VictorJuiz/thesis huggingface dataset:
Genetic and Biochemical Studies of Photosystem II Assembly

Photosystem II (PSII) is the protein-pigment complex in oxygenic photosynthesis that uses light energy to catalyze the oxidation of water. How the subunits and cofactors that make up this enzyme are properly assembled into a functional photosystem remains unknown. I sought to find and characterize previously unknown proteins involved in this process by screening a population of insertional mutants of the unicellular green alga Chlamydomonas reinhardtii. One mutant, which I named the second photosystem assembly component (2pac), contained a deletion of a gene encoding a membrane-bound rubredoxin (RBD1) and, as a result, displayed a PSII-specific phenotype. I then characterized plant and cyanobacterial mutants lacking the RBD1 ortholog and found that they too displayed a PSII-specific phenotype./nTo uncover the precise role of this rubredoxin in the assembly of PSII, I further characterized the 2pac mutant and found that PSII subunits were translated in the mutant but unstable. I found that the low level of PSII subunits that did accumulate in 2pac were assembled into PSII monomers but not dimers. By analyzing 2D-PAGE gels, I observed a comigration of RBD1 and the PSII subunit CP43, supporting a possible interaction between the two proteins. We attempted to further characterize interacting partners of RBD1 by coexpression of RBD1 and genes encoding PSII subunits in yeast and found an interaction between RBD1 and the PsbI protein. Taken together, the data are consistent with a model in which RBD1 aids in the fusion of a CP43-containing precomplex with the nascent PSII reaction center during formation of the PSII monomer./nBecause rubredoxins are known to be redox-active proteins in non-photosynthetic organisms, we hypothesized that RBD1 might be required for a redox modification of PSII during its biogenesis. We tested this by combining the 2pac mutation with a mutation in the gene encoding the chloroplast protease FtsH1 (which is known to degrade damaged or misassembled PSII) in order to accumulate more PSII in the 2pac mutant background for study. We found that PSII did indeed accumulate to a higher level in this double mutant strain (2pac ftsh1-1) than in the 2pac mutant. We also found the PSII in this strain to be much more light-sensitive than a wild-type PSII, supporting our hypothesis. We were unable to resolve any differences in cofactor or subunit composition, but we were able to rule out several candidate subunits and a cofactor./nIn order to find other genes like RBD1 that are responsible for PSII function, I devised a phylogenomic approach to search the publicly available genomes of oxygenic photoautotrophs for genes that had a specific phylogenetic signature. I hypothesized that genes required for PSII function would be present in the genomes of all oxygenic photoautotrophs except for the cyanobacterium UCYN-A, which lacks genes for PSII due to its symbiotic relationship with a diatom. The preliminary results indicated that some genes found through this approach might indeed be associated with PSII.

Advisor: Niyogi, Krishna
Enacting Sincerity: Nerval and the Cultural Politics of Imagination

This dissertation proposes a new reading of the work of Gérard de Nerval (1808-1855), placing him alongside Walter Benjamin’s Baudelaire as an insightful critic of modern life. During the 1840s and 1850s, the literary field in France was increasingly shaped by bourgeois values like sincerity, originality, and authenticity, and by the individualism that they underpinned, restricting authorized forms of writing and of subjectivity. I argue that Nerval’s writing constitutes an astute opposition to this transformation of literary subjectivity and the limitations it placed on imaginative experience and practice. Rather than merely reflecting the author’s own psychological crises (as is usually claimed), Nerval’s writings strategically reinvent the literary text as a site of new forms of collective imaginative practice./nBy considering Nerval’s work as a journalist, playwright, critic, and travel writer, as well as a poet, I draw out Nerval’s engagements with specific institutions and discourses, from censorship and intellectual property law to the national philosophy curriculum and literary criticism journals. From these local engagements emerges a shrewd critical voice that speaks directly and explicitly to the influence of bourgeois culture on the literary field. I argue that, though he is traditionally read as a figure of Romantic isolation and eccentricity, Nerval should rather be understood in relation to figures like George Sand and Maurice Barrès, writers who advocated a renewal of communal ties (albeit from very different political perspectives). Unlike these contemporaries, however, Nerval approaches community as a formal challenge, as well as a theme. He explodes the framework of the individual writing subject through, for example, a pervasive intertertextuality that constantly relates his texts to other writing and reading experiences. My project thus rejoins the critical tradition that emphasizes the failure to coincide with oneself as the essential feature of Nerval’s writing practice. However, I give this “failure” a productive and strategic value rather than the tragic valence attributed to it by psychoanalytic readings, be they psycho-biographical or post-structuralist. The mobility and porousness of the Nervalian writing subject are a formal innovation that generates a literature of community rather than self-expression.

