Browsing by Author "Bravo, Graciela"

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    Developing and Implementing Cloud-Based Tutorials That Combine Bioinformatics Software, Interactive Coding, and Visualization Exercises for Distance Learning on Structural Bioinformatics
    (2021) Engelberger, Felipe; Galaz-Davison, Pablo; Bravo, Graciela; Rivera, Maira; Ramirez-Sarmiento, Cesar A.
    The COVID-19 pandemic has swiftly forced a change in learning strategies across educational institutions, from extensively relying on in-person activities toward online teaching. It is particularly difficult to adapt courses that depend on physical equipment to be now carried out remotely. This is the case for bioinformatics, which typically requires dedicated computer classrooms, as the logistics of granting remote access to a workstation or relying on the computational resources of each student is not trivial. A possible workaround is using cloud server-based computing resources, such as Google Colaboratory, a free web browser application that allows the writing and execution of Python programming through Jupyter notebooks, integrating text, images, and code cells. Following a cloud-based approach, we migrated the practical activities of a course on molecular modeling and simulation into the Google Colaboratory environment resulting in 12 tutorials that introduce students to topics such as phylogenetic analysis, molecular modeling, molecular docking, several flavors of molecular dynamics, and coevolutionary analysis. Each of these notebooks includes a brief introduction to the topic, software installation, execution of the required tools, and analysis of results, with each step properly described. Using a Likert scale questionnaire, a pool of students positively evaluated these tutorials in terms of the time required for their completion, their ability to understand the content and exercises developed in each session, and the practical significance and impact that these computational tools have on scientific research. All tutorials are freely available at https: //github.com/pb3lab/ibm3202.
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    Royal Jelly Derived Extracellular Vesicles Modulate Microglial Nanomechanics and Inflammatory Responses
    (2025) Zavala, Gabriela; Berríos, Pablo; Sandoval, Felipe; Bravo, Graciela; Barrera, Nelson P.; Alarcón Moyano, Jéssica; Díaz Calderón, Paulo; Aguayo, Sebastián; Schuh, Christina
    BACKGROUND Microglia, the braińs resident immune cells, undergo profound mechanical and functional changes upon activation contributing to neuroinflammation, a pathological signature of many neurological diseases. Thus, new anti-inflammatory treatment options are needed that tackle these mechanobiological alterations in microglia, which remain strongly understudied. In this context, extracellular vesicles (EVs) are crucial mediators of intercellular and interkingdom communication, yet their influence on the mechanobiological properties of recipient cells remains largely unknown. Honeybee-derived Royal Jelly EVs (RJEVs) have demonstrated remarkable anti-inflammatory properties, but their impact on microglial cellular nanomechanics and uptake mechanisms remains unclear. RESULTS In this study, we used a multi-disciplinary approach to analyze the resulting biological and nanomechanical changes following the activation of human microglia and the potential effect of RJEV treatment on these mechanobiological parameters. We observed that LPS treatment was associated with decreased cellular Young’s modulus, increased membrane fluidity, and enhanced motility of microglia, indicating a more migratory and pro-inflammatory phenotype. Additionally, LPS exposure altered cellular EV uptake mechanisms by shifting preference from an equilibrium of four mechanisms to the predominance of macropinocytosis and clathrin-dependent endocytosis. Remarkably, RJEV treatment counteracted these mechanobiological changes by, in turn, increasing microglial stiffness, reducing motility, and decreasing secretion of pro-inflammatory cytokines. CONCLUSION This is the first study to demonstrate that microglial activation state dictates EV uptake mechanisms and to establish a direct link between inflammation, cellular and membrane mechanics, and EV-mediated modulation. Our findings highlight RJEVs as promising candidates for regulating neuroinflammation by targeting microglial mechanobiology as well as opening new strategies for EV-based therapeutics
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    The Adsorption of P2X2 Receptors Interacting with IgG Antibodies Revealed by Combined AFM Imaging and Mechanical Simulation
    (2024) Santander, Eduardo A.; Bravo, Graciela; Chang-Halabi, Yuan; Olguin-Orellana, Gabriel J.; Naulin, Pamela A.; Barrera, Mario J.; Montenegro, Felipe A.; Barrera, Nelson P.
    The adsorption of proteins onto surfaces significantly impacts biomaterials, medical devices, and biological processes. This study aims to provide insights into the irreversible adsorption process of multiprotein complexes, particularly focusing on the interaction between anti-His6 IgG antibodies and the His6-tagged P2X2 receptor. Traditional approaches to understanding protein adsorption have centered around kinetic and thermodynamic models, often examining individual proteins and surface coverage, typically through Molecular Dynamics (MD) simulations. In this research, we introduce a computational approach employing Autodesk Maya 3D software for the investigation of multiprotein complexes' adsorption behavior. Utilizing Atomic Force Microscopy (AFM) imaging and Maya 3D-based mechanical simulations, our study yields real-time structural and kinetic observations. Our combined experimental and computational findings reveal that the P2X2 receptor-IgG antibody complex likely undergoes absorption in an 'extended' configuration. Whereas the P2X2 receptor is less adsorbed once is complexed to the IgG antibody compared to its individual state, the opposite is observed for the antibody. This insight enhances our understanding of the role of protein-protein interactions in the process of protein adsorption.