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Essays on Empirical Market Design in Higher Education
No full textCentralized assignment mechanisms are widely used and present in many markets. The empirical evaluation of these markets is an essential and challenging task. For instance, in college admissions, students may report their preferences strategically, making it difficult to evaluate policy changes. Also, it is unclear whether students make mistakes when applying to college and if this has consequences on their welfare. Finally, little is known if the market design can affect students’ downstream outcomes. In my dissertation, I shed light on these issues, by analyzing the Chilean centralized college admissions system. In the first chapter, with I. Rios, we document strong evidence of strategic behavior in students’ applications, even though students face no incentives to misreport their preferences. Taking this into account, we build anew methodology that recovers students’ preferences from observed application lists, even when students face a large number of choices. In the second chapter, with I. Rios, we analyze the effects of centralized assignment mechanisms on downstream outcomes. We evaluate two channels that can explain students’ dynamic choices: (i) students might switch programs or drop out due to initial mismatches, and (ii) students might switch or drop out due to learning about their match-qualities. Based on these facts, we build a structural model of students’ college progression in the presence of a centralized system. We use the estimated model to analyze the impact of changing the market design on the system’s efficiency. We find that policies that elicit information on students’ cardinal preferences and leverage dynamic incentives can significantlyimprove the system’s efficiency. Finally, in the third chapter, with M. Martinez, C. Neilson, and I. Rios, we analyze the prevalence and relevance of application mistakes in college admissions. Using survey data, we find that a significant fraction of students makes welfare-relevant mistakes due to a lack of information and biased beliefs. We use these insights to design and evaluate an information policy to reduce application mistakes. We find that showing information aboutadmission probabilities has a causal effect on improving students’ outcomes
Serotonergic Modulation of the Central GLP-1 System
No full textThe prevalence of metabolic and stress-related disorders has been on the rise for decades and has reached epidemic proportions globally. The high degree of comorbidity between these pathological states is likely due, at least in part, to the significant overlap in neural circuitry that governs energy balance and stress-related physiological and behavioral responses. The future of pharmacotherapies aimed at treating these and other disorders relies on a more comprehensive understanding of the molecular interaction between different neuro-transmitter / -peptide systems. Of particular interest is a growing body of literature that supports an interaction between serotonin (5-HT) and the central glucagon-like peptide-1 (GLP-1) system, both of which are involved in the control of stress and energy balance. The research presented in this doctoral dissertation investigates the role of 5-HT as an endogenous modulator of the central GLP-1 system and its effects on feeding behavior and stress-induced neuronal activation. In Chapter 2, I establish that the anorectic and body weight changes induced by administration of exogenous hindbrain 5-HT are dependent on central GLP-1 receptor (GLP-1R) signaling. Second, I provide anatomical evidence of 5-HT2C and 5-HT3 receptor mRNA expression on GLP-1-producing preproglucagon (PPG) neurons in the medial nucleus tractus solitarius (NTS). Additionally, I show that hindbrain activation of these 5-HT receptors induces hypophagia in rats and that this effect is achieved via central GLP-1R signaling. Finally, a role for the 5-HT3 receptor was identified in mediating anorectic effect induced by the interoceptive stressor, lithium chloride (LiCl). Chapter 3 explores the 5-HT modulation of the central GLP-1 system in the context of acute stressors and the potential source of 5-HT driving the 5-HT/GLP-1 hindbrain interaction. 5-HT2C and 5-HT3 receptors were demonstrated to mediate the activation of NTS PPG neurons that results from exposure to LiCl and novel restraint. These acute stressors activate 5-HT activity in the Raphe magnus (RMg), a sub-nuclei of the caudal raphe (CR), as measured by increased c-Fos expression. Lastly, using a viral tracing technique I confirm that RMg neurons innervate NTS PPG neurons and that a sub-population of these PPG neurons lie in close proximity to 5-HT axons. Taken together, the results presented in this document expand the current understanding of both the central 5-HT and the GLP-1 systems. This collective body of work underscores the complexity of interactions between two different neural substrates and calls attention to the relevance such interactions play in the modulation behavioral and physiology
Synthetic Studies of Biologically Active Molecules: IRL 2500, Bruceantin, and Biliatresone
