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- All Subjects: healthcare
- All Subjects: Molecular Biology
- Creators: School of Life Sciences
Description
Nucleic acids encode the information required to create life, and polymerases are the gatekeepers charged with maintaining the storage and flow of this genetic information. Synthetic biologists utilize this universal property to modify organisms and other systems to create unique traits or improve the function of others. One of the many realms in synthetic biology involves the study of biopolymers that do not exist naturally, which is known as xenobiology. Although life depends on two biopolymers for genetic storage, it may be possible that alternative molecules (xenonucleic acids – XNAs), could be used in their place in either a living or non-living system. However, implementation of an XNA based system requires the development of polymerases that can encode and decode information stored in these artificial polymers. A strategy called directed evolution is used to modify or alter the function of a protein of interest, but identifying mutations that can modify polymerase function is made problematic by their size and overall complexity. To reduce the amount of sequence space that needs to be samples when attempting to identify polymerase variants, we can try to make informed decisions about which amino acid residues may have functional roles in catalysis. An analysis of Family B polymerases has shown that residues which are involved in substrate specificity are often highly conserved both at the sequence and structure level. In order to validate the hypothesis that a strong correlation exists between structural conservation and catalytic activity, we have selected and mutated residues in the 9°N polymerase using a loss of function mutagenesis strategy based on a computational analysis of several homologues from a diverse range of taxa. Improvement of these models will hopefully lead to quicker identification of loci which are ideal engineering targets.
ContributorsHaeberle, Tyler Matthew (Author) / Chaput, John (Thesis director) / Chen, Julian (Committee member) / Larsen, Andrew (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Introduction: Human papillomavirus (HPV) infection is seen in up to 90% of cases of cervical cancer, the third leading cancer cause of death in women. Current HPV screening focuses on only two HPV types and covers roughly 75% of HPV-associated cervical cancers. A protein based assay to test for antibody biomarkers against 98 HPV antigens from both high and low risk types could provide an inexpensive and reliable method to screen for patients at risk of developing invasive cervical cancer. Methods: 98 codon optimized, commercially produced HPV genes were cloned into the pANT7_cGST vector, amplified in a bacterial host, and purified for mammalian expression using in vitro transcription/translation (IVTT) in a luminescence-based RAPID ELISA (RELISA) assay. Monoclonal antibodies were used to determine immune cross-reactivity between phylogenetically similar antigens. Lastly, several protein characteristics were examined to determine if they correlated with protein expression. Results: All genes were successfully moved into the destination vector and 86 of the 98 genes (88%) expressed protein at an adequate level. A difference was noted in expression by gene across HPV types but no correlation was found between protein size, pI, or aliphatic index and expression. Discussion: Further testing is needed to express the remaining 12 HPV genes. Once all genes have been successfully expressed and purified at high concentrations, DNA will be printed on microscope slides to create a protein microarray. This microarray will be used to screen HPV-positive patient sera for antibody biomarkers that may be indicative of cervical cancer and precancerous cervical neoplasias.
ContributorsMeshay, Ian Matthew (Author) / Anderson, Karen (Thesis director) / Magee, Mitch (Committee member) / Katchman, Benjamin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Emerging Information Technology, Storage and Evaluation within Healthcare: A Discerning IMT Analysis
Description
The introduction of novel information technology within contemporary healthcare settings presents a critical juncture for the industry and thus lends itself to the importance of better understanding the impact of this emerging "health 2.0" landscape. Simply, how such technology may affect the healthcare system is still not fully realized, despite the ever-growing need to adopt it in order to serve a growing patient population. Thus, two pertinent questions are posed: is HIT useful and practical and, if so, what is the best way to implement it? This study examined the clinical implementation of specific instances of health information technology (HIT) so as to weigh its benefits and risks to ultimately construct a proposal for successful widespread adoption. Due to the poignancy of information analysis within HIT, Information Measurement Theory (IMT) was used to measure the effectiveness of current HIT systems as well as to elucidate improvements for future implementation. The results indicate that increased transparency, attention to patient-focused approaches and proper IT training will not only allow HIT to better serve the community, but will also decrease inefficient healthcare expenditure.
