6 research outputs found

    Multikingdom microscale models.

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    Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous multiple protease activities

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    Matrix metalloproteinases (MMPs) and A Disintegrin and Metalloproteinases (ADAMs) are two related protease families that play key roles in matrix remodeling and growth factor ligand shedding. Directly ascertaining the proteolytic activities of particular MMPs and ADAMs in physiological environments in a non-invasive, real-time, multiplex manner remains a challenge. This work describes Proteolytic Activity Matrix Analysis (PrAMA), an integrated experimental measurement and mathematical analysis framework for simultaneously determining the activities of particular enzymes in complex mixtures of MMPs and ADAMs. The PrAMA method interprets dynamic signals from panels of moderately specific FRET-based polypeptide protease substrates to deduce a profile of specific MMP and ADAM proteolytic activities. Deconvolution of signals from complex mixtures of proteases is accomplished using prior data on individual MMP/ADAM cleavage signatures for the substrate panel measured with purified enzymes. We first validate PrAMA inference using a compendium of roughly 4000 measurements involving known mixtures of purified enzymes and substrates, and then demonstrate application to the live-cell response of wildtype, ADAM10−/−, and ADAM17−/− fibroblasts to phorbol ester and ionomycin stimulation. Results indicate PrAMA can distinguish closely related enzymes from each other with high accuracy, even in the presence of unknown background proteolytic activity. PrAMA offers a valuable tool for applications ranging from live-cell in vitro assays to high-throughput inhibitor screening with complex enzyme mixtures. Moreover, our approach may extend to other families of proteases, such as caspases and cathepsins, that also can lack highly-specific substrates.Andrew and Edna Viterbi Fellowship in Computational BiologyNational Science Foundation (U.S.). Graduate Research Fellowship ProgramNational Science Foundation (U.S.) (grant 1R01EB010246-01)National Science Foundation (U.S.) (grant 5R01GM081336-02

    How microscale approaches can be applied to model the complex host pathogen microenvironment.

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    <p>(A) Virulence strategies of pathogens meet defense strategies of the host at the epithelial barrier. The infectious milieu can be incredibly complex, with organisms from different kingdoms interacting both with each other and with the host. Ideally, an accurate representation of the host, including the epithelium, vascular compartment, interstitial compartment, stromal cells, resident immune cells, and cytokines, would be exposed to an accurate representation of the invading pathogens, including a mixture of bacteria, fungi, viruses, and all sorts of soluble factors. In vitro methods now focus on making this complex environment experimentally tractable, modeling 1 or 2 components of the milieu. (B) Four aspects of the infection microenvironment that can be readily modeled using microfluidic approaches. 1. Microscale techniques simplify the process of modeling the fluid flows and shear forces that occur along the apical surface of the epithelium. 2. Gradients are easy to generate precisely and reproducibly in microscale and are ideal for performing chemotaxis assays. 3. Device geometry is customizable at microscale and offers control over coculture environments, allowing for soluble factor communication between 2 or more populations, as well as coculture between microbes from different kingdoms. 4. Microscale approaches can be used to create organotypic models that recapitulate aspects of tissue structure and function, which may better represent the host in host–pathogen interaction studies. Future microscale approaches may target entirely different aspects of the complex infection microenvironment depicted in (A).</p
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