VictorJuiz/thesis huggingface dataset:
Biomaterials for Cell Engineering and Regenerative Medicine

The promise of regenerative medicine relies on the ability to tightly control cell behavior. Given the broad influence of epigenetics in cell behavior and phenotype determination, it is critical to better understand how interactions with the physiological microenvironment and/or implanted materials affect cell's epigenetic state and, thus, identity. In this dissertation we demonstrate, for the first time, that biophysical cues (e.g., matrix topography and stiffness) can significantly improve the efficiency of cell reprogramming, the process of reverting somatic cells back to pluripotency, by inducing key epigenetic changes in adult fibroblasts. To help elucidate the role of biophysical factors in cell reprogramming we have utilized induced pluripotent stem cell (iPSC) technology in conjunction with various bioengineered substrates. These substrates include poly(dimethyl siloxane) (PDMS) microgrooves, aligned nanofibrous membranes, and polyacrylamide hydrogels. Our data largely suggest that cytoskeletal proteins play an important role in the process of cell reprogramming and that manipulation of the biophysical microenvironment can induce dramatic changes in histone acetylation and methylation patterns. These epigenetic changes significantly improve iPSC generation efficiency and replace the effects of potent small molecule epigenetic modifiers valproic acid (VPA) and tranylcypromine (TCP). Furthermore, we identify specific mediators of this epigenetic mechanomodulation, while distinguishing the role of cell shape in the observed histone modifications. This novel biophysical regulation of epigenetics has important implications in cell biology and in the optimization of materials for broad biological application. Finally, this dissertation work describes how drug-eluting microfibrous patches and nanofibrous scaffolds, in conjunction with iPSC-derived stem cells, can be utilized to combine the effects of biophysical guidance cues, therapeutic drug delivery, and cell engineering for the study and repair of spinal cord injury after both traumatic insult and neural tube defect.

Advisor: Li, Song
Development and Applications of New Chemical Tools for Studying the Cell Biology of Metals

Cells have evolved intricate mechanisms that coordinate the activity of transporters, chaperones, and small-molecule ligands to control the spatial and temporal positioning of metal ions. Alkali and alkaline earth metal ions are known to play essential roles in cellular signaling and charge balance whereas transition metals are typically found in the active sites of enzymes to carry out organic transformations. In order to carry out these functions the cell maintains static and labile metal ion pools. These pools can be characterized by bulk molecular biology and bioinorganic techniques on fixed samples in combination with fluorescent indicators that afford the ability to track metal ions in real-time through molecular imaging. In this regard, cellular calcium has been well characterized in variety of biological contexts, but methods to monitor biologically relevant transition metal ions in real-time have not been well established. This dissertation describes the synthesis, characterization, and applications of new fluorescent sensors for Ni(II) and Cu(I), as well as approaches to discover new roles of biological copper in cell signaling. Nickelsensor-1 is a new water-soluble, turn-on fluorescent sensor that is capable of selectively responding to Ni(II) in aqueous solution and in living cells. Coppersensor-3 and X-ray fluorescence microscopy reveal that neuronal cells mobilize significant pools of copper from their cell bodies to peripheral processes in a calcium dependent fashion upon depolarization with KCl. Mitochondrial Coppersensor-1 (Mito-CS1) is a bifunctional reporter that combines a Cu(I)-responsive fluorescent platform with a mitochondrial-targeting triphenylphosphonium moiety for the reversible detection of endogenous, exchangeable mitochondrial Cu(I) pools. Mito-CS1 in conjunction with ICP metal analyses, show that both the exchangeable Cu(I) and total mitochondrial copper pools are only mildly perturbed in fibroblasts with mutant SCO1 and SCO2 mitochondrial copper chaperones. Molecular imaging of neural calcium transients reveals that that endogenous copper is used to tune inhibitory and excitatory inputs during neural circuit development through the dynamic functions of CTR1. Finally, methods for high-throughput RNAi screening and immunofluorescence have been optimized to understand how the kinome regulates the copper mediated mobilization of ATP7A in mammalian cells.

