VictorJuiz/thesis huggingface dataset:
Encapsulation of Biomolecules in Bacteriophage MS2 Viral Capsids

Nanometer-scale molecular assemblies have numerous applications in materials, catalysis, and medicine. Self-assembly has been used to create many structures, but approaches can match the extraordinary combination of stability, homogeneity, and chemical flexibility found in viral capsids. In particular, the bacteriophage MS2 capsid has provided a porous scaffold for several engineered nanomaterials for drug delivery, targeted cellular imaging, and photodynamic therapy by chemical modification of the inner and outer surfaces of the shell. This work describes the development of new methods for reassembly of the capsid with concomitant encapsulation of large biomolecules. These methods were then used to encapsulate a variety of interesting cargoes, including RNA, DNA, protein-nucleic acid and protein-polymer conjugates, metal nanoparticles, and enzymes./nTo develop a stable, scalable method for encapsulation of biomolecules, the assembly of the capsid from its constituent subunits was analyzed in detail. It was found that combinations of negatively charged biomolecules and protein stabilizing agents could enhance reassembly, while electrostatic interactions of the biomolecules with the positively charged inner surface led to encapsulation. To investigate the role protein shells play in encapsulated enzymatic processes, this method was then used to a model enzyme in a series of capsids with altered characteristics around the pores. The method was then used to develop a potential system for delivery of therapeutic proteins to the cytoplasm of cancer cells by encapsulating conjugates of these proteins to a negatively charged, membrane-lysing polymer.

Advisor: Francis, Matthew B
Tullman-Ercek, Danielle
Mechanisms of RNA Recognition and Cleavage in RNA Interference

Proteins that harbor double stranded RNA-binding domains (dsRBDs) play/nfunctional roles in processes as diverse as RNA localization, RNA splicing, RNA editing,/nnuclear export of RNA and translation, yet the mechanistic basis and functional/nsignificance of dsRBDs remain unclear. To unravel this enigma, we investigated/ntransactivation response (TAR) RNA-binding protein (TRBP), comprising three dsRBDs,/nwhich has functions in HIV replication, PKR-mediated immune response and RNA/nsilencing. In collaborative studies using single-molecule methods, I found that TRBP/nexhibits an ATP-independent diffusion activity exclusively on double-stranded RNA/n(dsRNA) in a length-dependent manner. The first two dsRBDs of TRBP are essential for/ndiffusion, whereas the third dsRBD is dispensable. Two homologs of TRBP, PKR/nactivator (PACT) and R3D1-L, displayed the same behavior, implying that the ability to/ndiffuse along dsRNA is a universal property of this protein family. Furthermore, a Dicer-/nTRBP complex on dsRNA exhibited dynamic diffusion, which was correlated with/nDicer's catalytic activity, suggesting that the dsRNA-specific diffusion activity of TRBP/ncontributes to enhancing small interfering RNA (siRNA) and microRNA (miRNA)/nprocessing by Dicer./nThe enzyme Dicer generates 21-25 nucleotide-long dsRNAs that target specific/nmRNAs for silencing during RNA interference and related pathways. Although the active/nsite and RNA-binding regions of Dicer are functionally conserved within eukaryotes, the/nhelicase domain has distinct activities in the context of different Dicer enzymes. To/nexamine the evolutionary origins of Dicer helicase functions, we investigated two related/nDicer enzymes from the thermophilic fungus Sporotrichum thermophile. RNA cleavage/nassays showed that S. thermophile Dicer-1 (StDicer-1) can process hairpin precursors/nto miRNAs, whereas StDicer-2 can only cleave linear dsRNAs. Furthermore, only/nStDicer-2 possesses robust ATP hydrolytic activity in the presence of dsRNA. Deletion/nof the StDicer-2 helicase domain increases both StDicer-2 cleavage activity and affinity/nfor hairpin RNA. Notably, the full-length forms (but not truncated versions lacking their/nhelicase domain) of both StDicer-1 and StDicer-2 could complement the phenotype of a/nmutant of a distantly related yeast Schizosaccharomyces pombe lacking its endogenous/nDicer gene, underscoring the importance of the helicase domain for Dicer function./nThese results further suggest that an in vivo regulatory function for the helicase domain/nmay be conserved from fungi to humans.

