Cell Biology

Phagoptosis is a prevalent type of programmed cell death (PCD) in adult tissues in which phagocytes non-autonomously eliminate viable cells. Therefore, phagoptosis can only be studied in the context of the entire tissue that includes both the phagocyte executors and the targeted cells doomed to die. Here, we describe an ex vivo live imaging protocol of Drosophila testis to study the dynamics of phagoptosis of germ cell progenitors that are spontaneously removed by neighboring cyst cells. Using this approach, we followed the pattern of exogenous fluorophores with endogenously expressed fluorescent proteins and revealed the sequence of events in germ cell phagoptosis. Although optimized for Drosophila testis, this easy-to-use protocol can be adapted to a wide variety of organisms, tissues, and probes, thus providing a reliable and simple means to study phagoptosis.

Adult muscle stem cells (MuSCs) show remarkable capability in repairing injured tissues. Studying MuSCs in suitable model organisms, which show strong homology with vertebrate counterparts, helps in dissecting the mechanisms regulating their behavior. Additionally, ease of handling and access to technological tools make model organisms well suited for studying biological processes that are conserved across species. MuSCs quiescence, proliferation, and migration are regulated by various input of signals from the surrounding tissues that constitute the MuSCs niche. Observing MuSCs along with their niche in vivo through live imaging provides key information on how MuSCs behave in quiescent and activated states. Drosophila melanogaster is well known for its genetic tool arsenal and the similarity of its different biological processes with vertebrates. Hence, it is widely used to study different types of stem cells. Gained knowledge could then be extrapolated to the vertebrate/mammalian homologous systems to enhance our knowledge in stem cell fields. In this protocol, we discuss how to perform live cell imaging of Drosophila MuSCs, called adult muscle precursors (AMPs) at embryonic stages, using dual-color labelling to visualize both AMPs and the surrounding tissues. This dual-color fluorescent labelling enables the observation of in vivo behavior of two types of cells simultaneously and provides key information on their interactions. The originality of this protocol resides in its biological application to MuSCs and their niche.

Lysosomes play a central role in signaling, nutrient sensing, response to stress, and the degradation and recycling of cellular content. Defects in lysosomal digestive enzymes or structural components can impair lysosomal function with dire consequences to the cell, such as neurodegeneration. A number of methods exist to assess lysosomal stress in the model Drosophila, such as specific driver and reporter strains, transmission electron microscopy, and the investigation of gene expression. These methods, however, can be time consuming and, in some cases, costly. The procedure described here provides a quick, reliable, and low-cost approach to measure lysosomal stress in the Drosophila brain. Using fluorescence confocal microscopy and the LysoTracker staining, this protocol allows for the direct measurement of lysosome size and number. This method can be used to assess lysosomal stress under a number of different genetic and environmental scenarios in the Drosophila brain.

Sphingolipids are important structural components of cellular membranes. They also function as prominent signaling molecules to control a variety of cellular events, such as cell growth, differentiation, and apoptosis. Impaired sphingolipid metabolism, particularly defects in sphingolipid degradation, has been associated with many human diseases. Fluorescence sphingolipid analogs have been widely used as efficient probes to study sphingolipid metabolism and intracellular trafficking in living mammalian cells. Compared with nitrobenzoxadiazole fluorophores (NBD FL), the boron dipyrromethene difluoride fluorophores (BODIPY FL) have much higher absorptivity and fluorescence quantum. These features allow more intensive labeling of cells for fluorescence microscopy imaging and flow cytometry analysis. Here, we describe a protocol employing BODIPY FL-labeled sphingolipid analogs to elucidate sphingolipid internalization, trafficking, and endocytosis in mouse embryonic stem cells.

Graphical abstract:

Subcellular structures exhibit diverse behaviors in different cellular processes, including changes in morphology, abundance, and relative spatial distribution. Faithfully tracking and quantifying these changes are essential to understand their functions. However, most freely accessible methods lack integrated features for tracking multiple objects in different spectral channels simultaneously. To overcome these limitations, we have developed TRACES (Tracking of Active Cellular Structures), a customizable and open-source pipeline capable of detecting, tracking, and quantifying fluorescently labeled cellular structures in up to three spectral channels simultaneously at single-cell level. Here, we detail step-by-step instructions for performing the TRACES pipeline, including image acquisition and segmentation, object identification and tracking, and data quantification and visualization. We believe that TRACES will be a valuable tool for cell biologists, enabling them to track and measure the spatiotemporal dynamics of subcellular structures in a robust and semi-automated manner.

