VictorJuiz/thesis huggingface dataset:
High-throughput analysis and protein engineering using microcapillary arrays [electronic resource]

Over the past decade, high-throughput technologies have allowed researchers to gain unprecedented insights into intrinsically complex and interconnected biological systems. As examples, whole-genome sequencing has enabled the identification of crucial genes and mutations underlying disease pathophysiology, DNA microarrays have been used to elucidate transcription patterns involved in healthy and diseased states, and large-scale proteomics methods have helped map the connectivity of cell signaling networks that orchestrate responses to growth factors and other external stimuli. In contrast, analogously powerful approaches for rapidly and deeply interrogating the sequence-structure-activity relationship of proteins, with functional read-outs that span a range of biophysical and biochemical measurements, have lagged because of technical challenges. In this dissertation, I describe the development of a new technology platform, termed µSCALE (microcapillary single-cell analysis and laser extraction), that aims to improve high-throughput protein characterization and engineering. The µSCALE platform is built around a microcapillary array, automated fluorescence imaging, and a novel laser-based sample recovery method. The platform spatially segregates millions of cells or their protein products in a microcapillary array and interrogates the dense array within minutes. µSCALE also enables recovery of target sample from the microcapillary array using a precise laser-based extraction technique. To showcase capabilities and breadth of µSCALE, I applied it to three distinct protein-analysis and engineering applications, using libraries expressed in yeast or bacteria. In each case, I demonstrated feasibility and then engineered a novel protein variant, identifying new binders against a clinical target, creating a novel fluorescent protein biosensor, or reducing inhibition of an enzyme. Compared to conventional screening techniques, such as FACS and plate-based screens, the µSCALE affords several distinctions advantages, including a five orders of magnitude improvement in throughput, direct cell imaging, and high sorting purity and yield. Collectively, these benefits present µSCALE as an exciting, novel technology to the field of protein engineering and beyond.

Keywords: Bioengineering.
Advisor: Cochran Jennifer R. primary advisor. Thesis advisor
Baer Thomas
Endy Andrew D. advisor. Thesis advisor
Holography of de sitter space and disordered systems [electronic resource]

This dissertation is devoted to the study of models that capture the intricate dynamics of two different physical setups: exponentially expanding universes and disordered systems. We explore late time divergences in the perturbative corrections of wavefunctions of interacting light fields on a fixed de Sitter background. The divergences are holographically interpreted as shifts in the conformal weights of dual CFT operators. We then compute functional determinants in a Euclidean CFT for various non-perturbative deformations. According to the dS/CFT correspondence, these functional determinants calculate the late time Hartle-Hawking wavefunctional of asymptotically de Sitter space in higher spin gravity as a function of the profile of the fields in the bulk. Numerical experiments suggest that upon fixing the average of the bulk scalar profile, the wavefunction becomes normalizable in all the other (infinite) directions of the deformations we study. For disordered systems, we investigate the extent to which quiver quantum mechanics models encode the complex dynamics of multicentered black holes in string theory. In a certain limit of the quiver system we display the emergence of a conformal symmetry, which mimics the emergence of conformal symmetry in the near-horizon geometries of extremal black holes. Finally, we take a Newtonian multiparticle limit of the quiver system away from the conformal regime. We study the dynamics of the system numerically to look for signs of ergodicity breaking, cages, and transitions to chaos.

Keywords: Physics.
Advisor: Shenker Stephen Hart
Hartnoll Sean
Silverstein Eva
Host-centric proteomics of stool [electronic resource] : monitoring global host responses to the gut microbiota

The diverse community of microbes that inhabits the human bowel, known as the gut microbiota, is vitally important to human health. While the identity and abundance of the microbes has been widely studied, little is known about the ways in which they interact with their host. The breakdown of the host-microbiota symbiosis has been linked to numerous diseases, including inflammatory bowel diseases, autoimmune diseases and even autism. Host-expressed proteins are essential for maintaining this mutualistic relationship and serve as reporters on the status of host-microbiota interactions. Previously, a global means for non-invasively monitoring the expression of proteins by the host in the gastrointestinal tract has not been described. In this thesis, I elucidate the need for an unbiased method to monitor host responses to the microbiota and describe a mass spectrometry-based method we developed, called host-centric proteomics of stool, which can simultaneously measure hundreds of host secreted proteins. I then illustrate how this method can be used to study host protein secretions in various regions of the gastrointestinal tract and the host responses to antibiotic-associated pathogens.

