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Description
Yellow-bellied marmots (Marmota flavivent) are semi-fossorial ground-dwelling sciurid rodents native to the western United States. They are facultatively social and live in colonies that may contain over 50 individuals. Marmot populations are well studied in terms of their diet, life cycle, distribution, and behavior, however, knowledge about viruses associated with marmots is very limited. In this study we aim to identify DNA viruses by non-invasive sampling of their feces. Viral DNA was extracted from fecal material of 35 individual marmots collected in Colorado and subsequently submitted to rolling circle amplification for circular molecule enrichment. Using a viral metagenomics approach which included high-throughput sequencing and verification of viral genomes using PCR, cloning and sequencing, a diverse group of single-stranded (ss) DNA viruses were identified. Diverse ssDNA viruses were identified that belong to two established families, Genomoviridae (n=7) and Anelloviridae (n=1) and several others that belong to unclassified circular replication associated encoding single-stranded (CRESS) DNA virus groups (n=19). There were also circular DNA molecules extracted (n=4) that appear to encode one viral-like gene and are composed of <1545 nt. The viruses that belonged to the family Genomoviridae clustered with those in the Gemycircularvirus genus. The genomoviruses were extracted from 6 samples. These clustered with gemycircularvirus extracted from arachnids and feces. The anellovirus, extracted from one sample, identified here has a genome sequence that is most similar to those from other rodent species, lagomorphs, and mosquitos. The CRESS viruses identified here were extracted from 9 samples and are novel and cluster with others identified from avian species. This study gives a snapshot of viruses associated with marmots based on fecal sampling.
ContributorsKhalifeh, Anthony (Author) / Varsani, Arvind (Thesis director) / Kraberger, Simona (Committee member) / Dolby, Greer (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Dielectrophoresis has been shown in the recent past to successfully separate bioparticles of very subtle differences at high resolutions using biophysical forces. In this study, we test the biophysical differences of methicillin resistant and susceptible Staph. aureus that are known to have very similar genomes by using a modified gradient insulator-based dielectrophoresis device (g-iDEP). MRSA is commonly seen in hospitals and is the leading killer of infectious bacteria, claiming the lives of around 10,000 people annually. G-iDEP improves many capabilities within the DEP field including sample size, cost, ease of use and analysis time. This is a promising foundation to creating a more clinically optimized diagnostic tool for both separation and detection of bacteria in the healthcare field. The capture on-set potential for fluorescently tagged MRSA (801 ± 34V) is higher than fluorescently tagged MSSA (610 ± 32V), resulting in a higher electrokinetic to dielectrophoretic mobility ratio for MRSA. Since the strains have proven to be genomically similar through sequencing, it is reasonable to attribute this significant biophysical difference to the added PBP2a enzyme in MRSA. These results are consistent with other bacterial studied within in this device and have proven to be reproducible.
ContributorsSmithers, Jared (Author) / Hayes, Mark (Thesis director) / Woodbury, Neal (Committee member) / School of Criminology and Criminal Justice (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Diabesity is a global epidemic affecting millions worldwide. Diabesity is the term given to the link between obesity and Type II diabetes. It is estimated that ~90% of patients diagnosed with Type II diabetes are overweight or have struggled with excess body fat in the past. Type II diabetes is characterized by insulin resistance which is an impaired response of the body to insulin that leads to high blood glucose levels. Adipose tissue, previously thought of as an inert tissue, is now recognized as a major endocrine organ with an important role in the body's immune response and the development of chronic inflammation. It is speculated that adipose tissue inflammation is a major contributor to insulin resistance particular to Type II diabetes. This literature review explores the popular therapeutic targets and marketed drugs for the treatment of Type II diabetes and their role in decreasing adipose tissue inflammation. rAGE is currently in pre-clinical studies as a possible target to combat adipose tissue inflammation due to its relation to insulin resistance. Metformin and Pioglitazone are two drugs already being marketed that use unique chemical pathways to increase the production of insulin and/or decrease blood glucose levels. Sulfonylureas is one of the first FDA approved drugs used in the treatment of Type II diabetes, however, it has been discredited due to its life-threatening side effects. Bariatric surgery is a form of invasive surgery to rid the body of excess fat and has shown to normalize blood glucose levels. These treatments are all secondary to lifestyle changes, such as diet and exercise which can help halt the progression of Type II diabetes patients.
