseball, an opportunity for exists for teams with limited financial resources to sign players under team control to long-term contracts before other teams can bid for their services in free agency. If small and mid-market clubs can successfully identify talented players early, clubs can save money, achieve cost certainty and remain competitive for longer periods of time. These deals are also advantageous to players since they receive job security and greater financial dividends earlier in their career. The objective of this paper is to develop a regression-based predictive model that teams can use to forecast the performance of young baseball players with limited Major League experience. There were several tasks conducted to achieve this goal: (1) Data was obtained from Major League Baseball and Lahman's Baseball Database and sorted using Excel macros for easier analysis. (2) Players were separated into three positional groups depending on similar fielding requirements and offensive profiles: Group I was comprised of first and third basemen, Group II contains second basemen, shortstops, and center fielders and Group III contains left and right fielders. (3) Based on the context of baseball and the nature of offensive performance metrics, only players who achieve greater than 200 plate appearances within the first two years of their major league debut are included in this analysis. (4) The statistical software package JMP was used to create regression models of each group and analyze the residuals for any irregularities or normality violations. Once the models were developed, slight adjustments were made to improve the accuracy of the forecasts and identify opportunities for future work. It was discovered that Group I and Group III were the easiest player groupings to forecast while Group II required several attempts to improve the model.
ContributorsJack, Nathan Scott (Author) / Shunk, Dan (Thesis director) / Montgomery, Douglas (Committee member) / Borror, Connie (Committee member) / Industrial, Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2013-05