Both genetic and environment factors influence susceptibility to substance use disorders. However, the genetic basis of these disorders is largely unknown. We previously identified Hnrnph1 (heterogeneous nuclear ribonucleoprotein H1) as a quantitative trait gene for reduced methamphetamine (MA) stimulant sensitivity. Mutation (heterozygous deletion of a small region in the first coding exon) in Hnrnph1 also decreased MA reinforcement, reward, and dopamine release. 5’UTR genetic variants in Hnrnph1 support reduced 5’UTR usage and hnRNP H protein expression as a molecular mechanism underlying the reduced MA-induced psychostimulant response. Interestingly, Hnrnph1 mutant mice show a two-fold increase in hnRNP H protein in the striatal synaptosome with no change in whole tissue level. Proteome profiling of the synaptosome identified an increase in mitochondrial complex I and V proteins that rapidly decreased with MA in Hnrnph1 mutants. In contrast, the much lower level of basal mitochondrial proteins in the wild-type mice showed a rapid, MA-induced increase. Altered mitochondrial proteins associated with the Hnrnph1 mutation may contribute to reductions in MA behaviors. hnRNP H1 is an abundant RNA-binding protein in the brain, involved in all aspect of post-transcriptional regulation. We examined both baseline and MA-induced changes in hnRNP H-RNA interactions to identify targets of hnRNP H that could comprise the neurobiological mechanisms of cellular adaptations occurring following MA exposure. hnRNP H post-transcriptionally regulates a set of mRNA transcripts in the striatum involved in psychostimulant-induced synaptic plasticity. MA treatment induced opposite changes in binding of hnRNP H to these mRNA transcripts between Hnrnph1 mutants versus wild-types. RNA-binding, transcriptome, and spliceome analyses triangulated on hnRNP H binding to the 3’UTR of Cacna2d2, an upregulation of Cacna2d2 transcript, and decreased 3’UTR usage of Cacna2d2 in response to MA in the Hnrnph1 mutants. Cacna2d2 codes for a presynaptic, voltage-gated calcium channel subunit that could plausibly regulate MA-induced dopamine release and behavior. The multi-omics datasets point to a dysregulation of mitochondrial function and interrelated calcium signaling as potential mechanisms underlying MA-induced dopamine release and behavior in Hnrnph1 mutants.

Understanding the mapping between stimulus, behavior, and neural responses is vital for understanding sensory, motor, and general neural processing. We can examine this relationship through the complementary methods of encoding (predicting neural responses given the stimulus) and decoding (reconstructing the stimulus given the neural responses). The work presented in this thesis proposes, evaluates, and analyzes several nonlinear approaches for encoding and decoding that leverage recent advances in machine learning to achieve better accuracy. We first present and analyze a recurrent neural network encoding model to predict retinal ganglion cell responses to natural scenes, followed by a decoding approach that uses neural networks for approximate Bayesian decoding of natural images from these retinal cells. Finally, we present a probabilistic framework to distill behavioral videos into useful low-dimensional variables and to decode this behavior from neural activity.

It is estimated that one in 59 children in the US are affected by autism spectrum disorder (ASD). ASD is distinguished by social and communication deficits that can be displayed throughout a wide range of severity. This resulting spectrum of behaviors observed in ASD suggests that a complex etiology is involved. Previous studies have shown a genetic susceptibility to autism including paternal age, twin and sibling concordance. Genetic sequencing of those affected as well as first order relatives have identified alterations in genes associated with neuronal synaptic communication. However, very little information is available regarding the pathophysiology of synapses in ASD. Neuronal communication between anterior cingulate cortical neurons via synapses with other brain regions is vital in the execution of social behaviors in individuals. The aim of this study was to evaluate the protein expression of the synaptic marker spinophilin and post-synaptic density protein-95 (PSD-95) in postmortem ASD gray matter brain tissue from the anterior cingulate and frontal cortex to compare to typically developing (TD) control brain tissue. Postmortem brain tissue of ASD and TD subjects was acquired from nationally funded brain repositories previously matched by brain area, age and gender. Immunoblotting for spinophilin and PSD-95 was performed using anterior cingulate and frontal cortical gray matter brain tissue from matched ASD and TD brain tissue. Spinophilin and PSD-95 protein amounts for all donors were normalized using GAPDH. Frontal cortical tissue demonstrated no significant differences in spinophilin protein expression between TD and ASD groups (N=6). Anterior cingulate tissue demonstrated no significant differences in spinophilin protein expression between TD and ASD groups (N=5). PSD-95 protein expression levels did not result in any significant differences between ASD donors and their control pairs for either brain tissue region. Although no changes were detected in the frontal cortex or anterior cingulate cortex, more brain areas and subjects must be evaluated to determine if spinophilin or PSD-95 can be reliable markers for synaptic alterations in ASD. These data are critical in determining synaptic pathology in ASD which may lead to future treatments.

