abstract: MicroRNAs are small, non-coding transcripts that post-transcriptionally regulate expression of multiple genes. Recently microRNAs have been linked to the etiology of neuropsychiatric disorders, including drug addiction. Following genome-wide sequence analyses, microRNA-495 (miR-495) was found to target several genes within the Knowledgebase of Addiction-Related Genes (KARG) database and to be highly expressed in the nucleus accumbens (NAc), a pivotal brain region involved in reward and motivation. The central hypothesis of this dissertation is that NAc miR-495 regulates drug abuse-related behavior by targeting several addiction-related genes (ARGs). I tested this hypothesis in two ways: 1) by examining the effects of viral-mediated miR-495 overexpression or inhibition in the NAc of rats on cocaine abuse-related behaviors and gene expression, and 2) by examining changes in NAc miR-495 and ARG expression as a result of brief (i.e., 1 day) or prolonged (i.e., 22 days) cocaine self-administration. I found that behavioral measures known to be sensitive to motivation for cocaine were attenuated by NAc miR-495 overexpression, including resistance to extinction of cocaine conditioned place preference (CPP), cocaine self-administration on a high effort progressive ratio schedule of reinforcement, and cocaine-seeking behavior during both extinction and cocaine-primed reinstatement. These effects appeared specific to cocaine, as there was no effect of NAc miR-495 overexpression on a progressive ratio schedule of food reinforcement. In contrast, behavioral measures known to be sensitive to cocaine reward were not altered, including expression of cocaine CPP and cocaine self-administration under a low effort FR5 schedule of reinforcement. Importantly, the effects were accompanied by decreases in NAc ARG expression, consistent with my hypothesis. In further support, I found that NAc miR-495 levels were reduced and ARG levels were increased in rats following prolonged, but not brief, cocaine self-administration experience. Surprisingly, inhibition of NAc miR-495 expression also decreased both cocaine-seeking behavior during extinction and NAc ARG expression, which may reflect compensatory changes or unexplained complexities in miR-495 regulatory effects. Collectively, the findings suggest that NAc miR-495 regulates ARG expression involved in motivation for cocaine. Therefore, using microRNAs as tools to target several ARGs simultaneously may be useful for future development of addiction therapeutics. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2016

abstract: Biological and biomedical measurements, when adequately analyzed and processed, can be used to impart quantitative diagnosis during primary health care consultation to improve patient adherence to recommended treatments. For example, analyzing neural recordings from neurostimulators implanted in patients with neurological disorders can be used by a physician to adjust detrimental stimulation parameters to improve treatment. As another example, biosequences, such as sequences from peptide microarrays obtained from a biological sample, can potentially provide pre-symptomatic diagnosis for infectious diseases when processed to associate antibodies to specific pathogens or infectious agents. This work proposes advanced statistical signal processing and machine learning methodologies to assess neurostimulation from neural recordings and to extract diagnostic information from biosequences. For locating specific cognitive and behavioral information in different regions of the brain, neural recordings are processed using sequential Bayesian filtering methods to detect and estimate both the number of neural sources and their corresponding parameters. Time-frequency based feature selection algorithms are combined with adaptive machine learning approaches to suppress physiological and non-physiological artifacts present in neural recordings. Adaptive processing and unsupervised clustering methods applied to neural recordings are also used to suppress neurostimulation artifacts and classify between various behavior tasks to assess the level of neurostimulation in patients. For pathogen detection and identification, random peptide sequences and their properties are first uniquely mapped to highly-localized signals and their corresponding parameters in the time-frequency plane. Time-frequency signal processing methods are then applied to estimate antigenic determinants or epitope candidates for detecting and identifying potential pathogens. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2016

