VictorJuiz/thesis huggingface dataset:
Biochemical Analysis of Strains of α-Synuclein Aggregates

The synucleinopathies are progressive, neurodegenerative diseases of aging characterized by the accumulation of α-synuclein aggregates. α-Synuclein aggregates are prion-like and amplify in a prion-like manner. A key feature of prions is the existence of different strains, where depending on the conformation, a different prion disease is manifested. The existence of α-synuclein aggregate strains is an area of active research and provides a potential explanation for the clinical heterogeneity of the synucleinopathies. The overarching aim of this project was to investigate α-synuclein’s ability to form strains and understand their biological consequences. Using recombinant protein, we created and characterized two unique strains of α-synuclein fibrils, which induced different clinicopathological disease phenotypes in a mouse model (TgM83 mice). This approach provides evidence that conformational differences alone are sufficient for causing different disease phenotypes, demonstrating α-synuclein’s ability to form strains and that strains may be biologically relevant to disease pathogenesis.

Keywords: Neurodegeneration
Prion-like
Protein misfolding
Strains
Synucleinopathies
α-Synuclein
Advisor: Watts, Joel
ATOMISTIC INVESTIGATION OF DEFORMATION TWINNING IN NC FCC AND BCC MULTILAYERS

The deformation twinning is observed to increase both ductility and strength of nanocrystalline (NC) materials. Hence, deformation twinning in NC materials is very important and can be used to improve structural performance of NC materials and of those materials which employ both CG and NC layers, e.g. Multilayers (MLs). This thesis is focused on finding twinning trends in NC FCC materials and study interface-mediated deformation twinning in BCC ML using molecular dynamics. The first study investigates the competition between twin nucleation and twin thickening in NC FCC materials. The second study extends the FCC ML code to BCC materials and investigates CG-NC interface-mediated deformation twinning in BCC Ta ML material. The results of both studies provide insight into the work hardening behavior of the NC FCC and BCC ML due to deformation twinning.

Advisor: Singh, Chandra Veer
Analysis of Specialized Subcellular Regions in Cardiac Myocytes in Health and Disease

The nucleoplasmic reticulum (NR) and sarcoplasmic reticulum (SR) are critical intracellular subdomains within the cardiomyocyte. Despite their importance, there are large gaps of knowledge regarding these compartments. Here, I elucidated some of the molecular constituents within the NR of mouse ventricular cardiomyocytes, which contain SR and endoplasmic reticulum (ER) proteins, including SERCA2A, RyR2, and calnexin. For the first time, I revealed the presence of STIM1 within these invaginations, suggesting the existence of store-operated Ca2+ entry (SOCE) mechanisms within nuclei. Furthermore, super-resolution imaging (dSTORM) quantitatively assessed nanoscale changes in SR protein cluster properties with pressure-overload cardiac hypertrophy. DHPR and RyR2 reorganized into dispersed, low-density protein clusters; in contrast, SERCA2A became sequestered into highly dense protein clusters. Moreover, the amount and size of SERCA2A-containing nuclear invaginations increased in pathological hypertrophy. These findings shed light on the molecular constituents of the NR and reveal the dynamic nature of the SR in disease.

Keywords: Cardiac
Nucleoplasmic reticulum
Pressure-overload cardiac hypertrophy
Super-resolution microscopy
Advisor: Gramolini, Anthony O
Microbe and host-derived mechanisms of protection from autoimmune diabetes in non-obese diabetic mice

Autoimmune diabetes results from T cell-mediated destruction of insulin-producing pancreatic β cells in both humans and non-obese diabetic (NOD) mice. Our lab previously observed that cecal microbial transfer from male NOD mice into weanling females (MF) conferred protection in the recipients. The goal of this thesis was to investigate the effects of microbial transfer on autoantigen presentation and islet-reactive CD4+ T cell responses. We found that the proliferation of islet-reactive T cells did not vary in response to autoantigen presentation in MF recipients compared to controls. However, peripheral antigen presenting cells from MF recipients promoted a more activated T cell phenotype ex vivo compared to controls. Moreover, CD4+ T cells with major diabetogenic potential were identified in the islets. Since CD4+ T cells are central to immunological events in autoimmune diabetes, analysis of islet-reactive CD4+ T cell responses will shed light in mechanisms of microbe-dependent protection from autoimmune diabetes.

