Matching Items (12)
Filtering by
- All Subjects: Microbiology
- All Subjects: SOLS
- All Subjects: Mycobacterium tuberculosis--Genetics.
- Creators: Haydel, Shelley
- Member of: Theses and Dissertations
- Status: Published
Description
2D fetal echocardiography (ECHO) can be used for monitoring heart development in utero. This study’s purpose is to empirically model normal fetal heart growth and function changes during development by ECHO and compare these to fetuses diagnosed with and without cardiomyopathy with diabetic mothers. There are existing mathematical models describing fetal heart development but they warrant revalidation and adjustment. 377 normal fetuses with healthy mothers, 98 normal fetuses with diabetic mothers, and 37 fetuses with cardiomyopathy and diabetic mothers had their cardiac structural dimensions, cardiothoracic ratio, valve flow velocities, and heart rates measured by fetal ECHO in a retrospective chart review. Cardiac features were fitted to linear functions, with respect to gestational age, femur length, head circumference, and biparietal diameter and z-scores were created to model normal fetal growth for all parameters. These z-scores were used to assess what metrics had no difference in means between the normal fetuses of both healthy and diabetic mothers, but differed from those diagnosed with cardiomyopathy. It was found that functional metrics like mitral and tricuspid E wave and pulmonary velocity could be important predictors for cardiomyopathy when fitted by gestational age, femur length, head circumference, and biparietal diameter. Additionally, aortic and tricuspid annulus diameters when fitted to estimated gestational age showed potential to be predictors for fetal cardiomyopathy. While the metrics overlapped over their full range, combining them together may have the potential for predicting cardiomyopathy in utero. Future directions of this study will explore creating a classifier model that can predict cardiomyopathy using the metrics assessed in this study.
ContributorsNumani, Asfia (Co-author) / Mishra, Shambhavi (Co-author) / Sweazea, Karen (Thesis director) / Plasencia, Jon (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
This study examines the effect of the translation of traditional scientific vocabulary into plain English, a process referred to as Anglicization, on student learning in the context of introductory microbiology instruction. Data from Anglicized and Classical-vocabulary lab sections were collected. Data included exam scores as well as pre and post-course surveys on reasoning skills, impressions of biology, science and the course, and microbiology knowledge. Students subjected to Anglicized instruction performed significantly better on exams that assessed their abilities to apply and analyze knowledge from the course, and gained similar amounts of knowledge during the course when compared to peers instructed with standard vocabulary. Their performance in upper-level courses was also better than that of their traditionally educated peers. Hypotheses related to the effect are presented and evaluated; implications for instruction are discussed.
ContributorsRichter, Emily (Author) / Lawson, Anton (Thesis advisor) / Stout, Valerie (Committee member) / Haydel, Shelley (Committee member) / Atkinson, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
Pseudomonas aeruginosa is an opportunistic bacterial pathogen commonly associated with increased morbidity and mortality in cystic fibrosis (CF) patients. To adapt to the CF lung environment, P. aeruginosa undergoes multiple genetic changes as it moves from an acute to a chronic infection. The resultant phenotypes have been associated with chronic infection and can provide important information to track the patient’s individualized disease progression. This study examines the link between the accumulation of QS genetic mutations and phenotypic expression in P. aeruginosa laboratory strains and clinical isolates. We utilized several plate-based and colorimetric assays to quantify the production of pyocyanin, rhamnolipids, and protease from paired clinical early- and late-stage chronic infection isolates across 16 patients. Exoproduct production of each isolate was compared to the mean production of pooled isolates to classify high producing (QS-sufficient) and low producing (QS-deficient) isolates. We found that over time P. aeruginosa isolates exhibit a reduction in QS-related phenotypes during chronic infections. Future research of the QS regulatory networks will identify whether reversion of genotype will result in corresponding phenotypic changes in QS-deficient chronic infection isolates.
ContributorsKaranjia, Ava Vispi (Author) / Bean, Heather (Thesis director) / Haydel, Shelley (Committee member) / Davis, Trenton (Committee member) / School of Life Sciences (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Cystic Fibrosis (CF) is a genetic disorder that disrupts the hydration of mucous of the lungs, which promotes opportunistic bacterial infections that begin in the affected person’s childhood, and persist into adulthood. One of the bacteria that infect the CF lung is Pseudomonas aeruginosa. This gram-negative bacterium is acquired from the environment of the CF lung, changing the expression of phenotypes over the course of the infection. As P. aeruginosa infections become chronic, some phenotype changes are known to be linked with negative patient outcomes. An important exoproduct phenotype is rhamnolipid production, which is a glycolipid that P. aeruginosa produces as a surfactant for surface-mediated travel. Over time, the expression of this phenotype decreases in expression in the CF lung.