Advisor: Chang, Christopher J
Letters from the past: Molecular time travel to the origins of photosynthesis, RuBisCO, and the cyanobacterial phylum

The invention of oxygenic photosynthesis has forever changed the face of the Earth by producing the oxygen present in our atmosphere. It is thought that this unique metabolism arose from the bacterial phylum, Cyanobacteria. Moreover, this group has significantly contributed to eukaryotic diversity via endosymbiosis, as a cyanobacterium is considered to be the progenitor of the original plastid organelle, more commonly recognized as chloroplasts in plants. The antiquity of these events, dearth of convincing methodologies, and lack of conclusive evidence all contribute to the considerable challenges we face in understanding the timing of these major evolutionary and geological transitions. In order to address these problems, I have employed various techniques focusing on improving our understanding of the role of cyanobacteria and photosynthesis in shaping the world we have today./nEvolutionary relationships are difficult to reconstruct due to phylogenetic noise (e.g. horizontal gene transfer and homoplasy), resulting in uncertainty in our ability to build accurate phylogenetic trees. In order to address this issue, fifty-four strains of cyanobacteria were chosen for genome sequencing based on improving the phylogenetic coverage of the phylum. Not only does the diversity-driven and phylum-level approach identify many novel genes, but it also clarifies the phylogenetic placement of various cyanobacterial subclades, protein families, and endosymbiosis events./nThe timing of ancient events, such as primary endosymbiosis events, has primarily been dependent on the fossil record. This is problematic as microfossils are difficult to interpret and assign to extant lineages. Conversely, molecular clock methods have been just as widely varying. We devised a new approach to increase the amount of dating information incorporated into molecular clock analyses, improving the accuracy of the predicted dates. We date the plastid and mitochondrial endosymbiosis events to approximately 900 and 1200 million years ago, respectively./nFinally, I focus on the protein evolution of a specific protein crucial to photosynthesis: RuBisCO. Here, I use ancestral sequence reconstruction methods to predict, synthesize, and characterize ancestral versions of RuBisCO. We show that ancestral RuBisCOs have lower rates of carboxylation, reflective of the high CO2 and low O2 Precambrian atmosphere.

Advisor: Niyogi, Krishna K
Kerfeld, Cheryl A
Understanding Kinesin's Gating Mechanism by Optical Trap

Kinesin is a molecular motor that walks on microtubules by taking 8 nm steps towards the plus end in a hand over hand manner. The processive motility of kinesin requires its two motor domains (heads) to coordinate with each other. Interhead coordination involves a gating mechanism, where one of the heads cannot proceed until the other head goes through a certain act. Recent studies suggested that neck linker orientation is involved in coordination of the nucleotide binding and stepping motion of the two heads. In the leading head, the neck-linker is pointing backward, and inhibiting nucleotide binding. In the trailing head, the neck-linker is pointing forward, which allows the release of hydrolysis products and stepping towards the next tubulin binding site. To test this hypothesis, I used a novel optical trapping assay to directly measure microtubule release rate of the motor under a large range of constant forces. In the absence of nucleotide, the microtubule release increased as a function of force in both directions, with the release towards the plus-end was slightly faster than the minus-end under the same force. Addition of ATP resulted in faster release in both directions, consistent with nucleotide induced release properties of the kinesin motor. When kinesin was pulled from its linker in the forward direction, we observed faster release in the presence of ADP, which mimics the microtubule release. Remarkably, release was relatively slow when the linker was oriented in the backward direction by trap. Such asymmetry in the presence of ADP was not observed when kinesin was pulled from its head by a short DNA tether. These results suggest that geometrical constraints of the neck linker domains in a walking kinesin dimer break the symmetry of the two identical heads, such that the trailing head is free to move when the leading head is unable to bind nucleotide.