Advisor: Guerlac, Suzanne
Looking through dark lenses: How those with a history of nonsuicidal self-injury experience positive emotional situations

Theories suggest that nonsuicidal self-injury (NSSI) is strongly related to heightened negative emotion. However, it is unclear when and why those who engage in NSSI experience heightened negative emotion. In a series of studies, I examined whether individuals with a history of NSSI (versus controls) experience greater negative emotion in response to positive (but not negative) contexts. Results showed that in community, clinical, and college samples, after controlling for depression and anxiety, those with a history of NSSI (versus controls) do not experience heightened negative emotions in negative situations (Studies 1, 2, and 4). However, they consistently experience heightened negative emotions in positive situations (Studies 1-5) even when controlling for depression and anxiety symptoms (Studies 2-4). Heightened negative emotion persists across both high and low-arousal positive situations (Studies 3-4). Furthermore, the association between NSSI and negative emotion in positive situations is mediated by negative self-beliefs (Studies 5 and 6). However, experimentally manipulating negative self-beliefs was not shown to reduce negative self-beliefs or negative emotion in positive situations (Study 6). These findings suggest that NSSI is associated with heightened negative emotion in positive, but not negative, situations and that heightened negative self-beliefs contribute to these negative emotions. However, interventions that directly target negative self-beliefs may not be the most effective way to reduce negative emotions in NSSI.

Advisor: Mauss, Iris
Overlapping and Disconnected Social Spheres: A Multi-contextual Model of the Link Between School Choice and Neighborhood Effects on Adolescents

Because of the rise of public school choice programs, children who share a neighborhood are increasingly going to different schools. I explore the effects of overlapping and disconnected neighborhood and school spheres via two linked questions; first, whether and how the conjuncture/disjuncture of neighborhoods and schools affects the types of friendship opportunities available to students both at school and within their residential areas; and second, whether and how the conjuncture/disjuncture of neighborhoods and schools mediate children’s exposure to neighborhood disadvantages like violence. What I find is that school choice amplifies the disadvantages that children encounter in their neighborhoods by fragmenting local adolescent community networks and exacerbating the violent conditions that children face at their neighborhood schools./nMy data consist of 74 in-depth interviews with students from five public high schools in Philadelphia. Of these students, 45 attend a public magnet high school; the remaining 29 student interviewees live in the same neighborhoods as my magnet school sample but attend neighborhood schools in their local areas./nMy findings suggest that school choice policies concentrate the advantages of children who are able to exercise choice while leaving behind a substantially larger population of children who are consigned to local schools that contend with a disproportionate load of student misconduct and school violence. Instead of closing educational gaps for all, these reforms further stratify poor neighborhoods by creating a new class of even more disadvantaged children who are becoming increasingly disconnected from positive peer role models both within their neighborhoods and at school.

Advisor: Fischer, Claude S
Randomized Pivoting and Spectrum-Revealing Bounds in Numerical Linear Algebra

In the first part of this dissertation, we explore a novel randomized pivoting strategy to efficiently improve the reliability and quality of the LU factorization. Gaussian elimination with partial pivoting (GEPP) has long been among the most widely used methods for computing the LU factorization of a given matrix. However, this method is also known to fail for matrices that induce large element growth during the factorization process. We propose a new scheme, Gaussian elimination with randomized complete pivoting (GERCP) for the efficient and reliable LU factorization of a given matrix. GERCP satisfies GECP (Gaussian elimination with complete pivoting) style element growth bounds with high probability, yet costs only marginally more than GEPP in terms of algorithmic complexity and run-time. Our numerical experimental results strongly suggest that GERCP is as reliable as GECP and as efficient as GEPP for computing the LU factorization. In the second part, this dissertation provides tighter and simplified analyses of various popular low-rank matrix approximation algorithms included randomized subspace iteration and column/row selection based methods. We derive new bounds and unify them with other existing bounds under the title Spectrum-Revealing Bounds. These bounds demonstrate how certain structure in the decay of the spectrum of a matrix help to ``reveal'' an increasingly accurate estimate to the low-rank matrix approximation. We provide real world applications that demonstrate the qualitative value of our bounds for anyone using low-rank matrix approximations. In the case of randomized subspace iteration, we also dramatically improve and simplify the probabilistic analysis from previous works using intuitive and concise techniques. Lastly, we apply the idea of efficient low-rank matrix approximation in the presence of spectral decay to help speed up sparse principle components analysis (SPCA). We also develop novel lower bounds on the variance captured by each sparse principle component obtained after deflation.