Keywords: autoimmune
CD4
diabetes
islet
microbiota
Advisor: Danska, Jayne
Differential Atrial and Ventricular Remodeling in Response to Endurance Exercise

Cardiac remodeling, classified as physiological (i.e.exercise) or pathophysiological (i.e.heart disease), refers to biochemical, genetic, structural and functional cardiac changes that occur in response to stress. We have identified distinct remodeling patterns in mouse atria and ventricles in response to endurance swim exercise: exercise induced fibrosis, inflammation and atrial fibrillation(AF) in atria, while improving contractility and reducing arrhythmia vulnerability in ventricles. Although there is a strong link between AF and endurance exercise in humans, the underlying mechanisms are unknown. Pharmacological TNFÎą inhibition at 3-weeks after exercise commencement does not reverse the pathological atrial remodeling, indicating that remodeling occurs quickly and early. RNA-sequencing on 2-week exercised mouse atria and ventricles suggested that the ventricle undergoes a lesser degree of exercise-induced transcriptomic remodeling compared to the atria, and that TNFÎą-mediated atrial(but not ventricular) remodeling by TNFÎą is associated to changes in cell-cell adhesion and mechanotransduction-associated pathways(i.e.focal adhesion and integrin).

Keywords: Atrial Fibrillation
Cardiac remodeling
Endurance exercise
Mechanotransduction
TNFÎą
WNT
Advisor: Backx, Peter H
The Okapi (Oka) FERM Domain Protein Regulates Somatic Stem Cell Numbers and Cell Intercalation during Drosophila Oogenesis

Okapi (Oka) is a Drosophila melanogaster FERM domain protein that is essential for oogenesis. oka (CG34347) mutants are viable but display defects during oogenesis. Mutant ovaries showed enlarged and multilayered interfollicular stalks and germline disorganization. I generated endogenously and exogenously GFP-tagged Oka protein to examine the distribution of Oka. Oka was present in somatic cells of the ovary and localized to adherens junctions (AJs) in the germarium and follicles, including cap cells, follicular epithelium, intercalating cells that form the interfollicular stalk, and in migratory border cell clusters and centripetal cells. I found that oka mutant ovaries contained an increased number of follicle stem cells (FSCs), which could explain the increased somatic cell numbers, and is reminiscent of overactive signalling pathways such as Hippo and Hedgehog. My findings suggest that Oka is a component of AJs that negatively regulates FSC numbers and is required for the intercalation of interfollicular stalk cells.

Keywords: Drosophila melanogaster
FERM Domain Protein
Intercalation
Oogenesis
Proliferation
Stem Cells
Advisor: Tepass, Ulrich
Identifying novel urinary tract pacemaker cell markers sheds insight into the development and function of those cells

Non-obstructive hydronephrosis, defined as dilatation of the urinary pelvis is the most commonly detected antenatal abnormality. Previously, our lab demonstrated that reduced Hedgehog-signaling in the metanephric kidney causes non-obstructive hydronephrosis with abnormal urinary tract peristalsis and loss of urinary-tract-pacemaker-cell (utPMC) markers. Our lab also demonstrated that utPMCs develop from the neural-crest-cell (NCC) lineage. UtPMCs are comprised of HCN3+ cells, and cKIT+ cells. Investigations of utPMCs are hindered by a lack of knowledge of markers and earlier developmental markers expressed before E15.5 (the onset of HCN3/cKIT expression). Markers enriched in HCN3+ utPMC RNA-sequencing were verified by qPCR and analyzed in cKIT+ cells. This identified 9 HCN3-cell markers, 2 of which were shared with cKIT-cells. Immunofluorescence revealed that PTK2Î˛ is expressed in NCCs at E12.5 and sustained till adulthood. Functional analysis revealed that PTK2Î˛ contributes to utPMC function. Identifying markers expressed earlier than E15.5 allows studies on utPMCs and hydronephrosis.

Keywords: hydronephrosis
Kidney
Urinary tract pacemaker cells
Advisor: Rosenblum, Norman
Co-delivery of Chondroitinase ABC and Pre-differentiated Progeny of Human Neuroepithelial Cells in Hydrogels to the Injured Spinal Cord

The inability of injured axons to regenerate across the lesion that forms following a spinal cord injury is largely attributed to their reduced growth capacity, and the inhibitory microenvironment surrounding the lesion. To overcome these obstacles, a combinatorial strategy was designed involving the delivery of the enzyme chondroitinase ABC (chABC), from a methylcellulose hydrogel to degrade inhibitory molecules, and the transplantation of neuronal precursor cells in a hyaluronan-methylcellulose hydrogel to bridge the lesion. Although motor and sensory functionality was not recovered through this strategy in rat models of spinal cord injury, high levels of transplanted cells remained 8 weeks after transplantation, the cells retained a neuronal phenotype and migrated toward the lesion, despite being injected 1 mm away from the injury site. Future work involves determining the effect that chABC had in this system, and what modifications can be made to achieve functional recovery through this type of combinatorial strategy.

