Doctor of Philosophy

dissertationPrecise optical neural stimulation is an essential element in the use of optogenetics to elicit predictable neural action potentials within the brain, but accessing specific neocortical layers, light scattering, columniation, and ease of tissue damage pose unique challenges to the device engineer. This dissertation presents the design, simulation, microfabrication, and characterization of the Utah Optrode Array (UOA) for precise neural tissue targeting through three main objectives: 1. Maskless wafer-level microfabrication of optical penetrating neural arrays out of soda- lime glass: Utah Optrode Array. 2. Utah Optrode Array customization using stereotactic brain atlases and 3D CAD modeling for optogenetic neocortical interrogation in small rodents and nonhuman primates. 3. Single optrode characterization of the UOA for neocortical illumination. Maskless microfabrication techniques were used to create 169 individual 9 × 9 arrays 3.85 mm × 3.85 mm with 1.1 mm long optrodes from a single two inch glass wafer. The 9 × 9 UOA was too large for precise targeting of the upper layers of the cortex in smaller animals such as mice, so an array customization method was developed using Solidworks and off-the-shelf brain atlases to create 8 × 6 arrays 3.45 mm × 2.45 mm with 400 μm long optrodes. Stereotactic atlases were imported into Solidworks, splined, and lofted together to create a single 3D CAD model of a specific region of interest in the brain. Chronic and acute brain trauma showed excellent results for the 8 × 6 arrays in C57BL/6 wild-type mice (Mus musculus) and macaque monkey (Macaca fascicularis). Simulation, characterization, and radiometric testing of a single optrode of the 9 × 9 array was necessary to prove the ability to transmit light directly to specific tissue. Zemax optical design software was used to predict the light transmission capabilities, and then these results were compared to actual bench-top results. Insertion loss was both predicted and measured to be 3.7 dB. Power budgeting showed 9% of the light was lost at the interfaces of the UOA's backplane and tip in air, and 48% was lost through back-scattering, leaving 43% transmitting through the optrode with no measurable taper loss. Scanning electron microscopy showed small amounts of devitrification of the glass, and atomic force microscopy showed average surface roughness to be 13.5 nm and a root mean square roughness of 20.6 nm. The output beam was profiled in fluorescein dye with a total divergence angle of 63◦ with a cross over distance to adjacent beams at 255 μm

Optical Neural Interfaces for Optogenetic Interrogation

Precise optical neural stimulation is an essential element in the use of optogenetics to elicit predictable neural action potentials within the brain, but accessing specific neocortical layers, light scattering, columniation, and ease of tissue damage pose unique challenges to the device engineer. This dissertation presents the design, simulation, microfabrication, and characterization of the Utah Optrode Array (UOA) for precise neural tissue targeting through three main objectives: 1. Maskless wafer-level microfabrication of optical penetrating neural arrays out of soda- lime glass: Utah Optrode Array. 2. Utah Optrode Array customization using stereotactic brain atlases and 3D CAD modeling for optogenetic neocortical interrogation in small rodents and nonhuman primates. 3. Single optrode characterization of the UOA for neocortical illumination. Maskless microfabrication techniques were used to create 169 individual 9 × 9 arrays 3.85 mm × 3.85 mm with 1.1 mm long optrodes from a single two inch glass wafer. The 9 × 9 UOA was too large for precise targeting of the upper layers of the cortex in smaller animals such as mice, so an array customization method was developed using Solidworks and off-the-shelf brain atlases to create 8 × 6 arrays 3.45 mm × 2.45 mm with 400 μm long optrodes. Stereotactic atlases were imported into Solidworks, splined, and lofted together to create a single 3D CAD model of a specific region of interest in the brain. Chronic and acute brain trauma showed excellent results for the 8 × 6 arrays in C57BL/6 wild-type mice (Mus musculus) and macaque monkey (Macaca fascicularis). Simulation, characterization, and radiometric testing of a single optrode of the 9 × 9 array was necessary to prove the ability to transmit light directly to specific tissue. Zemax optical design software was used to predict the light transmission capabilities, and then these results were compared to actual bench-top results. Insertion loss was both predicted and measured to be 3.7 dB. Power budgeting showed 9% of the light was lost at the interfaces of the UOA’s backplane and tip in air, and 48% was lost through back-scattering, leaving 43% transmitting through the optrode with no measurable taper loss. Scanning electron microscopy showed small amounts of devitrification of the glass, and atomic force microscopy showed average surface roughness to be 13.5 nm and a root mean square roughness of 20.6 nm. The output beam was profiled in fluorescein dye with a total divergence angle of 63◦ with a cross over distance to adjacent beams at 255 μm

Using stereotactic brain atlases for small rodents and nonhuman primates for optrode array customization

