104 Result(s)
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Protocol
Polyvinylamine and Its Derivative as Effective Carrier for Targeted Delivery of Small RNAs
Polymeric delivery systems could enable the fast- and low-side-effect transport of various RNA classes. Previously, we demonstrated that polyvinylamine (PVAm), a cationic polymer, transfects many kinds of RNAs...
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Protocol
Detecting DNA Loops Using Tethered Particle Motion
The range of motion of a micron-sized bead tethered by a single polymer provides a dynamic readout of the effective length of the polymer. The excursions of the bead may reflect the intrinsic flexibility and/o...
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Protocol
Imaging CAR-T Synapse as a Quality Control for CAR Engineering
The chimeric antigen receptor (CAR) evolves as a powerful tool to reprogram T cells for targeted killing. CAR-T therapy succeeded in treating certain types of blood cancers, and its application is now expandin...
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Protocol
High-Throughput and In-Depth Proteomic Profiling of 5 μL Plasma and Serum Using TMTpro 16-Plex
High-throughput and in-depth proteomic analysis of plasma and serum samples remains challenging due to the presence of multiple high-abundance proteins. Here, we provide a detailed protocol for proteomic analy...
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Protocol
Twitching Motility Assays of Lysobacter enzymogenes OH11 Under a Light Microscope
Bacterial twitching motility is a peculiar way of adherence and surface translocation on moist solid or semisolid surfaces. Although the twitching motility has been detected in various flagellated bacteria, su...
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Protocol
Characterization of SARS-CoV-2 Glycoprotein Using a Quantitative Cell–Cell Fusion System
Coronaviruses (CoVs) infect host cells through the fusion of viral and cellular membrane and may also spread to the neighboring uninfected cells from infected cells through cell–cell fusion. The viral spike (S...
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Protocol
Assessment of Ferroptosis in Hematopoietic Stem and Progenitor Cells
Hematopoietic stem cells (HSCs) are critical for maintaining hematopoiesis throughout life by utilizing their self-renewing and multipotent capabilities. Ferroptosis is a type of cell death characterized by th...
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Protocol
3D-Autologous Culture Method for Precision Oncology
The 3D-autologous culture method (3D-ACM) for patient-derived cancer samples utilizes a patient’s own body fluid or serum to prepare a 3D scaffold and for the culture medium. 3D-ACM enables tumor cells and/or ...
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Protocol
Visualize the Distribution and Dynamics of Mitochondrial DNA (mtDNA) Nucleoids with Multiple Labeling Strategies
Mitochondrial DNA (mtDNA) encodes a variety of rRNAs, tRNAs, and respiratory chain complex proteins. The integrity of mtDNA supports the mitochondrial functions and plays an essential role in numerous physiolo...
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Protocol
Single-Molecule Nanomechanical Genoty** with DNA Origami-Based Shape IDs
Atomic force microscopy (AFM)-based nanomechanical imaging provides a sub-10-nm-resolution approach for imaging biomolecules under ambient conditions. Here we describe how to generate a set of DNA origami-base...
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Protocol
A Lentiviral Pseudotype System to Characterize SARS-CoV-2 Glycoprotein
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2 causes worldwide COVID-19 pandemic and poses a great threat to global public health. Due to its high pathogenicity and infectivity, live SARS-CoV-2 i...
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Protocol
Statistics and Machine Learning in Mass Spectrometry-Based Metabolomics Analysis
In this chapter, we review the cutting-edge statistical and machine learning methods for missing value imputation, normalization, and downstream analyses in mass spectrometry metabolomics studies, with illustr...
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Protocol
Network-Based Structural Alignment of RNA Sequences Using TOPAS
TOPAS (TOPological network-based Alignment of Structural RNAs) is a network-based alignment algorithm that predicts structurally sound pairwise alignment of RNAs. In order to take advantage of recent advances in ...
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Protocol
Detection of Ferroptosis in Models of Brain Diseases
Ferroptosis is a regulated form of non-apoptotic cell death driven by iron-dependent lipid peroxidation. In the past decade, ferroptosis has been reported to be involved in the pathological role in the central...
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Protocol
Membrane and Nuclear Yeast Two-Hybrid Systems
The yeast two-hybrid (Y2H) system is an effective means of detecting protein–protein interactions through the activation of reporter gene expression. This system has also displayed several useful applications,...
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Protocol
An Automatic Stage Identification MATLAB Tool to Reveal Notch Expression Pattern in Drosophila Egg Chambers
Many highly conserved pathways control the development and determine cell fate in organisms. One of these pathways is the Notch signaling pathway that allows for local cell–cell communication. Researchers have...
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Protocol
Highly Efficient Genome Editing in Clostridium difficile Using the CRISPR-Cpf1 System
Clostridium difficile is often the primary cause of nosocomial diarrhea, leading to thousands of deaths annually worldwide. The availability of an efficient genome editing tool for C. difficile is essential to un...
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Protocol
Investigating Fungal Biosynthetic Pathways Using Pichia pastoris as a Heterologous Host
Fungal natural products have extensive biological activities, and thus have been largely commercialized in the pharmaceutical, agricultural, and food industries. Recently, heterologous expression has become an...
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Protocol
Quantitative Mass Spectrometry Imaging with Liquid Microjunction Surface Sampling
Mass spectrometry imaging (MSI) could provide chemical spatial distribution within a diverse range of samples, but absolute quantitation with those techniques is still challenging. Recent years, ambient liquid...
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Protocol
Detection of 5-Formylcytosine and 5-Formyluracil Based on Photo-Assisted Domino Reaction
5-Formylcytosine (5fC) is a recently identified DNA modification in mammalian genome, derived from 5-methylcytosine (5mC) by TET-mediated oxidation. It has been demonstrated to be a critical intermediate durin...