<p> Behavior in higher eukaryotes is a complex process which integrates signals in the environment, the genetic makeup of the organism, and connectivity in the nervous system to produce extremely diverse adaptations to the phenomenon of existence. Unraveling the subcellular components that contribute to behavioral output is important for both understanding how behavior occurs in an unperturbed state, as well as understanding how behavior changes when the underlying systems that generate it are altered. Of the numerous molecular species that make up a cell, the regulation of messenger RNAs (mRNAs), the coding template of all proteins, is of key importance to the proper maintenance and functioning of cells of the brain, and thus the synaptic signals and information integration which underlie behavior. RNA binding proteins, a class of regulatory molecules, associate with mRNAs and facilitate their maturation from pre-spliced nascent transcripts, their stabilization and degradation ensuring appropriate levels are maintained, as well as their translation and subcellular compartmentalization, which ensures that proteins are translated at the appropriate level and in the places where they are required to fulfill their cellular functions. Our laboratory identified polymorphisms in the gene coding for the CUGBP and ELAV-like Factor 6 (CELF6) RNA binding protein to be associated with Autism Spectrum Disorder risk in humans. ASD is a spectrum of disorders of early neurodevelopment which present with lowered sociability and communication skills as well as restricted patterns of interests. When expression of the <i>Celf6</i> gene was ablated in mice, we found that they exhibited reductions to early communication as well as altered aspects of their exploratory behavior. In this dissertation, I explore the communication changes in young mouse pups with loss of CELF6 protein and identify that despite being able to produce vocalization patterns similar to their wild-type littermates, they nevertheless exhibit reduced response to maternal separation. Despite a history of literature on other CELF family proteins, the functions of the CELF6 protein in the brain have not been previously described. I provide characterization of the mRNA binding targets of CELF6 in the brain, and show that they share common UGU-containing sequence motifs which has been noted for other CELF proteins, and that CELF6 binding occurs primarily in the 3' untranslated regions (3' UTR) of mRNA. I hypothesized that this mode of interaction would result in regulation of mRNA degradation or translation efficiency as 3' UTR regions are known for providing binding sites for numerous regulators of such processes. In order to answer this question, I cloned sequence elements from the 3' UTRs of target mRNAs into a massively parallel reporter assay which has enabled me to test the effect of CELF6 expression on hundreds of binding targets simultaneously. When expressed in vitro, I found that CELF6 induced reduction to reporter library levels but exhibited few effects on translation efficiency, and I was able to rescue effects to reporter abundance mutation of binding motifs. Intriguingly, like CELF6, CELF3, CELF4, and CELF5 were all able to produce the same effect. CELF5 and CELF6 both showed similar, intermediate repression of reporter library mRNAs, while CELF3 and CELF4 exerted the strongest levels of repression. The level of repression under these conditions was somewhat predicted by number of motifs present per element, however a large amount of the variance in reporter levels is still unexplained and a mechanism for CELF6's action is unknown. Nevertheless, the work I present in this dissertation shows that CELF6 and other members of its family are key regulators of mRNA abundance levels which has direct implications to downstream consequence in the cell. As several of CELF6 binding target mRNAs are known regulators of neuronal signaling and synaptic function, the information I present is crucial for future experimentation. This work well help lead us to understand how behavior is altered when this protein is absent, along the way uncovering important mechanistic steps connecting the molecular landscape of cells to the behavior of organisms.</p><p>

