Matching Items (40)
Description
The entire history of HIV-1 is hidden in its ten thousand bases, where information regarding its evolutionary traversal through the human population can only be unlocked with fine-scale sequence analysis. Measurable footprints of mutation and recombination have imparted upon us a wealth of knowledge, from multiple chimpanzee-to-human transmissions to patterns of neutralizing antibody and drug resistance. Extracting maximum understanding from such diverse data can only be accomplished by analyzing the viral population from many angles. This body of work explores two primary aspects of HIV sequence evolution, point mutation and recombination, through cross-sectional (inter-individual) and longitudinal (intra-individual) investigations, respectively. Cross-sectional Analysis: The role of Haiti in the subtype B pandemic has been hotly debated for years; while there have been many studies, up to this point, no one has incorporated the well-known mechanism of retroviral recombination into their biological model. Prior to the use of recombination detection, multiple analyses produced trees where subtype B appears to have first entered Haiti, followed by a jump into the rest of the world. The results presented here contest the Haiti-first theory of the pandemic and instead suggest simultaneous entries of subtype B into Haiti and the rest of the world. Longitudinal Analysis: Potential N-linked glycosylation sites (PNGS) are the most evolutionarily dynamic component of one of the most evolutionarily dynamic proteins known to date. While the number of mutations associated with the increase or decrease of PNGS frequency over time is high, there are a set of relatively stable sites that persist within and between longitudinally sampled individuals. Here, I identify the most conserved stable PNGSs and suggest their potential roles in host-virus interplay. In addition, I have identified, for the first time, what may be a gp-120-based environmental preference for N-linked glycosylation sites.
ContributorsHepp, Crystal Marie, 1981- (Author) / Rosenberg, Michael S. (Thesis advisor) / Hedrick, Philip (Committee member) / Escalante, Ananias (Committee member) / Kumar, Sudhir (Committee member) / Arizona State University (Publisher)
Created2013
Description
Cyanovirin-N (CVN) is a cyanobacterial lectin with potent anti-HIV activity, mediated by binding to the N-linked oligosaccharide moiety of the envelope protein gp120. CVN offers a scaffold to develop multivalent carbohydrate-binding proteins with tunable specificities and affinities. I present here biophysical calculations completed on a monomeric-stabilized mutant of cyanovirin-N, P51G-m4-CVN, in which domain A binding activity is abolished by four mutations; with comparisons made to CVNmutDB, in which domain B binding activity is abolished. Using Monte Carlo calculations and docking simulations, mutations in CVNmutDB were considered singularly, and the mutations E41A/G and T57A were found to impact the affinity towards dimannose the greatest. 15N-labeled proteins were titrated with Manα(1-2)Manα, while following chemical shift perturbations in NMR spectra. The mutants, E41A/G and T57A, had a larger Kd than P51G-m4-CVN, matching the trends predicted by the calculations. We also observed that the N42A mutation affects the local fold of the binding pocket, thus removing all binding to dimannose. Characterization of the mutant N53S showed similar binding affinity to P51G-m4-CVN. Using biophysical calculations allows us to study future iterations of models to explore affinities and specificities. In order to further elucidate the role of multivalency, I report here a designed covalent dimer of CVN, Nested cyanovirin-N (Nested CVN), which has four binding sites. Nested CVN was found to have comparable binding affinity to gp120 and antiviral activity to wt CVN. These results demonstrate the ability to create a multivalent, covalent dimer that has comparable results to that of wt CVN.
WW domains are small modules consisting of 32-40 amino acids that recognize proline-rich peptides and are found in many signaling pathways. We use WW domain sequences to explore protein folding by simulations using Zipping and Assembly Method. We identified five crucial contacts that enabled us to predict the folding of WW domain sequences based on those contacts. We then designed a folded WW domain peptide from an unfolded WW domain sequence by introducing native contacts at those critical positions.
