Publicly accessible Penn Dissertations Copyright (c) 2013 University of Pennsylvania All rights reserved. http://repository.upenn.edu/edissertations Recent documents in Publicly accessible Penn Dissertations en-us Wed, 23 Jan 2013 20:09:28 PST 3600 The Process of Adoption of Small Scale Irrigation in Rural Mexico http://repository.upenn.edu/edissertations/466 http://repository.upenn.edu/edissertations/466 Thu, 08 Mar 2012 08:18:37 PST ABSTRACT

THE PROCESS OF ADOPTION OF SMALL SCALE IRRIGATION IN RURAL MEXICO

Case studies about the process of production in agriculture in four Mexican communities with small scale irrigation are presented.

Peasantry is viewed as a sui-generis system of production with a rationality which guides productive decisions for the obtention of a culturally defined subsistence level, which cannot be measured by the common factor of money. Peasant economic units are seen as subordinated parts of a dominant socio-economic system. Relations of domination are explained by the concept of articulation, which is manifested by the asymmetry of exchanges with the larger system in detriment of the peasants. Exchange imply transference of economic surplus of peasants to the rest of society by means of the intervention of agents and institutions, the mechanisms of operation of which tend to increase polarization between peasant producers and between agriculture and other sections of society. The dependent development of national economy tends to reproduce polarization and structural need.

Irrigation was considered as an innovation to be induced in the process of production. The adoption was not only a function of the advantages for more profitable production. The issue of subsistence was a central parameter in the adoption of new agricultural projects. The decision to adopt surpassed the limits of peasant rationality because the articulation of peasant economies with external factors set the limits within which they could manage their resources. Such restrictions were partly offset by the communitarian norms that regulated exchanges between peasant economic units.

A comparative analysis of case studies was made; two main concepts were taken: “managing logic” that lies behind the productive decisions and “control” that contextual factors exert upon peasant production. Field information was structured along those concepts and their intervening variables; then, four types of economies were extracted: infra-subsistence , surplus, appointed and peasant economy of decomposition.

The communities studied evolved to one of the four types. In the process, irrigation was a co-producer; however, it has not played the role expected by the government. In general, surplus generated by irrigated crops has been extracted from the communities, therefore it has not been used for their own development.

]]> ELVIA MARTINEZ-DE-BENITEZ UTILIZING GENETICALLY ENGINEERED MOUSE MODELS OF PANCREATIC CANCER: EVALUATING THE ROLE OF CATHEPSIN B AND THE EFFICACY OF FARNESYL THIOSALICYLIC ACID http://repository.upenn.edu/edissertations/465 http://repository.upenn.edu/edissertations/465 Mon, 27 Feb 2012 15:00:53 PST I have utilized genetically engineered mouse models of pancreatic cancer to identify a potential new therapeutic target, and to test the efficacy of a putative ras inhibitor. In the first part, I show that cathepsin B is upregulated during disease progression in the mouse pancreas, as is overall cathepsin activity. Loss of cathepsin B decreases preinvasive disease burden and imparts a significant survival benefit, with a consistent decrease in proliferation. In addition, lack of cathepsin B also decreases the burden of liver metastasis. Phospho-Erk localization appears to be affected by cathepsin B loss, which may account for the defect in proliferation. Cathepsin B null tumours also have increased active cathepsin L, which may compensate for cathepsin B in tumour progression and metastasis. Finally, a cysteine protease inhibitor in combination with gemcitabine confers a significant increase in survival in tumour-bearing mice. In the second part of this work, I have investigated the effect of farnesylthiosalicylic acid (FTS) in pancreatic tumour-bearing mice. In combination with gemcitabine, FTS significantly increases survival and decreases tumour kinetics and proliferation, and inhibits liver metastasis. Although FTS has previously been reported as a ras inhibitor, there is no evidence of modulation of ras activity or signaling in primary tumours after long-term or short-term intervention, or in liver metastases. In short, the therapeutic effects of FTS in this mouse model of pancreatic cancer do not appear to be ras-related, and the target of FTS remains to be elucidated.