The objective of this investigation is to evaluate how environmental changes that are related to the growth environment in the CF lung alters rhamnolipid production. Thirty-five P. aeruginosa isolates from Dartmouth College and Seattle Children’s Hospital were selected to observe the impact of temperature, presence of Staphylococcus aureus metabolites, and oxygen availability on rhamnolipid production. It was found that the rhamnolipid production significantly decreased for 30C versus 37C, but not at 40C. The addition of S. aureus spent media, in any of the tested conditions, did not influence rhamnolipid production. Finally, the change in oxygen concentration from normoxia to hypoxia significantly reduced rhamnolipid production. These results were compared to swarming assay data to understand how changes in rhamnolipid production impact surface-mediated motility.
The objective of this investigation is to evaluate how environmental changes that are related to the growth environment in the CF lung alters rhamnolipid production. Thirty-five P. aeruginosa isolates from Dartmouth College and Seattle Children’s Hospital were selected to observe the impact of temperature, presence of Staphylococcus aureus metabolites, and oxygen availability on rhamnolipid production. It was found that the rhamnolipid production significantly decreased for 30C versus 37C, but not at 40C. The addition of S. aureus spent media, in any of the tested conditions, did not influence rhamnolipid production. Finally, the change in oxygen concentration from normoxia to hypoxia significantly reduced rhamnolipid production. These results were compared to swarming assay data to understand how changes in rhamnolipid production impact surface-mediated motility.
ContributorsKiermayr, Jonathan Patrick (Author) / Bean, Heather (Thesis director) / Misra, Rajeev (Committee member) / Haydel, Shelley (Committee member) / School of International Letters and Cultures (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
The prrAB two-component system has been shown to be essential for viability in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To study this system, several prrAB mutants of Mycobacterium smegmatis, a close relative of Mtb, were created for study. These mutants included a deletion mutant complemented with prrA from Mtb controlled by Pmyc1_tetO, a deletion mutant, and a deletion mutant complemented with prrAB from M. smegmatis controlled by the native prrAB promoter sequence (~167 bp upstream sequence of prrAB). In a previous study, the prrAB deletion mutant clumped excessively relative to the wild-type strain when cultured in a nitrogen-limited medium. To address this irregularity, the lipid profiles of these mutants were analyzed through several experimental methods. Untargeted lipidomic profiles were analyzed by Electrospray Ionization Mass Spectrometry (ESI-MS). The ESI-MS data suggested the deletion mutant accumulates triacylglycerol species relative to the wild-type strain. This data was verified by thin-layer chromatography (TLC) and densitometry of the TLC images. The mycolic acid profile of each mutant was also analyzed by TLC but no noteworthy differences were found. High-throughput RNA-Seq analysis revealed several genes involved in lipid biosynthetic pathways upregulated in the prrAB deletion mutant, thus corroborating the ESI-MS and TLC data.
ContributorsOlson, Alexandra Nadine (Author) / Haydel, Shelley (Thesis director) / Bean, Heather (Committee member) / Maarsingh, Jason (Committee member) / School of Social Transformation (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
The spread of antibiotic resistant bacteria is currently a pressing global health concern, especially considering the prevalence of multi-drug resistance. Efflux pumps, bacterial machinery involved in various active transport functions, are capable of removing a broad range of antibiotics from the periplasmic space and the outer leaflet of the inner membrane, frequently conferring multi-drug resistance. Many aspects of efflux machinery’s structure, functions, and inter-protein interactions are still not fully understood; further characterization of these components of efflux will provide a strong foundation for combating this resistance mechanism. In this project, I further characterize the channel protein TolC as a part of the AcrAB-TolC efflux pump complex in Escherichia coli by first determining the specificity of compensatory mutations in TolC against defective AcrA and AcrB, and then identifying TolC residues that might influence TolC aperture dynamics or stability when altered. Specificity of compensatory mutations was determined using an array of TolC mutants, previously generated from defective AcrA or AcrB, against a different mutant AcrB protein; these new mutant combinations were then analyzed by real-time efflux and antibiotic susceptibility assays. A vancomycin susceptible TolC mutant—a phenotype that has been associated with constitutively open TolC channels—was then used to generate vancomycin-resistant revertants which were evaluated with DNA sequencing, protein quantification by Western blots, and real-time efflux assays to identify residues important for TolC aperture dynamics and protein stability and complex activity. Mutations identified in revertant strains corresponded to residues located in the lower half of the periplasmic domain of TolC; generally, these revertants had poorer efflux than wild-type TolC in the mutant AcrB background, and all revertants had poorer efflux activity than the parental mutant strain.
