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Item The Addicted Phenotype: Protein Phosphorylation Status and Dopamine Receptor Responsiveness(2007-05-22) Edwards, Scott; Self, David W.Up-regulation of cAMP/PKA signaling by drugs of abuse may contribute to escalation and relapse, possibly by differentially altering dopamine receptor-responsiveness in the mesolimbic dopamine system. To investigate this hypothesis, our initial studies measured alterations in cAMP-dependent and -independent protein phosphorylation in vivo produced by chronic cocaine and heroin self-administration, changes in mesolimbic protein phosphorylation compared to individual differences in the propensity for escalating cocaine self-adminstration, and, ultimately, dopamine receptor-mediated regulation of relapse to cocaine seeking in withdrawal. Chronic cocaine self-administration can produce either tolerance or sensitization to certain cocaine-regulated behaviors, but whether differential alterations develop in the biochemical response to cocaine is less clear. In Chapter 2, we studied cocaine-induced phosphorylation of multiple cAMP-dependent and -independent protein substrates in mesolimbic dopamine terminal regions following chronic self-administration. Changes in self-administering rats were compared to changes produced by passive yoked injection to identify regulation related to the context of behavioral reinforcement, whereas acute and chronic yoked groups were compared to identify the development tolerance or sensitization in the biochemical response to cocaine. Microwave-fixed brain tissue was collected immediately following 4 hrs of intravenous cocaine administration, and subjected to western blot analysis of phosphorylated and total protein substrates. Chronic cocaine produced region- and substrate-specific tolerance to cAMP-dependent protein phosphorylation, including phosphorylation of the AMPA GluR1 receptor subunit at serine 845 in striatal and amygdala subregions, and the NMDA NR1 receptor subunit at serine 897 in the CA1 subregion of hippocampus. Tolerance also developed to cAMP-independent GluR1S831 phosphorylation in the prefrontal cortex. In contrast, sensitization to cocaine-induced phosphorylation of the pre-synaptic vesicle protein synapsin I at serine 9 developed in amygdala and hippocampal subregions, while cAMP-dependent phosphorylation of the dopamine-synthesizing enzyme tyrosine hydroxylase at serine 40 decreased in pre-synaptic striatal dopamine terminals in striatal subregions. Cocaine-induced phosphorylation of extracellular signal-regulated kinase (ERK) was dissociated from downstream phosphorylation of the transcription factor cAMP-response element binding protein (CREB) in many brain regions, and failed to develop either tolerance or sensitization with chronic administration, and failed to develop either tolerance or sensitization with chronic administration. Positive reinforcement-related correlations between cocaine intake and protein phosphorylation were found only in self-administering animals, while negative dose-related correlations were found primarily with passive yoked administration. These regional- and substrate-specific adaptations in cocaine-induced protein phosphorylation are discussed in lieu of their potential impact on the development of cocaine addiction. In Chapter 3, we studied alterations in protein kinase A (PKA)-dependent and PKA-independent phosphorylation in multiple brain regions in rats undergoing either spontaneous or naltrexone-precipitated withdrawal (WD) from chronic intravenous heroin self-administration. Spontaneous WD from heroin self-administration produced region-specific increases in PKA-dependent GluR1S845 phosphorylation in the nucleus accumbens shell, basolateral amygdala, hippocampal CA1 and CA3 regions, and premotor cortex after 24 but not 12 hrs, and there were no changes in prefrontal cortex, nucleus accumbens core or caudate-putamen. Increased GluR1S845 phosphorylation occurred earlier (12 hrs) in the central amygdala, ventral tegmental area, and substantia nigra. In contrast, prominent ERK phosphorylation was found in both prefrontal and premotor cortex, CA1 and CA3, caudate-putamen, and basolateral amygdala, but not in nucleus accumbens, or central amygdala in spontaneous WD. Phosphorylation of striatal CREB increased in caudate-putamen but not in nucleus accumbens, paralleling ERK rather than PKA activity in heroin WD. Naltrexone administration potentiated GluR1S845 and ERK phosphorylation in the central amygdala, and ERK phosphorylation in nucleus accumbens core and shell. Thus, spontaneous WD from heroin self-administration produces region- and time-dependent changes in PKA and ERK activity that could contribute to the behavioral manifestation of opiate dependence. In Chapter 4 we studied PKA-dependent GluR1S845 phosphorylation and ERK phosphorylation mediated by ERK kinase in striatal subregions in an animal model of cocaine craving. Here, animals with chronic cocaine self-administration experience were re-exposed to the self-administration test chambers for 1 hr in the absence of cocaine to measure phosphorylation induced by the environmental context paired with cocaine reinforcement. After 1 day WD, GluR1S845 levels were elevated in both self-administering and yoked groups in the nucleus accumbens shell, but this effect persisted only in self-administering animals after 3 weeks WD. In the nucleus accumbens core, context-induced phosphorylation of both GluR1S845 and ERK increased from early to late WD from chronic cocaine self-administration, implicating this region in mediating the intensification of cocaine craving with longer periods of abstinence. These differential region- and substrate-specific adaptations to withdrawal- and context-induced protein phosphorylation could underlie the maintenance of cocaine addiction by exacerbating the potential for drug relapse in withdrawal. Finally, as a behavioral correlate, studies in Chapter 5 sought to compare these changes in protein phosphorylation status with alterations in dopamine-receptor mediated regulation of relapse to cocaine seeking in withdrawal. Here, the cocaine-addicted phenotype was modeled in rats based on individual differences in preferred levels of cocaine intake and a propensity for relapse in withdrawal. Since these cocaine-taking and -seeking behaviors are strongly but differentially regulated by postsynaptic dopamine D1 and D2 receptors in the mesolimbic system, we determined whether the development of cocaine addiction would be related to differential