No full textPart 1: Carbon monoxide (CO) is a poisonous gas that binds to hemoglobin, preventing oxygen transport to the tissues. CO poisoning causes ~50,000 emergency room visits per year. Treatments for CO poisoning are extremely limited. IRL 2500 is a small molecule allosteric effector of hemoglobin that has been shown to decrease the half-life of CO-bound hemoglobin (COHb). Herein we describe the synthesis of a novel, structurally constrained derivative of IRL 2500 and its effect on COHb. Part 2: Bruceantin is a natural product that has long been studied for its anticancer activity. Inspired by the structure of bruceantin, we proposed to develop a homologous Pauson Khand reaction utilizing a strained bicyclic compound to generate bridged cyclohexenones via a [3+2+1] cycloaddition as a possible method to generate the bruceantin ring system. The synthesis of suitable bicyclic substrates for this reaction has been achieved, and their viability in a rhodium- catalyzed cycloaddition has been evaluated, with nitrogen-containing bicyclic compounds having been shown to undergo ring opening reactions. Progress towards the synthesis of substrates with stabilizing groups will also be discussed. Part 3: Biliary atresia is a rare disease that is the most common indication for liver transplant among the pediatric population. Biliatresone was discovered to be an environmental toxin that recapitulates the biliary atresia phenotype. Analogs of biliatresone the could be used to identify the cellular target of the toxin have been designed and synthesized for use in a photoaffinity pulldown experiment. The best analog has been shown to cause the biliary atresia phenotype in zebrafish and has been used in experiments aimed at determining the molecular target ofbiliatresone. Future study and determination of the molecular target will aid in our understanding of biliary atresia
A Genome-First Approach to Investigating the Biological and Clinical Relevance of Exome-Wide Rare Coding Variation Using Electronic Health Record Phenotypes
No full textGenome-wide association studies (GWAS) have successfully described the roles of common genetic variation on human diseases by analyzing large populations recruited based on a shared phenotype, but the biological and clinical relevance of numerous genes remain incompletely described through these ‘phenotype-first’ methodologies. Much of the unexplained genetic contribution to disease risk and variability in complex traits may belong to the very rare and private spectrum of alleles, a range traditionally ignored by GWAS. Furthermore, the phenotype-first approach is likely to miss unexpected phenotypic consequences of genetic variants, such as those that may not be feasible to study in a phenotype-first approach due to rarity of the condition. The Penn Medicine BioBank, a healthcare system-based database of genotype, whole-exome sequencing, and electronic health record data, allows for an unbiased, ‘genome-first’ approach to describing the relationships between genetic variants and human disease traits captured in the clinical setting. Through ‘gene burden’ tests that interrogate the cumulative effects of multiple rare and private variants in a gene that are predicted to affect gene function, this dissertation aims to characterize the clinical manifestations of diseases and traits caused by rare, predicted loss-of-function and predicted deleterious missense variants on an exome-wide and/or phenome-wide scale. These analyses uncover previously unsuspected medical and biological consequences of loss-of-function variants in multiple genes. In summary, this dissertation will investigate the biological and clinical relevance of disease-associated genes by investigating the association of rare coding variation found in whole-exome sequencing with phenotypes derived from the EHR
Understanding Gene Regulation in Development and Differentiation Using Single Cell Multi-Omics
No full textTranscriptional regulation is a major determinant of tissue-specific gene expression during development. My thesis research leverages powerful single-cell approaches to address this fundamental question in two developmental systems, C. elegans embryogenesis and mouse embryonic hematopoiesis. I have also developed much-needed computational algorithms for single-cell data analysis and exploration. C. elegans is an animal with few cells, but a striking diversity of cell types. In this thesis, I characterize the molecular basis for their specification by analyzing the transcriptomes of 86,024 single embryonic cells. I identified 502 terminal and pre-terminal cell types, mapping most single cell transcriptomes to their exact position in C. elegans’ invariant lineage. Using these annotations, I find that: 1) the correlation between a cell’s lineage and its transcriptome increases from mid to late gastrulation, then falls dramatically as cells in the nervous system and pharynx adopt their terminal fates; 2) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and 3) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state. Next, I studied the development of hematopoietic stem cells (HSCs). All HSCs come from a specialized type of endothelial cells in the major arteries of the embryo called hemogenic endothelium (HE). To examine the cellular and molecular transitions underlying the formation of HSCs, we profiled nearly 40,000 rare single cells from the caudal arteries of embryonic day 9.5 (E9.5) to E11.5 mouse embryos using single-cell RNA-Seq and single-cell ATAC-Seq. I identified a continuous developmental trajectory from endothelial cells to early precursors of HSCs, and several critical transitional cell types during this process. The intermediate stage most proximal to HE, which we termed pre-HE, is characterized by increased accessibility of chromatin enriched for SOX, FOX, GATA, and SMAD binding motifs. I also identified a developmental bottleneck separates pre-HE from HE, and RUNX1 dosage regulates the efficiency of the pre-HE to HE transition. A distal enhancer of Runx1 shows high accessibility in pre-HE cells at the bottleneck, but loses accessibility thereafter. Once cells pass the bottleneck, they follow distinct developmental trajectories leading to an initial wave of lympho-myeloid-biased progenitors, followed by precursors of HSCs. During the course of both projects, I have developed novel computational methods for analyzing single-cell multi-omics data, including VERSE, PIVOT and VisCello. Together, these tools constitute a comprehensive single cell data analysis suite that facilitates the discovery of novel biological mechanisms
Automating Program Analysis for Differential Privacy
