VictorJuiz/thesis huggingface dataset:
Quantitative characterization of meiotic chromosome organization

Sexual reproduction relies on a specialized program of cell division called meiosis to generate haploid gametes from diploid germ cells. In order for chromosome segregation to occur accurately, homologous chromosomes must pair, synapse, and undergo crossover recombination. These physical and biochemical interactions occur in coordination with large-scale reorganization of meiotic chromosomes. To understand the relationship between chromosome organization and the regulation of recombination, we developed an automated image analysis pipeline that combines the throughput of population-based biochemical assays with the temporal and contextual information provided by cytological methods. This new technique enables us to monitor temporal changes in the distribution of meiotic double strand breaks (DSBs) on a chromosome-wide basis and to correlate that distribution with features of meiotic chromosome organization. We applied this technique to meiotic chromosomes in the nematode Caenorhabditis elegans and observed that the distribution of DSBs is dynamic during prophase and shifts from a distribution that mirrors the distribution of crossovers to one that is more uniform. This shift correlates with isotropic, recombination-independent elongation of chromosomes along the axis and is insensitive to defects in recombination, variation in the number of DSBs, and variation in chromosome axis length. This work reveals a novel dynamic aspect of meiotic DSB formation and quantifies, for the first time, statistical features of meiotic chromosome organization in C. elegans.

Advisor: Dernburg, Abby F
Implementation & Optimization of Parallel Imaging and Compressed Sensing Techniques for Faster Acquisition of Multi-Channel Magnetic Resonance Spectroscopic Imaging for Brain Tumor Patients

Primary brain tumors are typically aggressive lesions that are difficult to treat and have a relatively poor prognosis for many patients. Magnetic resonance imaging (MRI) tools have been commonly utilized in the management of patients diagnosed with gliomas. Functional and metabolic MRI techniques have been proposed to add information regarding the tissue characteristics and biochemistry for better tumor localization, treatment planning and follow up of the disease./nMagnetic resonance spectroscopic imaging (MRSI) is a metabolic imaging technique used to analyze brain tissue chemistry. By showing metabolically active infiltrative tumor that can look similar to surrounding tissues on conventional MR images, MRSI allows for a more accurate definition of the extent of the disease. Despite those benefits, MRSI has not been widely used to care for patients with brain tumors./nThree major difficulties encountered in using MRSI in a clinical setting are limited cover- age, coarse spatial resolution and long data acquisition time. The possibility of combining compressed sensing and parallel imaging techniques to accelerate the acquisition time, in- crease coverage of the brain or resolution while ensuring high quality data without loss of information was the primary goal of this dissertation./nSeveral new techniques have been developed to accelerate MRSI acquisition in addition to reconstruct and optimally combine the accelerated multi-channel whole-brain 3D-MRSI data accurately and robustly. These techniques were validated on healthy volunteers and patients with brain tumors. They allowed the acquisition of MRSI data from a much larger brain volumes and finer spatial resolution than the conventional methods. The proposed AVD- GRAPPA technique reduced the 20min acquisition to < 5min with clinically interpretable spectra (high correlation to the full sampling). The improved coverage and spatial resolution will be useful for evaluating heterogeneous and infiltrative tumors, which are difficult to evaluate with current protocols. This advancement should make possible a more accurate assessment of the progression of tumors in serial studies./nThe result of this dissertation suggests that magnetic resonance spectroscopic imaging is an important technique for spatially characterizing brain tumors that can be acquired in a shorter time to obtain equivalent disease related information. It is expected that shorter scan times will result in less patient discomfort, motion artifacts and will increase the scanner throughput and the usage of MRSI data in treatment management of the patients with brain tumor.

Advisor: Nelson, Sarah
Conolly, Steve
Petro-Socialism and Agrarianism: Agrarian Reform, Food, and Oil in Chavista Venezuela