]]> Aarthi Gopinathan HIV IMMUNOPATHOGENESIS: INHIBITION OF CD4+ T CELL ACTIVATION http://repository.upenn.edu/edissertations/464 http://repository.upenn.edu/edissertations/464 Mon, 27 Feb 2012 15:00:46 PST Human immunodeficiency virus (HIV) infection causes profound impairment of CD4+ T cell immunity. Anti-retroviral therapy (ART) restores CD4+ T cell responses to common antigens, but HIV-specific responses remain deficient. The immunization of chronically HIV infected, ART treated subjects also leads to poor HIV-specific CD4+ T cell responses. The mechanisms are not fully understood. In this thesis, I demonstrate that HIV envelope glycoprotein (Env), when delivered in the form of a vaccine or when present on free viral particles, suppresses antigen-stimulated CD4+ T cell proliferation. I investigate the potential involvement of human T regulatory cells (Treg) using an in vitro model system. I show that Env exposure neither changes the frequency nor the suppressive activity of Treg cells in human PBMC, and that Env-induced suppression of CD4+ T cell proliferation is independent of Tregs. The studies of HIV-induced inhibition of CD4+ T cell immunity were then moved to an in vivo model to determine physiological significance. A macaque model of HIV-infected individuals treated with ART during chronic infection was used to study the effect of SIV antigen stimulation in lymph nodes early after immunization. CMV seropositive rhesus macaques were infected with pathogenic SIVmac251 and after 4 months, treated with D4T and PMPA for viral control and immune reconstitution. I studied the immune and viral responses to SIV and CMV antigen immunization in draining lymph nodes. Animals were immunized with both SIV gag and CMV pp65 encoding plasmids in both arms and legs, which allowed draining lymph nodes for each antigen to be obtained at the same time, thus allowing direct comparisons of the effect of each antigen stimulation in the same animal. I observed that both SIV and CMV antigen immunizations stimulated antigen-specific T cell responses in draining lymph nodes. The CMV-specific responses were found in the periphery for 50 days post-immunization, while the SIV-specific responses transiently appeared. The SIV antigen stimulation also induced transient SIV viral replication in the draining lymph nodes, suggesting a mechanism for the early loss and poor HIV-specific CD4+ T cell response observed in HIV-infected progressors.

]]> Haitao Hu Native Functions of the Androgen Receptor are Essential to Pathogenesis in a Drosophila Model of Spinobulbar Muscular Atrophy http://repository.upenn.edu/edissertations/463 http://repository.upenn.edu/edissertations/463 Mon, 27 Feb 2012 15:00:39 PST Spinobulbar muscular atrophy (SBMA) is a progressive, late-onset disease characterized by degeneration of motor neurons in the brainstem and spinal cord. The disease is caused by expansion of a polyglutamine tract in the androgen receptor (AR) and is dependent on exposure to AR ligand. The expanded polyglutamine tract confers toxic function to the protein through unknown mechanisms, although the ligand-dependent nature of SBMA suggests that the mechanism of pathogenesis may be tied to ligand-dependent alterations in AR function. However, whether toxicity is mediated by native AR function or a novel AR function is unknown. We systematically investigated ligand-dependent modifications of AR in a Drosophila model of SBMA. We demonstrate in vivo that nuclear translocation of mutant AR is necessary but not sufficient for toxicity and that DNA binding by AR is necessary for toxicity. Mutagenesis studies demonstrated that a functional AF-2 domain is essential for toxicity, a finding corroborated by a genetic screen that identified AF-2 interactors as dominant modifiers of degeneration. As proof of this principle, we perform epistasis experiments using the AR coregulator limpet, which we find modifies polyglutamine-expanded AR toxicity in an AF-2-dependent manner. In addition, we use expression profiling to examine the molecular phenotype of polyglutamine-expanded AR degeneration, revealing that expression of wild-type AR results in a molecular phenotype that is very similar to that caused by polyglutamine-expanded AR. These findings suggest that expanded-polyglutamine AR toxicity may be mediated by amplification of normal function, a mechanism that may be broadly applicable to other polyglutamine diseases.

]]> Natalia B. Nedelsky CHARACTERIZATION OF THAP10 AND THAP11 AS TRANSCRIPTIONAL REPRESSORS IN DNA DAMAGE AND COLON CANCER PROGRESSION http://repository.upenn.edu/edissertations/462 http://repository.upenn.edu/edissertations/462 Mon, 27 Feb 2012 15:00:32 PST The THAP (Thanatos associated protein) domain is an evolutionarily conserved zinc-finger motif highly similar to the sequence specific DNA binding domain of Drosophila P element transposase. Emerging data suggest THAP proteins may function in DNA and chromatin dependent processes, including transcription. However, the transcriptional regulatory function, mechanisms of action, and role of most THAP proteins in normal and aberrant cellular processes remain largely unknown.

In this thesis, we demonstrate that several human THAP proteins contain transcriptional repressor activity and specifically identify THAP10 and THAP11 as differentially expressed in human DNA damage and colon cancer progression, respectively. THAP10 and THAP11 repressed basal and VP16 activator driven transcription when tethered to promoters as heterologous Gal4-DNA binding domain fusion proteins and physically associated with histone deacetylases in vitro and in vivo. THAP11 was found to be differentially expressed in the SW480/SW620 cell culture model of human colon cancer progression and immunohistochemical analysis of tissue microarrays similarly revealed increased THAP11 expression concomitant with disease progression. The increase in THAP11 expression in colon cancer tumors and cell lines suggests that THAP11 dependent transcriptional repression may contribute to disease progression. Consistent with this hypothesis we find that knockdown of THAP11 in metastatic SW620 colon cancer cells results in a modest but significant decrease in cell proliferation. Gene expression profiling in THAP11 depleted SW620 cells identified 80 differentially expressed genes, 70% of which were de-repressed by THAP11 knockdown. Directly repressed THAP11 gene targets were found to contain chromatin bound THAP11 near their transcription start sites. THAP11 mediated repression requires the multi-functional transcriptional regulator HCF-1 (Host cell factor-1). THAP11 physically associates with and recruits HCF-1 to repressed promoters and knockdown of HCF-1 is sufficient to de-repress THAP11 target genes.

