VictorJuiz/thesis huggingface dataset:
In vitro reconstitution of the 6-deoxyerythronolide B synthase [electronic resource] : insights into the mechanism and engineering of polyketide synthases

Polyketides are a large class of natural product metabolites with incredible structural diversity and remarkable medicinal utility. While existing polyketides have met a wide variety of therapeutic needs, society will continue to have a steady demand for new medicinal polyketides. Our hope is that by studying the detailed biochemistry involved in the biosynthesis of polyketides, we will be able to develop informed strategies for rationally engineering new therapeutic molecules. Polyketides are assembled by enzymatic complexes known as polyketide synthases (PKSs), which can vary widely in their overall protein architecture. Bacteria are known to harbor enormous, multimodular PKSs that build their polyketides by sequential chemical transformations in a manner that is reminiscent of the automobile assembly line. The modular architecture of these enzymes makes them attractive candidates for protein engineering and gives hope to the idea of generating novel polyketides through combinatorial biosynthesis. Arguably the most-well characterized multimodular PKS is the 6-deoxyerythronolide B synthase (DEBS) which produces the macrocyclic core, 6-deoxyerythronolide B (6-dEB), to the erythromycin family of antibiotics. Notwithstanding over 20 years of research, DEBS (or any other assembly line PKS) has never been completely reconstituted in vitro using purified protein components. In this dissertation, we present first the full, in vitro reconstitution and biochemical analysis of the full DEBS assembly line. This reconstituted system has enabled three unprecedented studies into the mechanism and engineering of PKSs. First, we have analyzed the full DEBS assembly line from a kinetic perspective, demonstrating that the entire complex features a turnover frequency of approximately 1 min-1, which is in good agreement with in vivo productivity estimates. This analysis also demonstrated that the full assembly line has a degree of relaxed substrate specificity for which we report the structural characterization of a chemical analog of the 6-dEB. In addition, we have used the reconstituted system to test a key hypothesis relating to the assembly line processing of polyketide intermediates by the DEBS complex. In particular, our results indicate that a module within DEBS can carry no more than one growing polyketide chain at any point during its catalytic cycle. Finally, as an extension of the reconstituted system, we have developed and tested protein engineering strategies for the construction of non-natural (or "hybrid") bimodular PKSs, giving insights into the design considerations for building novel PKS assembly lines. We hope that this work will inspire the continued study of these remarkable biocatalysts as a gateway to developing new polyketides.

Keywords: Chemical Engineering.
Advisor: Khosla Chaitan
Dunn Alexander Robert advisor. Thesis advisor
Sattely Elizabeth advisor. Thesis advisor
Increased Reprogramming Efficiency of Aged Fibroblasts to Functional Neurons Through Loss of FoxO3

Our lab has previously demonstrated that mouse fibroblasts can be converted into functional induced neuronal (iN) cells through the forced expression of three transcription factors Ascl1, Brn2, and Myt1. We have further shown that human fibroblasts can also be reprogrammed with additional transcription factors. However, it would be desirable to generate iN cells from adult and aged fibroblasts for use in neurological disease modeling and regenerative medicine. One major challenge is the reduced efficiency of iN cell formation in aged fibroblasts. Here we show that increased cellular senescence and p16/p19 levels, decreased proliferation, and ageing-associated FoxO3 transcription factor levels correlated with reduced reprogramming efficiency. We show that germline loss of the known Ascl1-inhibitor, and longevity-associated, transcription factor FoxO3 increased the functional maturation and reprogramming efficiency of iN cells derived from adult and aged fibroblasts. Our results indicate that the epigenetic impairment of reprogramming in aged cells can be overcome by simple genetic manipulation. The data presented here provides novel insight into iN cell reprogramming from aged fibroblasts and delineates a process to improve the reprogrammability of aged fibroblasts—a step closer towards the ultimate goal of using patient-specific iN cells in therapeutic applications and disease modeling.