WW domains are small modules consisting of 32-40 amino acids that recognize proline-rich peptides and are found in many signaling pathways. We use WW domain sequences to explore protein folding by simulations using Zipping and Assembly Method. We identified five crucial contacts that enabled us to predict the folding of WW domain sequences based on those contacts. We then designed a folded WW domain peptide from an unfolded WW domain sequence by introducing native contacts at those critical positions.
ContributorsWoodrum, Brian William (Author) / Ghirlanda, Giovanna (Thesis advisor) / Redding, Kevin (Committee member) / Wang, Xu (Committee member) / Arizona State University (Publisher)
Created2014
Description
Pre-Exposure Prophylaxis (PrEP) is any medical or public health procedure used before exposure to the disease causing agent, its purpose is to prevent, rather than treat or cure a disease. Most commonly, PrEP refers to an experimental HIV-prevention strategy that would use antiretrovirals to protect HIV-negative people from HIV infection. A deterministic mathematical model of HIV transmission is developed to evaluate the public-health impact of oral PrEP interventions, and to compare PrEP effectiveness with respect to different evaluation methods. The effects of demographic, behavioral, and epidemic parameters on the PrEP impact are studied in a multivariate sensitivity analysis. Most of the published models on HIV intervention impact assume that the number of individuals joining the sexually active population per year is constant or proportional to the total population. In the second part of this study, three models are presented and analyzed to study the PrEP intervention, with constant, linear, and logistic recruitment rates. How different demographic assumptions can affect the evaluation of PrEP is studied. When provided with data, often least square fitting or similar approaches can be used to determine a single set of approximated parameter values that make the model fit the data best. However, least square fitting only provides point estimates and does not provide information on how strongly the data supports these particular estimates. Therefore, in the third part of this study, Bayesian parameter estimation is applied on fitting ODE model to the related HIV data. Starting with a set of prior distributions for the parameters as initial guess, Bayes' formula can be applied to obtain a set of posterior distributions for the parameters which makes the model fit the observed data best. Evaluating the posterior distribution often requires the integration of high-dimensional functions, which is usually difficult to calculate numerically. Therefore, the Markov chain Monte Carlo (MCMC) method is used to approximate the posterior distribution.
ContributorsZhao, Yuqin (Author) / Kuang, Yang (Thesis advisor) / Taylor, Jesse (Committee member) / Armbruster, Dieter (Committee member) / Tang, Wenbo (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
Description
The AIDS epidemic has tremendously impacted the population of Mozambique. The rate of newly infected young women continues to grow disproportionately which is why consideration of health interventions specific to this population to combat the spread of the disease is critical. The Health Belief Model emphasizes the importance of self efficiency in the process of health related behavioral changes. Previous research has found that low levels of autonomy increase one's risk of contracting HIV/AIDS. This research uses data from a study conducted in 2006 in Mozambique to test whether higher levels of autonomy are associated with the practice of self protective behaviors related to the contraction of HIV/AIDS. Results suggest that some measures of autonomy such as education are positively associated with the practice of self protective behaviors. However, higher levels of decision making powers were negatively associated with the practice of self protective behaviors.