ContributorsRobles, Alondra Maria (Author) / Woodbury, Neal (Thesis director) / Redding, Kevin (Committee member) / Allen, James (Committee member) / Hendrickson, Kirstin (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
To date, there have been few, if any, studies evaluating the venom toxin levels in dogs that have been naturally envenomated by pit vipers. Understanding venom toxin pharmacokinetics in a clinical setting is important for a variety of reasons, including the potential to better elucidate treatment options, prognosis, and other factors associated with pit viper envenomation. In addition, dogs serve as a comparative species to humans for evaluating pit viper envenomations. This pilot study’s primary objective was to address the question of “What do we see?” in dogs presenting for rattlesnake envenomation. To answer this question, we obtained serum from envenomated dogs presenting at three veterinary clinics, then used enzyme-linked immunosorbent assay (ELISA) and western blot analysis to measure total venom and key toxins in sera. Phospholipase A2, a primary venom toxin, was identified in a few samples by the western blot, and contributed to the positive correlation between percent echinocytes in the blood and venom concentration. Medical data records were compared to venom concentrations measured using ELISA to determine whether there were any significant correlations. First, the hematological results were compared. Clotting times showed a strong positive correlation, clotting times and platelets showed a negative correlation, while echinocytes and platelets showed no correlation. When compared to venom concentration, clotting times showed a negative correlation, while age showed a positive correlation. Weight and platelets were also compared to venom concentration, but no significant correlations were found. The logistics of this study provided a real-world model where time elapsed between envenomation and hospital admission, thus giving a realistic look at what occurs in both animal and human medicine.
ContributorsNelson, Alexis (Co-author, Co-author) / DeNardo, Dale (Thesis director) / Woods, Craig (Thesis director) / Varsani, Arvind (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Human papillomavirus (HPV) is the causative agent of cervical cancer. Persistent infection with high-risk HPV 16, 18 or 45 species is associated with the development and progression of cervical cancer. HPV genotyping and Pap smear tests are the regular methods used to detect pre-invasive cervical lesions, but there is a need for developing a rapid biomarker to profile immunity to these viruses. The viral E7 oncogene is expressed in most HPV-associated cancers and anti-E7 antibodies can be detected in the blood of patients with cervical cancer. This research was focused on viral E7 oncogene expression to be used in development of low-cost point of care tests, enabling patients from low resource settings to detect the asymptotic stage of cervical cancer and be able to seek treatment early. In order to produce the E7 protein in vitro to measure antibody levels, GST tagged E7 genes from HPV 16, 18 and 45 species were inserted into the pDEST15 vector and expressed in E. coli BL21DE3 cells that were induced with 1mM of IPTG. The E7-GST fused expressed protein was then purified using glutathione beads and resolved on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Protein expression was 5.8 \u03bcg/ml for HPV 16E7 in 500 ml culture and for the 500 ml culture of HPV 18 E7 and 45 E7 were 10.5 \u03bcg/ml and 10.5 \u03bcg/ml for HPV 18E7 and 45E7 respectively. High yield values are showing high expression levels of GST-tagged E7 recombinant protein which can be used for serotyping a number of individuals. This shows that HPV E7 can be produced in large quantities that can potentially be used in point of care tests that can help identify women at risk of cervical cancer. In conclusion, the E7 protein produced in this study can potentially be used to induce humoral responses in patients\u2019 sera for understanding the immune response of cervical cancer.
ContributorsMakuyana, Ntombizodwa (Author) / Anderson, Karen (Thesis director) / Ewaisha, Radwa (Committee member) / Varsani, Arvind (Committee member) / Hou, Ching-Wen (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
The Heliobacterial Reaction Center (HbRC) is the simplest Type I Reaction Center (RC) known today. However, upon illumination it has been found to produce menaquinol, and this has led to experiments investigating the function of this reduction scheme. The goal of the experiment was to investigate the mechanisms of menaquinol production through the use of Photosystem II (PSII) herbicides that are known to inhibit the QB quinone site in Type II RCs. Seven herbicides were chosen, and out of all of them terbuthylazine showed the greatest effect on the RC in isolated membranes when Transient Absorption Spectroscopy was used. In addition, terbuthylazine decreased menaquinone reduction to menaquinol by ~72%, slightly more than the reported effect of teburtryn (68%)1. In addition, terbuthylazine significantly impacted growth of whole cells under high light more than terbutryn.
ContributorsOdeh, Ahmad Osameh (Author) / Redding, Kevin (Thesis director) / Woodbury, Neal (Committee member) / Allen, James (Committee member) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Background:
The positive impacts of yoga on stress, pain, and chronic disease has recently led to the integration of yoga as part of physical therapy (PT) treatment. Due to the lack of training for PTs related to yoga, there is currently a need to provide knowledge and education about how to safely and easily implement therapeutic yoga (TY) as a complementary treatment approach.