No full textThis dissertation explores techniques for automating program analysis, with a focus on validating and securely executing differentially private programs. Differential privacy allows analysts to study general patterns among individuals, while providing strong protections against identity leakage. To automatically check differential privacy for programs, we develop Fuzzi: a three-level logic for differential privacy. Fuzzi’s lowest level is a general-purpose logic; its middle level is apRHL, a program logic for mechanical construction of differential privacy proofs; and its top level is a novel sensitivity logic for tracking sensitivity bounds, a fundamental building block of differential privacy. Some differentially private algorithms have sophisticated proofs that cannot be derived by a compositional typechecking process. To detect incorrect implementations for these algorithms, we develop DPCheck for testing differential privacy automatically. Adapting a well-known “pointwise” proof technique for differential privacy, DPCheck observes runtime program behaviors, and derives formulas that constrain potential privacy proofs. Once we are convinced that a program is differentially private, we often still have to trust that the machine executing the program does not misbehave and leak sensitive results. For analytics at scale, computation is often delegated to networked computers that may become compromised. To securely run differentially private analytics at scale, we develop Orchard, a system that can answer many differentially private queries over data distributed among millions of user devices. Orchard leverages cryptographic primitives to employ untrusted computers, while preventing untrusted computers from observing sensitive results
Compartment-Specific Regulation of Autophagy in Neurons
No full textMacroautophagy (hereafter autophagy) is a fundamental catabolic process that delivers damaged cytoplasmic proteins and organelles to the lysosome for turnover. In this capacity, autophagy controls the composition and integrity of organelles and the cellular proteome. Autophagy is vital for the development, functionality, and survival of the nervous system. Autophagy is also essential for learning and memory, suggesting critical roles for autophagy at the neuronal synapse. The mechanisms and cellular processes that regulate autophagy in neurons and astrocytes, however, are poorly understood. In this thesis we have elucidated how synaptic activity, which is a fundamental aspect of neuronal physiology, regulates the dynamics and function of autophagic vacuoles in primary hippocampal neurons using live-cell confocal microscopy. We found that synaptic activity regulates the motility of autophagic vacuoles (AVs) in dendrites. Stimulation of synaptic activity dampened AV motility, whereas silencing synaptic activity induced AV motility. Activity-dependent effects on dendritic AV motility are local and reversible. Importantly, these effects are compartment-specific, occurring in dendrites and not in axons. Most strikingly, synaptic activity increases the presence of degradative autolysosomes in dendrites and not in axons. We have further defined the molecular underpinnings of autophagy in primary cortical neurons and astrocytes in response to metabolic stress, using a combination of confocal microscopy and immunoblotting. We found that inducing metabolic stress by nutrient deprivation or pharmacological inhibition of MTOR (mechanistic target of rapamycin kinase) robustly activates autophagy in astrocytes, but have less pronounced effects on autophagy in neurons. Combined, our studies indicate how different cellular processes regulate autophagy in two dominant cell types of the brain. These findings raise important implications for how neurons and glia manage cellular stress, and how they may collaborate to maintain homeostasis in the brain
A Proteomics Approach Identifies Novel Resident Zebrafish Balbiani Body Proteins Cirbpa and Cirbpb
No full textThe Balbiani body (Bb) is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects, fish, amphibians, and mammals. During early zebrafish oogenesis, the Bb assembles as a transient aggregate of mRNA, proteins, and membrane-bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops, the Bb appears to grow slowly until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins at the cortex. In fish and frogs, this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable, solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity, little is known about the mechanism behind the Bb’s action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles, translocates, and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 80 proteins associated with the Bb sample, including known Bb proteins and novel RNA-binding proteins. In particular, we identified Cirbpa and Cirbpb, which have both an RNA-binding domain and a predicted self-aggregation domain. In stage I oocytes, Cirbpa and Cirbpb localize to the Bb rather than the nucleus (as in somatic cells), indicating that they may have a specialized function in the germ line. Both the RNA-binding domain and the self-aggregation domain are sufficient to localize to the Bb, suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb, our proteomics dataset presents many candidates for further study, making it a valuable resource for building a comprehensive mechanism for Bb function at a protein level
Structures Formed by Colloids by Capillarity on Curved Interfaces