This dissertation examines the policy and socio-economic dynamics of the Venezuelan agrarian reform in the Chavista era. As a self-proclaimed socialist state, the Chavista government has framed its agrarian policies as a reordering of the food system that prioritized land redistribution, smallholder agriculture, and sustainable forms of production. The agrarian reform purported to place peasant farmers at the core of a new agricultural regime that would build national food sovereignty. Yet despite increased state support for smallholders, aggressive pro-peasant rhetoric, popular support for the Chavista party in rural areas, and oil wealth to fund agriculture development, rural dynamics have been characterized by conflict over land and a geographically and temporally uneven process of policy development in the countryside./nThis dissertation argues that the land reform program in Venezuela has plateaued as a redistributive process and has to come to serve as primarily social rather than productive policy in rural areas. In this study I seek to analyze the determining factors that have impacted and restricted the agrarian reform process and produced this limited outcome./nTo understand the limits of the agrarian reform I argue that it is necessary to examine policy processes within an analysis of the broader political economy of Venezuela as an oil state with a mixed economy. I also posit that analyses of agrarian dynamics that focus on peasant-state relationships without addressing the commercial agriculture sector have omitted a critical dimension of the agro-food system. I therefore take a multi-sectoral approach to agro-food policy that draws these understudied components of agrarian Venezuela—petro-state dynamics and the commercial agriculture sector—into an analysis anchored on peasant-state policy relationships./nThrough this multi-sectoral approach I argue that the complex and often contradictory objectives of state policy in the agrarian realm are illustrative of macro-level, petro-state constraints on progressive reform more broadly, as well as tensions between political and economic development objectives of state policy. I show how oil dynamics create political economic challenges to structural change and feed into the construction of particular state ‘needs’ for agriculture, food production and agrarian reform. These dynamics help to explain the apparent contradiction of why much of state agricultural policy in Venezuela contributes to maintaining the viability and local economic position of large farmers even as government discourse continues to highlight the state’s promotion of agrarian reform and smallholder production./nI propose the term ‘petro-socialism’ to refer to the political economy emerging from the amalgam of oil state dynamics and the anti-neoliberal/socialist framing of the government’s policies. The concept of petro-socialism connotes that the shape of state reforms in the Chavista period were inherently constrained and often contradictory in nature.

Advisor: Carr, Claudia
Translating Brazil: From Transnational Periodicals to Hemispheric Fictions, 1808-2010

This dissertation analyzes how travel and translation informed the construction of Brazil as modern in the 19th century, and how similar processes of transnational translation continue to shape the cultural visibility of the nation abroad in the contemporary moment. By reading journals, literary works, and cultural criticism, this study inserts Brazilian literature and culture into recent debates about translatability, world literature, and cosmopolitanism, while also underscoring the often-overlooked presence of Brazilians in the United States. The first half of the dissertation contends that Portuguese-language periodicals Correio Braziliense (London, 1808-1822), Revista Nitheroy (Paris, 1836), and O Novo Mundo (New York, 1870-1879) translated European and North American ideas of technology and education to a readership primarily in Brazil. The transnational circulation of these periodicals contributed to the self-fashioning of intellectuals who came to define the nation. To suggest parallels between Brazil and the United States in the late 19th century, the analysis of O Novo Mundo focuses on discourses of nation, modernity, and technological progress emerging in the hemispheric travels of scientists, intellectuals, and the Brazilian empire Dom Pedro II, and in the national displays at the 1876 Centennial Exhibition in Philadelphia./nThe second half of the dissertation proposes a counterpoint to the 19th century by analyzing literature, cultural criticism, and art from the late 20th and early 21st centuries. The national coexists with the transnational in both historical periods as Brazilian intellectuals and artists look beyond Brazil in order to refine their definitions of the nation as modern. Contemporary writers like Silviano Santiago and Adriana Lisboa find themselves at home not in Brazil, but rather within the translation zones of the Americas. For Santiago, translating French theory to the Latin American context informs his concept of the space in-between, which in turn manifests itself in his fiction about Brazilians in the United States. This analysis examines how Santiago and Lisboa develop translational aesthetics in their narratives through code switching and cultural references in order to better capture the displacement experienced by their transnational characters. The relative success in translation of Lisboa’s tales of immigrant lives suggests a preference for translatability in the global literary market. The dissertation concludes by arguing that Nuno Ramos represents an alternative mode for artistic visibility beyond Brazil as a translator between genres and media whose work contests assumptions of translatability

Advisor: Brizuela, Natalia
Slater, Candace
Regulated activation of the CUL3 ubiquitin ligase by a calcium-dependent co-adaptor complex

