Matching Items (91)
Description
Methicillin-Resistant Staphylococcus aureus (MRSA) infections are a major challenge to healthcare professionals. Treatment of MRSA is expensive, and otherwise avoidable deaths occur every year in the United States due to MRSA infections. Additionally, such infections lengthen patients’ stays in hospitals, keeping them out of work and adversely affecting the economy. Beta lactam antibiotics used to be highly effective against S. aureus infections, but resistance mechanisms have rendered methicillin, oxacillin, and other beta lactam antibiotics ineffective against these infections. A promising avenue for MRSA treatment lies in the use of synthetic antibodies—molecules that bind with specificity to a given compound. Synbody 14 is an example of such a synbody, and has been designed with MRSA treatment in mind. Mouse model studies have even associated Syn14 treatment with reduced weight loss and morbidity in MRSA-infected mice. In this experiment, in vitro activity of Syn 14 and oxacillin was assessed. Early experiments measured Syn 14 and oxacillin’s effectiveness in inhibiting colony growth in growth media, mouse serum, and mouse blood. Syn14 and oxacillin had limited efficacy against USA300 strain MRSA, though interestingly it was noted that Syn14 outperformed oxacillin in mouse serum and whole mouse blood, indicating the benefits of its binding properties. A second experiment measured the impact that a mix of oxacillin and Syn 14 had on colony growth, as well as the effect of adding them simultaneously or one after the other. While use of either bactericidal alone did not show a major inhibitory effect on USA300 MRSA colony growth, their use in combination showed major decreases in colony growth. Moreover, it was found that unlike other combination therapies, Syn14 and oxacillin did not require simultaneous addition to MRSA cells to achieve inhibition of cell growth. They merely required that Syn14 be added first. This result suggests Syn14’s possible utility in therapeutic settings, as the time insensitivity of synergy removes a major hurdle to clinical use—the difficulty in ensuring that two drugs reach an affected area at the same time. Syn14 remains a promising antimicrobial agent, and further study should focus on its precise mechanism of action and suitability in clinical treatment of MRSA infections.
ContributorsMichael, Alexander (Author) / Diehnelt, Chris (Thesis director) / Stafford, Phillip (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
Description
The purpose of this study is to aid in the Career Development of the Millennial Generation within the University setting through the use of the Career Services online Career Guide. To connect Millennials, also called Digital Natives, with a fulfilling career, Career Services must be open to relating to them through the use of technology and providing more effective online resources. The power to quickly communicate information using web-based services and social media is rendering in-person student services a thing of the past. In order to make recommendations on the subject, current literature will be reviewed pertaining to the Millennial generation's background, adaptation to modern technology, work ideology, and generational personality characteristics. Next, the information will be analyzed and applied to a project updating the Career Services website, more effectively educating Millennials on how to use a degree to find a career and by recommending ways in which student services and receptive employers may change to better facilitate the needs of this rising generation.
ContributorsSyfritt, Hannah Rebeka (Author) / Kirby, Andrew (Thesis director) / Kim, Linda (Committee member) / Berren, Scott (Committee member) / Barrett, The Honors College (Contributor) / School of Social and Behavioral Sciences (Contributor)
Created2015-05
Description
Critical flicker fusion thresholds (CFFTs) describe when quick amplitude modulations of a light source become undetectable as the frequency of the modulation increases and are thought to underlie a number of visual processing skills, including reading. Here, we compare the impact of two vision-training approaches, one involving contrast sensitivity training and the other directional dot-motion training, compared to an active control group trained on Sudoku. The three training paradigms were compared on their effectiveness for altering CFFT. Directional dot-motion and contrast sensitivity training resulted in significant improvement in CFFT, while the Sudoku group did not yield significant improvement. This finding indicates that dot-motion and contrast sensitivity training similarly transfer to effect changes in CFFT. The results, combined with prior research linking CFFT to high-order cognitive processes such as reading ability, and studies showing positive impact of both dot-motion and contrast sensitivity training in reading, provide a possible mechanistic link of how these different training approaches impact reading abilities.