<p> Abuse of psychostimulants including cocaine and new synthetic formulations remains an international public health problem and economic burden. Addiction develops consequential to positive and negative drives that underlie &ldquo;getting&rdquo; and &ldquo;staying&rdquo; high. Dopamine (DA), arising from ventral tegmental area (VTA), projects to ventral striatal targets to encode reward signals and reward prediction. Mesolimbic DA is implicated in both the immediate rewarding effects of psychostimulants, and its hypoactivity underlies negative affect as drug levels decline. Accordingly, modulating inputs to midbrain DA possesses capacity to mediate positive/rewarding and negative/aversive effects of drugs. Hypocretin/orexin (hcrt/ox) is a family of excitatory hypothalamic peptides that projects widely throughout the central nervous system including to VTA DA cells, and hcrt/ox mediates brain reward function and motivation for self-administered drugs. Notably, the first-in-class hcrt/ox receptor antagonist (suvorexant) was approved for management of insomnia in the summer of 2014. Also within the past decade, the caudal division of VTA (termed &ldquo;tail of VTA&rdquo; and &ldquo;rostromedial tegmental nucleus [RMTg]&rdquo;) was detailed for its ability to negatively regulate VTA DA. Functionally, stimulation of the GABA-producing RMTg population encodes aversion and responds to aversive cues. Curiously, anatomy work depicts the hypothalamus as a principal input to the RMTg although the cellular phenotypes and functions of hypothalamic projections to RMTg have not been fully resolved. </p><p> Work in this thesis was designed to map hcrt/ox projections to VTA and RMTg in effort to understand functionally-relevant topographical arrangement. In preliminary assessments, we test for the first time the ability of suvorexant to modulate reward and reinforcement associated with psychostimulant use in rats. Additionally, we profile how self-administered cocaine and &ldquo;bath salt&rdquo; synthetic cathinone 3,4-methylenedioxypyrovalerone (MDPV) influence affective states in rats by measuring ultrasonic vocalizations (USVs) and comparing patterns of responding. Subsequently, we test the ability of suvorexant to influence MDPV-taking and affective changes that promote self-administration. Finally, we utilize direct-site pharmacology to assess the degree to which hcrt/ox transmission within VTA and RMTg contributes to motivated responding for and affective processing of self-administered cocaine across two doses. Specifically, we hypothesized that intra-VTA suvorexant would suppress drug-taking by reducing the rewarding value of self-administered cocaine, whereas intra-RMTg hcrt/ox peptide injection would suppress drug-taking by increasing aversive value of self-administered cocaine. </p><p> We observed that systemic suvorexant effectively reduces motivated cocaine-taking, and that this reduction relates in part to reductions in subjective reward of self-administered cocaine as interpreted by reductions in positively-valenced 50-kHz USVs. Retrograde tracing supports that hcrt/ox projects to both VTA and RMTg without discernible topographical arrangement. Target-site pharmacology finds that intra-VTA suvorexant has no appreciable effects on motivated cocaine-taking but tends to elevate 50-kHz USVs during the pre-drug &ldquo;anticipation&rdquo; time epoch in low-dose cocaine self-administering rats (0.375 mg/kg/inf). While intra-RMTg hcrt/ox pre-treatment sparsely affected USVs, 0.3 nmol/hemisphere hcrt/ox significantly enhanced cocaine-taking in low-dose cocaine self-administering rats, and, in high-dose (0.750 mg/kg/inf) cocaine self-administering rats, intra-RMTg hcrt/ox significantly suppressed responding when pre-treated with 1.0 and 3.0 nmol/hemisphere. </p><p> Collectively, studies within this thesis promote the use of hcrt/ox receptor antagonists as adjunct pharmacotherapy in managing psychostimulant use disorders, although the circuitries through which aberrant motivated behaviors are modulated are not entirely clear. Future work will need to be performed to understand how hcrt/ox transmits to neurochemically-defined cell populations residing within VTA and RMTg&mdash;these pathways are recruited for processing stimuli as &ldquo;rewarding&rdquo; and &ldquo;aversive&rdquo; which are critical contributors in the development of substance use disorders and other psychiatric disorders characterized by dysregulated reward processing.</p><p>