As the optogenetic field expands its need to target with high specificity only grows more crucial. This work will show a method for customizing soda-lime glass optrode arrays so that fine structures within the brains of small rodents and nonhuman primates can be optically interrogated below the outer cortical layer. An 8 × 6 array is customized for optrode length (400 μm ), optrode width (75 μm ), optrode pitch (400 μm ), backplane thickness (500 μm ), and overall form factor (3.45 mm × 2.65 mm ). The 400 μm long optrode is capable of illuminating the cortical Layer IV of rhesus macaque ( Macaca Fascicularis ) and the motor cortex of small mice ( Mus Musculus )

Charge Pumped MEMS Actuation for High Force and Large Displacement

Charge-pumping represents an unusual approach to MEMS actuation with the potential benefits of large displacement coupled with high force, as well as simple out-of-plane motions, large-scale self-assembly, simple single contact and even the possibility of non-contact actuation. Charge pumping is conducive to energy scavenging techniques such as tribolectric harvesting, useful in aerospace and satellite applications, but it comes at the cost of modifications to the electronics control infrastructure now based on two-terminal (power/ground) voltage and current paradigms. Non-contact examples will be shown, including devices that can be used for microscale biomimetic optics

Utah optrode array customization using stereotactic brain atlases and 3-D CAD modeling for optogenetic neocortical interrogation in small rodents and nonhuman primates

As the optogenetic field expands, the need for precise targeting of neocortical circuits only grows more crucial. This work demonstrates a technique for using Solidworks® computer-aided design (CAD) and readily available stereotactic brain atlases to create a three-dimensional (3-D) model of the dorsal region of area visual cortex 4 (V4D) of the macaque monkey (Macaca fascicularis) visual cortex. The 3-D CAD model of the brain was used to customize an 8 × 6 Utah optrode array (UOA) after it was determined that a high-density (13 × 13) UOA caused extensive damage to marmoset (Callithrix jacchus) primary visual cortex as assessed by electrophysiological recording of spiking activity through a 1.5-mm-diameter through glass via. The 8 × 6 UOA was customized for optrode length (400 μm), optrode width (≤100 μm), optrode pitch (400 μm), backplane thickness (500 μm), and overall form factor (3.45 mm × 2.65 mm). Two 8 × 6 UOAs were inserted into layer VI of macaque V4D cortices with minimal damage as assessed in fixed tissue cytochrome oxidase staining in nonrecoverable surgeries. Additionally, two 8 × 6 arrays were implanted in mice (Mus musculus) motor cortices, providing early evidence for long-term tolerability (over 6 months), and for the ability to integrate the UOA with a Holobundle light delivery system toward patterned optogenetic stimulation of cortical networks

Neuroproteomics and Systems Biology Approach to Identify Temporal Biomarker Changes Post Experimental Traumatic Brain Injury in Rats

Traumatic brain injury (TBI) represents a critical health problem of which diagnosis, management and treatment remain challenging. TBI is a contributing factor in approximately 1/3 of all injury-related deaths in the United States. The Centers for Disease Control and Prevention (CDC) estimate that 1.7 million TBI people suffer a TBI in the United States annually. Efforts continue to focus on elucidating the complex molecular mechanisms underlying TBI pathophysiology and defining sensitive and specific biomarkers that can aid in improving patient management and care. Recently, the area of neuroproteomics-systems biology is proving to be a prominent tool in biomarker discovery for central nervous system (CNS) injury and other neurological diseases. In this work, we employed the controlled cortical impact (CCI) model of experimental TBI in rat model to assess the temporal-global proteome changes after acute (1 day) and for the first time, subacute (7 days), post-injury time frame using the established CAX-PAGE LC-MS/MS platform for protein separation combined with discrete systems biology analyses to identify temporal biomarker changes related to this rat TBI model. Rather than focusing on any one individual molecular entities, we used in silico systems biology approach to understand the global dynamics that govern proteins that are differentially altered post-injury. In addition, gene ontology analysis of the proteomic data was conducted in order to categorize the proteins by molecular function, biological process, and cellular localization. Results show alterations in several proteins related to inflammatory responses and oxidative stress in both acute (1 day) and subacute (7 days) periods post TBI. Moreover, results suggest a differential upregulation of neuroprotective proteins at 7-days post-CCI involved in cellular functions such as neurite growth, regeneration, and axonal guidance. Our study is amongst the first to assess temporal neuroproteome changes in the CCI model. Data presented here unveil potential neural biomarkers and therapeutic targets that could be used for diagnosis, treatment and, most importantly, for temporal prognostic assessment following brain injury. Of interest, this work relies on in silico bioinformatics approach to draw its conclusion; further work is conducted for functional studies to validate and confirm the omics data obtained