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- Creators: Harrington Bioengineering Program
Description
Transgene expression in mammalian cells has been shown to meet resistance in the form of silencing due to chromatin buildup within the cell. Interactions of proteins with chromatin modulate gene expression profiles. Synthetic Polycomb transcription factor (PcTF) variants have the potential to reactivate these silence transgenes as shown in Haynes & Silver 2011. PcTF variants have been constructed via TypeIIS assembly to further investigate this ability to reactive transgenes. Expression in mammalian cells was confirmed via fluorescence microscopy and red fluorescent protein (RFP) expression in cell lysate. Examination of any variation in conferment of binding strength of homologous Polycomb chromodomains (PCDs) to its trimethylated lysine residue target on histone three (H3K27me3) was investigated using a thermal shift assay. Results indicate that PcTF may not be a suitable protein for surveying with SYPRO Orange, a dye that produces a detectable signal when exposed to the hydrophobic domains of the melting protein. A cell line with inducible silencing of a chemiluminescent protein was used to determine the effects PcTF variants had on gene reactivation. Results show down-regulation of the target reporter gene. We propose this may be due to PcTF not binding to its target; this would cause PcTF to deplete transcriptional machinery in the nucleus. Alternatively, the CMV promoter could be sequestering transcriptional machinery in its hyperactive transcription of PcTF leading to widespread down-regulation. Finally, the activation domain used may not be appropriate for this cell type. Future PcTF variants will address these hypotheses by including multiple Polycomb chromodomains (PCDs) to alter the binding dynamics of PcTF to its target, and by incorporating alternative promoters and activation domains.
ContributorsGardner, Cameron Lee (Author) / Haynes, Karmella (Thesis director) / Stabenfeldt, Sarah (Committee member) / Barrett, The Honors College (Contributor) / Department of Finance (Contributor) / Harrington Bioengineering Program (Contributor)
Created2015-05
Description
Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The global population over the age of 60 is estimated to rise to 23% by 2050 only increase the prevalence of functional neurological disorders and stroke. Increase in cases of functional neurological disorders and strokes will place a greater burden on the healthcare industry, specifically physical therapy. Physical therapy is vital for a patient’s recovery of motor function which is time demanding and taxing on the physical therapist. Wearable robotics have been proven to improve functional outcomes in gait rehabilitation by providing controlled high dosage and high-intensity training. Accurate control strategies for assistive robotic exoskeletons are vital for repetitive high precisions assistance for cerebral plasticity to occur.
This thesis presents a preliminary determination and design of a control algorithm for an assistive ankle device developed by the ASU RISE Laboratory. The assistive ankle device functions by compressing a spring upon heel strike during gait, remaining compressed during mid-stance and then releasing upon initiation of heel-off. The relationship between surface electromyography and ground reactions forces were used for identification of user-initiated heel-off. The muscle activation of the tibialis anterior combined with the ground reaction forces of the heel pressure sensor generated potential features that will be utilized in the revised control algorithm for the assistive ankle device. Work on this project must proceed in order to test and validate the revised control algorithm to determine its accuracy and precision.
This thesis presents a preliminary determination and design of a control algorithm for an assistive ankle device developed by the ASU RISE Laboratory. The assistive ankle device functions by compressing a spring upon heel strike during gait, remaining compressed during mid-stance and then releasing upon initiation of heel-off. The relationship between surface electromyography and ground reactions forces were used for identification of user-initiated heel-off. The muscle activation of the tibialis anterior combined with the ground reaction forces of the heel pressure sensor generated potential features that will be utilized in the revised control algorithm for the assistive ankle device. Work on this project must proceed in order to test and validate the revised control algorithm to determine its accuracy and precision.
ContributorsGaytan-Jenkins, Daniel Rinaldo (Author) / Zhang, Wenlong (Thesis director) / Tyler, Jamie (Committee member) / Harrington Bioengineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Synthetic biology is an emerging engineering disciple, which designs and controls biological systems for creation of materials, biosensors, biocomputing, and much more. To better control and engineer these systems, modular genetic components which allow for highly specific and high dynamic range genetic regulation are necessary. Currently the field struggles to demonstrate reliable regulators which are programmable and specific, yet also allow for a high dynamic range of control. Inspired by the characteristics of the RNA toehold switch in E. coli, this project attempts utilize artificial introns and complementary trans-acting RNAs for gene regulation in a eukaryote host, S. cerevisiae. Following modification to an artificial intron, splicing control with RNA hairpins was demonstrated. Temperature shifts led to increased protein production likely due to increased splicing due to hairpin loosening. Progress is underway to demonstrate trans-acting RNA interaction to control splicing. With continued development, we hope to provide a programmable, specific, and effective means for translational gene regulation in S. cerevisae.