Advisor: Zhang, Xiang
Youthful Transgressions: Teenagers, Sexuality, and the Contested Path to Adulthood in Postwar America

"Youthful Transgressions" examines teenage sexual culture in the United States after World War II, with a particular focus on the ways that changing notions of childhood and adulthood influenced the place of sexually precocious adolescents in American society. This dissertation argues that between the 1940s and the 1980s, teenage sexuality transformed from a private problem that was seen as leading children into premature adulthood, to a public problem that kept adolescents in a pathologized version of childhood./nThis dissertation addresses the question of how Americans decided who was an adult and who was a child, as well as the consequences of those decisions. In the immediate postwar years, sexually active teenagers were reclassified as adults and hidden from public view through hasty marriages and mandatory expulsions from schools. In the 1960s and 1970s, married and pregnant youth took advantage of a newly expansive concept of childhood to fight their way back into schools and reclaim many of the legal and social rights of children. By the late 1970s and 1980s, lawmakers became convinced that teenage childbearing was an epidemic and responded with federal programs that intervened into the personal and sexual lives of youth and redefined teenage mothers as dependent children./n"Youthful Transgressions" draws from a range of institutional, legal, popular and personal sources, including school records, court documents, congressional testimony, newspaper and magazine articles, advice literature, popular music, and diaries. These sources reveal that ideas about age categories and sexuality evolved in tandem. Teenagers created their own definitions of childhood, adulthood, and age-appropriate sexuality that coexisted with adult views, challenged conventional norms, and evolved to meet their needs over the course of the twentieth century.

Advisor: Fass, Paula S
State Imaginaries and the Movements against the Vietnam and Iraq Wars

The question animating this dissertation concerns the very different trajectories evinced by the movements against the Vietnam and Iraq Wars: the former growing steadily from modest beginnings, the latter displaying an initial burst of intensity before largely disappearing from public view. Offering a complement and counterpoint to political process theory, I construct an account of these different trajectories by foregrounding the way that the larger political-cultural milieu shapes political subjectivities and hence capacities and styles of action. I focus particularly on the dominant set of assumptions about the state and citizenship in each era, which I call "state imaginaries." Weaving together original archival research and insights from social movement studies and political theory, I argue that the dominant state imaginary shifted in the years between the Vietnam War and the Iraq War, from an imaginary of the state based fundamentally on consent, in which actors understood themselves to be complicit citizens, to an imaginary of the state as an alien and invasive force, in which actors worried about being potential prey. I draw out the implications of these different state imaginaries for the form of politics in each era, through case studies of the draft resistance and counter-recruitment movements.

Advisor: Burawoy, Michael
Essays on Entrepreneurial Choice and Non-Market Strategy

In this dissertation, I explore strategic choices and outcomes and what drives them at both the individual and firm levels./nFirst, I introduce a new empirical setting for the study of entrepreneurship at the individual level. Next, the central study in the dissertation and posits that prospective entrepreneurs face a spectrum of entrepreneurial choices rather than a binary employment-entrepreneurship decision. Using novel panel data in an industry in which the individuals are all self-employed but some own businesses whereas others are more employee-like, I show that talent, risk attitudes and overconfidence predict selection into a rich set of entrepreneurial choices that vary by risk, autonomy and returns to talent. My results, which reveal both talent and risk interaction effects and differences in the effects between specialized and general talent, also shed light on the mixed empirical findings in prior research regarding the effect of talent and risk attitudes on entrepreneurship. These findings suggest that research over the last three decades that rely solely on a self-employment definition of entrepreneurship or on uni-dimensional drivers obscures complex choices and incompletely measures the determinants of entrepreneurial choice./nThe last essay investigates firm-level characteristics and their influence on strategic outcomes, particularly responses from the firms' external environment. Business operations of many firms, from apparel firms in the 1990s to Apple Inc. in this decade, have been disrupted due to anti-sweatshop activism. It has been argued that firms that have a record of recalcitrance may deter targeting by activists who consider a campaign against difficult targets too costly (Baron and Diermeier 2007). We use a unique database of anti-sweatshop targeting in the global apparel industry from 1990 to 2005 and indicators of recalcitrance or responsiveness in regards to domestic labor issues for the same period to test whether recalcitrance actually deters targeting. We find that firms that are recalcitrant in responding to Occupational Safety and Health Administration (OSHA) citations draw the attention of anti-sweatshop campaigners, whereas responsive firms and those that work with domestic unions are no more likely to be targeted.