ContributorsMcFeely, Megan Elizabeth (Author) / Misra, Rajeev (Thesis director) / Haydel, Shelley (Committee member) / Stout, Valerie (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Abstract The BIO 189 Life Sciences Career Paths course is a seminar course that is intended to acclimate incoming freshmen into the School of Life Sciences (SOLS). While there are instructors who organize and present in the class, upper division undergraduate students are primarily responsible for facilitating lectures and discussions and mentoring the freshmen. Prior research has demonstrated that the mentor-mentee relationship is a very important predictor of success and retention within all university first-year programs. While past studies focused on the student mentor-mentee relationships, there is limited research that measures student satisfaction within freshmen seminar courses, especially in areas of science, technology, engineering, and mathematics (STEM). The purpose of this project is to survey students about their perception of the BIO 189 course. The effort of the project is on pre-health students, as they initiate their undergraduate careers and attempt to achieve acceptance into professional school four years later. Analysis of Likert scale surveys distributed to 561 freshmen revealed that students with an emphasis on "medicine" in their majors preferred a BIO 189 course geared to pre-health interests whereas students seeking an emphasis on research (ecology and cell biology/genetics) sought a BIO 189 course focused on internship and employment opportunities. Assessment of the mentor-mentee relationship revealed that students (n = 561) preferred one-on-one meetings with mentors outside of class (44%) compared to those who preferred interaction in class (30%). A sizable 61.68% of students (n = 548) were most concerned with attaining favorable GPAs, highlighting strong emphasis on academic performance. Overall, 61% of respondents (n = 561) expressed satisfaction with SOLS resources and involvement opportunities, which was hypothesized. These results give substantial insight into the efficacy of a first-year success seminar-mentoring program for college freshmen in STEM.
ContributorsMaalouf, Nicholas Elie (Author) / Haydel, Shelley (Thesis director) / Harrell, Carita (Committee member) / Capco, David (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The need for new tuberculocidal drugs is crucial with drug resistance on the rise as the tuberculosis epidemic rages on. One new potential drug target is the PrrAB two component system (TCS) since it does not exist in humans and is essential to viability in Mycobacterium tuberculosis. This project examines Mycobacterium smegmatis, and this nonpathogenic and fast-growing organism possesses two full length PrrAB orthologs, in addition to an orphaned PrrB sensor histidine kinase. While it was determined that PrrAB1 and PrrAB2 are nonessential, the lone PrrB3 is not yet characterized for essentiality. To confirm individual dispensability of PrrAB1 and PrrAB2 and investigate the essentiality of PrrB3 and the full M. smegmatis PrrAB multiplex, we utilized CRISPRi dCas9 to repress the expression (knockdown) of prrAB1 (MSMEG_5662-5663), prrAB2 (MSMEG_0244-0246), and the lone prrB3 (MSMEG_2793) in M. smegmatis independently and simultaneously. Repression of prrAB1 resulted in the greatest growth defect, with a lag of 17 cellular division cycles compared to the control, a strain generated with an empty vector. However, the knockdown of prrAB1 was not lethal to M. smegmatis. The inhibition of all three prrAB orthologs simultaneously, also known as a multiplex knockdown, lagged the control by 13 cellular division cycles. At the 48-hour point, both the single ortholog repression of prrAB1 as well as the whole prrAB system knockdown had a growth defect of 13 replication cycles behind the control. However, the multiplex knockdown stabilized growth at 48 hours, revealing a possible compensatory mechanism in M. smegmatis. Conclusively, we show that the PrrAB TCS is globally inessential for viability in M. smegmatis.
ContributorsHeiligenstein, Piper (Author) / Haydel, Shelley (Thesis director) / Shrivastava, Abhishek (Committee member) / Haller, Yannik (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2023-12
Description
Antibiotic resistant bacteria are a worldwide epidemic threatening human survival. Antimicrobial susceptibility tests (ASTs) are important for confirming susceptibility to empirical antibiotics and detecting resistance in bacterial isolates. Current ASTs are based on bacterial culturing, which take 2-14 days to complete depending on the microbial growth rate. Considering the high mortality and morbidity rates for most acute infections, such long time frames are clinically impractical and pose a huge risk to a patient's life. A faster AST will reduce morbidity and mortality rates, as well as help healthcare providers, administer narrow spectrum antibiotics at the earliest possible treatment stage.