sensitivity in functional D1 and D2 receptor responses. Using a population of 40 outbred Sprague-Dawley rats trained to self-administer cocaine for 3 weeks, we found that animals with higher preferred levels of cocaine intake exhibited a vertical and rightward shift in the self-administration dose-response function, and were more resistant to extinction from cocaine self-administration, similar to phenotypic changes reported in other models of cocaine addiction. After 3 weeks of withdrawal from cocaine self-administration, high intake rats were subsensitive to the ability of the D1 agonist SKF 81297 to inhibit cocaine-seeking behavior, but supersensitive to cocaine seeking triggered by the D2 agonist quinpirole, when compared to low intake rats. Additionally, high intake rats developed profound increases in locomotor responses to D2 receptor challenge from early to late withdrawal times, whereas low intake rats developed increased responsiveness to D1 receptor challenge. In a second experiment, responses to the mixed D1/D2 agonist apomorphine and the NMDA glutamate receptor antagonist MK-801 failed to differ between low and high intake rats. These findings suggest that cocaine addiction is specifically related to differential alterations in functional D1 and D2 receptors that mediate opposing influences on cocaine-seeking behavior. Alterations in dopamine receptor signaling may issue from an enduring up-regulation of cAMP/PKA signaling in drug withdrawal. The potential for reduced D1 receptor (Gs/Golf-coupled) sensitivity to account for tolerance to cocaine-regulated PKA-dependent protein phosphorylation during self-administration (Chapter 2) is discussed in Chapter 6. Conversely, it is possible that PKA up-regulation in cocaine WD (Chapter 4) could account for the paradoxical sensitization of subsequent Gi/Go-coupled D2 receptor responses. Thus, addiction-related alterations in D1 and D2 dopamine receptor responses may ultimately involve complex reciprocal interactions between adaptations in PKA signaling pathways that differentially influence D1 and D2 receptor signaling.Item Analyses of the Link Between Amyloid and Tau Pathology in an AD Mouse Model (3xtg-AD): Disease Progression with Increased Levels of Abeta and Tau Peptides(2018-01-23) Zapata, Lucio, Jr.; Ismail, Hannah; Lambracht-Washington, DorisINTRODUCTION: Pathological features of Alzheimer's disease (AD) include the accumulation of extracellular amyloid plaques composed of aggregated amyloid-β (Aβ) peptide and intracellular neurofibrillary tangles consisting of phosphorylated tau protein. Mutations in the genes that encode amyloid precursor protein (APP), and presenilin 1 and 2 (PS1/PS2) have been shown to cause familial AD in humans. Studies provided evidence that Aβ accumulation may initiate phosphorylation of tau protein, via the Ras/MEK/Extracellular Signal-regulated Kinase (ERK) signaling cascade, activation of the mitogen-activated protein kinase (p38 MAPK), Cyclin dependent kinase 5 (CDK5) and/or glycogen synthase kinase-3β (GSK3β). We studied distribution of Aβ and tau oligomers, Erk activity in different brain lysate fractions from different age groups of a triple transgenic mouse model (3xTg-AD) and wild-type mice, and Erk activity in DNA Abeta42 immunized mice. METHODS: Brain lysates of 4-, 6-, 12-, and 20-month-old 3xTg-AD and wild-type mice were prepared via a 4-step extraction protocol in TBS (soluble), TBS-T, SDS, and formic acid. DNA Abeta42 vaccination administered via gene gun. Abeta and Tau concentrations and Tau phosphorylation levels were monitored by Dot blot, Semidenaturing detergent agarose gel electrophoresis (SDD-AGE), and ELISA using anti-Abeta and anti-Tau antibodies. Erk1/2 levels were monitored by Western blot using monoclonal antibodies. RESULTS: There was a significant increase of total tau concentrations with increasing age and we found also an increasing insolubility (more tau in the non-soluble brain lysate fractions). 4- and 20-month-old 3xTg-AD soluble brain lysates indicated the presence of aggregated tau peptide, which was not present in wild-type control mice. Kinases involved with tau phosphorylation were measured and showed an increase of activated/phosphorylated Erk1/2 with increasing age, with a drop in concentration at 12 months in half of the mice analyzed (n=5). Immunized 3xTg-AD mice showed a decrease in activated Erk1/2 when compared to non-immunized, age matched mice. DISCUSSION: The 3xTg-AD mouse model provides a good model to study pathologies and possible treatments for human Alzheimer's disease. Abeta 42 peptide and tau increase due to age in this mouse model. A link between the amyloid pathology is likely found in the wide spectrum of cellular kinases which are upregulated due to Abeta in Alzheimer's disease. Therefore, immunization against Abeta and generation of anti-Abeta antibody will indirectly reduce tau pathology.Item Assessment of Brain Perfusion and Vascular Compliance with Magnetic Resonance Imaging(2018-02-28) Li, Yang; Choi, Changho; Lu, Hanzhang; Vinogradov, Elena; Shang, Ty; Liu, HanliBrain perfusion is an index that reflects the amount of blood received by the brain tissue in a given time period. Normal brain perfusion ensures that sufficient oxygen, glucose, and other nutrients are delivered to the neurons and glial cells in the brain. While perfusion is relatively static index of brain vascular function, vascular compliance represents the dynamic ability of arteries to dilate or retract in response to blood pressure alternations. An artery vessel with high compliance can better buffer the pulsatility of blood flow, thereby protecting the downstream arterioles and capillaries from damage. Consequently, brain perfusion and vascular compliance are complementary properties of brain's vascular system and may be important indicators of cerebrovascular health. Therefore, noninvasive imaging of brain perfusion and vascular compliance will provide valuable biomarkers to study cerebral physiology and function. Furthermore, these biomarkers may also yield crucial pathophysiological knowledge and guide therapies in brain disorders, such as stroke, small-vessel disease, and neurodegenerative disease. This thesis consists of three novel tools toward brain perfusion and vascular compliance imaging. I first developed a cardiac-triggered Arterial-Spin-Labeling (ASL) technique to enhance the sensitivity of brain perfusion MRI without using exogenous contrast agent. I demonstrated its utility in several experimental settings, including single-shot acquisition, multi-shot