Advisor: Tadelis, Steven
Tourism and Territory in the Mayan World

In post Peace Accords Guatemala, tourism development is engendering new claims and claimants to territory in a climate of land tenure insecurity and enduring inequality. Through ethnographical research, this dissertation explores the territoriality of tourism development through the empirical lens of an archaeological site called Mirador in the Maya Biosphere Reserve. I develop a process-based understanding of territoriality to analyze tourism related struggles over identity, boundary making, land use, heritage claims, and territorial rule at the frontier of state power. In theorizing tourism's territoriality, I argue that the intertwined practices of capitalist spatial colonization and the commodification of place uniquely characterize the industry. I identify five manifestations of tourism's territoriality in the Maya Biosphere: practices of historical and geographical erasure in Mirador tourism imaginaries, territory-based identity production, tourism-enabled practices of enclosure and land dispossession, the "scaling up" of heritage claims through the social construction of global heritage, and the militarization of conservation spaces through tactics of counterinsurgency eco-tourism development./nIn conceptualizing tourism's territoriality, this project contributes to the fields of political ecology, critical tourism studies, political geography, and spatial theories of territory. At the chapter level, analytical contributions include analyses of identity formation in contemporary Guatemala, the role of tourism development in driving the global land grab, how implicit ideas of scale in global heritage discourses usurp local claims to natural and cultural resources, and the revival of counterinsurgency methods in the making of paradisiacal places. In Guatemala's booming post-war tourism sector, this dissertation argues that ongoing struggles over territory are taking deceptively innocuous forms of national park creation, world heritage designation, and environmental conservation.

Advisor: Hart, Gillian
Watts, Michael
Enantioselective Hydroarylation of Unactivated Ketones with Aryl Pinacolboronic Esters and A Hydrindanone-Based Approach Toward Natural Products

The first section of this dissertation describes our efforts to further develop the rhodium–catalyzed 1,2–addition of pinacolboronic ester nucleophiles into unactivated ketones. This reaction represents a mild and efficient alternative for performing this carbon–carbon forming transformation, which traditionally employs harsh conditions, and is especially useful in the context of total synthesis. Our observation that bisphosphine ligands are a beneficial additive in this transformation led to its elaboration into an asymmetric reaction manifold. The second section of this dissertation centers on the use of a key hydrindanone intermediate as a valuable synthetic precursor to the diterpenoid alkaloids and the phragmalin–type limonoids. Chapter 2 begins with a discussion of the isolation and classification of the diterpenoid alkaloids. In addition, major synthetic contributions made by others toward the synthesis of these natural products are also discussed. Our own synthetic approach to these compounds is then detailed, including the construction of the versatile denudatine type core. Central to the success of this strategy was a highly diastereoselective Diels–Alder cycloaddition to furnish a functionalized hydrindanone, the stereochemical information of which was relayed throughout the rest of the synthesis. Chapter 3 focuses on the phragmalin–type limonoids. Previous landmark syntheses of limonoid natural products are first summarized following a brief overview of their isolation and classification. Our strategy for accessing the bridging framework of these natural products is then disclosed. Key to the success of this approach was the concept of network analysis allowing for disconnection of the bridging framework into a fused [6,5] system, thus simplifying its construction.

