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Protocol
Use of Bastion for the Identification of Secreted Substrates
Bacteria use secretion systems to translocate numerous proteins into and across cell membranes, but have evolved more specialized secretion systems that can disrupt the normal cellular processes of host cells ...
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Protocol
Prediction of Peptide and TCR CDR3 Loops in Formation of Class I MHC-Peptide-TCR Complexes Using Molecular Models with Solvation
Formation of major histocompatibility (MHC)-peptide-T cell receptor (TCR) complexes is central to initiation of an adaptive immune response. These complexes form through initial stabilization of the MHC fold v...
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Protocol
Lysosome Imaging Based on Fluorescent Carbon Dots
Lysosomes play key roles in different cellular processes such as autophagy, phagocytosis, and apoptosis. Lysosomal dysfunction is related to many diseases. Fluorescence lysosome staining strategy is valuable f...
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Protocol
Genome-Wide Native R-Loop Profiling by R-Loop Cleavage Under Targets and Tagmentation (R-Loop CUT&Tag)
R-loops are three-stranded nucleic acid structures that consist of a DNA–RNA hybrid and a displaced single-stranded DNA. R-loops occur during transcription and participate in multiple physiological processes s...
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Protocol
Using Differential Scanning Fluorimetry (DSF) to Detect Ligand Binding with Purified Protein
Differential scanning fluorimetry (DSF) can be used to detect the binding of a small molecule ligand to a purified target protein. Upon binding with certain ligands, the protein can be stabilized from thermal ...
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Protocol
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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Protocol
Quantum Dots-Based Lateral Flow Test Strip for Glutathione Detection
Lateral flow test strips (LFTSs) are particularly attractive for assaying targets due to their ability for fast response, simple equipment, portability, and straightforward signal readout. In this work, we des...
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Protocol
Knockdown of Chimeric RNA by RNAi
Knockdown assays are widely used to study the functions of a gene of interest. RNA interference (RNAi) describes a set of well-known methods used to reduce the expression of a target gene by degrading its mRNA...
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Protocol
Separation of Nuclear and Cytoplasmic Fractions for Chimeric RNA Characterization
Cellular organelle fractionation, a basic technique in molecular biology, has been devised to separate various cell components, which can then be purified and analyzed biochemically. Isolation of proteins or R...
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Protocol
Detection and Measurement of Chimeric RNAs by RT-PCR
Reverse-transcription polymerase chain reaction (RT-PCR) is a powerful combination of assays useful in detection and measurement of expressed RNA transcripts. RT-PCR consists of RNA isolation and reverse trans...
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Protocol
RNase Protection Assay
Unbound, single-stranded RNA can be digested by RNase (A or T1) to ribonucleotides, whereas double-stranded RNA is not digested by RNase. Based on this principle, the RNase Protection Assay (RPA) is used to va...
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Protocol
Case Study: The Recurrent Fusion RNA DUS4L-BCAP29 in Noncancer Human Tissues and Cells
Traditional gene fusions are involved in the development of various neoplasias. DUS4L-BCAP29, a chimeric fusion RNA, has been reported to be a cancer-related fusion in prostate and gastric cancers. This chimeric ...
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Protocol
Prediction, Characterization, and In Silico Validation of Chimeric RNAs
Many chimeric RNA prediction software packages are available to assist the scientific community in searching for cancer-specific chimeric RNAs. These packages predict a large number of false positive events, w...
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Protocol
Overexpression of Chimeric RNA by Retroviral Transduction
Cloning the open reading frame (ORF) of a protein-coding chimeric RNA into a mammalian expression vector is a simple, practiced way to study the function of the chimeric RNA. Here, we provide procedures for th...
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Protocol
Confirmation of Transcriptional Read-Through Events by RT-PCR
Chimeric RNAs can be formed by trans-splicing from different transcripts or cis-splicing of adjacent genes (cis-SAGe). Cis-SAGe results from read-through transcription of two neighbor genes. To investigate the...
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Protocol
Detection of Tetanus Antibody Applying a Cu-Zn-In-S/ZnS Quantum Dot-Based Lateral Flow Immunoassay
Lateral flow test strip (LFTS) enables rapid, portable, and low-cost point-of-care testing (POCT) diagnosis. Quantum dots (QDs), which are fluorescent semiconductor nanocrystals with distinctive and unique pho...
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Protocol
Case Study: Landscape of Chimeric RNAs in Bladder Cancer
Chimeric RNAs and their products have been shown to be closely associated with tumorigenicity and development in a variety of tumors, making them attractive diagnostic markers and therapeutic targets. In previ...
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Protocol
Validation of Chimeric Fusion Peptides Using Proteomics Data
Chimeric RNAs as well as their fused protein products have therapeutic applications ranging from diagnostics to being used as therapeutic target. Many algorithms have been developed to identify chimeric RNAs, ...
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Protocol
Computational Methods for Biochemical Simulations Implemented in GAMESS
Computational methods for modeling biochemical processes implemented in GAMESS package are reviewed; in particular, quantum mechanics combined with molecular mechanics (QM/MM), semi-empirical, and fragmentatio...
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Protocol
CRISPR/Cas9-Mediated Gene Tagging: A Step-by-Step Protocol
CRISPR/Cas9 provides a simple and powerful tool for modifying almost any DNA of interest. One promising application of the CRISPR/Cas9 system is for tagging genes with a fluorescence marker or tag peptides. Fo...
