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Book
308 pages ; 24 cm.
Green Library
Book
1 online resource.
Regeneration is a process that requires tightly regulated proliferation, differentiation, and tissue remodeling. Classical model organisms such as C. elegans, D. melanogaster, and M. musculus have limited regenerative capabilities therefore we present the freshwater planarian Schmidtea mediterranea, which provides an ideal system to study the role of stem cells in regeneration. This immortal adult organism boasts excellent regenerative capabilities driven by a stem cell population called neoblasts. The neoblast population is the only mitotically active cell type in planarians and can be easily manipulated without concern for embryonic requirements. This unique model also allows for the study of human embryonic stem cell genes in a simpler in vivo system. Thus S. mediterranea offers the opportunity to accelerate the studies and understanding of stem cell biology and regeneration in the environment of a living organism. GATA transcription factors are DNA binding proteins that are well-known master regulators of development. Through the activation and repression of transcription, these factors direct cellular differentiation toward lineage specification. Here we used loss-of-function experiments to understand the role of the GATA4/5/6 subfamily in the differentiation of neoblasts. S. mediterranea has a single homolog of mammalian GATA-4, -5, and -6, Smed-gata4/5/6, which is expressed primarily in the planarian intestine and in some neoblasts. Smed-gata4/5/6 knockdown results in perturbed homeostasis and regeneration, eventually leading to planarian death. Loss of Smed-gata4/5/6 disrupts intestinal differentiation and also affects non-intestinal lineages. During late time points of regeneration, Smed-gata4/5/6 loss leads to decreased neoblast proliferation and gene expression of neoblast subpopulations. These data support the conserved role of Smed-gata4/5/6 in intestinal differentiation and indicate the intestine may act as a neoblast niche. Our preliminary work on Experimental Evolution through irradiation exposure shows a sub-lethal dose of irradiation eliminates neoblast expression after 24 hours and expression recovery occurs after 3-4 weeks. This demonstrates S. mediterranea is a malleable model organism that can be used to study the link between regeneration and cancer.
Book
220 pages ; 24 cm.
Green Library
Book
231 pages ; 23 cm.
Green Library
Book
x, 277 pages ; 21 cm.
Green Library
Book
348 pages : illustrations ; 24 cm.
Green Library
Book
478 pages : music ; 25 cm.
Music Library
Book
1 online resource.
This dissertation explores two major lines of research concerning ultrafast electron dynamics in atoms and molecules. The first part investigates the dynamics of photoionization in intense laser fields on the attosecond time scale. A new technique using a weak probing field at half the frequency of the strong ionizing laser field reveals attosecond delays in the above-threshold ionization process. We observe the influence of the combined Coulomb-laser potential on the spectral phase of the photoelectron. In the second part, an experiment which imaged the uncoupling of electron motion from the molecular frame in rotating molecules is described. A coherent wave packet in the 4f Rydberg manifold of molecular nitrogen is created and its motion is probed in time. This allows for a direct observation in the time domain of a non-Born-Oppenheimer regime, known as the l-uncoupling regime, that up until now has only been inferred from spectroscopic data.
Book
1 online resource.