Keywords:  Department of Biology
Ahlenius, Henrik
iN cells
reprogramming
aging
direct lineage conversion
neuron
transcription factor
FoxO3
Thesis
Advisor: Wernig Marius
Shen Kang
Inducing and mapping cellular reprogramming by transcription factor overexpression [electronic resource]

The capability to directly convert one cell type into another by transcription factor overexpression is a modern marvel of biology. Recent advances have suggested that this process can principally convert any cell type to any cell type without restriction to germline origin or tissue. In this thesis, I demonstrate that FoxG1, Sox2 and Brn2 can directly convert fibroblasts into neural precursor cells. These cells can self-renew, differentiate into functional neurons, astrocytes and oligodendrocytes and integrate into the mouse brain. Additionally, this thesis demonstrates my work in induced pluripotent stem cell reprogramming where I identified a series of early intermediates that allowed us to interrogate the mechanism involved during early reprogramming induction.

Keywords: Genetics.
Advisor: Wernig Marius primary advisor. Thesis advisor
Baker Julie (Professor of genetics) advisor. Thesis advisor
Fire Andrew Zachary advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Industrial Agriculture and the Potential for Sustainability: An Ethnography of Iowa Farmers

This thesis explores how central Iowa mid-sized industrial farmers formed and maintain their ties to the agribusiness industry and through this analysis illuminates possibilities for sustainable alternatives. In the context of widespread debate about the best way our agricultural systems can "feed the world" without sacrificing local autonomy, it examines central Iowa as a case study, in order to examine the way global processes situated within late capitalism create particular experiences and affect in daily life. It shows how the agriculture industry became naturalized in farmers' everyday lives and how this produced a set of dispositions that became evident in farmers' affective responses to the "battle for representation" of agriculture. As farmers connected with favorable industry representations of their work and lauded their own efforts for sustainability, they opened the possibility for unlikely alliances with groups advocating for sustainable agriculture.

Keywords:  Department of Anthropology
Anthropology
agriculture
sustainability
ethnography
globalization
Thesis
Advisor: Ebron Paulla
Thiranagama Sharika
Influencing the design decision process [electronic resource] : information visualization in multi-criteria decision support systems for early-stage building design

This thesis investigates the challenges associated with the implementation of multi-criteria decision support systems (MCDSS) for early-stage building design. To support this effort, a method is proposed to compare the influence of the MCDSS user interface on design decision-making processes based on effectiveness, efficiency, and diversity metrics identified in and modified from the multi-criteria decision-making and design process literature. The use of the metrics is demonstrated in multi-objective parametric design charrettes with human subjects. Analysis of the charrette data reveals that visualization methods affect the efficiency and diversity of the design process but have no influence on effectiveness unless decision maker expertise is taken into account. The interaction between decision maker characteristics and information visualization is further examined to show how the background and current state of the decision maker can modify the design process. The results suggest that information visualization in MCDSS could be tailored according to user discipline and experience to improve performance across all dimensions of the design process.

Keywords: Civil and Environmental Engineering.
Advisor: Lepech Michael primary advisor. Thesis advisor
Kiremidjian Anne S. (Anne Setian) advisor. Thesis advisor
Levitt Raymond E. advisor. Thesis advisor
Inhibition of the RSK-CREB Signaling Axis as a Therapeutic Strategy for Acute Myeloid Leukemia