acquisition, and detection of cerebral blood flow (CBF) changes. Next, I worked on the analysis strategies of perfusion MRI data. I developed a cloud-based tool for ASL data processing that is free from any software installation, compatible with file formats from all major MRI manufacturers, and publicly accessible. Quantitative CBF maps and region-specific reports are available for download within minutes. I have launched this cloud service recently and received initial feedback from researchers around the world. Finally, I developed a technique to measure vascular compliance in larger cerebral arteries. I used a time-resolved vascular-space-occupancy technique to obtain 3D maps of cerebral arterial compliance and then applied the technique to study arterial stiffness in aging.Item BDNF-Producing B Cells Mediate Plasticity in the Recovering Brain After Stroke(2021-11-29) Torres, Vanessa; Monson, Nancy L.; Stowe, Ann; Goldberg, Mark P.; Vitetta, Ellen S.; Volk, Lenora J.; Satterthwaite, Anne B.Neuronal networks require significant neurotrophic support for functional plasticity after stroke, but the delivery of neurotrophins has failed thus far in clinical trials. Therefore, identifying endogenous mechanisms that could enhance neurotrophic support in the recovering brain after stroke is essential. B cells, a lymphocyte known to infiltrate the post-stroke brain, possess the ability to produce neurotrophins, including brain-derived neurotrophic factor (BDNF). Depleting B cells after stroke results in motor and cognitive deficits that are mediated by specific brain regions (e.g., hippocampus) outside the initial infarct. We propose that B cells migrate to specific brain regions after stroke and respond to local signals that enhance their neurotrophic capacities to promote neuroplasticity. To investigate whether B cells are a potential source of endogenous BDNF support after stroke, we must identify 1.) the spatial distribution of B cells within the post-stroke brain, 2.) the type of neurotrophic support B cells provide to ischemic-injured neurons and 3.) the impact that the post-stroke microenvironment exerts on the neurotrophic capacity of B cells. Using whole brain microscopy, we discovered that B cells migrate to specific remote brain regions areas outside of the initial infarct that regulate motor and cognitive function after stroke. To understand how B cells support ischemic-injured neurons, we used ex vivo electrophysiology and in vitro models of ischemic injury to assess functional and structural neuroplasticity in the presence or absence of B cells. We discovered that B cells support synaptic transmission in the dentate gyrus region of the hippocampus after stroke and through the production of BDNF, B cells protect against the ischemic-induced loss of neurons and neuronal dendrites. After stroke, neuronal BDNF production is dependent on glutamate-induced activity of the N-methyl-D-aspartate receptor (NMDAR) downstream of the GluN2A subunit. Given that B cells also express NMDARs, we investigated whether glutamate can similarly upregulate BDNF in B cells downstream of their NMDARs. Using microscopy, flow cytometry and qPCR, we discovered that stroke and glutamate differentially regulate B cell gene and surface expression of GluN2A. Additionally, both mouse and human B cells elicit a functional response to glutamate and can induce autocrine BDNF signaling. Collectively, the data presented in this thesis are the first to demonstrate a glutamate-induced neurotrophic role for B cells in the ischemic brain. Understanding the mechanisms by which neuroinflammation supports neuroplasticity after stroke enables the development of immune-based therapeutics that harness endogenous neurotrophic support from B cells to ameliorate pathology.Item The Capabilities of Neural Systems Depend on a Hierarchically Structured World(August 2021) Blazek, Paul Joseph; Reynolds, Kimberly A.; Pfeiffer, Brad E.; Toprak, Erdal; Zinn, Andrew R.; Lin, MiloThe study of the human mind spans thousands of years, from the earliest philosophers to modern neuroscience. However, there still remains an incredible gap in our understanding of how cognitive functions arise from the biology of the brain. This has greatly hampered attempts to understand how the brain works, what its limitations are, and how to replicate it in artificial intelligence systems. Here I propose a general framework to understand how cognitive processes can be encoded by networks of interconnected neurons. I have taken a theoretical and computational approach, using artificial neural networks as a high-level quantitative model of basic neuroscientific principles. Neural networks are capable of reasoning by means of a series of specialized distinctions made by individual neurons that are integrated hierarchically. This framework enables the study of how the capabilities of neural systems are dependent on structural and functional constraints. Biological constraints on neural coding and network size and topology limit the complexity of stimuli that can be comprehended by the network. Surprisingly, though, neural networks are capable of comprehending much more complex stimuli than has been previously described, provided that the inherent distinctions between these stimuli are hierarchically structured. Functional constraints on neural networks require that they be able to perform cognitive processes and be able to reason in a way that can be communicated with other people. I have proposed a novel neurocognitive model which, when implemented in deep neural networks, is able to simulate a wide variety of cognitive processes. It is consistent with experimental evidence from neuroscience and theories from philosophy and psychology. By directly implementing symbolic reasoning within the structure and function of the network, it becomes possible to overcome many of the fundamental problems that face modern artificial intelligence systems, including their lack of explainability, robustness, and generalizability. This culminated in a novel algorithm that translates neural networks to human-understandable code, providing a complete picture of how neural networks can reason. All of these results suggest that neural systems require the world to be hierarchically structured in order to comprehend it, a direct reflection of their own hierarchical organization.Item Cardiovascular Risk Factors Predict the Spatial Distribution of White Matter Hyperintensities(2014-02-04) Banerjee, Soham; King, Kevin; McColl, Roderick; Whittemore, Anthony; Hulsey, Keith; Peshock, Ronald