The world's ever-increasing needs for energy, currently fulfilled primarily by the combustion of hydrocarbon fuels, are demanding development of more efficient and cleaner combustion processes, which ultimately requires improved knowledge of fundamental combustion kinetics. Present in the combustion of most hydrocarbon fuels, aldehydes are important intermediate species that hold key information to such knowledge. Recognizing the critical role of aldehydes in combustion research, the current study presents (1) an advanced aldehydes diagnostic system for use in combustion environments, (2) a set of improved rate constant measurements for several key reactions of aldehydes, and (3) a toolbox that will facilitate future kinetics studies of aldehydes. A system of continuous-wavelength (CW) laser absorption diagnostic methods was developed for the quantitative measurement of formaldehyde (CH2O) and acetaldehyde (CH3CHO) in shock tube kinetic studies. Investigation of the high-temperature CH2O spectrum showed that the optimal wavelength for CH2O detection using commercially available lasers was near 2896 cm−1. By exploiting the structural difference between the absorption spectra of CH2O and that of broadband interfering species, the current study proposed a two-color (2895.92 and 2895.60 cm−1) interference-free detection scheme for CH2O sensing in combustion environments. A third color (32601.10 cm−1) was also added to develop a UV/IR detection scheme for combined CH3CHO/CH2O measurements. Aldehyde absorption cross-sections at all three colors were measured behind reflected shock waves over a wide range of temperatures (600--1800 K) and pressures (0.8--3.6 atm), with an uncertainty of ±5%. The diagnostic system was then validated in two well-controlled experiments, and demonstrated in shock tube pyrolysis experiments of 1,3,5-trioxane, CH2O and CH3CHO. The rate constant of acetaldehyde thermal dissociation, CH3CHO (+M) = CH3 + HCO (+M), was measured behind reflected shock waves at temperatures of 1273 - 1618 K using a sensitive CO diagnostic. Example simulations of existing reaction mechanisms updated with the current rate constant values demonstrated substantial improvements with regard to the acetaldehyde pyrolysis chemistry. The rate constant of the H-abstraction reaction of formaldehyde (CH2O) by hydrogen atoms (H), CH2O + H = H2 + HCO, was also studied behind reflected shock waves using the same CO absorption diagnostic, over temperatures of 1304--2006 K. These experiments were carefully designed to maintain relatively constant H radical concentrations, which significantly boosted the measurement sensitivity of the target reaction and suppressed the influence of interfering reactions. Compared to previous studies, the current work has significantly reduced the measurement uncertainty. The overall rate constants of the H-abstraction reactions of 10 different aldehydes, namely formaldehyde (CH2O), acetaldehyde (CH3CHO), propionaldehyde (C2H5CHO) and n-butyraldehyde (n-C3H7CHO), isobutyraldehyde (i-C3H7CHO), n-valeraldehyde (n-C4H9CHO), isovaleraldehyde (i-C4H9CHO), trans-2-pentenal (C2H5CHCHCHO), trimethylacetaldehyde ((CH3)3CCHO) and benzaldehyde (C6H5CHO), by hydroxyl radicals (OH), were studied behind reflected shock waves at temperatures of 958 -- 1391 K, using UV laser absorption at 306.69 nm. The current study reported the first direct rate constant measurement for C2 and higher aldehydes + OH at temperatures above 1000 K. To aid future kinetics research in shock tubes, a novel toolset of advanced laser absorption diagnostics, namely shock-tube-integrated cavity-enhanced absorption spectroscopy (CEAS), was also developed in the current study. This CEAS technique utilized high reflectivity mirrors directly mounted on the shock tube to enhance the effective optical pathlength in shock tube/laser absorption measurements by factors of about 50 - 90, thereby greatly improving the species detection limits in shock tube kinetics studies. A CW laser CEAS method was explored and applied to ultra-sensitive CO detection in rate constant measurements for the acetone thermal dissociation reaction, CH3COCH3 (+ M) = CH3 + CH3CO (+ M), over 1004-1094 K. A pulsed-laser CEAS was also explored in the current study to develop an improved laser absorption diagnostic for CH3 at 216.62 nm. Example application of this diagnostic was demonstrated in rate constant measurements for the thermal dissociation reaction of methane, CH4 + M = CH3 + H + M over 1487 - 1866 K. This CEAS toolset should prove very useful in future shock tube kinetics studies, including but not limited to, the studies of aldehydes.
Book
xxxi, 262 pages ; 21 cm.
Law Library (Crown)
Collection
Undergraduate Theses, Department of Biology, 2015-2016
Noncoding RNAs can orchestrate eukaryotic gene expression programs through diverse yet only partially understood mechanisms. One noncoding RNA in particular, 7SK, is known to repress mRNA transcription by blocking RNA polymerase II activity at gene promoters. Recent studies suggest that 7SK may be physically associated with chromatin, the target of RNA polymerase II, but the functional significance of this association has not been explored. Here we discover novel roles for 7SK at distinct genomic loci and find that it coordinates the functions of multiple protein complexes. 7SK binds both promoters and enhancers across the genome. At enhancers, mass spectrometry and co-immunoprecipitation reveal a direct, previously unknown interaction between 7SK and a major eukaryotic chromatin remodeling complex called BAF. Depletion of 7SK disrupts the BAF complex, causing aberrant transcription as well as increased DNA damage signaling at thousands of enhancers. These results suggest that 7SK has a multifaceted role in controlling gene regulation. By scaffolding at least two separate nuclear protein complexes at distinct genomic elements, 7SK provides a conceptual framework for how noncoding RNAs may operate as versatile regulators of information flow through the nucleus.