ContributorsZhou, Tianyou (Author) / Nanez, Jose (Author) / Zimmerman, Daniel (Author) / Holloway, Steven (Author) / Seitz, Aaron (Author) / New College of Interdisciplinary Arts and Sciences (Contributor)
Created2016-10-26
Description
Although autism spectrum disorder (ASD) is a serious lifelong condition, its underlying neural mechanism remains unclear. Recently, neuroimaging-based classifiers for ASD and typically developed (TD) individuals were developed to identify the abnormality of functional connections (FCs). Due to over-fitting and interferential effects of varying measurement conditions and demographic distributions, no classifiers have been strictly validated for independent cohorts. Here we overcome these difficulties by developing a novel machine-learning algorithm that identifies a small number of FCs that separates ASD versus TD. The classifier achieves high accuracy for a Japanese discovery cohort and demonstrates a remarkable degree of generalization for two independent validation cohorts in the USA and Japan. The developed ASD classifier does not distinguish individuals with major depressive disorder and attention-deficit hyperactivity disorder from their controls but moderately distinguishes patients with schizophrenia from their controls. The results leave open the viable possibility of exploring neuroimaging-based dimensions quantifying the multiple-disorder spectrum.
ContributorsYahata, Noriaki (Author) / Morimoto, Jun (Author) / Hashimoto, Ryuichiro (Author) / Lisi, Giuseppe (Author) / Shibata, Kazuhisa (Author) / Kawakubo, Yuki (Author) / Kuwabara, Hitoshi (Author) / Kuroda, Miho (Author) / Yamada, Takashi (Author) / Megumi, Fukuda (Author) / Imamizu, Hiroshi (Author) / Nanez, Jose (Author) / Takahashi, Hidehiko (Author) / Okamoto, Yasumasa (Author) / Kasai, Kiyoto (Author) / Kato, Nobumasa (Author) / Sasaki, Yuka (Author) / Watanabe, Takeo (Author) / Kawato, Mitsuo (Author) / New College of Interdisciplinary Arts and Sciences (Contributor)
Created2016-04-14
Description
Peptides offer great promise as targeted affinity ligands, but the space of possible peptide sequences is vast, making experimental identification of lead candidates expensive, difficult, and uncertain. Computational modeling can narrow the search by estimating the affinity and specificity of a given peptide in relation to a predetermined protein target. The predictive performance of computational models of interactions of intermediate-length peptides with proteins can be improved by taking into account the stochastic nature of the encounter and binding dynamics. A theoretical case is made for the hypothesis that, because of the flexibility of the peptide and the structural complexity of the target protein, interactions are best characterized by an ensemble of possible bound configurations rather than a single “lock and key” fit. A model incorporating these factors is proposed and evaluated. A comprehensive dataset of 3,924 peptide-protein interface structures was extracted from the Protein Data Bank (PDB) and descriptors were computed characterizing the geometry and energetics of each interface. The characteristics of these interfaces are shown to be generally consistent with the proposed model, and heuristics for design and selection of peptide ligands are derived. The curated and energy-minimized interface structure dataset and a relational database containing the detailed results of analysis and energy modeling are made publicly available via a web repository. A novel analytical technique based on the proposed theoretical model, Virtual Scanning Probe Mapping (VSPM), is implemented in software to analyze the interaction between a target protein of known structure and a peptide of specified sequence, producing a spatial map indicating the most likely peptide binding regions on the protein target. The resulting predictions are shown to be superior to those of two other published methods, and support the validity of the stochastic binding model.