abstract: Humans' ability to perform fine object and tool manipulation is a defining feature of their sensorimotor repertoire. How the central nervous system builds and maintains internal representations of such skilled hand-object interactions has attracted significant attention over the past three decades. Nevertheless, two major gaps exist: a) how digit positions and forces are coordinated during natural manipulation tasks, and b) what mechanisms underlie the formation and retention of internal representations of dexterous manipulation. This dissertation addresses these two questions through five experiments that are based on novel grip devices and experimental protocols. It was found that high-level representation of manipulation tasks can be learned in an effector-independent fashion. Specifically, when challenged by trial-to-trial variability in finger positions or using digits that were not previously engaged in learning the task, subjects could adjust finger forces to compensate for this variability, thus leading to consistent task performance. The results from a follow-up experiment conducted in a virtual reality environment indicate that haptic feedback is sufficient to implement the above coordination between digit position and forces. However, it was also found that the generalizability of a learned manipulation is limited across tasks. Specifically, when subjects learned to manipulate the same object across different contexts that require different motor output, interference was found at the time of switching contexts. Data from additional studies provide evidence for parallel learning processes, which are characterized by different rates of decay and learning. These experiments have provided important insight into the neural mechanisms underlying learning and control of object manipulation. The present findings have potential biomedical applications including brain-machine interfaces, rehabilitation of hand function, and prosthetics. / Dissertation/Thesis / Ph.D. Bioengineering 2013

abstract: Reaching movements are subject to noise in both the planning and execution phases of movement production. Although the effects of these noise sources in estimating and/or controlling endpoint position have been examined in many studies, the independent effects of limb configuration on endpoint variability have been largely ignored. The present study investigated the effects of arm configuration on the interaction between planning noise and execution noise. Subjects performed reaching movements to three targets located in a frontal plane. At the starting position, subjects matched one of two desired arm configuration 'templates' namely "adducted" and "abducted". These arm configurations were obtained by rotations along the shoulder-hand axis, thereby maintaining endpoint position. Visual feedback of the hand was varied from trial to trial, thereby increasing uncertainty in movement planning and execution. It was hypothesized that 1) pattern of endpoint variability would be dependent on arm configuration and 2) that these differences would be most apparent in conditions without visual feedback. It was found that there were differences in endpoint variability between arm configurations in both visual conditions, but these differences were much larger when visual feedback was withheld. The overall results suggest that patterns of endpoint variability are highly dependent on arm configuration, particularly in the absence of visual feedback. This suggests that in the presence of vision, movement planning in 3D space is performed using coordinates that are largely arm configuration independent (i.e. extrinsic coordinates). In contrast, in the absence of vision, movement planning in 3D space reflects a substantial contribution of intrinsic coordinates. / Dissertation/Thesis / M.S. Bioengineering 2013

abstract: Our eyes never stop moving, even during attempted gaze fixation. Fixational eye movements, which include tremor, drift, and microsaccades, are necessary to prevent retinal image adaptation, but may also result in unstable vision. Fortunately, the nervous system can suppress the retinal displacements induced by fixational eye movements and consequently keep our vision stable. The neural correlates of perceptual suppression during fixational eye movements are controversial. Also, the contribution of retinal versus extraretinal inputs to microsaccade-induced neuronal responses in the primary visual cortex (i.e. area V1) remain unclear. Here I show that V1 neuronal responses to microsaccades are different from those to stimulus motions simulating microsaccades. Responses to microsaccades consist of an initial excitatory component followed by an inhibitory component, which may be attributed to retinal and extraretinal signals, respectively. I also discuss the effects of the fixation target's size and luminance on microsaccade properties. Fixation targets are frequently used in psychophysical and electrophysiological research, and may have uncontrolled influences on experimental results. I found that microsaccade rates and magnitudes change linearly with fixation target size, but not with fixation target luminance. Finally, I present ion a novel variation of the Ouchi-Spillmann illusion, in which fixational eye movements may play a role. / Dissertation/Thesis / M.S. Biology 2013