Collection
Undergraduate Theses, Department of Biology, 2015-2016
The Wnt pathway is an instructive signaling system in development, tissue homeostasis, and cancer. Although many core components of the canonical Wnt signaling cascade have been identified, additional layers of regulation likely remain undiscovered. To identify genes and regulatory elements involved in Wnt signaling, we performed unbiased forward genetic screens in a human haploid cell line using insertional mutagenesis with a retrovirus. The work in this thesis is divided into two experimental sections based on the analysis of these haploid genetic screens: 1) design and implementation of an improved and generally applicable computational pipeline to map the genomic insertion sites of the retroviral mutagen used in these screens and 2) the experimental analysis of a class of unexpected mutants we discovered using this pipeline. Analysis of insertional genetic screens in cultured cells has traditionally been “gene-centric”, focused on mapping the insertions in genomic regions with annotated, protein-coding transcripts. We hypothesized that recurrent insertions in non-protein coding regions or unexpected patterns of insertions in coding regions of the genome may identify regulatory elements or cryptic transcripts that regulate Wnt signaling. Therefore, we developed a bioinformatics pipeline designed to be “gene blind” by identifying recurrent insertions in one-thousand base-pair bins across the human genome, chosen consecutively across each chromosome without regard to gene boundaries. Using this pipeline, we found several genomic regions, including unannotated areas near the genes LRP6, TCF7L2, TFAP4 and APC, that are strong candidates to play important regulatory roles in Wnt responsiveness. These genomic regions may represent regulatory elements such as enhancers, promoters, or cis-acting non-coding RNAs (ncRNAs). A human tumor suppressor gene that is a central negative regulator of the Wnt pathway, the adenomatous polyposis coli (APC) gene is one of the most commonly mutated genes in colorectal cancer. Therefore, we designed a screen to search for genes that positively regulate the high-level oncogenic signaling observed when the APC gene is inactivated using CRISPR/Cas9 engineering. Our bioinformatics pipeline identified a perplexing pattern of retroviral insertions in the APC gene that were enriched for in cells selected for reduced Wnt signaling in the absence of APC. This was paradoxical since APC had already been engineered to contain a frameshift mutation in these cells. We found that these insertions somehow increase the level of APC protein, leading to the suppression of signaling in cells still containing a putatively inactivating lesion in the APC gene. In summary, the combined use of haploid screens and a custom bioinformatics pipeline has the potential to probe the genomic regulome of a signaling pathway that plays a central role in development and cancer. Future detailed understanding of these genetic elements and their mechanism of function may reveal new strategies that could be used to target human cancers resulting from deregulation of the Wnt pathway.
Collection
Undergraduate Theses, Department of Biology, 2015-2016
Autism spectrum disorders (ASDs) are fundamentally social and behavioral disorders with a range of comorbidities and social and financial impacts. Recent studies have estimated ASDs to have a heritability of around 50%, while indicating that there is also a significant environmental component. It is clear that neither genes nor environment in isolation can explain the etiology of autism. Large-scale genomics studies have identified a set of genes that have been shown to have a high association with ASDs. In addition, recent studies have identified certain environmental factors associated with an increased risk for developing ASDs, with pre- and perinatal hypoxia as one of the more salient factors. However, the interaction between genes and environment through the lens of hypoxia has yet to be evaluated. This study aimed to find and characterize the intersection between genes associated with autism and the genes associated with the cellular response to hypoxia. Every gene in a database of autism-associated genes was interrogated, through a thorough literature search and comparison with a set of microarray data, for evidence of its regulation by hypoxia. This process created a set of genes associated with both autism and the hypoxia response. A statistical test for overrepresentation indicated that hypoxia-regulated genes were overrepresented in the ASD database; the proportion of ASD genes also responsive to hypoxia was roughly twice what would be expected by chance. Functional and network analyses then showed that specific biological functions were overrepresented in the ASD/Hypoxia gene set, indicating that the number of hypoxia-regulated genes among all ASD genes, were indeed greater than would be expected by chance, and fell into specific networks and pathways. This lays the groundwork for functional characterization of variations in these genes in a population affected with autism as well as a neurotypical population. With a better understanding of how variations in certain genes can affect an individual’s response to a potential hypoxic event, researchers and medical professionals alike can open up better therapeutic avenues for children and adults affected by ASDs.
