VictorJuiz/thesis huggingface dataset:
Measurement of the effect of force on the helix-coil transition using hybrid smFRET-magnetic tweezers

The alpha helix is the predominant element of secondary structure in proteins and is involved in a number of force-dependent biological processes. Despite its importance, direct measurements of its response to force have not been made. Investigations of the mechanical properties of biomolecules usually rely on force spectroscopic techniques such as optical tweezers or atomic force spectroscopy, but these techniques have failed to detect the unfolding/folding signature of the alpha helix, presumably because the cooperativity of the helix-coil transition is broad and the expected extension change is small./nThis research describes the development of an instrument combining magnetic tweezers and total internal reflection fluorescence microscopy (TIRF) with the goal of capturing the effect of force on an isolated alpha helix. Changes in extension are reported by single-molecule Förster resonance energy transfer (smFRET) between small-molecule fluorophores conjugated near the middle of such a helix. This technique provides an extremely sensitive probe of conformation that is unaffected by the DNA handles typically used in optical tweezers experiments and is amenable to both nucleic acid and protein constructs. Calibration is performed and verified using the known worm-like chain (WLC) force-extension behavior of DNA, its overstretching transition, and the opening and closing of a previously characterized DNA hairpin./nUsing this instrument, the alpha helix is observed to unfold cooperatively and reversibly from 11 pN to 17 pN, indicating rapid equilibrium between the helix and coil states. This contrasts with the behavior of an unstructured polypeptide that exhibits a steady, non- cooperative FRET decrease across the 1-30 pN range of applied force. The behavior of the unstructured polypeptide is well described by a WLC model, reformulated here in terms of root-mean square displacement. The helix-prediction algorithm AGADIR, when modified to incorporate the effect of force and a WLC model of the unfolded state, successfully explains the observed folding signature of the alpha helix.

Advisor: Marqusee, Susan
Bustamante, Carlos J
Leveraging Students’ Prior Knowledge in Attaining Deep Structural Understanding of Domain General Models

The Next Generation Science Standards charge U.S. teachers with the task of including patterns, as a crosscutting concept, in their science curricula. This study explores the learning processes and outcomes of a pattern-based curriculum that engages middle school students in the construction of models of particular patterns. These patterns are general behaviors or processes that can be found in a range of phenomena; examples of such patterns include threshold, equilibration, and oscillation. The study investigates 1) the development of students’ pattern models in response to instruction, 2) the productivity of prior knowledge in students' construction of pattern models and 3) the features of instruction that support the process of pattern model construction. It addresses research questions through analysis of data collected during the implementation of a pattern-based curriculum. Findings show that students have a wealth of prior knowledge that can be leveraged by instruction toward their construction of models of threshold, equilibration, and oscillation patterns. These findings contribute to literatures concerned with deep structural and domain-general knowledge, the productive role of prior knowledge in conceptual change, and the design of constructivist instruction.

Advisor: diSessa, Andrea A
Paying for What You'll Like? The Uncertain Value of Uncertainty

Risk and uncertainty can be perceived in seemingly contradicting ways. Receiving a surprise gift can be exciting, whereas not knowing the outcome of a job interview can be incredibly anxiety-provoking. Even the same uncertain event, such as gambling, can simultaneously evoke positive and negative emotions. When is uncertainty positive, and when is it negative? We find that how much people value uncertainty depends on the context, and in particular, how value is measured. Namely, when considering pricing measures (e.g., willingness-to-pay), uncertainty is evaluated negatively, whereas when considering rating measures (e.g., enjoyment), uncertainty is evaluated positively. This effect holds when the outcomes are positive or negative, and even when changing the amount of uncertainty, uncertainty remains negative with pricing measures and positive with rating measures. We explore possible explanations, such as perceived selling price of uncertain prospects, and discuss crucial implications for both theory and applications.

