1,552 research outputs found

    Mechanisms contributing to RNA localization and translation: study of neuronal zipcodes in primary cortical neurons, and translational changes in neurodegeneration

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    The regulation of gene expression in terms of space and time is governed by the distribution of RNA and proteins within a cell. This tightly controlled regulation is necessary for mediating cellular development and function. The localization of RNA is also a highly controlled process that is influenced by specific cis and trans-acting elements. In polarized cells, such as neurons, the localization of transcripts towards axons and dendrites (neurites) enables the immediate and efficient local synthesis of proteins in response to external stimuli. This thesis focuses on the examination of the cis-elements, or "zipcodes," that contribute to the localization of RNA towards the neurites and the translational defects that result in the peripheral neuropathy Charcot-Marie-Tooth (CMT) disease

    Characterization of a cytoplasmic mRNA-transport complex from yeast

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    Molecular Mechanisms Of Mrna Transport By A Class V Myosin And Cytoplasmic Dynein

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    mRNA localization ensures correct spatial and temporal control of protein synthesis in the cell. Using a single molecule in vitro approach, we provide insight into the mechanisms by which localizing mRNAs are carried by molecular motors on cytoskeletal tracks to their destination. Budding yeast serves as a model system for studying the mechanisms of mRNA transport because localizing mRNAs are moved on actin tracks in the cell by a single class V myosin motor, Myo4p. Molecular motors that specialize in cargo transport are generally double-headed so that they can walk for many microns without dissociating, a feature known as processivity. Thus, is was surprising when Myo4p purified from yeast was shown by in vitro assays to be non-processive. The reason for its inability to move processively is that the Myo4p heavy chain does not dimerize with itself, but instead binds tightly to the adapter protein She3p to form a single-headed motor complex. The mRNA-binding adapter protein She2p links Myo4p to mRNA cargo by binding She3p. To understand the molecular mechanisms of mRNA transport in budding yeast, we fully reconstituted a messenger ribonucleoprotein (mRNP) complex from purified proteins and a localizing mRNA (ASH1) found in budding yeast. Using single molecule in vitro assays, we find that She2p recruits two Myo4p-She3p complexes, forming a processive double-headed motor complex that is stabilized by mRNA at physiological ionic strength. Thus, only in the presence of mRNA is Myo4p capable of continuous mRNA transport, an elegant mechanism that ensures that only cargo bound motors are motile. We next wished to understand if the principles of mRNA transport in budding yeast are conserved in higher eukaryotes. In Drosophila, mRNA is transported on microtubule tracks by cytoplasmic dynein, and the adapters that link the motor to localizing transcripts are well-defined. The adapter protein bicaudal D (BicD) coordinates dynein motor activity with mRNA cargo binding. The N-terminus of BicD binds dynein, and the C-terminus interacts with the mRNA-binding protein Egalitarian. Unlike mammalian dynein alone, it was recently shown that an N-terminal fragment of BicD (BicD2CC1), in combination with a large 1.2MDa multi-subunit accessory complex called dynactin, forms a complex (DDBCC1) that is activated for long processive runs. But unlike the constitutively activated BicD2CC1 fragment, the full-length BicD molecule fails to recruit dynein-dynactin because it is auto-inhibited by interactions between the N-terminal dynein binding domain and the C-terminal cargo binding domain. To understand how dynein is activated by native cargo and full-length adapters, we fully reconstituted a mRNP complex in vitro from tissue-purified dynein and dynactin, expressed full-length adapters BicD and Egalitarian, and a synthesized localizing mRNA found in Drosophila. We find that only mRNA-bound Egalitarian is capable of relieving BicD auto-inhibition for the recruitment of dynein-dynactin, and activation of mRNA transport in vitro. Thus, the presence of an mRNA cargo for activation of motor complexes is a conserved mechanism in both budding yeast and higher eukaryotes to ensure that motor activity is tightly coupled to cargo selection

    Handwritten character recognition by combining multiple recognizers using conditional probabilities

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    This research mainly focuses on recognizing the handwritten characters on a form in order to automate the Medical Form processing. Several efficient algorithms have been developed by us so far, to separate the handwritten characters from printed text character; to separate the lines, words and each character. In this thesis, we concentrate on the recognition of the segmented handwritten characters. Different feature recognition algorithms are employed and their performance on a given training set is analyzed. We find a way to combine all these individual feature recognition algorithms by incorporating their interdependence. The reliability of these algorithms is determined in terms of Conditional Probabilities and a rule for classifying the input character based on the outputs of each individual feature recognition algorithms is identified from the observations

    Site-Agnostic 3D Dose Distribution Prediction with Deep Learning Neural Networks

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    Typically, the current dose prediction models are limited to small amounts of data and require re-training for a specific site, often leading to suboptimal performance. We propose a site-agnostic, 3D dose distribution prediction model using deep learning that can leverage data from any treatment site, thus increasing the total data available to train the model. Applying our proposed model to a new target treatment site requires only a brief fine-tuning of the model to the new data and involves no modifications to the model input channels or its parameters. Thus, it can be efficiently adapted to a different treatment site, even with a small training dataset

    Outside the Frame: Mapping and Urban Space in the United States, c. 1920-2014

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    In this thesis, I will focus on the way in which maps have developed and been used in or by the United States, specifically government and academic institutions, in the past century to create, control, and shape urban space. I will make use of formal analysis and historical context to examine three case studies in which “conventional” maps, meaning institutional (namely, government and academic) cartography, have been used, and, it will be argued, misused, to selectively include and exclude information and collectively shape our environment. Additionally, this thesis will follow chronologically alongside the simultaneous development and refinement of mapping technologies, focusing on how these advancements in technology were fueled by, and subsequently fed into, certain understandings of the production of space. In order, the case studies I examine are the Home Owners\u27 Loan Corporation (HOLC) and Federal Housing Association (FHA) redlining maps of Philadelphia, military mappings and the development of Geographic Information Systems (GIS), and the Million-Dollar Blocks project by Columbia\u27s Spatial Information Design Lab. I am investigating what – meaning what people, narratives, and experiences – is left outside of the frame of the map and to what effect. Keywords: mapping, critical cartography, GIS, Philadelphia, incarceration, urban space

    Progression of a large syphilis outbreak in rural North Carolina through space and time: Application of a Bayesian Maximum Entropy graphical user interface

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    In 2001, the primary and secondary syphilis incidence rate in rural Columbus County, North Carolina was the highest in the nation. To understand the development of syphilis outbreaks in rural areas, we developed and used the Bayesian Maximum Entropy Graphical User Interface (BMEGUI) to map syphilis incidence rates from 1999–2004 in seven adjacent counties in North Carolina. Using BMEGUI, incidence rate maps were constructed for two aggregation scales (ZIP code and census tract) with two approaches (Poisson and simple kriging). The BME maps revealed the outbreak was initially localized in Robeson County and possibly connected to more urban endemic cases in adjacent Cumberland County. The outbreak spread to rural Columbus County in a leapfrog pattern with the subsequent development of a visible low incidence spatial corridor linking Roberson County with the rural areas of Columbus County. Though the data are from the early 2000s, they remain pertinent, as the combination of spatial data with the extensive sexual network analyses, particularly in rural areas gives thorough insights which have not been replicated in the past two decades. These observations support an important role for the connection of micropolitan areas with neighboring rural areas in the spread of syphilis. Public health interventions focusing on urban and micropolitan areas may effectively limit syphilis indirectly in nearby rural areas
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