Collectively, this data provides the first characterization of a directly regulated, THAP11 dependent gene expression program in human cells and suggests THAP11 may be an important transcriptional regulator in human colon cancer. These results, in conjunction with previous findings from our laboratory and others, suggest THAP proteins likely function as biologically relevant transcriptional regulators.

]]> James B. Parker THE DEVELOPMENT, CHARACTERIZATION AND IMPLEMENTATION OF A REACTIVE OXYGEN SPECIES-RESPONSIVE RATIOMETRIC BIOLUMINESCENT REPORTER AND ITS USE AS A SENSOR FOR PROGRAMMED CELL DEATH http://repository.upenn.edu/edissertations/461 http://repository.upenn.edu/edissertations/461 Mon, 27 Feb 2012 15:00:25 PST The process of programmed cell death (PCD) is a prevalent area of scientific research and is characterized by a highly complex proteolytic cascade. PCD is involved in development, homeostasis and the immune response. Further, unregulated PCD has been implicated in various, often, devastating pathologies including cancer, autoimmune diseases and neurodegenerative disorders. The importance of PCD in human health and disease has led to the widespread utilization of genetically encoded reporters for the non-invasive imaging of PCD in vitro and in vivo; however, it is currently not well understood whether the reporters themselves are susceptible to inactivation and/or degradation during PCD. Molecular reporters that do exhibit an unexpected sensitivity to their environment could lead to ambiguous findings and/or inaccurate conclusions. Interestingly, we have found that the commonly used bioluminescent reporter protein, Firefly Luciferase (fLuc), exhibits a rapid loss in activity in cells undergoing PCD. In contrast, a variant of Renilla Luciferase, RLuc8, demonstrated quite stable activity under the same conditions. Following extensive inhibition analyses, it was determined that reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), play a large role in the disparity between fLuc and RLuc8 activity, in cells undergoing PCD. ROS are natural byproducts of oxygen metabolism that are normally regulated by antioxidants; if the balance between ROS and antioxidants becomes skewed, cells can enter a state of ‘oxidative stress.’ It has been reported that many cases of PCD are associated with elevated levels of ROS. Consistent with these reports, when fLuc and RLuc8 were intracellularly coexpressed, it was found that the bioluminescence ratio, RLuc8:fLuc, served as a useful metric to report on caspase-dependent and –independent PCD in vitro and in vivo in an ROS-mediated manner. It is envisioned that this ratiometric reporter could have widespread impact on research endeavors involving the aforementioned maladies, including therapeutic development and evaluation.

]]> Julie Czupryna The Basis of VCP-Mediated Degeneration: Insights From a Drosophila Model of Disease http://repository.upenn.edu/edissertations/460 http://repository.upenn.edu/edissertations/460 Mon, 27 Feb 2012 15:00:18 PST Valosin-containing protein (VCP) is a highly conserved molecular chaperone that regulates a wide array of essential cellular processes. Mutations in VCP are causative of degenerative disease that can affect muscle, brain and bone. Despite VCP being implicated in many major pathways in the cell, the mechanism of disease pathogenesis is unknown. To gain insight into the degeneration associated with mutations in VCP, we developed and characterized a Drosophila model of disease that recapitulated VCP mutation-dependent toxicity. VCP is involved in a diverse array of activities, many of which we may not know. Therefore we employed an unbiased genetic screening method that has the potential to uncover unanticipated pathways affected in the disease. Using this approach, we identified four proteins that dominantly suppressed degeneration; one of which was Ube4b, one of the many known ancillary proteins that bind to VCP and determine its function. The three remaining dominant modifiers identified were all RNA-binding proteins including TBPH, the Drosophila orthologue of TAR (trans-activating response region) DNA-binding protein (TDP-43). TDP-43 has been identified as a major component of the ubiquitinated inclusions characteristic of an emerging spectrum of proteinopathies, including degeneration associated with VCP mutations. Redistribution of TDP-43 from the nucleus to the cytoplasm has been demonstrated in these proteinopathies but the significance of this was unknown. Here we demonstrated that TDP-43 and VCP interact genetically and disease-causing VCP mutations led to redistribution of TDP-43 to the cytoplasm in vitro and in vivo, replicating the major pathology observed in TDP-43 proteinopathies. Furthermore, we demonstrated that TDP-43 redistribution is sufficient to induce cytotoxicity. Together our results show that degeneration associated with VCP mutations is mediated, in part, by toxic gain of function of TDP-43 in the cytoplasm where its redistribution is possibly due to the altered binding repertoire of VCP. This work acts to further our understanding of the pathogenic mechanism of, not only VCP-related disease but also a broad array of TDP-43 proteinopathies that include frontotemporal dementia, inclusion body myopathies and amyotrophic lateral sclerosis.

