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    An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking
    Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that ...
    Preparation of Amyloid Fibril Networks
    Authors:  Mirren Charnley , Jay Gilbert, Owen G. Jones and Nicholas P. Reynolds, date: 02/20/2018, view: 40, Q&A: 0
    Networks of amyloid nanofibrils fabricated from common globular proteins such as lysozyme and β-lactoglobulin have material properties that mimic the extracellular microenvironment of many cell types. Cells cultured on such amyloid fibril networks ...
    Characterization of Amyloid Fibril Networks by Atomic Force Microscopy
    Authors:  Mirren Charnley , Jay Gilbert, Owen G. Jones and Nicholas P. Reynolds, date: 02/20/2018, view: 38, Q&A: 0
    Dense networks of amyloid nanofibrils fabricated from common globular proteins adsorbed to solid supports can improve cell adhesion, spreading and differentiation compared to traditional flat, stiff 2D cell culture substrates like Tissue Culture ...
    An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking
    [Abstract] Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that are typically made do not provide unambiguous information about the dynamic properties of these ...
    Preparation of Amyloid Fibril Networks
    Authors:  Mirren Charnley , Jay Gilbert, Owen G. Jones and Nicholas P. Reynolds, date: 02/20/2018, view: 40, Q&A: 0
    [Abstract] Networks of amyloid nanofibrils fabricated from common globular proteins such as lysozyme and β-lactoglobulin have material properties that mimic the extracellular microenvironment of many cell types. Cells cultured on such amyloid fibril networks show improved attachment, spreading and in the case of mesenchymal stem cells improved ...
    Characterization of Amyloid Fibril Networks by Atomic Force Microscopy
    Authors:  Mirren Charnley , Jay Gilbert, Owen G. Jones and Nicholas P. Reynolds, date: 02/20/2018, view: 38, Q&A: 0
    [Abstract] Dense networks of amyloid nanofibrils fabricated from common globular proteins adsorbed to solid supports can improve cell adhesion, spreading and differentiation compared to traditional flat, stiff 2D cell culture substrates like Tissue Culture Polystyrene (TCPS). This is due to the fibrous, nanotopographic nature of the amyloid fibril networks ...
    Measuring Nucleosome Assembly Activity in vitro with the Nucleosome Assembly and Quantification (NAQ) Assay
    Authors:  Francesca Mattiroli, Yajie Gu and Karolin Luger, date: 02/05/2018, view: 135, Q&A: 0
    [Abstract] Nucleosomes organize the eukaryotic genome into chromatin. In cells, nucleosome assembly relies on the activity of histone chaperones, proteins with high binding affinity to histones. At least a subset of histone chaperones promotes histone deposition in vivo. However, it has been challenging to characterize this activity, due to the lack ...
    FRET-based Stoichiometry Measurements of Protein Complexes in vitro
    Authors:  Francesca Mattiroli, Yajie Gu and Karolin Luger, date: 02/05/2018, view: 180, Q&A: 0
    [Abstract] For a complete understanding of biochemical reactions, information on complex stoichiometry is essential. However, measuring stoichiometry is experimentally challenging. Our lab has developed a FRET-based assay to study protein complex stoichiometry in vitro. This assay, also known as Job plot, is set up as a continuous variation of the ...
    Radioactive Tracer Feeding Experiments and Product Analysis to Determine the Biosynthetic Capability of Comfrey (Symphytum officinale) Leaves for Pyrrolizidine Alkaloids
    Authors:  Thomas Stegemann, Lars H. Kruse and Dietrich Ober, date: 02/05/2018, view: 85, Q&A: 0
    [Abstract] This protocol delivers a method to determine the biosynthetic capability of comfrey leaves for pyrrolizidine alkaloids independently from other organs like roots or flowers.

    The protocol applies and combines radioactive tracer experiments with standard and modern techniques like thin layer chromatography (TLC), solid-phase extraction ...
    Detection of Protein Interactions in the Cytoplasm and Periplasm of Escherichia coli by Förster Resonance Energy Transfer
    [Abstract] This protocol was developed to qualitatively and quantitatively detect protein-protein interactions in Escherichia coli by Förster Resonance Energy Transfer (FRET). The described assay allows for the previously impossible in vivo screening of periplasmic protein-protein interactions. In FRET, excitation of a donor fluorescent ...
    Infectious Subviral Particle-induced Hemolysis Assay for Mammalian Orthoreovirus
    Authors:  Anthony J. Snyder and Pranav Danthi, date: 01/20/2018, view: 165, Q&A: 0
    [Abstract] Mammalian orthoreovirus (reovirus) utilizes pore forming peptides to penetrate host cell membranes. This step is essential for delivering its genome containing core particle during viral entry. This protocol describes an in vitro assay for measuring reovirus-induced pore formation.
    Infectious Subviral Particle to Membrane Penetration Active Particle (ISVP-to-ISVP*) Conversion Assay for Mammalian Orthoreovirus
    Authors:  Anthony J. Snyder and Pranav Danthi, date: 01/20/2018, view: 168, Q&A: 0
    [Abstract] The mammalian orthoreovirus (reovirus) outer capsid undergoes a series of conformational changes prior to or during viral entry. These transitions are necessary for delivering the genome-containing core across host cell membranes. This protocol describes an in vitro assay for monitoring the transition into a membrane penetration-active ...
    Fish Bile Clean-up for Subsequent Zymography and Mass Spectrometry Proteomic Analyses
    Author:  Rachel Ann Hauser-Davis, date: 01/20/2018, view: 281, Q&A: 0
    [Abstract] Biliary excretion offers a way to analyze various contaminants in aquatic organisms, and fish bile has been used as a biomarker for environmental contamination. The use of the fish bile proteome as a tool for monitoring the impact of environmental contaminants has been recently validated. However, scarce studies in this context are available, and ...