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Protocol
Structural Determination of Glucosyltransferase C by Cryo-Electron Microscopy
Biofilm formation is a critical factor in the development of cariogenic virulence of Streptococcus mutans. S. mutans has evolved a concerted mechanism to synthesize a biofilm matrix from dietary sugars by a famil...
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Protocol
Dissecting the Role of the Ccr4–Not Deadenylase Complex in Pluripotency and Differentiation
In this chapter, we describe methods and assays to examine the role of the Ccr4–Not mRNA deadenylase complex in regulating mouse embryonic stem cell (ESC) pluripotency and differentiation. We present the follo...
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Protocol
Characterization of Small Molecule–Protein Interactions Using SPR Method
Surface plasmon resonance (SPR) is an optical phenomenon being used to monitor molecular binding events. With the advantages of being label-free, real-time, and sensitive, SPR assays have become one of the mos...
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Protocol
Characterization of Z-DNA by Infrared Spectroscopy
Infrared spectrum stems from the matter’s absorption of light in the infrared (IR) light region. Generally, this infrared light absorption is due to the transition of vibrational and rotational energy levels o...
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Protocol
Cellular Thermal Shift Assay for the Detection of Small Molecule–Target Interactions in Arabidopsis Cells
Chemical genetics takes advantage of small molecule–protein interactions to explore various biological processes. Although an attractive alternative to classical genetics in plants, the identification of small...
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Protocol
Dynamic Measurement of Endosome-Lysosome Fusion in Neurons Using High-Content Imaging
Endocytosis is a dynamic cellular process that actively transports particles into a cell. Late endosome fusion with the lysosome is a crucial step in the delivery of newly synthesized lysosomal proteins and en...
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Protocol
Analysis of Actin Array Rearrangement During the Plant Response to Bacterial Stimuli
Plants are constantly exposed to various environmental stresses, among which, microbial pathogens are one of the major threats. Studies have shown that the host actin cytoskeleton undergoes active rearrangemen...
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Protocol
Live-Imaging Detection of Multivesicular Body-Plasma Membrane Fusion and Exosome Release in Cultured Primary Neurons
Exosomes represent a class of extracellular vesicles (EVs) derived from the endocytic pathway that is important for cell-cell communication and implicated in the spread of pathogenic protein aggregates associa...
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Protocol
Plant Cytogenetics: From Chromosomes to Cytogenomics
Chromosomes have been studied since the late nineteenth century in the disciplines of cytology and cytogenetics. Analyzing their numbers, features, and dynamics has been tightly linked to the technical develop...
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Protocol
Noncanonical Amino Acid Incorporation in Mice
Genetic code expansion enables in cellulo biosynthesis of curative proteins with enhanced specificity, improved stability, and even novel functions, due to the incorporation of artificial, designed, noncanonical ...
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Protocol
A Powerful Method for Studying Protein–Protein Interactions in Plants: Coimmunoprecipitation (Co-IP) Assay
With the continuous application of molecular biology technologies in the field of plant virology, growing evidence shows that the interactions between viral proteins or virus and host are essential in almost a...
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Protocol
The Yin-Yang Dynamics in Cardiovascular Pharmacogenomics and Personalized Medicine
Studies of genetic variants and systems biology have indicated that Yin-Yang dynamics are especially meaningful for cardiovascular pharmacogenomics and personalized therapeutic strategies. The comprehensive co...
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Protocol
Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes
Computational tool composites alternative way to identify essential genes and it is low-cost and time-efficient. Based on experimental essentiality sets deposited in the databases DEG and OGEE as reference, we...
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Protocol
Determination of N6-Methyladenine in DNA of Mammals and Plants by Dpn I Digestion Combined with Size-Exclusion Ultrafiltration and Mass Spectrometry Analysis
DNA adenine methylation (N6-methyladenine, 6mA) widely exists in bacteria and regulates various biological processes including gene transcription and restriction-modification system. In recent years, it has been ...
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Protocol
Determination of Cytosine Modifications in DNA by Chemical Labeling-Mass Spectrometry Analysis
In active DNA demethylation, DNA cytosine methylation (5-methylcytosine, 5-mC) can be converted to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and 5-carboxylcytosine (5-caC) by ten-eleven translo...
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Protocol
The Yin-Yang Dynamics in Cancer Pharmacogenomics and Personalized Medicine
The enormous heterogeneity of cancer systems has made it very challenging to overcome drug resistance and adverse reactions to achieve personalized therapies. Recent developments in systems biology, especially...
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Protocol
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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Protocol
Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome
The organization of the genome inside the nucleus facilitates many nuclear processes. Because the nuclear genome is highly dynamic and often regulated by essential proteins, rapid depletion strategies are nece...
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Protocol
Measurement of Cellulase and Xylanase Activities in Trichoderma reesei
The microbial cellulase system is responsible for the generation of glucose from cellulose. Cellulases are comprised of at least three major groups of enzymes, namely endoglucanases, exoglucanases, and β-gluco...
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Protocol
Retroviral Transduction of NKT Hybridoma Cells
Natural killer T (NKT) cells have been shown to bridge innate and adaptive immunity. However, the rare population and hard-to-transfect of primary NKT cells slow down our understanding of cellular and molecula...