ContributorsMaietta, Myles Anthony (Author) / Kashiwagi, Dean (Thesis director) / Kashiwagi, Jacob (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The Intercellular Adhesion Molecule-1 (ICAM-1, known as CD54) is a cell surface type I transmembrane glycoprotein with a molecular weight of 85 to 110 kDa. The primary function of ICAM-1 is to provide adhesion between endothelial cells and leukocytes after injury or stress. ICAM-1 is used as a receptor for various pathogens such as rhinoviruses, coxsackievirus A21 and the malaria parasite Plasmodium falciparum. ICAM-1 contains five immunoglobulin (Ig) domains in its long N-terminal extracellular region, a hydrophobic transmembrane domain, and a small C-terminal cytoplasmic domain. The Ig domains 1-2 and Ig domains 3-4-5 have been crystallized separately and their structure solved, however the full ICAM-1 structure has not been solved. Because ICAM-1 appears to be important for the mediation of cell-to-cell communication in physiological and pathological conditions, gaining a structural understanding of the full-length membrane anchored ICAM-1 is desirable. In this context, we have transiently expressed a plant-optimized gene encoding human ICAM-1 in Nicotiana benthamiana plants using the MagnICON expression system. The plant produced ICAM-1 is forming aggregates according to previous data. Thus, the current extraction and purification protocols have been altered to include TCEP, a reducing agent. The protein was purified using TALON metal affinity resin and partially characterized using various biochemical techniques. Our results show that there is a reduction in aggregation formation with the use of TCEP.
ContributorsPatel, Heeral (Author) / Mor, Tsafrir (Thesis director) / Mason, Hugh (Committee member) / Kannan, Latha (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Variants of human butyrylcholinesterase (BChE) have been designed to have high cocaine hydrolytic activity. These variants have potential pharmacological applications toward treating cocaine overdose and addiction. These enzymes must be stable in the human body over fairly long periods of time in order to be effective at treating cocaine addiction. Recombinantly expressed BChE, however, tends to be in monomer or dimer oligomeric forms, which are far less stable than the tetramer form of the enzyme. When BChE is transiently expressed in Nicotiana benthamiana, it is produced mainly as monomers and dimers. However, when the protein is expressed through stable transformation, it produces much greater proportions of tetramers. Tetramerization of WT human plasma derived BChE is facilitated by the binding of a proline rich peptide. In this thesis, I investigated if a putative plant-derived analog of the mammalian proline-rich attachment domain caused stably expressed cocaine hydrolase variants of human BChE to undergo tetramerization. I also examined if co-expression of peptides with known proline-rich attachment domains further shifted the monomer-tetramer ratio toward the tetramer.
ContributorsKendle, Robert Player (Author) / Mor, Tsafrir (Thesis director) / Mason, Hugh (Committee member) / Larrimore, Kathy (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Efforts to quantify the diversity of the T cell repertoire have generally been unsuccessful because not all factors accounting for diversity have been considered. In order to get an accurate representation of the T cell repertoire, one must incorporate analysis of germline gene diversity, diversity from somatic recombination, joining diversity from N- and P- nucleotides, and TCR chain pairing diversity. Because of advances in high-throughput sequencing techniques, estimates have been able to account for diversity from TCR genes. However the ability to account for chain pairing diversity has been more difficult. In order to do so, single cell sorting techniques must be employed. These techniques, though effective, are time consuming and expensive. For this reason, no large-scale analyses have been done on the immune repertoires using these techniques. In this study, we propose a novel method for linking the two TCR chain sequences from an individual cell. DNA origami nanostructure technology is employed to capture and bind the TCRγ and TCRδ chain mRNA inside individual cells using probe strands complementary to the C-region of those sequences. We then use a dual-primer RT and ligation molecular strategy to link the two sequences together. The result is a single amplicon containing the CDR3 region of the TCRγ and TCRδ. This amplicon can then be easily PCR amplified using sequence specific primers, and sequenced. DNA origami nanostructures offer a rapid, cost-effective method alternative to conventional single cell sorting techniques, as both TCR mRNA can be captured on one origami molecule inside a single cell. At present, this study outlines a proof-of-principle analysis of the method to determine its functionality. Using known TCRγ and TCRδ sequences, the DNA origami and RT/PCR method was tested and resulting sequence data proved the effectiveness of the method. The original TCRγ and TCRδ sequences were linked together as a single amplicon containing both CDR3 regions of the genes. Thus, this method can be employed in further research to elucidate the γδ T cell repertoire. This technology is also easily adapted to any gene target or cell type and therefore presents a large opportunity to be used in other immune repertoire analysis and other immunological studies (such as the rapid identification and subsequent production of antibodies).
ContributorsPoindexter, Morgan Elizabeth (Author) / Blattman, Joseph (Thesis director) / Yan, Hao (Committee member) / Schoettle, Louis (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The Performance Based Studies Research Studies Group (PBSRG) at Arizona State University aims to evaluate and provide solutions to problems by using concepts derived from deductive logic. The research group identified that problems in most industries are due to the traditional approach of management, direction and control, and offers a practical contrasting model. The author is a biological sciences major interested in the health care industry. As a volunteer at a local non-profit pregnancy clinic in Tempe, AZ, the author noticed characteristics of the clinic structure that resembled both the traditional approach of management, direction and control and the best value (BV) approach. Although the pregnancy clinic has existed for 30 years and has high patient satisfaction, it faces problems that jeopardize its long term sustainability. This study analyzes the stereotypical structure of non-profit health clinics through literature review and through a case study of a local non-profit pregnancy clinic in Tempe, Arizona. The study identified and analyzed the factors that contribute to inefficiency within non-profit health clinics. The conclusions of the research demonstrate that characteristics of non-profit health clinics that resemble the traditional model perform in a manner that is unsustainable. Recommendations were based on concepts derived from Information Measurement Theory (IMT) and aimed to improve efficiency and effectiveness. The study identifies sources of risks and examines the performance of such organizations; the study concludes that rejection of traditional models and adaptation of the new approach is preferable in improving performance and increasing patient, employee, and volunteer satisfaction.