ContributorsWilliams, Kelli (Author) / Hayford, Sarah (Thesis advisor) / Agadjanian, Victor (Committee member) / Yabiku, Scott (Committee member) / Arizona State University (Publisher)
Created2011
Description
HIV/AIDS is the sixth leading cause of death worldwide and the leading cause of death among women of reproductive age living in low-income countries. Clinicians in industrialized nations monitor the efficacy of antiretroviral drugs and HIV disease progression with the HIV-1 viral load assay, which measures the copy number of HIV-1 RNA in blood. However, viral load assays are not widely available in sub-Saharan Africa and cost between 50-$139 USD per test on average where available. To address this problem, a mixed-methods approach was undertaken to design a novel and inexpensive viral load diagnostic for HIV-1 and to evaluate barriers to its adoption in a developing country. The assay was produced based on loop-mediated isothermal amplification (LAMP). Blood samples from twenty-one individuals were spiked with varying concentrations of HIV-1 RNA to evaluate the sensitivity and specificity of LAMP. Under isothermal conditions, LAMP was performed with an initial reverse-transcription step (RT-LAMP) and primers designed for HIV-1 subtype C. Each reaction generated up to a few billion copies of target DNA within an hour. Presence of target was detected through naked-eye observation of a fluorescent indicator and verified by DNA gel electrophoresis and real-time fluorescence. The assay successfully detected the presence of HIV in samples with a broad range of HIV RNA concentration, from over 120,000 copies/reaction to 120 copies/reaction. In order to better understand barriers to adoption of LAMP in developing countries, a feasibility study was undertaken in Tanzania, a low-income country facing significant problems in healthcare. Medical professionals in Northern Tanzania were surveyed for feedback regarding perspectives of current HIV assays, patient treatment strategies, availability of treatment, treatment priorities, HIV transmission, and barriers to adoption of the HIV-1 LAMP assay. The majority of medical providers surveyed indicated that the proposed LAMP assay is too expensive for their patient populations. Significant gender differences were observed in response to some survey questions. Female medical providers were more likely to cite stigma as a source problem of the HIV epidemic than male medical providers while males were more likely to cite lack of education as a source problem than female medical providers.
ContributorsSalamone, Damien Thomas (Author) / Jacobs, Bertram L (Thesis advisor) / Marsiglia, Flavio (Committee member) / Stout, Valerie (Committee member) / Johnson, Crista (Committee member) / Arizona State University (Publisher)
Created2011
Description
Over the past two decades, a significant amount of research has been conducted investigating cyanovirin-N (CVN), which has been shown to be an effective antiviral agent by inhibiting entry of HIV into the cell. The virucidal activity of CVN is attributed to the tight binding interactions with the glycosylated surfaces of the envelope protein gp120. In this study we investigated how the incorporation of various single point mutations in the glycan binding site would ultimately affect the overall binding affinity of the protein with the glycan. These mutations were predicted through computational methods. Using a BP-docking program and molecular dynamics (MD) simulation, the free energy change upon the ligand binding to the each protein was determined. Experimental work and Isothermal Titration Calorimetry (ITC) was used to determine the Kd values for each protein mutant. A total of three different CVN mutants, T57S, S52T, and a double mutant T57S-S52T, or simply TS, were investigated on the background of P51G-m4-CVN. After conducting the experimental work, it was concluded that the overall fold and stability of the protein was conserved for each mutant. ITC data showed that T57S displayed the lowest dissociation constant valued in the micromolar range. In fact, T57S had a much lower Kd value in comparison to P51G-m4. In contrast, the double mutant TS, showed poor binding affinity for the glycan. When comparing experimental data with the data provided by MD simulation and BP-docking, the results were fairly correlated for all mutants, except for that of the double mutant, TS. According to information provided by MD simulation and BP docking, the binding of the sugar to TS is a very exergonic reaction, which is indicative of very negative free energy change (ΔG). However, the experimental Kd, which was very high, contradicts this data and is thus indicative of lower binding affinity for the glycan. This contradiction is currently being investigated.
ContributorsAllen, Denysia Monique (Author) / Ghirlanda, Giovanna (Thesis director) / Ozkan, S. Banu (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2015-05
Description
Curanderos are Hispanic traditional healers who attend to their clients through spiritual, natural, and physical techniques. Recent studies have shown that a subset of the Hispanic population refer to these healers for HIV and STD treatment and believe they are important in a collaborative targeted HIV intervention. Thus, curanderos were interviewed and the lay population of Phoenix was sampled in order to get a better idea of the utility of these healers in an HIV prevention effort targeted at the Hispanic community. Due to the limitations of this study there was not sufficient enough data to make significant conclusions; however the interviews with the curanderos were surprising in the they had significant roles as healers in the Phoenix area, patients have referred to them for HIV and STD treatment, and a couple of the healers have integrated western medical knowledge into their practice.