ContributorsDorr, Brandon Arthur (Author) / Wang, Xiao (Thesis director) / Green, Alexander (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This paper begins by exploring the prior research that has shown how eating a plant-based diet can affect the human body. Some of these effects include: improved mood, energy levels, gut health, alkalized urine pH, as well as, lowering the risk of hormonal imbalance, kidney stones, diabetes, cancer, and coronary artery disease. The worries that generally accompany eating a fully vegan diet, which include, malnutrition and protein deficiency, are also addressed in the background research. In attempt to build upon previous research, a weeklong experiment was conducted testing 3 different factors, which include: gut health, improved mood, and urine pH. Mood states were measured quantifiably using a POMS (profile of mood states) test. Gut health was measured using several factors, including consistency and frequency of bowel movements, as well as, GI discomfort. Two 24-hour urine samples were collected from each of the subjects to compare the pH of their urine before and after the study. The sample size of this study included 15 healthy, non-smoking, subjects, between 18-30 years of age. The subjects were split up into 3 stratified random samples, including, an omnivore control group, vegan control group, and experimental vegan group. The experimental vegans had eaten meat/eggs/dairy regularly for their whole lives before the start of the study, and had consented to eating a vegan diet for the entirety of one week. While the data from the control groups remained mostly constant as predicted, the results from the experimental group were shown to have a significantly better mood (P<0.05) after one week, as well as, a significantly higher urine pH (P < 0.025) than they did before the study. However, the experimental group did not show a significant change in stool frequency, consistency, or GI discomfort within one week. The vegan control group, which included subjects who had eaten a plant-based diet for 1-3 years, had much better gut health scores. This leads us to believe that the vegan gut microbiome takes much longer to transform into than just one week unlike urine pH and mood, which can take as little as one week. These findings warrant further investigation.
ContributorsMacias, Lindsey Kaori (Author) / Johnston, Carol (Thesis director) / Katsanos, Christos (Committee member) / Harrington Bioengineering Program (Contributor) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
A Personal Journey Through Physical Fitness chronicles one individual's academic and physical journey through fitness. An ex college gymnast after exiting formal sports looks to academics for the answers to accomplish the goal of working out one hour a day and feeling as well as being physically fit as a result. This research resulted in finding the five pillars of physical fitness; which are Endurance, Flexibility, Strength, Balance, and Agility. After determining that these were the five primary pillars of physical fitness a workout plan was made based on and focused on improving them. This work out plan included running and hiking for endurance, high intensity interval training for agility, endurance and strength, stretching at the end of every work out, and a weightlifting program that utilized push, pull, and lower body days. It also utilized yoga for flexibility, recovery, and balance. Additionally, gymnastic ring strength was included to help develop balance and strength. Then a four-week trial period was executed taking measurements at the beginning and end of the plan. The results of the five-pillar plan were quantified using physical metrics. There was improvement in all of the pillars: Endurance, Flexibility, Strength, Balance, and Agility. However it should be noted there was not a direct measure for balance making its improvement much more subjective and qualitative than quantitative. In addition to having physical metrics of health and increased fitness there were mental side effects such as of feeling good and more relaxed throughout the process. At the end of each week of the four-week workout trial mental and physical feelings were recorded and included in the study. The method and plan were successful and created in a way that others could follow this four-week plan to improve their own physical health.
ContributorsVlastos, Joseph Nicholas (Author) / Kaplan, Robert (Thesis director) / Roses-Thema, Cynthia (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Concussions and traumatic brain injuries are mechanical events which can derive from no specific activity or event. However, these injuries occur often during athletic and sporting events but many athletes experiencing these symptoms go undiagnosed and continue playing without proper medical attention. The current gold standard for diagnosing athletes with concussions is to have medical professionals on the sidelines of events to perform qualitative standardized assessments which may not be performed frequently enough and are not specialized for each athlete. The purpose of this report is to discuss a study sanctioned by Arizona State University's Project HoneyBee and additional affiliations to validate a third-party mouth guard device product to recognize and detect force impacts blown to an athlete's head during athletic activity. Current technology in health monitoring medical devices can allow users to apply this device as an additional safety mechanism for early concussion awareness and diagnosis. This report includes the materials and methods used for experimentation, the discussion of its results, and the complications which occurred and areas for improvement during the preliminary efforts of this project. Participants in the study were five non-varsity ASU Wrestling athletes who volunteered to wear a third-party mouth guard device during sparring contact at practice. Following a needed calibration period for the devices, results were recorded both through visual observation and with the mouth guard devices using an accelerometer and gyroscope. This study provided a sound understanding for the operation and functionality of the mouth guard devices. The mouth guard devices have the capability to provide fundamental avenues of research for future investigations.