Keywords: Chemical and Systems Biology.
Advisor: Elias Joshua
Khosla Chaitan
Relman David A. advisor. Thesis advisor
Sonnenburg Justin
Wandless Thomas advisor. Thesis advisor
Wysocka Joanna
How does politics affect central banking? [electronic resource] : evidence from the Federal Reserve

My dissertation investigates the ways in which political dynamics influence decision-making at central banks. I address this question by looking at the different mechanisms through which political influence occurs. I devote a chapter to examining this topic in each of the following contexts: the evolution of the structure of the Federal Reserve, the preferences of monetary policymakers around elections, and the Federal Reserve's lending during the 2008 financial crisis. Through this series of chapters, I find that politicians designed the American central bank in such a way that political considerations are able to consistently affect monetary policymakers. However, stemming from the partial compromises inherent in its design, this influence is constrained in such a way to ensure its stability, as too much would lead to a new equilibrium in which the central bank is more apolitical.

Keywords: Political Science.
Advisor: Haber Stephen H.
Hainmueller Jens advisor. Thesis advisor
Weingast Barry R. advisor. Thesis advisor
How Milton's Rhythms Work

This thesis, which takes as its subject John Milton's epic poem Paradise Lost, is a marriage of prosody and reader-response theory: against critics who argue that Milton's rhythms demonstrate his political beliefs, this thesis argues that Milton's rhythms create certain tasks that train the reader in the qualities he needs to become the ideal republican and the ideal Christian.

Keywords: Milton
Paradise Lost
prosody
rhythm
reader-response theory
Thesis
Advisor: Hoxby Blair
The human dimensions of wave resource management in California [electronic resource]

The California coast is a complex coupled social-ecological system: managing its many people, industries, and natural resources is a daunting challenge. Breaking waves are an important resource on California's coast, where they support the recreation of 1.1 million surfers, inject millions of dollars into local economies, and define the culture and character of many individuals and communities. Sustainably managing wave resources for the benefit of both healthy coastal ecosystems and present and future generations of resource users requires understanding the human dimensions of wave resources within this social-ecological context. My research advances this understanding by investigating new sources of management-relevant knowledge of wave resources, projecting the future impacts of human activities on these resources, and exploring the effects of such impacts on the users themselves. Based on a survey of more than 1,000 California surfers, I find that these resource users develop valuable local ecological knowledge--wave knowledge--of the coastal system and, as a result, could contribute meaningfully to coastal research and management efforts. By combining this knowledge with oceanographic principles, I project that one-third of wave resources ("surf-spots") evaluated in California through the survey are vulnerable and could disappear as a result of sea level rise by 2100. I also find that surfers nurture deep, personal attachments to specific surf-spots and thus, as important stakeholders and potential stewards, are likewise susceptible to changing conditions of wave resources. Review of California's coastal governance setting reveals that while formal institutions for managing coastal resources exist and have significant implications for wave resource quality, these institutions typically do not directly address wave resource quality. I conclude that waves are vital and vulnerable natural resources in California. This research enhances our understanding of California's coastal social-ecological system and lays the groundwork for further study of the human dimensions of wave resources.