Gene expression regulation is a set of critical biological processes that give rise to the diversity of cell types across tissues and development stages. Noncoding regions of the genome (intergenic + intronic, >98% of genome) play an important role in these processes, with noncoding genetic variation quantitatively affecting transcriptional activity, splicing of pre-mRNA, and localization, stability, and translational control of mRNA transcripts. Previous genetic studies of human disease have implicated numerous common noncoding loci with small but significant effect in common conditions. Recently, we and others have reported evidence supporting a role of rare noncoding variants with larger effect in early onset conditions such as birth defects and neurodevelopmental disorders. These early onset conditions are quite common in aggregate, affecting over 3% of young children. A better understanding of the functional impact of rare regulatory noncoding variants will enable novel genetic discovery, give insights of disease mechanisms, and ultimately improve diagnosis, treatment, and clinical care. In this thesis dissertation, I describe three related projects. First, we used a combinatorial multi-testing framework to find excess burden of noncoding de novo mutations in congenital heart disease (impacting both transcriptional and post-transcriptional regulatory stages). This finding was central to the rest of my work, motivating the development of new computational approaches to predict genetic effect of noncoding variants through the lens of post-transcriptional regulation. Second, we used convolutional neural networks to model and understand sequence specific RBP binding processes. Finally, we designed a graphical neural network model capable of integrating cause and consequence to predict genetic effect of rare noncoding variants. In summary, we developed new machine learning methods to analyze multimodal human genome sequencing data, uncover deeper insights into post-transcriptional gene regulatory processes, and advance genomic medicine.

Circadian clocks are endogenous timekeeping mechanisms, which give the sense of time-of-day to most organisms. To help the organisms to adapt to daily fluctuations in the environment, circadian clocks are reset by various environmental cues. Light is one of the cardinal environmental cues that synchronize circadian clocks. In a standard 12:12 light-dark condition, Drosophila exhibits bimodal activity pattern in the anticipation of lights-on and -off. The morning peak of activity is generated by Pigment Dispersing Factor (PDF) positive small ventro-lateral neurons (sLNvs) called the M-oscillators, while the evening peak of activity is generated by the dorsolateral neurons (LNds) and the 5th sLNv together referred to as the E-oscillators. Since the Drosophila circadian clock is extremely sensitive to light, a brief light exposure can robustly shift the phase of circadian behavior. The model for this resetting posits that circadian photoreception is cell-autonomous: the photoreceptor CRYPTOCHROME (CRY) senses light, binds to TIMELESS (TIM) and promotes its degradation via JETLAG (JET). However, it was more recently proposed that interactions between circadian neurons are also required for phase resetting. The goal of my thesis was to map the neuronal circuitry controlling circadian photoreception in Drosophila. In the first half of my dissertation (Chapter II), using a novel severe jetset mutant and JET RNAi, we identified M- and E-oscillators as critical light sensing neurons. We also found that JET functions cell-autonomously to promote TIM degradation in M- and E-oscillators, and non-autonomously in E-oscillators when expressed in M-oscillators. However, JET expression was required in both groups of neurons to phase-shift locomotor rhythms in response to light input. Thus M- and E-oscillators cooperate to shift circadian behavior in response to photic cues. In chapter III, unexpectedly, we found that light can delay or advance circadian behavior even when the M- or E-oscillators are genetically ablated or incapacitated suggesting that behavioral phase shifts in response to light are largely a consequence of cell autonomous light detection by CRY and governed by the molecular properties of the pacemaker. Nevertheless, neural interactions are integral in modulating light responses. The M-oscillator neurotransmitter, PDF was important in coordinating M- and E-oscillators for circadian behavioral response to light input. Moreover, we uncover a potential role for a subset of Dorsal neurons in control of phase advances specifically. Hence, neural modulation of cell autonomous light detection contributes to plasticity of circadian behavior and facilitates its adaptation to environmental inputs.

