Mammalia

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    Protocols in Current Issue
    BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
    Authors:  Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo, date: 09/05/2020, view: 752, Q&A: 0
    [Abstract] Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein conformational analysis and ligand binding calculations, using vetted methods and protocols can be a ...
    Isolation and Quantification of Extracellular DNA from Biofluids
    Authors:  Ľubica Janovičová, Barbora Konečná, Barbora Vlková and Peter Celec, date: 08/20/2020, view: 617, Q&A: 0
    [Abstract] Extracellular DNA is studied as a diagnostic biomarker, but also as a factor involved in the pathophysiology of several diseases due to its pro-inflammatory properties. Extracellular DNA can be extracted from plasma, urine, saliva or other biofluids using standard DNA isolation procedures and specialized commercial kits. Sample preparation for ...
    A Quantitative Single-cell Flow Cytometry Assay for Retrograde Membrane Trafficking Using Engineered Cholera Toxin
    Authors:  Mariska Simpson, Wayne I. Lencer and Phi Luong, date: 08/05/2020, view: 669, Q&A: 0
    [Abstract] The organization and distribution of proteins, lipids, and nucleic acids in eukaryotic cells is an essential process for cell function. Retrograde trafficking from the plasma membrane to the Golgi and endoplasmic reticulum can greatly modify cell membrane composition and intracellular protein dynamics, and thus typifies a key sorting step. ...
    Preparation and Characterization of Ginger Lipid-derived Nanoparticles for Colon-targeted siRNA Delivery
    Authors:  Junsik Sung, Chunhua Yang, James F. Collins and Didier Merlin, date: 07/20/2020, view: 400, Q&A: 0
    [Abstract] Synthetic nanoparticle-based drug delivery system is widely known for its ability to increase the efficacy and specificity of loaded drugs, but it often suffers from relatively higher immunotoxicity and higher costs as compared to traditional drug formulations. Contrarily, plant-derived nanoparticles appear to be free from these limitations of ...
    Calcein Release Assay to Measure Membrane Permeabilization by Recombinant Alpha-Synuclein
    Authors:  Sayan Dutta, Ben G. Watson, Seema Mattoo and Jean-Christophe Rochet, date: 07/20/2020, view: 464, Q&A: 0
    [Abstract] Lipid membranes are involved in regulating biochemical and biological processes and in modulating the selective permeability of cells, organelles, and vesicles. Membrane composition, charge, curvature, and fluidity all have concerted effects on cellular signaling and homeostasis. The ability to prepare artificial lipid assemblies that mimic ...
    Tyramide Signal-Amplified Immunofluorescence of MYCN and MYC in Human Tissue Specimens and Cell Line Cultures
    Authors:  Johanna M. Schafer and Jennifer A. Pietenpol, date: 07/05/2020, view: 687, Q&A: 0
    [Abstract] MYC family members, MYC, MYCN, and MYCL, are oncogenic transcription factors that regulate the expression of genes involved in normal development, cell growth, proliferation, metabolism, and survival. While MYC is amplified and/or overexpressed across a variety of tissue types, MYCN is often overexpressed in tumors of the nervous system ...
    Microscopy-based Methods for Rosetting Assay in Malaria Research
    Authors:  Wenn-Chyau Lee and Laurent Rénia, date: 07/05/2020, view: 887, Q&A: 0
    [Abstract] In malaria, rosetting phenomenon is a condition where a Plasmodium-infected erythrocyte stably adheres to at least an uninfected erythrocyte. This phenomenon that occurs in all species of human malaria parasite is likely to be an immune escape mechanism for the parasite. However, it has been associated with malaria pathogenesis, possibly ...
    Quantitative Nucleocytoplasmic Transport Assays in Cellular Models of Neurodegeneration
    [Abstract] Nucleocytoplasmic transport deficits are suggested to play a role in neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Given the importance and complexity of this process, understanding when these aberrations occur and which pathways are involved is of great importance. Here, we make use of CRISPR-Cas9 technology to ...
    In vitro Measurement of CMP-Sialic Acid Transporter Activity in Reconstituted Proteoliposomes
    Authors:  James Cahill, Shivani Ahuja and Matthew R. Whorton, date: 03/20/2020, view: 1062, Q&A: 0
    [Abstract] Nucleotide-sugar transporters (NSTs) facilitate eukaryotic cellular glycosylation by transporting nucleotide-sugar conjugates into the Golgi lumen and endoplasmic reticulum for use by glycosyltransferases, while also transferring nucleotide monophosphate byproducts to the cytoplasm. Mutations in this family of proteins can cause a number of ...
    Expression and Purification of Adeno-associated Virus Virus-like Particles in a Baculovirus System and AAVR Ectodomain Constructs in E. coli
    [Abstract] Adeno-associated virus (AAV) is a promising gene therapy vector and the biophysical characterization of its interactions with host proteins is a critical foundation for engineering tissue targeting and immune escape. Presented here are protocols for the production of: (a) the outer protein shells (virus-like particles or VLPs) for serotype 2 ...



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