The small protein ubiquitin is an essential post-translational modification that regulates a vast number of cellular processes in eukaryotes. Through a cascade of enzymatic steps, ubiquitin is transferred from a ubiquitin activating enzyme (E1) to a ubiquitin conjugating enzyme (E2), which interacts with a ubiquitin ligase (E3) that stimulates transfer of ubiquitin to a substrate. Conjugation of ubiquitin to a substrate can result in a variety of outcomes, including changes in protein stability, localization, or binding partners. This modification is utilized to control a diversity of processes, including protein trafficking, cell division, DNA damage response, immune signaling, transcriptional regulation, and many others./nCullin-RING-ligases (CRLs) are the largest class of ubiquitin E3 ligases. CRLs are comprised of one of seven Cullin scaffold proteins (CUL1, CUL2, CUL3, CUL4A, CUL4B, CUL5, and CUL7). The functions of these ligases are nearly as diverse as the function of ubiquitin itself. In particular, CUL3 has functions in developmental processes, mitosis, autophagy, organelle formation, endocytosis, and more. CUL3 exerts its many roles by pairing with at least 90 substrate receptors that recruit proteins to be ubiquitylated. When in complex with the substrate receptor KLHL12, CUL3 transfers a single ubiquitin to its substrate, SEC31, a structural component of the COPII vesicle coat that helps transport proteins from the endoplasmic reticulum to the Golgi apparatus. SEC31 ubiquitylation triggers an increase in COPII vesicle size, allowing for the packaging and transport of large proteins such as collagen./nIn this work, I examine the mechanisms by which SEC31 ubiquitylation by CUL3KLHL12 is regulated. CUL3KLHL12 activity requires the calcium-binding proteins PEF1 and ALG2. PEF1 and ALG2 form a target-specific co-adaptor that acts as a calcium sensor. Together PEF1 and ALG2 are an integral part of the CUL3KLHL12 ubiquitin ligase and allow for SEC31 targeting only in the presence of elevated cellular calcium concentrations. This translates a short-lived rise in cytosolic calcium levels into sustained ubiquitylation of SEC31, which in turn triggers formation of large COPII coats and collagen secretion. As calcium signaling is also known to control chondrocyte differentiation and collagen synthesis, the regulated activation of CUL3KLHL12 could allow organisms to integrate collagen secretion into programs of craniofacial bone formation. This work shows that target-specific co-adaptors provide a mechanism for rapid and signal-dependent activation of CUL3 complexes important for human development and disease.

Advisor: Rape, Michael
Modeling of Flow and Thermal Energy Transport of High and Low Temperature Applications with Thermal Energy Storage

A 3D model simulation using computational fluid dynamics (ANSYS) was used to assess the heat transfer from the molten glass to incoming air at ambient temperature. A system model was developed to simulate an experimental helical coil counter-flow test heat exchanger. The molten glass is also implemented as a falling thin film (< 3mm) to absorb thermal energy in a concentrating solar power plant. The phosphorous pentoxide glass flow is treated as a laminar, Newtonian and gravity-driven flow over a slightly inclined flat plate using an explicit finite difference scheme to evaluate important heat transfer performance./nIn the cold regime (~30 oC), a transient unit that uses solid-liquid phase change for thermal cold storage was analyzed. Computational fluid dynamics (Fluent-ANSYS) was used to model the phase change behavior of lithium nitrate trihydrate (LiNO3H2O) by modeling a unit cell of a thermal energy storage heat exchanger. In this analysis, the time required to input thermal energy (melt) the phase change material is calculated to assess its heat transfer performance. By modeling different unit cell domains, the overall heat transfer coefficient and mean conductance are calculated for two different heat exchanger designs.

Advisor: Carey, Van P
Literality: The Question of Contemporary Poetry

The history of French poetry has been marked by crisis. Frequently a mode of critical thought, poetry has drawn attention to the specificity of its historical and literary contexts, seeking to address the question of itself as a mode of critical agency and autonomous thought rather than as an extension of a determining social or cultural order. Poetry’s continued engagement with the question of its autonomy and viable place in the world has been coupled with a history of breakdowns of poetic form, leading up to, in the 1970s, a poetry qualified by formal minimalism, a refusal of metaphor and image, and an apparent distancing with respect to traditional lyric. This poetry’s attentiveness to language as written (or “à la lettre”) defines its loyalty to the literal. Consequently, this poetry has frequently been misunderstood as self-absorbed, coldly formalist, and elitist in its apparent inaccessibility, as the poets Jean-Marie Gleize and Jacques Roubaud have remarked. Taking up their observations, I address the question of contemporary poetry’s difficulty and the pertinence of this question to this poetry’s contemporaneity by examining the work of three poets whose work belongs to those concerned with literality: the late Anne-Marie Albiach, Emmanuel Hocquard, and Claude Royet-Journoud. In doing so, I show what literality means for each of these poets. I suggest that despite criticisms against it, this poetry is the form taken by individuals’ lived attempts to situate themselves autonomously within the world and within their own moment while taking into consideration the necessity to listen to voices other than their own and granting integrity to the present. This work of conscious self-situation is also the work of constructing a relationship to the past that is not based on linear narrative, or a determining form. My analysis is framed by and draws on the work of Robert Kaufman, who articulates modernism in terms of a “reinvention of lyric-Romantic critical agency.”