M.PURPOSE: Increased volume of brain white matter hyperintensities (WMH) seen on MRI is associated with cardiovascular risk factors; however, WMH have also been attributed to normal aging. Recent studies have suggested that WMH in some brain regions are more strongly associated with specific risk factors. The purpose of this study was to create a map of every individual brain voxel that was significantly associated with risk factors (hypertension, diabetes, hyper-cholesterolemia) as compared to those without each risk factor. The aim of the study is to create a predictive model, which uses the WMH distribution to determine the associated underlying risk factor. METHODS: The MRI brain images used for analysis were obtained from 2066 participants in the Dallas Heart Study, a population based study. Each MRI brain was transformed onto a standard template that adjusts for participant variation in brain volume and shape, using the FSL SIENAX software. The participant's WMH distributions were then generated from their MRIs using an automated algorithm. For each risk factor, the subjects were divided into a case group and a control group. Each voxel of WMH was compared between the two groups using a two tailed nonparametric permutation test. A map of every voxel significantly associated with each risk factor was created. RESULTS: Of the total of 431891 voxels that comprise the distribution of WMH over the entire population, 26064 voxels (6%) were significantly associated with hypertension only. These hypertensive-associated voxels were prevalent anterior to the frontal horns of the lateral ventricles. Similarly, 22527 voxels (5%) were associated with diabetes only with a prevalence near the longitudinal cerebral fissure as well as lateral to the posterior horns of the lateral ventricles. 8088 voxels (2%) were associated with hyper-cholesterolemia only and were abundant posterior to the posterior horns of the lateral ventricles. 331588 voxels (77%) were not associated with a risk factor. CONCLUSIONS: For hypertension, diabetes, and hyper-cholesterolemia, certain voxels were significantly associated with a risk factor, and maps of these voxels were created. Knowing the WMH distribution significantly associated with each risk factor will improve the specificity for evaluating patients for risk factor associated white matter injury. Importantly, this approach makes no a priori assumptions which divide the brain into functional regions or vascular territories.Item Cdk5-Dependent Regulation of Neuronal MEK1(2013-01-22) Krishnan, Govind; Benavides, David; Tassin, Tara; Bibb, James A.INTRODUCTION: Cyclin-dependent protein kinase 5 (Cdk5) is a member of the Cdk family that is implicated in many regulatory pathways in post-mitotic neurons. The kinase plays an important role in neuronal development and synaptic transmission; its disregulation contributes to neurodegenerative diseases such as Alzheimer's disease. Cdk5 is involved in the regulation of the Ras-Raf-MEK-ERK signaling pathway. It is hypothesized that Cdk5 serves a neuroprotective role by preventing the prolonged stimulation of ERK from inducing cell cycle reentry and, hence, neuronal apoptosis. In order to address whether Cdk5 phosphorylation of MEK1 affects its in vitro kinase activity, we sought to confirm the Cdk5-phosphorylation site of MEK1. Although it has been previously shown that Cdk5 phosphorylates MEK1-T286, our previous unpublished mass spectometry analysis of in vitro kinase reactions identifies the site as T292. We corroborated this data with Western blot analysis of the in vitro Cdk5 phosphorylation of MEK with phosphate-specific antibodies to sites T286 and T292. METHODS: Glutathione S-transferase (GST)-tagged MEK1 was expressed and purified from E.coli. The tagged protein was run through column fractions, with glutathione beads that would attach to the GST tag, such that GST-MEK1 would be purified out of the bacterial lysates. This was then run through gel electrophoresis to confirm that MEK1 had indeed been purified, by comparing the bands seen in the gels to the known molecular weights of GST-MEK1. The protein concentration was determined using a Bradford assay. Non-radioactive and radioactive Cdk5 kinase assays of MEK1 were then performed. MEK1 was incubated in the absence or presence of Cdk5 with Mg2+/ATP or Mg2+/ATP plus trace amounts of [gamma-32P]-ATP, respectively. The non-radiolabeled kinase reactions were subjected to polyacrylamide gel electrophoresis (PAGE) on a 10-20% acrylamide gradient gel, followed by electrophoretic transfer and Western blot analysis with phospho-T286 and phospho-T292 MEK1 antibodies. Phosphorimages of radiolabeled kinase reactions were generated by PAGE, dried gels and standards were exposed to a phosphorimager screen and analyzed on a phosphorimager. RESULTS: Our results confirm that T292 is indeed the Cdk5 site of MEK1. The identity of this site is important because it is the location at which control can be exercised over the ERK pathway.Item Cell-Free Formation of RNA Granules(2012-07-16) Han, Tina Wei; McKnight, Steven L.Asymmetric RNA localization is a mechanism by which a cell can spatially and temporally regulate the translation of RNAs. This mechanism is essential for many developmental processes such as germ cell formation in Drosophila embryos, as well as establishment of cell polarity and synaptic plasticity in the brain. In many instances, asymmetric RNA localization is achieved through transport and sequestration by RNA granules. RNA granules are large, non-membrane bound ribonucleoparticles that have been observed in various biological contexts. Unfortunately, because RNA granules are highly heterogeneous and weakly associating aggregates, they can be difficult to study biochemically, which constitutes a major impediment for gaining a more detailed understanding of the mechanisms governing RNA granule assembly. Here we describe two in vitro models for studying RNA granule assembly. The first method is based on the precipitation activity of a 3,5-disubstituted isoxazole compound that can be used as a quick and efficient pharmacological tool to probe the function and regulation of RNA granules. The second method utilizes a three-dimensional protein-retaining hydrogel formed from a recombinant protein. Polypeptides of low amino acid complexity were found to be the sequence determinants of isoxazole precipitation and hydrogel retention. Next generation sequencing was used to identify RNAs that partitioned with granule components in both isoxazole and hydrogel