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.
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- All Subjects: Bioengineering
Description
Autoimmunity develops when the immune system targets self-antigens within the body. Rheumatoid arthritis (RA) is a common autoimmune disease, and its progression is characterized by pro-inflammatory immune cells rapidly proliferating, migrating, and infiltrating joint tissue to provoke inflammation. In order to fulfill this taxing autoreactive response, an increase in energy metabolism is required by immune cells, such as dendritic cells (DCs). Therefore, a shift in DC energy reliance from the Krebs cycle toward glycolysis occurs. This metabolic shift phenotypically transitions DCs from anti-inflammatory properties toward an aggressive pro-inflammatory phenotype, in turn activating pro-inflammatory T cells and promoting RA pathogenesis. If the disease persists uncontrollably, further complications and eventual joint dysfunction can occur. Although, clinically approved drugs can prevent RA progression, they require frequent administration for temporary symptom relief. Furthermore, current approved biological products for RA are not known to have a direct modulatory effect on immunometabolism. Given that cellular metabolism controls immune cell function, this work aims to harness perturbations within RA immune cell energy metabolism and utilizes it as a therapeutic target by reprogramming immune cell metabolism via the delivery of metabolite-based particles. The two-time delivery of these particles reduced RA inflammation in a RA collagen-induced arthritis (CIA) mouse model and generated desired responses with long-term effects. Specifically, this work was achieved by:
Aim 1 – developing and delivering metabolite-based polymeric microparticles synthesized from the Krebs cycle metabolite, alpha-ketoglutarate (aKG; termed paKG MPs) to DCs to modulate their energy metabolism and promote anti-inflammatory properties (in context of RA).
Aim 2 – exploiting the encapsulation ability of paKG MPs to inhibit DC glycolysis in the presence of the CIA self-antigen (collagen type II (bc2)) for the treatment of RA in CIA mice. Herein, paKG MPs encapsulating a glycolytic inhibitor and bc2 induce an anti-inflammatory DC phenotype in vitro and generate suppressive bc2-specific T cell responses and reduce paw inflammation in CIA mice.
ContributorsMangal, Joslyn Lata (Author) / Acharya, Abhinav P (Thesis advisor) / Florsheim, Esther B (Committee member) / Wu, Hsin-Jung Joyce (Committee member) / Anderson, Karen (Committee member) / Arizona State University (Publisher)
Created2022
Description
Diffuse pleural mesothelioma (DPM) is a devastating lung cancer most commonly diagnosed at an advanced stage with a poor prognosis for patients. Therapies available to patients after diagnosis currently include surgical resection, radiotherapy, immunotherapy, and chemotherapy. However, these therapies only prolong life for about a year and a half on average. DPM patients desperately need effective therapies in the form of drugs, drug combinations, and miRNA-based therapies, that could lengthen overall survival and provide a better quality of life. I hypothesized that focusing on DPM tumor biology would streamline the process for discovering new therapies that will have a lasting impact for patients. I have applied systems biology methods to mine multiomic data from patient DPM tumors to discover new therapeutic options. I began by developing a somatic mutation integration pipeline, which created a comprehensive somatic mutational profile of DPM tumors from patient genomic and transcriptomic data. The somatic mutational profile was used in the generation of dpmSYGNAL, a disease-relevant gene regulatory network (GRN) trained on patient tumor multiomic data. I integrated this GRN with functional genomics screens performed on two low-passage primary DPM tumor cell lines and identified gene vulnerabilities that could be targeted by FDA-approved inhibitors and drug combinations. I also developed a pipeline to integrate miRNA target genes from biotinylated pulldowns with RNA-seq data from a study re-expressing the miRNA hsa-miR-497-5p in DPM cell lines. I determined that the re-expression of hsa-miR-497-5p had early pro-apoptotic effects and inhibited the cell cycle at later time points. The identification of inhibitors, combinations of inhibitors, and a therapeutic miRNA demonstrates that DPM biology can be used as a guide to discover new therapeutics for DPM.