Objective:
The purpose of this study was to assess the readiness of PTs (those who do not currently prescribe TY to patients) to integrate TY into treatment, and secondly, the feasibility (i.e., acceptability, demand, and practicality) of a 5-week online TY training to improve the readiness of PT’s to utilize TY in their practice.
Methods:
Licensed Physical Therapist’s (n=103) were recruited nationally through social media and email. Eligible and consented participants were asked to register in a 5-week online TY training course, Readiness for Integrating Yoga Therapeutics into Rehabilitation for PTs (intervention). PTs perceptions of TY and the role of safety and confidence in prescribing TY to patients were measured at baseline and post-intervention using a customized survey. Feasibility outcomes were measured after completion of the 5-week online training course with a survey. Feasibility was measured with acceptability, demand, and practicality. Our benchmarks included: (1) at least 70% of PTs would find the course acceptable, (2) at least 60% would finish the course (i.e., demand) and (3) there would be significant improvements in PTs perceptions of TY.
Results:
A total of 95 licensed PTs registered in the 5-week online TY training course, with 60 PTs (63%) completing the intervention and surveys. Of the PTs who completed the 5-week online training course, most PTs felt they were not ready (n=19/60, 31.7%) or somewhat ready (n=25/60, 41.7%) to integrate TY prior to taking the online training. Over half of PTs thought the online training was acceptable (n= 50/60, 83.3%) and finished the course (n=60/95, 63%). There were significant improvements in personal readiness to prescribe TY, safety prescribing TY, confidence to prescribe TY, current understanding/knowledge of TY and feeling adequately trained and educated to use some form of TY techniques with patients.
Conclusion:
Findings suggest a 5-week online TY training course is feasible in improving PTs readiness to prescribe TY, safety prescribing TY, confidence to prescribe TY, current understanding/knowledge of TY and feeling adequately trained and educated to use some form of TY techniques with patients. Future studies are proposed to test the effectiveness of TY training and education opportunities with PTs to further advance the adoption of TY into PT practice.
The positive impacts of yoga on stress, pain, and chronic disease has recently led to the integration of yoga as part of physical therapy (PT) treatment. Due to the lack of training for PTs related to yoga, there is currently a need to provide knowledge and education about how to safely and easily implement therapeutic yoga (TY) as a complementary treatment approach.
Objective:
The purpose of this study was to assess the readiness of PTs (those who do not currently prescribe TY to patients) to integrate TY into treatment, and secondly, the feasibility (i.e., acceptability, demand, and practicality) of a 5-week online TY training to improve the readiness of PT’s to utilize TY in their practice.
Methods:
Licensed Physical Therapist’s (n=103) were recruited nationally through social media and email. Eligible and consented participants were asked to register in a 5-week online TY training course, Readiness for Integrating Yoga Therapeutics into Rehabilitation for PTs (intervention). PTs perceptions of TY and the role of safety and confidence in prescribing TY to patients were measured at baseline and post-intervention using a customized survey. Feasibility outcomes were measured after completion of the 5-week online training course with a survey. Feasibility was measured with acceptability, demand, and practicality. Our benchmarks included: (1) at least 70% of PTs would find the course acceptable, (2) at least 60% would finish the course (i.e., demand) and (3) there would be significant improvements in PTs perceptions of TY.
Results:
A total of 95 licensed PTs registered in the 5-week online TY training course, with 60 PTs (63%) completing the intervention and surveys. Of the PTs who completed the 5-week online training course, most PTs felt they were not ready (n=19/60, 31.7%) or somewhat ready (n=25/60, 41.7%) to integrate TY prior to taking the online training. Over half of PTs thought the online training was acceptable (n= 50/60, 83.3%) and finished the course (n=60/95, 63%). There were significant improvements in personal readiness to prescribe TY, safety prescribing TY, confidence to prescribe TY, current understanding/knowledge of TY and feeling adequately trained and educated to use some form of TY techniques with patients.
Conclusion:
Findings suggest a 5-week online TY training course is feasible in improving PTs readiness to prescribe TY, safety prescribing TY, confidence to prescribe TY, current understanding/knowledge of TY and feeling adequately trained and educated to use some form of TY techniques with patients. Future studies are proposed to test the effectiveness of TY training and education opportunities with PTs to further advance the adoption of TY into PT practice.