Advisor: Nelson, Leif D
Chen, Serena
Regulation of Autophagosome Biogenesis by the Autophagy Specific Class III Phosphatidylinostitol-3 Kinase Complex

Autophagy is a conserved pathway critical for homeostasis in all eukaryotic cells. Autophagy provides a mechanism for cells to respond to a large variety of cellular stresses through a vesicle-based degradation process. Most of the gene products and other factors required for the execution of autophagy have been elucidated, but the biochemical reactions by which these components work in concert to engulf cargo in a double membrane vesicle, called an autophagosome, is still unclear. In mammalian cells, the class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) is essential for early steps in autophagy because it generates a membrane lipid, phosphatidylinositol 3-phosphate (PtdIns3P), that is necessary to recruit downstream autophagy factors to cellular membranes. However, it was not known whether the PI3KC3-C1 also contributes to phagophore formation in other ways./nThe research described in this dissertation focused on one of the subunits of PI3KC3-C1, Atg14L, which is essential for the complex to initiate autophagy. I used an in vitro reconstitution assay where I added back purified PI3KC3-C1 or various mutant derivatives of the complex to extracts derived from a Cas9-generated Atg14L-deficient cell line. As a biochemical readout for examining the functions of Atg14L, I used a cell-free reaction that reproduces a key early step in autophagosome membrane generation, lipidation of a cytoplasmic protein, LC3. In this assay, I found that Atg14L (and the other subunits of PI3KC3-C1) are required for LC3 lipidation, whereas mutants of the complex that abrogate its catalytic activity and membrane curvature-sensing capability did not support LC3 lipidation. In addition, PI3KC3-C1 activity, through Atg14L and its membrane curvature- sensing motif, is required for efficient membrane recruitment of the downstream PtdIns3P-binding effector, WIPI2, but not for recruitment of Atg16L, a key factor required for LC3 lipidation./nIn an effort to find other cofactors that may also regulate PI3KC3-C1, I found that NRBF2 binds Atg14L and attenuates its autophagy-stimulating function and, hence, serves as a negative regulator of autophagy. Under fed conditions, however, NRBF2 is phosphorylated; phosphorylation null mutants show elevated autophagy under fed conditions. In another study, I uncovered that Atg14L acts as a vesicle tether that supports vesicle fusion when soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are incorporated into the vesicle. The fusogenic activity of Atg14L requires oligomerization through conserved cysteine repeats near the N-terminus of Atg14L.

Advisor: Schekman, Randy W
Motives to Exit: Career Choice or Disillusionment Among Young Charter School Teachers

Abstract/nMotives to Exit: Career Choice or Disillusionment Among Young Charter School Teachers/nby/nCatherine Alice Arenson/nDoctor of Education/nUniversity of California, Berkeley/nProfessor Heinrich Mintrop, Chair/nTeacher turnover is an urgent problem in many schools serving disadvantaged populations. Reform efforts strive to provide a consistently rigorous and stable academic environment for students, but constant teacher turnover impedes the development of a stable learning community, making it difficult to improve and successfully implement reform efforts. Teacher turnover can occur for a variety of reasons, and understanding these reasons was the purpose of this research study. The aim was to better understand teacher turnover among a particular group of young, idealistic, social justice–oriented teachers that staff many of the most challenging urban charter schools. These teachers enter the field with excitement and appear passionately dedicated to making a difference, but then leave the profession after only a few years./nMy research explored the motives of thirty teachers for entering and exiting the teaching profession. My initial hypothesis was that teachers possibly leave owing to career flexibility, reality shock, disillusionment, or burnout. I found the exit motives were most closely aligned with career flexibility and reality shock. The exit motives fell into three categories that were connected to the entrance motives: loss of passion or energy, shift in self-concept or self-identity, and loss of social connections. These motives blend and build on one another in the decision to leave the classroom./nA prosocial mindset and career uncertainty guided these young teachers to a temporary commitment to teaching. By choosing difficult school contexts they learned they could not make a positive impact. They left exhausted, though not to the degree of burnout, for work that better suited them./nTeaching is a profession that deserves the best of the best for our nation’s children. Pro-socially minded, ambitious, and hard-working people are a strong asset to our nation’s schools; however, commitment to the profession of teaching is essential. This study highlights the need for greater attention to recruiting, preparation, and structure of the work of teaching in order to secure teachers’ ongoing commitment to the profession.