ContributorsWilferd, Sierra Fe (Author) / Plaisier, Christopher L (Thesis advisor) / Anderson, Karen (Committee member) / Wilson, Melissa (Committee member) / Hoang, Chuong D (Committee member) / Arizona State University (Publisher)
Created2024
Description
Intracellular voltage recordings from single neurons in vitro and in vivo have been fundamental to our understanding of neuronal function. Conventional electrodes and associated positioning systems for intracellular recording in vivo are large and bulky, which has largely restricted their use to single-channel recording from anesthetized animals. Further, intracellular recordings are very cumbersome, requiring a high degree of skill not readily achieved in a typical laboratory. This dissertation presents a robotic, head-mountable, MEMS (Micro-Electro-Mechanical Systems) based intracellular recording system to overcome the above limitations associated with form-factor, scalability and highly skilled and tedious manual operations required for intracellular recordings. This system combines three distinct technologies: 1) novel microscale, polycrystalline silicon-based electrode for intracellular recording, 2) electrothermal microactuators for precise microscale navigation of the electrode and 3) closed-loop control algorithm for autonomous movement and positioning of electrode inside single neurons. First, two distinct designs of polysilicon-based microscale electrodes were fabricated and tested for intracellular recordings. In the first approach, tips of polysilicon microelectrodes were milled to nanoscale dimensions (<300 nm) using focused ion beam (FIB) to develop polysilicon nanoelectrodes. Polysilicon nanoelectrodes recorded >1.5 mV amplitude, positive-going action potentials and synaptic potentials from neurons in the abdominal ganglion of Aplysia Californica. In the second approach, polysilicon microelectrodes were integrated with miniaturized glass micropipettes filled with electrolyte to fabricate glass-polysilicon microelectrodes. These electrodes consistently recorded high fidelity intracellular potentials from neurons in the abdominal ganglion of Aplysia Californica (Resting Potentials < -35 mV, Action Potentials > 60 mV) as well as the rat motor cortex (Resting Potentials < -50 mV). Next, glass-polysilicon microelectrodes were coupled with microscale electrothermal actuators and controller for autonomous intracellular recordings from single neurons in the abdominal ganglion. Consistent resting potentials (< -35 mV) and action potentials (> 60 mV) were recorded after each successful penetration attempt with the controller and microactuated glass-polysilicon microelectrodes. The success rate of penetration and quality of recordings achieved using electrothermal microactuators were comparable to that of conventional positioning systems. Finally, the feasibility of this miniaturized system to obtain intracellular recordings from single neurons in the motor cortex of rats in vivo is also demonstrated. The MEMS-based system offers significant advantages: 1) reduction in overall size for potential use in behaving animals, 2) scalable approach to potentially realize multi-channel recordings and 3) a viable method to fully automate measurement of intracellular recordings.
ContributorsSampath Kumar, Swathy (Author) / Muthuswamy, Jit (Thesis advisor) / Abbas, James (Committee member) / Hamm, Thomas (Committee member) / Christen, Jennifer Blain (Committee member) / Buneo, Christopher (Committee member) / Arizona State University (Publisher)
Created2018
Description
Neural interfacing applications have advanced in complexity, with needs for increasingly high degrees of freedom in prosthetic device control, sharper discrimination in sensory percepts in bidirectional interfaces, and more precise localization of functional connectivity in the brain. As such, there is a growing need for reliable neurophysiological recordings at a fine spatial scale matching that of cortical columnar processing. Penetrating microelectrodes provide localization sufficient to isolate action potential (AP) waveforms, but often suffer from recorded signal deterioration linked to foreign body response. Micro-Electrocorticography (μECoG) surface electrodes elicit lower foreign body response and show greater chronic stability of recorded signals, though they typically lack the signal localization necessary to isolate individual APs. This dissertation validates the recording capacity of a novel, flexible, large area μECoG array with bilayer routing in a feline implant, and explores the ability of conventional μECoG arrays to detect features of neuronal activity in a very high frequency band associated with AP waveforms.