Keywords: Biomaterials
Cell Transplantation
Chondroitinase ABC
Hydrogels
Neuronal Precursor Cells
Spinal Cord Injury
Advisor: Shoichet, Molly S
The Role of Sphingosine-1-Phosphate in Regulation of Multidrug Resistance at the Developing Blood-brain Barrier

P-glycoprotein (P-gp) is an efflux transporter on brain endothelial cells (BECs) that protects the developing brain. Sphingosine-1-phosphate (S1P) can modify P-gp function in the adult blood- brain barrier (BBB). This thesis determined the effect of S1P on the developing BBB. We hypothesized that S1P reduces P-gp function in primary cultured guinea pig BECs dependent on developmental age. Treatment of BECs with exogenous S1P or FTY720P (S1P analog) had no effect on P-gp function. BECs treated with high doses of FTY720 (precursor of FTY720P and inhibitor of S1P production) decreased cellular S1P and decreased P-gp function. Extended incubation with the highest dose of FTY720 or SKi II (inhibitor of S1P production) increased P- gp function. These results indicate that S1P is important for maintaining P-gp activity and disruption of the S1P-ceramide rheostat can change P-gp function at the BBB, altering brain exposure to P-gp substrates and potentially adversely affecting brain development.

Keywords: Brain development
Endothelial
Multidrug resistance
P-glycoprotein
Sphingolipids
Sphingosine-1-phosphate
Advisor: Matthews, Stephen G
Constraining Deformation, Uplift, and Activity Along the Tuz Golu Fault Zone, Central Anatolia, Turkey

We use a combination of paleostress analysis, tectonic geomorphology, and 40Ar/39Ar geochronology along the Tuz Golu fault zone to constrain deformation and uplift in the Central Anatolian Plateau (CAP) interior. Paleostress analysis shows at least two principal phases of deformation - pre-upper Miocene compression and post-Miocene extension, suggesting a changeover from compression to extension in Anatolia that broadly coincides with the onset of regional uplift. Morphometric analysis provide evidence of a southeastward increase in footwall uplift rate that could be the result of a regional uplift gradient, block rotations, or a combination of these processes. Morphometrics suggest north-northwest tilting of catchments, which may be linked to regional tilting related to uplift of the CAP. We utilize 40Ar/39Ar dating of offset lava flows in the southeastern Tuz Golu fault zone to constrain strike-slip deformation, and derive dextral slip rates that range from 0.58 to 3.53 mm/yr since ~2 Ma.

Keywords: Anatolia
Geodynamics
Geology
Structural
Tectonics
Turkey
Advisor: Schoenbohm, Lindsay M
Community Connectedness Mediates the Link Between Attachment Avoidance and Internalized Heterosexism

For sexual minorities, social connection with other sexual minorities plays an important role in managing minority stress (Detrie Lease, 2007; Meyer, 2003) and buffering the effects of internalized heterosexism (Mason, Lewis, Winstead, Derlega, 2015; J. Puckett, Levitt, Horne, Hayes-skelton, 2015). Disrupted social connection could explain why past studies found links between attachment avoidance â a discomfort with closeness and intimacy â and internalized heterosexism (Brown Trevethan, 2010; Mohr Fassinger, 2003). Using structural equation modeling, I tested whether community connectedness might mediate the link between attachment avoidance and multiple components of internalized heterosexism. In Study 1, attachment avoidance predicted higher internalized heterosexism, but this was fully mediated by the negative association between avoidance and community connectedness. Study 2 largely replicated these results, however, connectedness only partially mediated a link between avoidance and identity concealment. Thus, attachment avoidance may be linked to negative identity because avoidance hinders community connectedness.

Keywords: Attachment
Collective Self-Esteem
Community Connectedness
Internalized Heterosexism
Sexual Identity
Sexual Minorities
Advisor: MacDonald, Geoff
The Inhibitory Role of Taurine through Glycine and GABAA Receptors in the Anoxia-tolerant Western Painted Turtle Brain (Chrysemys picta bellii)

Unlike anoxia-intolerant mammals, painted turtles survive extended periods of anoxia. This is partly accomplished by an increase in gamma-aminobutyric acid (GABA) which mediates spike arrest via shunting inhibition in brain. Taurine levels also increase; its purpose is unknown but is speculated to include actions similar to inhibitory neurotransmitters, acting through glycine and/or GABAA/B receptors. Given the general importance of inhibition in anoxia-tolerance, we investigated taurineâ s function as an inhibitory molecule in the turtle cerebrocortex. Using whole-cell patch-clamp electrophysiological methods we found that taurine depolarized membrane potential, increased whole cell conductance and induced an inward current similar to the effects of GABA and glycine. These effects were reduced when glycine and GABAA receptors but not GABAB or glutamatergic receptors were inhibited, suggesting that taurine mediates its effects through both glycine and GABAA receptors. Therefore, taurine may act as an inhibitory signaling molecule during anoxia in the turtle cortex.