]]> Gillian P. Ritson QUANTITATIVE MOLECULAR MRI OF INTERVERTEBRAL DISC DEGENERATION http://repository.upenn.edu/edissertations/459 http://repository.upenn.edu/edissertations/459 Mon, 27 Feb 2012 15:00:11 PST Degeneration of the intervertebral disc (IVD) is the most common cause of back-related disability among North American adults. Low-back-pain and associated disability costs the United States more than 100 billion dollars annually in health care expenditures and reduced productivity. The mechanism of IVD degeneration, especially its biomolecular aspect, is poorly understood in an in vivo setting. Thus there is increasingly a need for the non-invasive diagnosis and quantification of IVD degeneration. MRI is a non-invasive imaging modality capable of producing contrast sensitive to biomolecules. Therefore, the primary objective of this dissertation research project is to develop MRI techniques capable of non-invasive quantification of IVD biomolecular composition in vivo. We further developed three MRI techniques specifically for IVD imaging. Magnetization transfer (MT) MRI, T1ρ MRI and sodium MRI were first separately validated of their specificities for IVD biomolecular components. In doing so, we concluded that MT MRI is sensitive to IVD collagen content, T1ρ MRI is indicative of IVD osmotic pressure, and sodium MRI is sensitive to IVD proteoglycan (PG) content. Next, we applied all three techniques to human subjects in vivo. Due to the inherently low signal-to-noise ratio (SNR) efficiency of sodium MRI, we engineered a custom radio-frequency (RF) surface coil for sodium MRI of human lumbar spine on a 7 T MRI scanner. Cross-correlation of the MT MRI, T1ρ MRI and sodium MRI data with the corresponding Pfirrmann grade revealed that the relative collagen density of IVD increases with degeneration, the IVD osmotic pressure decreases with degeneration, and the IVD PG content decreases with degeneration. By establishing that in vivo MT MRI, T1ρ MRI and sodium MRI can be used to quantify multiple IVD biomolecular characteristics non-invasively, we open up the possibility to conduct longitudinal studies on human subjects as they undergo IVD degeneration. The combination of MT MRI, T1ρ MRI and sodium MRI provides scientists and clinicians with the diagnostic tool to improve our understanding of IVD degeneration, which could benefit future treatment and prognosis of IVD degeneration.

]]> CHENYANG WANG GAMMA OSCILLATIONS IN THE MOUSE PRIMARY VISUAL CORTEX AS AN ENDOPHENOTYPE OF SCHIZOPHRENIA http://repository.upenn.edu/edissertations/458 http://repository.upenn.edu/edissertations/458 Mon, 27 Feb 2012 14:59:58 PST Gamma oscillations (20-50 Hz) are a robust component of brain activity associated with information processing, but are also part of the background spontaneous activity during various brain states including sleep and anesthesia. Our goal was to examine the changes in gamma oscillations that result from pharmacological and genetic manipulations of glutamatergic transmission which produce endophenotypes of schizophrenia. We recorded local field potentials (LFP) and single units through the depth of the mouse primary visual cortex in vivo and examined the alterations in gamma frequency activity under both normal and pathological conditions. Our results indicate that both in awake and anesthetized animals, baseline gamma frequency power in the LFP is increased throughout the cortical lamina, and the signal-to-noise ratio of gamma oscillations produced by a visual stimulus is diminished, most notably in the superficial layers. In addition, the entrainment of single units to the local oscillations in the LFP is reduced in the supragranular (L2/3) and infragranular (L5/6) layers. This work supports the hypothesis that alterations in glutamatergic transmission result in changes to gamma oscillations in primary sensory areas and is consistent with the hypothesis that these changes are associated with disrupted sensory perception.