Recordings from both layers of the flexible μECoG array showed frequency features typical of cortical local field potentials (LFP) and were shown to be stable in amplitude over time. Recordings from both layers also showed consistent, frequency-dependent modulation after induction of general anesthesia, with large increases in beta and gamma band and decreases in theta band observed over three experiments. Recordings from conventional μECoG arrays over human cortex showed robust modulation in a high frequency (250-2000 Hz) band upon production of spoken words. Modulation in this band was used to predict spoken words with over 90% accuracy. Basal Ganglia neuronal AP firing was also shown to significantly correlate with various cortical μECoG recordings in this frequency band. Results indicate that μECoG surface electrodes may detect high frequency neuronal activity potentially associated with AP firing, a source of information previously unutilized by these devices.
Recordings from both layers of the flexible μECoG array showed frequency features typical of cortical local field potentials (LFP) and were shown to be stable in amplitude over time. Recordings from both layers also showed consistent, frequency-dependent modulation after induction of general anesthesia, with large increases in beta and gamma band and decreases in theta band observed over three experiments. Recordings from conventional μECoG arrays over human cortex showed robust modulation in a high frequency (250-2000 Hz) band upon production of spoken words. Modulation in this band was used to predict spoken words with over 90% accuracy. Basal Ganglia neuronal AP firing was also shown to significantly correlate with various cortical μECoG recordings in this frequency band. Results indicate that μECoG surface electrodes may detect high frequency neuronal activity potentially associated with AP firing, a source of information previously unutilized by these devices.
ContributorsBarton, Cody David (Author) / Greger, Bradley (Thesis advisor, Committee member) / Santello, Marco (Committee member) / Buneo, Christopher (Committee member) / Graudejus, Oliver (Committee member) / Artemiadis, Panagiotis (Committee member) / Arizona State University (Publisher)
Created2018
Description
Growing understanding of the neural code and how to speak it has allowed for notable advancements in neural prosthetics. With commercially-available implantable systems with bi- directional neural communication on the horizon, there is an increasing imperative to develop high resolution interfaces that can survive the environment and be well tolerated by the nervous system under chronic use. The sensory encoding aspect optimally interfaces at a scale sufficient to evoke perception but focal in nature to maximize resolution and evoke more complex and nuanced sensations. Microelectrode arrays can maintain high spatial density, operating on the scale of cortical columns, and can be either penetrating or non-penetrating. The non-penetrating subset sits on the tissue surface without puncturing the parenchyma and is known to engender minimal tissue response and less damage than the penetrating counterpart, improving long term viability in vivo. Provided non-penetrating microelectrodes can consistently evoke perception and maintain a localized region of activation, non-penetrating micro-electrodes may provide an ideal platform for a high performing neural prosthesis; this dissertation explores their functional capacity.
The scale at which non-penetrating electrode arrays can interface with cortex is evaluated in the context of extracting useful information. Articulate movements were decoded from surface microelectrode electrodes, and additional spatial analysis revealed unique signal content despite dense electrode spacing. With a basis for data extraction established, the focus shifts towards the information encoding half of neural interfaces. Finite element modeling was used to compare tissue recruitment under surface stimulation across electrode scales. Results indicated charge density-based metrics provide a reasonable approximation for current levels required to evoke a visual sensation and showed tissue recruitment increases exponentially with electrode diameter. Micro-scale electrodes (0.1 – 0.3 mm diameter) could sufficiently activate layers II/III in a model tuned to striate cortex while maintaining focal radii of activated tissue.
In vivo testing proceeded in a nonhuman primate model. Stimulation consistently evoked visual percepts at safe current thresholds. Tracking perception thresholds across one year reflected stable values within minimal fluctuation. Modulating waveform parameters was found useful in reducing charge requirements to evoke perception. Pulse frequency and phase asymmetry were each used to reduce thresholds, improve charge efficiency, lower charge per phase – charge density metrics associated with tissue damage. No impairments to photic perception were observed during the course of the study, suggesting limited tissue damage from array implantation or electrically induced neurotoxicity. The subject consistently identified stimulation on closely spaced electrodes (2 mm center-to-center) as separate percepts, indicating sub-visual degree discrete resolution may be feasible with this platform. Although continued testing is necessary, preliminary results supports epicortical microelectrode arrays as a stable platform for interfacing with neural tissue and a viable option for bi-directional BCI applications.
