Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
Displaying 1 - 10 of 11
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- All Subjects: Synthetic Biology
- All Subjects: EEG
- Creators: Harrington Bioengineering Program
Description
Brain-computer interface technology establishes communication between the brain and a computer, allowing users to control devices, machines, or virtual objects using their thoughts. This study investigates optimal conditions to facilitate learning to operate this interface. It compares two biofeedback methods, which dictate the relationship between brain activity and the movement of a virtual ball in a target-hitting task. Preliminary results indicate that a method in which the position of the virtual object directly relates to the amplitude of brain signals is most conducive to success. In addition, this research explores learning in the context of neural signals during training with a BCI task. Specifically, it investigates whether subjects can adapt to parameters of the interface without guidance. This experiment prompts subjects to modulate brain signals spectrally, spatially, and temporally, as well differentially to discriminate between two different targets. However, subjects are not given knowledge regarding these desired changes, nor are they given instruction on how to move the virtual ball. Preliminary analysis of signal trends suggests that some successful participants are able to adapt brain wave activity in certain pre-specified locations and frequency bands over time in order to achieve control. Future studies will further explore these phenomena, and future BCI projects will be advised by these methods, which will give insight into the creation of more intuitive and reliable BCI technology.
ContributorsLancaster, Jenessa Mae (Co-author) / Appavu, Brian (Co-author) / Wahnoun, Remy (Co-author, Committee member) / Helms Tillery, Stephen (Thesis director) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor) / Department of Psychology (Contributor)
Created2014-05
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
Cell fate is a complex and dynamic process with many genetic components. It has often been likened to “multistable” mathematical systems because of the numerous possible “stable” states, or cell types, that cells may end up in. Due to its complexity, understanding the process of cell fate and differentiation has proven challenging. A better understanding of cell differentiation has applications in regenerative stem cell therapies, disease pathologies, and gene regulatory networks.
A variety of different genes have been associated with cell fate. For example, the Nanog/Oct-4/Sox2 network forms the core interaction of a gene network that maintains stem cell pluripotency, and Oct-4 and Sox2 also play a role in the tissue types that stem cells eventually differentiate into. Using the CRISPR/cas9 based homology independent targeted integration (HITI) method developed by Suzuki et al., we can integrate fluorescent tags behind genes with reasonable efficiency via the non-homologous end joining (NHEJ) DNA repair pathway. With human embryonic kidney (HEK) 293T cells, which can be transfected with high efficiencies, we aim to create a three-parameter reporter cell line with fluorescent tags for three different genes related to cell fate. This cell line would provide several advantages for the study of cell fate, including the ability to quantitatively measure cell state, observe expression heterogeneity among a population of genetically identical cells, and easily monitor fluctuations in expression patterns.
The project is partially complete at this time. This report discusses progress thus far, as well as the challenges faced and the future steps for completing the reporter line.
A variety of different genes have been associated with cell fate. For example, the Nanog/Oct-4/Sox2 network forms the core interaction of a gene network that maintains stem cell pluripotency, and Oct-4 and Sox2 also play a role in the tissue types that stem cells eventually differentiate into. Using the CRISPR/cas9 based homology independent targeted integration (HITI) method developed by Suzuki et al., we can integrate fluorescent tags behind genes with reasonable efficiency via the non-homologous end joining (NHEJ) DNA repair pathway. With human embryonic kidney (HEK) 293T cells, which can be transfected with high efficiencies, we aim to create a three-parameter reporter cell line with fluorescent tags for three different genes related to cell fate. This cell line would provide several advantages for the study of cell fate, including the ability to quantitatively measure cell state, observe expression heterogeneity among a population of genetically identical cells, and easily monitor fluctuations in expression patterns.
The project is partially complete at this time. This report discusses progress thus far, as well as the challenges faced and the future steps for completing the reporter line.
ContributorsLoveday, Tristan Andre (Author) / Wang, Xiao (Thesis director) / Brafman, David (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Human potential is characterized by our ability to think flexibly and develop novel solutions to problems. In cognitive neuroscience, problem solving is studied using various tasks. For example, IQ can be tested using the RAVEN, which measures abstract reasoning. Analytical problem solving can be tested using algebra, and insight can be tested using a nine-dot test. Our class of problem-solving tasks blends analytical and insight processes. This can be done by measuring multiply-constrained problem solving (MCPS). MCPS occurs when an individual problem has several solutions, but when grouped with simultaneous problems only one correct solution presents itself. The most common test for MCPS is known at the CRAT, or compound remote associate task. For example, when given the three target words “water, skate, and cream” there are many compound associates that can be assigned each of the target words individually (i.e. salt-water, roller-skate, whipped-cream), but only one that works with all three (ice-water, ice-skate, ice-cream).
This thesis is a tutorial for a MATLAB user-interface, known as EEGLAB. Cognitive and neural correlates of analytical and insight processes were evaluated and analyzed in the CRAT using EEG. It was hypothesized that different EEG signals will be measured for analytical versus insight problem solving, primarily observed in the gamma wave production. The data was interpreted using EEGLAB, which allows psychological processes to be quantified based on physiological response. I have written a tutorial showing how to process the EEG signal through filtering, extracting epochs, artifact detection, independent component analysis, and the production of a time – frequency plot. This project has combined my interest in psychology with my knowledge of engineering and expand my knowledge of bioinstrumentation.