]]> Cristin G. Welle Prediction of Proapoptotic Anticancer Therapeutic Response Based On Visualization of Death Ligand-Receptor Interaction and Specific Marker of Cellular Proliferation http://repository.upenn.edu/edissertations/457 http://repository.upenn.edu/edissertations/457 Mon, 27 Feb 2012 14:59:52 PST Emerging targeted therapeutics hold great promise for the treatment of human cancer. However there are still challenges for selecting patients that most likely will benefit from targeted drugs. One of the major limitations of classical imaging methods is the significant delay to provide quantifiable and objective evidence of response to cancer therapy. Molecular imaging may be useful in targeted drug development by assessing the target expression and drug-target interaction, and predicting therapeutic response in both preclinical and clinical settings. The apoptosis pathway triggered by the Tumor Necrosis Factor (TNF)-Related Apoptosis-Inducing Ligand (TRAIL) receptors is a potential target for therapeutic intervention. TRAIL and its proapoptotic receptor agonistic monoclonal antibodies are being developed as targeted therapeutics in the treatment of human cancer. It is our hypothesis that visualization of proapoptotic receptors and binding of their agonists to proapoptotic receptors can noninvasively predict proapoptotic response if the pathway is intact. Hence the objective of this work is to develop efficient multimodality molecular imaging methods to predict proapoptotic anticancer therapy response before or at the very early stage of treatment. Towards this goal, we have labeled proapoptotic receptor agonists (PARAs) with near-infrared (NIR) fluorescent dyes to image PARAs binding to their targets expressed on the cell surface in cultured cells and in human tumor xenografts grown subcutaneously in immunodeficient mice. Both in vitro and in vivo studies demonstrated that imaging PARAs binding to their targets was well correlated with proapoptotic anticancer therapeutic response when TRAIL signaling pathway was intact. To pursue a more general molecular imaging marker that can predict anticancer therapeutic response even when the signaling pathway is impaired, we explored a novel radiotracer for positron emission tomography (PET) imaging [(18)F]-3'-fluoro-3'-deoxy-L-thymidine ([(18)F]-FLT), an analogue of thymidine and a specific marker of DNA replication and cellular proliferation. Our results suggested that early changes in [(18)F]-PET may not only predict the tumor histological response to anticancer therapeutics but also determine superiority of one treatment regimen over another. In summary our proof-of-concept studies show that multimodality molecular imaging will greatly aid in accelerating anticancer drug approval process and improving survival and response rates in hard-to-treat cancer.

]]> Lanlan Zhou GENOMIC METHODS FOR STUDYING THE POST-TRANSLATIONAL REGULATION OF TRANSCRIPTION FACTORS http://repository.upenn.edu/edissertations/456 http://repository.upenn.edu/edissertations/456 Thu, 02 Feb 2012 12:34:12 PST The spatiotemporal coordination of gene expression is a fundamental process in cellular biology. Gene expression is regulated, in large part, by sequence-specific transcription factors that bind to DNA regions in the proximity of each target gene. Transcription factor activity and specificity are, in turn, regulated post-translationally by protein-modifying enzymes. High-throughput methods exist to probe specific steps of this process, such as protein-protein and protein-DNA interactions, but few computational tools exist to integrate this information in a principled, model-oriented manner. In this work, I develop several computational tools for studying the functional implications of transcription factor modification. I establish the first publicly accessible database for known and predicted regulatory circuits that encompass modifying enzymes, transcription factors, and transcriptional targets. I also develop a model-based method for integrating heterogeneous genomic and proteomic data for the inference of modification-dependent transcriptional regulatory networks. The model-based method is thoroughly validated as a reliable and accurate computational genomic tool. Additionally, I propose and demonstrate fundamental improvements to computational proteomic methods for identifying modified protein forms. In summary, this work contributes critical methodological advances to the field of regulatory network inference.

]]> Logan J. Everett Mind Economy: Dynamic Graph Analysis of Communications http://repository.upenn.edu/edissertations/455 http://repository.upenn.edu/edissertations/455 Thu, 02 Feb 2012 12:34:06 PST Social networks are growing in reach and impact but little is known about their structure, dynamics, or users’ behaviors. New techniques and approaches are needed to study and understand why these networks attract users’ persistent attention, and how the networks evolve. This thesis investigates questions that arise when modeling human behavior in social networks, and its main contributions are:

• an infrastructure and methodology for understanding communication on graphs;

• identification and exploration of sub-communities;

• metrics for identifying effective communicators in dynamic graphs;

• a new definition of dynamic, reciprocal social capital and its iterative computation

• a methodology to study influence in social networks in detail, using

• a class hierarchy established by social capital

• simulations mixed with reality across time and capital classes

• various attachment strategies, e.g. via friends-of-friends or full utility optimization

• a framework for answering questions such as “are these influentials accidental”

• discovery of the “middle class” of social networks, which as shown with our new metrics and simulations is the real influential in many processes

Our methods have already lead to the discovery of “mind economies” within Twitter, where interactions are designed to increase ratings as well as promoting topics of interest and whole subgroups. Reciprocal social capital metrics identify the “middle class” of Twitter which does most of the “long-term” talking, carrying the bulk of the system-sustaining conversations. We show that this middle class wields the most of the actual influence we should care about — these are not “accidental influentials.” Our approach is of interest to computer scientists, social scientists, economists, marketers, recruiters, and social media builders who want to find and present new ways of exploring, browsing, analyzing, and sustaining online social networks.

]]> Alexy Khrabrov THE CYTOSKELETAL MECHANISMS OF CELL-CELL JUNCTION FORMATION IN ENDOTHELIAL CELLS http://repository.upenn.edu/edissertations/454 http://repository.upenn.edu/edissertations/454 Thu, 02 Feb 2012 12:34:00 PST Intercellular adhesions are essential for compartmentalization and integrity of tissues in an organism, cell-cell communication, and morphogenesis. The actin cytoskeleton and associated proteins play a vital role in establishing and maintaining cell-cell adhesion. However, the procedure by which cells establish adherens junctions remains largely unclear.

