43 Result(s)
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STAMP: Spatio-Temporal Association Map** of Proteins
We describe a tool, Spatio-Temporal Association Map** of Proteins (STAMP), for identifying protein interactomes via proximity labeling. For a proof-of-principle study, we use cytidine 5′-triphosphate synthas...
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Synthetic Biology Meets Machine Learning
This chapter outlines the myriad applications of machine learning (ML) in synthetic biology, specifically in engineering cell and protein activity, and metabolic pathways. Though by no means comprehensive, the...
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Monoclonal Antibodies Generation: Updates and Protocols on Hybridoma Technology
Since its inception in 1975, the hybridoma technology revolutionized science and medicine, facilitating discoveries in almost any field from the laboratory to the clinic. Many technological advancements have b...
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Strategies for Multienzyme Assemblies
Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to co-localize the functional partner...
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Quantification of Angiogenesis in Laser Choroidal Neovascularization
Murine laser-induced laser choroidal neovascularization is a widely used and robust model of wet (exudative) age-related macular degeneration (wAMD). wAMD is one of the leading causes of blindness in the Weste...
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Simple Gene Knockdown in Endothelial Cells Using Short Interfering RNA Oligonucleotides
Cell transfection using short interfering RNAs (siRNAs) is a widely used technique to perform loss of function studies by “knocking down” genes of interest. Oftentimes, primary cells can be difficult to transf...
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Long-Term Imaging and Dynamic Analysis of Cytoophidia in Yeast
Live-cell imaging is widely used by researchers to study cellular dynamics and obtain a deep understanding of cell biological processes. Kee** cells in the proper growing environment and immobilizing the cel...
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In Situ Hybridization and Immunostaining of Xenopus Brain
The dynamic expression pattern analysis provides the primary information of gene function. Differences of the RNA and/or protein location will provide valuable information for gene expression regulation. Gener...
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Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx
CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With this framework, single-cel...
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Imaging Neuronal Signal Transduction Using Multiphoton FRET-FLIM
Synaptic plasticity, the ability of neurons to modulate the strength of specific inputs, is critical for neural circuits to adapt to experience throughout life. In excitatory pyramidal neurons, plasticity is i...
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Assays to Measure the Activity of Influenza Virus Polymerase
Influenza viruses use an RNA-dependent RNA polymerase (RdRp) to transcribe and replicate their segmented negative-stranded RNA genomes. The influenza A virus RdRp consists of a heterotrimeric complex of the pr...
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Profiling Tumor Infiltrating Immune Cells with CIBERSORT
Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to therapy. Methods to enumerate immune subsets such as...
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In Vivo Evaluation of Dystrophin Exon Skip** in mdx Mice
Dystrophin exon skip** in mdx mice has been the key model for the development of antisense therapy in vivo. Evaluation of exon skip** in this model involves the following two aspects: (1) efficiency and accur...
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Biochemical Identification of Nonmethylated DNA by BioCAP-Seq
CpG islands are regions of vertebrate genomes that often function as gene regulatory elements and are associated with most gene promoters. CpG island elements usually contain nonmethylated CpG dinucleotides, w...
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Genomic Tagging of AGO1 Using CRISPR/Cas9-Mediated Homologous Recombination
Tagging of genes at the endogenous loci is a powerful strategy for the analysis of protein function. We have developed a homologous recombination-based approach for inserting epitope tag into Drosophila AGO1 locu...
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Deep Sequencing of the Hepatitis B Virus Genome: Analysis of Multiple Samples by Implementation of the Illumina Platform
The quasispecies variation of hepatitis B virus (HBV) was believed to be a viral response to antiviral treatment and host immune pressure. Sanger sequencing was previously the classic approach for quasispecies...
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Northern Blot Detection of Virus-Derived Small Interfering RNAs in Caenorhabditis elegans Using Nonradioactive Oligo Probes
Northern blot analysis has been widely used as a tool for detection and characterization of specific RNA molecules. When coupled with radioactive probe northern blot allows for robust detection and characteriz...
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Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems
In plant biology, transient expression systems have become valuable approaches used routinely to rapidly study protein expression, subcellular localization, protein-protein interactions, and transcriptional ac...
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Array-on-Array Strategy For Activity-Based Enzyme Profiling
We describe a novel array on array strategy intended to enhance the throughput of enzymatic activity screening using microarrays. This strategy consists of spotting a first array with large droplets of enzymes...
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Contractile Force Readout of hESC-Cardiomyocytes
Promising pharmaceuticals frequently fail clinical trials due to cardiotoxicity or a decline in heart function not indicated from preclinical animal models and in vitro tests. The development of low-cost, high...