ContributorsMartinez, Justin Anthony (Author) / Maupin, Jonathan (Thesis director) / Hruschka, Daniel (Committee member) / Aguilera, Miguel (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2013-05
DescriptionThis research evaluates the national HIV/AIDS policy of Ghana and compares it to the policies of other countries in the Economic Community of West African States.
ContributorsAlcaraz, Hailey Elizabeth (Author) / Alozie, Nicholas (Thesis director) / Fisher, Erik (Committee member) / Rothenberg, Daniel (Committee member) / Barrett, The Honors College (Contributor) / School of Community Resources and Development (Contributor) / School of Politics and Global Studies (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2013-05
Description
Studies have demonstrated that viruses such as human immunodeficiency virus [HIV], M13 bacteriophage, and murine cytomegalovirus [MCMV] have been effectively inactivated by exposure to ultra short-pulsed lasers (6,7,10,11,14,15,17). Ultra short pulse laser shows promise as a new method for non-invasive antiviral treatments (17). This method can be used to prevent problems such as drug resistance that is currently rising in numbers. According to the Center for Disease Control [CDC], there are more than two million people in the United States of America that are infected with antimicrobial-resistant infections and at least 23,000 deaths per year occur as a result (19). In this study, ultra-short pulses, specifically Ti-Sapphire Laser [USP Ti-Sapphire Laser] will be evaluated for viral inactivation. The virus chosen for this study was MS2 bacteriophage, which is a non- enveloped, icosahedral, single-stranded RNA [ssRNA] bacteriophages that infects F+ pilus Escherichia coli (16). It was hypothesized that ultrashort pulses from a Ti-Sapphire laser will inactivate MS2 bacteriophage. Inactivation was measured using plaque-forming units [PFU/mL] as an indicator. It was expected that there would be an increase in inactivation of MS2 bacteriophage with an increase in irradiation duration. The results indicated that MS2 bacteriophage was highly sensitive to irradiation treatments of the USP Ti-Sapphire Laser. The concentration of MS2 bacteriophage decreased by 107 PFU/mL after being treated for various time periods ranging from 5 minutes to 150 minutes. Longer duration of USP Ti- Sapphire Laser treatment inactivated more MS2 Bacteriophage.
ContributorsApablasa, Nayeli Aleysa (Author) / Stout, Valerie (Thesis director) / Jacobs, Bertram (Committee member) / Tsen, Kong-Thong (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Abstract HIV: An Evolutionary Perspective Arthur J. Stepp; April 2001 Human Immuno-deficiency Virus (HIV) poses a significant threat to global health. Despite the fact that the number of cases of HIV is growing exponentially, there is no known cure for the disease and little understanding of its mechanism of pathogenesis. An application of an evolutionary perspective understanding may provide new insight into how natural selection acts upon HIV to increase its level of virulence, and also HIV's pathogenesis. By applying the replication rate hypothesis theory developed by Paul Eward in 1994 to epidemiological evidence from Africa, it becomes clear that as the replication rate of the virus increases, the mutation rate increases simultaneously. People who have been infected for the longest amounts of time tend to have more virulent, powerful strains of HIV as the virus has gone through more replications and has thus developed more powerful mutations that tend to advance to AIDS more quickly. This has important implications for the best approach to combatting the spread of the virus, because it means that preventing unprotected contact with people with highly mutated strains of the virus will greatly reduce the virus's virulence. Thus, the reduction of unprotected sexual contact and needle-borne transmission will pay extra dividends, as highly virulent strains of HIV will be better contained.
ContributorsStepp, Arthur (Author) / Burke, William (Thesis director) / Schmidt, Jean (Committee member) / Barrett, The Honors College (Contributor)
Created2001-05