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Protocol
Native Circular RNA Pulldown Method to Simultaneously Profile RNA and Protein Interactions
Circular RNAs (circRNAs) are a widespread, cell-, tissue-, and disease-specific class of largely non-coding RNA transcripts. These single-stranded, covalently-closed transcripts arise through non-canonical spl...
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Protocol
Detection of Ligand-Induced Receptor Kinase and Signaling Component Phosphorylation with Mn2+-Phos-Tag SDS-PAGE
Plasma membrane-resident receptor kinases (RKs) are crucial for plants to sense endogenous and exogenous signals in regulating growth, development, and stress response. Upon perception of ligands by the extrac...
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Protocol
A Liquid Chromatography-Tandem Mass Spectrometry Assay for Quantification of Ethyl Glucuronide and Ethyl Sulfate in Urine
Ethyl glucuronide and ethyl sulfate emerged as the biomarkers of choice for detection of ethanol use as the required sample is urine, enabling easy and noninvasive collection. Further, these biomarkers have a ...
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Protocol
Characterization of T-Cell Epitopes in Food Allergens by Bioinformatic Tools
The identification of T-cell epitopes is a critical step in the understanding of the immunologic mechanisms such as food allergy. Epitope screening in silico by bioinformatic tools can be used to identify T-ce...
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Protocol
Delivery of mRNA with Histidine-Lysine Peptides
Transfection with mRNA has been considered superior to that with plasmids since the mRNA can be translated to a protein in the cytosol without entering the nucleus. One disadvantage of using mRNA is its suscep...
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Protocol
Surface Modification of Liposomes Using Folic Acid
Liposomes are usually defined as spherically shaped microscopic vesicles that consist of one or more phospholipid bilayer membranes. They are widely used in drug delivery due to their biocompatibility, biodegr...
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Protocol
In Vivo Investigation of Gene Function in Muscle Stem Cells by CRISPR/Cas9-Mediated Genome Editing
Skeletal muscle satellite cells (SCs) are adult stem cells responsible for muscle development and injury-induced muscle regeneration. Functional elucidation of intrinsic regulatory factors governing SC activit...
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Protocol
Exons 45–55 Skip** Using Antisense Oligonucleotides in Immortalized Human DMD Muscle Cells
Antisense oligonucleotides (AOs) have demonstrated high potential as a therapy for treating genetic diseases like Duchene muscular dystrophy (DMD). As a synthetic nucleic acid, AOs can bind to a targeted messe...
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Protocol
Measuring Enzyme Kinetics of Glycoside Hydrolases Using the 3,5-Dinitrosalicylic Acid Assay
Use of the 3,5-dinitrosalicylic acid reagent allows the simple, rapid quantification of reducing sugars. The method can be used for analysis of biological samples or in characterization of enzyme reactions, as...
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Protocol
Isolation and Differentiation of Adipocyte Precursors Derived from Neonatal Murine Brown Adipose Tissue
Brown adipose tissue (BAT) is an important regulator of energy homeostasis. Primary brown adipocyte culture provides a powerful and physiologically relevant tool for in vitro studies related to BAT. Here, we d...
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Protocol
Genetic Code Expansion in Mammalian Cells Through Quadruplet Codon Decoding
Genetic code expansion enables the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins both in vitro and in vivo. In addition to a widely applied nonsense suppression strategy, the us...
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Protocol
Site-Specific Incorporation of Sulfotyrosine into Proteins in Mammalian Cells
Protein (PTS) plays a crucial role in numerous extracellular protein-protein interactions. It is involved in diverse physiological processes and the development of human diseases, including AIDS and cancer. ...
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Protocol
Assessment of NLRP3 Inflammasome Activation and NLRP3-NEK7 Complex Assembly
The NLRP3 inflammasome is a critical component of innate immunity that activates caspase-1 to induce inflammation in response to a wide spectrum of endogenous and exogenous stimuli. NLRP3 inflammasome activati...
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Protocol
DPH Probe Method for Liposome-Membrane Fluidity Determination
A liposome is a sealing vesicle composed of a biofilm-like phospholipid bilayer. Continuous phospholipid exchange across the membrane causes spontaneous accumulation and deposition of liposome ions, resulting ...
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Protocol
LC-MS-Based Redox Phosphoipidomics Analysis in Ferroptosis
Ferroptosis is a regulated form of cell death characterized by the accumulation of oxidized phospholipids, particularly oxidized phosphatidylethanolamines (PE), which serve as important biomarkers in the progr...
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Protocol
Mathematically Modeling the Effect of Endocrine and Cdk4/6 Inhibitor Therapies on Breast Cancer Cells
Mathematical modeling of cancer systems is beginning to be used to design better treatment regimens, especially in chemotherapy and radiotherapy. The effectiveness of mathematical modeling to inform treatment ...
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Protocol
Single-Cell Transcriptomic Analysis of Mononuclear Cell Populations in Skeletal Muscle
Skeletal muscle possesses a remarkable regenerative capacity, mainly relying on a population of undifferentiated and unipotent muscle progenitors, called muscle stem cells (MuSCs) or satellite cells, and their...
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Protocol
Linear-Time Algorithms for RNA Structure Prediction
RNA secondary structure prediction is widely used to understand RNA function. Existing dynamic programming-based algorithms, both the classical minimum free energy (MFE) methods and partition function methods,...
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Protocol
Genome-Wide Association Studies (GWAS)
Most of the breeding targets are quantitative traits. In exploring the quantitative trait locus (QTL) system of a trait, linkage map** was established using sparse polymerase chain reaction (PCR) markers. Wi...
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Protocol
Vector Tropism
Recombinant viruses expand the neurobiology toolbox and offer researchers an assortment of gene delivery options. Each type of virus varies in its capabilities and limitations, and therefore, there are importa...