Collection
Undergraduate Honors Theses, Department of English
This paper analyzes recurring themes and patterns of thought in the nature poetry of W. H. Auden. This topic, typically neglected in most Auden criticism, focuses on the themes from Auden's nature poetry that persist throughout his poetic career. Divided into three sections--poetry about mines and mining, poetry about the body and the natural landscape, and poetry about places unknown--this paper argues that a more complete reading of Auden occurs when one examines his work in light of the subject, the natural world, rather than in a chronological way, as in most criticism. In combining the critical approaches of Edward Mendelson and John Fuller, this paper hopes to examine an atypical topic in a unique manner. In conclusion, Auden's poetry about the natural world keeps returning to the same concerns and anxieties. Though Auden is a poet characterized in part by the way that his poetry changes throughout his life, this paper examines how these recurring themes appear repeatedly in Auden's poetry about the natural world.
Collection
Undergraduate Theses, Department of Biology, 2015-2016
The microtubule cytoskeleton is spatially reorganized from the centrosomes to new subcellular sites during cell differentiation in many cell types, yet the importance of possessing distinct microtubule organizing centers (MTOCs) and the mechanisms governing MTOC reassignment remain poorly understood. Centrosomal and non-centrosomal microtubules are nucleated by a conserved nucleating complex, the γ-tubulin small complex (γ-TuSC), which is comprised of GIP-1/GCP3, GIP-2/GCP2, and TBG-1/γ-tubulin. Tissues of the nematode C. elegans display dualistic MTOC localization, in which γ-TuSC proteins are capable of localizing to both MTOCs, but do so at distinct times in development. This makes C. elegans an ideal system for studying the process of MTOC reassignment. We have proposed a model of MTOC reassignment whereby regulation of γ-TuSC protein localization dictates the sites of functional MTOCs. The gip-1 locus is predicted to encode multiple isoforms, presenting the possibility that differential expression of GIP-1 isoforms may play a role in this process. We therefore set out to investigate the role of GIP-1 in the developing C. elegans intestine. In this tissue, MTOC proteins are translocated from the centrosomes to the future apical cell membrane following their final round of divisions, resulting in a relatively simple dichotomy of MTOC function. Because a complete loss of functional MTOCs leads to an early arrest in embryonic development, we adapted an endogenous protein degradation pathway to deplete GIP-1 exclusively in the developing intestine around the time of MTOC reassignment. We found that GIP-1 is required for normal apical localization of GIP-2 and TBG-1, but not for apical localization of microtubules or the polarity protein PAR-3. Embryos depleted of intestinal GIP-1 have fewer and abnormally enlarged intestinal nuclei as compared to control embryos. Using a structure–function approach to identify GIP-1 domains required for MTOC localization and function, we have identified two domains (GIP-1[N], GIP-1a[G+C]) that localize to centrosomes but not apical membranes. Together, these results demonstrate that GIP-1 is vital for normal mitosis in the early embryonic intestine, and highlight the presence of redundant microtubule nucleating and anchoring mechanisms in this tissue. Furthermore, we provide the first evidence that GIP-1 may localize to centrosomal and apical membrane MTOCs through distinct protein domains. Future efforts focused on understanding the consequences of GIP-1 depletion for microtubule dynamics will greatly inform our understanding of the role of GIP-1 in regulating the microtubule cytoskeleton. With aberrant microtubule organization linked to some epithelial cancers and invasive cell behavior, understanding this basic cellular process may inform future efforts to inhibit cancer proliferation and metastasis.