This thesis is a tutorial for a MATLAB user-interface, known as EEGLAB. Cognitive and neural correlates of analytical and insight processes were evaluated and analyzed in the CRAT using EEG. It was hypothesized that different EEG signals will be measured for analytical versus insight problem solving, primarily observed in the gamma wave production. The data was interpreted using EEGLAB, which allows psychological processes to be quantified based on physiological response. I have written a tutorial showing how to process the EEG signal through filtering, extracting epochs, artifact detection, independent component analysis, and the production of a time – frequency plot. This project has combined my interest in psychology with my knowledge of engineering and expand my knowledge of bioinstrumentation.
ContributorsCobban, Morgan Elizabeth (Author) / Brewer, Gene (Thesis director) / Ellis, Derek (Committee member) / Harrington Bioengineering Program (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
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
It is unknown which regions of the brain are most or least active for golfers during a peak performance state (Flow State or "The Zone") on the putting green. To address this issue, electroencephalographic (EEG) recordings were taken on 10 elite golfers while they performed a putting drill consisting of hitting nine putts spaced uniformly around a hole each five feet away. Data was collected at three time periods, before, during and after the putt. Galvanic Skin Response (GSR) measurements were also recorded on each subject. Three of the subjects performed a visualization of the same putting drill and their brain waves and GSR were recorded and then compared with their actual performance of the drill. EEG data in the Theta (4 \u2014 7 Hz) bandwidth and Alpha (7 \u2014 13 Hz) bandwidth in 11 different locations across the head were analyzed. Relative power spectrum was used to quantify the data. From the results, it was found that there is a higher magnitude of power in both the theta and alpha bandwidths for a missed putt in comparison to a made putt (p<0.05). It was also found that there is a higher average power in the right hemisphere for made putts. There was not a higher power in the occipital region of the brain nor was there a lower power level in the frontal cortical region during made putts. The hypothesis that there would be a difference between the means of the power level in performance compared to visualization techniques was also supported.
ContributorsCarpenter, Andrea (Co-author) / Hool, Nicholas (Co-author) / Muthuswamy, Jitendran (Thesis director) / Crews, Debbie (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
By 2050, feeding the world will require a 70% increase in food production with fewer water resources due to climate change. New strategies are needed to replace current approaches. C3 photosynthesis is inefficient due to photorespiration, but synthetic biology offers a way to increase photosynthetic efficiency and crop yields, such as the tartronyl-CoA (TaCo) pathway. This project assesses the TaCo pathway in the chloroplast of Chlamydomonas reinhardtii and represents a pivotal step toward its practical application in higher plants for use in agriculture and biotechnology.
ContributorsSharma, Priyati (Author) / Cerna, Gabriella (Co-author) / Redding, Kevin (Thesis director) / Bartelle, Benjamin (Committee member) / Erb, Tobias (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)
Created2024-05
Description
This paper is a summarization of a year of projects in Dr. Xiao Wang's Synthetic Biology lab, following from initial computational projects and moving into more experimental projects under the mentorship of Dr. Kylie Standage-Beier, dealing with molecular cloning and dose response curves produced by measuring fluorescence via flow cytometry. This is then integrated with a novel computational flow cytometry analysis software based on public MATLAB functions that convert flow cytometry files into MATLAB variables.
ContributorsKasen, Daniel (Author) / Wang, Xiao (Thesis director) / Standage-Beier, Kylie (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)
Created2024-05
Description
The cocktail party effect describes the brain’s natural ability to attend to a specific voice or audio source in a crowded room. Researchers have recently attempted to recreate this ability in hearing aid design using brain signals from invasive electrocorticography electrodes. The present study aims to find neural signatures of auditory attention to achieve this same goal with noninvasive electroencephalographic (EEG) methods. Five human participants participated in an auditory attention task. Participants listened to a series of four syllables followed by a fifth syllable (probe syllable). Participants were instructed to indicate whether or not the probe syllable was one of the four syllables played immediately before the probe syllable. Trials of this task were separated into conditions of playing the syllables in silence (Signal) and in background noise (Signal With Noise), and both behavioral and EEG data were recorded. EEG signals were analyzed with event-related potential and time-frequency analysis methods. The behavioral data indicated that participants performed better on the task during the “Signal” condition, which aligns with the challenges demonstrated in the cocktail party effect. The EEG analysis showed that the alpha band’s (9-13 Hz) inter-trial coherence could potentially indicate characteristics of the attended speech signal. These preliminary results suggest that EEG time-frequency analysis has the potential to reveal the neural signatures of auditory attention, which may allow for the design of a noninvasive, EEG-based hearing aid.
ContributorsLaBine, Alyssa (Author) / Daliri, Ayoub (Thesis director) / Chao, Saraching (Committee member) / Barrett, The Honors College (Contributor) / College of Health Solutions (Contributor) / Harrington Bioengineering Program (Contributor)
Created2023-05