Advisor: Ardoin Nicole M. (Nicole Michele) primary advisor. Thesis advisor
Caldwell Margaret R.
Crowder Larry B.
Thomas Leif N. advisor. Thesis advisor
Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes as an In Vitro Model of Doxorubicin-Induced Cardiotoxicity

Doxorubicin (DOX; trade name Adriamycin) is an anthracycline antibiotic and widely used chemotherapeutic agent. Despite its powerful and wide-spectrum anticancer effects, its clinical utility is limited by its cardiotoxicity, which increases the risk of dilated cardiomyopathy and subsequent heart failure among DOX-treated cancer patients and survivors. Recent animal-based studies have suggested that DOX-induced cardiotoxicity (DIC) is due, at least in part, to iron accumulation and resulting oxidative stress, and that this is mediated by the downregulation of ABCB8, which encodes a mitochondrial iron transporter protein called ATP-binding cassette subfamily B member 8 (ABCB8). Circumventing the challenges of validating these findings in primary human heart tissue, this study applies human iPSC-derived cardiomyocytes (hiPSC-CMs) as a surrogate human platform to probe the pathogenic processes of DIC. I hypothesized that DOX causes dose-dependent ABCB8 downregulation and mitochondrial iron accumulation in hiPSC-CMs, consistent with studies performed on animal-based in vitro models. Patient-specific hiPSC-CMs, generated from DOX-treated breast cancer patients who experienced cardiotoxicity (DOX TOX) and those who did not (DOX CONTROL), were utilized to investigate whether patient-specific differences in the pattern and severity of ABCB8 expression and mitochondrial accumulation of iron could predict susceptibility to DIC. I found that, while high concentrations of DOX caused significant reduction of ABCB8 in hiPSC-CMs, modest and non-cytotoxic concentrations did not. Further, while no robust difference was observed between the baseline expression of ABCB8 in DOX CONTROL and DOX TOX cells, these two cancer patient-derived hiPSC-CM populations both expressed significantly lower levels of ABCB8 than their HEALTHY CONTROL counterparts. Finally, preliminary data suggested that DOX does not induce consistent dose-dependent trends in mitochondrial iron accumulation in hiPSC-CMs. As the first humanized model of DIC in the specific context of iron metabolism, this work represents a key step toward improving the clinical utility of DOX, by elucidating the molecular basis of both its cardiotoxic effects and patient-specific susceptibility to this condition.

Keywords:  Department of Biology
Biology
induced pluripotent stem cell
cardiomyocyte
cardiotoxicity
doxorubicin
iron
Thesis
Advisor: Wu Sean M.
Dixon Scott J.
Humor in fascist Italy [electronic resource]

In this dissertation I trace a cultural history of humor in fascist Italy by looking at novels, vignettes and articles through the lens of the humorous philosophies of Giacomo Leopardi, Luigi Pirandello, and Aldo Palazzeschi, and the political and cultural context of fascism. The Introduction lays the philosophical foundations of humor in Italian literature and finds Leopardian, Pirandellian and Palazzezchian influences in the works of Massimo Bontempelli and Achille Campanile. Chapter One finds similar echos of literary humor in editions of Il corriere della sera and Il popolo d'Italia printed around the March on Rome and during Mussolini's first months in power. Chapter Two delves into the more overt convergence of politics and humor in the humorous and politically engaged newspapers Il becco giallo and La libertà. It follows the two starkly antifascist publications through the assassination of Matteotti, Mussolini's famous January 3, 1925 speech to parliament, and comments upon the goal of creating political change through humor. Chapter Three looks at the fascinating and extremely perplexing strapaesista magazine Il selvaggio, whose irreverence and critique of fascism leaves the reader wondering how it thwarted regime-sanctioned censorship. Chapter Four returns to Il corriere della sera and Il popolo d'Italia to find the transformation of humor into traditional propaganda, and at times, irrelevant nonsense. The Conclusion looks at the humorous magazines Il bertoldo and the Marc'Aurelio and their biting critique of the failure of humor to effectively fight fascism, ultimately finding that humor unmasks, subverts and criticizes fascism, but remains a passive observer of reality.