Advisor: Smock, Ann
Kaufman, Robert
Light Absorbers and Catalysts for Solar to Fuel Conversion

Increasing fossil fuel consumption and the resulting consequences to the environment has propelled research into means of utilizing alternative, clean energy sources. Solar power is among the most promising of renewable energy sources but must be converted into an energy dense medium such as chemical bonds to render it useful for transport and energy storage. Photoelectrochemistry (PEC), the splitting of water into oxygen and hydrogen fuel or reducing CO2 to hydrocarbon fuels via sunlight is a promising approach towards this goal./nPhotoelectrochemical systems are comprised of several components, including light absorbers and catalysts. These parts must all synergistically function in a working device. Therefore, the continual development of each component is crucial for the overall goal. For PEC systems to be practical for large scale use, the must be efficient, stable, and composed of cost effective components. To this end, my work focused on the development of light absorbing and catalyst components of PEC solar to fuel converting systems./nIn the direction of light absorbers, I focused of utilizing Indium Phosphide (InP) nanowires (NWs) as photocathodes. I first developed synthetic techniques for InP NW solution phase and vapor phase growth. Next, I developed light absorbing photocathodes from my InP NWs towards PEC water splitting cells./nI studied cobalt sulfide (CoSx) as an earth abundant catalyst for the reductive hydrogen evolution half reaction. Using in situ spectroscopic techniques, I elucidated the active structure of this catalyst and offered clues to its high activity./nIn addition to hydrogen evolution catalysts, I established a new generation of earth abundant catalysts for CO2 reduction to CO fuel/chemical feedstock. I first worked with molecularly tunable homogeneous catalysts that exhibited high selectivity for CO2 reduction in non-aqueous media. Next, in order to retain molecular tunability while achieving stability and efficiency in aqueous solvents, I aimed to heterogenize a class of molecular porphyrin catalysts into a 3D mesoscopic porous catalytic structure in the form of a metal-organic framework (MOF).To do so, I initially developed a growth for thin film MOFs that were embedded with catalytic groups in their linkers.6 Next, I utilized these thin film MOFs grown on conductive substrates and functionalized with cobalt porphyrin units as 3D porous CO¬2 reduction catalysts. This new class of catalyst exhibited high efficiency, selectivity, and stability in neutral pH aqueous electrolytes./nFinally, as a last chapter of my work, I explored hybrid inorganic/biological CO2 reduction pathways. Specifically, I used time-resolved spectroscopic and biochemical techniques to investigate charge transfer pathways from light absorber to CO2-derived acetate in acetogenic self-sensitized bacteria.

Advisor: Yang, Peidong
Deep UV Second Harmonic Generation Studies of Thiocyanate at Hydrophobe/Water Interfaces

Abstract/nDeep UV Second Harmonic Generation Studies of Thiocyanate at Hydrophobe/Water Interfaces/nBy/nDebra Lynn McCaffrey/nDoctor of Philosophy in Chemistry/nUniversity of California, Berkeley/nProfessor Richard J. Saykally, Chair/nOur understanding of the air/water interface and ion adsorption to this interface has developed rapidly in the last decade. While tremendous progress has been made in this area, it is essential for the field to branch out into additional interfaces. This dissertation describes the work I’ve done to extend the field to additional hydrophobic interfaces./nChapter 1 gives historical context for the work done on the air/water interface. Macroscopic measurements, such as surface tension, suggested that ions should be depleted from the air/water interface. Microscopic measurements, such as molecular dynamics simulations and second harmonic generation spectroscopy, show that some ions are enhanced at the air/water interface and that the degree of enhancement follows the Hofmeister series. The mechanism that drives adsorption is a delicate balance between factors such as solvent repartitioning, electrostatics, capillary waves, and configurational entropy./nChapter 2 presents nonlinear optical spectroscopy theory and outlines the experimental apparatus. It also details the sample preparation and the data analysis procedure. The processed data are fit to a Langmuir model, derived therein./nChapter 3 details studies on hydrocarbon/water interfaces. Hydrocarbons provide a condensed phase analogue to the air/water interface. While the data are preliminary and need to be refined, the general trend is that thin layers of hydrocarbons have little effect on the free energy of adsorption of thiocyanate./nChapter 4 details studies on the graphene/water interface. While graphene has a high charge carrier mobility, it seems that graphene behaves like a hydrophobe in regards to thiocyanate adsorption. Experimental studies showed that the free energy of adsorption to the graphene/water interface is similar to that of the air/water interface. Molecular dynamics simulations reveal that the adsorption mechanism is drastically different, however./nChapter 5 evolved out of a concern to include a surface potential term in the Langmuir model. This created nested models that were compared with several model comparison metrics. The better model seems to depend on the dataset. The method of calculating errors for the fit parameters was also examined, but further work still needs to be done on finding the most accurate method./nChapter 6 presents some broad conclusions and directions for future study. It seems that thin, uncharged monolayers inserted into an interface have little effect on the free energy of adsorption, although the mechanism can change. This chapter also proposes a new study to help elucidate the effect of surface charge. Surfactants can mix with alkanes to form an ordered monolayer on water. Varying the concentration of the surfactant can vary the surface charge.

Advisor: Saykally, Richard J