Acute Myeloid Leukemia (AML) is one of the most challenging cancers to treat, with current therapies yielding a 5-year survival rate of approximately 70% for pediatric patients and 50% for adult patients. Even when curative, current therapies are highly toxic and can cause life-threatening acute and chronic toxicities. The poor overall survival associated with current regimens creates an impetus to develop more effective and less toxic therapies.
Previous studies have reported that CREB (cyclic AMP Response Element Binding protein), a transcription factor critical for hematopoietic cell survival and proliferation, is overexpressed in the majority of AML patients and is an independent predictor of poor clinical outcome. RSK (Ribosomal S6 Kinase), the primary activator of CREB in AML cells, additionally plays an independent role in preventing hematopoietic cell death, although the overall role of RSK signaling in AML cells is unknown. In this study, we explore a novel strategy for AML therapy by blocking the RSK-CREB signaling axis using small molecule inhibitors.
CREB inhibition induced cell cycle arrest and apoptosis of AML cells by downregulating CREB-driven genes and signaling pathways that promote AML cell survival. In vivo studies demonstrated that treatment with the CREB inhibitor prolonged survival in mouse models of AML without toxicity. Resistance to the CREB inhibitor was mediated by RSK activation and subsequent increased CREB phosphorylation. Independent blockade of RSK resulted in reduced AML cell survival in vitro, and AML cell lines with RSK knockdown exhibited decreased proliferation in vivo. Our results further define the role of CREB and RSK in AML and suggest that the RSK-CREB signaling pathway represents a potential therapeutic target for AML, laying the groundwork for development of a new family of chemotherapy drugs.

Keywords:  Department of Biology
Biology
AML
pediatric
Cancer Biology
Pediatric Hematology/Oncology
Thesis
Advisor: Sakamoto Kathleen
Simon Michael
Injectable Hydrogels and Regenerative Medicine: Enhancing Transplantation for Spinal Cord Repair

The innate spinal cord injury (SCI) repair mechanisms in humans are incapable of regenerating functional motor neurons. Cellular transplantation of neural progenitor cells (NPCs) has been suggested as a potential solution to this issue. Robust populations of NPCs cells may be derived from human induced pluripotent stem cells (hiPSCs) and can restore communication along injured axons by establishing relay grafts. However, developing efficient cell-delivery and engraftment mechanisms for transplantation remains a significant challenge. Previous research has shown that cell delivery within carrier gels improves cellular viability upon transplantation, but a majority of these gels are difficult to synthesize and incompatible with a diversity of cell types. A recently developed family of hydrogels (MITCH-PEG and SHIELD) may offer an attractive solution for enhancing transplantation in SCI repair. Not only are these biocompatible hydrogel materials capable of encapsulating hiPSC-NPCs at physiological conditions, they are also both reproducible and customizable in nature. Examining the behavior of hiPSC-NPCs encapsulated in the hydrogels demonstrated that the hydrogels were capable of protecting and supporting the hiPSC-NPCs. These results suggest that encapsulating hiPSC-NPCs in a hydrogel prior to transplantation may serve as an effective strategy for increasing functional regeneration in SCI repair. In the future, technologies like MITCH-PEG and SHIELD will improve transplantation techniques by serving as a platform for a variety of cell types and therapies, particularly in the central nervous system where regeneration is not generally common.

Keywords:  Department of Biology
Biology
spinal cord injury (SCI)
relay graft formation
functional regeneration
human induced pluripotent stem cell (hiPSC)
differentiation
neural progenitor cell (NPC)
hydrogel
encapsulation
cell-delivery
Thesis
Advisor: Plant Giles
Cyert Martha
INO80 Chromatin Remodeling Complex’s Role in Myocardial Development: A Phenotype Characterization

Comprised of two atria and two ventricles, the heart is responsible for the delivery of blood and nutrients to the different parts of the body. As a well-characterized chromatin-remodeling complex, INO80 is known to have a variety of functions in organisms, more recently including metabolic regulation. An endocardial knockout of Ino80, the ATPase subunit of the INO80 chromatin-remodeling complex, has been shown to result in reduced thickness in the myocardial wall of the heart during development. This is likely due to the disruption in the regulation of signaling pathways between the endocardium and myocardium. In light of this information, this study investigated the role of INO80 as a potential regulator of cardiac development, not just through regulation of signaling, but natively in the myocardium. In order to elucidate this function, this study characterized the myocardial Ino80 knockout in Mus musculus. This revealed a lack of a phenotype in the myocardial layer of the heart. This suggests that INO80 does not play a native role in the myocardium, rather its main function in cardiovascular development is signaling between the endocardial layer and the myocardial layer to promote development. This elucidates the importance in understanding the signaling pathways that INO80 plays during development, and narrows the potential function of INO80 in overall heart development.

