142 Result(s)
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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
Protein–Ligand Blind Docking Using CB-Dock2
Protein–ligand blind docking is a widely used method for studying the binding sites and poses of ligands and receptors in pharmaceutical and biological research. Recently, our new blind docking server named CB...
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Protocol
Neonatal Sepsis Is Diminished by Cervical Vagus Nerve Stimulation and Tracked Noninvasively by ECG: A Pilot Report and Dataset in the Piglet Model
Background: Vagus nerve stimulation (VNS) reduced inflammation induced by lipopolysaccharide (LPS) in an adult rat sepsis model. A multi-dimensional heart rate variability (HRV) index reliably tracked the inflamm...
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Base-Editor-Mediated circRNA Knockout by Targeting Predominantly Back-Splice Sites
Back-splicing of eukaryotic exon(s) leads to the production of covalently closed circular RNAs (circRNAs). Generally, most circRNAs contain overlap** sequences to their cognate linear RNAs from the same gene...
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Protocol
Vagus Nerve Manipulation and Microglial Plasticity in the Prenatal Brain
The efferent and afferent effects of the vagus nerve on the develo** brain have remained enigmatic. Here we review the evidence of such effects on microglial plasticity in the sheep model of human fetal deve...
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Protocol
Liquid Biopsy in Bladder Cancer
Fluid biopsy based on circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), exosome, and circulating RNA in blood and body fluids has gained attention. Here, the recent findings and issues related to ...
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Protocol
Somatic Cell Nuclear Transfer in Rabbits
Somatic cell nuclear transfer (SCNT) is a technology that enables differentiated somatic cells to acquire a totipotent state, thus making it of great value in developmental biology, biomedical research, and ag...
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Protocol
Ribosomal Profiling by Gradient Fractionation of Cell Lysates
Ribosomal profiling is a widely used technique for deep sequencing of ribosome-protected mRNA and for measuring ribosome status in cells. It is a powerful method that is typically employed for monitoring and m...
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Protocol
Detection of Single Non-small Cell Lung Cancer Cell Multidrug Resistance with Single-Cell Bioanalyzer
Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer death in the world. Despite the development of various lung cancer treatment methods, including surgery, radiation therapy, endocrine t...
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Protocol
Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics
Pediatric cancer multi-omics is a uniquely rewarding and challenging domain of biomedical research. Public generosity bestows an abundance of resources for the study of extremely rare diseases; this unique dyn...
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Protocol
Multivariate Analysis with the R Package mixOmics
The high-dimensional nature of proteomics data presents challenges for statistical analysis and biological interpretation. Multivariate analysis, combined with insightful visualization can help to reveal the u...
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Protocol
Recent Advances in Computational Modeling of Multi-targeting Inhibitors as Anti-Alzheimer Agents
Alzheimer’s disease (AD) is a neurodegenerative illness that affects the brain and is linked to cognitive decline, memory problems, and behavioral changes. It is highly prevalent in the elderly, with a constan...
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Protocol
Visualization of Myddosome Assembly in Live Cells
The Myddosome is an oligomeric protein complex composed of MyD88 and members of IL-1 receptor-associated kinase (IRAK) family that transduce signals from Toll-like and IL-1 family receptors. The molecular dyna...
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Combined FRET-FLIM and NAD(P)H FLIM to Analyze B Cell Receptor Signaling Induced Metabolic Activity of Germinal Center B Cells In Vivo
Affinity maturation of B cell clones within germinal centers constitutes an important mechanism for immune memory. During this process, B cell receptor signaling capacity is tested in multiple rounds of positi...
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AAV-Mediated Gene Delivery to Mouse Brown Adipose Tissue
Recombinant adeno-associated virus (AAV) vectors are attractive vehicles for gene therapy. Yet targeting adipose tissue is still a challenging task. We recently showed that a novel engineered hybrid serotype R...
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Protocol
Structural Variant Detection from Long-Read Sequencing Data with cuteSV
Structural Variation (SV) represents genomic rearrangements and is strongly associated with human health and disease. Recently, long-read sequencing technologies provide the opportunity to more comprehensive i...
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Protocol
Evaluating Reliability of DNA Methylation Measurement
DNA methylation is a widely studied epigenetic phenomenon. Alterations in methylation patterns influence human phenotypes and risk of disease. The Illumina Infinium HumanMethylation450 (HM450) and MethylationE...
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Protocol
Detection of Viroids by RT-PCR
Reverse transcription-polymerase chain reaction (RT-PCR) is an effective method for detecting the presence of viroids in plant tissue. Viroid RNA is converted to cDNA and amplified to detectable levels, making...
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Protocol
A Protocol for Gold Nanoparticle-Assisted Aptamer Selection for a Small Molecule Porphyrin to Develop DNAzyme
DNAzymes can be obtained by in vitro selection, when specific analytes such as porphyrins are used as targets. In this process, the immobilization of targets serving as a major step is not suitable for the sel...
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Protocol
High-Efficiency Differentiation of Human Pluripotent Stem Cells to Hematopoietic Stem/Progenitor Cells in Random Positioning Machine Bioreactors
Human pluripotent stem cells (PSCs) are known to differentiate into almost all the blood lineage cells in vitro and hold a great promise for studying human early hematopoietic development and have a huge poten...