Advisor: Doudna, Jennifer A
Making Matters: Teaching and Learning Literacies and Identities in Urban Schools

This qualitative study conducted over a 14-month period examined how teachers and students' identities influenced their learning and implementation of design thinking processes in conjunction with their technology use in urban classrooms. Design thinking is a learning approach through which students engage in hands-on project-based activities that solve complex problems (Carrol, et al., 2010). This research was an examination of teachers' professional development with design thinking principles to understand 1) how teachers' identities influenced their learning to use tools afforded in training, and 2) how teachers' took up the use of digital technologies in classroom practice. Additionally, this work examined 1) how access to technologies influenced 60 predominately Latino/a and African American students' identities and 2) how it also influenced these students' developing new and critical literacies. Findings revealed how teachers' identities differentially affected their learning of design thinking principles and how they facilitated the use of technologies in their classrooms. This work also revealed that students transformed negative self-perceptions by designing digitally mediated projects that facilitated the development of more positive identities. Finally, this work found that students' developing new and critical literacies were influenced by their lived experiences because students evidenced a predilection for making digitally mediated projects that relevantly connected to their personal lives. Implications of this work are that both teachers and students' identities play integral roles in how they learn and utilize principles of design thinking as well as digital technologies such that identity connections need to be much more central to the processes of learning for both teachers and students.

Advisor: Mahiri, Jabari
Visible Deliverances: The Fact and Figure of Miracle in Eighteenth-Century America

In my dissertation, "Visible Deliverances: The Fact and Figure of Miracle in Eighteenth-Century America," I argue that the idea of the miraculous was a vital resource for the representation of physical and spiritual experience in eighteenth century America. If the peculiar power of a miracle is that it can disrupt apparently fundamental systems like time and causation, that same unique power constituted its great virtue for the Protestant thinkers in my study. The idea of the miraculous suspension of natural law dramatized the subordination of all perceived order to the will of God. Consequently this shock of divine power was a useful construct for the purposes of pious exhortation. In a deeper sense, however, it allowed the clerical writers I focus on to imagine the link between divine power and the contingent structures of human understanding. In "Visible Deliverances" I argue that this work of writing the human relation to the divine through miracle took place in the imaginative space of literary representation. Faced with the incommensurability of human perception and divine force, these writers turned to allusive figural strategies. It was only figural comparison - a practice of spiritualizing analogy - that could place human experience in a defensible relation to the immensity of God's greatest works of power. In an initial chapter on miracles stories in Cotton Mather's medical writing, I argue that he advocated for these stories as necessary evidence for understanding the full scope of physical experience. In my second chapter I read George Whitefield's sermons on Christ's miracles in the context of early-eighteenth-century English religious controversies. In a final chapter, I describe the complexity of Jonathan Edwards' approach to the persistence of miraculous power in the world, an idea that he disavowed, but could not fully relinquish. Ultimately I argue that the principle of contemporary miracle is what allows these writers to describe the full power of the essential evangelical experience of spiritual rebirth.

Advisor: Breitwieser, Mitchell
Listening Genres: The Circulation of Psychoanalysis in Everyday Interactions in Buenos Aires, Argentina

Listening Genres: The Circulation of Psychoanalysis in Everyday Interactions in Buenos Aires, Argentina/nBy/nXochiquetzal Marsilli-Vargas/nDoctor of Philosophy in Anthropology/nUniversity of California, Berkeley/nProfessor Charles L. Briggs, Chair/nThis dissertation proposes the concept of listening genres as frameworks of relevance that surface at the moment of reception and orient the apprehension of sound. At the intersection of linguistic and psychological anthropology, sound studies, and Argentine cultural history, it argues that sound reception, far from being neutral and automatic, always involves a particular type of ideological and practice intervention. The listener, by focusing through a particular frame, creates a context, or more precisely a contextual configuration of reception that provides a unique interpretative lens. The argument is that through listening, sound images produce different contexts depending on the particular way in which an individual listens. Social actors, thus, listen both pragmatically and intentionally. Hearers listen with a purpose, they look for (directed) meanings, and the outcome of their interpretation transforms various social dimensions./nTo exemplify how listening genres are produced and reproduced, this dissertation explores psychoanalytic listening as a genre in Buenos Aires, Argentina. Based on ethnographic work conducted in a variety of social settings, it explains how and why psychoanalysis occupies an important position in Argentina, one that symbolically structures other fields and many discursive arenas. We can find psychoanalysis outside the clinical setting, in newspapers, TV and radio shows, sports, and casual conversations, among other forms. By contributing to the ongoing discussion about why psychoanalysis is so prevalent in Argentina, this dissertation proposes the idea that psychoanalytic listening as a genre has become a social fact. It has gone beyond the clinical setting, creating links to citizenship, civil society, and the state, as well as with national culture in general. This dissertation demonstrates that personal identities, conceptions of citizenship, and constructions of the political in Buenos Aires, are rooted less in the performativity associated with speaking than in particularly forms of listening based on psychoanalysis. This listening is social, produced by a collectivity of individuals, and performed in all sorts of interactions surpassing class, age, and gender classifications.