ContributorsTran, Yvonne Ho (Author) / Kashiwagi, Dean (Thesis director) / Kashiwagi, Jacob (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Healthcare systems and health insurance are both concepts implemented in every country to provide access to the general population. Countries undergo healthcare reforms in order to increase the performance of the system. In 2010, the Affordable Care Act (ACA) was introduced in the United States to increase coverage and create a more inclusive health insurance market. For comparison, the recent reforms in Chile and Singapore were observed as points to determine what concepts work well and what can be implemented in the U.S. system. Unlike the United States, Chile and Singapore completely altered the system that was previously in use. In Chile, the reforms began in the 1970s and made two more major changes in 1973 and early 2000s. Singapore began its reform in the 1960s and created the medical savings account system that is still in use today. To analyze the system further, the medical professions of neurology, physician assistants and optometry were compared in each country. In regards to neurology, the coverage of services in Chile and Singapore are similar in that select medical procedures are covered. In contrast, the United States offers coverage on a case-by-case basis. For physician assistants, such a profession does not exist in Chile or Singapore. In the United States, the profession is rapidly expanding, and coverage is offered for most services provided. Optometry is a stand-alone profession in both the U.S. and Singapore. The services provided by the optometrists are selectively covered by insurance, depending on whether it is considered a medical problem. Chile covers the services often provided by optometrists, however, the ophthalmologist is the provider, as optometry does not exist. This study concluded that the U.S. should continue to provide a more inclusive healthcare system that includes vision and dental care. The U.S., like Singapore, should also adopt a more integrative system. Under this system, patient care would be provided in a way that professionals specializing in the care are included in every step of the process.
ContributorsLa, Jenny (Co-author) / Feruj, Farihah (Co-author) / Morrison, Sarah (Co-author) / Gaughan, Monica (Thesis director) / Essary, Alison (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The Community Action Research Experiences (CARE) Program collaborated with the WellCare Foundation (WCF) to assess the referral sources of the clinic in order to more effectively reach additional potential patients. Archival data were analyzed from a 19-month period from the medical records of patients. Also, data were collected from interviews with the case manager of agencies that were a known referral source of WCF. These case manager interviews were completed over a one-month period. For the archival data part of the project, data were collected from 117 patients. Four representatives from community agencies participated in phone interviews. The results indicated that the most common referral sources were word of mouth, followed by community agency referrals. The results also indicated that WCF appears to have served a unique niche that is not served by other non-profit health clinics. These results led to implications for action and direction for future applied research.
ContributorsEbbing, Brittany Gabrielle (Author) / Spinrad, Tracy (Thesis director) / Dumka, Larry (Committee member) / Brougham, Jennifer (Committee member) / Barrett, The Honors College (Contributor) / T. Denny Sanford School of Social and Family Dynamics (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
In medical field today, current diagnostic tools for neurodegenerative diseases fail to diagnose patients prior to the occurrence of damaging neuronal loss. Oftentimes, this means that by the time a patient has been diagnosed with a disease such as Alzheimer's disease (AD) or Parkinson's disease (PD), they have already suffered severe, irreversible neurodegeneration. One of the significant weaknesses in the diagnosis and treatment of patients with AD and PD is the lack of viable biomarkers. Biomarkers are vital tools that can be utilized to identify patients who are in presymptomatic stages of a disease, track and quantify disease progression, and also determine whether or not a patient is responding to a particular treatment. RNAs are involved in all cellular processes, and due to their very specific spatial, temporal, and even cellular-level expression, abnormal expression signatures serve as key indicators of many diseases. Recently, cells have been shown to secrete nanometer-sized microvesicles, called exosomes, which moderate the horizontal transfer of mRNAs and miRNAs between cells. We hypothesize that exosomes obtained from human biofluids, such as cerebral spinal fluid (CSF) and blood plasma, can be used to determine extracellular RNA (exRNA) expression signatures associated with neurodegenerative disease. This experiment used pooled samples of CSF and plasma in order to investigate which of 3 sample enrichment methods would be most conducive to studying exRNA contained within exosomes. The results from this preliminary investigation will be used in later investigations that will seek to determine exRNA biomarkers of neurodegenerative disease.
ContributorsBeecroft, Taylor Alexandria (Author) / Capco, David (Thesis director) / Van Keuren-Jensen, Kendall (Committee member) / Huentelman, Matt (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05