ContributorsTielke, Austin Wyatt (Author) / Ross, Heather (Thesis director) / LaBelle, Jeffrey (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Current research into live-cell dynamics, particularly those relating to chromatin structure and remodeling, are limited. The tools that are used to detect state changes in chromatin, such as Chromatin Immunoprecipitation and qPCR, require that the cell be killed off. This limits the ability of researchers to pinpoint changes in live cells over a longer period of time. As such, there is a need for a live-cell sensor that can detect chromatin state changes. The Chromometer is a transgenic chromatin state sensor designed to better understand human cell fate and the chromatin changes that occur. HOXD11.12, a DNA sequence that attracts repressive Polycomb group (PCG) proteins, was placed upstream of a core promoter-driven fluorescent reporter (AmCyan fluorescent protein, CFP) to link chromatin repression to a CFP signal. The transgene was stably inserted at an ectopic site in U2-OS (osteosarcoma) cells. Expression of CFP should reflect the epigenetic state at the HOXD locus, where several genes are regulated by Polycomb to control cell differentiation. U2-OS cells were transfected with the transgene and grown under selective pressure. Twelve colonies were identified as having integrated parts from the transgene into their genomes. PCR testing verified 2 cell lines that contain the complete transgene. Flow cytometry indicated mono-modal and bimodal populations in all transgenic cell colonies. Further research must be done to determine the effectiveness of this device as a sensor for live cell state change detection.
ContributorsBarclay, David (Co-author) / Simper, Jan (Co-author) / Haynes, Karmella (Thesis director) / Brafman, David (Committee member) / School of Life Sciences (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The dilemma of the lack of prenatal and neonatal healthcare has been prevalent among third world countries for many years. The lack of prenatal healthcare has been shown to have direct links to spontaneous preterm births from which low-birth weight in babies can be a result. The World Health Organization has identified preterm birth as one of the biggest overseen burdens in developing countries.
This study seeks to answer the research questions: What are the major risk factors associated with the lack of prenatal and neonatal healthcare in developing countries? What are potential routes of intervention (ROI) to help these countries? The goal is to analyze the risk factors and determine if there are any ROIs available to minimize potential incidents or accidents associated with complications of preterm birth.
A few potential risk factors include: poverty, a mother’s lack of education, a lack of professional visitation during pregnancy, having a short cervix, and routine use of Ultrasound. This research paper has identified that keeping ultrasound diagnostics to a minimum, seeking professional help during pregnancy, incorporating corticosteroids for preterm births, implementing Kangaroo Mother Care, and Cervical Cerclage are interventions that can reduce preterm births and the associated complications that come with it. We believe that further research, regarding compliance of each of these interventions, would show reduction of preterm births and low birth weight in developing countries.
This study seeks to answer the research questions: What are the major risk factors associated with the lack of prenatal and neonatal healthcare in developing countries? What are potential routes of intervention (ROI) to help these countries? The goal is to analyze the risk factors and determine if there are any ROIs available to minimize potential incidents or accidents associated with complications of preterm birth.
A few potential risk factors include: poverty, a mother’s lack of education, a lack of professional visitation during pregnancy, having a short cervix, and routine use of Ultrasound. This research paper has identified that keeping ultrasound diagnostics to a minimum, seeking professional help during pregnancy, incorporating corticosteroids for preterm births, implementing Kangaroo Mother Care, and Cervical Cerclage are interventions that can reduce preterm births and the associated complications that come with it. We believe that further research, regarding compliance of each of these interventions, would show reduction of preterm births and low birth weight in developing countries.
ContributorsHuapaya, Eduardo Luciano (Author) / Muthuswamy, Jitendran (Thesis director) / Comar, William (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The primary goal of this paper is to analyze a tool used for measuring human
development on a global scale. Originally, development within a country was solely judged by the degree of economic growth by way of Gross National Product (GNP) and per capita income. Holistically, GNP measures the total extent of economic activity of a country’s people within a given time period. (Rutherford, 2012). Critics found several issues with this one-dimensional approach of measuring human development. What failed to be recognized was the distribution of income among the country’s citizens. Higher incomes often favor men within the majority when compared to women and people of minority groups (Feiner & Roberts, 1990). GNP also failed to recognize the social limitations under a government. In other words, are there limitations as to what goods can be bought and who can buy them?
development on a global scale. Originally, development within a country was solely judged by the degree of economic growth by way of Gross National Product (GNP) and per capita income. Holistically, GNP measures the total extent of economic activity of a country’s people within a given time period. (Rutherford, 2012). Critics found several issues with this one-dimensional approach of measuring human development. What failed to be recognized was the distribution of income among the country’s citizens. Higher incomes often favor men within the majority when compared to women and people of minority groups (Feiner & Roberts, 1990). GNP also failed to recognize the social limitations under a government. In other words, are there limitations as to what goods can be bought and who can buy them?
ContributorsSteeley, Emily Anne (Author) / Parmentier, Mary Jane (Thesis director) / Grgich, Traci (Committee member) / Harrington Bioengineering Program (Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05