Keywords:  Department of Biology
Biology
heart development
chromatin remodeler
metabolic regulation
myocardium
Thesis
Advisor: Morrison Ashby
Red-Horse Kristy
Insights from patient authored text [electronic resource] : from close reading to automated extraction

Millions of people collaborate online with others who share their health concerns. In the process, these users perform complex health-related tasks, such as differential diagnosis and treatment comparison. The result is a massive, growing and readily accessible corpus of patient authored text (PAT) that documents patients' behavior outside of the clinical environment. As a result, PAT can provide insights into otherwise obscure topics, such as why patients follow only certain parts of a treatment protocol, or how people self-treat stigmatized conditions such as prescription drug addiction. Despite the potential value of PAT, attempts to extract medically-relevant insights from it have been limited. PAT is notoriously noisy and challenging to work with, and there is a dearth of methods and tools for processing and analyzing it. Moreover, the specific research questions that PAT can support are not obvious: determining what data PAT encodes, and how, is a challenge in and of itself. In this thesis, I develop methods for automatically extracting medically-relevant data from PAT. I focus specifically on the topic of addiction: a stigmatized and prevalent medical condition. Building on close readings of source text to inform schema induction, data annotation, and feature engineering, I train classifiers that accurately identify (1) medically-relevant terms in PAT; (2) users' motivations for participating in an addiction-related online health community; (3) users' drugs of choice, and (4) users' transitions through relapse and recovery. Using these classifiers to scale analyses to large PAT corpora, I derive novel insights into the process of addiction, as well as the role that online health communities play in giving users informational and emotional support and, ultimately, in enabling recovery. In concert, these contributions both underscore PAT's latent value for illuminating poorly understood or clandestine medical topics, and offer viable methods that dramatically improve our ability to realize this value.

Advisor: Heer Jeffrey Michael
Bernstein Michael S.
Card Stuart K.
Manning Christopher D. advisor. Thesis advisor
Insights into prosocial behavior [electronic resource]

This dissertation proposes new behavioral motivations to explain prosocial behavior and examines how standard behavioral motivations often have more nuanced policy implications in the realm of prosocial behavior. Each chapter details the results from testing these motivations in laboratory experiments. The first chapter investigates the interaction between monetary incentives and volunteer reputations via a laboratory study entitled Incentives for Prosocial Behavior: The Role of Reputations. This study is motivated by the possibility that monetary incentives may introduce a "greedy" signal that crowds out the motivation to volunteer. As the empirical evidence on such crowd-out is mixed, this study proposes a potential explanation: the strength of the greedy signal depends on the reputations of volunteers. In particular, this study confirms that crowd out in response to monetary incentives is much less likely among those with public, as opposed to private, reputations. In joint work with Stephen Terry, the second chapter explores the role of reference points in charitable giving via a laboratory study entitled Wage Elasticities in Working and Volunteering: The Role of Reference Points in a Laboratory Study. This study demonstrates how targeting behavior, in the presence of expectations-based reference points, induces negative volunteer effort responses to high volunteer wages or productivity levels. This study thus suggests that charities should carefully consider the potentially counterproductive nature of reference points or "goals" for volunteer effort. The third chapter considers the role of risk in charitable giving via a laboratory study entitled Excusing Selfishness in Charity Giving: The Role of Risk. In particular, iv the study documents self-serving responses to risk in charitable giving, as participants appear to use even small risk of their donations having less impact as an excuse not to donate. In exploiting a within-subject experimental design, this study also provides evidence for an individual level of consistency in self-serving tendencies. This study concludes with several potential policy implications. For instance, charities may increase their donations by targeting past donors for risky projects and new donors, who are potentially more susceptible to excuses, for non-risky projects.

