Browsing by Subject "reprogramming"

Now showing 1 - 3 of 3
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    The design and implementation of mobile deluge on Android platform for wireless sensor network reprogramming
    (2017-11-28) Faruk, MD Omor; Liang, Yao; Tuceryan, Mihran; Mukhopadhyay, Snehasis
    Wireless Sensor Networks (WSN) is being used in various applications including environmental monitoring, site inspection and military. WSN is a distributed network of sensor devices that can be used to monitor temperature, humidity, light and other important metrics. The software that runs on the sensor devices define how the device should operate. In real world WSN deployment, device software update is required to maintain optimal operation. In this thesis, we propose a novel idea of updating the software of the sensor nodes using a mobile device running on Android Operating System. Our implementation builds upon Mobile Deluge with few enhancement which is a method of re-programming WSN with laptop computer. We have evaluated our application performance by lab experiments and in real world deployments of WSN and found the application stable and battery efficient.
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    The Direct Reprogramming of Somatic Cells: Establishment of a Novel System for Photoreceptor Derivation
    (2013-08-22) Steward, Melissa Mary; Meyer, Jason S.; Dai, Guoli; Randall, Stephen Karl, 1953-; Atkinson, Simon
    Photoreceptors are a class of sensory neuronal cells that are deleteriously affected in many disorders and injuries of the visual system. Significant injury or loss of these cells often results in a partial or complete loss of vision. While previous studies have determined many necessary components of the gene regulatory network governing the establishment, development, and maintenance of these cells, the necessary and sufficient profile and timecourse of gene expression and/or silencing has yet to be elucidated. Arduous protocols do exist to derive photoreceptors in vitro utilizing pluripotent stem cells, but only recently have been able to yield cells that are disease- and/or patient-specific. The discovery that mammalian somatic cells can be directly reprogrammed to another terminally-differentiated cell phenotype has inspired an explosion of research demonstrating the successful genetic reprogramming of one cell type to another, a process which is typically both more timely and efficient than those used to derive the same cells from pluripotent stem cell sources. Therefore, the emphasis of this study was to establish a novel system to be used to determine a minimal transcriptional network capable of directly reprogramming mouse embryonic fibroblasts (MEFs) to rod photoreceptors. The tools, assays, and experimental design chosen and established herein were designed and characterized to facilitate this determination, and preliminary data demonstrated the utility of this approach for accomplishing this aim.
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    A system for detecting high impact-low frequency mutations in primary tumors and metastases
    (Springer Nature, 2018-01-11) Anjanappa, Manjushree; Hao, Yangyang; Simpson, Edward R; Bhat-Nakshatri, Poornima; Nelson, Jennifer B; Tersey, Sarah A; Mirmira, Raghavendra G; Cohen-Gadol, Aaron A; Saadatzadeh, M. Reza; Li, Lang; Fang, Fang; Nephew, Kenneth P.; Miller, Kathy D.; Liu, Yunlong; Nakshatri, Harikrishna; Medical and Molecular Genetics, School of Medicine
    Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50% of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.