Advisor: Mintrop, Heinrich
Bridging the Hierarchical and Collaborative Divide: Learning in California's Integrated Regional Water Management Process

Collaborative governance holds promise for generating learning and innovative solutions to complex resource management challenges. However, attending to the cross-scale dynamics of many environmental problems requires local or regional-scale networks to engage with state or national level government agencies, which are often hierarchical in structure. California’s Integrated Regional Water Management process has sought to encourage local water agencies to collaborate at a regional level in order to build a collective understanding of water management problems and define their own priorities and actions. At the same time, to demonstrate public accountability, the state government has required regions to comply with complex requirements to develop plans and apply for project funds, which may constrain learning and innovation./nThis dissertation examines the extent to which learning is occurring in the midst of these tensions. It focuses particular attention on how regional-level capacity for managing a network can help to mediate between hierarchical and collaborative governance forms to enable learning. Analysis of a sample of 19 out of the 48 water planning regions in California revealed that centralized network structures were associated with higher levels of investment in network management activities. Learning was assessed in two case study regions in the Central Valley with respect to three IRWM program goals embedded in IRWM requirements: building a regional vision for water management, promoting environmental stewardship, and addressing the needs of disadvantaged communities. This analysis indicated that a committed and trusted lead agency with staff dedicated to managing a collaborative process played a crucial role in generating learning around these themes. This lead agency helped to bridge the hierarchical and collaborative divide in three ways: by brokering across regional and state-level interests, developing processes that transform external requirements into learning opportunities, and supporting the development of informal dynamics in addition to ensuring formal rule compliance. This research improves our understanding of how networks function in the context of hybrid governance arrangements with collaborative and hierarchical features. It also delineates critical elements of adaptive governance structures that can support learning to manage multi-scalar environmental problems.

Advisor: Romm, Jeffrey M
Becoming a Place of Institution: The Military Footprint of the Presidio of San Francisco

Abstract/nBecoming a Place of Institution: The Military Footprint of the Presidio of San Francisco/nby/nEric Brandan Blind/nDoctor of Philosophy in Anthropology/nUniversity of California, Berkeley/nProfessor Kent G. Lightfoot, Chair/nThis dissertation aims to illuminate the role of institutions in crafting a future that both enables and constrains future generations. Previous research on institutions has focused almost exclusively on physical institutions and more so on total institutions, such as prisons and asylums. A deeper examination of the literature shows another strain of institutional theory that uses the lens to look at more conceptual institutions, such as marriage or belief systems. In bridging the two, a more coherent model of institutional analysis is pursued./nThis dissertation involves an in-depth case study of the military institution at the Presidio of San Francisco. It focuses on the creation and re-creation of this place over generations and through imperial and national regimes, including the militaries of Spain, Mexico and the United States. Throughout this place-based analysis multiple lines of evidence are used and integrated through the device of storytelling using the biographical paths of individuals or life histories of artifacts to understand the larger institutional projects each intersected with and was instrumental in perpetuating./nThe approach illustrates how storytelling is not only an integrative device, but also an approach that elucidates the values that lie at the heart of any institutional project. It demonstrates how places are the locus for the manifestation of those values, one that is both setting for the social reproduction of the institution and the product of its reproduction./nThe findings prompt a re-thinking of place based-approaches and the role of institutional theory in examining historical trajectories. Given the import and magnitude of the US military presence in the world today it also calls for greater study of this institution to not only understand its impacts abroad, but also to better understand the role it plays at home. Finally, but most importantly, this study calls for more research into this institution, because as it is demonstrated in this study, the legitimacy and success of the US military institution today will surely lead it to be referenced in the future.

Advisor: Lightfoot, Kent G
"To Struggle and Battle and Overcome: The Educational Thought of Nannie Helen Burroughs, 1865-1961

Few twentieth century African American educators were as influential in their lifetime and as neglected by scholars in our day as Nannie Helen Burroughs. The founder of the National Training School for Women and Girls, she was admired by African American leaders ranging from Mary Church Terrell, Anna Julia Cooper, Carter G. Woodson, Ella Baker and Martin Luther King, Jr. Relying on Burroughs’ papers and other archival sources, this dissertation examines Burroughs’ educational thought and its relationship to her leadership of the Women’s Convention of the National Baptist Church, the International Council of Women of the Darker Races, the National Association of Wage Earners and other Black organizations. This dissertation argues that Burroughs both drew on the main currents of African American thought and developed a unique synthesis of practical education, prophetic Christian Pan Africanism and woman-centered leadership.