Keywords: French and Italian.
Advisor: Wittman Laura primary advisor. Thesis advisor
Fuller Mia
Springer Carolyn advisor. Thesis advisor
Hybrid rocket combustion and applications to space exploration missions [electronic resource]

A major focus of the NASA Technology Roadmaps (2015) is the development of new propulsion systems for in-space and launch applications. Hybrid propulsion systems, which have fuel and oxidizer stored in different phases, present a favorable alternative to conventional propulsion systems for many exploration missions. Hybrid propulsion systems enjoy a high specific impulse, are throttle-able, able to be stopped and restarted, and benefit from flexibility in their packaging configuration. However, the adoption of hybrid rocket systems has historically been inhibited by performance issues stemming from the use of slow-burning fuels. Many of these performance issues can be resolved through the use of paraffin-based fuels. The overarching goal of this thesis work is to improve the understanding of paraffin-based hybrid rockets in order to facilitate their adoption as a viable in-space propulsion system over existing liquid and solid chemical propulsion systems. This goal has been divided into two focus areas. 1. Investigate the feasibility of using hybrid rocket motors for exploration missions in order to determine the class of mission(s) for which they are best suited. A general approach for first pass hybrid propulsion system design is presented. This approach is applied to two missions, a very small-scale Mars aerocapture demonstration mission and a Flagship class Europa flyby mission. A propulsion system using a hybrid rocket motor is found to be viable for both classes of mission with potential benefits over the baseline propulsion systems in terms of total mass, power, and cost. 2. Improve the understanding of the combustion processes inside classical and fast-burning hybrid rocket motors. This task is conducted in order to facilitate improved performance models of these systems and to better inform designers as they evaluate these systems for specific missions. The approach to this work utilizes a combustion visualization experiment and various optics to explore the mass transfer phenomena, boundary layer growth rates and the flame location above combusting fuels at conditions representative of those in a typical hybrid rocket motor. This thesis provides strong confirmation of the basic droplet formation and entrainment mechanism for fast burning fuels at operating conditions representative of those within a typical hybrid rocket motor. Imaging diagnostics are successfully used to quantify the location of the flame within the boundary layer for classical and high regression rate fuels at a range of operating conditions.

Keywords: Aeronautics and Astronautics.
Advisor: Cantwell Brian primary advisor. Thesis advisor
Close Sigrid
Hubbard Scott
Jameson Antony
Zilliac Gregory G.
Hydroxylation of unactivated tertiary carbon-hydrogen bonds using organic and metal-based catalysts [electronic resource]

The selective hydroxylation of C--H bonds with complex substrates remains a grand challenge in modern synthetic chemistry. Selective methods for C--H oxidation have the potential to transform the field of natural product and complex molecule synthesis. While a variety of methods exist for the oxidation of C--H bonds, significant challenges in reaction efficiency, including catalyst turnover numbers and oxidant use, and positional selectivity still remain. One method that our laboratory has investigated for C--H hydroxylation uses 1,2,3-benzoxathiazine-2,2-dioxide-derived oxaziridines. By gaining an understanding of the off pathway processes that govern oxaziridine stability, significant improvements in reaction time, scope, and efficiency were obtained. Subsequent studies focused on elucidating the energetic requirements of the C--H bond oxidation event as well as probing the mechanism of the previously undescribed reduction of the oxaziridine intermediate in water and alcoholic solvents. The final chapter of this thesis details investigations into two metal-based approaches for catalyzing C--H hydroxylation, along with a comparative analysis of several methods for C--H hydroxylation that appear in the literature. These efforts serve to define the current scope and limitations of existing technologies for C--H hydroxylation and provide a reference for users of this technology.

Keywords: Chemistry.
Advisor: Du Bois Justin primary advisor. Thesis advisor
Waymouth Robert M. advisor. Thesis advisor
Wender Paul A. advisor. Thesis advisor
Identification of direct AMPK phosphorylation sites in cells reveals a role for AMPK in non-metabolic pathways [electronic resource]

AMP-activated protein kinase (AMPK) is a central energy gauge that regulates metabolism and has been increasingly involved in non-metabolic processes and diseases. However, AMPK's direct substrates in non-metabolic contexts are largely unknown. To better understand the AMPK network, we use a chemical genetics screen coupled to a peptide capture approach in whole cells, resulting in identification of direct AMPK phosphorylation sites. Interestingly, the high-confidence AMPK substrates contain many proteins involved in cell motility, adhesion, and invasion. AMPK phosphorylation of the RHOA guanine nucleotide exchange factor NET1A inhibits extracellular matrix degradation, an early step in cell invasion. The identification of direct AMPK phosphorylation sites also facilitates large-scale prediction of AMPK substrates. We provide an AMPK motif matrix and a pipeline to predict additional AMPK substrates from quantitative phosphoproteomics datasets. As AMPK is emerging as a critical node in aging and pathological processes, our study identifies potential targets for therapeutic strategies.

