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Protocol
Generating 2D Barcode for DNA Barcode Sequences
DNA barcode sequence is a short DNA sequence representing a sample from a particular species. The commonly used DNA barcodes are at least 200 bps long. This large number of characters cannot be encoded in two-...
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Protocol
A Robust In Vitro Co-culture Model for Studying the Intercellular Communication of Neutrophils
Communication among neutrophils plays critical roles during various phases of inflammatory responses, with clinical relevance to both acute and chronic inflammatory diseases. Despite its significance, underlyi...
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Protocol
Four-Color ImmunoSpot® Assays Requiring Only 1–3 mL of Blood Permit Precise Frequency Measurements of Antigen-Specific B Cells-Secreting Immunoglobulins of All Four Classes and Subclasses
The B lymphocyte response can encompass four immunoglobulin (Ig) classes and four IgG subclasses, each contributing fundamentally different effector functions. Production of the appropriate Ig class/subclass i...
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Protocol
Develo** Complex RNA Design Applications in the Infrared Framework
Applications in biotechnology and bio-medical research call for effective strategies to design novel RNAs with very specific properties. Such advanced design tasks require support by computational tools but at...
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Protocol
A Clickable NAD+ Analog-Based Assay of Poly(ADP-Ribosyl)ated Proteins
Poly(ADP-ribosyl)lation (PARylation) is a posttranslational modification that plays an important role in a variety of biological processes in both animals and plants. Identification of PARylated substrates is ...
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Protocol
Pseudouridine Identification and Functional Annotation with PIANO
Pseudouridine (Ψ) is the first-discovered RNA modification abundantly present in many classes of RNAs, which plays a pivotal role in a series of biological processes. Accurately identifying the location of Ψ s...
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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
Statistical and Machine Learning Methods for Discovering Prognostic Biomarkers for Survival Outcomes
Discovering molecular biomarkers for predicting patient survival outcomes is an essential step toward improving prognosis and therapeutic decision-making in the treatment of severe diseases such as cancer. Due...
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Protocol
Testing the Role of Focal Adhesion Kinase (FAK) in Topography-Mediated Stem Cell Differentiation by Inhibiting FAK Phosphorylation
Stem cell differentiation can be modulated by the substrate topographies. Focal adhesion kinase (FAK) has been identified as a key regulator in topography-induced stem cell mechanotransduction. This chapter wi...
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Protocol
Generation of Human iPSC-Derived Retinal Organoids for Assessment of AAV-Mediated Gene Delivery
Human retinal organoids derived from induced pluripotent stem cells (iPSCs) serve as a promising preclinical model for testing the safety and efficacy of viral gene therapy. Retinal organoids recapitulate the ...
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Protocol
Comprehensive Survey of ChIP-Seq Datasets to Identify Candidate Iron Homeostasis Genes Regulated by Chromatin Modifications
Vital biochemical reactions including photosynthesis to respiration require iron, which should be tightly regulated. Although increasing evidence reveals the importance of epigenetic regulation in gene express...
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Protocol
Fluorescence-Detection Size-Exclusion Chromatography-Based Thermostability Assay for Membrane Proteins
Green fluorescent proteins (GFPs) have lightened up almost every aspect of biological research including protein sciences. In the field of membrane protein structural biology, GFPs have been used widely to mon...
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Protocol
The Detection of Exosomal PD-L1 in Peripheral Blood
Peripheral blood is a source for liquid biopsy, which can meet the requirements of pretreatment disease ty** to determine precise targeted therapy and monitoring of posttreatment minimal residual disease mon...
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Protocol
Functional Interrogation of Ca2+ Signals in Human Cancer Cells In Vitro and Ex Vivo by Fluorescent Microscopy and Molecular Tools
Genetically encoded calcium indicators (GECIs) and high-resolution confocal microscopy enable dynamic visualization of calcium signals in cells and tissues. Two-dimensional and 3D biocompatible materials mimic...
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Protocol
Vascular Imaging in Small Animals Using Clinical Ultrasound Scanners
Conventional ultrasound with frequency (2–15 MHz) has been a global diagnostic and therapeutic tool in clinical medicine, and high-frequency ultrasound (>30 MHz) has been a powerful investigative device for pr...
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Protocol
A Simple Method for Generating, Clearing, and Imaging Pre-vascularized 3D Adipospheres Derived from Human iPS Cells
Beige/brite/brown-like adipocytes (BAs), dispersed in white adipose tissue, represent promising cell targets to counteract obesity and associated diseases. However, there are major limitations for a BA-based t...
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Protocol
A Plate Reader-Based Measurement of the Cellular ROS Production Using Dihydroethidium and MitoSOX
Intracellular reactive oxygen species (ROS) act as an important signaling transductor in cells, regulating almost every aspect of cell biology. Measurements of ROS production thus, offer links between oxidativ...
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Protocol
Rabbit Surgery Protocol for End-to-End and End-to-Side Vascular Graft Anastomosis
Preclinical testing in animal model is a required stage of vascular device development. Among small animal models, rabbits provide vasculature with relative larger caliber for anastomotic implantation of vascu...
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Protocol
Chemical Perturbation of Chloroplast Ca2+ Dynamics in Arabidopsis thaliana Suspension Cell Cultures and Seedlings
Ca2+ signaling is part of universal signal transduction pathways to respond to external and internal stimuli or stress and in plants plays a central role in chloroplasts, such as in the regulation of photosynthet...
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Protocol
Analysis of Clonal Composition in Human iPSC and ESC and Derived 2D and 3D Differentiated Cultures
Human induced pluripotent and embryonic stem cell cultures (hiPSC/hESC) are phenotypically heterogeneous and prone to clonal deviations during subculturing and differentiation. Clonal deviations often emerge u...