ContributorsEmery, Jack Scott (Author) / Pizziconi, Vincent B (Thesis advisor) / Woodbury, Neal W (Thesis advisor) / Guilbeau, Eric J (Committee member) / Stafford, Phillip (Committee member) / Taylor, Thomas (Committee member) / Towe, Bruce C (Committee member) / Arizona State University (Publisher)
Created2010
Description
Bacteria with antibiotic resistance are becoming a growing concern as the number of infections they are causing continue to increase. Many potential solutions are being researched in order to combat these pathogens. One such microbe is Pseudomonas aeruginosa, which causes acute and chronic human infections. It frequently colonizes the lungs of cystic fibrosis patients and is deadly. For these reasons, P. aeruginosa has been heavily studied in order to determine a solution to antibiotic resistance. One possible solution is the development of synbodies, which have been developed at the Biodesign Institute at Arizona State University. Synbodies are constructed from peptides that have antibacterial activity and were determined to have specificity for a target bacterium. These synbodies were tested in this study to determine whether or not some of them are able to inhibit P. aeruginosa growth. P. aeruginosa can also form multicellular communities called biofilms and these are known to cause approximately 65% of all human infections. After conducting minimum inhibitory assays, the efficacy of certain peptides and synbodies against biofilm inhibition was assessed. A recent study has shown that low concentrations of a specific peptide can cause biofilm disruption, where the biofilm structure breaks apart and the cells within it disperse into the supernatant. Taking into account this study and peptide data regarding biofilm inhibition from Dr. Aurélie Crabbé’s lab, screened peptides were tested against biofilm to see if dispersion would occur.
ContributorsPatel, Justin Hemant (Author) / Diehnelt, Chris (Thesis director) / Stafford, Phillip (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2015-05
Description
The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern web development technologies, Genie was developed as a simulator to help educators in biology, genetics, and evolution classrooms teach their students about population genetics. Because Genie was designed for the modern web, it is highly accessible to both educators and students, who can access the web application using any modern web browser on virtually any device. Genie demonstrates the efficacy of web devel- opment technologies for demonstrating and simulating complex processes, and it will be a unique educational tool for educators who teach population genetics.
ContributorsRoos, Benjamin Hirsch (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Mayron, Liam (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
Description
Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
ContributorsSchwartz, Rachel (Author) / Harkins, Kelly (Author) / Stone, Anne (Author) / Cartwright, Reed (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-06-11
Description
This thesis explores the likely impacts of climate change on agricultural production globally and in the state of Arizona, and on agricultural supply chains. It shows increases in severe weather, including hotter temperatures and droughts, will have a negative impact on crop production in the state and on global agricultural supply chains. It also shows the effects on the environment caused by our current cradle-to-grave supply chains. As a partial remedy, this thesis explores the benefits of vertical farming systems and shows how they could be of value to the residents of Arizona.
ContributorsKing, Emily Marie (Author) / Kirby, Andrew (Thesis director) / Carter, Craig (Committee member) / Department of Supply Chain Management (Contributor) / School of Sustainability (Contributor) / School of International Letters and Cultures (Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Callithrix penicillata, also known as the Black-tufted marmoset primarily lives in the Brazilian highlands and has had little research conducted on it. For this project I performed a genome curation on the newly assembled genome of this species. The scaffolds obtained by the Dovetail Genomics reads were organized and labeled into chromosomes using the 2014 Callithrix jacchus genome as a reference. Then, using that same genome as a reference, 13 of the chromosomes were reverse complimented to be continuous with the 2014 Callithrix jacchus genome. The N50 statistics of the assembly were calculated and found to be 124 Mb. Quality scores were run for the final genome using referee and visualized with a bar plot, with 99% of sites scoring above 0. Heterozygosity was also calculated and found to be 0.3%. Finally, the final version of the genome was visually compared to the 2017 Callithrix jacchus genome and the GRCh38 human genome. This genome was submitted to the NCBIs database to await further approval.
ContributorsJohnson, Joelle Genevieve (Author) / Cartwright, Reed (Thesis director) / Stone, Anne (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12