Advisor: Gu, Ming
Things Fall Apart: Faith, Prosperity and Division within the African American Community

During the past decades, tensions have emerged between a relatively new, highly popular theology focused on material prosperity and individual accountability, known as the prosperity gospel, versus a traditional African American doctrine that emphasizes humanitarianism and racial consciousness. Despite the diversity of interests and experiences within the African American community, none of these divisions have manifested themselves systematically in the political arena. I argue that considering the importance of the church in shaping African American political views, values, and norms, a significant shift in church doctrine could dramatically alter not only congregants’ own political values, but also could lead to a significant change in how the church interacts with its surrounding community. The prosperity gospel may be that significant shift. Based on interviews with community and church leaders, participant observation, sermon content analysis, and archival research, I present evidence to suggest that not only do churches that espouse the prosperity gospel reinforce humanitarianism and racial consciousness, in certain circumstances, they do so more aggressively than their traditional counterparts. This dissertation supports numerous scholars’ claims that the prosperity gospel emphasizes individualism and individual versus collective level solutions to societal problems; however, this bias toward individualism and self-accountability is found in all of the younger ministers who participated in the study, even when categorized as a traditional church. I argue that this is evidence of the global trend of the infiltration of neo-liberal ideas into religious institutions. The prosperity gospel provides an effective conduit for neo-liberal ideals, but no longer monopolizes the dispersion of these values.

Advisor: Stoker, Laura
Scattering Resonances for Convex Obstacles

In the setting of obstacle scattering in Euclidean spaces, the poles of meromorphic continuation of the resolvent of the Laplacian on the exterior region are called the resonances or scattering poles. Each resonance corresponds to a resonant wave. The real part of a resonance corresponds to the frequency of the wave, while the imaginary part corresponds to the decay rate of the wave. Consequently understanding the distribution of the resonances is important in understanding the long time behavior of the solution to wave equations in the exterior domain./nWe study the distribution of resonances in the case of a strictly convex obstacle with smooth boundary. In particular, under general boundary conditions, we prove the existence of the cubic resonance free regions near the real axis. Moreover, if the obstacle is close to a sphere, in the sense that it satisfies certain pinched curvature conditions, we prove that the resonances close to the real axis are separated into cubic bands and in each band, the counting function of resonances satisfies a Weyl law. We also generalize these results to totally convex obstacles in more general asymptotic Euclidean metrics.

Advisor: Zworski, Maciej R
Mechanism of Protein Unfolding and Polypeptide Translocation by the AAA+ Protease ClpXP

ATP-dependent proteases exist in all cells and are crucial regulators of the pro-/nteome. These biological nanomachines contain a homohexameric molecular motor/nwhich generates mechanical force to unfold proteins and translocate unstructured/npolypeptides into a degradation chamber for proteolysis. Using E. coli ClpXP as/na model system for investigating the function of ATP-dependent proteases, I used/nsingle-molecule optical tweezers to explore how individual subunits within the hex-/nameric motor convert the chemical energy from ATP hydrolysis into the mechanical/nwork required to perform protein unfolding and polypeptide translocation./nThese studies revealed key aspects of motor function that highlight how ATP-/ndependent proteases are tailored to serve their specific cellular tasks. My analyses/nindicated that ClpXP translocates in bursts resulting from highly coordinated con-/nformational changes in two to four ATPase subunits and that these bursts of translo-/ncation couple to the phosphate release step of the ATP hydrolysis cycle. I found/nthat firing of four ATPase subunits is required to successfully unfold GFP, but that/npolypeptide translocation robustly occurs even when only two ATPase subunits fire./nBecause this work pushed the envelope of single-molecule data analysis techniques,/nI developed new algorithms to detect steps in passive-mode optical tweezers data,/nwhere the noise statistics vary in time./nThe results discussed in this dissertation improve our understanding of how ClpXP/nmechanically operates. Strong structural similarities to other ATP-dependent pro-/nteases, as well as other ring translocases, suggest that the operating principles I have/ndiscerned and describe here may generalize to other biological molecular motors.