Advisor: Briggs, Charles L
Good as Gold: The Marin-Sonoma Artisan Cheese Cluster

The overall economic performance of rural communities across the United States is challenged by shifting patterns of production, consumption, and global competition. Recent research has identified clusters - geographically proximate group of interconnected companies and associated institutions in a particular field, linked by commonalities and complementaries - as a prominent feature of successful rural economies. This dissertation explores the emergence of an artisan cheese cluster from historic dairy roots in Marin and Sonoma Counties in the North Coast region of California. The artisan and farmstead cheese producers there provide an instructive case study to assess the social, cultural, and economic impacts of the artisan cheese clusters generally. Michael Porter's (1990) "Diamond Model of Competitive Advantage" is utilized as an analytic framework to consider factors that provided competitive advantages during various historical periods before and during the emergence of the cluster, as well as to assess its current business environment.The viability of encouraging such artisan cheese clusters in other rural regions as an economic development strategy is evaluated based on these findings.

Advisor: Gilless, J K
Spatiotemporal exposure modeling and epidemiological analyses of the 2008 northern California wildfires

Projections under likely climate change scenarios demonstrate that the area burned from wildfires and the length of the wildfire season will continue to increase in the western US and in many other parts of the world. Wildfires emit many air pollutants of concern for public health. In this dissertation, I systematically reviewed the scientific literature on which health effects were associated with wildfire smoke exposure, piloted the most sophisticated exposure model to date to estimate PM2.5 exposures during the 2008 northern California wildfires, and assessed the effect of these exposures on respiratory and cardiovascular hospitalizations. The scientific literature documents clear evidence of respiratory health effects from wildfire smoke, most specifically for exacerbations of asthma and chronic obstructive pulmonary disease (COPD). Only inconsistent evidence exists for cardiovascular effects. Several high-quality studies demonstrate significant associations between wildfire smoke exposure and all-cause mortality, but not for specific causes of mortality. To study the 2008 northern California wildfires, I created a spatiotemporal exposure model that used the latest in machine learning methods to combine information from satellites, output from a chemical transport model, and meteorological and other spatial and temporal variables to create an optimal exposure model. The best model had an out-of-sample cross-validated R2 of 0.80. Using this model, I could estimate exposures at any location on any day within the study area. To analyze the health effects of the 2008 northern California wildfires, I estimated exposure at all ZIP codes within the study region and found evidence of increased asthma, COPD, pneumonia, and all-cause respiratory hospitalizations associated with PM2.5 during the fire period. Only for asthma hospitalizations was this effect significantly different from effects for PM2.5 outside of the fire period. I also found some evidence of increased rates of hospitalization for asthma associated with PM2.5 during the wildfire period among women compared to men, and among adults compared to children and the elderly. I also found higher rates of hospitalizations for COPD and pneumonia in ZIP codes with lower levels of owner-occupied housing, but I did not find consistent differences along gradients of other measures of socio-economic status by ZIP code. My research piloted the first spatiotemporal exposure model to use machine learning methods to improve estimation of PM2.5 exposures during wildfires using a combination of satellite data, chemical transport model output, meteorological parameters, and land use information. The results from my epidemiological analysis confirm previous evidence of exacerbation of respiratory health effects from exposure to wildfire PM2.5 and highlight evidence of groups that are more vulnerable to this exposure.

Advisor: Jerrett, Michael LB
Mechanisms of Circuit Plasticity in the Developing Retina

Across the developing nervous system, immature networks generate spontaneous activity that is highly correlated amongst neighboring cells, which is required for the correct establishment of adult neural circuits. Remarkably, correlated activity persists following disruption of the underlying circuits that mediate it, indicating that plasticity mechanisms exist to ensure correlated activity is maintained. Here, we examine this phenomenon in the developing mouse retina, where correlated activity is mediated by cholinergic transmission and propagates across the retina as a wave. The absence of cholinergic signaling leads to the generation of "recovered" waves that propagate through a distinct, gap junction mediated circuit. Our findings show that stimulation of melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) facilitates recovery of correlated activity in the absence of cholinergic waves, which results in the emergence of a light-sensitive network. We tested whether pharmacological blockade of cholinergic waves altered retinal light-response properties. We observed an increase in the duration of light-evoked activity and number of light-responsive cells, which arose from signaling via gap junctions. These observations suggest that electrical coupling of ipRGCs increases in the absence of cholinergic input, allowing melanopsin-driven signals to propagate to other neurons. Furthermore, we show that light-sensitive waves are strongly modulated by dopamine signaling--a potent neuromodulator of gap junction coupling. We determine that this light-sensitive wave circuit is present but latent in wild type retina, where it is usually suppressed by a combination of cholinergic and dopaminergic signaling. Our observations indicate that dopamine signaling acts as a switch for network reconfiguration, where high dopamine silences the light-sensitive, gap junction coupled network under cholinergic waves and reduced dopamine activates it in the absence of cholinergic waves. We conclude that the wiring diagram of the developing retina includes several overconnected circuits, in which some circuits are closed and others activated depending on the internal state of the system.