We investigated the dynamics of cell-cell junction formation and the corresponding architecture of the underlying cytoskeleton in cultured human umbilical vein endothelial cells (HUVECs). We show that the initial interaction between cells is mediated by protruding lamellipodia. Upon their retraction, cells maintain contact through thin bridges formed by filopodia-like protrusions connected by VE-cadherin-rich junctions.

Bridges share multiple features with conventional filopodia, such as an internal actin bundle associated with fascin along the length and VASP at the tip. Strikingly, unlike conventional filopodia, transformation of actin organization from the lamellipodial network to filopodial bundle during bridge formation occurs in a proximal-to-distal direction and is accompanied by recruitment of fascin in the same direction. Subsequently, bridge bundles recruit nonmuscle myosin II and mature into stress fibers. Myosin II activity was important for bridge formation and accumulation of VE-cadherin in nascent adherens junctions. Our data reveal a mechanism of cell-cell junction formation in endothelial cells utilizing lamellipodia as the initial protrusive contact, subsequently transforming into filopodia-like bridges connected through adherens junctions. Moreover, a novel lamellipodia-to-filopodia transition is employed in this context.

]]> Matthew K. Hoelzle PLASMON ENHANCED PHOTOCONDUCTION IN PORPHYRIN-GOLD NANOPARTICLE ASSEMBLIES http://repository.upenn.edu/edissertations/453 http://repository.upenn.edu/edissertations/453 Thu, 02 Feb 2012 12:33:54 PST This thesis describes a series of experiments to both determine the origins of charge transport and enhanced photoconduction in metal nanoparticle arrays linked with zinc-porphyrin complexes, but to also determine the nucleation and growth mechanisms related to Ferroelectric Nanolithography (FNL) as a platform for hybrid devices. The development of test structures on glass substrates was undertaken to not only allow the study of the mechanisms controlling charge transport but the photoconduction of zinc-porphyrin linked gold nanoparticle (AuNP) arrays. In this study, the dominate charge transport mechanism was determined to be thermally assisted tunneling and the origins of enhanced photoconduction in these systems was attributed to three mechanisms: direct exciton formation in the molecules, hot electrons and a field effect (optical antenna) due to the excitation of surface plasmons. In the hope of developing a platform for hybrid devices, FNL was utilized to systematically vary the parameters that effect the deposition of metal nanoparticles through domain directed deposition on ferroelectric surfaces. The nucleation and growth mechanisms were determined through this work, where thevintegrated photon flux controlled the particle density and the interface between the particle and the ferroelectric surface determined the particles size. Finally, with the ability to control the deposition of AuNPs on a ferroelectric surface, hybrid devices of zinc-porphyrin linked AuNPs were realized with FNL.

]]> David Conklin Synthetic Studies Of (+)-Nodulisporic Acid A: Development Of An Efficient Route To Eastern Hemisphere Sub-Targets http://repository.upenn.edu/edissertations/452 http://repository.upenn.edu/edissertations/452 Thu, 02 Feb 2012 12:33:49 PST (+)-Nodulisporic Acid A (NsAA) is an indole diterpene of complex structure, isolated from the fungus nodulisporium sp., possessing potent insecticidal activity. Herein is described a new tactic for the construction of complex indoles employing a tandem palladium-mediated process between a haloindoline and a vinyl bromide or triflate.

Chapter 1 of this work will review the efforts by Merck and Co. that lead to the isolation and discovery of potent analogs of NsAA, as well as briefly review the history of complex indole synthesis in the Smith Research Group.

Chapter 2 will describe efforts to streamline the synthesis of the chiral, non-racemic material used to make different variants of the eastern hemisphere sub-target, the development of a new tactic for bringing the two hemispheres together, and efforts to synthesize an eastern hemisphere sub-target that contains the sidechain of NsAA.

]]> Stephen S. Gonzales Nancy as a Center of Art Nouveau Architecture, 1895-1914 http://repository.upenn.edu/edissertations/451 http://repository.upenn.edu/edissertations/451 Thu, 02 Feb 2012 12:33:43 PST The small city of Nancy, France, is arguably the center where Art Nouveau architecture had the most lasting impact. Nancy’s Art Nouveau was a divergent form of modernity that was defined by regionalism and a distinct sense of place, which its proponents championed as the key elements of an authentic architecture, allowing Nancy to challenge Paris as the dominant French artistic center in the two decades before World War I.

Most of Nancy’s architects were graduates of the Ecole des Beaux-Arts in Paris, and grounded in the language of classicism and its associated professional standards. Much of Nancy’s Art Nouveau had a conservative character that garnered praise from the national architectural press. Nancy’s architects were also disciples of Emile Gallé, the founder of a regional association of artists, industrialists, and designers called the Ecole de Nancy, dedicated to the promotion of Art Nouveau. Nancy’s architects freely collaborated with other artists of the Ecole on their buildings, and a sense of pride in their province led them to study local flora, the and regional legends and politics, using the iconography of plants and narratives to make architecture legible to a wide public.