Hypocretin/Orexin (HCRT) neurotransmission facilitates drug-seeking behavior. HCRT neurotransmission at HCRT-receptors 1 and 2 (HCRT-R1 and -R2, respectively) is implicated in addiction. During the shift to alcohol-dependency, adaptations in neurotransmitter systems occur in reward- and stress-related brain regions. Specifically, neurotransmission systems in the central amygdala (CeA) are modulated by alcohol drinking/exposure. Therefore, this study investigated Hcrtr1 and Hcrtr2 mRNA expression in the CeA of alcohol-dependent rats and in non-dependent controls during acute alcohol withdrawal. Fos mRNA expression in the CeA of alcohol-dependent and non-dependent rats was also determined to assess adaptations in neuronal activation. To our knowledge, this is the first study to utilize RNAscope to quantify Hcrtr1 and Hcrtr2 mRNA in a rodent model of alcohol dependence. However, Hcrtr1, Hcrtr2, and Fos mRNA levels were not found to be significantly different in alcohol-dependent rats compared to non-dependent controls, possibly due to the temporal dynamics of these neuroadaptations.

Individuals have suffered from depression for decades. Although depression is under diagnosed, it is one of the most common disorders seen by psychiatrists. The purpose of this research study was to understand whether students' perceived stress level was a significant predictor of students' depressive symptoms. The study explored social cognitive theory to assist in understanding the relationship between depressive symptoms and perceived stress in female minority students. Although depressive symptoms and perceived stress in students have been explored exhaustively, these variables had not been explored specifically among minority students and then compared to nonminority students. Using the Center for Epidemiologic Studies Depression Scale and the Perceived Stress Scale, depressive symptoms and perceived stress in a sample of 109 minority and nonminority, female, undergraduate students were measured. A quantitative analysis was conducted to answer the research questions. For the first research question, data analysis confirmed that perceived stress significantly predicted depressive symptoms in minority, female, undergraduate students. For the second research question, data analysis did not support moderation. Lastly, for the third research question, data analysis confirmed that perceived stress for minority students was significantly different from the distribution of perceived stress for nonminority students. Understanding depressive symptoms from a social cognitive perspective can be initiate positive social change. The results of the study can be used to design targeted interventions (e.g., support groups, cognitive therapy) for mental health in different areas, including colleges, universities, mental health agencies, and hospitals.

Microglia, the resident macrophages of the central nervous system (CNS), are dynamic cells, constantly extending and retracting their processes as they contact and functionally regulate neurons and other glial cells. There is far less known about how microglia interact with the CNS vasculature, particularly under healthy steady-state conditions. Here, I provide the first extensive characterization of juxtavascular microglia in the healthy, postnatal brain and identify a molecular mechanism regulating the timing of these interactions during development. Using the mouse cerebral cortex, I show that microglia are intimately associated with the vasculature in the CNS, directly contacting the basal lamina in vascular sites that are devoid of astrocyte endfeet. I demonstrate a high percentage of microglia are associated with the vasculature during the first week of postnatal development, which is concomitant with a peak in microglial colonization of the cortex and recruitment to synapses. I find that as microglia colonize the cortex, juxtavascular microglia are highly motile along vessels and become largely stationary as the brain matures. 2-photon live imaging in adult mice reveals that these vascular-associated microglia in the mature brain are stable and stationary for several weeks. Further, a decrease in microglia motility along the vasculature is tightly correlated with the expansion of astrocyte endfeet along the vasculature. Finally, I provide evidence that the timing of these microglia-vascular interactions during development is regulated by the microglial fractalkine receptor (CX3CR1). Together, these data support a model by which microglia use the vasculature as a scaffold to migrate and colonize the developing brain and the timing of these associations is modulated by CX3CR1. This migration along the vasculature becomes restricted as astrocyte vascular endfoot territory expands and, upon maturation, vascular-associated microglia become largely stationary.

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