Keywords: Anoxia
GABA
Glycine
Shunting Inhibition
Taurine
Western Painted Turtle
Advisor: Buck, Leslie
Identification and Validation of the Regulators of Riboneogenesis

The riboneogenesis pathway provides yeast with an alternate route for ribose production. Ribose is an essential precursor for nucleotide synthesis. Riboneogenesis connects glycolysis to the non-oxidative pentose phosphate pathway by the action of the key enzyme, Shb17, which converts sedoheptulose-1,7,-bisphosphate into sedoheptulose-7-phosphate. To understand why this pathway evolved and to gain insight into ribose metabolism in yeast, I used fluorescence based assays to identify genetic regulators of Shb17. Using reporter fluorescence, I probed the levels of Shb17 across the budding yeast prototrophic deletion collection using both a Typhoon fluorescent imager as well as flow cytometry. My screens identified genes involved in ribosome biogenesis as potential regulators of Shb17, which were validated by immunoblotting and further characterized by polysome profiling. My results raise the hypothesis that the relative level of the 60S to the 40S ribosomal subunit influence the regulation of Shb17.

Advisor: Caudy, Amy A
Factors Associated with In-hospital Growth Trajectories of Very Low Birth Weight Infants

Relationships between individual factors and in-hospital growth of very low birth weight (VLBW) infants have been previously investigated; however, examining these factors together and their association with growth rates during hospitalization is warranted. This study explores the relationship between infant demographics, morbidities, daily macronutrient and energy intakes, and in-hospital weight, length, and head circumference (HC) trajectories. Repeated measures linear regression models assessed the relationship between prospectively-collected factors and anthropometric measures over time of 316 VLBW infants. Weight was associated with all macronutrient and energy intakes over time, irrespective of the infantsâ postnatal age (p-values: .03-

Keywords: Human milk
Macronutrient intakes
Postnatal growth
Preterm infant
Very low birth weight
Advisor: O'Connor, Deborah L
Modeling, Numerical Simulation and Experimental Investigation of Ion Exchange and Diffusion-Coupled Drug Transport in Pharmaceutical Polymers

Ionic polymers are used in pharmaceutical products to achieve desired drug release properties. The ionic interaction between drugs and polymers complicates theoretical prediction of drug transport adding more difficulties in design of controlled release dosage forms. Therefore, this thesis investigates drug transport in membranes of Eudragit速 RS (RS) and Eudragit速 RL (RL) with different amounts of cationic groups. A mathematical model was developed to describe the ion-exchange and diffusion-coupled drug loading mechanism. The model was verified by loading two different anionic drugs, ibuprofen Na and diclofenac Na, into cationic RS/RL polymer membranes. The dependence of drug loading kinetic and equilibrium were investigated using numerical simulations and experiments on the different physicalchemical parameters. Thermodynamic and kinetic parameters of the system determined from this work can be used for the design of experiments to achieve target loading efficacy and efficiency and for prediction of drug release kinetics of coated dosage forms.

Keywords: Eudragit Polymer
Ion Exchange
Modeling
Advisor: Wu, Xiaoyu
Stromal Cells Control Nephron Formation in a Hedgehog-dependent Manner

In the mammalian kidney, Foxd1+ stromal cells signal to and control adjacent nephron progenitor (NP) differentiation. We have previously demonstrated that deletion of Hedgehog (HH) signaling from stromal cells is characterized by fewer nephrons and an expansion in NP. To elucidate the molecular mechanisms underlying this stromal-NP crosstalk, we performed RNA sequencing on E13.5 Foxd1Cre;SmoloxP/- mutant whole kidney tissue. I discovered that Tgfb2 and Tgfb3 were downregulated in mutant kidneys, and that TGFβ intracellular effector pSMAD2/3 was decreased in mutants. Ex vivo functional analysis demonstrated that TGFβ2 and TGFβ3 control nephron differentiation. Genetic deletion of Tgfbr2 (receptor for TGFβ ligands) in the NP population resulted in no phenotype. Conditional deletion of Tgfbr2 within the stromal compartment results in expanded NP and a disorganized stromal compartment. Together, these data suggest that TGFβ acts downstream of Hedgehog signaling in stromal-nephron progenitor crosstalk, and in a cell-autonomous role within the stroma.