abstract: Each year, millions of aging women will experience menopause, a transition from reproductive capability to reproductive senescence. In women, this transition is characterized by depleted ovarian follicles, declines in levels of sex hormones, and a dysregulation of gonadotrophin feedback loops. Consequently, menopause is accompanied by hot flashes, urogenital atrophy, cognitive decline, and other symptoms that reduce quality of life. To ameliorate these negative consequences, estrogen-containing hormone therapy is prescribed. Findings from clinical and pre-clinical research studies suggest that menopausal hormone therapies can benefit memory and associated neural substrates. However, findings are variable, with some studies reporting null or even detrimental cognitive and neurobiological effects of these therapies. Thus, at present, treatment options for optimal cognitive and brain health outcomes in menopausal women are limited. As such, elucidating factors that influence the cognitive and neurobiological effects of menopausal hormone therapy represents an important need relevant to every aging woman. To this end, work in this dissertation has supported the hypothesis that multiple factors, including post-treatment circulating estrogen levels, experimental handling, type of estrogen treatment, and estrogen receptor activity, can impact the realization of cognitive benefits with Premarin hormone therapy. We found that the dose-dependent working memory benefits of subcutaneous Premarin administration were potentially regulated by the ratios of circulating estrogens present following treatment (Chapter 2). When we administered Premarin orally, it impaired memory (Chapter 3). Follow-up studies revealed that this impairment was likely due to the handling associated with treatment administration and the task difficulty of the memory measurement used (Chapters 3 and 4). Further, we demonstrated that the unique cognitive impacts of estrogens that become increased in circulation following Premarin treatments, such as estrone (Chapter 5), and their interactions with the estrogen receptors (Chapter 6), may influence the realization of hormone therapy-induced cognitive benefits. Future directions include assessing the mnemonic effects of: 1) individual biologically relevant estrogens and 2) clinically-used bioidentical hormone therapy combinations of estrogens. Taken together, information gathered from these studies can inform the development of novel hormone therapies in which these parameters are optimized. / Dissertation/Thesis / Ph.D. Psychology 2013

abstract: Learning by trial-and-error requires retrospective information that whether a past action resulted in a rewarded outcome. Previous outcome in turn may provide information to guide future behavioral adjustment. But the specific contribution of this information to learning a task and the neural representations during the trial-and-error learning process is not well understood. In this dissertation, such learning is analyzed by means of single unit neural recordings in the rats' motor agranular medial (AGm) and agranular lateral (AGl) while the rats learned to perform a directional choice task. Multichannel chronic recordings using implanted microelectrodes in the rat's brain were essential to this study. Also for fundamental scientific investigations in general and for some applications such as brain machine interface, the recorded neural waveforms need to be analyzed first to identify neural action potentials as basic computing units. Prior to analyzing and modeling the recorded neural signals, this dissertation proposes an advanced spike sorting system, the M-Sorter, to extract the action potentials from raw neural waveforms. The M-Sorter shows better or comparable performance compared with two other popular spike sorters under automatic mode. With the sorted action potentials in place, neuronal activity in the AGm and AGl areas in rats during learning of a directional choice task is examined. Systematic analyses suggest that rat's neural activity in AGm and AGl was modulated by previous trial outcomes during learning. Single unit based neural dynamics during task learning are described in detail in the dissertation. Furthermore, the differences in neural modulation between fast and slow learning rats were compared. The results show that the level of neural modulation of previous trial outcome is different in fast and slow learning rats which may in turn suggest an important role of previous trial outcome encoding in learning. / Dissertation/Thesis / Ph.D. Electrical Engineering 2014

<p> In the past couple of decades we have seen remarkable advances in the integration of biological systems with artificial ones. Our knowledge of both of these worlds has grown exponentially, and in particular our knowledge of the human body. In recent years we have been able to understand and treat diseases we never thought we would, and we have even been able to interface with the body to restore lost functions. Direct interaction with the human brain to read and write information to it has been achieved thanks to the development of neural probes. The work presented in this thesis focused on improving the performance of such probes in regards to their operational lifetime. This work begins with a description and demonstration of how silicon carbide technologies are suitable and compatible with neural probes, and is a better material choice for device insulation. Then, a fabrication method for silicon carbide based electrode arrays is presented, in which conductive silicon carbide is integrated with insulating silicon carbide to form an electrode architecture in which the only exposed material is the superior silicon carbide. Following this, <i>in-vivo</i> demonstration of these silicon carbide based electrode arrays is done by recording from the nervous system of an animal model</p><p>