93 Result(s)
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Protocol
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Protocol
Studying Secretory Protein Synthesis in Nicotiana benthamiana Protoplasts
Transient gene expression in plant protoplasts facilitates the analysis of hybrid genes in a fast and reproducible manner. The technique is particularly powerful when studying basic conserved biochemical proce...
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Transplant and Care for In Vitro Orchid Seedlings
Transferring young orchid seedlings from in vitro culture to the external environment is critical for orchid micropropagation. This chapter introduces the techniques for transitioning orchid seedlings from tis...
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Analysis of Visual Recovery After Optic Nerve Crush in Adult Zebrafish
Zebrafish can successfully regenerate axons after optic nerve crush (ONC). Here, we describe two different behavioral tests to map visual recovery: the dorsal light reflex (DLR) test and the optokinetic respon...
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Genetically Encoded Noncanonical Amino Acids in Proteins to Investigate Lysine Benzoylation
Posttranslational modifications (PTMs) of lysine residues are major regulators of gene expression, protein–protein interactions, and protein localization and degradation. Histone lysine benzoylation is a recen...
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Single-Molecule Imaging of Enzymatic Reactions on DNA Origami
The interaction between enzymes is very important for understanding of enzyme functions and shed light on enzymatic reaction mechanisms. With the development of DNA nanotechnology, DNA origami has become a pow...
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Biogenesis of Mesoporous Silica Nanoparticles Enclosed in Extracellular Vesicles by Mouse Renal Adenocarcinoma Cells
Integrating the versatility of synthetic nanoparticles to natural biomaterials, such as cells or cell membranes, has gained considerable attention as promising alternative cargo delivery platforms in recent ye...
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Liquid Biopsy in Adverse Neurodevelopment of Children: Problems and Prospects
Neurodevelopmental disorders in children have an important impact on the quality of life in the whole life cycle. Severe neurodevelopmental disorders will become a serious social and family burden and an impor...
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Computational Analysis of Antibody Paratopes for Antibody Sequences in Antibody Libraries
To ensure the functionalities of the antibodies in phage-displayed synthetic antibody libraries, we use computational method to evaluate the designs of the antibody libraries. The computational methodologies d...
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Detection of Cell-Derived Exosomes Via Surface-Enhanced Raman Scattering Using Aggregated Silver Nanoparticles
Exosomes are small extracellular vesicles that contain RNA, lipids, and proteins and can act as cellular messengers, carrying information to cells and tissues in the body. Thus, sensitive, label-free, and mult...
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Analysis of Axonal Regrowth and Dendritic Remodeling After Optic Nerve Crush in Adult Zebrafish
Neurodegenerative diseases and central nervous system (CNS) injuries are frequently characterized by axonal damage, as well as dendritic pathology. In contrast to mammals, adult zebrafish show a robust regener...
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Density-Based Fractionation of Cell-Conditioned Medium to Prepare Proteomics Grade Extracellular Vesicles
The identification of the molecular composition of extracellular vesicles (EV) by omics approaches, including proteomics, requires the separation of EV from non-EV confounding factors present in the source bio...
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Quantitative Disaccharide Profiling of Glycosaminoglycans from Two Different Preparations by PMP and Deuterated PMP Labeling
Glycosaminoglycan (GAG) fine structures from the same animal cells and tissues are controlled not only by the biosynthetic and metabolic enzymes but also by other environmental factors, such as chemicals, grow...
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Identifying Somatic Mitochondrial DNA Mutations
Mitochondria are cellular organelles that play an essential role in eukaryotes, producing the energy needed for a cell to survive. Beyond the ~3.2 Gb of nuclear genomic DNA, each human cell has hundreds of mit...
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Multi-dimensional Fluorescence Live-Cell Imaging for Glucosome Dynamics in Living Human Cells
Fluorescence live-cell imaging that has contributed to our understanding of cell biology is now at the frontline of studying quantitative biochemistry in a cell. Particularly, technological advancements of flu...
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Phosphate-Methylated Oligonucleotides as a Novel Primer for PCR and RT-PCR
This chapter introduces neutralized DNA (nDNA) as a novel design for the primers of PCR and RT-PCR by methylating phosphate groups of some oligonucleotides in their structures. It starts with an introduction ...
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Functional Studies of Genetic Variants Associated with Human Diseases in Notch Signaling-Related Genes Using Drosophila
Rare variants in the many genes related to Notch signaling cause diverse Mendelian diseases that affect myriad organ systems. In addition, genome- and exome-wide association studies have linked common and rare...
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A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms
Especially in eukaryotes, the N-terminal acetylation status of a protein reveals translation initiation sites and substrate specificities and activities of N-terminal acetyltransferases (NATs). Here, we discus...
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Methods to Assess the Reproducibility and Similarity of Hi-C Data
Hi-C experiments are costly to perform and involve multiple complex experimental steps. Reproducibility of Hi-C data is essential for ensuring the validity of the scientific conclusions drawn from the data. In...
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In-Depth Glycan Characterization of Therapeutic Glycoproteins by Stepwise PGC SPE and LC-MS/MS
Glycosylation of biologics, an important factor in pharmacological functions such as efficacy, safety, and biological activity, is easily affected by subtle changes in the cellular environment. Therefore, comp...
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Extraction of Functional Mitochondria Based on Membrane Stiffness
The abnormal functionality of mitochondria has been linked to many life-threatening diseases such as cancers, failure of cardiovascular functions, and neurodegenerative disorders. Therefore, in vitro analysis ...