Advisor: Rosenblum, Norman
Do VLBW Infants Continue to Acquire Growth Deficits during their In-hospital Stay?

The purpose of this study was to determine whether very low birth weight (VLBW) infants continue to leave the hospital growth restricted, and to explore predictor variables affecting growth. Infant growth, demographics, morbidity, and mortality data were collected prospectively until hospital discharge or the 90th postnatal day. Anthropometric z scores were calculated. Multiple regression models with interaction terms were constructed to assess the association of potential predictor variables with absolute and z score measures of weight, length and head circumference over time. From birth to end of the study, weight (-0.73  1.06 to -1.5  0.85), length (-0.71  1.08 to -1.83  1.29) and head circumference (-0.87  1 to -1.11  1.03) z scores declined (P

Keywords: Growth
Infants
Preterm
Advisor: O'Connor, Deborah L
ARGLU1 is an RNA-binding Protein that has a Fundamental Role in Modulating Global Alternative Splicing Patterns

Alternative splicing (AS) is a key step of RNA maturation. More emerging evidence demonstrates RNA synthesis and processing are coupled, thus transcriptional coregulatory proteins are being studied in greater detail as mediators of both events. Nuclear receptors such as glucocorticoid receptor (GR) are ligand-dependent transcription factors dependent on coregualtor interaction. The role of GR in metabolism and immune function in response to synthetic glucocorticoids, such as Dexamethasone are well characterized. We identified a novel GR coactivator, arginine and glutamate rich 1 (ARGLU1) that potentiates GR transcriptional activity and interacts with splicing factors. ARGLU1 knockdown in a neuronal cell line and analysis of mRNA found ARGLU1 alters alternatively spliced events (ASEs). Dexamethasone-regulated ASEs were also identified and found to be largely dependent on ARGLU1 and GR. RNA immunoprecipitation found that ARGLU1 could bind pre-mRNA of ASEs. This thesis studied the role of ARGLU1 as a novel RNA-binding protein that modulates AS.

Keywords: Alternative splicing
Nuclear receptor coregulators
RNA-binding proteins
RNA processing
Advisor: Cummins, Carolyn L
Effects of TRPM2 Inhibition in Neuroprotection following Neonatal Hypoxic-Ischemic Brain Injury

Neonatal hypoxic-ischemic (HI) brain injury is a major cause of acute mortality and chronic neurological morbidity in infants and children. Studies indicate that transient receptor potential melastatin 2 or TRPM2 (a non-selective cation channel with high permeability to calcium that can be activated by intracellular adenosine diphosphoribose [ADPR] and H2O2) can mediate neuronal death following acute ischemic insults in adult mice as well as HI brain injury in neonatal mice. My study tested the effect of a newly described TRPM2 channel inhibitor AG490 by using a H2O2-induced neuronal cell death in vitro model and mouse HI brain injury in vivo model. I found that the inhibition of TRPM2 channels by AG490 demonstrates a neuroprotective effect both in vitro and in vivo. The neuroprotective effect of AG490 following post-injury treatment suggests the potential clinical implications of this drug, including the possible prevention of HI related neurological complications such as hypoxic-ischemic encephalopathy.

Keywords: AG490
hypoxic-ischemic
neuroprotective
TRPM2
Advisor: SUN, HONG-SHUO
CONSUMPTION OF NON-COW’S MILK BEVERAGES AND HEIGHT IN CHILDHOOD

ABSTRACT Background: Non-cow’s milk beverages among children are increasingly being consumed due to perceived health benefits. However, non-cow’s milk contains less protein and fat than cow’s milk and may not have the same effect on height. I hypothesized that consumption of non-cow’s milk beverages would be associated with lower childhood height. Methods: A cross-sectional analysis of TARGet Kids! data on healthy children 2-5 years of age was conducted. Multivariate linear regression models were used to test the association between daily volume of non-cow’s milk beverage consumption and height-for-age z-scores. Results: Higher non-cow’s milk consumption was associated with lower childhood height. Each daily cup of non-cow’s milk was associated with a lower height-for-age z-score of 0.11 (95% CI: 0.16, 0.05, P

Keywords: childhood
cow milk
height
noncow milk beverages
pediatrics
Advisor: Maguire, Jonathon L.