Book
478 pages : some illustrations ; 24 cm.
Green Library
Book
1 online resource.
This dissertation adds to the literature on Latinas in science, technology, engineering, and mathematics (STEM) fields. Furthermore, it is one of the few studies to focus on Latinas in STEM in graduate school and in the workforce. Each of the three qualitative studies in this dissertation uses academic resilience as a framework to explore Latinas' journeys through the STEM pipeline, identifying protective factors or sources of support and the risk factors or challenges they encountered. In the first study, twenty Latina graduate students were interviewed about their experiences from early childhood through their time in graduate programs in STEM fields. The participants were master's or doctoral students at the same private elite university at the time of the interviews. The following were some of the major themes that were identified: earliest STEM experience, special teachers and mentors, community college experiences, decision to attend graduate school, familismo, graduate school faculty advisors/mentors, sense of belonging, and ethnic/cultural identity. The findings point to four potential areas for intervention. In the second study, twelve Latinas were interviewed about their academic and career trajectories in STEM fields. The participants had received their doctoral degrees or were employed in STEM fields at Research I institutions. Some of the risk factors or challenges that these women faced included: their families' gendered expectations, undocumented status, inaccessible research advisors, and cultural taxation. The protective factors or strengths and support systems that helped participants overcome these challenges included: family support, undergraduate research experiences, and access to academic mentors and diversity offices. In addition to the risk and protective factors identified, the Happenstance Learning Theory is used to describe participants' academic and career paths in STEM. The third study examined Latinas' experiences with microaggressions and discrimination in STEM fields and explored how experiences varied by skin tone and field of study. This study combined the participant samples of the first two studies and included analysis of survey data and interview responses. Survey results indicated that participants with lighter skin tones reported fewer experiences with microaggressions. In addition, women in science fields reported fewer microaggressions than the women in engineering fields. Responses to microaggressions included ignoring the events, confronting the offender, and relying upon protective factors such as external sources of support. Findings draw attention to colorism and phenotyping as barriers to success in STEM fields. Together, the three studies in this dissertation confirm previous findings about Latinas in STEM fields and identify new risk and protective factors.
Book
353 pages
SAL3 (off-campus storage)
Book
1 online resource.
This doctoral dissertation analyzes the surprisingly common presence of Homer in imperial literary symposia, i.e. fictionalized dinner conversations in the early Roman Empire, where characters often cite the already ancient poetry. Unlike past studies of text reuse at these dinner parties, this dissertation takes the setting seriously and treats these quotations from the standpoint of performance. Through the societally approved use of Homer the elite justifies its privileged position and establishes a hierarchy within itself, and these texts either accept this ideology or reject it through parody. Such an approach not only explains the role of Homer at table, but also why learning how to present and interpret poetry is a vital skill cross-culturally.
Book
1 online resource.
Integration of optical devices into modern CMOS electronics processes offers a wide range of opportunities and challenges for optical design. Modern foundry processes provide an enormous amount of design freedom in feature shapes and sizes; such freedom is rarely fully exploited by traditional human-directed design methods. At the same time, fabrication considerations greatly limit the material selection available for on-chip optics, making integration of most existing light sources infeasible. The first part of this dissertation focuses on the use of strained germanium (Ge) as a Si-compatible light source. While Ge is naturally an indirect bandgap material and thus poorly suited to light emission, application of tensile strain can be used to modify the bandstructure of Ge, greatly increasing light emission efficiency. To this end, we present design and experimental analysis of an optical device which integrates 2.4% uniaxial tensile strain, a single-material pseudo-heterostructure, and a Q > 2,000 cavity in a Ge-on-insulator material system. The second part of this dissertation presents a method for computational inverse design of active optical devices. Rather than relying on a small number of human-chosen design parameters to determine the structure of the device, inverse design begins with an arbitrary structure and then adjusts all available degrees of freedom to create a working device. To illustrate the effectiveness of this method, we present inverse-design of an all-optical switch, resulting in a device that uses 22x less power, 2.5x less power density, and 8x less device area than similar devices reported in recent literature.