The rooting of the work of Nancy’s architects in their region and the alliance they formed with local industry were successes that Parisian Art Nouveau architects were never able to match. Consequently, in Paris, Art Nouveau was quickly discarded, while in Nancy it was celebrated as an integral piece of regional identity and an important national achievement until 1914.

]]> Peter Clericuzio Inhaled Oxygen as a Quantitative Intravascular MRI Contrast Agent http://repository.upenn.edu/edissertations/450 http://repository.upenn.edu/edissertations/450 Thu, 02 Feb 2012 11:52:19 PST Increasing the fraction of inspired oxygen (FiO2) generates MR contrast by two distinct mechanisms: increased T2 from deoxyhemoglobin dilution in venous compartments (blood oxygenation level-dependent effect or BOLD) and reduced T­1 from paramagnetic molecular oxygen dissolved in blood plasma and tissues. Many research and clinical applications using hyperoxic contrast have recently emerged, including delineating ischemic stroke penumbra, oxygen delivery to tumors, and functional MRI data calibration. However, quantitative measurements using this contrast agent depend on the precise knowledge of its effects on the MR signal – of which there remain many crucial missing pieces.

This thesis aims to obtain a more quantitative understanding of intravascular hyperoxic contrast in vivo, with the hope of increasing its precision and utility. Specifically, our work focuses on the following areas: (1) paramagnetic effects of molecular oxygen BOLD and arterial spin labeling (ASL) data, (2) degree and temporal characteristics of hyperoxia-induced reductions in cerebral blood flow (CBF), (3) use of oxygen in quantitative measurements of metabolism, and (4) biophysical mechanisms of hyperoxic T1 contrast.

In Chapter 2, the artifactual influence of paramagnetic molecular oxygen on BOLD-modulated hyperoxic gas studies is characterized as a function of static field strength, and we show that optimum reduction in FiO2 mitigates this effect while maintaining BOLD contrast. Since ASL measurements are highly sensitive to arterial blood T­1 (T1a), the value of T1a in vivo is determined as a function of arterial oxygen partial pressure in Chapter 3. The effect of both the degree and duration of hyperoxic exposure on absolute CBF are quantified using simultaneous ASL and in vivo T1a measurements, as described in Chapter 4. In Chapter 5, hyperoxic gas calibration of BOLD/ASL data is used to measure cerebral oxygen metabolism in a hypermetabolic swine model, with our results comparing favorably to 17O2 measurements of absolute metabolism. In Chapter 6, a model to describe the relationship between CBF, oxygen consumption, and hyperoxic T1 reduction is developed, which allows for a more rigorous physiological interpretation of these data. Taken together, this work represents several important steps towards making hyperoxia a more quantitative MRI contrast agent for research and clinical applications.

]]> David T. Pilkinton DYNAMIC VERTICAL CLIMBING: BIOINSPIRATION, DESIGN, AND ANALYSIS http://repository.upenn.edu/edissertations/449 http://repository.upenn.edu/edissertations/449 Thu, 02 Feb 2012 11:52:16 PST Biologists have proposed a pendulous climbing model, the Full-Goldman (F-G) template, that abstracts remarkable similarities in dynamic wall scaling behavior exhibited by radically different animal species. This thesis presents a progression of work related to dynamic vertical climbing based on that model.

We begin by describing the inspiration, design, implementation of and experimentation with the first dynamical vertical climbing robot. We study numerically a version of the pendulous climbing template dynamically re-scaled for applicability to utilitarian payloads with conventional electronics and actuation, revealing that the incorporation of passive compliance can compensate for an artifact’s poorer power density and scale disadvantages relative to biology. However, the introduction of these dynamical elements raises new concerns about stability regarding both the power stroke and limb coordination that we allay via mathematical analysis. Combining these numerical and analytical insights into a series of design prototypes, we document the correspondence of the various models to the variously scaled platforms and report that our approximately two kilogram platform, DynoClimber, climbs dynamically at vertical speeds up to 1.5 bodylengths per second — in particular, the final 2.6 kg prototype climbs at an average steady state speed of 0.66 m/s against gravity on a carpeted vertical wall, in rough agreement with our various models’ predictions.

We establish whether the success of the robot is inherent to the morphology suggested by the F-G template or, instead, to a fortuitous set of parameter choices during the robot’s design. Thus we examine the effects of (i) actuator dynamics and (ii) lateral force generation on climber stability by investigating a sequence of reduced order variants of the F-G template. We prove analytically that a purely vertical climber is stable for a general class of actuator force functions, and use that result to further simplify our models by allowing the prescription of leg length. We use that simplification to demonstrate that a sprawled posture stabilizes vertical climbing by damping rotational motion during stride transitions. We also notably demonstrate through simulation that a climber’s stability does not depend on the actuation frequency it employs.