Advisor: Feller, Marla B
Modeling and Applications of Highly-Scaled Gravure Printing

Pattern printing techniques have advanced rapidly in the last decade, driven by their potential applications in printed electronics. Several printing techniques have realized printed features ≤10 µm, but unfortunately they suffer from disadvantages that prevent their deployment in real applications; in particular, process throughput is a significant concern. Direct gravure printing delivers high throughput and has a proven history of being manufacturing worthy. Unfortunately, it suffers from scalability challenges due to limitations in roll manufacturing and lack of understanding of the relevant printing mechanisms. Gravure printing relies on individual processes namely filling, wiping, transferring and spreading to achieve high quality printing. As gravure printed features are scaled, the associated complexities are increased, and a detailed study of the various processes involved is needed./nIn this thesis, the various gravure-related fluidic mechanisms are studied using a novel inverse direct gravure printer. The underlying mechanisms of gravure printing are presented. A simple model of gravure printing is proposed. This model demonstrates that individual fluidic processes can be studied separately and a comprehensive understanding of the wiping process in gravure printing is analyzed carefully due to the importance of this process in producing high-fidelity patterns. We report two critical wiping mechanisms that generate drag-out and lubrication residues, which are fundamental scaling limitations for highly-scaled gravure printing. Third, the filling process is investigated, leaded to explanations of air entrapment in gravure cells. In addition, we provide designs and operation conditions for the ultimate reduction of the residues, leading significant scaling of printed features. Printed lines as small as 2 µm are realized at printing speeds as high as ~1 m/s, attesting to the potential of highly-scaled gravure printing./nIn addition to comprehensive printing mechanism studies, we demonstrate a fabrication process for a high-resolution roll based on advanced microfabrication techniques. The fabrication process incorporates the design guidelines developed previously to deliver the optimized cell geometry and pattern arrangement. Furthermore, electrically functional high-resolution lines are integrated in a fabrication process for fully printed high performance thin film transistors (TFTs). Highly-scaled TFTs demonstrated with channel lengths as small as 3 µm, leading to devices with transition frequency above 1 MHz; this represents a significant advancement over the state of the art.

Advisor: Subramanian, Vivek
The dynamic role of magnetic fields in galaxy evolution

Magnetic fields are present in a variety of astrophysical environments, where they can affect the motions and structure of matter. Observations of magnetic fields in the Milky Way show that magnetic fields are an important force acting on gas in the interstellar medium. Observing magnetic fields outside of the Milky Way is challenging, and the most reliable observations of extragalactic magnetic fields are in galaxies similar to the Milky Way./nThis dissertation focuses on results from observations of magnetic fields in galaxies at a very different stage of their evolution than the Milky Way. There are two main types of galaxies described here: starburst galaxies and early-type galaxies. Starburst galaxies are galaxies that are very rapidly forming stars as a result of a merger, and represent a short lived, but dramatic, phase during galaxy evolution. Early-type galaxies have limited star formation, and typically have little remaining gas. The three main approaches I use to study extragalactic magnetic fields are: (i) directly measuring magnetic fields via Zeeman splitting, targeting starburst galaxies that host such strong OH maser lines that they are called OH megamasers (OHMs); (ii) exploring the excitation of OH in both starburst galaxies and early-type galaxies, in order to understand how and where OHMs are produced; and (iii) assessing the quality of an alternative method of measuring magnetic fields in galaxies based on measuring synchrotron fluxes, looking in starburst galaxies and one early-type galaxy./nUsing both single dish and interferometric observations of Zeeman splitting in OHMs, I find that magnetic fields are dynamically important within starburst galaxies, both on scales relevant to star formation (roughly a parsec), and on larger scales with the interstellar medium of starburst galaxies. I discuss observations of OH lines in starburst galaxies and in early-type galaxies, and conclude that they support models in which OHMs are excited radiatively through far-infrared emission. I present evidence that estimates of magnetic fields from applying the minimum energy argument to observations of synchrotron fluxes are wrong in two very different environments: the interstellar medium of starburst galaxies and a radio jet in an early-type galaxy.

Advisor: Heils, Carl