The scale at which non-penetrating electrode arrays can interface with cortex is evaluated in the context of extracting useful information. Articulate movements were decoded from surface microelectrode electrodes, and additional spatial analysis revealed unique signal content despite dense electrode spacing. With a basis for data extraction established, the focus shifts towards the information encoding half of neural interfaces. Finite element modeling was used to compare tissue recruitment under surface stimulation across electrode scales. Results indicated charge density-based metrics provide a reasonable approximation for current levels required to evoke a visual sensation and showed tissue recruitment increases exponentially with electrode diameter. Micro-scale electrodes (0.1 – 0.3 mm diameter) could sufficiently activate layers II/III in a model tuned to striate cortex while maintaining focal radii of activated tissue.
In vivo testing proceeded in a nonhuman primate model. Stimulation consistently evoked visual percepts at safe current thresholds. Tracking perception thresholds across one year reflected stable values within minimal fluctuation. Modulating waveform parameters was found useful in reducing charge requirements to evoke perception. Pulse frequency and phase asymmetry were each used to reduce thresholds, improve charge efficiency, lower charge per phase – charge density metrics associated with tissue damage. No impairments to photic perception were observed during the course of the study, suggesting limited tissue damage from array implantation or electrically induced neurotoxicity. The subject consistently identified stimulation on closely spaced electrodes (2 mm center-to-center) as separate percepts, indicating sub-visual degree discrete resolution may be feasible with this platform. Although continued testing is necessary, preliminary results supports epicortical microelectrode arrays as a stable platform for interfacing with neural tissue and a viable option for bi-directional BCI applications.
ContributorsOswalt, Denise (Author) / Greger, Bradley (Thesis advisor) / Buneo, Christopher (Committee member) / Helms-Tillery, Stephen (Committee member) / Mirzadeh, Zaman (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2018
Description
The ultimate goal of human movement control research is to understand how natural movements performed in daily reaching activities, are controlled. Natural movements require coordination of multiple degrees of freedom (DOF) of the arm. Patterns of arm joint control were studied during daily functional tasks, which were performed through the rotation of seven DOF in the arm. Analyzed movements which imitated the following 3 activities of daily living: moving an empty soda can from a table and placing it on a further position; placing the empty soda can from initial position at table to a position at shoulder level on a shelf; and placing the empty soda can from initial position at table to a position at eye level on a shelf. Kinematic and kinetic analyses were conducted for these three movements. The studied kinematic characteristics were: hand trajectory in the sagittal plane, displacements of the 7 DOF, and contribution of each DOF to hand velocity. The kinetic analysis involved computation of 3-dimensional vectors of muscle torque (MT), interaction torque (IT), gravity torque (GT), and net torque (NT) at the shoulder, elbow, and wrist. Using the relationship NT = MT + GT + IT, the role of active control and passive factors (gravitation and inter-segmental dynamics) in rotation of each joint by computing MT contribution (MTC) to NT was assessed. MTC was computed using the ratio of the signed MT projection on NT to NT magnitude. Despite a variety of joint movements available across the different tasks, 3 patterns of shoulder and elbow coordination prevailed in each movement: 1) active rotation of the shoulder and predominantly passive rotation of the elbow; 2) active rotation of the elbow and predominantly passive rotation of the shoulder; and 3) passive rotation of both joints. Analysis of wrist control suggested that MT mainly compensates for passive torque and provides adjustment of wrist motion according to requirements of each task. In conclusion, it was observed that the 3 shoulder-elbow coordination patterns (during which at least one joint moved) passively represented joint control primitives, underlying the performance of well-learned arm movements, although these patterns may be less prevalent during non-habitual movements.
ContributorsSansgiri, Dattaraj (Author) / Dounskaia, Natalia (Thesis advisor) / Schaefer, Sydney (Thesis advisor) / Buneo, Christopher (Committee member) / Arizona State University (Publisher)
Created2018