Theses - Honors College
Permanent URI for this collectionhttps://hdl.handle.net/2104/8111
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Browsing Theses - Honors College by Author "Adair, Tamarah"
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Item Determining the correlation between accessory gene regulator polymorphisms and Staphylococcus aureus sensitivity to 470 nm blue light(2016-08-11) Yuen, Sarah; Adair, Tamarah; University Scholars.; University Scholars.Staphylococcus aureus is a Gram-positive pathogen responsible for minor skin infections, deep tissue infections, and even death. Due to the increasing resistance of S. aureus strains to antibiotics, it is important to investigate and develop alternative modes of treatment for bacterial infections. Photodynamic therapy using 470 nm blue light has been identified as a viable alternative to antibiotic treatment, however significant differences in the sensitivity of strains to blue light have been found. This project investigated the role of a genetic component, the accessory gene regulator (agr), found to be down-regulated in S. aureus isolates exposed to blue light. A statistically significant difference was found between the response of S. aureus isolates among agr groups, indicating that there exists a genetic basis for the varying responses of isolates to blue light therapy. However, further studies must be conducted to further elucidate the role of agr in the response to photodynamic therapy.Item The Effects of Blue Light on the Biofilm Formation and Disruption of Staphylococcus aureus(2013-05-24) Fricke, Kayla; Adair, Tamarah; Biology.; Honors College.The formation of biofilm complicates the treatment of Staphylococcus aureus infections. This experiment measured the effect of 470 nm blue light, a possible antimicrobial agent, on biofilm formation using a biofilm assay. Blue light irradiation for 2 hours on dilute cultures inhibited biofilm formation, and irradiation on saturated cultures after 48 hours of growth resulted in strain-specific changes in the amount of biofilm. There was a positive correlation between cell count and biofilm formation and no correlation between cell count and biofilm disruption. Strain specific variation is observed for the formation of biofilm per cell on blue light treated cultures. It is hypothesized that molecular and genetic variability among strains led to these results. Blue light has the potential to serve as a preventative for infections in a clinical setting, but further investigation into the variation seen in this study is needed to make progress in treating disease.Item Genome-wide analysis of codon usage in Mycobacteriophage and S. aureusBoys, Ian; Adair, Tamarah; University Scholars.; Honors College.The molecular genetics of microbial life, including viruses and bacteria, is of great relevance to medicine, evolutionary theory, and other areas of science. Here, we study the implications of codon bias, the non-random usage of synonymous codons, and GC3, the frequency of codons with guanine or cytosine in the third nucleotide position. Biased codon usage frequently is the result of adaptation for optimal expression, reflecting tRNA abundance. It has previously been suggested that GC3 is similarly of functional significance, with implications for transcription and translation. We make use of the HHMI’s mycobacteriophage genome database to analyze trends in codon bias and GC3 content in a diverse set of viruses with a common host. To this end we utilize genome landscapes to observe trends in genome-wide GC3 usage, and find that patterns in GC3 content can be informative in the difficult process of unraveling the complex relationships between mycobacteriophages. Similarly, we show that codon bias is likewise informative, though it in some instances contradicts the evidence provided by GC3 analysis. In a second portion of the study, we investigate the relationship between codon bias, GC3 content, and gene expression in S. aureus BUSA 2288. We find that codon bias is correlated with gene expression in S. aureus, suggesting that it does indeed reflect selection for expression. GC3 is, however, not tied to any trend in expression.Item Heterogeneous Response to 470 nm Blue Light Amongst 25 Staphylococcus aureus Isolates(2014-05-02) Rosenthal, Meredith; Adair, Tamarah; Biology.; Baylor University.; Honors College.Staphylococcus aureus infections are an increasing concern for the United States as it is currently the most prevalent cause of hospital acquired infections. The growing antibiotic resistance amongst these bacteria has called for new treatments, including photodynamic therapy, which uses light to kill microorganisms. We tested the variance of the response to blue light of 25 different isolates of S. aureus. Using 470 nm blue LEDs with an approximate forward power of 80 mW and an average luminance of 4.22 klux, we exposed 1 ml S. aureus cultures for 30 minutes and measured the optical density at 600 nm 18 hours after treatment. We compared the blue light treatment to a control group and found that there was a wide degree of variance with inhibition values ranging from 97% to an increased growth rate of 8%. Using flow cytometry, we measured cell counts at 4 hours after exposure to blue light for 3 strains identified as highly sensitive and 3 strains identified as highly resistant. There was a range of 80-99.9% inhibition when examining live cell counts. However, the discrepancy between the more and less sensitive strains was still apparent when examining live to dead cell ratios. A variation in susceptibility to blue light indicates