Keywords: Economics.
Advisor: Bernheim B. Douglas primary advisor. Thesis advisor
Niederle Muriel primary advisor. Thesis advisor
Roth Alvin E.
Sprenger Charles
Insights into the growth and decay of orogenic wedges from foreland basin successions [electronic resource]

Convergent plate margins are dynamic settings where the evolution of sedimentary basins is influenced by a variety of interrelated autogenic and allogenic processes. These include plate tectonic-scale processes such as plate subduction and the development of a volcanic arc, fold-thrust belt, and associated basins; the development of climatic gradients across the orogen; shallow-crustal structural partitioning of the basins into discrete depocenters; and the surficial (topographic) responses to such events. This dissertation examines the interplay of tectonic, sedimentary, and climatic processes during the evolution of two retroarc foreland basin systems: the Late Cretaceous-Eocene Magallanes-Austral basin of Patagonia (Chapters 2 and 3) and the Late Cretaceous-Oligocene Rocky Mountain foreland basin of southwestern Montana (Chapter 4). These chapters investigate a variety of geologic processes that occur at different temporal and spatial scales. Specifically, major goals of this dissertation include (1) generating a paleogeographic reconstruction of latest Cretaceous depositional environments in the Magallanes-Austral basin to better understand the termination of the long-lived deep-marine foreland basin (Chapter 2); (2) utilizing detrital zircon U-Pb ages to understand variations in sediment dispersal patterns and long-term average sedimentation rates during shoaling of the Magallanes-Austral basin (Chapter 3); and (3) integrating structural, stratigraphic, sediment provenance, and stable isotope ([delta] 18O, [delta] 13C) data to better understand the spatial and temporal relationships of tectonic activity and climate (Chapter 4). Data types and methods are diverse, and include detailed outcrop description, detrital zircon U-Pb geochronology, thin-section petrography, 1-D subsidence modelling, and stable isotope ([delta] 18O, [delta] 13C) stratigraphy from calcic paleosols.

Keywords: Geological and Environmental Sciences.
Advisor: Graham S. A. (Stephan Alan)
Chamberlain C. Page advisor. Thesis advisor
Lowe Donald R.
Integrated analysis using molecular-scale and imaging-scale data to identify prognostic subgroups in glioblastoma [electronic resource]

Glioblastoma (GBM, World Health Organization [WHO] grade IV) is the most common and most aggressive brain cancer in adults, with a median survival of approximately one year, despite multimodal therapy of microsurgical resection, radiation, and chemotherapy. Previous molecular studies have classified patients into four subtypes based solely on gene expression. However, heterogeneity can be seen within these GBM subtypes, and there is no significant survival difference between the subtypes; thus, there is a pressing need to find better ways of defining disease subtypes based on biological characteristics that impact clinical outcome. We believe that this goal can be accomplished by developing methods to integrate, analyze, and make inferences from multi-scale datasets that span the visible (imaging-based) and molecular (genomic) scales to link imaging phenotype to genomic features. In my thesis, I describe my work developing computational methods to identify imaging-scale markers in combination with molecular-scale markers that better stratify patients into prognostic subgroups than current methods. First, I present imaging informatics methods to quantify two imaging phenotypes, tumor location and cerebral blood perfusion, to stratify patients in GBM. As an extension of perfusion analysis, I also examined inter-vendor and inter-reader variability in perfusion quantification. Second, to relate molecular data to alterations in metabolic activity, I extended an existing pathway analysis framework to incorporate metabolic pathways, enabling interrogation of deregulated energy metabolism in cancer. Third, I developed algorithms for integrating the quantitative imaging phenotypic and biological activity data to identify associations between molecular-scale features and imaging-scale features.

Keywords: Biomedical Informatics.
Advisor: Rubin Daniel
Gevaert Olivier Michel Simonne
Napel Sandy advisor. Thesis advisor