Advisor: Martin, Andreas
Inference of population history and mutation biology from human genetic variation

Human genetic diversity bears many imprints of our species’ migration out of Africa. When our ancestral population expanded across the globe and settled into nearly every habitable environment, genetic diversity was reduced, distributed and redistributed by an intricate series of population bottlenecks and migrations. The coalescent process is a mathematical model that describes the probability distribution of modern DNA sequences that could have evolved from a common ancestor following a specific demographic scenario; in principle, this gives us the means to infer the history that is most consistent with large datasets of genomes sequenced from living people. In practice, however, the coalescent is such a complicated model that such calculations are intractable to perform exactly. Here, I introduce several new techniques for performing approximate demographic inference under the coalescent; these operate by condensing samples of genomes into more compact summary statistics and then mathematically approximating the probability distributions that these statistics should follow. I then use these techniques to infer joint demographic histories from European and African genomes, describing a complex out-of-Africa migration that involved multiple pop- ulation size changes as well as a long period of migration between the diverging continental groups. The good match between predicted and observed genomic samples indicates that the coalescent is a useful framework for describing the evolution of humans; however, I also note systematic discrepancies between the model and the data. In the last two chapters of this thesis, I go on to show that some deviations of human data from coalescent predictions stem from the coalescent’s oversimplication of the way mutations are generated. One stan- dard assumption is that mutations occur independently; in contrast, at least 2% of human occur in linked clusters and are likely to have been generated by multinucleotide mutation events (MNMs). Examining the derived and ancestral alleles of these MNMs, I show that they are enriched for transversions and that many bear the specific signature of error-prone Polymerase ζ. A second assumption I show to be violated is that the mutation rate has not changed over time and is constant across populations. I show this indirectly by demon- strating that C→T transitions, particularly in the context TCC→TTC, are more frequent in Europeans than in other populations. Although it is not clear whether this mutation rate change was functionally significant or driven by selection, it demonstrates that the process of genome evolution has not stayed constant during recent human history, but has been regionally differentiated by the forces that shape our primary genome sequences.

Advisor: Nielsen, Rasmus
Evans, Steven
A Phenomenological Study of High-Field Optically Pumped 13C NMR in Diamond

Nuclear magnetic resonance (NMR) is a powerful spectroscopic technique capable of probing the local electronic environment in a wide array of materials. The sensitivity of an NMR experiment is proportional to a net nuclear spin polarization that is often generated by placing the sample of interest in a static external magnetic field and allowing the spin state populations to come to thermal equilibrium. Unfortunately these thermal polarizations are exceedingly small. Even with a 23.5 Tesla magnet, the strongest currently available, the room temperature 1H polarization is only 0.0081%. Significant sensitivity enhancements can be achieved by hyperpolarizing the nuclear spin system. Transferring polarization from electrons to nuclei, also known as dynamic nuclear polarization (DNP), is one method by which this hyperpolarization is achieved. Optically pumped NMR (OPNMR) is a form of DNP, which uses laser light to athermally polarize a reservoir of electron spins which in turn athermally polarize coupled nuclei./nFor much of its history solid state OPNMR involved transferring polarization from photo-excited conduction electrons to hyperfine coupled nuclei in zincblende semiconductors at temperatures ≤ ~80 K. Within the last decade it was found that OPNMR of 15N, 14N, and 13C in single crystal diamond is possible via optically polarized negatively charged nitrogen vacancy (NV-) defects. The best characterized form of OPNMR in diamond is a hyperfine-mediated phenomenon that takes advantage of the NV- excited state level anti-crossing that occurs when the external field is set to ~50 mT. A high-field form of 13C optical pumping has been observed at 7.05 and 9.4 T, well beyond the level anti-crossing. Polarization rates, lifetimes, and magnitudes are influenced by the concentrations of NV- and P1 defects in the diamond. Two of the samples characterized in this study have defect concentrations that allow for the generation of room temperature 13C polarizations up to 200 times that of thermal equilibrium. Both positive and negative polarizations are observed. The sign and magnitude of the polarization exhibit an extraordinary sensitivity to the orientation of the crystal with respect to the polarization of the electric field vector of the optical illumination incident on the sample. For example, the sign of the polarization can flip with as little as a 0.5° change in the orientation of the crystal./nThe mechanism responsible for this high-field pumping process remains unknown. Progress in developing a theoretical model is hindered by the simultaneous presence of four defect orientations for every orientation of the crystal.

Advisor: Reimer, Jeffrey A
Pines, Alexander