a genetic trait may be responsible for this phenotype. Future studies will explore the genetic differences in these strains.Item The Induction, Purification and Host Range of 4 Lysogenic Staphylococcus aureus Bacteriophages(2013-05-23) Manzana, Carlo; Adair, Tamarah; Biology.; Baylor University.; Honors College.This research examined a possible correlation between bacteriophage resistance of Staphylococcus aureus and the presence of integrase genes. Four lysogenic Staphylococcus aureus bacteriophages were isolated and their lytic ability was determined. Phages were obtained through Mitomycin C phage induction and verified through positive spot tests on a panel of 10 different isolates. Phages were then assayed for their host range and compared to a well-known S. aureus phage, Phage K. The 4 induced phages exhibited less lytic activity than Phage K. Moreover, the results suggest that there is no clear correlation between phage resistance and the type or number of prophage integrase genes present in the host bacteria.Item Introduction and Initial Analysis of the Ciliate Investigative Learning Initiative Classroom-Based Undergraduate Research Experience(2017-05-23) Minick, Josephine; Adair, Tamarah; University Scholars.; Honors College.Due to inherent shortcomings in the traditional laboratory structure, inquiry-based laboratories have increasingly been adopted to increase student engagement in science and provide an early research experience. At Baylor University, a new inquiry-based introductory biology laboratory, the Ciliate Investigative Learning Initiative Classroom-Based Undergraduate Research Experience (CILI-CURE), has been designed to address these learning goals. In this study, the first group of student outcomes from this initiative are evaluated by the Test of Scientific Literacy Skills, Course-Based Undergraduate Research Experience Survey, and the Baylor Course Evaluation. Statistical analyses indicate significant gains in students’ skills in data analysis, accessing primary literature, identifying the validity of scientific arguments, collecting data, and learning laboratory techniques. While supporting the concept that inquiry-based courses improve students’ perception of science, thus providing an improved way to teach the process of science, these outcomes also indicate areas for improvement in qualitative skills.Item Investigating Inhibitory Synergy between Blue Light Irradiation and Antibiotic Treatment of Staphylococcus aureus(2013-05-24) Fox, Gregg; Adair, Tamarah; Biology.; Honors College.Staphylococcus aureus is a Gram-positive pathogen responsible for significant infections in both the hospital and the community. Rising antibiotic resistance has led to increased infection rates, while the ability of S. aureus to form protective biofilms on medical implants continues to contribute to life-threatening instances of recurrent bacteremia. In an effort to better combat these enhanced defenses, recent research has focused particularly on biofilm disruptors and other alternative treatment methods such as antimicrobial photodynamic therapy (aPDT), all of which have demonstrated synergistic inhibitory effects when combined with antibiotic therapy. This experiment was conducted to search for similar synergistic effects when irradiation with visible blue light, another emerging technique, is coupled with standard antibiotic treatments of oxacillin, neomycin, and ciprofloxacin. During testing, bacterial samples in 24-well plates were exposed to uniform 470nm blue light via an adjustable lightbox. The effects of combined therapy were ascertained through a modified broth microdilution assay with CFUs/mL measured periodically. Data from these tests reveal that the inhibitory effect of blue light alone is relatively dose-independent in the short term, with dosages as low as 5 minutes showing significant inhibition four hours after the beginning of treatment. Combined therapy is even more promising, evincing synergy between blue light and all tested antibiotics in the short-term and between blue light and all but neomycin in the long-term.Item RNA-SEQ Reveals Changes in the Staphylococcus aureus Transcriptome Following Blue Light Illumination(2014-05-02) Drum, Bayless; Adair, Tamarah; Biology.; Honors College.Staphylococcus aureus infections are becoming a more serious human health concern as antibiotic resistance among S. aureus strains increases. As a result, alternatives to antibiotic treatments are being explored, including photodynamic therapies. It has been shown that blue light exposure will inhibit the growth of both Gram-positive and Gram-negative bacteria, including S. aureus growing in culture. However, the mechanism of this inhibition is not well characterized. In an effort to better understand the mechanism of blue light inhibition, a whole transcriptome analysis of S. aureus isolate BUSA2288 was performed using RNA-seq to analyze the response to blue light exposure. RNA was extracted from S. aureus cultures illuminated with blue light, and control cultures grown in the dark. Transcriptomic comparisons using a cutoff of 5 fold identified a total of 28 down-regulated genes and 6 up-regulated genes in the samples that were exposed to blue light. The differentially regulated genes fall into 8 functional categories with 4 genes of unknown function. These results indicate that blue light does have an effect on the transcriptome of S. aureus. Pathways involving reactive oxygen intermediates generated in the broth and excitation and damage to membrane proteins are proposed to explain the killing effect of blue light on S. aureus.