12 Result(s)
within
Protocol
Wenjun **ao
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Protocol
Modeling and Simulation of the NMDA Receptor at Coarse-Grained and Atomistic Levels
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. While high-resolution structures were solved for an allosterically inhibited form of ...
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Defining Selective Neuronal Resilience and Identifying Targets of Neuroprotection and Axon Regeneration Using Single-Cell RNA Sequencing: Computational Approaches
We describe a computational workflow to analyze single-cell RNA-sequencing (scRNA-seq) profiles of axotomized retinal ganglion cells (RGCs) in mice. Our goal is to identify differences in the dynamics of survi...
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Analysis of Interleukin-4-Induced Class Switch Recombination in Mouse Myeloma CH12F3-2 Cells
Affinity maturation of B lymphocytes is a process that includes somatic hypermutation and class switch recombination. Class switch recombination is a fundamental factor of the human adaptive immunity. The pert...
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Next-Generation Sequencing for MicroRNA Expression Profile
Sequencing technologies have made considerable advancements. From the Sanger sequencing method to the next-generation sequencing (NGS) methods, and from the NGS methods to the third-generation sequencing metho...
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Handling High-Dimension (High-Feature) MicroRNA Data
High-dimensional data, or high-feature variables, are often used to describe the characteristics of microRNA sequence and microarray data. As a consequence, the curse of high dimension often becomes a problem....
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Exploring MicroRNA::Target Regulatory Interactions by Computing Technologies
MiRNA genes (miRNA precursor genes) share some common structural elements with protein genes. As with protein genes, the promoters of miRNA genes are necessary to regulate the expression of miRNA. The computat...
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Assessment of Phagocytic Activity of Cultured Macrophages Using Fluorescence Microscopy and Flow Cytometry
Phagocytosis is the process by which phagocytes, including macrophages, neutrophils and monocytes, engulf and kill invading pathogens, remove foreign particles, and clear cell debris. Phagocytes and their abil...
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Analysis of Protein Conformational Transitions Using Elastic Network Model
In this chapter, we demonstrate the usage of a coarse-grained elastic network model to analyze protein conformational transitions in the NS3 helicase (NS3hel) of Hepatitis C virus (HCV). This analysis allows u...
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Quantitative Analysis of miRNA Expression in Epithelial Cells and Tissues
Reliable detection of the microRNA (miRNA) precursor and mature form expression levels is a fundamental starting block for more focused studies of the biogenesis and functional roles of these important post-tr...
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Computer Modeling of Helicases Using Elastic Network Model
In this chapter, we will demonstrate the usage of a suite of computational techniques based on a coarse-grained elastic network model by applying them to a monomeric helicase—the NS3 helicase of hepatitis C vi...
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Detection and Measurement of Membrane-Bound Protein Tyrosine Kinases in the Zebrafish Egg
The study of the biochemical events involved in fertilization and egg activation has historically been directed toward marine invertebrate and amphibian eggs (1), although recent progress has been made in the ana...
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Zymographic Method for the Measurement of Gelatinase Activity in Brain Tissue
Specific recognition of cell-surface molecules with other cells or extracellular matrix (ECM) is fundamental for cellular motility, reorganization, and proliferation. To carry out these actions, cells often di...