No full textThe trapping and interaction of nano- and micro-particles at fluid interfaces is broadly important in technology, including established technologies like froth flotation to recover ores and emulsion stabilization by adsorbed particle layers, or the formation of Pickering emulsions. Particle trapping and organization at interfaces is also important in advanced materials processing, for example, in the formation of ordered nanoparticle structures at fluid interfaces in Langmuir troughs. Capillary interactions are ubiquitous between microscale colloids trapped at fluid interfaces. These interactions are particularly interesting because they depend on the shape of the interface shape and the shape of the particle’s contact line. This latter quantity depends on the particles’ shape, its surface chemistry and topography, but not on its bulk materials properties. Thus, these interaction are “materials agnostic”, and can be used to organize finely divided materials of diverse bulk properties. Generally, colloids become trapped at fluid interfaces because upon adsorption, they eliminate a patch of liquid-liquid or liquid-vapor interface, significantly reducing the free energy of the system. Particles trapped at fluid interfaces generally have pinned, undulated contact lines that distort the interface around them. To minimize the area, and therefore the energy of these distortions, colloids interact and assemble. These interactions are significant at planar interfaces, and depend strongly on the shape of the host interface. In particular, on curved fluid interfaces, capillary interactions direct isolated colloid motion along paths defined by deviatoric curvature gradients. This directed motion relies on the leading order, long-ranged quadrupolar distortions made by the colloids\u27 undulated pinned contact lines, and the underlying “saddle-like” shape of the interface that is also described by a quadrupolar term in the limit of small interfacial slopes. While the importance of curvature for isolated particles on curved interfaces is now well appreciated, its role in guiding structure formation has not been well studied. In my thesis, I study the organization of microparticles trapped on curved interfaces using theory and experiment. I first focus on pair interactions between particles with pinned contact lines trapped on interfaces with curvature gradients. I derive closed-form expressions for the interaction potential between spherical or disk-like particles with nearly circular contact lines. Gradients in this potential predict the forces on the particles and hence particle paths. The particles are attracted to each other, and are also attracted to zones of high deviatoric curvature. Depending on the relative magnitudes of their attraction and the strength of the local curvature gradient, particle pairs are predicted to dimerize, co-migrate without dimerization but in each other’s influence, or to migrate independently. On curved oil-water interfaces, I study pair interactions and dimer formation of spherical microparticles. These particles induce significant nanometric deformation on the interface. Particles are attracted to each other and come to apparent contact. I use the analytical pair potentials to understand dimerization and to identify criteria for dimers to form. When many particles are present on the curved interface, they organize in nearly trapped structures that reflect the underlying curvature field. To model this process, I use Monte Carlo simulations in which the energy landscape is determined by the analytical pair potential in the curved interface, extended to have higher order modes in the particle contact line undulation and in the local expansion of the interface. By randomly adding particles with given contact line undulations, the Monte Carlo simulations generate structures with qualitative features similar to those formed in experiment. Lastly, I address pair interactions of elongated particles on curved fluid interfaces. The leading order disturbance made by each particle in the interface is a quadrupole in elliptical coordinates. The analytical pair potential now captures the alignment of the particle’s major axis with respect to the underlying curvature field. I compare prediction to the paths taken by cylindrical microparticle pairs in a curvature field. The study of structure formation by Monte Carlo is left for future work
Molecular Control of Synaptic Efficacy Within Striatal Circuits
No full textAs the input nucleus of the basal ganglia, the striatum integrates diverse excitatory projections governing cognitive and motor control. Over the last decade, substantial progress has been made in the identification of striatal cell-types, distinguishing their molecular profiles and local connectivity patterns. Nevertheless, our understanding of the functional organization of striatal circuits remains limited. The studies presented in this thesis focus on delineating the synaptic properties of excitatory inputs originating from dorsal prefrontal cortex and parafascicular thalamus innervating neuronal populations within dorsal medial striatum. In these studies, we use quantitative optogenetic measures to investigate striatal projections in an input-specific manner onto distinct striatal neuronal populations. In the first study, we find a divergence between cell-type specific anatomical connectivity and measures of excitatory strength. Furthermore, we find that synaptic strength is modified according to both presynaptic region and postsynaptic cell type. As a substantial degree of synaptic function is determined by the molecular composition of individual neurons and their synapses, the second study examines the role of a cell-adhesion molecule, Neurexin1ɑ, at these synapses. We found Neurexin1ɑ, a gene with broad neuropsychiatric disease association, regulates synaptic efficacy at these synapses in an input- and postsynaptic cell type manner. Together, these studies demonstrate a significant amount of diversity observed in physiological connectivity can be attributed to presynaptic-postsynaptic interactions and their underlying molecular composition. Ultimately, forming a comprehensive map of striatal circuits will be essential in understanding how the convergence of inputs from various sources convey information for distinct behavioral functions