Advisor: Perlstein, Daniel H
Field and Laboratory Investigations on Seismic Properties of Unconsolidated Saline Permafrost

Saline permafrost is mechanically weak and very sensitive to temperature disturbances, which makes its degradation particularly worrisome in a warming climate. For the purposes of hazard mitigation and prevention, it is crucial to gain knowledge about the properties and distributions of saline permafrost. However, one major challenge is that saline permafrost is hard to access, as it often is covered with a surficial layer of non-saline permafrost. Seismic methods are cost-effective methods for detecting and delineating saline permafrost, but research on seismic properties of unconsolidated saline permafrost is lacking./nThe body of work comprising this dissertation is the first systematic study to investigate seismic properties of unconsolidated saline permafrost. Encompassing field and laboratory components, the study reveals pervasive presence of saline permafrost across the Barrow Environmental Observatory (BEO) in Alaska, and illustrates saline permafrost’s striking vulnerability to temperature disturbances. Besides these findings regarding the distributions and properties of saline permafrost, other key deliverables of this dissertation include 1) rich seismic datasets for field and laboratory investigations of unconsolidated saline permafrost, 2) full-wavefield-based workflow for delineating irregularly dispersive media, and 3) improved microstructural realization regarding pore-scale distributions of ice in saturated frozen sediments./nThrough this work we hope to call attention to the possibly ubiquitous presence of saline permafrost along the polar coasts. Considering the potentially large impact of saline permafrost degradation in a warming climate, we advocate future research needs in regional-scale mapping of saline permafrost and assessing its influences in climate modeling.

Advisor: Dreger, Douglas
Unjust environments: Racial inequalities in environmental exposures and their implications for health

Some of us grow up surrounded by trees, good schools, and opportunity. Others play in the shadow of heavy industry or near abandoned brownfields, surrounded by a high concentration of poverty. Unequal – and unjust – environments shape our opportunities for good health and too often add to the hardships of socially disadvantaged groups. Research on environmental justice considers how a long history of racial discrimination in the U.S. has insured that people of color are more likely to live in neighborhoods with less desirable and less healthful environments./nIn this dissertation I contribute to scholarship on environmental justice by investigating/ncumulative environmental hazards, chemical body burden, and the health implications of climate change from an environmental justice perspective. Chapter 1 describes my approach and how it is situated within prior research on environmental inequalities, differential vulnerability to the health impacts of pollution by socioeconomic status, and racial/ethnic disparities in health. Chapter 2 investigates social inequalities in residential proximity to cumulative environmental and social stressors to health across the state of California. It innovates upon previous work by incorporating measures of social vulnerability and geographically comparing the degree to which multiple environmental hazards are inequitably distributed in a framework that can be used to identify opportunities to reduce inequality and track progress towards environmental justice goals./nIn Chapter 3 I analyze biomonitoring data to examine socio-demographic differences in chemical body burden during pregnancy, considering the number and concentrations of over 80 toxic compounds detected in blood and urine by race, ethnicity, country of origin, and educational attainment. Biomonitoring data gives an indication of possible differences in exposures to multiple toxic chemicals that can reveal inequities with implications for maternal and child health. Chapter 4 considers the potential health implications of climate change from an environmental justice perspective. Using a recent heat wave in Texas, I investigate whether extremely hot temperatures are associated with an elevated risk of preterm birth and examine the possibility that climate change could worsen existing racial and ethnic disparities in reproductive health. The research and policy implications of my findings are discussed in Chapter 5, where I stress the need to incorporate differential vulnerability and cumulative exposures into environmental regulatory policy, exercise precaution in the face of uncertainty, and focus on remedying the upstream drivers of social inequality that lead to unjust environments.

Advisor: Morello-Frosch, Rachel A
Templated Dry Printing of Conductive Metal Nanoparticles

Printed electronics can lower the cost and increase the ubiquity of electrical components such as batteries, sensors, and telemetry systems. Unfortunately, the advance of printed electronics has been held back by the limited minimum resolution, aspect ratio, and feature fidelity of present printing techniques such as gravure, screen printing and inkjet printing. Templated dry printing offers a solution to these problems by patterning nanoparticle inks into templates before drying./nThis dissertation shows advancements in two varieties of templated dry nanoprinting. The first, advective micromolding in vapor-permeable templates (AMPT) is a microfluidic approach that uses evaporation-driven mold filling to create submicron features with a 1:1 aspect ratio. We will discuss submicron surface acoustic wave (SAW) resonators made through this process, and the refinement process in the template manufacturing process necessary to make these devices. We also present modeling techniques that can be applied to future AMPT templates./nWe conclude with a modified templated dry printing that improves throughput and isolated feature patterning by transferring dry-templated features with laser ablation. This method utilizes surface energy-defined templates to pattern features via doctor blade coating. Patterned and dried features can be transferred to a polymer substrate with an Nd:YAG MOPA fiber laser, and printed features can be smaller than the laser beam width.

Advisor: Pisano, Albert P