In this study, we present a detailed protocol for live imaging and quantitative analysis of floral meristem development in Aquilegia coerulea, a member of the buttercup family (Ranunculaceae). Using confocal microscopy and the image analysis software MorphoGraphX, we were able to examine the cellular growth dynamics during floral organ primordia initiation, and the transition from floral meristem proliferation to termination. This protocol provides a powerful tool to study the development of the meristem and floral organ primordia, and should be easily adaptable to many plant lineages, including other emerging model systems. It will allow researchers to explore questions outside the scope of common model systems.

Membraneless organelles, such as germ granules and stress granules, are liquid-like condensates formed by phase transition. Recently, we and others have adopted proximity-based labeling methods to determine the composition of these membraneless compartments. Here, we describe the use of TurboID—an engineered promiscuous biotin ligase—to label and purify proteins localizing to Caenorhabditis elegans germ granules, known as P granules. We provide a detailed protocol for visualization of the subcellular localization of biotinylated proteins from dissected gonads, assessment of TurboID enrichment using streptavidin blots, and enrichment of biotinylated proteins under stringent conditions. Altogether, this protocol provides a workflow to unravel the proteome of C. elegans germ granules. Importantly, the assays described here can be applied to interrogate many membraneless organelles, in a diversity of living multicellular organisms.

Graphical abstract:

The Drosophila larval haematopoietic organ or lymph gland consists of multiple cell types arranged in zones. The smallest stem cell compartment consists of 40-45 cells that constitute the haematopoietic niche. In order to analyse the haematopoietic niche, it needs to be labelled with a specific antibody to differentiate it from the other cell types. To characterise a phenotype, it is often necessary to investigate the expression of a gene in a particular stem cell compartment within the lymph gland. In such a situation, in-situ hybridization is performed, as it indicates the localization of gene expression. Although chromogenic in-situ hybridization enables us to compare the signal and tissue morphology simultaneously, it fails to harness the information related to the degree of gene expression. Dual immunofluorescence and in-situ hybridization (IF-FISH) serves as the powerful technique that helps to visualize both protein and mRNA expression within the same cell type. This technique also provides reliable quantification regarding mRNA expression levels. When dealing with a few cells within the organ, like the niche of the larval lymph gland, fluorescently labelled riboprobes allows us to localize and assess the magnitude of gene expression within the niche cells, which are also immunolabelled with a niche-specific marker, to distinguish them from the adjoining cell types.

Roots are the prime organ for nutrient and water uptake and are therefore fundamental to the growth and development of plants. However, physical challenges of a heterogeneous environment and diverse edaphic stresses affect root growth in soil. Compacted soil is a serious global problem, causing inhibition of root elongation, which reduces surface area and impacts resource foraging. Visualisation and quantification of roots in soil is difficult due to this growth substrate’s opaque nature; however, non-destructive imaging technologies are now becoming more widely available to plant and soil scientists working to address this challenge. We have recently developed an integrated approach, combining X-ray Computed Tomography (X-ray CT) and confocal microscopy to image roots grown in compacted soil conditions from a plant to a cellular scale. The method is suited to visualize cellular responses of root tips grown in both non-compacted and compacted soils. This protocol presents a fully integrated workflow, including soil column preparation, creation of compaction conditions, plant growth, imaging, and quantification of root adaptive responses at a cellular scale.

This protocol describes a method for high-resolution confocal imaging of pericytes with the far-red fluorophore TO-PRO^TM-3 Iodide 642/661 in cerebral slices of murine. Identification of pericytes with TO-PRO-3 is a short time-consuming, high cost-effective and robust technique to label pericytes with no need for immunostaining or generation of reporter mice. Since the TO-PRO-3 stain resists immunofluorescence, and lacks spectral overlap, the probe is well suited for multiple labelling. Our procedures also combine TO-PRO-3-staining of pericytes with fluorescent markers for astrocytes and vessels in brain slices. These approaches should enable the assessment of pericyte biology in gliovascular unit.