Journal of Visualized Experiments. JoVE

Journal: Journal of Visualized Experiments. JoVE

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J Vis Exp

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JoVE

ISSN

1940-087X

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Publications 1 - 10 of 34

A Comprehensive Protocol and Step-by-Step Guide for Multi-Omics Integration in Biological Research
Adam, Elodie; Zanoaga, Mihaela-Diana; Rota, Riccardo; et al. (2025)
Journal of Visualized Experiments. JoVE
This manuscript provides a comprehensive step-by-step guide for integrating multi-omics data in biological research. Multi-omics data integration refers to the process of combining and analyzing data measured on the same set of biological samples with different omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomes, lipidomics, and glycomics. Even though multi-omics approaches have similar objectives as single-block or single-omics analyses (for instance, description, discrimination, classification, or prediction), they are able to capture a broader spectrum of molecular information, thus providing a deeper understanding of biological systems and their complex interactions. Indeed, the combination of multiple-omics datasets enables the improvement of prediction accuracy and yields more robust results, especially in cases where the number of available samples is limited. Moreover, thanks also to the most recent development of machine learning techniques, multi-omics analyses are nowadays suitable to uncover hidden patterns and complex phenomena arising among different biological compounds. The primary aim of this work is to present the full protocol that is commonly used in multi-omics studies, from the initial formulation of the problem to the tools useful for the biological interpretation of the results. The manuscript describes in detail the various methods of integrating multi-omics data, including concatenation-based (low-level), transformation-based (mid-level), and model-based (high-level) approaches, and highlights their limitations and advantages, along with the presentation of general visualization and diagnostic tools.
Experimental and Data Analysis Workflow for Soft Matter Nanoindentation
Ciccone, Giuseppe; Gonzalez Oliva, Mariana Azevedo; Antonovaite, Nelda; et al. (2022)
Journal of Visualized Experiments. JoVE
Nanoindentation refers to a class of experimental techniques where a micrometric force probe is used to quantify the local mechanical properties of soft biomaterials and cells. This approach has gained a central role in the fields of mechanobiology, biomaterials design and tissue engineering, to obtain a proper mechanical characterization of soft materials with a resolution comparable to the size of single cells (μm). The most popular strategy to acquire such experimental data is to employ an atomic force microscope (AFM); while this instrument offers an unprecedented resolution in force (down to pN) and space (sub-nm), its usability is often limited by its complexity that prevents routine measurements of integral indicators of mechanical properties, such as Young's Modulus (E). A new generation of nanoindenters, such as those based on optical fiber sensing technology, has recently gained popularity for its ease of integration while allowing to apply sub-nN forces with µm spatial resolution, therefore being suitable to probe local mechanical properties of hydrogels and cells. In this protocol, a step-by-step guide detailing the experimental procedure to acquire nanoindentation data on hydrogels and cells using a commercially available ferrule-top optical fiber sensing nanoindenter is presented. Whereas some steps are specific to the instrument used herein, the proposed protocol can be taken as a guide for other nanoindentation devices, granted some steps are adapted according to the manufacturer's guidelines. Further, a new open-source Python software equipped with a user-friendly graphical user interface for the analysis of nanoindentation data is presented, which allows for screening of incorrectly acquired curves, data filtering, computation of the contact point through different numerical procedures, the conventional computation of E, as well as a more advanced analysis particularly suited for single-cell nanoindentation data.
Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers
James, Daniel; Weinert, Tobias; Skopintsev, Petr; et al. (2019)
Journal of Visualized Experiments. JoVE
Fabrication procedures and birefringence measurements for designing magnetically responsive lanthanide ion chelating phospholipid assemblies
Isabettini, Stéphane; Baumgartner, Mirjam E.; Fischer, Peter; et al. (2018)
Journal of Visualized Experiments. JoVE
High-Resolution C. elegans Imaging Across All Larval Stages
Berger, Simon; Spiri, Silvan; deMello, Andrew; et al. (2025)
Journal of Visualized Experiments. JoVE