In this dissertation, I developed a nonculture-based AST using an imaging and cell tracking technology. I track individual Escherichia coli O157:H7 (E. coli O157:H7) Uropathogenic Escherichia Coli (UPEC) cells, widely implicated in food-poisoning outbreaks and urinary tract infections respectively. Cells tethered to a surface are tracked on the nanometer scale, and phenotypic motion is correlated with bacterial metabolism. Antibiotic action significantly slows down motion of tethered bacterial cells, which is used to perform antibiotic susceptibility testing. Using this technology, the clinical minimum bactericidal concentration of an antibiotic against UPEC pathogens was calculated within 2 hours directly in urine samples as compared to 3 days using current gold standard tools.
Such technologies can make a tremendous impact to improve the efficacy and efficiency of infectious disease treatment. This has the potential to reduce the antibiotic mis-prescription steeply, which can drastically decrease the annual 2M+ hospitalizations and 23,000+ deaths caused due to antibiotic resistance bacteria along with saving billions of dollars to payers, patients, and hospitals.
In this dissertation, I developed a nonculture-based AST using an imaging and cell tracking technology. I track individual Escherichia coli O157:H7 (E. coli O157:H7) Uropathogenic Escherichia Coli (UPEC) cells, widely implicated in food-poisoning outbreaks and urinary tract infections respectively. Cells tethered to a surface are tracked on the nanometer scale, and phenotypic motion is correlated with bacterial metabolism. Antibiotic action significantly slows down motion of tethered bacterial cells, which is used to perform antibiotic susceptibility testing. Using this technology, the clinical minimum bactericidal concentration of an antibiotic against UPEC pathogens was calculated within 2 hours directly in urine samples as compared to 3 days using current gold standard tools.
Such technologies can make a tremendous impact to improve the efficacy and efficiency of infectious disease treatment. This has the potential to reduce the antibiotic mis-prescription steeply, which can drastically decrease the annual 2M+ hospitalizations and 23,000+ deaths caused due to antibiotic resistance bacteria along with saving billions of dollars to payers, patients, and hospitals.
ContributorsSyal, Karan (Author) / Tao, Nongjian (Thesis advisor) / Haydel, Shelley (Committee member) / Rege, Kaushal (Committee member) / Wang, Shaopeng (Committee member) / Haynes, Karmella (Committee member) / Arizona State University (Publisher)
Created2017
Description
Many Fic domain proteins, through catalyzing post translational modifications (PTM) of protein substrates, functionally contribute to bacterial pathogenesis and the regulation of bacterial growth. Furthermore, one form of Fic-mediated regulation is the Fic toxin-antitoxin system, whereby an antitoxin interacts with and inhibits the Fic toxin. This study sought to determine the functional importance of Mycobacterium tuberculosis Fic and its putative antitoxin protein, Rv3642c. Using M. tuberculosis H37Rv genetic deletion mutants, fic and Rv3642c were demonstrated to promote intracellular survival in human THP-1 macrophage-like cells. Unlike other Fic toxins, of Fic toxin-antitoxin systems, Fic did not inhibit bacterial growth in vitro in the absence of Rv3642c. Notably, Fic demonstrated in vitro AMPylation of a THP-1 cell extract protein as shown by immunodetection. Fic also exhibited auto-AMPylation activity. Interestingly, a mutation of the conserved histidine in the Fic domain motif, a residue previously shown to be critical for AMPylation, had no effect on Fic-mediated ATP hydrolysis or AMPylation activity. Rv3642c was demonstrated to form a complex with Fic when co-expressed in Escherichia coli, indicating a toxin-antitoxin interaction. Screening M. tuberculosis protein fractions and culture filtrate with α-Fic and α-Rv3642c rabbit antisera did not detect monomers of Fic or Rv3642c, thus the cellular localization of Fic and the Rv3642c-Fic complex remains unclear. The results of this study provide insight into the function of M. tuberculosis Fic, and suggest that Fic and Rv3642c are important for M. tuberculosis survival in the intracellular macrophage environment. Furthermore, these findings challenge the current dogma that Fic domain catalysis is dependent on the conserved histidine of the Fic motif.
ContributorsLaMarca, Ryan (Author) / Haydel, Shelley (Thesis advisor) / Lake, Douglas (Committee member) / Nickerson, Cheryl (Committee member) / Arizona State University (Publisher)
Created2017