models and were found to be enriched in mRNAs known to be constituents of neuronal transport granules for dendritic localization. The overrepresented gene ontology categories for these RNAs included cell adhesion, extracellular matrix, and synaptic proteins. The average length of the 3’UTR of these RNAs was found to be longer than the 3’UTRs of RNAs excluded from the cell-free RNA granule preparations. These two in vitro models for studying RNA granule assembly offer a novel approach to identify candidate targets recruited to RNA granules by specific RNA-binding proteins.Item Correcting Biases in Multi-Module Neural Networks, Through Efficient Hyperparameter Optimization and Statistically Meaningful Uncertainty Quantification, with Applications to Neurological Disorders(2023-05-01T05:00:00.000Z) Treacher, Alex H.; Lin, Milo; Rajaram, Satwik; Jaqaman, Khuloud; Vinogradov, Elena; Montillo, Albert A.Deep learning is a branch of machine learning that employs artificial neural networks to produce inferences from data. These networks have been successfully applied to a plethora of clinically and biologically related problems, including prognosis and diagnosis for a broad spectrum of diseases. However, many applications have focused on single tasks and/or single modal data, and thus use networks consisting of a single module. Modules are sections of a complete network, each that carries out a specific task. Multi-module artificial neural networks take inspiration from mammalian brains that process different types of input via dedicated brain regions (e.g. optical information by the visual cortex, sound, and language via Broca's and Wernicke's areas) and subsequently integrates them into a unified representation of our surroundings. While much work has been done on networks with a single module, significantly less work has focused on multi-module networks. Such networks are especially important in clinical problems that require the integration of multi-modal information and/or extracting multiple representations from the same input to provide high predictive performance. This dissertation corrects biases in multi-module networks for clinically relevant neurological problems. It develops novel hyperparameter search strategies with significantly improved performance of multi-module networks for diagnoses and prognoses, and adds uncertainty quantification to empower multi-module mixed effects deep learning models with the ability to produce statistically meaningful measures of covariate significance and principled probabilistic prediction confidence. Concretely, in this dissertation, I demonstrate the ability of multi-module deep learning networks to integrate spatial and temporal information and automate the detection of artifacts in magnetoencephalography (MEG) brain recordings of subjects including control subjects and those with a head injury. Recognizing how important the optimization of the network architecture was to achieve high predictive performance motivated the development of a novel module adaptive hyperparameter optimization (MA) hyperparameter search framework, which increases the efficiency of architecture optimization of multi-module networks. This approach is demonstrated to identify more optimal architectures when compared to other search strategies and to significantly increase the predictive performance of Alzheimer's and Parkinson's disease prognoses. Finally, I empower mixed effects deep learning (MEDL) models, which explicitly use multi-module networks, with uncertainty quantification allowing for the calculation of fundamental statistical metrics of model fit, covariate coefficient estimation, and prediction confidence. This model is then applied to predict which subjects will convert from mild cognitive impairment to Alzheimer's disease.Item Deep brain stimulation enhances control and restores valued personality characteristics(2022-11-08) Kubu, Cynthia S.Questions related to what constitutes personality, and how those conceptualizations interface with notions of self, identity, and autonomy, have fascinated psychologists, philosophers, and ethicists for hundreds of years. Since 2008, several studies have asserted that deep brain stimulation (DBS) results in patients’ loss of control, particularly related to undesired personality changes. Inherent in this argument is the thesis that DBS negatively impacts patients’ identity, autonomy, and personality. Our lab has relied on empirical methods to examine questions related to control in patients who undergo DBS to treat motor symptoms. Our data refute the claims that DBS results in a loss of control. We rely on the American philosophical tradition of pragmatism to conduct our work, particularly the emphasis on different ways of knowing, including the perspectives of various disciplines as well as different stakeholders in understanding, studying, and ultimately implementing practices based on good data.Item Diffusion Kurtosis Imaging as a Diagnostic Tool for Parkinson's Disease(2015-01-26) Vento, Joseph; Cardoso, Ellison; Otaduy, MariaReliable diagnosis of Parkinson's disease requires long-term assessment of a patient's motor performance tests and response to medication. Though the development of magnetic resonance imaging (MRI) presents an additional tool in making a diagnosis, limited imaging biomarkers have been reported that support a clinical diagnosis of Parkinson's disease or its differentiation from similarly presenting diseases. Diffusion Kurtosis Imaging (DKI) is an MRI method that quantifies deviation of water diffusion from normal Gaussian distribution. DKI is a more sensitive technique than conventional diffusion tensor imaging (DTI) for assessing tissue microstructure. The parameters provided by DKI analysis, particularly the mean kurtosis, reflect structural changes within brain regions and demonstrate potential as a diagnostic tool for Parkinson's disease where the basal ganglia are known to markedly change. Here we examine the DKI maps of 86 patients from Hospital das Clinicas da FMUSP in Sao Paulo, Brazil. 