Finally, we explore the potential benefits of pendulous dynamical climbing in animals and in robots by examining the stability and power advantages of variously more and less sprawled limb morphologies when driven by conventional motors in contrast with animal-like muscles. For quadratic-in-velocity power output actuation models typical of commercially available electromechanical actuators, our results suggest the new hypothesis that sprawled posture may confer significant energetic advantage. In notable contrast, muscle-powered climbers do not experience an energetic benefit from sprawled posture due to their sufficiently distinct actuator characteristics and operating regimes. These results suggest that the benefits of sprawled posture climbing may be distinctly different depending upon the details of the climber’s sensorimotor endowment. This study also shows that even minimally intelligent foot placement improves stability when compared to the template-derived rigid sprawl.

]]> Goran Lynch THE NANOAQUARIUM: A NANOFLUIDIC PLATFORM FOR IN SITU TRANSMISSION ELECTRON MICROSCOPY IN LIQUID MEDIA http://repository.upenn.edu/edissertations/448 http://repository.upenn.edu/edissertations/448 Thu, 02 Feb 2012 11:52:13 PST There are many scientifically interesting and technologically relevant nanoscale phenomena that take place in liquid media. Examples include aggregation and assembly of nanoparticles; colloidal crystal formation; liquid phase growth of structures such as nanowires; electrochemical deposition and etching for fabrication processes and battery applications; interfacial phenomena; boiling and cavitation; and biological interactions. Understanding of these fields would benefit greatly from real-time, in situ transmission electron microscope (TEM) imaging with nanoscale resolution. Most liquids cannot be imaged by traditional TEM due to evaporation in the high vacuum environment and the requirement that samples be very thin. Liquid-cell in situ TEM has emerged as an exciting new experimental technique that hermetically seals a thin slice of liquid between two electron transparent membranes to enable TEM imaging of liquid-based processes. This work presents details of the fabrication of a custom-made liquid-cell in situ TEM device, dubbed the nanoaquarium. The nanoaquarium’s highlights include an exceptionally thin sample cross section (10s to 100s of nm); wafer scale processing that enables high-yield mass production; robust hermetic sealing that provides leak-free operation without use of glue, epoxy, or any polymers; compatibility with lab-on-chip technology; and on-chip integrated electrodes for sensing and actuation. The fabrication process is described, with an emphasis on direct wafer bonding. Experimental results involving direct observation of colloid aggregation using an aqueous solution of gold nanoparticles are presented. Quantitative analysis of the growth process agrees with prior results and theory, indicating that the experimental technique does not radically alter the observed phenomenon. For the first time, in situ observations of nanoparticles at a contact line and in an evaporating thin film of liquid are reported, with applications for techniques such as dip-coating and drop-casting, commonly used for depositing nanoparticles on a surface via convective-capillary assembly. Theoretical analysis suggests that the observed particle motion and aggregation are caused by gradients in surface tension and disjoining pressure in the thin liquid film.

]]> Joseph M. Grogan Optimization and Translation of MSC-Based Hyaluronic Acid Hydrogels for Cartilage Repair http://repository.upenn.edu/edissertations/447 http://repository.upenn.edu/edissertations/447 Thu, 02 Feb 2012 11:52:09 PST Traumatic injury and disease disrupt the ability of cartilage to carry joint stresses and, without an innate regenerative response, often lead to degenerative changes towards the premature development of osteoarthritis. Surgical interventions have yet to restore long-term mechanical function. Towards this end, tissue engineering has been explored for the de novo formation of engineered cartilage as a biologic approach to cartilage repair. Research utilizing autologous chondrocytes has been promising, but clinical limitations in their yield have motivated research into the potential of mesenchymal stem cells (MSCs) as an alternative cell source. MSCs are multipotent cells that can differentiate towards a chondrocyte phenotype in a number of biomaterials, but no combination has successfully recapitulated the native mechanical function of healthy articular cartilage. The broad objective of this thesis was to establish an MSC-based tissue engineering approach worthy of clinical translation.

Hydrogels are a common class of biomaterial used for cartilage tissue engineering and our initial work demonstrated the potential of a photo-polymerizable hyaluronic acid (HA) hydrogel to promote MSC chondrogenesis and improved construct maturation by optimizing macromer and MSC seeding density. The beneficial effects of dynamic compressive loading, high MSC density, and continuous mixing (orbital shaker) resulted in equilibrium modulus values over 1 MPa, well in range of native tissue.

While compressive properties are crucial, clinical translation also demands that constructs stably integrate within a defect. We utilized a push-out testing modality to assess the in vitro integration of HA constructs within artificial cartilage defects. We established the necessity for in vitro pre-maturation of constructs before repair to achieve greater integration strength and compressive properties in situ. Combining high MSC density and gentle mixing resulted in integration strength over 500 kPa, nearly 10-fold greater than previous reports of integration with MSC-based constructs. Furthermore, we demonstrated the durability of this repair system by applying dynamic loading and showed its functional contribution to the distribution of compressive loads across the repair space.

Overall, the studies contained within this thesis offer the first MSC-based tissue engineering strategy that successfully recapitulates native mechanical function while also demonstrating the potential for complete functional cartilage repair.

]]> Isaac E. Erickson