Advisor: Sarpong, Richmond
Numerical Investigations of Star Formation and Interstellar Clouds

This thesis explores several related questions on the physics of star formation and interstellar clouds. Chapter 2 addresses the remarkable independence of the stellar initial mass function to gas metallicity across a wide a range of galactic and extra-galactic environments. I perform analytic calculations that suggest the temperature structure of a centrally heated, dusty gas cloud should be relatively insensitive to the dust-to-gas ratio over the range of variation probed by observations. I support these calculations with full radiation-hydrodynamic simulations. Chapter 3 investigates the fragmentation of magnetized, massive cores via direct numerical simulation, finding that a combination of magnetic fields and protostellar heating strongly suppresses core fragmentation. These results could explain why the stellar initial mass function so closely resembles the dense core mass function, even at very high core masses. Chapter 4 analyzes the magnetic field structure around a rotationally-dominated protostellar disk formed in the above simulations. I present a map of the column density, magnetic field vectors, and outflow lobes at various length scales and viewing angles that can be compared against observations. I find that the disk begins to influence the geometry of the magnetic field on ∼ 100 AU scales, which should begin to be probed in nearby stellar cores by the next generation of radio interferometers. Chapter 5 addresses the long-standing question of the high CH+ abundance along diffuse molecular sight lines. I compute the CH+ abundance in a turbulent, diffuse molecular cloud by post-processing numerical simulations of magnetohydrodynamic turbulence. The results agree well with observations of the column densities of CH+ and of rotationally-excited H2. Finally, Chapter 6 presents the results of radiation-magnetohydrodynamic simulations of star formation at the cluster scale. The results show that the magnetic field plays a role in determining the star formation rate, the degree of fragmentation, and the characteristic stellar mass.

Advisor: McKee, Christopher
Klein, Richard
Tunneling in low-power device-design: A bottom-up view of issues, challenges, and opportunities

Simulation of electronic transport in nanoscale devices plays a pivotal role in shedding light on underlying physics, and in guiding device-design and optimization. The length scale of the problem and the physical mechanism of device operation guide the choice of formalism. In the sub-20 nanometer regime, semi-classical approaches start breaking down, thus necessitating a quantum-mechanical treatment of the electronic transport problem. Non-equilibrium Green's function (NEGF) is a theoretical framework for investigating quantum-mechanical systems - interacting with surroundings through exchange of quasiparticles - far from equilibrium. Although hugely computation-intensive with a realistic device-representation, it provides a rigorous way to include particle-particle interactions and to model phenomena that are inherently quantum-mechanical./nWe build the Berkeley Quantum Transport Simulator (BQTS) - a massively parallel, generic, NEGF-based numerical simulator - to explore low-power device-design opportunities. Demonstrating scalability and benchmarking results with experimental tunnel diode data, we set out to understand tunneling in devices and to leverage it for both digital and analog applications./nInvestigating InAs short-channel band-to-band tunneling transistors (TFETs), we show that direct source-to-drain tunneling sets the leakage-floor in such devices, thereby limiting the minimum subthreshold swing (SS) in spite of excellent electrostatics. A heterojunction TFET with a halo doping in the source-channel overlap region is proposed and is shown to achieve steep SS as well as large ON current. We discover that by band-offset engineering, the steepness therein could be controlled primarily by the modulation of heterojunction-barrier. Subsequently, exploring layered materials for analog applications, we demonstrate that doping the drain underlap region in graphene FETs prolongs the onset of tunneling in their output characteristics, and hence significantly increases their output resistance (r0) and intrinsic gain (gmr0). Due to large bandgap, and consequently, large r0, monolayer-MoS2 FETs exhibit a significant enhancement in maximum oscillation frequency (fmax) over their graphene counterparts.

Advisor: Salahuddin, Sayeef
PhaseLift: A Novel Methodology for Phase Retrieval

In many physical settings, it is difficult or impossible to measure the phase of a signal. The problem is then to recover a signal from intensity measurements only. This phase retrieval problem has challenged physicists, mathematicians and engineers for decades, being notoriously difficult to solve numerically. We propose a novel framework for phase retrieval, which recasts the problem as a low rank matrix recovery problem and provide theoretical guarantees and empirical demonstrations of its performance, as well as connections of our results to quantum mechanics and random matrix theory.

Advisor: Strain, John
Candes, Emmanuel