49 patients presented with a previous diagnosis of Parkinson's disease based on the UK Parkinson's Brain Bank criteria (mean age, 65.3 + 8.7 [standard deviation]), 19 patients with a previous diagnosis of essential tremor based on the Movement Disorder Society standards (mean age, 64.7 + 6.7) and 27 patients were age-matched healthy controls (mean age, 64.5 + 10.9). All patients underwent the same 3T MRI procedure, consisting of a DTI scan with 32 different gradient directions and b values of 0, 1000, and 2000 s/mm2, necessary to construct a DKI map. Using a region of interest (ROI) analysis on the substantia nigra (rostral, middle, and caudal) and putamen for each patient and comparing mean kurtosis values, we find no significant differentiation of Parkinson's disease patients in the substantia nigra, but significantly higher mean kurtosis values in the putamen of Parkinson's patients (0.82 + 0.05 [standard deviation]) than healthy controls (0.60 + 0.04, p = 0.0158). Neither analysis demonstrated significant difference from essential tremor patients. Higher mean kurtosis estimates in the basal ganglia of Parkinson's disease patients may reflect changes in the microstructural environment of these structures related to disease progression. Further studies should investigate the histological correlates of these values and the reliability of DKI estimates as a diagnostic tool in various stages of the disease.Item Distinct Tau Strains: Exploring Variability in Cell Uptake and Seeding Using Heparinoids(2018-01-23) Prueitt, William; Stopschinski, Barbara; Diamond, MarcBACKGROUND: Tauopathies (including Alzheimer's Disease) are incurable, progressive neurodegenerative diseases caused by tau protein aggregation. Evidence suggests that tau aggregates spread pathology as do prions, infectious proteins that transmit a pathologic conformation to native proteins via disease-specific conformers (strains). Evidence shows tau aggregates enter cells through heparan sulfate proteoglycan (HSPG) mediated macropinocytosis. In this project, I explored whether distinct tau strains bind cell surface HSPGs uniquely or generically to trigger uptake and used heparinoids to measure the relative importance of heparin size and sulfation patterns. METHODS: I used a "biosensor" cell line responsive to tau aggregates that scores induction of intracellular aggregation based on FRET flow cytometry. Using cell lysate from various strains of tau, I measured (1) the ability of different heparin-like molecules to block tau aggregate uptake and seeding, and (2) seeding in HSPG gene knockout cells. RESULTS: All tau strains tested were highly sensitive to heparin inhibition of seeding and most maintained a highly similar dose response. Some strains, however, showed subtle differences. At maximal heparin concentrations, noticeably higher seeding vs baseline was observed in DS 5 & 6 (17%, 9%) as compared to the other strains (<5%). Heparinoid titrations revealed highly similar inhibition patterns between DS 9 and 10. Seeding reduction: DS 9: dp4= 21%; dp8= 27%; dp12= 70%; dp16= 63%; De-2-O=65%; De-6-O= 52%; De-N= 35%. For DS 10: dp4= 19%; dp8= 33%; dp12= 64%; dp16=46%; De-2-O= 53%; De-6-O= 25%; De-N= 13%. Seeding in HSPG genetic knockout cells was reduced substantially in two knockouts, but increased in another. CONCLUSIONS: Cellular uptake of many tau strains is similarly inhibited by heparin, hinting that the same heparinoid (or small molecule analog) could be used to treat diverse tauopathies. But the unique behavior of some strains suggests a one-size-fits-all treatment approach may not always be sufficient. Certain size and sulfation patterns on heparin have specific importance for tau binding. Larger heparinoids better inhibit tau seeding (dp16 & dp12 > dp8 & dp4) and the importance of N-sulfation > 6-O-sulfation > 2-O-sulfation. This pattern remains consistent in recombinant tau, DS 9, DS 10, and in the genetic knockout data gathered here (using strains) and by others in the lab (using recombinant tau). This data shows many similarities and some differences between strains of tau. Parsing these differences could have important implications for understanding the diversity of tauopathies and finding unique approaches to diagnosis and treatment.Item Does Reelin Affect Recovery from a Stroke?(2016-01-19) DeSai, Charisma; Herz, Joachium; Stowe Ann M.; Lane-Donovan, CourtneyReelin is an extraceullular glycoprotein that modulates synaptic plasticity and increases long-term potentiation. Since Reelin has neuroprotective effects, we were interested to see if Reelin plays a role in recovery after significant neurological damage. Earlier studies with reeler mice showed that mice lacking Reelin have increased susceptibility to stroke and suffer more damage post-stroke. Since Reelin is important in neuronal migration during development, it is possible that the effects seen were due to improper brain development, instead of Reelin deficiency itself. Instead of using Reeler mice, we used the Reelin conditional knockout(cKO) mouse model. Thus, we were able to see the effects of Reelin loss while permitting normal brain development. Stroke size and post-stroke behavior were investigated after inducing transient middle cerebral artery occlusion in four-month-old Reelin cKO mice. No significant difference was seen between wild type and Reelin cKO mice in infarct size or behavior, suggesting that while Reelin does play in important function in the brain, it does not play a significant role in post-stroke recovery.Item Donald W. Seldin, M.D., Research Symposium finalist presentations(2022-04-29) Almonte, Matthew; Duvalyan, Angela; McAdams, Meredith; Onyirioha, Kristeen; Saez-Calveras, Nil; Triana, TaylorThis edition of the UT Southwestern Internal Medicine Grand Rounds features presentations by the six Foster Fellows selected as finalists from the Seventh Annual Donald W. Seldin, M.D. Research Symposium, which was held on April 21, 2022. These Foster Fellows presented work that spanned the breadth and depth of scholarly activity across the department, and at the close of Grand Rounds, one will be selected as the 2022 Seldin Scholar, in honor of Dr. Donald W. Seldin. The Grand Rounds presentation includes additional award presentations recognizing Clinical Vignettes, as well as the Award for Research in Quality and Education at Parkland Hospital and the Social Impact Award.Item Effects of Alcohol Use on Cognition During Later Adulthood(2020-12-01T06:00:00.000Z) Becker, Joshua Eric; Brown, E. Sherwood; Rossetti, Heidi; Denney, David; Palka, Jayme; Cullum, C. Munro; Adinoff, Byron H.Alcohol is one of the most widely used psychoactive substance in the world, yet there are conflicting findings related to its long-term effect on cognition. Some research has identified a U-shaped relationship between alcohol consumption and cognition, while negative relationships have been identified in other studies. Methodological issues, particularly the time at which alcohol consumption was measured relative to when cognition was measured, wide variability