Caenorhabditis elegans has become one of the most widely studied and best-understood animal models in biology. Three features are key to C. elegans' success as a model organism: its invariant cell lineage, transparency, and genetic tractability. These render it ideal for a diverse range of microscopy-based studies directly in vivo. Live C. elegans larvae and adults often need to be immobilized during image acquisition. Traditional immobilization methods adversely affect animal development, especially in time-lapse imaging applications. Here, a detailed setup and operation protocol for a novel microfluidic imaging method is introduced, which addresses the limitations associated with traditional agar-pad-based immobilization and other microfluidic strategies. This approach enables simultaneous live imaging across various larval stages while preserving worm orientation and identity over time. To achieve this, a microfluidic trap channel array is employed, with its geometry precisely designed to maintain a stable worm orientation while accommodating growth and molting. Immobilization is facilitated by an active hydraulic valve that applies pressure to secure worms against the cover glass solely during image acquisition. This design allows high-resolution imaging with minimal effects on worm viability or developmental timing.
Generating controlled, dynamic chemical landscapes to study microbial behavior
Carrara, Francesco; Brumley, Douglas R.; Hein, Andrew M.; et al. (2020)
Journal of Visualized Experiments. JoVE
An optimized hemagglutination inhibition (HI) assay to quantify influenzaspecific antibody titers
Kaufmann, Lukas; Syedbasha, Mohammedyaseen; Vogt, Dominik; et al. (2017)
Journal of Visualized Experiments. JoVE
Microfluidic Approach to Resolve Simultaneous and Sequential Cytokine Secretion of Individual Polyfunctional Cells
Linder, Aline; Portmann, Kevin; Schlotheuber, Luca Johannes; et al. (2024)
Journal of Visualized Experiments. JoVE
Infections, autoimmune diseases, desired and adverse immunological responses to treatment can lead to a complex and dynamic cytokine response in vivo. This response involves numerous immune cells secreting various cytokines to orchestrate the immune reaction. However, the secretion dynamics, amounts, and co-occurrence of the different cytokines by various cell subtypes remain poorly understood due to a lack of appropriate tools to study them. Here, we describe a protocol using a microfluidic droplet platform that allows the time-resolved quantitative measurement of secretion dynamics for several cytokines in parallel on the single-cell level. This is enabled by the encapsulation of individual cells into microfluidic droplets together with a multiplexed immunoassay for parallel quantification of cytokine concentrations, their immobilization for dynamic fluorescent imaging, and the analysis of the respective images to derive secreted quantities and dynamics. The protocol describes the preparation of functionalized magnetic nanoparticles, calibration experiments, cell preparation, and the encapsulation of the cells and nanoparticles into droplets for fluorescent imaging and subsequent image and data analysis using the example of lipopolysaccharide-stimulated human peripheral blood mononuclear cells. The presented platform identified distinct cytokine secretion behavior for single and co-secreting cells, characterizing the expected phenotypic heterogeneity in the measured cell sample. Furthermore, the modular nature of the assay allows its adaptation and application to study a variety of proteins, cytokines, and cell samples, potentially leading to a deeper understanding of the interplay between different immune cell types and the role of the different cytokines secreted dynamically to shape the tightly regulated immune response. These new insights could be particularly interesting in the studies of immune dysregulations or in identifying target populations in therapy and drug development.
Intracerebral Transplantation and In Vivo Bioluminescence Tracking of Human Neural Progenitor Cells in the Mouse Brain
Weber, Rebecca Z.; Bodenmann, Chantal; Uhr, Daniela; et al. (2022)
Journal of Visualized Experiments. JoVE
Cell therapy has long been an emerging treatment paradigm in experimental neurobiology. However, cell transplantation studies often rely on end-point measurements and can therefore only evaluate longitudinal changes of cell migration and survival to a limited extent. This paper provides a reliable, minimally invasive protocol to transplant and longitudinally track neural progenitor cells (NPCs) in the adult mouse brain. Before transplantation, cells are transduced with a lentiviral vector comprising a bioluminescent (firefly-luciferase) and fluorescent (green fluorescent protein [GFP]) reporter. The NPCs are transplanted into the right cortical hemisphere using stereotaxic injections in the sensorimotor cortex. Following transplantation, grafted cells were detected through the intact skull for up to five weeks (at days 0, 3, 14, 21, 35) with a resolution limit of 6,000 cells using in vivo bioluminescence imaging. Subsequently, the transplanted cells are identified in histological brain sections and further characterized with immunofluorescence. Thus, this protocol provides a valuable tool to transplant, track, quantify, and characterize cells in the mouse brain.
Easy and accurate mechano-profiling on micropost arrays
Goedecke, Nils; Bollhalder, Maja; Bernet, Remo; et al. (2015)
Journal of Visualized Experiments. JoVE

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