Biological Engineering

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    Protocols in Current Issue
    VirScan: High-throughput Profiling of Antiviral Antibody Epitopes
    Authors:  Ellen L. Shrock, Christine L. Shrock and Stephen J. Elledge, date: 07/05/2022, view: 35, Q&A: 0

    Profiling the specificities of antibodies can reveal a wealth of information about humoral immune responses and the antigens they target. Here, we present a protocol for VirScan, an application of the phage immunoprecipitation sequencing (PhIP-Seq)

    ...
    A Robust Nanoparticle-based Magnetic Separation Method for Intact Lysosomes
    Authors:  The Son Le, Mari Takahashi and Shinya Maenosono, date: 07/05/2022, view: 35, Q&A: 0

    Lysosome isolation is a preresiquite for identifying lysosomal protein composition by mass spectroscopic analysis, to reveal lysosome functions, and their involvement in some diseases. Magnetic nanoparticle-based fractionation has received great

    ...
    Serological Measurement of Poly-IgA Immune Complex Levels in IgA Nephropathy and IgA Vasculitis
    Authors:  Xue Zhang, Jicheng Lv, Pan Liu, Xinfang Xie, Xinyan Li, Hong Zhang and Jing Jin, date: 07/05/2022, view: 34, Q&A: 0

    Both IgA nephropathy and IgA vasculitis, formerly known as Henoch-Schӧnlein purpura, are immune deposition diseases. IgA nephropathy is caused by the deposition of aberrantly formed poly-IgA complexes from blood circulation to the kidney

    ...
    In vivo Characterization of Endogenous Protein Interactomes in Drosophila Larval Brain, Using a CRISPR/Cas9-based Strategy and BioID-based Proximity Labeling
    Authors:  Ezgi Uçkun, Georg Wolfstetter, Johannes Fuchs and Ruth H. Palmer, date: 07/05/2022, view: 22, Q&A: 0

    Understanding protein-protein interactions (PPIs) and interactome networks is essential to reveal molecular mechanisms mediating various cellular processes. The most common method to study PPIs in vivo is affinity purification combined with mass

    ...
    VirScan: High-throughput Profiling of Antiviral Antibody Epitopes
    Authors:  Ellen L. Shrock, Christine L. Shrock and Stephen J. Elledge, date: 07/05/2022, view: 35, Q&A: 0
    [Abstract]

    Profiling the specificities of antibodies can reveal a wealth of information about humoral immune responses and the antigens they target. Here, we present a protocol for VirScan, an application of the phage immunoprecipitation sequencing (PhIP-Seq) method for profiling the specificities of human antiviral antibodies. Accompanying this protocol is

    ...
    A Robust Nanoparticle-based Magnetic Separation Method for Intact Lysosomes
    Authors:  The Son Le, Mari Takahashi and Shinya Maenosono, date: 07/05/2022, view: 35, Q&A: 0
    [Abstract]

    Lysosome isolation is a preresiquite for identifying lysosomal protein composition by mass spectroscopic analysis, to reveal lysosome functions, and their involvement in some diseases. Magnetic nanoparticle-based fractionation has received great attention for lysosome isolation, owing to its high efficiency, purity, and preservation of lysosomal

    ...
    Serological Measurement of Poly-IgA Immune Complex Levels in IgA Nephropathy and IgA Vasculitis
    Authors:  Xue Zhang, Jicheng Lv, Pan Liu, Xinfang Xie, Xinyan Li, Hong Zhang and Jing Jin, date: 07/05/2022, view: 34, Q&A: 0
    [Abstract]

    Both IgA nephropathy and IgA vasculitis, formerly known as Henoch-Schӧnlein purpura, are immune deposition diseases. IgA nephropathy is caused by the deposition of aberrantly formed poly-IgA complexes from blood circulation to the kidney glomerulus; IgA vasculitis is characterized by IgA-dominant immune deposits to small vessels of the skin

    ...
    In vivo Characterization of Endogenous Protein Interactomes in Drosophila Larval Brain, Using a CRISPR/Cas9-based Strategy and BioID-based Proximity Labeling
    Authors:  Ezgi Uçkun, Georg Wolfstetter, Johannes Fuchs and Ruth H. Palmer, date: 07/05/2022, view: 22, Q&A: 0
    [Abstract]

    Understanding protein-protein interactions (PPIs) and interactome networks is essential to reveal molecular mechanisms mediating various cellular processes. The most common method to study PPIs in vivo is affinity purification combined with mass spectrometry (AP–MS). Although AP–MS is a powerful method, loss of weak and transient

    ...
    Protocol for High Throughput Screening of Antibody Phage Libraries
    [Abstract]

    Phage display is a proven and widely used technology for selecting specific antibodies against desired targets. However, an immense amount of effort is required to identify and screen the desired positive clones from large and diverse combinatorial libraries. On the other hand, the selection of positive binding clones

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    Labelling of Active Transcription Sites with Argonaute NRDE-3—Image Active Transcription Sites in vivo in Caenorhabditis elegans
    Authors:  Antoine Barrière and Vincent Bertrand, date: 06/05/2022, view: 519, Q&A: 0
    [Abstract]

    Live labelling of active transcription sites is critical to our understanding of transcriptional dynamics. In the most widely used method, RNA sequence MS2 repeats are added to the transcript of interest, on which fluorescently tagged Major Coat Protein binds, and labels transcription sites and transcripts. Here we describe another strategy, using

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    Patterned Substrate of Mobile and Immobile Ligands to Probe EphA2 Receptor Clustering
    Authors:  Zhongwen Chen, Kabir H. Biswas and Jay T. Groves, date: 06/05/2022, view: 779, Q&A: 0
    [Abstract]

    A multitude of membrane-localized receptors are utilized by cells to integrate both biochemical and physical signals from their microenvironment. The clustering of membrane receptors is widely presumed to have functional consequences for subsequent signal transduction. However, it is experimentally challenging to selectively manipulate receptor

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    Preparation of Cas9 Ribonucleoproteins for Genome Editing
    Authors:  Sheng-Wei Lin, Viet Quoc Nguyen and Steven Lin, date: 05/20/2022, view: 1333, Q&A: 0
    [Abstract]

    Genome editing by the delivery of pre-assembled Cas9 ribonucleoproteins (Cas9 RNP) is an increasingly popular approach for cell types that are difficult to manipulate genetically by the conventional plasmid and viral methods. Cas9 RNP editing is robust, precise, capable of multiplexing, and free of genetic materials. Its transient presence in

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    Immunomagnetic Isolation and Enrichment of Microvascular Endothelial Cells from Human Adipose Tissue
    [Abstract]

    Human adipose tissue-resident microvascular endothelial cells are not only garnering attention for their emergent role in the pathogenesis of obesity-related metabolic disorders, but are also of considerable interest for vascular tissue engineering due, in part, to the abundant, accessible, and uniquely dispensable nature of the tissue. Here, we

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    A System to Easily Manage Metadata in Biomedical Research Labs Based on Open-source Software
    Author:  Manuel A. Castro-Alamancos, date: 05/05/2022, view: 584, Q&A: 0
    [Abstract]

    In most biomedical labs, researchers gather metadata (i.e., all details about the experimental data) in paper notebooks, spreadsheets, or, sometimes, electronic notebooks. When data analyses occur, the related details usually go into other notebooks or spreadsheets, and more metadata are available. The whole thing rapidly becomes very complex and

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