in definitions of "moderate" alcohol consumption, and selecting appropriate comparison groups, have made exploring the effects of alcohol on cognition during aging difficult. The current study examined the relationship between drinking at three separate time points (between the ages of 50 and 74) and cognition in older adulthood. Results revealed that the quantity of self-reported drinks over the three time points was a significant predictor of cognition in older adulthood (b=0.001; p<.001), although the effect sizes were very small and not meaningful. Subsequent analyses examined this relationship among heavy drinkers and binge drinkers compared to moderate drinkers and non-binge drinkers, but heavy and binge drinking were not significant predictors of cognition in older adulthood (all ps>0.05). Overall, the results suggest no that there is not a meaningful relationship between alcohol consumption and cognitive functioning in older adulthood in this sample. There were few consistent heavy drinkers (n=71), but a large number of consistent moderate drinkers (n=1,847), although even the moderate drinkers did not consume much alcohol (mean alcohol consumption = 15.3 drinks/month; median alcohol consumption = 5.0 drinks/month). This may have limited the ability to detect clinically meaningful differences. Future studies should rely on more standardized alcohol measures, large, diverse samples, and inclusion of cognitive measures assessing visuospatial abilities and executive functioning, in order to better explore the relationship of alcohol in the aging brain.Item Effects of Regional Deletion of Rab3A-interacting Molecule and PTEN on Brain Function(2013-04-16) Haws, Michael; Eisch, Amelia J.; Powell, Craig M.; Huber, Kimberly M.; Goldberg, Matthew S.This dissertation describes experiments designed to delete/knockdown molecules from targeted neuronal populations to study brain region-specific behavioral functions. To this end, I utilized two different conditional knockdown techniques to study the role of the presynaptic active zone molecule Rab3A-interacting Molecule (RIM1) and the phosphatase and tensin homologue on chromosome 10 (PTEN). The cre-lox system was used to eliminate RIM1 from the hippocampal dentate gyrus and area CA3, while adeno-associated virus expressing PTEN-directed interference RNA was injected into the basolateral amygdala to knockdown PTEN in local pyramidal neurons. In the case of RIM1, I hypothesized that deletion of RIM1 from the dentate gyrus or from area CA3 would replicate a subset of the learning and memory deficits found in RIM1α-/- mice. Though the conditional RIM1 knockout mice were not completely selective for the dentate gyrus or for area CA3, both conditional knockouts induced a different behavioral abnormality present in RIM1α-/- mice. My results help narrow the potential brain regions involved in key RIM1α-/- mice behavioral aberrations. In the case of PTEN, I hypothesized that deletion of PTEN specifically in the basolateral amygdala (BLA) would cause increased anxiety and neuronal hypertrophy. Knockdown of PTEN in the BLA did not induce anxiogenesis though it did increase soma volume, dendritic caliber, spine size, mushroom:thin spine ratio, and the frequency of spontaneous miniature excitatory post-synaptic currents. These findings are in contrast to previous findings of increased spine density with PTEN knockdown. This difference likely represents the more sensitive techniques employed in the present studies to ascertain dendritic spine type and density. Though PTEN knockdown had synaptic effects I did not observe any behavioral effects. However, limitations in viral knockdown of PTEN transcripts or viral infection rate may be responsible for the lack of effect. Indeed, limitations exist for both the transgenic and viral approaches used which proved to be challenging obstacles to designing experiments, interpreting data and coming to more extensive concrete conclusions. Transgene expression is often not as selective as desired. Virus injections may not localize to target region or may not infect enough neurons. Understanding and characterizing these and other limitations is vital.Item Evidence of B Cell Dysregulation in Early Multiple Sclerosis Patients(2017-04-04) Rivas, Jacqueline Ruth; Satterthwaite, Anne B.; Monson, Nancy L.; Stowe, Ann; Cowell, Lindsay G.; Greenberg, Benjamin M.Plasmablasts are a highly differentiated, antibody secreting B cell subset whose prevalence correlates with disease activity in Multiple Sclerosis (MS). For many patients experiencing partial transverse myelitis symptoms, plasmablasts are elevated in the blood and cerebrospinal fluid (CSF) at the first clinical presentation of disease. Plasmablasts are a transient subset, representing the portion of B cells currently participating in an antibody-mediated immune response. However, it has not been investigated whether these cells have the potential to participate in the autoimmune response through the expression of autoreactive receptors. In these studies, we found genetic evidence of B cell dysregulation in early MS patients, likely from a loss of peripheral tolerance, and the development of affinity maturated, autoreactive plasmablasts. Plasmablasts from these early MS patients over-utilize immunoglobulin heavy chain V-region subgroup 4 (VH4) genes, exhibit excess light chain receptor editing, and have increased mutation accumulation in IgG utilizing VH4+ cells. Many highly mutated antibodies utilizing VH4 gene segments from both CSF B cells and peripheral plasmablasts recognize neurons and glial cells. Certain peripheral cells are polyreactive, while those in the CSF are typically specific for central nervous system antigens. Other V gene families have the potential for autoreactivity as well, although the strongest binding was observed in VH4+ antibodies. The peripheral plasmablast response is directed toward cytoplasmic neuronal antigens, and this autoreactivity is detectable in the serum IgG antibody pool. Interestingly, certain mutations in six key codons along the VH4 domain correlate with polyreactivity, neuron reactivity, or glial cell reactivity. Previous work identified that the prevalence of mutations at these codons in CSF B cells predicts conversion to MS, demonstrating their likely role in progression of disease. Plasmablasts may provide a useful biomarker of B cell activation in MS, or may be direct participants in autoimmunity. In either case, the study of plasmablasts provides insight to the development of the autoreactive B cell response in