ContributorsThompson, Abigail Ann (Co-author) / Thompson, Abigail (Co-author) / Huberty, Jennifer (Thesis director) / Taylor, Matthew (Committee member) / Ortiz, Alexis (Committee member) / College of Health Solutions (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Predicting the binding sites of proteins has historically relied on the determination of protein structural data. However, the ability to utilize binding data obtained from a simple assay and computationally make the same predictions using only sequence information would be more efficient, both in time and resources. The purpose of this study was to evaluate the effectiveness of an algorithm developed to predict regions of high-binding on proteins as it applies to determining the regions of interaction between binding partners. This approach was applied to tumor necrosis factor alpha (TNFα), its receptor TNFR2, programmed cell death protein-1 (PD-1), and one of its ligand PD-L1. The algorithms applied accurately predicted the binding region between TNFα and TNFR2 in which the interacting residues are sequential on TNFα, however failed to predict discontinuous regions of binding as accurately. The interface of PD-1 and PD-L1 contained continuous residues interacting with each other, however this region was predicted to bind weaker than the regions on the external portions of the molecules. Limitations of this approach include use of a linear search window (resulting in inability to predict discontinuous binding residues), and the use of proteins with unnaturally exposed regions, in the case of PD-1 and PD-L1 (resulting in observed interactions which would not occur normally). However, this method was overall very effective in utilizing the available information to make accurate predictions. The use of the microarray to obtain binding information and a computer algorithm to analyze is a versatile tool capable of being adapted to refine accuracy.
ContributorsBrooks, Meilia Catherine (Author) / Woodbury, Neal (Thesis director) / Diehnelt, Chris (Committee member) / Ghirlanda, Giovanna (Committee member) / Department of Psychology (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Abstract Objective: The purpose of this study was to determine the feasibility (e.g., practicality and demand) of a 4-week series of yoga classes in a homeless shelter. Participants: Five current residents of Central Arizona Shelter Services (CASS) and the Chief of Programming at CASS. Methods: Each shelter resident participated in a 5-minute interview answering questions regarding the demand of implementing a yoga program at CASS. The Chief of Programming participated in a 30-minute interview answering questions regarding the practicality of implementing a 4-week series yoga program at the homeless shelter. Results: CASS residents reported a strong desire to attend a yoga program. The Chief of Programming at CASS reported that implementing a yoga program would conflict with the overall goal of the shelter. Conclusion: Implementing a 4-week series yoga program is not feasible at CASS although there is a strong demand for a yoga program among the homeless population of the Phoenix metro area.
ContributorsSamuels, Jasmyne Angelique (Author) / Hart, Teresa (Thesis director) / Huberty, Jennifer (Committee member) / Pearl, Julia (Committee member) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Recent research has confirmed and revealed many physical and mental benefits of yoga. The practice of yoga has spread throughout the western world, where it is widely used for the purpose of exercise and fitness. Due to its rise in popularity, there is a need for research regarding the energy expenditure required for different types of yoga. The majority of the literature cites yoga as being an effective exercise for light intensity activity, but there are not as many studies attempting to determine if there are postures and sequences that can meet the requirements for moderate physical activity. In addition, there is a need to validate mobile devices with which to measure energy expenditure (EE) that are compatible with the dynamic movements that occur during yoga. The purpose of this study was to measure energy expenditure of twenty-two yoga practitioners of varying experience during a 30-minute Vinyasa flow yoga practice and from this data collection determine: if an ashtanga-based vinyasa yoga class meets the criteria for moderate intensity physical activity, the reliability between the Actigraph and Oxycon Mobile and the validity of an Actigraph GT3X device worn on the hip in estimating energy expenditure for ashtanga-based vinyasa flow yoga. The Actigraph GT3X and the Oxycon mobile were used to measure energy expenditure. Mean values for energy expenditure recorded by the Oxycon and Actigraph were 3.19 ± 0.42 METs and 1.16 ± 0.23 METs respectively, exhibiting a significant difference in data collection. There was no correlation between the values recorded by the two devices, indicating that the Actigraph was not consistent with the Oxycon Mobile (previously validated for measurement of EE). Results of this study indicate that this Vinyasa flow yoga sequence does satisfy the criteria for moderate intensity physical activity as defined by ACSM with an average EE of 3.19 ± 0.42 METs, and that the Actigraph GT3X is not an accurate device for measurement of EE for yoga.
ContributorsHand, Lindsay Gabrielle (Author) / Huberty, Jennifer (Thesis director) / Buman, Matthew (Committee member) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12