Advisor: Brunet Anne
Elias Joshua
Ferrell James Ellsworth advisor. Thesis advisor
Snyder Michael
Winslow Monte advisor. Thesis advisor
Identification of environment specific chromatin state in Drosophila melanogaster and its relationship to seasonal adaptation

A growing body of research suggests that balancing selection is an important evolutionary force acting in natural populations. Balancing selection typically occurs when conditionally beneficial alleles are maintained in a population via varying spatial or temporal selection pressures. One species that exhibits balancing selection is Drosophila melanogaster, which rapidly evolves in response to seasonal fluctuations among seasons. Previous work has shown that seasonal adaptation causes frequency oscillations in approximately 2000 single nucleotide polymorphisms (SNPs) and phenotypic traits (e.g. metabolic and reproduction profiles) across winter and summer seasons. We hypothesize that variation at cis-regulatory regions (cis-eQTL), regions regulating mRNA expression, contributes to rapid and cyclic seasonal adaptation via modulation of environment-dependent gene expression. To test this hypothesis, we used two sequencing methods on winter-summer hybrid Drosophila populations that were subjected to either winter-like or summer-like conditions. The first technique, RNA-Seq, is a method that creates gene expression profiles and the second, FAIRE-Seq, is a process that isolates and enriches openly-transcribed chromatin through phenol-chloroform separation. While FAIRE-Seq has been used successfully in the past, this project elucidates the various means by which the protocol must be trouble-shot and adjusted for individual experiments. Consideration of other chromatin sequencing methods, such as ATAC-Seq and DNase-Seq, may be more practical for future experiments involving open-chromatin research.

Keywords:  Department of Biology
Drosophila melanogaster
biology
molecular evolution
seasonal adaptation
cis-eQTL
chromatin state
FAIRE-Seq
Thesis
Advisor: Petrov Dmitri
Fraser Hunter
Identifying a role for IQGAP1 in Ras-mediated tumorigenesis [electronic resource]

Targeting cancer cells while sparing normal cellular function is the elusive target of all cancer researchers. The ERK1/2 MAPK pathway is critical for cellular survival and over 30% of all human cancers have mutations or altered expression of these pathway members. Two cancers are particularly dependent on this pathway for survival, melanoma (~60% BrafV600E mutations) and pancreatic cancer (> 90% KrasG12D mutations). Our previous work describes the identification of an ERK1/2 MAPK scaffold, IQGAP1, that appears to function in a tumor-specific fashion and is not required for normal cellular function. However, it is unclear how targeting this scaffold-kinase interaction will affect tumorigenesis in-vivo as well as how it will affect the ERK1/2 MAPK pathway downstream. The work in this thesis expands previous in-vitro validation of IQGAP1 as a cancer specific target by characterizing tumor response in the context of PLX4032 resistance in melanoma as well as in mouse models of pancreatic cancer. Our work also identifies a key alteration in the phosphorylation of the linker region of SMAD2 downstream of TGFβ when IQGAP1 is depleted or targeted therapeutically. This has important consequences for tumor behavior as well as changes in the extracellular matrix within tumors, which could make tumors more invasive and resistant to therapy. We additionally examine the validity of IQGAP1 as a therapeutic target in canine melanoma, an alternative model of melanoma that recapitulates many of the characteristics of human melanoma, but in a Braf and Nras wild-type setting. Through this work, we have improved the understanding of the relationship between ERK1/2 and TGFβ pathways in cancer as well as paved the way for additional clinical development of this novel cancer therapeutic.

Advisor: Khavari Paul A. primary advisor. Thesis advisor
Oro Anthony
Sage Julien advisor. Thesis advisor
Sweet-Cordero Eric advisor. Thesis advisor