early MS patients.Item Exploring a Functional Disconnect Between Nestin-Expressing Type-1 Cells and Adult Hippocampal Neurogenesis(2010-05-14) DeCarolis, Nathan Anthony; Eisch, Amelia J.The subgranular zone of the hippocampal dentate gyrus generates new neurons throughout adulthood. The process of adult neurogenesis is well-described, but the source of proliferating progenitors is unknown. One potential source is the Type-1 cell, which is morphologically reminiscent of embryonic radial stem cells and expresses protein markers like nestin. However, there is no direct evidence that Type-1 cells are the source of neurogenesis. For this doctoral research, I asked two questions to gain more insight into the role of Type-1 cells in adult The subgranular zone of the hippocampal dentate gyrus generates new neurons throughout adulthood. The process of adult neurogenesis is well-described, but the source of proliferating progenitors is unknown. One potential source is the Type-1 cell, which is morphologically reminiscent of embryonic radial stem cells and expresses protein markers like nestin. However, there is no direct evidence that Type-1 cells are the source of neurogenesis. For this doctoral research, I asked two questions to gain more insight into the role of Type-1 cells in adult GL-YFP but not Nes-YFP mice showed recovery of YFP+ progenitors, suggesting that GL-YFP cells are stem-like while Nes-YFP cells are progenitor-like. This correlative and causative evidence that nestin-expressing Type-1 cells are not the source of neurogenesis significantly advances our understanding of the neurogenic process.Item Factors Affecting Resting-State Functional Connectivity Across Three Intrinsically Connected Networks in Traumatic Brain Injury(2014-07-28) Bosworth, Christopher Charles; Marquez de la Plata, Carlos; Cullum, C. Munro; Krawczyk, Daniel; Aslan, Sina; Spence, JeffreyThis study investigated the factors that influence post-TBI functional connectivity within three intrinsically connected networks; the default mode network (DMN), central executive network (CEN), and salience network (SN). The aim was to develop a predictive model for each network, based off a combination of cognitive performance, brain volumetric factors, aging/demographic factors, and TBI-related factors. A secondary aim was to examine the relationship between the SN and the anticorrelation (i.e., between-network BOLD signal correlation) between the DMN and CEN. Participants (n=63) sustained a mild-to-moderate TBI within six-months of participating in the study. They completed a cognitive assessment battery consisting of measures of executive functioning, language, memory, reasoning, and intelligence estimates. They also underwent structural MRI, resting-state fMRI, and completed mood symptom questionnaires. A seed-based, resting-state functional connectivity analysis was conducted for the DMN, CEN, and SN. Measures of brain volumetrics were calculated from the structural MRI. Stepwise multiple linear regressions using cognitive factors, demographic and injury factors, functional outcomes, brain volumetric factors, and symptoms of depression were preformed in order to develop predictive models of DMN, CEN, and SN functional connectivity. A Pearson correlation was used to examine the relationship between SN functional connectivity and DMN/CEN anticorrelation. The predictive model for the DMN accounted for approximately 50% of the variance within the network, and was comprised of factors which included TBI severity, age at assessment, volumetric factors, and cognitive factors (including attention and abstract verbal reasoning). The predictive model for the CEN accounted for 37% of the network’s variance, and was comprised solely of cognitive factors, including verbal ability, attention, and inhibition. The SN model accounted for 45% of the variance, and was comprised of factors that included gender, functional outcomes, volumetric factors, and cognitive factors (including attention and cognitive switching). The functional connectivity within the SN had a trending positive correlation with the degree of anticorrelation between the DMN and CEN. These results not only reveal the factors that contribute to functional connectivity, but they also highlight the differences between networks, including that the DMN may be more sensitive to volumetric changes and TBI severity than the CEN or SN.Item Increased Amyloid Deposition after TBI Correlates with Cognitive Deficits and Symptom Worsening(2016-01-19) Sherman, Matt; Gatson, Joshua; Stebbins, Cari; Kilianski, Joseph; Madden, Christopher; Wolf, Steven E.; Diaz-Arrastia, Ramon; Batjer, Hunt; Minei, JosephBACKGROUND: Traumatic brain injury (TBI) is a risk factor for Alzheimer's disease (AD). The primary objective of this case-series study was to conduct early 18F-AV-45 (florbetapir F18) positron emission tomography (PET) imaging in mild-to-moderate TBI subjects after injury to determine if amyloid plaque load predicts cognitive deficits. METHODS: Serial florbetapir F18 PET imaging was conducted in 7 individuals with a mild or moderate TBI (as indicated by their Glasgow Coma Scale [GCS] score between 13 and 15) at day 14 and at 12 months after injury. Of the 7 subjects that were tested, only one had a moderate TBI. Amyloid plaque levels were measured in the cerebral cortex of each individual. To screen for cognitive deficits, the symbol match test was administered at 12 months after TBI. RESULTS: At day 14 after injury, compared to healthy controls, the mild and moderate TBI subjects (N=7) had a 10% increase in amyloid plaque load within the cerebral cortex. When stratified by cognitive outcomes, at day 14 after injury, the subjects with poor outcomes (n=3) experienced a 20% and 13% increase in brain amyloid compared to healthy controls and TBI subjects with good outcomes, respectively. With respect to cognition, at 12 months after injury, the subjects with poor outcomes exhibited a negative correlation (r= -0.71) between amyloid plaque load and cognitive performance. Also, a positive correlation (r=+0.78) was detected between increased brain amyloid load and symptom scores at 12 months. CONCLUSIONS: Individuals with early, substantial increases in brain amyloid experience poor outcomes in the form of memory dysfunction and heightened symptoms (memory deficits, headaches, difficulty concentrating, etc.) at 12 months post-injury. Data presented here suggests that florbetapir F18 PET imaging may be a sensitive biomarker for predicting outcomes within the mild and moderate TBI population.